Sample records for quantitative tomography simulations

  1. Two schemes for quantitative photoacoustic tomography based on Monte Carlo simulation

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Liu, Yubin; Yuan, Zhen, E-mail: zhenyuan@umac.mo

    Purpose: The aim of this study was to develop novel methods for photoacoustically determining the optical absorption coefficient of biological tissues using Monte Carlo (MC) simulation. Methods: In this study, the authors propose two quantitative photoacoustic tomography (PAT) methods for mapping the optical absorption coefficient. The reconstruction methods combine conventional PAT with MC simulation in a novel way to determine the optical absorption coefficient of biological tissues or organs. Specifically, the authors’ two schemes were theoretically and experimentally examined using simulations, tissue-mimicking phantoms, ex vivo, and in vivo tests. In particular, the authors explored these methods using several objects withmore » different absorption contrasts embedded in turbid media and by using high-absorption media when the diffusion approximation was not effective at describing the photon transport. Results: The simulations and experimental tests showed that the reconstructions were quantitatively accurate in terms of the locations, sizes, and optical properties of the targets. The positions of the recovered targets were accessed by the property profiles, where the authors discovered that the off center error was less than 0.1 mm for the circular target. Meanwhile, the sizes and quantitative optical properties of the targets were quantified by estimating the full width half maximum of the optical absorption property. Interestingly, for the reconstructed sizes, the authors discovered that the errors ranged from 0 for relatively small-size targets to 26% for relatively large-size targets whereas for the recovered optical properties, the errors ranged from 0% to 12.5% for different cases. Conclusions: The authors found that their methods can quantitatively reconstruct absorbing objects of different sizes and optical contrasts even when the diffusion approximation is unable to accurately describe the photon propagation in biological tissues. In particular

  2. 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

  3. 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. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. 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).

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

    PubMed

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

    2015-09-01

    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.

  6. Electron tomography and 3D molecular simulations of platinum nanocrystals

    NASA Astrophysics Data System (ADS)

    Florea, Ileana; Demortière, Arnaud; Petit, Christophe; Bulou, Hervé; Hirlimann, Charles; Ersen, Ovidiu

    2012-07-01

    This work reports on the morphology of individual platinum nanocrystals with sizes of about 5 nm. By using the electron tomography technique that gives 3D spatial selectivity, access to quantitative information in the real space was obtained. The morphology of individual nanoparticles was characterized using HAADF-STEM tomography and it was shown to be close to a truncated octahedron. Using molecular dynamics simulations, this geometrical shape was found to be the one minimizing the nanocrystal energy. Starting from the tomographic reconstruction, 3D crystallographic representations of the studied Pt nanocrystals were obtained at the nanometer scale, allowing the quantification of the relative amount of the crystallographic facets present on the particle surface.This work reports on the morphology of individual platinum nanocrystals with sizes of about 5 nm. By using the electron tomography technique that gives 3D spatial selectivity, access to quantitative information in the real space was obtained. The morphology of individual nanoparticles was characterized using HAADF-STEM tomography and it was shown to be close to a truncated octahedron. Using molecular dynamics simulations, this geometrical shape was found to be the one minimizing the nanocrystal energy. Starting from the tomographic reconstruction, 3D crystallographic representations of the studied Pt nanocrystals were obtained at the nanometer scale, allowing the quantification of the relative amount of the crystallographic facets present on the particle surface. Electronic supplementary information (ESI) available. See DOI: 10.1039/c2nr30990d

  7. 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

  8. Quantitative validation of an air-coupled ultrasonic probe model by Interferometric laser tomography

    NASA Astrophysics Data System (ADS)

    Revel, G. M.; Pandarese, G.; Cavuto, A.

    2012-06-01

    The present paper describes the quantitative validation of a finite element (FE) model of the ultrasound beam generated by an air coupled non-contact ultrasound transducer. The model boundary conditions are given by vibration velocities measured by laser vibrometry on the probe membrane. The proposed validation method is based on the comparison between the simulated 3D pressure field and the pressure data measured with interferometric laser tomography technique. The model details and the experimental techniques are described in paper. The analysis of results shows the effectiveness of the proposed approach and the possibility to quantitatively assess and predict the generated acoustic pressure field, with maximum discrepancies in the order of 20% due to uncertainty effects. This step is important for determining in complex problems the real applicability of air-coupled probes and for the simulation of the whole inspection procedure, also when the component is designed, so as to virtually verify its inspectability.

  9. 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

  10. Physically corrected forward operators for induced emission tomography: a simulation study

    NASA Astrophysics Data System (ADS)

    Viganò, Nicola Roberto; Solé, Vicente Armando

    2018-03-01

    X-ray emission tomography techniques over non-radioactive materials allow one to investigate different and important aspects of the matter that are usually not addressable with the standard x-ray transmission tomography, such as density, chemical composition and crystallographic information. However, the quantitative reconstruction of these investigated properties is hindered by additional problems, including the self-attenuation of the emitted radiation. Work has been done in the past, especially concerning x-ray fluorescence tomography, but this has always focused on solving very specific problems. The novelty of this work resides in addressing the problem of induced emission tomography from a much wider perspective, introducing a unified discrete representation that can be used to modify existing algorithms to reconstruct the data of the different types of experiments. The direct outcome is a clear and easy mathematical description of the implementation details of such algorithms, despite small differences in geometry and other practical aspects, but also the possibility to express the reconstruction as a minimization problem, allowing the use of variational methods, and a more flexible modeling of the noise involved in the detection process. In addition, we look at the results of a few selected simulated data reconstructions that describe the effect of physical corrections like the self-attenuation, and the response to noise of the adapted reconstruction algorithms.

  11. Hybrid model based unified scheme for endoscopic Cerenkov and radio-luminescence tomography: Simulation demonstration

    NASA Astrophysics Data System (ADS)

    Wang, Lin; Cao, Xin; Ren, Qingyun; Chen, Xueli; He, Xiaowei

    2018-05-01

    Cerenkov luminescence imaging (CLI) is an imaging method that uses an optical imaging scheme to probe a radioactive tracer. Application of CLI with clinically approved radioactive tracers has opened an opportunity for translating optical imaging from preclinical to clinical applications. Such translation was further improved by developing an endoscopic CLI system. However, two-dimensional endoscopic imaging cannot identify accurate depth and obtain quantitative information. Here, we present an imaging scheme to retrieve the depth and quantitative information from endoscopic Cerenkov luminescence tomography, which can also be applied for endoscopic radio-luminescence tomography. In the scheme, we first constructed a physical model for image collection, and then a mathematical model for characterizing the luminescent light propagation from tracer to the endoscopic detector. The mathematical model is a hybrid light transport model combined with the 3rd order simplified spherical harmonics approximation, diffusion, and radiosity equations to warrant accuracy and speed. The mathematical model integrates finite element discretization, regularization, and primal-dual interior-point optimization to retrieve the depth and the quantitative information of the tracer. A heterogeneous-geometry-based numerical simulation was used to explore the feasibility of the unified scheme, which demonstrated that it can provide a satisfactory balance between imaging accuracy and computational burden.

  12. Geographic and demographic variabilities of quantitative parameters in stress myocardial computed tomography perfusion.

    PubMed

    Park, Jinoh; Kim, Hyun-Sook; Hwang, Hye Jeon; Yang, Dong Hyun; Koo, Hyun Jung; Kang, Joon-Won; Kim, Young-Hak

    2017-09-01

    To evaluate the geographic and demographic variabilities of the quantitative parameters of computed tomography perfusion (CTP) of the left ventricular (LV) myocardium in patients with normal coronary artery on computed tomography angiography (CTA). From a multicenter CTP registry of stress and static computed tomography, we retrospectively recruited 113 patients (mean age, 60 years; 57 men) without perfusion defect on visual assessment and minimal (< 20% of diameter stenosis) or no coronary artery disease on CTA. Using semiautomatic analysis software, quantitative parameters of the LV myocardium, including the myocardial attenuation in stress and rest phases, transmural perfusion ratio (TPR), and myocardial perfusion reserve index (MPRI), were evaluated in 16 myocardial segments. In the lateral wall of the LV myocardium, all quantitative parameters except for MPRI were significantly higher compared with those in the other walls. The MPRI showed consistent values in all myocardial walls (anterior to lateral wall: range, 25% to 27%; p = 0.401). At the basal level of the myocardium, all quantitative parameters were significantly lower than those at the mid- and apical levels. Compared with men, women had significantly higher values of myocardial attenuation and TPR. Age, body mass index, and Framingham risk score were significantly associated with the difference in myocardial attenuation. Geographic and demographic variabilities of quantitative parameters in stress myocardial CTP exist in healthy subjects without significant coronary artery disease. This information may be helpful when assessing myocardial perfusion defects in CTP.

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

    PubMed Central

    Pang, Wei; Coghill, George M.

    2015-01-01

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

  14. 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. Copyright © 2015 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

  15. Utility of Quantitative Parameters from Single-Photon Emission Computed Tomography/Computed Tomography in Patients with Destructive Thyroiditis.

    PubMed

    Kim, Ji-Young; Kim, Ji Hyun; Moon, Jae Hoon; Kim, Kyoung Min; Oh, Tae Jung; Lee, Dong-Hwa; So, Young; Lee, Won Woo

    2018-01-01

    Quantitative parameters from Tc-99m pertechnetate single-photon emission computed tomography/computed tomography (SPECT/CT) are emerging as novel diagnostic markers for functional thyroid diseases. We intended to assess the utility of SPECT/CT parameters in patients with destructive thyroiditis. Thirty-five destructive thyroiditis patients (7 males and 28 females; mean age, 47.3 ± 13.0 years) and 20 euthyroid patients (6 males and 14 females; mean age, 45.0 ± 14.8 years) who underwent Tc-99m pertechnetate quantitative SPECT/CT were retrospectively enrolled. Quantitative parameters from the SPECT/CT (%uptake, standardized uptake value [SUV], thyroid volume, and functional thyroid mass [SUVmean × thyroid volume]) and thyroid hormone levels were investigated to assess correlations and predict the prognosis for destructive thyroiditis. The occurrence of hypothyroidism was the outcome for prognosis. All the SPECT/CT quantitative parameters were significantly lower in the 35 destructive thyroiditis patients compared to the 20 euthyroid patients using the same SPECT/CT scanner and protocol ( p < 0.001 for all parameters). T3 and free T4 did not correlate with any SPECT/CT parameters, but thyroid-stimulating hormone (TSH) significantly correlated with %uptake ( p = 0.004), SUVmean ( p < 0.001), SUVmax ( p = 0.002), and functional thyroid mass ( p < 0.001). Of the 35 destructive thyroiditis patients, 16 progressed to hypothyroidism. On univariate and multivariate analyses, only T3 levels were associated with the later occurrence of hypothyroidism ( p = 0.002, exp(β) = 1.022, 95% confidence interval: 1.008 - 1.035). Novel quantitative SPECT/CT parameters could discriminate patients with destructive thyroiditis from euthyroid patients, suggesting the robustness of the quantitative SPECT/CT approach. However, disease progression of destructive thyroiditis could not be predicted using the parameters, as these only correlated with TSH, but not with T3, the sole predictor of

  16. On iterative algorithms for quantitative photoacoustic tomography in the radiative transport regime

    NASA Astrophysics Data System (ADS)

    Wang, Chao; Zhou, Tie

    2017-11-01

    In this paper, we present a numerical reconstruction method for quantitative photoacoustic tomography (QPAT), based on the radiative transfer equation (RTE), which models light propagation more accurately than diffusion approximation (DA). We investigate the reconstruction of absorption coefficient and scattering coefficient of biological tissues. An improved fixed-point iterative method to retrieve the absorption coefficient, given the scattering coefficient, is proposed for its cheap computational cost; the convergence of this method is also proved. The Barzilai-Borwein (BB) method is applied to retrieve two coefficients simultaneously. Since the reconstruction of optical coefficients involves the solutions of original and adjoint RTEs in the framework of optimization, an efficient solver with high accuracy is developed from Gao and Zhao (2009 Transp. Theory Stat. Phys. 38 149-92). Simulation experiments illustrate that the improved fixed-point iterative method and the BB method are competitive methods for QPAT in the relevant cases.

  17. 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.

  18. Ventilation inhomogeneity in obstructive lung diseases measured by electrical impedance tomography: a simulation study.

    PubMed

    Schullcke, B; Krueger-Ziolek, S; Gong, B; Jörres, R A; Mueller-Lisse, U; Moeller, K

    2017-10-10

    Electrical impedance tomography (EIT) has mostly been used in the Intensive Care Unit (ICU) to monitor ventilation distribution but is also promising for the diagnosis in spontaneously breathing patients with obstructive lung diseases. Beside tomographic images, several numerical measures have been proposed to quantitatively assess the lung state. In this study two common measures, the 'Global Inhomogeneity Index' and the 'Coefficient of Variation' were compared regarding their capability to reflect the severity of lung obstruction. A three-dimensional simulation model was used to simulate obstructed lungs, whereby images were reconstructed on a two-dimensional domain. Simulations revealed that minor obstructions are not adequately recognized in the reconstructed images and that obstruction above and below the electrode plane may result in misleading values of inhomogeneity measures. EIT measurements on several electrode planes are necessary to apply these measures in patients with obstructive lung diseases in a promising manner.

  19. Utility of Quantitative Parameters from Single-Photon Emission Computed Tomography/Computed Tomography in Patients with Destructive Thyroiditis

    PubMed Central

    Kim, Ji-Young; Kim, Ji Hyun; Moon, Jae Hoon; Kim, Kyoung Min; Oh, Tae Jung; Lee, Dong-Hwa; So, Young

    2018-01-01

    Objective Quantitative parameters from Tc-99m pertechnetate single-photon emission computed tomography/computed tomography (SPECT/CT) are emerging as novel diagnostic markers for functional thyroid diseases. We intended to assess the utility of SPECT/CT parameters in patients with destructive thyroiditis. Materials and Methods Thirty-five destructive thyroiditis patients (7 males and 28 females; mean age, 47.3 ± 13.0 years) and 20 euthyroid patients (6 males and 14 females; mean age, 45.0 ± 14.8 years) who underwent Tc-99m pertechnetate quantitative SPECT/CT were retrospectively enrolled. Quantitative parameters from the SPECT/CT (%uptake, standardized uptake value [SUV], thyroid volume, and functional thyroid mass [SUVmean × thyroid volume]) and thyroid hormone levels were investigated to assess correlations and predict the prognosis for destructive thyroiditis. The occurrence of hypothyroidism was the outcome for prognosis. Results All the SPECT/CT quantitative parameters were significantly lower in the 35 destructive thyroiditis patients compared to the 20 euthyroid patients using the same SPECT/CT scanner and protocol (p < 0.001 for all parameters). T3 and free T4 did not correlate with any SPECT/CT parameters, but thyroid-stimulating hormone (TSH) significantly correlated with %uptake (p = 0.004), SUVmean (p < 0.001), SUVmax (p = 0.002), and functional thyroid mass (p < 0.001). Of the 35 destructive thyroiditis patients, 16 progressed to hypothyroidism. On univariate and multivariate analyses, only T3 levels were associated with the later occurrence of hypothyroidism (p = 0.002, exp(β) = 1.022, 95% confidence interval: 1.008 – 1.035). Conclusion Novel quantitative SPECT/CT parameters could discriminate patients with destructive thyroiditis from euthyroid patients, suggesting the robustness of the quantitative SPECT/CT approach. However, disease progression of destructive thyroiditis could not be predicted using the parameters, as these only correlated

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Wang, Hongchang, E-mail: hongchang.wang@diamond.ac.uk; Kashyap, Yogesh; Sawhney, Kawal

    2016-03-21

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-07-01

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

  2. Quantitative computed tomography and aerosol morphometry in COPD and alpha1-antitrypsin deficiency.

    PubMed

    Shaker, S B; Maltbaek, N; Brand, P; Haeussermann, S; Dirksen, A

    2005-01-01

    Relative area of emphysema below -910 Hounsfield units (RA-910) and 15th percentile density (PD15) are quantitative computed tomography (CT) parameters used in the diagnosis of emphysema. New concepts for noninvasive diagnosis of emphysema are aerosol-derived airway morphometry, which measures effective airspace dimensions (EAD) and aerosol bolus dispersion (ABD). Quantitative CT, ABD and EAD were compared in 20 smokers with chronic obstructive pulmonary disease (COPD) and 22 patients with alpha1-antitrypsin deficiency (AAD) with a similar degree of airway obstruction and reduced diffusion capacity. In both groups, there was a significant correlation between RA-910 and PD15 and pulmonary function tests (PFTs). A significant correlation was also found between EAD, RA-910 and PD15 in the study population as a whole. Upon separation into two groups, the significance disappeared for the smokers with COPD and strengthened for those with AAD, where EAD correlated significantly with RA-910 and PD15. ABD was similar in the two groups and did not correlate with PFT and quantitative CT in either group. In conclusion, based on quantitative computed tomography and aerosol-derived airway morphometry, emphysema was significantly more severe in patients with alpha1-antitrypsin deficiency compared with patients with usual emphysema, despite similar measures of pulmonary function tests.

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

    PubMed

    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; Albrecht, Philipp

    2016-06-14

    To develop consensus recommendations for reporting of quantitative optical coherence tomography (OCT) study results. 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. 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. 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. © 2016 American Academy of Neurology.

  4. 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

  5. Optical coherence tomography for the quantitative study of cerebrovascular physiology

    PubMed Central

    Srinivasan, Vivek J; Atochin, Dmitriy N; Radhakrishnan, Harsha; Jiang, James Y; Ruvinskaya, Svetlana; Wu, Weicheng; Barry, Scott; Cable, Alex E; Ayata, Cenk; Huang, Paul L; Boas, David A

    2011-01-01

    Doppler optical coherence tomography (DOCT) and OCT angiography are novel methods to investigate cerebrovascular physiology. In the rodent cortex, DOCT flow displays features characteristic of cerebral blood flow, including conservation along nonbranching vascular segments and at branch points. Moreover, DOCT flow values correlate with hydrogen clearance flow values when both are measured simultaneously. These data validate DOCT as a noninvasive quantitative method to measure tissue perfusion over a physiologic range. PMID:21364599

  6. Quantitative computed tomography assessment of transfusional iron overload.

    PubMed

    Wood, John C; Mo, Ashley; Gera, Aakansha; Koh, Montre; Coates, Thomas; Gilsanz, Vicente

    2011-06-01

    Quantitative computed tomography (QCT) has been proposed for iron quantification for more than 30 years, however there has been little clinical validation. We compared liver attenuation by QCT with magnetic resonance imaging (MRI)-derived estimates of liver iron concentration (LIC) in 37 patients with transfusional siderosis. MRI and QCT measurements were performed as clinically indicated monitoring of LIC and vertebral bone-density respectively, over a 6-year period. Mean time difference between QCT and MRI studies was 14 d, with 25 studies performed on the same day. For liver attenuation outside the normal range, attenuation values rose linearly with LIC (r(2) = 0·94). However, intersubject variability in intrinsic liver attenuation prevented quantitation of LIC <8 mg/g dry weight of liver, and was the dominant source of measurement uncertainty. Calculated QCT and MRI accuracies were equivalent for LIC values approaching 22 mg/g dry weight, with QCT having superior performance at higher LIC's. Although not suitable for monitoring patients with good iron control, QCT may nonetheless represent a viable technique for liver iron quantitation in patients with moderate to severe iron in regions where MRI resources are limited because of its low cost, availability, and high throughput. © 2011 Blackwell Publishing Ltd.

  7. Evaluation of the BreastSimulator software platform for breast tomography

    NASA Astrophysics Data System (ADS)

    Mettivier, G.; Bliznakova, K.; Sechopoulos, I.; Boone, J. M.; Di Lillo, F.; Sarno, A.; Castriconi, R.; Russo, P.

    2017-08-01

    The aim of this work was the evaluation of the software BreastSimulator, a breast x-ray imaging simulation software, as a tool for the creation of 3D uncompressed breast digital models and for the simulation and the optimization of computed tomography (CT) scanners dedicated to the breast. Eight 3D digital breast phantoms were created with glandular fractions in the range 10%-35%. The models are characterised by different sizes and modelled realistic anatomical features. X-ray CT projections were simulated for a dedicated cone-beam CT scanner and reconstructed with the FDK algorithm. X-ray projection images were simulated for 5 mono-energetic (27, 32, 35, 43 and 51 keV) and 3 poly-energetic x-ray spectra typically employed in current CT scanners dedicated to the breast (49, 60, or 80 kVp). Clinical CT images acquired from two different clinical breast CT scanners were used for comparison purposes. The quantitative evaluation included calculation of the power-law exponent, β, from simulated and real breast tomograms, based on the power spectrum fitted with a function of the spatial frequency, f, of the form S(f)  =  α/f   β . The breast models were validated by comparison against clinical breast CT and published data. We found that the calculated β coefficients were close to that of clinical CT data from a dedicated breast CT scanner and reported data in the literature. In evaluating the software package BreastSimulator to generate breast models suitable for use with breast CT imaging, we found that the breast phantoms produced with the software tool can reproduce the anatomical structure of real breasts, as evaluated by calculating the β exponent from the power spectral analysis of simulated images. As such, this research tool might contribute considerably to the further development, testing and optimisation of breast CT imaging techniques.

  8. [Quantitative assessment on artifacts of dental restorative materials in cone beam computed tomography].

    PubMed

    Yuan, Fu-song; Sun, Yu-chun; Xie, Xiao-yan; Wang, Yong; Lv, Pei-jun

    2013-12-18

    To quantitatively evaluate the artifacts appearance of eight kinds of common dental restorative materials, such as zirconia. For the full-crown tooth preparation of mandibular first molar, eight kinds of full-crowns, such as zirconia all-ceramic crown, glass ceramic crown, ceramage crown, Au-Pt based porcelain-fused-metal (PFM) crown, Pure Titanium PFM crown, Co-Cr PFM crown, Ni-Cr PFM crown, and Au-Pd metal crown were fabricated. And natural teeth in vitro were used as controls. These full-crown and natural teeth in vitro were mounted an ultraviolet-curable resin fixed plate. High resolution cone beam computed tomography (CBCT) was used to scan all of the crowns and natural teeth in vitro, and their DICOM data were imported into software MIMICS 10.0. Then, the number of stripes and the maximum diameters of artifacts around the full-crowns were evaluated quantitatively in two-dimensional tomography images. In the two-dimensional tomography images,the artifacts did not appear around the natural teeth in vitro, glass ceramic crown, and ceramage crown. But thr artifacts appeared around the zirconia all-ceramic and metal crown. The number of stripes of artifacts was five to nine per one crown. The maximum diameters of the artifacts were 2.4 to 2.6 cm and 2.2 to 2.7 cm. In the two-dimensional tomography images of CBCT, stripe-like and radical artifacts were caused around the zirconia all-ceramic crown and metal based porcelain-fused-metal crowns. These artifacts could lower the imaging quality of the full crown shape greatly. The artifact was not caused around the natural teeth in vitro, glass ceramic crown, and ceramage crown.

  9. Novel Application of Quantitative Single-Photon Emission Computed Tomography/Computed Tomography to Predict Early Response to Methimazole in Graves' Disease

    PubMed Central

    Kim, Hyun Joo; Bang, Ji-In; Kim, Ji-Young; Moon, Jae Hoon; So, Young

    2017-01-01

    Objective Since Graves' disease (GD) is resistant to antithyroid drugs (ATDs), an accurate quantitative thyroid function measurement is required for the prediction of early responses to ATD. Quantitative parameters derived from the novel technology, single-photon emission computed tomography/computed tomography (SPECT/CT), were investigated for the prediction of achievement of euthyroidism after methimazole (MMI) treatment in GD. Materials and Methods A total of 36 GD patients (10 males, 26 females; mean age, 45.3 ± 13.8 years) were enrolled for this study, from April 2015 to January 2016. They underwent quantitative thyroid SPECT/CT 20 minutes post-injection of 99mTc-pertechnetate (5 mCi). Association between the time to biochemical euthyroidism after MMI treatment and %uptake, standardized uptake value (SUV), functional thyroid mass (SUVmean × thyroid volume) from the SPECT/CT, and clinical/biochemical variables, were investigated. Results GD patients had a significantly greater %uptake (6.9 ± 6.4%) than historical control euthyroid patients (n = 20, 0.8 ± 0.5%, p < 0.001) from the same quantitative SPECT/CT protocol. Euthyroidism was achieved in 14 patients at 156 ± 62 days post-MMI treatment, but 22 patients had still not achieved euthyroidism by the last follow-up time-point (208 ± 80 days). In the univariate Cox regression analysis, the initial MMI dose (p = 0.014), %uptake (p = 0.015), and functional thyroid mass (p = 0.016) were significant predictors of euthyroidism in response to MMI treatment. However, only %uptake remained significant in a multivariate Cox regression analysis (p = 0.034). A %uptake cutoff of 5.0% dichotomized the faster responding versus the slower responding GD patients (p = 0.006). Conclusion A novel parameter of thyroid %uptake from quantitative SPECT/CT is a predictive indicator of an early response to MMI in GD patients. PMID:28458607

  10. 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.

  11. 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.

  12. Clinical results of computerized tomography-based simulation with laser patient marking.

    PubMed

    Ragan, D P; Forman, J D; He, T; Mesina, C F

    1996-02-01

    Accuracy of a patient treatment portal marking device and computerized tomography (CT) simulation have been clinically tested. A CT-based simulator has been assembled based on a commercial CT scanner. This includes visualization software and a computer-controlled laser drawing device. This laser drawing device is used to transfer the setup, central axis, and/or radiation portals from the CT simulator to the patient for appropriate patient skin marking. A protocol for clinical testing is reported. Twenty-five prospectively, sequentially accessioned patients have been analyzed. The simulation process can be completed in an average time of 62 min. Under many cases, the treatment portals can be designed and the patient marked in one session. Mechanical accuracy of the system was found to be within +/- 1mm. The portal projection accuracy in clinical cases is observed to be better than +/- 1.2 mm. Operating costs are equivalent to the conventional simulation process it replaces. Computed tomography simulation is a clinical accurate substitute for conventional simulation when used with an appropriate patient marking system and digitally reconstructed radiographs. Personnel time spent in CT simulation is equivalent to time in conventional simulation.

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

    PubMed Central

    Fromson, B H; Denison, D M

    1988-01-01

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

  14. 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.

  15. Accuracy of volumetric measurement of simulated root resorption lacunas based on cone beam computed tomography.

    PubMed

    Wang, Y; He, S; Guo, Y; Wang, S; Chen, S

    2013-08-01

    To evaluate the accuracy of volumetric measurement of simulated root resorption cavities based on cone beam computed tomography (CBCT), in comparison with that of Micro-computed tomography (Micro-CT) which served as the reference. The State Key Laboratory of Oral Diseases at Sichuan University. Thirty-two bovine teeth were included for standardized CBCT scanning and Micro-CT scanning before and after the simulation of different degrees of root resorption. The teeth were divided into three groups according to the depths of the root resorption cavity (group 1: 0.15, 0.2, 0.3 mm; group 2: 0.6, 1.0 mm; group 3: 1.5, 2.0, 3.0 mm). Each depth included four specimens. Differences in tooth volume before and after simulated root resorption were then calculated from CBCT and Micro-CT scans, respectively. The overall between-method agreement of the measurements was evaluated using the concordance correlation coefficient (CCC). For the first group, the average volume of resorption cavity was 1.07 mm(3) , and the between-method agreement of measurement for the volume changes was low (CCC = 0.098). For the second and third groups, the average volumes of resorption cavities were 3.47 and 6.73 mm(3) respectively, and the between-method agreements were good (CCC = 0.828 and 0.895, respectively). The accuracy of 3-D quantitative volumetric measurement of simulated root resorption based on CBCT was fairly good in detecting simulated resorption cavities larger than 3.47 mm(3), while it was not sufficient for measuring resorption cavities smaller than 1.07 mm(3) . This method could be applied in future studies of root resorption although further studies are required to improve its accuracy. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Watanabe, Norio; Tsuburaya, Yuji; Shimada, Akihiro

    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.

  17. Effects of the approximations of light propagation on quantitative photoacoustic tomography using two-dimensional photon diffusion equation and linearization

    NASA Astrophysics Data System (ADS)

    Okawa, Shinpei; Hirasawa, Takeshi; Kushibiki, Toshihiro; Ishihara, Miya

    2017-12-01

    Quantitative photoacoustic tomography (QPAT) employing a light propagation model will play an important role in medical diagnoses by quantifying the concentration of hemoglobin or a contrast agent. However, QPAT by the light propagation model with the three-dimensional (3D) radiative transfer equation (RTE) requires a huge computational load in the iterative forward calculations involved in the updating process to reconstruct the absorption coefficient. The approximations of the light propagation improve the efficiency of the image reconstruction for the QPAT. In this study, we compared the 3D/two-dimensional (2D) photon diffusion equation (PDE) approximating 3D RTE with the Monte Carlo simulation based on 3D RTE. Then, the errors in a 2D PDE-based linearized image reconstruction caused by the approximations were quantitatively demonstrated and discussed in the numerical simulations. It was clearly observed that the approximations affected the reconstructed absorption coefficient. The 2D PDE-based linearized algorithm succeeded in the image reconstruction of the region with a large absorption coefficient in the 3D phantom. The value reconstructed in the phantom experiment agreed with that in the numerical simulation, so that it was validated that the numerical simulation of the image reconstruction predicted the relationship between the true absorption coefficient of the target in the 3D medium and the reconstructed value with the 2D PDE-based linearized algorithm. Moreover, the the true absorption coefficient in 3D medium was estimated from the 2D reconstructed image on the basis of the prediction by the numerical simulation. The estimation was successful in the phantom experiment, although some limitations were revealed.

  18. Bayesian parameter estimation in spectral quantitative photoacoustic tomography

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

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

    PubMed Central

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

    2010-01-01

    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. PMID:20799770

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

    PubMed

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

    2010-06-07

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

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

    NASA Astrophysics Data System (ADS)

    Harrison, Robert L.

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

  2. Quantitative reconstructions in multi-modal photoacoustic and optical coherence tomography imaging

    NASA Astrophysics Data System (ADS)

    Elbau, P.; Mindrinos, L.; Scherzer, O.

    2018-01-01

    In this paper we perform quantitative reconstruction of the electric susceptibility and the Grüneisen parameter of a non-magnetic linear dielectric medium using measurement of a multi-modal photoacoustic and optical coherence tomography system. We consider the mathematical model presented in Elbau et al (2015 Handbook of Mathematical Methods in Imaging ed O Scherzer (New York: Springer) pp 1169-204), where a Fredholm integral equation of the first kind for the Grüneisen parameter was derived. For the numerical solution of the integral equation we consider a Galerkin type method.

  3. 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. © IMechE 2014.

  4. The Influence of Reconstruction Kernel on Bone Mineral and Strength Estimates Using Quantitative Computed Tomography and Finite Element Analysis.

    PubMed

    Michalski, Andrew S; Edwards, W Brent; Boyd, Steven K

    2017-10-17

    Quantitative computed tomography has been posed as an alternative imaging modality to investigate osteoporosis. We examined the influence of computed tomography convolution back-projection reconstruction kernels on the analysis of bone quantity and estimated mechanical properties in the proximal femur. Eighteen computed tomography scans of the proximal femur were reconstructed using both a standard smoothing reconstruction kernel and a bone-sharpening reconstruction kernel. Following phantom-based density calibration, we calculated typical bone quantity outcomes of integral volumetric bone mineral density, bone volume, and bone mineral content. Additionally, we performed finite element analysis in a standard sideways fall on the hip loading configuration. Significant differences for all outcome measures, except integral bone volume, were observed between the 2 reconstruction kernels. Volumetric bone mineral density measured using images reconstructed by the standard kernel was significantly lower (6.7%, p < 0.001) when compared with images reconstructed using the bone-sharpening kernel. Furthermore, the whole-bone stiffness and the failure load measured in images reconstructed by the standard kernel were significantly lower (16.5%, p < 0.001, and 18.2%, p < 0.001, respectively) when compared with the image reconstructed by the bone-sharpening kernel. These data suggest that for future quantitative computed tomography studies, a standardized reconstruction kernel will maximize reproducibility, independent of the use of a quantitative calibration phantom. Copyright © 2017 The International Society for Clinical Densitometry. Published by Elsevier Inc. All rights reserved.

  5. Variable pixel size ionospheric tomography

    NASA Astrophysics Data System (ADS)

    Zheng, Dunyong; Zheng, Hongwei; Wang, Yanjun; Nie, Wenfeng; Li, Chaokui; Ao, Minsi; Hu, Wusheng; Zhou, Wei

    2017-06-01

    A novel ionospheric tomography technique based on variable pixel size was developed for the tomographic reconstruction of the ionospheric electron density (IED) distribution. In variable pixel size computerized ionospheric tomography (VPSCIT) model, the IED distribution is parameterized by a decomposition of the lower and upper ionosphere with different pixel sizes. Thus, the lower and upper IED distribution may be very differently determined by the available data. The variable pixel size ionospheric tomography and constant pixel size tomography are similar in most other aspects. There are some differences between two kinds of models with constant and variable pixel size respectively, one is that the segments of GPS signal pay should be assigned to the different kinds of pixel in inversion; the other is smoothness constraint factor need to make the appropriate modified where the pixel change in size. For a real dataset, the variable pixel size method distinguishes different electron density distribution zones better than the constant pixel size method. Furthermore, it can be non-chided that when the effort is spent to identify the regions in a model with best data coverage. The variable pixel size method can not only greatly improve the efficiency of inversion, but also produce IED images with high fidelity which are the same as a used uniform pixel size method. In addition, variable pixel size tomography can reduce the underdetermined problem in an ill-posed inverse problem when the data coverage is irregular or less by adjusting quantitative proportion of pixels with different sizes. In comparison with constant pixel size tomography models, the variable pixel size ionospheric tomography technique achieved relatively good results in a numerical simulation. A careful validation of the reliability and superiority of variable pixel size ionospheric tomography was performed. Finally, according to the results of the statistical analysis and quantitative comparison, the

  6. Quantitative computed tomography for the prediction of pulmonary function after lung cancer surgery: a simple method using simulation software.

    PubMed

    Ueda, Kazuhiro; Tanaka, Toshiki; Li, Tao-Sheng; Tanaka, Nobuyuki; Hamano, Kimikazu

    2009-03-01

    The prediction of pulmonary functional reserve is mandatory in therapeutic decision-making for patients with resectable lung cancer, especially those with underlying lung disease. Volumetric analysis in combination with densitometric analysis of the affected lung lobe or segment with quantitative computed tomography (CT) helps to identify residual pulmonary function, although the utility of this modality needs investigation. The subjects of this prospective study were 30 patients with resectable lung cancer. A three-dimensional CT lung model was created with voxels representing normal lung attenuation (-600 to -910 Hounsfield units). Residual pulmonary function was predicted by drawing a boundary line between the lung to be preserved and that to be resected, directly on the lung model. The predicted values were correlated with the postoperative measured values. The predicted and measured values corresponded well (r=0.89, p<0.001). Although the predicted values corresponded with values predicted by simple calculation using a segment-counting method (r=0.98), there were two outliers whose pulmonary functional reserves were predicted more accurately by CT than by segment counting. The measured pulmonary functional reserves were significantly higher than the predicted values in patients with extensive emphysematous areas (<-910 Hounsfield units), but not in patients with chronic obstructive pulmonary disease. Quantitative CT yielded accurate prediction of functional reserve after lung cancer surgery and helped to identify patients whose functional reserves are likely to be underestimated. Hence, this modality should be utilized for patients with marginal pulmonary function.

  7. 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.

  8. 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.

  9. DMD-based quantitative phase microscopy and optical diffraction tomography

    NASA Astrophysics Data System (ADS)

    Zhou, Renjie

    2018-02-01

    Digital micromirror devices (DMDs), which offer high speed and high degree of freedoms in steering light illuminations, have been increasingly applied to optical microscopy systems in recent years. Lately, we introduced DMDs into digital holography to enable new imaging modalities and break existing imaging limitations. In this paper, we will first present our progress in using DMDs for demonstrating laser-illumination Fourier ptychographic microscopy (FPM) with shotnoise limited detection. After that, we will present a novel common-path quantitative phase microscopy (QPM) system based on using a DMD. Building on those early developments, a DMD-based high speed optical diffraction tomography (ODT) system has been recently demonstrated, and the results will also be presented. This ODT system is able to achieve video-rate 3D refractive-index imaging, which can potentially enable observations of high-speed 3D sample structural changes.

  10. Simultaneous Neutron and X-ray Tomography for Quantitative analysis of Geological Samples

    NASA Astrophysics Data System (ADS)

    LaManna, J.; Hussey, D. S.; Baltic, E.; Jacobson, D. L.

    2016-12-01

    Multiphase flow is a critical area of research for shale gas, oil recovery, underground CO2 sequestration, geothermal power, and aquifer management. It is critical to understand the porous structure of the geological formations in addition to the fluid/pore and fluid/fluid interactions. Difficulties for analyzing flow characteristics of rock cores are in obtaining 3D distribution information on the fluid flow and maintaining the cores in a state for other analysis methods. Two powerful non-destructive methods for obtaining 3D structural and compositional information are X-ray and neutron tomography. X-ray tomography produces information on density and structure while neutrons excel at acquiring the liquid phase and produces compositional information. These two methods can offer strong complementary information but are typically conducted at separate times and often at different facilities. This poses issues for obtaining dynamic and stochastic information as the sample will change between analysis modes. To address this, NIST has developed a system that allows for multimodal, simultaneous tomography using thermal neutrons and X-rays by placing a 90 keVp micro-focus X-ray tube 90° to the neutron beam. High pressure core holders that simulate underground conditions have been developed to facilitate simultaneous tomography. These cells allow for the control of confining pressure, axial load, temperature, and fluid flow through the core. This talk will give an overview the simultaneous neutron and x-ray tomography capabilities at NIST, the benefits of multimodal imaging, environmental equipment for geology studies, and several case studies that have been conducted at NIST.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    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 opticalmore » 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

  12. Toward Quantitative Small Animal Pinhole SPECT: Assessment of Quantitation Accuracy Prior to Image Compensations

    PubMed Central

    Chen, Chia-Lin; Wang, Yuchuan; Lee, Jason J. S.; Tsui, Benjamin M. W.

    2011-01-01

    Purpose We assessed the quantitation accuracy of small animal pinhole single photon emission computed tomography (SPECT) under the current preclinical settings, where image compensations are not routinely applied. Procedures The effects of several common image-degrading factors and imaging parameters on quantitation accuracy were evaluated using Monte-Carlo simulation methods. Typical preclinical imaging configurations were modeled, and quantitative analyses were performed based on image reconstructions without compensating for attenuation, scatter, and limited system resolution. Results Using mouse-sized phantom studies as examples, attenuation effects alone degraded quantitation accuracy by up to −18% (Tc-99m or In-111) or −41% (I-125). The inclusion of scatter effects changed the above numbers to −12% (Tc-99m or In-111) and −21% (I-125), respectively, indicating the significance of scatter in quantitative I-125 imaging. Region-of-interest (ROI) definitions have greater impacts on regional quantitation accuracy for small sphere sources as compared to attenuation and scatter effects. For the same ROI, SPECT acquisitions using pinhole apertures of different sizes could significantly affect the outcome, whereas the use of different radii-of-rotation yielded negligible differences in quantitation accuracy for the imaging configurations simulated. Conclusions We have systematically quantified the influence of several factors affecting the quantitation accuracy of small animal pinhole SPECT. In order to consistently achieve accurate quantitation within 5% of the truth, comprehensive image compensation methods are needed. PMID:19048346

  13. 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.

  14. Clinical application of quantitative computed tomography in osteogenesis imperfecta-suspected cat.

    PubMed

    Won, Sungjun; Chung, Woo-Jo; Yoon, Junghee

    2017-09-30

    One-year-old male Persian cat presented with multiple fractures and no known traumatic history. Marked decrease of bone radiopacity and thin cortices of all long bones were identified on radiography. Tentative diagnosis was osteogenesis imperfecta, a congenital disorder characterized by fragile bone. To determine bone mineral density (BMD), quantitative computed tomography (QCT) was performed. The QCT results revealed a mean trabecular BMD of vertebral bodies of 149.9 ± 86.5 mg/cm 3 . After bisphosphonate therapy, BMD of the same site increased significantly (218.5 ± 117.1 mg/cm 3 , p < 0.05). QCT was a useful diagnostic tool to diagnose osteopenia and quantify response to medical treatment.

  15. Measurement of lung expansion with computed tomography and comparison with quantitative histology.

    PubMed

    Coxson, H O; Mayo, J R; Behzad, H; Moore, B J; Verburgt, L M; Staples, C A; Paré, P D; Hogg, J C

    1995-11-01

    The total and regional lung volumes were estimated from computed tomography (CT), and the pleural pressure gradient was determined by using the milliliters of gas per gram of tissue estimated from the X-ray attenuation values and the pressure-volume curve of the lung. The data show that CT accurately estimated the volume of the resected lobe but overestimated its weight by 24 +/- 19%. The volume of gas per gram of tissue was less in the gravity-dependent regions due to a pleural pressure gradient of 0.24 +/- 0.08 cmH2O/cm of descent in the thorax. The proportion of tissue to air obtained with CT was similar to that obtained by quantitative histology. We conclude that the CT scan can be used to estimate total and regional lung volumes and that measurements of the proportions of tissue and air within the thorax by CT can be used in conjunction with quantitative histology to evaluate lung structure.

  16. CatSim: a new computer assisted tomography simulation environment

    NASA Astrophysics Data System (ADS)

    De Man, Bruno; Basu, Samit; Chandra, Naveen; Dunham, Bruce; Edic, Peter; Iatrou, Maria; McOlash, Scott; Sainath, Paavana; Shaughnessy, Charlie; Tower, Brendon; Williams, Eugene

    2007-03-01

    We present a new simulation environment for X-ray computed tomography, called CatSim. CatSim provides a research platform for GE researchers and collaborators to explore new reconstruction algorithms, CT architectures, and X-ray source or detector technologies. The main requirements for this simulator are accurate physics modeling, low computation times, and geometrical flexibility. CatSim allows simulating complex analytic phantoms, such as the FORBILD phantoms, including boxes, ellipsoids, elliptical cylinders, cones, and cut planes. CatSim incorporates polychromaticity, realistic quantum and electronic noise models, finite focal spot size and shape, finite detector cell size, detector cross-talk, detector lag or afterglow, bowtie filtration, finite detector efficiency, non-linear partial volume, scatter (variance-reduced Monte Carlo), and absorbed dose. We present an overview of CatSim along with a number of validation experiments.

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

  18. Software for simulation of a computed tomography imaging spectrometer using optical design software

    NASA Astrophysics Data System (ADS)

    Spuhler, Peter T.; Willer, Mark R.; Volin, Curtis E.; Descour, Michael R.; Dereniak, Eustace L.

    2000-11-01

    Our Imaging Spectrometer Simulation Software known under the name Eikon should improve and speed up the design of a Computed Tomography Imaging Spectrometer (CTIS). Eikon uses existing raytracing software to simulate a virtual instrument. Eikon enables designers to virtually run through the design, calibration and data acquisition, saving significant cost and time when designing an instrument. We anticipate that Eikon simulations will improve future designs of CTIS by allowing engineers to explore more instrument options.

  19. 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.

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

    PubMed

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

    2010-05-01

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

  1. 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

  2. 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.

  3. Quantitative Comparison of Virtual Monochromatic Images of Dual Energy Computed Tomography Systems: Beam Hardening Artifact Correction and Variance in Computed Tomography Numbers: A Phantom Study.

    PubMed

    Wu, Rongli; Watanabe, Yoshiyuki; Satoh, Kazuhiko; Liao, Yen-Peng; Takahashi, Hiroto; Tanaka, Hisashi; Tomiyama, Noriyuki

    2018-05-21

    The aim of this study was to quantitatively compare the reduction in beam hardening artifact (BHA) and variance in computed tomography (CT) numbers of virtual monochromatic energy (VME) images obtained with 3 dual-energy computed tomography (DECT) systems at a given radiation dose. Five different iodine concentrations were scanned using dual-energy and single-energy (120 kVp) modes. The BHA and CT number variance were evaluated. For higher iodine concentrations, 40 and 80 mgI/mL, BHA on VME imaging was significantly decreased when the energy was higher than 50 keV (P = 0.003) and 60 keV (P < 0.001) for GE, higher than 80 keV (P < 0.001) and 70 keV (P = 0.002) for Siemens, and higher than 40 keV (P < 0.001) and 60 keV (P < 0.001) for Toshiba, compared with single-energy CT imaging. Virtual monochromatic energy imaging can decrease BHA and improve CT number accuracy in different dual-energy computed tomography systems, depending on energy levels and iodine concentrations.

  4. Simulation study on compressive laminar optical tomography for cardiac action potential propagation

    PubMed Central

    Harada, Takumi; Tomii, Naoki; Manago, Shota; Kobayashi, Etsuko; Sakuma, Ichiro

    2017-01-01

    To measure the activity of tissue at the microscopic level, laminar optical tomography (LOT), which is a microscopic form of diffuse optical tomography, has been developed. However, obtaining sufficient recording speed to determine rapidly changing dynamic activity remains major challenges. For a high frame rate of the reconstructed data, we here propose a new LOT method using compressed sensing theory, called compressive laminar optical tomography (CLOT), in which novel digital micromirror device-based illumination and data reduction in a single reconstruction are applied. In the simulation experiments, the reconstructed volumetric images of the action potentials that were acquired from 5 measured images with random pattern featured a wave border at least to a depth of 2.5 mm. Consequently, it was shown that CLOT has potential for over 200 fps required for the cardiac electrophysiological phenomena. PMID:28736675

  5. The Role of High-resolution Peripheral Quantitative Computed Tomography as a Biomarker for Joint Damage in Inflammatory Arthritis.

    PubMed

    Tam, Lai-Shan

    2016-10-01

    Since 2011, members of the SPECTRA Collaboration (Study grouP for xtrEme-Computed Tomography in Rheumatoid Arthritis) have investigated the validity, reliability, and responsiveness of high-resolution peripheral quantitative computed tomography (HR-pQCT) as a biomarker for joint damage in inflammatory arthritis. Presented in this series of articles are a systematic review of HR-pQCT-related findings to date, a review of selected images of cortical and subchondral trabecular bone of metacarpophalangeal (MCP) joints, results of a consensus process to standardize the definition of erosions and their quantification, as well as an examination of the effect of joint flexion on width and volume assessment of the joint space.

  6. 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. © 2016 American Heart Association, Inc.

  7. 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.

  8. Simulation of a small muon tomography station system based on RPCs

    NASA Astrophysics Data System (ADS)

    Chen, S.; Li, Q.; Ma, J.; Kong, H.; Ye, Y.; Gao, J.; Jiang, Y.

    2014-10-01

    In this work, Monte Carlo simulations were used to study the performance of a small muon Tomography Station based on four glass resistive plate chambers(RPCs) with a spatial resolution of approximately 1.0mm (FWHM). We developed a simulation code to generate cosmic ray muons with the appropriate distribution of energies and angles. PoCA and EM algorithm were used to rebuild the objects for comparison. We compared Z discrimination time with and without muon momentum measurement. The relation between Z discrimination time and spatial resolution was also studied. Simulation results suggest that mean scattering angle is a better Z indicator and upgrading to larger RPCs will improve reconstruction image quality.

  9. [Dosimetric evaluation of eye lense shieldings in computed tomography examination--measurements and Monte Carlo simulations].

    PubMed

    Wulff, Jorg; Keil, Boris; Auvanis, Diyala; Heverhagen, Johannes T; Klose, Klaus Jochen; Zink, Klemens

    2008-01-01

    The present study aims at the investigation of eye lens shielding of different composition for the use in computed tomography examinations. Measurements with thermo-luminescent dosimeters and a simple cylindrical waterfilled phantom were performed as well as Monte Carlo simulations with an equivalent geometry. Besides conventional shielding made of Bismuth coated latex, a new shielding with a mixture of metallic components was analyzed. This new material leads to an increased dose reduction compared to the Bismuth shielding. Measured and Monte Carlo simulated dose reductions are in good agreement and amount to 34% for the Bismuth shielding and 46% for the new material. For simulations the EGSnrc code system was used and a new application CTDOSPP was developed for the simulation of the computed tomography examination. The investigations show that a satisfying agreement between simulation and measurement with the chosen geometries of this study could only be achieved, when transport of secondary electrons was accounted for in the simulation. The amount of scattered radiation due to the protector by fluorescent photons was analyzed and is larger for the new material due to the smaller atomic number of the metallic components.

  10. Quantitative 3D high resolution transmission ultrasound tomography: creating clinically relevant images (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Wiskin, James; Klock, John; Iuanow, Elaine; Borup, Dave T.; Terry, Robin; Malik, Bilal H.; Lenox, Mark

    2017-03-01

    There has been a great deal of research into ultrasound tomography for breast imaging over the past 35 years. Few successful attempts have been made to reconstruct high-resolution images using transmission ultrasound. To this end, advances have been made in 2D and 3D algorithms that utilize either time of arrival or full wave data to reconstruct images with high spatial and contrast resolution suitable for clinical interpretation. The highest resolution and quantitative accuracy result from inverse scattering applied to full wave data in 3D. However, this has been prohibitively computationally expensive, meaning that full inverse scattering ultrasound tomography has not been considered clinically viable. Here we show the results of applying a nonlinear inverse scattering algorithm to 3D data in a clinically useful time frame. This method yields Quantitative Transmission (QT) ultrasound images with high spatial and contrast resolution. We reconstruct sound speeds for various 2D and 3D phantoms and verify these values with independent measurements. The data are fully 3D as is the reconstruction algorithm, with no 2D approximations. We show that 2D reconstruction algorithms can introduce artifacts into the QT breast image which are avoided by using a full 3D algorithm and data. We show high resolution gross and microscopic anatomic correlations comparing cadaveric breast QT images with MRI to establish imaging capability and accuracy. Finally, we show reconstructions of data from volunteers, as well as an objective visual grading analysis to confirm clinical imaging capability and accuracy.

  11. Survival Prediction in Pancreatic Ductal Adenocarcinoma by Quantitative Computed Tomography Image Analysis.

    PubMed

    Attiyeh, Marc A; Chakraborty, Jayasree; Doussot, Alexandre; Langdon-Embry, Liana; Mainarich, Shiana; Gönen, Mithat; Balachandran, Vinod P; D'Angelica, Michael I; DeMatteo, Ronald P; Jarnagin, William R; Kingham, T Peter; Allen, Peter J; Simpson, Amber L; Do, Richard K

    2018-04-01

    Pancreatic cancer is a highly lethal cancer with no established a priori markers of survival. Existing nomograms rely mainly on post-resection data and are of limited utility in directing surgical management. This study investigated the use of quantitative computed tomography (CT) features to preoperatively assess survival for pancreatic ductal adenocarcinoma (PDAC) patients. A prospectively maintained database identified consecutive chemotherapy-naive patients with CT angiography and resected PDAC between 2009 and 2012. Variation in CT enhancement patterns was extracted from the tumor region using texture analysis, a quantitative image analysis tool previously described in the literature. Two continuous survival models were constructed, with 70% of the data (training set) using Cox regression, first based only on preoperative serum cancer antigen (CA) 19-9 levels and image features (model A), and then on CA19-9, image features, and the Brennan score (composite pathology score; model B). The remaining 30% of the data (test set) were reserved for independent validation. A total of 161 patients were included in the analysis. Training and test sets contained 113 and 48 patients, respectively. Quantitative image features combined with CA19-9 achieved a c-index of 0.69 [integrated Brier score (IBS) 0.224] on the test data, while combining CA19-9, imaging, and the Brennan score achieved a c-index of 0.74 (IBS 0.200) on the test data. We present two continuous survival prediction models for resected PDAC patients. Quantitative analysis of CT texture features is associated with overall survival. Further work includes applying the model to an external dataset to increase the sample size for training and to determine its applicability.

  12. 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…

  13. Quantitative chest computed tomography as a means of predicting exercise performance in severe emphysema.

    PubMed

    Crausman, R S; Ferguson, G; Irvin, C G; Make, B; Newell, J D

    1995-06-01

    We assessed the value of quantitative high-resolution computed tomography (CT) as a diagnostic and prognostic tool in smoking-related emphysema. We performed an inception cohort study of 14 patients referred with emphysema. The diagnosis of emphysema was based on a compatible history, physical examination, chest radiograph, CT scan of the lung, and pulmonary physiologic evaluation. As a group, those who underwent exercise testing were hyperinflated (percentage predicted total lung capacity +/- standard error of the mean = 133 +/- 9%), and there was evidence of air trapping (percentage predicted respiratory volume = 318 +/- 31%) and airflow limitation (forced expiratory volume in 1 sec [FEV1] = 40 +/- 7%). The exercise performance of the group was severely limited (maximum achievable workload = 43 +/- 6%) and was characterized by prominent ventilatory, gas exchange, and pulmonary vascular abnormalities. The quantitative CT index was markedly elevated in all patients (76 +/- 9; n = 14; normal < 4). There were correlations between this quantitative CT index and measures of airflow limitation (FEV1 r2 = .34, p = 09; FEV1/forced vital capacity r2 = .46, p = .04) and between maximum workload achieved (r2 = .93, p = .0001) and maximum oxygen utilization (r2 = .83, p = .0007). Quantitative chest CT assessment of disease severity is correlated with the degree of airflow limitation and exercise impairment in pulmonary emphysema.

  14. TOWARD QUANTITATIVE OPTICAL COHERENCE TOMOGRAPHY ANGIOGRAPHY: Visualizing Blood Flow Speeds in Ocular Pathology Using Variable Interscan Time Analysis.

    PubMed

    Ploner, Stefan B; Moult, Eric M; Choi, WooJhon; Waheed, Nadia K; Lee, ByungKun; Novais, Eduardo A; Cole, Emily D; Potsaid, Benjamin; Husvogt, Lennart; Schottenhamml, Julia; Maier, Andreas; Rosenfeld, Philip J; Duker, Jay S; Hornegger, Joachim; Fujimoto, James G

    2016-12-01

    Currently available optical coherence tomography angiography systems provide information about blood flux but only limited information about blood flow speed. The authors develop a method for mapping the previously proposed variable interscan time analysis (VISTA) algorithm into a color display that encodes relative blood flow speed. Optical coherence tomography angiography was performed with a 1,050 nm, 400 kHz A-scan rate, swept source optical coherence tomography system using a 5 repeated B-scan protocol. Variable interscan time analysis was used to compute the optical coherence tomography angiography signal from B-scan pairs having 1.5 millisecond and 3.0 milliseconds interscan times. The resulting VISTA data were then mapped to a color space for display. The authors evaluated the VISTA visualization algorithm in normal eyes (n = 2), nonproliferative diabetic retinopathy eyes (n = 6), proliferative diabetic retinopathy eyes (n = 3), geographic atrophy eyes (n = 4), and exudative age-related macular degeneration eyes (n = 2). All eyes showed blood flow speed variations, and all eyes with pathology showed abnormal blood flow speeds compared with controls. The authors developed a novel method for mapping VISTA into a color display, allowing visualization of relative blood flow speeds. The method was found useful, in a small case series, for visualizing blood flow speeds in a variety of ocular diseases and serves as a step toward quantitative optical coherence tomography angiography.

  15. A calibrated iterative reconstruction for quantitative photoacoustic tomography using multi-angle light-sheet illuminations

    NASA Astrophysics Data System (ADS)

    Wang, Yihan; Lu, Tong; Zhang, Songhe; Song, Shaoze; Wang, Bingyuan; Li, Jiao; Zhao, Huijuan; Gao, Feng

    2018-02-01

    Quantitative photoacoustic tomography (q-PAT) is a nontrivial technique can be used to reconstruct the absorption image with a high spatial resolution. Several attempts have been investigated by setting point sources or fixed-angle illuminations. However, in practical applications, these schemes normally suffer from low signal-to-noise ratio (SNR) or poor quantification especially for large-size domains, due to the limitation of the ANSI-safety incidence and incompleteness in the data acquisition. We herein present a q-PAT implementation that uses multi-angle light-sheet illuminations and a calibrated iterative multi-angle reconstruction. The approach can acquire more complete information on the intrinsic absorption and SNR-boosted photoacoustic signals at selected planes from the multi-angle wide-field excitations of light-sheet. Therefore, the sliced absorption maps over whole body can be recovered in a measurementflexible, noise-robust and computation-economic way. The proposed approach is validated by the phantom experiment, exhibiting promising performances in image fidelity and quantitative accuracy.

  16. Fourier phase in Fourier-domain optical coherence tomography.

    PubMed

    Uttam, Shikhar; Liu, Yang

    2015-12-01

    Phase of an electromagnetic wave propagating through a sample-of-interest is well understood in the context of quantitative phase imaging in transmission-mode microscopy. In the past decade, Fourier-domain optical coherence tomography has been used to extend quantitative phase imaging to the reflection-mode. Unlike transmission-mode electromagnetic phase, however, the origin and characteristics of reflection-mode Fourier phase are poorly understood, especially in samples with a slowly varying refractive index. In this paper, the general theory of Fourier phase from first principles is presented, and it is shown that Fourier phase is a joint estimate of subresolution offset and mean spatial frequency of the coherence-gated sample refractive index. It is also shown that both spectral-domain phase microscopy and depth-resolved spatial-domain low-coherence quantitative phase microscopy are special cases of this general theory. Analytical expressions are provided for both, and simulations are presented to explain and support the theoretical results. These results are further used to show how Fourier phase allows the estimation of an axial mean spatial frequency profile of the sample, along with depth-resolved characterization of localized optical density change and sample heterogeneity. Finally, a Fourier phase-based explanation of Doppler optical coherence tomography is also provided.

  17. Fourier phase in Fourier-domain optical coherence tomography

    PubMed Central

    Uttam, Shikhar; Liu, Yang

    2015-01-01

    Phase of an electromagnetic wave propagating through a sample-of-interest is well understood in the context of quantitative phase imaging in transmission-mode microscopy. In the past decade, Fourier-domain optical coherence tomography has been used to extend quantitative phase imaging to the reflection-mode. Unlike transmission-mode electromagnetic phase, however, the origin and characteristics of reflection-mode Fourier phase are poorly understood, especially in samples with a slowly varying refractive index. In this paper, the general theory of Fourier phase from first principles is presented, and it is shown that Fourier phase is a joint estimate of subresolution offset and mean spatial frequency of the coherence-gated sample refractive index. It is also shown that both spectral-domain phase microscopy and depth-resolved spatial-domain low-coherence quantitative phase microscopy are special cases of this general theory. Analytical expressions are provided for both, and simulations are presented to explain and support the theoretical results. These results are further used to show how Fourier phase allows the estimation of an axial mean spatial frequency profile of the sample, along with depth-resolved characterization of localized optical density change and sample heterogeneity. Finally, a Fourier phase-based explanation of Doppler optical coherence tomography is also provided. PMID:26831383

  18. 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.

  19. 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.

  20. 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

  1. Precision of quantitative computed tomography texture analysis using image filtering: A phantom study for scanner variability.

    PubMed

    Yasaka, Koichiro; Akai, Hiroyuki; Mackin, Dennis; Court, Laurence; Moros, Eduardo; Ohtomo, Kuni; Kiryu, Shigeru

    2017-05-01

    Quantitative computed tomography (CT) texture analyses for images with and without filtration are gaining attention to capture the heterogeneity of tumors. The aim of this study was to investigate how quantitative texture parameters using image filtering vary among different computed tomography (CT) scanners using a phantom developed for radiomics studies.A phantom, consisting of 10 different cartridges with various textures, was scanned under 6 different scanning protocols using four CT scanners from four different vendors. CT texture analyses were performed for both unfiltered images and filtered images (using a Laplacian of Gaussian spatial band-pass filter) featuring fine, medium, and coarse textures. Forty-five regions of interest were placed for each cartridge (x) in a specific scan image set (y), and the average of the texture values (T(x,y)) was calculated. The interquartile range (IQR) of T(x,y) among the 6 scans was calculated for a specific cartridge (IQR(x)), while the IQR of T(x,y) among the 10 cartridges was calculated for a specific scan (IQR(y)), and the median IQR(y) was then calculated for the 6 scans (as the control IQR, IQRc). The median of their quotient (IQR(x)/IQRc) among the 10 cartridges was defined as the variability index (VI).The VI was relatively small for the mean in unfiltered images (0.011) and for standard deviation (0.020-0.044) and entropy (0.040-0.044) in filtered images. Skewness and kurtosis in filtered images featuring medium and coarse textures were relatively variable across different CT scanners, with VIs of 0.638-0.692 and 0.430-0.437, respectively.Various quantitative CT texture parameters are robust and variable among different scanners, and the behavior of these parameters should be taken into consideration.

  2. Grating-based tomography applications in biomedical engineering

    NASA Astrophysics Data System (ADS)

    Schulz, Georg; Thalmann, Peter; Khimchenko, Anna; Müller, Bert

    2017-10-01

    For the investigation of soft tissues or tissues consisting of soft and hard tissues on the microscopic level, hard X-ray phase tomography has become one of the most suitable imaging techniques. Besides other phase contrast methods grating interferometry has the advantage of higher sensitivity than inline methods and the quantitative results. One disadvantage of the conventional double-grating setup (XDGI) compared to inline methods is the limitation of the spatial resolution. This limitation can be overcome by removing the analyser grating resulting in a single-grating setup (XSGI). In order to verify the performance of XSGI concerning contrast and spatial resolution, a quantitative comparison of XSGI and XDGI tomograms of a human nerve was performed. Both techniques provide sufficient contrast to allow for the distinction of tissue types. The spatial resolution of the two-fold binned XSGI data set is improved by a factor of two in comparison to XDGI which underlies its performance in tomography of soft tissues. Another application for grating-based X-ray phase tomography is the simultaneous visualization of soft and hard tissues of a plaque-containing coronary artery. The simultaneous visualization of both tissues is important for the segmentation of the lumen. The segmented data can be used for flow simulations in order to obtain information about the three-dimensional wall shear stress distribution needed for the optimization of mechano-sensitive nanocontainers used for drug delivery.

  3. 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.

  4. Quantitative 3D imaging of yeast by hard X-ray tomography.

    PubMed

    Zheng, Ting; Li, Wenjie; Guan, Yong; Song, Xiangxia; Xiong, Ying; Liu, Gang; Tian, Yangchao

    2012-05-01

    Full-field hard X-ray tomography could be used to obtain three-dimensional (3D) nanoscale structures of biological samples. The image of the fission yeast, Schizosaccharomyces pombe, was clearly visualized based on Zernike phase contrast imaging technique and heavy metal staining method at a spatial resolution better than 50 nm at the energy of 8 keV. The distributions and shapes of the organelles during the cell cycle were clearly visualized and two types of organelle were distinguished. The results for cells during various phases were compared and the ratios of organelle volume to cell volume can be analyzed quantitatively. It showed that the ratios remained constant between growth and division phase and increased strongly in stationary phase, following the shape and size of two types of organelles changes. Our results demonstrated that hard X-ray microscopy was a complementary method for imaging and revealing structural information for biological samples. Copyright © 2011 Wiley Periodicals, Inc.

  5. Quantitative 3D analysis of bone in hip osteoarthritis using clinical computed tomography.

    PubMed

    Turmezei, Tom D; Treece, Graham M; Gee, Andrew H; Fotiadou, Anastasia F; Poole, Kenneth E S

    2016-07-01

    To assess the relationship between proximal femoral cortical bone thickness and radiological hip osteoarthritis using quantitative 3D analysis of clinical computed tomography (CT) data. Image analysis was performed on clinical CT imaging data from 203 female volunteers with a technique called cortical bone mapping (CBM). Colour thickness maps were created for each proximal femur. Statistical parametric mapping was performed to identify statistically significant differences in cortical bone thickness that corresponded with the severity of radiological hip osteoarthritis. Kellgren and Lawrence (K&L) grade, minimum joint space width (JSW) and a novel CT-based osteophyte score were also blindly assessed from the CT data. For each increase in K&L grade, cortical thickness increased by up to 25 % in distinct areas of the superolateral femoral head-neck junction and superior subchondral bone plate. For increasing severity of CT osteophytes, the increase in cortical thickness was more circumferential, involving a wider portion of the head-neck junction, with up to a 7 % increase in cortical thickness per increment in score. Results were not significant for minimum JSW. These findings indicate that quantitative 3D analysis of the proximal femur can identify changes in cortical bone thickness relevant to structural hip osteoarthritis. • CT is being increasingly used to assess bony involvement in osteoarthritis • CBM provides accurate and reliable quantitative analysis of cortical bone thickness • Cortical bone is thicker at the superior femoral head-neck with worse osteoarthritis • Regions of increased thickness co-locate with impingement and osteophyte formation • Quantitative 3D bone analysis could enable clinical disease prediction and therapy development.

  6. Noncontact quantitative biomechanical characterization of cardiac muscle using shear wave imaging optical coherence tomography

    PubMed Central

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

    2014-01-01

    We report on a quantitative optical elastographic method based on shear wave imaging optical coherence tomography (SWI-OCT) for biomechanical characterization of cardiac muscle through noncontact elasticity measurement. The SWI-OCT system employs a focused air-puff device for localized loading of the cardiac muscle and utilizes phase-sensitive OCT to monitor the induced tissue deformation. Phase information from the optical interferometry is used to reconstruct 2-D depth-resolved shear wave propagation inside the muscle tissue. Cross-correlation of the displacement profiles at various spatial locations in the propagation direction is applied to measure the group velocity of the shear waves, based on which the Young’s modulus of tissue is quantified. The quantitative feature and measurement accuracy of this method is demonstrated from the experiments on tissue-mimicking phantoms with the verification using uniaxial compression test. The experiments are performed on ex vivo cardiac muscle tissue from mice with normal and genetically altered myocardium. Our results indicate this optical elastographic technique is useful as a noncontact tool to assist the cardiac muscle studies. PMID:25071943

  7. A quantitative approach to evaluating caring in nursing simulation.

    PubMed

    Eggenberger, Terry L; Keller, Kathryn B; Chase, Susan K; Payne, Linda

    2012-01-01

    This study was designed to test a quantitative method of measuring caring in the simulated environment. Since competency in caring is central to nursing practice, ways of including caring concepts in designing scenarios and in evaluation of performance need to be developed. Coates' Caring Efficacy scales were adapted for simulation and named the Caring Efficacy Scale-Simulation Student Version (CES-SSV) and Caring Efficacy Scale-Simulation Faculty Version (CES-SFV). A correlational study was designed to compare student self-ratings with faculty ratings on caring efficacy during an adult acute simulation experience with traditional and accelerated baccalaureate students in a nursing program grounded in caring theory. Student self-ratings were significantly correlated with objective ratings (r = 0.345, 0.356). Both the CES-SSV and the CES-SFV were found to have excellent internal consistency and significantly correlated interrater reliability. They were useful in measuring caring in the simulated learning environment.

  8. 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.

  9. 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.

  10. Automated high resolution full-field spatial coherence tomography for quantitative phase imaging of human red blood cells

    NASA Astrophysics Data System (ADS)

    Singla, Neeru; Dubey, Kavita; Srivastava, Vishal; Ahmad, Azeem; Mehta, D. S.

    2018-02-01

    We developed an automated high-resolution full-field spatial coherence tomography (FF-SCT) microscope for quantitative phase imaging that is based on the spatial, rather than the temporal, coherence gating. The Red and Green color laser light was used for finding the quantitative phase images of unstained human red blood cells (RBCs). This study uses morphological parameters of unstained RBCs phase images to distinguish between normal and infected cells. We recorded the single interferogram by a FF-SCT microscope for red and green color wavelength and average the two phase images to further reduced the noise artifacts. In order to characterize anemia infected from normal cells different morphological features were extracted and these features were used to train machine learning ensemble model to classify RBCs with high accuracy.

  11. 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

  12. A qualitative and quantitative assessment for a bone marrow harvest simulator.

    PubMed

    Machado, Liliane S; Moraes, Ronei M

    2009-01-01

    Several approaches to perform assessment in training simulators based on virtual reality have been proposed. There are two kinds of assessment methods: offline and online. The main requirements related to online training assessment methodologies applied to virtual reality systems are the low computational complexity and the high accuracy. In the literature it can be found several approaches for general cases which can satisfy such requirements. An inconvenient about those approaches is related to an unsatisfactory solution for specific cases, as in some medical procedures, where there are quantitative and qualitative information available to perform the assessment. In this paper, we present an approach to online training assessment based on a Modified Naive Bayes which can manipulate qualitative and quantitative variables simultaneously. A special medical case was simulated in a bone marrow harvest simulator. The results obtained were satisfactory and evidenced the applicability of the method.

  13. Quantitative Simulation of QARBM Challenge Events During Radiation Belt Enhancements

    NASA Astrophysics Data System (ADS)

    Li, W.; Ma, Q.; Thorne, R. M.; Bortnik, J.; Chu, X.

    2017-12-01

    Various physical processes are known to affect energetic electron dynamics in the Earth's radiation belts, but their quantitative effects at different times and locations in space need further investigation. This presentation focuses on discussing the quantitative roles of various physical processes that affect Earth's radiation belt electron dynamics during radiation belt enhancement challenge events (storm-time vs. non-storm-time) selected by the GEM Quantitative Assessment of Radiation Belt Modeling (QARBM) focus group. We construct realistic global distributions of whistler-mode chorus waves, adopt various versions of radial diffusion models (statistical and event-specific), and use the global evolution of other potentially important plasma waves including plasmaspheric hiss, magnetosonic waves, and electromagnetic ion cyclotron waves from all available multi-satellite measurements. These state-of-the-art wave properties and distributions on a global scale are used to calculate diffusion coefficients, that are then adopted as inputs to simulate the dynamical electron evolution using a 3D diffusion simulation during the storm-time and the non-storm-time acceleration events respectively. We explore the similarities and differences in the dominant physical processes that cause radiation belt electron dynamics during the storm-time and non-storm-time acceleration events. The quantitative role of each physical process is determined by comparing against the Van Allen Probes electron observations at different energies, pitch angles, and L-MLT regions. This quantitative comparison further indicates instances when quasilinear theory is sufficient to explain the observed electron dynamics or when nonlinear interaction is required to reproduce the energetic electron evolution observed by the Van Allen Probes.

  14. Quantitative X-ray computed tomography peritoneography in malignant peritoneal mesothelioma patients receiving intraperitoneal chemotherapy.

    PubMed

    Leinwand, Joshua C; Zhao, Binsheng; Guo, Xiaotao; Krishnamoorthy, Saravanan; Qi, Jing; Graziano, Joseph H; Slavkovic, Vesna N; Bates, Gleneara E; Lewin, Sharyn N; Allendorf, John D; Chabot, John A; Schwartz, Lawrence H; Taub, Robert N

    2013-12-01

    Intraperitoneal chemotherapy is used to treat peritoneal surface-spreading malignancies. We sought to determine whether volume and surface area of the intraperitoneal chemotherapy compartments are associated with overall survival and posttreatment glomerular filtration rate (GFR) in malignant peritoneal mesothelioma (MPM) patients. Thirty-eight MPM patients underwent X-ray computed tomography peritoneograms during outpatient intraperitoneal chemotherapy. We calculated volume and surface area of contrast-filled compartments by semiautomated computer algorithm. We tested whether these were associated with overall survival and posttreatment GFR. Decreased likelihood of mortality was associated with larger surface areas (p = 0.0201) and smaller contrast-filled compartment volumes (p = 0.0341), controlling for age, sex, histologic subtype, and presence of residual disease >0.5 cm postoperatively. Larger volumes were associated with higher posttreatment GFR, controlling for pretreatment GFR, body surface area, surface area, and the interaction between body surface area and volume (p = 0.0167). Computed tomography peritoneography is an appropriate modality to assess for maldistribution of intraperitoneal chemotherapy. In addition to identifying catheter failure and frank loculation, quantitative analysis of the contrast-filled compartment's surface area and volume may predict overall survival and cisplatin-induced nephrotoxicity. Prospective studies should be undertaken to confirm and extend these findings to other diseases, including advanced ovarian carcinoma.

  15. Validation of a low dose simulation technique for computed tomography images.

    PubMed

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

    2014-01-01

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

  16. Positron emission tomography

    NASA Astrophysics Data System (ADS)

    Yamamoto, Y. Lucas; Thompson, Christopher J.; Diksic, Mirko; Meyer, Ernest; Feindel, William H.

    One of the most exciting new technologies introduced in the last 10 yr is positron emission tomography (PET). PET provides quantitative, three-dimensional images for the study of specific biochemical and physiological processes in the human body. This approach is analogous to quantitative in-vivo autoradiography but has the added advantage of permitting non-invasive in vivo studies. PET scanning requires a small cyclotron to produce short-lived positron emitting isotopes such as oxygen-15, carbon-11, nitrogen-13 and fluorine-18. Proper radiochemical facilities and advanced computer equipment are also needed. Most important, PET requires a multidisciplinary scientific team of physicists, radiochemists, mathematicians, biochemists and physicians. This review analyzes the most recent trends in the imaging technology, radiochemistry, methodology and clinical applications of positron emission tomography.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Amirifar, Nooshin; Lardé, Rodrigue, E-mail: rodrigue.larde@univ-rouen.fr; Talbot, Etienne

    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 showmore » that the laser pulse energy has to be well tuned to obtain reliable quantitative chemical composition measurements of undoped and doped ZnO nanomaterials.« less

  18. 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.

  19. Quantitative analysis of the right auricle with 256-slice computed tomography.

    PubMed

    Li, Cai-Ying; Gao, Bu-Lang; Pan, Tong; Xiang, Cheng; Zhang, Xue-Jing; Liu, Xiao-Wei; Fan, Qiong-Ying

    2017-04-01

    To quantitatively measure the morphology parameters of the right auricle with 256-slice multidetector computed tomography angiography (MDCTA) in healthy people. A retrospective analysis of 200 patients who had undergone coronary MDCTA with negative findings was performed. The raw imaging data were reconstructed and the right auricular volume, right atrial volume, right auricle height, base long and short axes, base perimeter and area, normal angle, and distance were quantitatively measured. Men had significantly (P < 0.05) greater values than women in the right auricular volume (13.3 ± 4.0 vs. 11.7 ± 3.7 mL) and height (33.0 ± 5.0 vs. 30.5 ± 5.2 mm), the base long axis (34.4 ± 4.1 vs. 33.2 ± 3.9 mm), area (787.6 ± 177.6 vs. 771.0 ± 143.2 mm 2 ) and perimeter (119.2 ± 17.5 vs. 115.0 ± 13.0), and the normal distance (22.4 ± 6.6 vs. 20.2 ± 6.7 mm). The normal 95 % reference range for the right auricular parameters was put forward. The right auricular parameters had a good correlation with the right atrium volume, aortic diameter, the body weight, height, and body surface area but a bad correlation with the vertebral body height. Significantly (P < 0.05) greater values were found in the normal angle and distance in subjects below than over 40 years of age. No other significant (P > 0.05) difference existed in the other right auricular parameters. Quantitative measurements of the right auricle can help us get a good understanding of the right auricular morphology and its relationship with surrounding structures and are helpful for cardiac interventions of electrophysiology and radiofrequency ablation.

  20. Quantitative Oxygenation Venography from MRI Phase

    PubMed Central

    Fan, Audrey P.; Bilgic, Berkin; Gagnon, Louis; Witzel, Thomas; Bhat, Himanshu; Rosen, Bruce R.; Adalsteinsson, Elfar

    2014-01-01

    Purpose To demonstrate acquisition and processing methods for quantitative oxygenation venograms that map in vivo oxygen saturation (SvO2) along cerebral venous vasculature. Methods Regularized quantitative susceptibility mapping (QSM) is used to reconstruct susceptibility values and estimate SvO2 in veins. QSM with ℓ1 and ℓ2 regularization are compared in numerical simulations of vessel structures with known magnetic susceptibility. Dual-echo, flow-compensated phase images are collected in three healthy volunteers to create QSM images. Bright veins in the susceptibility maps are vectorized and used to form a three-dimensional vascular mesh, or venogram, along which to display SvO2 values from QSM. Results Quantitative oxygenation venograms that map SvO2 along brain vessels of arbitrary orientation and geometry are shown in vivo. SvO2 values in major cerebral veins lie within the normal physiological range reported by 15O positron emission tomography. SvO2 from QSM is consistent with previous MR susceptometry methods for vessel segments oriented parallel to the main magnetic field. In vessel simulations, ℓ1 regularization results in less than 10% SvO2 absolute error across all vessel tilt orientations and provides more accurate SvO2 estimation than ℓ2 regularization. Conclusion The proposed analysis of susceptibility images enables reliable mapping of quantitative SvO2 along venograms and may facilitate clinical use of venous oxygenation imaging. PMID:24006229

  1. 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.

  2. Inverse transport problems in quantitative PAT for molecular imaging

    NASA Astrophysics Data System (ADS)

    Ren, Kui; Zhang, Rongting; Zhong, Yimin

    2015-12-01

    Fluorescence photoacoustic tomography (fPAT) is a molecular imaging modality that combines photoacoustic tomography with fluorescence imaging to obtain high-resolution imaging of fluorescence distributions inside heterogeneous media. The objective of this work is to study inverse problems in the quantitative step of fPAT where we intend to reconstruct physical coefficients in a coupled system of radiative transport equations using internal data recovered from ultrasound measurements. We derive uniqueness and stability results on the inverse problems and develop some efficient algorithms for image reconstructions. Numerical simulations based on synthetic data are presented to validate the theoretical analysis. The results we present here complement these in Ren K and Zhao H (2013 SIAM J. Imaging Sci. 6 2024-49) on the same problem but in the diffusive regime.

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

    PubMed Central

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

    2014-01-01

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

  4. Peri-implant assessment via cone beam computed tomography and digital periapical radiography: an ex vivo study.

    PubMed

    Silveira-Neto, Nicolau; Flores, Mateus Ericson; De Carli, João Paulo; Costa, Max Dória; Matos, Felipe de Souza; Paranhos, Luiz Renato; Linden, Maria Salete Sandini

    2017-11-01

    This research evaluated detail registration in peri-implant bone using two different cone beam computer tomography systems and a digital periapical radiograph. Three different image acquisition protocols were established for each cone beam computer tomography apparatus, and three clinical situations were simulated in an ex vivo fresh pig mandible: buccal bone defect, peri-implant bone defect, and bone contact. Data were subjected to two analyses: quantitative and qualitative. The quantitative analyses involved a comparison of real specimen measures using a digital caliper in three regions of the preserved buccal bone - A, B and E (control group) - to cone beam computer tomography images obtained with different protocols (kp1, kp2, kp3, ip1, ip2, and ip3). In the qualitative analyses, the ability to register peri-implant details via tomography and digital periapical radiography was verified, as indicated by twelve evaluators. Data were analyzed with ANOVA and Tukey's test (α=0.05). The quantitative assessment showed means statistically equal to those of the control group under the following conditions: buccal bone defect B and E with kp1 and ip1, peri-implant bone defect E with kp2 and kp3, and bone contact A with kp1, kp2, kp3, and ip2. Qualitatively, only bone contacts were significantly different among the assessments, and the p3 results differed from the p1 and p2 results. The other results were statistically equivalent. The registration of peri-implant details was influenced by the image acquisition protocol, although metal artifacts were produced in all situations. The evaluators preferred the Kodak 9000 3D cone beam computer tomography in most cases. The evaluators identified buccal bone defects better with cone beam computer tomography and identified peri-implant bone defects better with digital periapical radiography.

  5. Quantitative evaluation of retinal degeneration in royal college of surgeons rats by contrast enhanced ultrahigh resolution optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Syu, Jia-Pu; Su, Min-Jyun; Chen, Po-Wei; Ke, Chang-Chih; Chiou, Shih-Hwa; Kuo, Wen-Chuan

    2018-02-01

    This study presents a spectral domain optical coherence tomography (SD-OCT) using supercontinuum laser combined with a fundus photography for in vivo high-resolution imaging of retinal degeneration in Royal College of Surgeons (RCS-/- rat). These findings were compared with the Sprague-Dawley (SD) rats and the corresponding histology. Quantitative measurements show that changes in thickness were not significantly different between SD control and young RCS retinas (4 weeks). However, in old RCS rats (55 weeks), the thickness of photoreceptor layer decreased significantly as compared to young RCS rats (both 4 weeks and 5 weeks). After contrast enhancement method, this platform will be useful for the quantitative evaluation of the degree of retinal degeneration, treatment outcome after therapy, and drug screening development in the future.

  6. Experimental validation of a Monte-Carlo-based inversion scheme for 3D quantitative photoacoustic tomography

    NASA Astrophysics Data System (ADS)

    Buchmann, Jens; Kaplan, Bernhard A.; Prohaska, Steffen; Laufer, Jan

    2017-03-01

    Quantitative photoacoustic tomography (qPAT) aims to extract physiological parameters, such as blood oxygen saturation (sO2), from measured multi-wavelength image data sets. The challenge of this approach lies in the inherently nonlinear fluence distribution in the tissue, which has to be accounted for by using an appropriate model, and the large scale of the inverse problem. In addition, the accuracy of experimental and scanner-specific parameters, such as the wavelength dependence of the incident fluence, the acoustic detector response, the beam profile and divergence, needs to be considered. This study aims at quantitative imaging of blood sO2, as it has been shown to be a more robust parameter compared to absolute concentrations. We propose a Monte-Carlo-based inversion scheme in conjunction with a reduction in the number of variables achieved using image segmentation. The inversion scheme is experimentally validated in tissue-mimicking phantoms consisting of polymer tubes suspended in a scattering liquid. The tubes were filled with chromophore solutions at different concentration ratios. 3-D multi-spectral image data sets were acquired using a Fabry-Perot based PA scanner. A quantitative comparison of the measured data with the output of the forward model is presented. Parameter estimates of chromophore concentration ratios were found to be within 5 % of the true values.

  7. Simulation-based artifact correction (SBAC) for metrological computed tomography

    NASA Astrophysics Data System (ADS)

    Maier, Joscha; Leinweber, Carsten; Sawall, Stefan; Stoschus, Henning; Ballach, Frederic; Müller, Tobias; Hammer, Michael; Christoph, Ralf; Kachelrieß, Marc

    2017-06-01

    Computed tomography (CT) is a valuable tool for the metrolocical assessment of industrial components. However, the application of CT to the investigation of highly attenuating objects or multi-material components is often restricted by the presence of CT artifacts caused by beam hardening, x-ray scatter, off-focal radiation, partial volume effects or the cone-beam reconstruction itself. In order to overcome this limitation, this paper proposes an approach to calculate a correction term that compensates for the contribution of artifacts and thus enables an appropriate assessment of these components using CT. Therefore, we make use of computer simulations of the CT measurement process. Based on an appropriate model of the object, e.g. an initial reconstruction or a CAD model, two simulations are carried out. One simulation considers all physical effects that cause artifacts using dedicated analytic methods as well as Monte Carlo-based models. The other one represents an ideal CT measurement i.e. a measurement in parallel beam geometry with a monochromatic, point-like x-ray source and no x-ray scattering. Thus, the difference between these simulations is an estimate for the present artifacts and can be used to correct the acquired projection data or the corresponding CT reconstruction, respectively. The performance of the proposed approach is evaluated using simulated as well as measured data of single and multi-material components. Our approach yields CT reconstructions that are nearly free of artifacts and thereby clearly outperforms commonly used artifact reduction algorithms in terms of image quality. A comparison against tactile reference measurements demonstrates the ability of the proposed approach to increase the accuracy of the metrological assessment significantly.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    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 formore » 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.« less

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

    PubMed

    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.

  10. Quantitative characterization of mechanically indented in vivo human skin in adults and infants using optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Huang, Pin-Chieh; Pande, Paritosh; Shelton, Ryan L.; Joa, Frank; Moore, Dave; Gillman, Elisa; Kidd, Kimberly; Nolan, Ryan M.; Odio, Mauricio; Carr, Andrew; Boppart, Stephen A.

    2017-03-01

    Influenced by both the intrinsic viscoelasticity of the tissue constituents and the time-evolved redistribution of fluid within the tissue, the biomechanical response of skin can reflect not only localized pathology but also systemic physiology of an individual. While clinical diagnosis of skin pathologies typically relies on visual inspection and manual palpation, a more objective and quantitative approach for tissue characterization is highly desirable. Optical coherence tomography (OCT) is an interferometry-based imaging modality that enables in vivo assessment of cross-sectional tissue morphology with micron-scale resolution, which surpasses those of most standard clinical imaging tools, such as ultrasound imaging and magnetic resonance imaging. This pilot study investigates the feasibility of characterizing the biomechanical response of in vivo human skin using OCT. OCT-based quantitative metrics were developed and demonstrated on the human subject data, where a significant difference between deformed and nondeformed skin was revealed. Additionally, the quantified postindentation recovery results revealed differences between aged (adult) and young (infant) skin. These suggest that OCT has the potential to quantitatively assess the mechanically perturbed skin as well as distinguish different physiological conditions of the skin, such as changes with age or disease.

  11. 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

  12. Data analysis in emission tomography using emission-count posteriors

    NASA Astrophysics Data System (ADS)

    Sitek, Arkadiusz

    2012-11-01

    A novel approach to the analysis of emission tomography data using the posterior probability of the number of emissions per voxel (emission count) conditioned on acquired tomographic data is explored. The posterior is derived from the prior and the Poisson likelihood of the emission-count data by marginalizing voxel activities. Based on emission-count posteriors, examples of Bayesian analysis including estimation and classification tasks in emission tomography are provided. The application of the method to computer simulations of 2D tomography is demonstrated. In particular, the minimum-mean-square-error point estimator of the emission count is demonstrated. The process of finding this estimator can be considered as a tomographic image reconstruction technique since the estimates of the number of emissions per voxel divided by voxel sensitivities and acquisition time are the estimates of the voxel activities. As an example of a classification task, a hypothesis stating that some region of interest (ROI) emitted at least or at most r-times the number of events in some other ROI is tested. The ROIs are specified by the user. The analysis described in this work provides new quantitative statistical measures that can be used in decision making in diagnostic imaging using emission tomography.

  13. Quantitative observation of tracer transport with high-resolution PET

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

    Transport processes in natural porous media are typically heterogeneous over various scales. This heterogeneity is caused by the complexity of pore geometry and molecular processes. Heterogeneous processes, like diffusive transport, conservative advective transport, mixing and reactive transport, can be observed and quantified with quantitative tomography of tracer transport patterns. Positron Emission Tomography (PET) is by far the most sensitive method and perfectly selective for positron-emitting radiotracers, therefore it is suited as reference method for spatiotemporal tracer transport observations. The number of such PET-applications is steadily increasing. However, many applications are afflicted by the low spatial resolution (3 - 5 mm) of the clinical scanners from cooperating nuclear medical departments. This resolution is low in relation to typical sample dimensions of 10 cm, which are restricted by the mass attenuation of the material. In contrast, our GeoPET-method applies a high-resolution scanner with a resolution of 1 mm, which is the physical limit of the method and which is more appropriate for samples of the size of soil columns or drill cores. This higher resolution is achieved at the cost of a more elaborate image reconstruction procedure, especially considering the effects of Compton scatter. The result of the quantitative image reconstruction procedure is a suite of frames of the quantitative tracer distribution with adjustable frame rates from minutes to months. The voxel size has to be considered as reference volume of the tracer concentration. This continuous variable includes contributions from structures far below the spatial resolution, as far as a detection threshold, in the pico-molar range, is exceeded. Examples from a period of almost 10 years (Kulenkampff et al. 2008a, Kulenkampff et al. 2008b) of development and application of quantitative GeoPET-process tomography are shown. These examples include different transport processes

  14. Toward standardized quantitative image quality (IQ) assessment in computed tomography (CT): A comprehensive framework for automated and comparative IQ analysis based on ICRU Report 87.

    PubMed

    Pahn, Gregor; Skornitzke, Stephan; Schlemmer, Hans-Peter; Kauczor, Hans-Ulrich; Stiller, Wolfram

    2016-01-01

    Based on the guidelines from "Report 87: Radiation Dose and Image-quality Assessment in Computed Tomography" of the International Commission on Radiation Units and Measurements (ICRU), a software framework for automated quantitative image quality analysis was developed and its usability for a variety of scientific questions demonstrated. The extendable framework currently implements the calculation of the recommended Fourier image quality (IQ) metrics modulation transfer function (MTF) and noise-power spectrum (NPS), and additional IQ quantities such as noise magnitude, CT number accuracy, uniformity across the field-of-view, contrast-to-noise ratio (CNR) and signal-to-noise ratio (SNR) of simulated lesions for a commercially available cone-beam phantom. Sample image data were acquired with different scan and reconstruction settings on CT systems from different manufacturers. Spatial resolution is analyzed in terms of edge-spread function, line-spread-function, and MTF. 3D NPS is calculated according to ICRU Report 87, and condensed to 2D and radially averaged 1D representations. Noise magnitude, CT numbers, and uniformity of these quantities are assessed on large samples of ROIs. Low-contrast resolution (CNR, SNR) is quantitatively evaluated as a function of lesion contrast and diameter. Simultaneous automated processing of several image datasets allows for straightforward comparative assessment. The presented framework enables systematic, reproducible, automated and time-efficient quantitative IQ analysis. Consistent application of the ICRU guidelines facilitates standardization of quantitative assessment not only for routine quality assurance, but for a number of research questions, e.g. the comparison of different scanner models or acquisition protocols, and the evaluation of new technology or reconstruction methods. Copyright © 2015 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

  15. Quantification of Wear and Deformation in Different Configurations of Polyethylene Acetabular Cups Using Micro X-ray Computed Tomography

    PubMed Central

    Affatato, Saverio; Zanini, Filippo; Carmignato, Simone

    2017-01-01

    Wear is currently quantified as mass loss of the bearing materials measured using gravimetric methods. However, this method does not provide other information, such as volumetric loss or surface deviation. In this work, we validated a technique to quantify polyethylene wear in three different batches of ultrahigh-molecular-polyethylene acetabular cups used for hip implants using nondestructive microcomputed tomography. Three different configurations of polyethylene acetabular cups, previously tested under the ISO 14242 parameters, were tested on a hip simulator for an additional 2 million cycles using a modified ISO 14242 load waveform. In this context, a new approach was proposed in order to simulate, on a hip joint simulator, high-demand activities. In addition, the effects of these activities were analyzed in terms of wear and deformations of those polyethylenes by means of gravimetric method and micro X-ray computed tomography. In particular, while the gravimetric method was used for weight loss assessment, microcomputed tomography allowed for acquisition of additional quantitative information about the evolution of local wear and deformation through three-dimensional surface deviation maps for the entire cups’ surface. Experimental results showed that the wear and deformation behavior of these materials change according to different mechanical simulations. PMID:28772616

  16. Mapping Site Remediation with Electrical Resistivity Tomography Explored via Coupled-Model Simulations

    NASA Astrophysics Data System (ADS)

    Power, C.; Gerhard, J. I.; Tsourlos, P.; Giannopoulos, A.

    2011-12-01

    Remediation programs for sites contaminated with dense non-aqueous phase liquids (DNAPLs) would benefit from an ability to non-intrusively map the evolving volume and extent of the DNAPL source zone. Electrical resistivity tomography (ERT) is a well-established geophysical tool, widely used outside the remediation industry, that has significant potential for mapping DNAPL source zones. However, that potential has not been realized due to challenges in data interpretation from contaminated sites - in either a qualitative or quantitative way. The objective of this study is to evaluate the potential of ERT to map realistic, evolving DNAPL source zones within complex subsurface environments during remedial efforts. For this purpose, a novel coupled model was developed that integrates a multiphase flow model (DNAPL3D-MT), which generates realistic DNAPL release scenarios, with 3DINV, an ERT model which calculates the corresponding resistivity response. This presentation will describe the developed model coupling methodology, which integrates published petrophysical relationships to generate an electrical resistivity field that accounts for both the spatial heterogeneity of subsurface soils and the evolving spatial distribution of fluids (including permeability, porosity, clay content and air/water/DNAPL saturation). It will also present an example in which the coupled model was employed to explore the ability of ERT to track the remediation of a DNAPL source zone. A field-scale, three-dimensional release of chlorinated solvent DNAPL into heterogeneous clayey sand was simulated, including the subsurface migration and subsequent removal of the DNAPL source zone via dissolution in groundwater. Periodic surveys of this site via ERT applied at the surface were then simulated and inversion programs were used to calculate the subsurface distribution of electrical properties. This presentation will summarize this approach and its potential as a research tool exploring the range

  17. Simulation of FRET dyes allows quantitative comparison against experimental data

    NASA Astrophysics Data System (ADS)

    Reinartz, Ines; Sinner, Claude; Nettels, Daniel; Stucki-Buchli, Brigitte; Stockmar, Florian; Panek, Pawel T.; Jacob, Christoph R.; Nienhaus, Gerd Ulrich; Schuler, Benjamin; Schug, Alexander

    2018-03-01

    Fully understanding biomolecular function requires detailed insight into the systems' structural dynamics. Powerful experimental techniques such as single molecule Förster Resonance Energy Transfer (FRET) provide access to such dynamic information yet have to be carefully interpreted. Molecular simulations can complement these experiments but typically face limits in accessing slow time scales and large or unstructured systems. Here, we introduce a coarse-grained simulation technique that tackles these challenges. While requiring only few parameters, we maintain full protein flexibility and include all heavy atoms of proteins, linkers, and dyes. We are able to sufficiently reduce computational demands to simulate large or heterogeneous structural dynamics and ensembles on slow time scales found in, e.g., protein folding. The simulations allow for calculating FRET efficiencies which quantitatively agree with experimentally determined values. By providing atomically resolved trajectories, this work supports the planning and microscopic interpretation of experiments. Overall, these results highlight how simulations and experiments can complement each other leading to new insights into biomolecular dynamics and function.

  18. 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.

  19. Improving diffuse optical tomography with structural a priori from fluorescence diffuse optical tomography

    NASA Astrophysics Data System (ADS)

    Ma, Wenjuan; Gao, Feng; Duan, Linjing; Zhu, Qingzhen; Wang, Xin; Zhang, Wei; Wu, Linhui; Yi, Xi; Zhao, Huijuan

    2012-03-01

    We obtain absorption and scattering reconstructed images by incorporating a priori information of target location obtained from fluorescence diffuse optical tomography (FDOT) into the diffuse optical tomography (DOT). The main disadvantage of DOT lies in the low spatial resolution resulting from highly scattering nature of tissue in the near-infrared (NIR), but one can use it to monitor hemoglobin concentration and oxygen saturation simultaneously, as well as several other cheomphores such as water, lipids, and cytochrome-c-oxidase. Up to date, extensive effort has been made to integrate DOT with other imaging modalities such as MRI, CT, to obtain accurate optical property maps of the tissue. However, the experimental apparatus is intricate. In this study, DOT image reconstruction algorithm that incorporates a prior structural information provided by FDOT is investigated in an attempt to optimize recovery of a simulated optical property distribution. By use of a specifically designed multi-channel time-correlated single photon counting system, the proposed scheme in a transmission mode is experimentally validated to achieve simultaneous reconstruction of the fluorescent yield, lifetime, absorption and scattering coefficient. The experimental results demonstrate that the quantitative recovery of the tumor optical properties has doubled and the spatial resolution improves as well by applying the new improved method.

  20. 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. Copyright © 2014. Published by Elsevier B.V.

  1. Automated Quantitative Analysis of Retinal Microvasculature in Normal Eyes on Optical Coherence Tomography Angiography.

    PubMed

    Lupidi, Marco; Coscas, Florence; Cagini, Carlo; Fiore, Tito; Spaccini, Elisa; Fruttini, Daniela; Coscas, Gabriel

    2016-09-01

    To describe a new automated quantitative technique for displaying and analyzing macular vascular perfusion using optical coherence tomography angiography (OCT-A) and to determine a normative data set, which might be used as reference in identifying progressive changes due to different retinal vascular diseases. Reliability study. A retrospective review of 47 eyes of 47 consecutive healthy subjects imaged with a spectral-domain OCT-A device was performed in a single institution. Full-spectrum amplitude-decorrelation angiography generated OCT angiograms of the retinal superficial and deep capillary plexuses. A fully automated custom-built software was used to provide quantitative data on the foveal avascular zone (FAZ) features and the total vascular and avascular surfaces. A comparative analysis between central macular thickness (and volume) and FAZ metrics was performed. Repeatability and reproducibility were also assessed in order to establish the feasibility and reliability of the method. The comparative analysis between the superficial capillary plexus and the deep capillary plexus revealed a statistically significant difference (P < .05) in terms of FAZ perimeter, surface, and major axis and a not statistically significant difference (P > .05) when considering total vascular and avascular surfaces. A linear correlation was demonstrated between central macular thickness (and volume) and the FAZ surface. Coefficients of repeatability and reproducibility were less than 0.4, thus demonstrating high intraobserver repeatability and interobserver reproducibility for all the examined data. A quantitative approach on retinal vascular perfusion, which is visible on Spectralis OCT angiography, may offer an objective and reliable method for monitoring disease progression in several retinal vascular diseases. Copyright © 2016 Elsevier Inc. All rights reserved.

  2. Combining Ultrasound Pulse-Echo and Transmission Computed Tomography for Quantitative Imaging the Cortical Shell of Long Bone Replicas

    NASA Astrophysics Data System (ADS)

    Shortell, Matthew P.; Althomali, Marwan A. M.; Wille, Marie-Luise; Langton, Christian M.

    2017-11-01

    We demonstrate a simple technique for quantitative ultrasound imaging of the cortical shell of long bone replicas. Traditional ultrasound computed tomography instruments use the transmitted or reflected waves for separate reconstructions but suffer from strong refraction artefacts in highly heterogenous samples such as bones in soft tissue. The technique described here simplifies the long bone to a two-component composite and uses both the transmitted and reflected waves for reconstructions, allowing the speed of sound and thickness of the cortical shell to be calculated accurately. The technique is simple to implement, computationally inexpensive and sample positioning errors are minimal.

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

    PubMed Central

    Wang, Dongxu; Mackie, T Rockwell

    2015-01-01

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

  4. Correlative Energy-Dispersive X-Ray Spectroscopic Tomography and Atom Probe Tomography of the Phase Separation in an Alnico 8 Alloy.

    PubMed

    Guo, Wei; Sneed, Brian T; Zhou, Lin; Tang, Wei; Kramer, Matthew J; Cullen, David A; Poplawsky, Jonathan D

    2016-12-01

    Alnico alloys have long been used as strong permanent magnets because of their ferromagnetism and high coercivity. Understanding their structural details allows for better prediction of the resulting magnetic properties. However, quantitative three-dimensional characterization of the phase separation in these alloys is still challenged by the spatial quantification of nanoscale phases. Herein, we apply a dual tomography approach, where correlative scanning transmission electron microscopy (STEM) energy-dispersive X-ray spectroscopic (EDS) tomography and atom probe tomography (APT) are used to investigate the initial phase separation process of an alnico 8 alloy upon non-magnetic annealing. STEM-EDS tomography provides information on the morphology and volume fractions of Fe-Co-rich and Νi-Al-rich phases after spinodal decomposition in addition to quantitative information of the composition of a nanoscale volume. Subsequent analysis of a portion of the same specimen by APT offers quantitative chemical information of each phase at the sub-nanometer scale. Furthermore, APT reveals small, 2-4 nm Fe-rich α 1 phases that are nucleated in the Ni-rich α 2 matrix. From this information, we show that phase separation of the alnico 8 alloy consists of both spinodal decomposition and nucleation and growth processes. The complementary benefits and challenges associated with correlative STEM-EDS and APT are discussed.

  5. Quantitative coronary plaque analysis predicts high-risk plaque morphology on coronary computed tomography angiography: results from the ROMICAT II trial.

    PubMed

    Liu, Ting; Maurovich-Horvat, Pál; Mayrhofer, Thomas; Puchner, Stefan B; Lu, Michael T; Ghemigian, Khristine; Kitslaar, Pieter H; Broersen, Alexander; Pursnani, Amit; Hoffmann, Udo; Ferencik, Maros

    2018-02-01

    Semi-automated software can provide quantitative assessment of atherosclerotic plaques on coronary CT angiography (CTA). The relationship between established qualitative high-risk plaque features and quantitative plaque measurements has not been studied. We analyzed the association between quantitative plaque measurements and qualitative high-risk plaque features on coronary CTA. We included 260 patients with plaque who underwent coronary CTA in the Rule Out Myocardial Infarction/Ischemia Using Computer Assisted Tomography (ROMICAT) II trial. Quantitative plaque assessment and qualitative plaque characterization were performed on a per coronary segment basis. Quantitative coronary plaque measurements included plaque volume, plaque burden, remodeling index, and diameter stenosis. In qualitative analysis, high-risk plaque was present if positive remodeling, low CT attenuation plaque, napkin-ring sign or spotty calcium were detected. Univariable and multivariable logistic regression analyses were performed to assess the association between quantitative and qualitative high-risk plaque assessment. Among 888 segments with coronary plaque, high-risk plaque was present in 391 (44.0%) segments by qualitative analysis. In quantitative analysis, segments with high-risk plaque had higher total plaque volume, low CT attenuation plaque volume, plaque burden and remodeling index. Quantitatively assessed low CT attenuation plaque volume (odds ratio 1.12 per 1 mm 3 , 95% CI 1.04-1.21), positive remodeling (odds ratio 1.25 per 0.1, 95% CI 1.10-1.41) and plaque burden (odds ratio 1.53 per 0.1, 95% CI 1.08-2.16) were associated with high-risk plaque. Quantitative coronary plaque characteristics (low CT attenuation plaque volume, positive remodeling and plaque burden) measured by semi-automated software correlated with qualitative assessment of high-risk plaque features.

  6. Magnetic resonance electrical impedance tomography (MREIT): simulation study of J-substitution algorithm.

    PubMed

    Kwon, Ohin; Woo, Eung Je; Yoon, Jeong-Rock; Seo, Jin Keun

    2002-02-01

    We developed a new image reconstruction algorithm for magnetic resonance electrical impedance tomography (MREIT). MREIT is a new EIT imaging technique integrated into magnetic resonance imaging (MRI) system. Based on the assumption that internal current density distribution is obtained using magnetic resonance imaging (MRI) technique, the new image reconstruction algorithm called J-substitution algorithm produces cross-sectional static images of resistivity (or conductivity) distributions. Computer simulations show that the spatial resolution of resistivity image is comparable to that of MRI. MREIT provides accurate high-resolution cross-sectional resistivity images making resistivity values of various human tissues available for many biomedical applications.

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

    ERIC Educational Resources Information Center

    Punch, Raymond J.

    2012-01-01

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

  8. Quantitative Electron Tomography of Rubber Composites

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

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

  9. 3D noninvasive ultrasound Joule heat tomography based on acousto-electric effect using unipolar pulses: a simulation study

    PubMed Central

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

    2012-01-01

    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 acouto-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 acouto-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 any 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. PMID:23123757

  10. Compressed sensing for ultrasound computed tomography.

    PubMed

    van Sloun, Ruud; Pandharipande, Ashish; Mischi, Massimo; Demi, Libertario

    2015-06-01

    Ultrasound computed tomography (UCT) allows the reconstruction of quantitative tissue characteristics, such as speed of sound, mass density, and attenuation. Lowering its acquisition time would be beneficial; however, this is fundamentally limited by the physical time of flight and the number of transmission events. In this letter, we propose a compressed sensing solution for UCT. The adopted measurement scheme is based on compressed acquisitions, with concurrent randomised transmissions in a circular array configuration. Reconstruction of the image is then obtained by combining the born iterative method and total variation minimization, thereby exploiting variation sparsity in the image domain. Evaluation using simulated UCT scattering measurements shows that the proposed transmission scheme performs better than uniform undersampling, and is able to reduce acquisition time by almost one order of magnitude, while maintaining high spatial resolution.

  11. Determining Metacarpophalangeal Flexion Angle Tolerance for Reliable Volumetric Joint Space Measurements by High-resolution Peripheral Quantitative Computed Tomography.

    PubMed

    Tom, Stephanie; Frayne, Mark; Manske, Sarah L; Burghardt, Andrew J; Stok, Kathryn S; Boyd, Steven K; Barnabe, Cheryl

    2016-10-01

    The position-dependence of a method to measure the joint space of metacarpophalangeal (MCP) joints using high-resolution peripheral quantitative computed tomography (HR-pQCT) was studied. Cadaveric MCP were imaged at 7 flexion angles between 0 and 30 degrees. The variability in reproducibility for mean, minimum, and maximum joint space widths and volume measurements was calculated for increasing degrees of flexion. Root mean square coefficient of variance values were < 5% under 20 degrees of flexion for mean, maximum, and volumetric joint spaces. Values for minimum joint space width were optimized under 10 degrees of flexion. MCP joint space measurements should be acquired at < 10 degrees of flexion in longitudinal studies.

  12. A quantitative reconstruction software suite for SPECT imaging

    NASA Astrophysics Data System (ADS)

    Namías, Mauro; Jeraj, Robert

    2017-11-01

    Quantitative Single Photon Emission Tomography (SPECT) imaging allows for measurement of activity concentrations of a given radiotracer in vivo. Although SPECT has usually been perceived as non-quantitative by the medical community, the introduction of accurate CT based attenuation correction and scatter correction from hybrid SPECT/CT scanners has enabled SPECT systems to be as quantitative as Positron Emission Tomography (PET) systems. We implemented a software suite to reconstruct quantitative SPECT images from hybrid or dedicated SPECT systems with a separate CT scanner. Attenuation, scatter and collimator response corrections were included in an Ordered Subset Expectation Maximization (OSEM) algorithm. A novel scatter fraction estimation technique was introduced. The SPECT/CT system was calibrated with a cylindrical phantom and quantitative accuracy was assessed with an anthropomorphic phantom and a NEMA/IEC image quality phantom. Accurate activity measurements were achieved at an organ level. This software suite helps increasing quantitative accuracy of SPECT scanners.

  13. Impact of Dynamic Specimen Shape Evolution on the Atom Probe Tomography Results of Doped Epitaxial Oxide Multilayers: Comparison of Experiment and Simulation

    DOE PAGES

    Madaan, Nitesh; Bao, Jie; Nandasiri, Manjula I.; ...

    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.

  14. Massively parallel simulator of optical coherence tomography of inhomogeneous turbid media.

    PubMed

    Malektaji, Siavash; Lima, Ivan T; Escobar I, Mauricio R; Sherif, Sherif S

    2017-10-01

    An accurate and practical simulator for Optical Coherence Tomography (OCT) could be an important tool to study the underlying physical phenomena in OCT such as multiple light scattering. Recently, many researchers have investigated simulation of OCT of turbid media, e.g., tissue, using Monte Carlo methods. The main drawback of these earlier simulators is the long computational time required to produce accurate results. We developed a massively parallel simulator of OCT of inhomogeneous turbid media that obtains both Class I diffusive reflectivity, due to ballistic and quasi-ballistic scattered photons, and Class II diffusive reflectivity due to multiply scattered photons. This Monte Carlo-based simulator is implemented on graphic processing units (GPUs), using the Compute Unified Device Architecture (CUDA) platform and programming model, to exploit the parallel nature of propagation of photons in tissue. It models an arbitrary shaped sample medium as a tetrahedron-based mesh and uses an advanced importance sampling scheme. This new simulator speeds up simulations of OCT of inhomogeneous turbid media by about two orders of magnitude. To demonstrate this result, we have compared the computation times of our new parallel simulator and its serial counterpart using two samples of inhomogeneous turbid media. We have shown that our parallel implementation reduced simulation time of OCT of the first sample medium from 407 min to 92 min by using a single GPU card, to 12 min by using 8 GPU cards and to 7 min by using 16 GPU cards. For the second sample medium, the OCT simulation time was reduced from 209 h to 35.6 h by using a single GPU card, and to 4.65 h by using 8 GPU cards, and to only 2 h by using 16 GPU cards. Therefore our new parallel simulator is considerably more practical to use than its central processing unit (CPU)-based counterpart. Our new parallel OCT simulator could be a practical tool to study the different physical phenomena underlying OCT

  15. Monte Carlo Simulation for Polychromatic X-Ray Fluorescence Computed Tomography with Sheet-Beam Geometry

    PubMed Central

    Jiang, Shanghai

    2017-01-01

    X-ray fluorescence computed tomography (XFCT) based on sheet beam can save a huge amount of time to obtain a whole set of projections using synchrotron. However, it is clearly unpractical for most biomedical research laboratories. In this paper, polychromatic X-ray fluorescence computed tomography with sheet-beam geometry is tested by Monte Carlo simulation. First, two phantoms (A and B) filled with PMMA are used to simulate imaging process through GEANT 4. Phantom A contains several GNP-loaded regions with the same size (10 mm) in height and diameter but different Au weight concentration ranging from 0.3% to 1.8%. Phantom B contains twelve GNP-loaded regions with the same Au weight concentration (1.6%) but different diameter ranging from 1 mm to 9 mm. Second, discretized presentation of imaging model is established to reconstruct more accurate XFCT images. Third, XFCT images of phantoms A and B are reconstructed by filter back-projection (FBP) and maximum likelihood expectation maximization (MLEM) with and without correction, respectively. Contrast-to-noise ratio (CNR) is calculated to evaluate all the reconstructed images. Our results show that it is feasible for sheet-beam XFCT system based on polychromatic X-ray source and the discretized imaging model can be used to reconstruct more accurate images. PMID:28567054

  16. Correlative Energy-Dispersive X-Ray Spectroscopic Tomography and Atom Probe Tomography of the Phase Separation in an Alnico 8 Alloy

    DOE PAGES

    Guo, Wei; Sneed, Brian T.; Zhou, Lin; ...

    2016-12-21

    Alnico alloys have long been used as strong permanent magnets because of their ferromagnetism and high coercivity. Understanding their structural details allows for better prediction of the resulting magnetic properties. However, quantitative three-dimensional characterization of the phase separation in these alloys is still challenged by the spatial quantification of nanoscale phases. Herein, we apply a dual tomography approach, where correlative scanning transmission electron microscopy (STEM) energy-dispersive X-ray spectroscopic (EDS) tomography and atom probe tomography (APT) are used to investigate the initial phase separation process of an alnico 8 alloy upon non-magnetic annealing. STEM-EDS tomography provides information on the morphology andmore » volume fractions of Fe–Co-rich and Νi–Al-rich phases after spinodal decomposition in addition to quantitative information of the composition of a nanoscale volume. Subsequent analysis of a portion of the same specimen by APT offers quantitative chemical information of each phase at the sub-nanometer scale. Furthermore, APT reveals small, 2–4 nm Fe-rich α 1 phases that are nucleated in the Ni-rich α 2 matrix. From this information, we show that phase separation of the alnico 8 alloy consists of both spinodal decomposition and nucleation and growth processes. Lastly, we discuss the complementary benefits and challenges associated with correlative STEM-EDS and APT.« less

  17. Comparison of low- and ultralow-dose computed tomography protocols for quantitative lung and airway assessment.

    PubMed

    Hammond, Emily; Sloan, Chelsea; Newell, John D; Sieren, Jered P; Saylor, Melissa; Vidal, Craig; Hogue, Shayna; De Stefano, Frank; Sieren, Alexa; Hoffman, Eric A; Sieren, Jessica C

    2017-09-01

    Quantitative computed tomography (CT) measures are increasingly being developed and used to characterize lung disease. With recent advances in CT technologies, we sought to evaluate the quantitative accuracy of lung imaging at low- and ultralow-radiation doses with the use of iterative reconstruction (IR), tube current modulation (TCM), and spectral shaping. We investigated the effect of five independent CT protocols reconstructed with IR on quantitative airway measures and global lung measures using an in vivo large animal model as a human subject surrogate. A control protocol was chosen (NIH-SPIROMICS + TCM) and five independent protocols investigating TCM, low- and ultralow-radiation dose, and spectral shaping. For all scans, quantitative global parenchymal measurements (mean, median and standard deviation of the parenchymal HU, along with measures of emphysema) and global airway measurements (number of segmented airways and pi10) were generated. In addition, selected individual airway measurements (minor and major inner diameter, wall thickness, inner and outer area, inner and outer perimeter, wall area fraction, and inner equivalent circle diameter) were evaluated. Comparisons were made between control and target protocols using difference and repeatability measures. Estimated CT volume dose index (CTDIvol) across all protocols ranged from 7.32 mGy to 0.32 mGy. Low- and ultralow-dose protocols required more manual editing and resolved fewer airway branches; yet, comparable pi10 whole lung measures were observed across all protocols. Similar trends in acquired parenchymal and airway measurements were observed across all protocols, with increased measurement differences using the ultralow-dose protocols. However, for small airways (1.9 ± 0.2 mm) and medium airways (5.7 ± 0.4 mm), the measurement differences across all protocols were comparable to the control protocol repeatability across breath holds. Diameters, wall thickness, wall area fraction

  18. Depth-Dependent Glycosaminoglycan Concentration in Articular Cartilage by Quantitative Contrast-Enhanced Micro–Computed Tomography

    PubMed Central

    Mittelstaedt, Daniel

    2015-01-01

    Objective A quantitative contrast-enhanced micro–computed tomography (qCECT) method was developed to investigate the depth dependency and heterogeneity of the glycosaminoglycan (GAG) concentration of ex vivo cartilage equilibrated with an anionic radiographic contrast agent, Hexabrix. Design Full-thickness fresh native (n = 19 in 3 subgroups) and trypsin-degraded (n = 6) articular cartilage blocks were imaged using micro–computed tomography (μCT) at high resolution (13.4 μm3) before and after equilibration with various Hexabrix bathing concentrations. The GAG concentration was calculated depth-dependently based on Gibbs-Donnan equilibrium theory. Analysis of variance with Tukey’s post hoc was used to test for statistical significance (P < 0.05) for effect of Hexabrix bathing concentration, and for differences in bulk and zonal GAG concentrations individually and compared between native and trypsin-degraded cartilage. Results The bulk GAG concentration was calculated to be 74.44 ± 6.09 and 11.99 ± 4.24 mg/mL for native and degraded cartilage, respectively. A statistical difference was demonstrated for bulk and zonal GAG between native and degraded cartilage (P < 0.032). A statistical difference was not demonstrated for bulk GAG when comparing Hexabrix bathing concentrations (P > 0.3214) for neither native nor degraded cartilage. Depth-dependent GAG analysis of native cartilage revealed a statistical difference only in the radial zone between 30% and 50% Hexabrix bathing concentrations. Conclusions This nondestructive qCECT methodology calculated the depth-dependent GAG concentration for both native and trypsin-degraded cartilage at high spatial resolution. qCECT allows for more detailed understanding of the topography and depth dependency, which could help diagnose health, degradation, and repair of native and contrived cartilage. PMID:26425259

  19. 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.

  20. Thoracoscopic anatomical lung segmentectomy using 3D computed tomography simulation without tumour markings for non-palpable and non-visualized small lung nodules.

    PubMed

    Kato, Hirohisa; Oizumi, Hiroyuki; Suzuki, Jun; Hamada, Akira; Watarai, Hikaru; Sadahiro, Mitsuaki

    2017-09-01

    Although wedge resection can be curative for small lung tumours, tumour marking is sometimes required for resection of non-palpable or visually undetectable lung nodules as a method for identification of tumours. Tumour marking sometimes fails and occasionally causes serious complications. We have performed many thoracoscopic segmentectomies using 3D computed tomography simulation for undetectable small lung tumours without any tumour markings. The aim of this study was to investigate whether thoracoscopic segmentectomy planned with 3D computed tomography simulation could precisely remove non-palpable and visually undetectable tumours. Between January 2012 and March 2016, 58 patients underwent thoracoscopic segmentectomy using 3D computed tomography simulation for non-palpable, visually undetectable tumours. Surgical outcomes were evaluated. A total of 35, 14 and 9 patients underwent segmentectomy, subsegmentectomy and segmentectomy combined with adjacent subsegmentectomy, respectively. All tumours were correctly resected without tumour marking. The median tumour size and distance from the visceral pleura was 14 ± 5.2 mm (range 5-27 mm) and 11.6 mm (range 1-38.8 mm), respectively. Median values related to the procedures were operative time, 176 min (range 83-370 min); blood loss, 43 ml (range 0-419 ml); duration of chest tube placement, 1 day (range 1-8 days); and postoperative hospital stay, 5 days (range 3-12 days). Two cases were converted to open thoracotomy due to bleeding. Three cases required pleurodesis for pleural fistula. No recurrences occurred during the mean follow-up period of 44.4 months (range 5-53 months). Thoracoscopic segmentectomy using 3D computed tomography simulation was feasible and could be performed to resect undetectable tumours with no tumour markings. © The Author 2017. Published by Oxford University Press on behalf of the European Association for Cardio-Thoracic Surgery. All rights reserved.

  1. Simulated linear test applied to quantitative proteomics.

    PubMed

    Pham, T V; Jimenez, C R

    2016-09-01

    Omics studies aim to find significant changes due to biological or functional perturbation. However, gene and protein expression profiling experiments contain inherent technical variation. In discovery proteomics studies where the number of samples is typically small, technical variation plays an important role because it contributes considerably to the observed variation. Previous methods place both technical and biological variations in tightly integrated mathematical models that are difficult to adapt for different technological platforms. Our aim is to derive a statistical framework that allows the inclusion of a wide range of technical variability. We introduce a new method called the simulated linear test, or the s-test, that is easy to implement and easy to adapt for different models of technical variation. It generates virtual data points from the observed values according to a pre-defined technical distribution and subsequently employs linear modeling for significance analysis. We demonstrate the flexibility of the proposed approach by deriving a new significance test for quantitative discovery proteomics for which missing values have been a major issue for traditional methods such as the t-test. We evaluate the result on two label-free (phospho) proteomics datasets based on ion-intensity quantitation. Available at http://www.oncoproteomics.nl/software/stest.html : t.pham@vumc.nl. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  2. Quantitative analysis of iris parameters in keratoconus patients using optical coherence tomography.

    PubMed

    Bonfadini, Gustavo; Arora, Karun; Vianna, Lucas M; Campos, Mauro; Friedman, David; Muñoz, Beatriz; Jun, Albert S

    2015-01-01

    To investigate the relationship between quantitative iris parameters and the presence of keratoconus. Cross-sectional observational study that included 15 affected eyes of 15 patients with keratoconus and 26 eyes of 26 normal age- and sex-matched controls. Iris parameters (area, thickness, and pupil diameter) of affected and unaffected eyes were measured under standardized light and dark conditions using anterior segment optical coherence tomography (AS-OCT). To identify optimal iris thickness cutoff points to maximize the sensitivity and specificity when discriminating keratoconus eyes from normal eyes, the analysis included the use of receiver operating characteristic (ROC) curves. Iris thickness and area were lower in keratoconus eyes than in normal eyes. The mean thickness at the pupillary margin under both light and dark conditions was found to be the best parameter for discriminating normal patients from keratoconus patients. Diagnostic performance was assessed by the area under the ROC curve (AROC), which had a value of 0.8256 with 80.0% sensitivity and 84.6% specificity, using a cutoff of 0.4125 mm. The sensitivity increased to 86.7% when a cutoff of 0.4700 mm was used. In our sample, iris thickness was lower in keratoconus eyes than in normal eyes. These results suggest that tomographic parameters may provide novel adjunct approaches for keratoconus screening.

  3. A novel approach for quantitative harmonization in PET.

    PubMed

    Namías, M; Bradshaw, T; Menezes, V O; Machado, M A D; Jeraj, R

    2018-05-04

    Positron emission tomography (PET) imaging allows for measurement of activity concentrations of a given radiotracer in vivo. The quantitative capabilities of PET imaging are particularly important in the context of monitoring response to treatment, where quantitative changes in tracer uptake could be used as a biomarker of treatment response. Reconstruction algorithms and settings have a significant impact on PET quantification. In this work we introduce a novel harmonization methodology requiring only a simple cylindrical phantom and show that it can match the performance of more complex harmonization approaches based on phantoms with spherical inserts. Resolution and noise measurements from cylindrical phantoms are used to simulate the spherical inserts from NEMA image quality phantoms. An optimization algorithm was used to find the optimal smoothing filters for the simulated NEMA phantom images to identify those that best harmonized the PET scanners. Our methodology was tested on seven different PET models from two manufacturers installed at five institutions. Our methodology is able to predict contrast recovery coefficients (CRCs) from NEMA phantoms with errors within  ±5.2% for CRCmax and  ±3.7% for CRCmean (limits of agreement  =  95%). After applying the proposed harmonization protocol, all the CRC values were within the tolerances from EANM. Quantitative harmonization in compliance with the EARL FDG-PET/CT accreditation program is achieved in a simpler way, without the need of NEMA phantoms. This may lead to simplified scanner harmonization workflows more accessible to smaller institutions.

  4. What can we learn from in-soil imaging of a live plant: X-ray Computed Tomography and 3D numerical simulation of root-soil system

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Yang, Xiaofan; Varga, Tamas; Liu, Chongxuan

    Plant roots play a critical role in plant-soil-microbe interactions that occur in the rhizosphere, as well as processes with important implications to farming, forest management and climate change. X-ray computed tomography (XCT) has been proven to be an effective tool for non-invasive root imaging and analysis. A combination of XCT, open-source software, and our own code was used to noninvasively image a prairie dropseed (Sporobolus heterolepis) specimen, segment the root data to obtain a 3D image of the root structure at 31µm resolution, and extract quantitative information (root volume and surface area) from the 3D data, respectively. Based on themore » mesh generated from the root structure, computational fluid dynamics (CFD) simulations were applied to numerically investigate the root-soil-groundwater system. The plant root conductivity, soil hydraulic conductivity and transpiration rate were shown to control the groundwater distribution. The flow variability and soil water distributions under different scenarios were investigated. Parameterizations were evaluated to show their impacts on the average conductivity. The pore-scale modeling approach provides realistic simulations of rhizosphere flow processes and provides useful information that can be linked to upscaled models.« less

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

    PubMed

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

    2017-02-01

    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. 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. 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. 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.

  6. 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. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  7. Weight Multispectral Reconstruction Strategy for Enhanced Reconstruction Accuracy and Stability With Cerenkov Luminescence Tomography.

    PubMed

    Hongbo Guo; Xiaowei He; Muhan Liu; Zeyu Zhang; Zhenhua Hu; Jie Tian

    2017-06-01

    Cerenkov luminescence tomography (CLT) provides a novel technique for 3-D noninvasive detection of radiopharmaceuticals in living subjects. However, because of the severe scattering of Cerenkov light, the reconstruction accuracy and stability of CLT is still unsatisfied. In this paper, a modified weight multispectral CLT (wmCLT) reconstruction strategy was developed which split the Cerenkov radiation spectrum into several sub-spectral bands and weighted the sub-spectral results to obtain the final result. To better evaluate the property of the wmCLT reconstruction strategy in terms of accuracy, stability and practicability, several numerical simulation experiments and in vivo experiments were conducted and the results obtained were compared with the traditional multispectral CLT (mCLT) and hybrid-spectral CLT (hCLT) reconstruction strategies. The numerical simulation results indicated that wmCLT strategy significantly improved the accuracy of Cerenkov source localization and intensity quantitation and exhibited good stability in suppressing noise in numerical simulation experiments. And the comparison of the results achieved from different in vivo experiments further indicated significant improvement of the wmCLT strategy in terms of the shape recovery of the bladder and the spatial resolution of imaging xenograft tumors. Overall the strategy reported here will facilitate the development of nuclear and optical molecular tomography in theoretical study.

  8. 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. © 2013 American College of Veterinary Radiology.

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

    PubMed

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

    2016-06-01

    An in vitro study of morphological alterations between sound dental structure and artificially induced white spot lesions in human teeth, was performed through the loss of fluorescence by Quantitative Light-Induced Fluorescence (QLF) and the alterations of the light attenuation coefficient by Optical Coherence Tomography (OCT). To analyze the OCT images using a commercially available system, a special algorithm was applied, whereas the QLF images were analyzed using the software available in the commercial system employed. When analyzing the sound region against white spot lesions region by QLF, a reduction in the fluorescence intensity was observed, whilst an increase of light attenuation by the OCT system occurred. Comparison of the percentage of alteration between optical properties of sound and artificial enamel caries regions showed that OCT processed images through the attenuation of light enhanced the tooth optical alterations more than fluorescence detected by QLF System. QLF versus OCT imaging of enamel caries: a photonics assessment. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Amendt, P.; Estabrook, K.; Everett, M.

    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 sphericalmore » 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.« less

  11. Quantitative optical coherence tomography analysis for late in-stent restenotic lesions.

    PubMed

    Fu, Qiang; Suzuki, Nobuaki; Kozuma, Ken; Miyagawa, Mutsuki; Nomura, Takahiro; Kawashima, Hideyuki; Shiratori, Yoshitaka; Ishikawa, Shuichi; Kyono, Hiroyuki; Isshiki, Takaaki

    2015-01-01

    Coronary optical coherence tomography (OCT) has the potential to identify in-stent neoatherosclerosis, which is a possible risk factor for late acute coronary events after drug-eluting stent implantation. The purpose of this study was to investigate differences between mid-term and late in-stent restenosis after stent implantation by quantitative and semiautomated tissue property analysis using OCT. In total, 1063 OCT image frames of 16 lesions in 15 patients were analyzed. This included 346 frames of 6 lesions in late in-stent restenosis, which was defined as restenosis that was not detected at 6 to 12 months but ≥ 12 months after follow-up coronary angiography. Signal attenuation was circumferentially analyzed using a dedicated semiautomated software. Attenuation was assessed along 200 lines delineated radially for analysis of the in-stent restenotic lesions (between the lumen and stent contours). All lines were anchored by the image wire to avoid artifacts resulting from wire location. Stronger signal attenuation at the frame level (2.46 ± 0.78 versus 1.47 ± 0.32, P < 0.001) and higher maximum signal intensity at the lesion level (9.19 ± 0.19 versus 8.84 ± 0.32, P = 0.018) were observed in late in-stent restenotic lesions than in mid-term in-stent restenotic lesions. OCT demonstrated stronger signal attenuation and higher maximum signal intensity in late in-stent restenotic lesions than in mid-term in-stent restenotic lesions, indicating the possibility of neoatherosclerosis.

  12. 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

  13. Quantitative computed tomography versus spirometry in predicting air leak duration after major lung resection for cancer.

    PubMed

    Ueda, Kazuhiro; Kaneda, Yoshikazu; Sudo, Manabu; Mitsutaka, Jinbo; Li, Tao-Sheng; Suga, Kazuyoshi; Tanaka, Nobuyuki; Hamano, Kimikazu

    2005-11-01

    Emphysema is a well-known risk factor for developing air leak or persistent air leak after pulmonary resection. Although quantitative computed tomography (CT) and spirometry are used to diagnose emphysema, it remains controversial whether these tests are predictive of the duration of postoperative air leak. Sixty-two consecutive patients who were scheduled to undergo major lung resection for cancer were enrolled in this prospective study to define the best predictor of postoperative air leak duration. Preoperative factors analyzed included spirometric variables and area of emphysema (proportion of the low-attenuation area) that was quantified in a three-dimensional CT lung model. Chest tubes were removed the day after disappearance of the air leak, regardless of pleural drainage. Univariate and multivariate proportional hazards analyses were used to determine the influence of preoperative factors on chest tube time (air leak duration). By univariate analysis, site of resection (upper, lower), forced expiratory volume in 1 second, predicted postoperative forced expiratory volume in 1 second, and area of emphysema (< 1%, 1% to 10%, > 10%) were significant predictors of air leak duration. By multivariate analysis, site of resection and area of emphysema were the best independent determinants of air leak duration. The results were similar for patients with a smoking history (n = 40), but neither forced expiratory volume in 1 second nor predicted postoperative forced expiratory volume in 1 second were predictive of air leak duration. Quantitative CT is superior to spirometry in predicting air leak duration after major lung resection for cancer. Quantitative CT may aid in the identification of patients, particularly among those with a smoking history, requiring additional preventive procedures against air leak.

  14. Automated Quantitative Computed Tomography Versus Visual Computed Tomography Scoring in Idiopathic Pulmonary Fibrosis: Validation Against Pulmonary Function.

    PubMed

    Jacob, Joseph; Bartholmai, Brian J; Rajagopalan, Srinivasan; Kokosi, Maria; Nair, Arjun; Karwoski, Ronald; Raghunath, Sushravya M; Walsh, Simon L F; Wells, Athol U; Hansell, David M

    2016-09-01

    The aim of the study was to determine whether a novel computed tomography (CT) postprocessing software technique (CALIPER) is superior to visual CT scoring as judged by functional correlations in idiopathic pulmonary fibrosis (IPF). A total of 283 consecutive patients with IPF had CT parenchymal patterns evaluated quantitatively with CALIPER and by visual scoring. These 2 techniques were evaluated against: forced expiratory volume in 1 second (FEV1), forced vital capacity (FVC), diffusing capacity for carbon monoxide (DLco), carbon monoxide transfer coefficient (Kco), and a composite physiological index (CPI), with regard to extent of interstitial lung disease (ILD), extent of emphysema, and pulmonary vascular abnormalities. CALIPER-derived estimates of ILD extent demonstrated stronger univariate correlations than visual scores for most pulmonary function tests (PFTs): (FEV1: CALIPER R=0.29, visual R=0.18; FVC: CALIPER R=0.41, visual R=0.27; DLco: CALIPER R=0.31, visual R=0.35; CPI: CALIPER R=0.48, visual R=0.44). Correlations between CT measures of emphysema extent and PFTs were weak and did not differ significantly between CALIPER and visual scoring. Intriguingly, the pulmonary vessel volume provided similar correlations to total ILD extent scored by CALIPER for FVC, DLco, and CPI (FVC: R=0.45; DLco: R=0.34; CPI: R=0.53). CALIPER was superior to visual scoring as validated by functional correlations with PFTs. The pulmonary vessel volume, a novel CALIPER CT parameter with no visual scoring equivalent, has the potential to be a CT feature in the assessment of patients with IPF and requires further exploration.

  15. 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. © 2014 Japanese Society of Hepato-Biliary-Pancreatic Surgery.

  16. Diversity of respiratory impedance based on quantitative computed tomography in patients with COPD.

    PubMed

    Wada, Yosuke; Kitaguchi, Yoshiaki; Yasuo, Masanori; Ueno, Fumika; Kawakami, Satoshi; Fukushima, Kiyoyasu; Fujimoto, Keisaku; Hanaoka, Masayuki

    2018-01-01

    This study was conducted in order to investigate the diversity of respiratory physiology, including the respiratory impedance and reversibility of airway obstruction, based on quantitative computed tomography (CT) in patients with COPD. Medical records of 174 stable COPD patients were retrospectively reviewed to obtain the patients' clinical data, including the pulmonary function and imaging data. According to the software-based quantification of the degree of emphysema and airway wall thickness, the patients were classified into the "normal by CT" phenotype, the airway-dominant phenotype, the emphysema-dominant phenotype, and the mixed phenotype. The pulmonary function, including the respiratory impedance evaluated by using the forced oscillation technique (FOT) and the reversibility of airway obstruction in response to inhaled short-acting β 2 -agonists, was then compared among the four phenotypes. The respiratory system resistance at 5 and 20 Hz (R5 and R20) was significantly higher, and the respiratory system reactance at 5 Hz (X5) was significantly more negative in the airway-dominant and mixed phenotypes than in the other phenotypes. The within-breath changes of X5 (ΔX5) were significantly greater in the mixed phenotype than in the "normal by CT" and emphysema-dominant phenotypes. The FOT parameters (R5, R20, and X5) were significantly correlated with indices of the degree of airway wall thickness and significantly but weakly correlated with the reversibility of airway obstruction. There was no significant correlation between the FOT parameters (R5, R20, and X5) and the degree of emphysema. There is a diversity of respiratory physiology, including the respiratory impedance and reversibility of airway obstruction, based on quantitative CT in patients with COPD. The FOT measurements may reflect the degree of airway disease and aid in detecting airway remodeling in patients with COPD.

  17. Correlation of quantitative dual-energy computed tomography iodine maps and abdominal computed tomography perfusion measurements: are single-acquisition dual-energy computed tomography iodine maps more than a reduced-dose surrogate of conventional computed tomography perfusion?

    PubMed

    Stiller, Wolfram; Skornitzke, Stephan; Fritz, Franziska; Klauss, Miriam; Hansen, Jens; Pahn, Gregor; Grenacher, Lars; Kauczor, Hans-Ulrich

    2015-10-01

    Study objectives were the quantitative evaluation of whether conventional abdominal computed tomography (CT) perfusion measurements mathematically correlate with quantitative single-acquisition dual-energy CT (DECT) iodine concentration maps, the determination of the optimum time of acquisition for achieving maximum correlation, and the estimation of the potential for radiation exposure reduction when replacing conventional CT perfusion by single-acquisition DECT iodine concentration maps. Dual-energy CT perfusion sequences were dynamically acquired over 51 seconds (34 acquisitions every 1.5 seconds) in 24 patients with histologically verified pancreatic carcinoma using dual-source DECT at tube potentials of 80 kVp and 140 kVp. Using software developed in-house, perfusion maps were calculated from 80-kVp image series using the maximum slope model after deformable motion correction. In addition, quantitative iodine maps were calculated for each of the 34 DECT acquisitions per patient. Within a manual segmentation of the pancreas, voxel-by-voxel correlation between the perfusion map and each of the iodine maps was calculated for each patient to determine the optimum time of acquisition topt defined as the acquisition time of the iodine map with the highest correlation coefficient. Subsequently, regions of interest were placed inside the tumor and inside healthy pancreatic tissue, and correlation between mean perfusion values and mean iodine concentrations within these regions of interest at topt was calculated for the patient sample. The mean (SD) topt was 31.7 (5.4) seconds after the start of contrast agent injection. The mean (SD) perfusion values for healthy pancreatic and tumor tissues were 67.8 (26.7) mL per 100 mL/min and 43.7 (32.2) mL per 100 mL/min, respectively. At topt, the mean (SD) iodine concentrations were 2.07 (0.71) mg/mL in healthy pancreatic and 1.69 (0.98) mg/mL in tumor tissue, respectively. Overall, the correlation between perfusion values and

  18. In vivo classification of human skin burns using machine learning and quantitative features captured by optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Singla, Neeru; Srivastava, Vishal; Singh Mehta, Dalip

    2018-02-01

    We report the first fully automated detection of human skin burn injuries in vivo, with the goal of automatic surgical margin assessment based on optical coherence tomography (OCT) images. Our proposed automated procedure entails building a machine-learning-based classifier by extracting quantitative features from normal and burn tissue images recorded by OCT. In this study, 56 samples (28 normal, 28 burned) were imaged by OCT and eight features were extracted. A linear model classifier was trained using 34 samples and 22 samples were used to test the model. Sensitivity of 91.6% and specificity of 90% were obtained. Our results demonstrate the capability of a computer-aided technique for accurately and automatically identifying burn tissue resection margins during surgical treatment.

  19. X-ray Micro-Tomography of Ablative Heat Shield Materials

    NASA Technical Reports Server (NTRS)

    Panerai, Francesco; Ferguson, Joseph; Borner, Arnaud; Mansour, Nagi N.; Barnard, Harold S.; MacDowell, Alastair A.; Parkinson, Dilworth Y.

    2016-01-01

    X-ray micro-tomography is a non-destructive characterization technique that allows imaging of materials structures with voxel sizes in the micrometer range. This level of resolution makes the technique very attractive for imaging porous ablators used in hypersonic entry systems. Besides providing a high fidelity description of the material architecture, micro-tomography enables computations of bulk material properties and simulations of micro-scale phenomena. This presentation provides an overview of a collaborative effort between NASA Ames Research Center and Lawrence Berkeley National Laboratory, aimed at developing micro-tomography experiments and simulations for porous ablative materials. Measurements are carried using x-rays from the Advanced Light Source at Berkeley Lab on different classes of ablative materials used in NASA entry systems. Challenges, strengths and limitations of the technique for imaging materials such as lightweight carbon-phenolic systems and woven textiles are discussed. Computational tools developed to perform numerical simulations based on micro-tomography are described. These enable computations of material properties such as permeability, thermal and radiative conductivity, tortuosity and other parameters that are used in ablator response models. Finally, we present the design of environmental cells that enable imaging materials under simulated operational conditions, such as high temperature, mechanical loads and oxidizing atmospheres.Keywords: Micro-tomography, Porous media, Ablation

  20. 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.

  1. Electrodeposition of Highly Porous Pt Nanoparticles Studied by Quantitative 3D Electron Tomography: Influence of Growth Mechanisms and Potential Cycling on the Active Surface Area.

    PubMed

    Ustarroz, Jon; Geboes, Bart; Vanrompay, Hans; Sentosun, Kadir; Bals, Sara; Breugelmans, Tom; Hubin, Annick

    2017-05-17

    Nanoporous Pt nanoparticles (NPs) are promising fuel cell catalysts due to their large surface area and increased electrocatalytic activity toward the oxygen reduction reaction (ORR). Herein, we report on the influence of the growth mechanisms on the surface properties of electrodeposited Pt dendritic NPs with large surface areas. The electrochemically active surface was studied by hydrogen underpotential deposition (H UPD) and compared for the first time to high-angle annular dark field scanning transmission electron microscopy (HAADF-STEM) quantitative 3D electron tomography of individual nanoparticles. Large nucleation overpotential leads to a large surface coverage of roughened spheroids, which provide a large roughness factor (R f ) but low mass-specific electrochemically active surface area (EASA). Lowering the nucleation overpotential leads to highly porous Pt NPs with pores stretching to the center of the structure. At the expense of smaller R f , the obtained EASA values of these structures are in the range of those of large surface area supported fuel cell catalysts. The active surface area of the Pt dendritic NPs was measured by electron tomography, and it was found that the potential cycling in the H adsorption/desorption and Pt oxidation/reduction region, which is generally performed to determine the EASA, leads to a significant reduction of that surface area due to a partial collapse of their dendritic and porous morphology. Interestingly, the extrapolation of the microscopic tomography results in macroscopic electrochemical parameters indicates that the surface properties measured by H UPD are comparable to the values measured on individual NPs by electron tomography after the degradation caused by the H UPD measurement. These results highlight that the combination of electrochemical and quantitative 3D surface analysis techniques is essential to provide insights into the surface properties, the electrochemical stability, and, hence, the

  2. 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.

  3. What can we learn from in-soil imaging of a live plant: X-ray Computed Tomography and 3D numerical simulation of root-soil system

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Yang, Xiaofan; Varga, Tamas; Liu, Chongxuan

    Plant roots play a critical role in plant-soil-microbe interactions that occur in the rhizosphere. X-ray Computed Tomography (XCT) has been proven to be an effective tool for non-invasive root imaging and analysis. A combination of XCT, open-source software, and in-house developed code was used to non-invasively image a prairie dropseed (Sporobolus heterolepis) specimen, segment the root data to obtain a 3D image of the root structure, and extract quantitative information from the 3D data, respectively. Based on the explicitly-resolved root structure, pore-scale computational fluid dynamics (CFD) simulations were applied to numerically investigate the root-soil-groundwater system. The plant root conductivity, soilmore » hydraulic conductivity and transpiration rate were shown to control the groundwater distribution. Furthermore, the coupled imaging-modeling approach demonstrates a realistic platform to investigate rhizosphere flow processes and would be feasible to provide useful information linked to upscaled models.« less

  4. What can we learn from in-soil imaging of a live plant: X-ray Computed Tomography and 3D numerical simulation of root-soil system

    DOE PAGES

    Yang, Xiaofan; Varga, Tamas; Liu, Chongxuan; ...

    2017-05-04

    Plant roots play a critical role in plant-soil-microbe interactions that occur in the rhizosphere. X-ray Computed Tomography (XCT) has been proven to be an effective tool for non-invasive root imaging and analysis. A combination of XCT, open-source software, and in-house developed code was used to non-invasively image a prairie dropseed (Sporobolus heterolepis) specimen, segment the root data to obtain a 3D image of the root structure, and extract quantitative information from the 3D data, respectively. Based on the explicitly-resolved root structure, pore-scale computational fluid dynamics (CFD) simulations were applied to numerically investigate the root-soil-groundwater system. The plant root conductivity, soilmore » hydraulic conductivity and transpiration rate were shown to control the groundwater distribution. Furthermore, the coupled imaging-modeling approach demonstrates a realistic platform to investigate rhizosphere flow processes and would be feasible to provide useful information linked to upscaled models.« less

  5. Monte-Carlo-based phase retardation estimator for polarization sensitive optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Duan, Lian; Makita, Shuichi; Yamanari, Masahiro; Lim, Yiheng; Yasuno, Yoshiaki

    2011-08-01

    A Monte-Carlo-based phase retardation estimator is developed to correct the systematic error in phase retardation measurement by polarization sensitive optical coherence tomography (PS-OCT). Recent research has revealed that the phase retardation measured by PS-OCT has a distribution that is neither symmetric nor centered at the true value. Hence, a standard mean estimator gives us erroneous estimations of phase retardation, and it degrades the performance of PS-OCT for quantitative assessment. In this paper, the noise property in phase retardation is investigated in detail by Monte-Carlo simulation and experiments. A distribution transform function is designed to eliminate the systematic error by using the result of the Monte-Carlo simulation. This distribution transformation is followed by a mean estimator. This process provides a significantly better estimation of phase retardation than a standard mean estimator. This method is validated both by numerical simulations and experiments. The application of this method to in vitro and in vivo biological samples is also demonstrated.

  6. 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

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

    NASA Astrophysics Data System (ADS)

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

    2008-10-01

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

  8. Mapping Bone Mineral Density Obtained by Quantitative Computed Tomography to Bone Volume Fraction

    NASA Technical Reports Server (NTRS)

    Pennline, James A.; Mulugeta, Lealem

    2017-01-01

    Methods for relating or mapping estimates of volumetric Bone Mineral Density (vBMD) obtained by Quantitative Computed Tomography to Bone Volume Fraction (BVF) are outlined mathematically. The methods are based on definitions of bone properties, cited experimental studies and regression relations derived from them for trabecular bone in the proximal femur. Using an experimental range of values in the intertrochanteric region obtained from male and female human subjects, age 18 to 49, the BVF values calculated from four different methods were compared to the experimental average and numerical range. The BVF values computed from the conversion method used data from two sources. One source provided pre bed rest vBMD values in the intertrochanteric region from 24 bed rest subject who participated in a 70 day study. Another source contained preflight vBMD values from 18 astronauts who spent 4 to 6 months on the ISS. To aid the use of a mapping from BMD to BVF, the discussion includes how to formulate them for purpose of computational modeling. An application of the conversions would be used to aid in modeling of time varying changes in vBMD as it relates to changes in BVF via bone remodeling and/or modeling.

  9. Accurate and quantitative polarization-sensitive OCT by unbiased birefringence estimator with noise-stochastic correction

    NASA Astrophysics Data System (ADS)

    Kasaragod, Deepa; Sugiyama, Satoshi; Ikuno, Yasushi; Alonso-Caneiro, David; Yamanari, Masahiro; Fukuda, Shinichi; Oshika, Tetsuro; Hong, Young-Joo; Li, En; Makita, Shuichi; Miura, Masahiro; Yasuno, Yoshiaki

    2016-03-01

    Polarization sensitive optical coherence tomography (PS-OCT) is a functional extension of OCT that contrasts the polarization properties of tissues. It has been applied to ophthalmology, cardiology, etc. Proper quantitative imaging is required for a widespread clinical utility. However, the conventional method of averaging to improve the signal to noise ratio (SNR) and the contrast of the phase retardation (or birefringence) images introduce a noise bias offset from the true value. This bias reduces the effectiveness of birefringence contrast for a quantitative study. Although coherent averaging of Jones matrix tomography has been widely utilized and has improved the image quality, the fundamental limitation of nonlinear dependency of phase retardation and birefringence to the SNR was not overcome. So the birefringence obtained by PS-OCT was still not accurate for a quantitative imaging. The nonlinear effect of SNR to phase retardation and birefringence measurement was previously formulated in detail for a Jones matrix OCT (JM-OCT) [1]. Based on this, we had developed a maximum a-posteriori (MAP) estimator and quantitative birefringence imaging was demonstrated [2]. However, this first version of estimator had a theoretical shortcoming. It did not take into account the stochastic nature of SNR of OCT signal. In this paper, we present an improved version of the MAP estimator which takes into account the stochastic property of SNR. This estimator uses a probability distribution function (PDF) of true local retardation, which is proportional to birefringence, under a specific set of measurements of the birefringence and SNR. The PDF was pre-computed by a Monte-Carlo (MC) simulation based on the mathematical model of JM-OCT before the measurement. A comparison between this new MAP estimator, our previous MAP estimator [2], and the standard mean estimator is presented. The comparisons are performed both by numerical simulation and in vivo measurements of anterior and

  10. Preliminary experiments on pharmacokinetic diffuse fluorescence tomography of CT-scanning mode

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

    In vivo tomographic imaging of the fluorescence pharmacokinetic parameters in tissues can provide additional specific and quantitative physiological and pathological information to that of fluorescence concentration. This modality normally requires a highly-sensitive diffuse fluorescence tomography (DFT) working in dynamic way to finally extract the pharmacokinetic parameters from the measured pharmacokinetics-associated temporally-varying boundary intensity. This paper is devoted to preliminary experimental validation of our proposed direct reconstruction scheme of instantaneous sampling based pharmacokinetic-DFT: A highly-sensitive DFT system of CT-scanning mode working with parallel four photomultiplier-tube photon-counting channels is developed to generate an instantaneous sampling dataset; A direct reconstruction scheme then extracts images of the pharmacokinetic parameters using the adaptive-EKF strategy. We design a dynamic phantom that can simulate the agent metabolism in living tissue. The results of the dynamic phantom experiments verify the validity of the experiment system and reconstruction algorithms, and demonstrate that system provides good resolution, high sensitivity and quantitativeness at different pump speed.

  11. Geoscientific process monitoring with positron emission tomography (GeoPET)

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

    Transport processes in geomaterials can be observed with input-output experiments, which yield no direct information on the impact of heterogeneities, or they can be assessed by model simulations based on structural imaging using µ-CT. Positron emission tomography (PET) provides an alternative experimental observation method which directly and quantitatively yields the spatio-temporal distribution of tracer concentration. Process observation with PET benefits from its extremely high sensitivity together with a resolution that is acceptable in relation to standard drill core sizes. We strongly recommend applying high-resolution PET scanners in order to achieve a resolution on the order of 1 mm. We discuss the particularities of PET applications in geoscientific experiments (GeoPET), which essentially are due to high material density. Although PET is rather insensitive to matrix effects, mass attenuation and Compton scattering have to be corrected thoroughly in order to derive quantitative values. Examples of process monitoring of advection and diffusion processes with GeoPET illustrate the procedure and the experimental conditions, as well as the benefits and limits of the method.

  12. Changes in bone structure of Corriedale sheep with inherited rickets: a peripheral quantitative computed tomography assessment.

    PubMed

    Dittmer, Keren E; Firth, Elwyn C; Thompson, Keith G; Marshall, Jonathan C; Blair, Hugh T

    2011-03-01

    An inherited skeletal disease with gross and microscopic features of rickets has been diagnosed in Corriedale sheep in New Zealand. The aim of this study was to quantify the changes present in tibia from sheep with inherited rickets using peripheral quantitative computed tomography. In affected sheep, scans in the proximal tibia, where metaphysis becomes diaphysis, showed significantly greater trabecular bone mineral content (BMC) and bone mineral density (BMD). The sheep with inherited rickets had significantly greater BMC and bone area in the mid-diaphysis of the proximal tibia compared to control sheep. However, BMD in the mid-diaphysis was significantly less in affected sheep than in controls, due to the greater cortical area and lower voxel density values in affected sheep. From this it was concluded that the increased strain on under-mineralised bone in sheep with inherited rickets led to increased bone mass in an attempt to improve bone strength. Copyright © 2010 Elsevier Ltd. All rights reserved.

  13. Electron tomography simulator with realistic 3D phantom for evaluation of acquisition, alignment and reconstruction methods.

    PubMed

    Wan, Xiaohua; Katchalski, Tsvi; Churas, Christopher; Ghosh, Sreya; Phan, Sebastien; Lawrence, Albert; Hao, Yu; Zhou, Ziying; Chen, Ruijuan; Chen, Yu; Zhang, Fa; Ellisman, Mark H

    2017-05-01

    Because of the significance of electron microscope tomography in the investigation of biological structure at nanometer scales, ongoing improvement efforts have been continuous over recent years. This is particularly true in the case of software developments. Nevertheless, verification of improvements delivered by new algorithms and software remains difficult. Current analysis tools do not provide adaptable and consistent methods for quality assessment. This is particularly true with images of biological samples, due to image complexity, variability, low contrast and noise. We report an electron tomography (ET) simulator with accurate ray optics modeling of image formation that includes curvilinear trajectories through the sample, warping of the sample and noise. As a demonstration of the utility of our approach, we have concentrated on providing verification of the class of reconstruction methods applicable to wide field images of stained plastic-embedded samples. Accordingly, we have also constructed digital phantoms derived from serial block face scanning electron microscope images. These phantoms are also easily modified to include alignment features to test alignment algorithms. The combination of more realistic phantoms with more faithful simulations facilitates objective comparison of acquisition parameters, alignment and reconstruction algorithms and their range of applicability. With proper phantoms, this approach can also be modified to include more complex optical models, including distance-dependent blurring and phase contrast functions, such as may occur in cryotomography. Copyright © 2017 Elsevier Inc. All rights reserved.

  14. Quantitative Evaluation of PET Respiratory Motion Correction Using MR Derived Simulated Data

    NASA Astrophysics Data System (ADS)

    Polycarpou, Irene; Tsoumpas, Charalampos; King, Andrew P.; Marsden, Paul K.

    2015-12-01

    The impact of respiratory motion correction on quantitative accuracy in PET imaging is evaluated using simulations for variable patient specific characteristics such as tumor uptake and respiratory pattern. Respiratory patterns from real patients were acquired, with long quiescent motion periods (type-1) as commonly observed in most patients and with long-term amplitude variability as is expected under conditions of difficult breathing (type-2). The respiratory patterns were combined with an MR-derived motion model to simulate real-time 4-D PET-MR datasets. Lung and liver tumors were simulated with diameters of 10 and 12 mm and tumor-to-background ratio ranging from 3:1 to 6:1. Projection data for 6- and 3-mm PET resolution were generated for the Philips Gemini scanner and reconstructed without and with motion correction using OSEM (2 iterations, 23 subsets). Motion correction was incorporated into the reconstruction process based on MR-derived motion fields. Tumor peak standardized uptake values (SUVpeak) were calculated from 30 noise realizations. Respiratory motion correction improves the quantitative performance with the greatest benefit observed for patients of breathing type-2. For breathing type-1 after applying motion correction, SUVpeak of 12-mm liver tumor with 6:1 contrast was increased by 46% for a current PET resolution (i.e., 6 mm) and by 47% for a higher PET resolution (i.e., 3 mm). Furthermore, the results of this study indicate that the benefit of higher scanner resolution is small unless motion correction is applied. In particular, for large liver tumor (12 mm) with low contrast (3:1) after motion correction, the SUVpeak was increased by 34% for 6-mm resolution and by 50% for a higher PET resolution (i.e., 3-mm resolution. This investigation indicates that there is a high impact of respiratory motion correction on tumor quantitative accuracy and that motion correction is important in order to benefit from the increased resolution of future PET

  15. 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.

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

    PubMed Central

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

    2016-01-01

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

  17. Quantitative X-ray fluorescence computed tomography for low-Z samples using an iterative absorption correction algorithm

    NASA Astrophysics Data System (ADS)

    Huang, Rong; Limburg, Karin; Rohtla, Mehis

    2017-05-01

    X-ray fluorescence computed tomography is often used to measure trace element distributions within low-Z samples, using algorithms capable of X-ray absorption correction when sample self-absorption is not negligible. Its reconstruction is more complicated compared to transmission tomography, and therefore not widely used. We describe in this paper a very practical iterative method that uses widely available transmission tomography reconstruction software for fluorescence tomography. With this method, sample self-absorption can be corrected not only for the absorption within the measured layer but also for the absorption by material beyond that layer. By combining tomography with analysis for scanning X-ray fluorescence microscopy, absolute concentrations of trace elements can be obtained. By using widely shared software, we not only minimized the coding, took advantage of computing efficiency of fast Fourier transform in transmission tomography software, but also thereby accessed well-developed data processing tools coming with well-known and reliable software packages. The convergence of the iterations was also carefully studied for fluorescence of different attenuation lengths. As an example, fish eye lenses could provide valuable information about fish life-history and endured environmental conditions. Given the lens's spherical shape and sometimes the short distance from sample to detector for detecting low concentration trace elements, its tomography data are affected by absorption related to material beyond the measured layer but can be reconstructed well with our method. Fish eye lens tomography results are compared with sliced lens 2D fluorescence mapping with good agreement, and with tomography providing better spatial resolution.

  18. Simulating the influence of scatter and beam hardening in dimensional computed tomography

    NASA Astrophysics Data System (ADS)

    Lifton, J. J.; Carmignato, S.

    2017-10-01

    Cone-beam x-ray computed tomography (XCT) is a radiographic scanning technique that allows the non-destructive dimensional measurement of an object’s internal and external features. XCT measurements are influenced by a number of different factors that are poorly understood. This work investigates how non-linear x-ray attenuation caused by beam hardening and scatter influences XCT-based dimensional measurements through the use of simulated data. For the measurement task considered, both scatter and beam hardening are found to influence dimensional measurements when evaluated using the ISO50 surface determination method. On the other hand, only beam hardening is found to influence dimensional measurements when evaluated using an advanced surface determination method. Based on the results presented, recommendations on the use of beam hardening and scatter correction for dimensional XCT are given.

  19. Imaging of pharmacokinetic rates of indocyanine green in mouse liver with a hybrid fluorescence molecular tomography/x-ray computed tomography system.

    PubMed

    Zhang, Guanglei; Liu, Fei; Zhang, Bin; He, Yun; Luo, Jianwen; Bai, Jing

    2013-04-01

    Pharmacokinetic rates have the potential to provide quantitative physiological and pathological information for biological studies and drug development. Fluorescence molecular tomography (FMT) is an attractive imaging tool for three-dimensionally resolving fluorophore distribution in small animals. In this letter, pharmacokinetic rates of indocyanine green (ICG) in mouse liver are imaged with a hybrid FMT and x-ray computed tomography (XCT) system. A recently developed FMT method using structural priors from an XCT system is adopted to improve the quality of FMT reconstruction. In the in vivo experiments, images of uptake and excretion rates of ICG in mouse liver are obtained, which can be used to quantitatively evaluate liver function. The accuracy of the results is validated by a fiber-based fluorescence measurement system.

  20. A Quantitative Approach to Distinguish Pneumonia From Atelectasis Using Computed Tomography Attenuation.

    PubMed

    Edwards, Rachael M; Godwin, J David; Hippe, Dan S; Kicska, Gregory

    2016-01-01

    It is known that atelectasis demonstrates greater contrast enhancement than pneumonia on computed tomography (CT). However, the effectiveness of using a Hounsfield unit (HU) threshold to distinguish pneumonia from atelectasis has never been shown. The objective of the study is to demonstrate that an HU threshold can be quantitatively used to effectively distinguish pneumonia from atelectasis. Retrospectively identified CT pulmonary angiogram examinations that did not show pulmonary embolism but contained nonaerated lungs were classified as atelectasis or pneumonia based on established clinical criteria. The HU attenuation was measured in these nonaerated lungs. Receiver operating characteristic (ROC) analysis was performed to determine the area under the ROC curve, sensitivity, and specificity of using the attenuation to distinguish pneumonia from atelectasis. Sixty-eight nonaerated lungs were measured in 55 patients. The mean (SD) enhancement was 62 (18) HU in pneumonia and 119 (24) HU in atelectasis (P < 0.001). A threshold of 92 HU diagnosed pneumonia with 97% sensitivity (confidence interval [CI], 80%-99%) and 85% specificity (CI, 70-93). Accuracy, measured as area under the ROC curve, was 0.97 (CI, 0.89-0.99). We have established that a threshold HU value can be used to confidently distinguish pneumonia from atelectasis with our standard CT pulmonary angiogram imaging protocol and patient population. This suggests that a similar threshold HU value may be determined for other scanning protocols, and application of this threshold may facilitate a more confident diagnosis of pneumonia and thus speed treatment.

  1. Facilitating arrhythmia simulation: the method of quantitative cellular automata modeling and parallel running

    PubMed Central

    Zhu, Hao; Sun, Yan; Rajagopal, Gunaretnam; Mondry, Adrian; Dhar, Pawan

    2004-01-01

    Background Many arrhythmias are triggered by abnormal electrical activity at the ionic channel and cell level, and then evolve spatio-temporally within the heart. To understand arrhythmias better and to diagnose them more precisely by their ECG waveforms, a whole-heart model is required to explore the association between the massively parallel activities at the channel/cell level and the integrative electrophysiological phenomena at organ level. Methods We have developed a method to build large-scale electrophysiological models by using extended cellular automata, and to run such models on a cluster of shared memory machines. We describe here the method, including the extension of a language-based cellular automaton to implement quantitative computing, the building of a whole-heart model with Visible Human Project data, the parallelization of the model on a cluster of shared memory computers with OpenMP and MPI hybrid programming, and a simulation algorithm that links cellular activity with the ECG. Results We demonstrate that electrical activities at channel, cell, and organ levels can be traced and captured conveniently in our extended cellular automaton system. Examples of some ECG waveforms simulated with a 2-D slice are given to support the ECG simulation algorithm. A performance evaluation of the 3-D model on a four-node cluster is also given. Conclusions Quantitative multicellular modeling with extended cellular automata is a highly efficient and widely applicable method to weave experimental data at different levels into computational models. This process can be used to investigate complex and collective biological activities that can be described neither by their governing differentiation equations nor by discrete parallel computation. Transparent cluster computing is a convenient and effective method to make time-consuming simulation feasible. Arrhythmias, as a typical case, can be effectively simulated with the methods described. PMID:15339335

  2. MCNP6 simulation of radiographs generated from megaelectron volt X-rays for characterizing a computed tomography system

    NASA Astrophysics Data System (ADS)

    Dooraghi, Alex A.; Tringe, Joseph W.

    2018-04-01

    To evaluate conventional munition, we simulated an x-ray computed tomography (CT) system for generating radiographs from nominal x-ray energies of 6 or 9 megaelectron volts (MeV). CT simulations, informed by measured data, allow for optimization of both system design and acquisition techniques necessary to enhance image quality. MCNP6 radiographic simulation tools were used to model ideal detector responses (DR) that assume either (1) a detector response proportional to photon flux (N) or (2) a detector response proportional to energy flux (E). As scatter may become significant with MeV x-ray systems, simulations were performed with and without the inclusion of object scatter. Simulations were compared against measurements of a cylindrical munition component principally composed of HMX, tungsten and aluminum encased in carbon fiber. Simulations and measurements used a 6 MeV peak energy x-ray spectrum filtered with 3.175 mm of tantalum. A detector response proportional to energy which includes object scatter agrees to within 0.6 % of the measured line integral of the linear attenuation coefficient. Exclusion of scatter increases the difference between measurement and simulation to 5 %. A detector response proportional to photon flux agrees to within 20 % when object scatter is included in the simulation and 27 % when object scatter is excluded.

  3. GePEToS: A Geant4 Monte Carlo Simulation Package for Positron Emission Tomography

    NASA Astrophysics Data System (ADS)

    Jan, S.; Collot, J.; Gallin-Martel, M.-L.; Martin, P.; Mayet, F.; Tournefier, E.

    2005-02-01

    GePEToS is a simulation framework developed over the last few years for assessing the instrumental performance of future positron emission tomography (PET) scanners. It is based on Geant4, written in object-oriented C++ and runs on Linux platforms. The validity of GePEToS has been tested on the well-known Siemens ECAT EXACT HR+ camera. The results of two application examples are presented: the design optimization of a liquid Xe /spl mu/PET camera dedicated to small animal imaging as well as the evaluation of the effect of a strong axial magnetic field on the image resolution of a Concorde P4 /spl mu/PET camera.

  4. Material characterization using ultrasound tomography

    NASA Astrophysics Data System (ADS)

    Falardeau, Timothe; Belanger, Pierre

    2018-04-01

    Characterization of material properties can be performed using a wide array of methods e.g. X-ray diffraction or tensile testing. Each method leads to a limited set of material properties. This paper is interested in using ultrasound tomography to map speed of sound inside a material sample. The velocity inside the sample is directly related to its elastic properties. Recent develop-ments in ultrasound diffraction tomography have enabled velocity mapping of high velocity contrast objects using a combination of bent-ray time-of-flight tomography and diffraction tomography. In this study, ultrasound diffraction tomography was investigated using simulations in human bone phantoms. A finite element model was developed to assess the influence of the frequency, the number of transduction positions and the distance from the sample as well as to adapt the imaging algorithm. The average velocity in both regions of the bone phantoms were within 5% of the true value.

  5. Characterizing root system characteristics with Electrical resistivity Tomography: a virtual rhizotron simulation

    NASA Astrophysics Data System (ADS)

    Rao, Sathyanarayan; Ehosioke, Solomon; Lesparre, Nolwenn; Nguyen, Frédéric; Javaux, Mathieu

    2017-04-01

    Electrical Resistivity Tomography (ERT) is more and more used for monitoring soil water content in a cropped soil. Yet, the impact of roots on the signal is often neglected and a topic of controversy. In several studies related to soil-root system, it has been showed that the measured root mass density statistically correlates with the electrical conductivity (EC) data obtained from ERT. In addition, some studies suggest that some roots are more electrically conductive than soil for most water content. Thus, higher EC of roots suggest that it might have a measurable impact on ERT signals. In this work, virtual rhizotrons are simulated using the software package called R-SWMS that solves water and solute transport in plant root-soil system, including root growth. The distribution of water content obtained from R-SWMS simulation is converted into EC data using pedo-physical models. The electrical properties of roots and rhizosphere are explicitly included in the EC data to form a conductivity map (CM) with a very detailed spatial resolution. Forward ERT simulations is then carried out for CM generated for various root architectures and soil conditions to study the impact of roots on ERT forward (current and voltage patterns) and inverse solutions. It is demonstrated that under typical injection schemes with lateral electrodes, root system is hardly measurable. However, it is showed that adding electrodes and constraints on the ERT inversion based on root architecture help quantifying root system mass and extent.

  6. Quantitative Tomography for Continuous Variable Quantum Systems

    NASA Astrophysics Data System (ADS)

    Landon-Cardinal, Olivier; Govia, Luke C. G.; Clerk, Aashish A.

    2018-03-01

    We present a continuous variable tomography scheme that reconstructs the Husimi Q function (Wigner function) by Lagrange interpolation, using measurements of the Q function (Wigner function) at the Padua points, conjectured to be optimal sampling points for two dimensional reconstruction. Our approach drastically reduces the number of measurements required compared to using equidistant points on a regular grid, although reanalysis of such experiments is possible. The reconstruction algorithm produces a reconstructed function with exponentially decreasing error and quasilinear runtime in the number of Padua points. Moreover, using the interpolating polynomial of the Q function, we present a technique to directly estimate the density matrix elements of the continuous variable state, with only a linear propagation of input measurement error. Furthermore, we derive a state-independent analytical bound on this error, such that our estimate of the density matrix is accompanied by a measure of its uncertainty.

  7. A method for volume determination of the orbit and its contents by high resolution axial tomography and quantitative digital image analysis.

    PubMed Central

    Cooper, W C

    1985-01-01

    The various congenital and acquired conditions which alter orbital volume are reviewed. Previous investigative work to determine orbital capacity is summarized. Since these studies were confined to postmortem evaluations, the need for a technique to measure orbital volume in the living state is presented. A method for volume determination of the orbit and its contents by high-resolution axial tomography and quantitative digital image analysis is reported. This procedure has proven to be accurate (the discrepancy between direct and computed measurements ranged from 0.2% to 4%) and reproducible (greater than 98%). The application of this method to representative clinical problems is presented and discussed. The establishment of a diagnostic system versatile enough to expand the usefulness of computerized axial tomography and polytomography should add a new dimension to ophthalmic investigation and treatment. Images FIGURE 8 FIGURE 9 FIGURE 10 A FIGURE 10 B FIGURE 11 A FIGURE 11 B FIGURE 12 FIGURE 13 FIGURE 14 FIGURE 15 FIGURE 16 FIGURE 17 FIGURE 18 FIGURE 19 FIGURE 20 FIGURE 21 FIGURE 22 FIGURE 23 FIGURE 24 FIGURE 25 FIGURE 26 A FIGURE 26 B FIGURE 27 FIGURE 28 FIGURE 29 FIGURE 30 FIGURE 31 FIGURE 32 PMID:3938582

  8. Simulation of a current source with a Cole-Cole load for multi-frequency electrical impedance tomography.

    PubMed

    Aguiar Santos, Susana; Schlebusch, Thomas; Leonhardt, Steffen

    2013-01-01

    An accurate current source is one of the keys in the hardware of Electrical impedance Tomography systems. Limitations appear mainly at higher frequencies and for non-simple resistive loads. In this paper, we simulate an improved Howland current source with a Cole-Cole load. Simulations comparing two different op-amps (THS4021 and OPA843) were performed at 1 kHz to 1 MHz. Results show that the THS4021 performed better than the OPA843. The current source with THS4021 reaches an output impedance of 20 MΩ at 1 kHz and above 320 kΩ at 1 MHz, it provides a constant and stable output current up to 4 mA, in the complete range of frequencies, and for Cole-Cole (resistive and capacitive) load.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Oliver, J; Budzevich, M; Moros, E

    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),more » 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

  10. Multicenter study of quantitative computed tomography analysis using a computer-aided three-dimensional system in patients with idiopathic pulmonary fibrosis.

    PubMed

    Iwasawa, Tae; Kanauchi, Tetsu; Hoshi, Toshiko; Ogura, Takashi; Baba, Tomohisa; Gotoh, Toshiyuki; Oba, Mari S

    2016-01-01

    To evaluate the feasibility of automated quantitative analysis with a three-dimensional (3D) computer-aided system (i.e., Gaussian histogram normalized correlation, GHNC) of computed tomography (CT) images from different scanners. Each institution's review board approved the research protocol. Informed patient consent was not required. The participants in this multicenter prospective study were 80 patients (65 men, 15 women) with idiopathic pulmonary fibrosis. Their mean age was 70.6 years. Computed tomography (CT) images were obtained by four different scanners set at different exposures. We measured the extent of fibrosis using GHNC, and used Pearson's correlation analysis, Bland-Altman plots, and kappa analysis to directly compare the GHNC results with manual scoring by radiologists. Multiple linear regression analysis was performed to determine the association between the CT data and forced vital capacity (FVC). For each scanner, the extent of fibrosis as determined by GHNC was significantly correlated with the radiologists' score. In multivariate analysis, the extent of fibrosis as determined by GHNC was significantly correlated with FVC (p < 0.001). There was no significant difference between the results obtained using different CT scanners. Gaussian histogram normalized correlation was feasible, irrespective of the type of CT scanner used.

  11. Magnetoacoustic Tomography with Magnetic Induction (MAT-MI) for Breast Tumor Imaging: Numerical Modeling and Simulation

    PubMed Central

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

    2011-01-01

    Magnetoacoustic tomography with magnetic induction (MAT-MI) was recently introduced as a noninvasive electrical conductivity imaging approach with high spatial resolution close to ultrasound imaging. In the present study, we test the feasibility of the MAT-MI method for breast tumor imaging using numerical modeling and computer simulation. Using the finite element method, we have built three dimensional numerical breast models with varieties of embedded tumors for this simulation study. In order to obtain an accurate and stable forward solution that does not have numerical errors caused by singular MAT-MI acoustic sources at conductivity boundaries, we first derive an integral forward method for calculating MAT-MI acoustic sources over the entire imaging volume. An inverse algorithm for reconstructing the MAT-MI acoustic source is also derived with spherical measurement aperture, which simulates a practical setup for breast imaging. With the numerical breast models, we have conducted computer simulations under different imaging parameter setups and all the results suggest that breast tumors that have large conductivity contrast to its surrounding tissues as reported in literature may be readily detected in the reconstructed MAT-MI images. In addition, our simulations also suggest that the sensitivity of imaging breast tumors using the presented MAT-MI setup depends more on the tumor location and the conductivity contrast between the tumor and its surrounding tissues than on the tumor size. PMID:21364262

  12. Hyper-spectrum scanning laser optical tomography

    NASA Astrophysics Data System (ADS)

    Chen, Lingling; Li, Guiye; Li, Yingchao; Liu, Lina; Liu, Ang; Hu, Xuejuan; Ruan, Shuangchen

    2018-02-01

    We describe a quantitative fluorescence projection tomography technique which measures the three-dimensional fluorescence spectrum in biomedical samples with size up to several millimeters. This is achieved by acquiring a series of hyperspectral images, by using laser scanning scheme, at different projection angles. We demonstrate that this technique provide a quantitative measure of the fluorescence signal by comparing the spectrum and intensity profile of a fluorescent bead phantom and also demonstrate its application to differentiating the extrinsic label and the autofluorescence in a mouse embryo.

  13. Peripheral Quantitative Computed Tomography: Measurement Sensitivity in Persons With and Without Spinal Cord Injury

    PubMed Central

    Shields, Richard K.; Dudley-Javoroski, Shauna; Boaldin, Kathryn M.; Corey, Trent A.; Fog, Daniel B.; Ruen, Jacquelyn M.

    2012-01-01

    Objectives To determine (1) the error attributable to external tibia-length measurements by using peripheral quantitative computed tomography (pQCT) and (2) the effect these errors have on scan location and tibia trabecular bone mineral density (BMD) after spinal cord injury (SCI). Design Blinded comparison and criterion standard in matched cohorts. Setting Primary care university hospital. Participants Eight able-bodied subjects underwent tibia length measurement. A separate cohort of 7 men with SCI and 7 able-bodied age-matched male controls underwent pQCT analysis. Interventions Not applicable. Main Outcome Measures The projected worst-case tibia-length–measurement error translated into a pQCT slice placement error of ±3mm. We collected pQCT slices at the distal 4% tibia site, 3mm proximal and 3mm distal to that site, and then quantified BMD error attributable to slice placement. Results Absolute BMD error was greater for able-bodied than for SCI subjects (5.87mg/cm3 vs 4.5mg/cm3). However, the percentage error in BMD was larger for SCI than able-bodied subjects (4.56% vs 2.23%). Conclusions During cross-sectional studies of various populations, BMD differences up to 5% may be attributable to variation in limb-length–measurement error. PMID:17023249

  14. FIB–SEM tomography of 4th generation PWA 1497 superalloy

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Ziętara, Maciej, E-mail: zietara@agh.edu.pl; Kruk, Adam, E-mail: kruczek@agh.edu.pl; Gruszczyński, Adam, E-mail: gruszcz@agh.edu.pl

    2014-01-15

    The effect of creep deformation on the microstructure of the PWA 1497 single crystal Ni-base superalloy developed for turbine blade applications was investigated. The aim of the present study was to characterize quantitatively a superalloy microstructure and subsequent development of rafted γ′ precipitates in the PWA 1497 during creep deformation at 982 °C and 248 MPa up to rupture. The PWA1497 microstructure was characterized by scanning electron microscopy and FIB–SEM electron tomography. The 3D reconstruction of the PWA1497 microstructure is presented and discussed. - Highlights: • The microstructure of PWA1497 superalloy was examined using FIB–SEM tomography. • In case ofmore » modern single crystal superalloys, measurements of A{sub A} are adequate for V{sub V}. • During creep the γ channel width increases from 65 to 193 nm for ruptured specimen. • Tomography is a useful technique for quantitative studies of material microstructure.« less

  15. Ab initio structure determination and quantitative disorder analysis on nanoparticles by electron diffraction tomography.

    PubMed

    Krysiak, Yaşar; Barton, Bastian; Marler, Bernd; Neder, Reinhard B; Kolb, Ute

    2018-03-01

    Nanoscaled porous materials such as zeolites have attracted substantial attention in industry due to their catalytic activity, and their performance in sorption and separation processes. In order to understand the properties of such materials, current research focuses increasingly on the determination of structural features beyond the averaged crystal structure. Small particle sizes, various types of disorder and intergrown structures render the description of structures at atomic level by standard crystallographic methods difficult. This paper reports the characterization of a strongly disordered zeolite structure, using a combination of electron exit-wave reconstruction, automated diffraction tomography (ADT), crystal disorder modelling and electron diffraction simulations. Zeolite beta was chosen for a proof-of-principle study of the techniques, because it consists of two different intergrown polymorphs that are built from identical layer types but with different stacking sequences. Imaging of the projected inner Coulomb potential of zeolite beta crystals shows the intergrowth of the polymorphs BEA and BEB. The structures of BEA as well as BEB could be extracted from one single ADT data set using direct methods. A ratio for BEA/BEB = 48:52 was determined by comparison of the reconstructed reciprocal space based on ADT data with simulated electron diffraction data for virtual nanocrystals, built with different ratios of BEA/BEB. In this way, it is demonstrated that this smart interplay of the above-mentioned techniques allows the elaboration of the real structures of functional materials in detail - even if they possess a severely disordered structure.

  16. Optimization of dual-energy xenon-computed tomography for quantitative assessment of regional pulmonary ventilation.

    PubMed

    Fuld, Matthew K; Halaweish, Ahmed F; Newell, John D; Krauss, Bernhard; Hoffman, Eric A

    2013-09-01

    Dual-energy x-ray computed tomography (DECT) offers visualization of the airways and quantitation of regional pulmonary ventilation using a single breath of inhaled xenon gas. In this study, we sought to optimize scanning protocols for DECT xenon gas ventilation imaging of the airways and lung parenchyma and to characterize the quantitative nature of the developed protocols through a series of test-object and animal studies. The Institutional Animal Care and Use Committee approved all animal studies reported here. A range of xenon/oxygen gas mixtures (0%, 20%, 25%, 33%, 50%, 66%, 100%; balance oxygen) were scanned in syringes and balloon test-objects to optimize the delivered gas mixture for assessment of regional ventilation while allowing for the development of improved 3-material decomposition calibration parameters. In addition, to alleviate gravitational effects on xenon gas distribution, we replaced a portion of the oxygen in the xenon/oxygen gas mixture with helium and compared gas distributions in a rapid-prototyped human central-airway test-object. Additional syringe tests were performed to determine if the introduction of helium had any effect on xenon quantitation. Xenon gas mixtures were delivered to anesthetized swine to assess airway and lung parenchymal opacification while evaluating various DECT scan acquisition settings. Attenuation curves for xenon were obtained from the syringe test-objects and were used to develop improved 3-material decomposition parameters (Hounsfield unit enhancement per percentage xenon: within the chest phantom, 2.25 at 80 kVp, 1.7 at 100 kVp, and 0.76 at 140 kVp with tin filtration; in open air, 2.5 at 80 kVp, 1.95 at 100 kVp, and 0.81 at 140 kVp with tin filtration). The addition of helium improved the distribution of xenon gas to the gravitationally nondependent portion of the airway tree test-object, while not affecting the quantitation of xenon in the 3-material decomposition DECT. The mixture 40% Xe/40% He/20% O2

  17. 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.

  18. 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.

  19. Quantitative EEG and low resolution electromagnetic tomography (LORETA) imaging of patients with persistent auditory hallucinations.

    PubMed

    Lee, Seung-Hwan; Wynn, Jonathan K; Green, Michael F; Kim, Hyun; Lee, Kang-Joon; Nam, Min; Park, Joong-Kyu; Chung, Young-Cho

    2006-04-01

    Electrophysiological studies have demonstrated gamma and beta frequency oscillations in response to auditory stimuli. The purpose of this study was to test whether auditory hallucinations (AH) in schizophrenia patients reflect abnormalities in gamma and beta frequency oscillations and to investigate source generators of these abnormalities. This theory was tested using quantitative electroencephalography (qEEG) and low-resolution electromagnetic tomography (LORETA) source imaging. Twenty-five schizophrenia patients with treatment refractory AH, lasting for at least 2 years, and 23 schizophrenia patients with non-AH (N-AH) in the past 2 years were recruited for the study. Spectral analysis of the qEEG and source imaging of frequency bands of artifact-free 30 s epochs were examined during rest. AH patients showed significantly increased beta 1 and beta 2 frequency amplitude compared with N-AH patients. Gamma and beta (2 and 3) frequencies were significantly correlated in AH but not in N-AH patients. Source imaging revealed significantly increased beta (1 and 2) activity in the left inferior parietal lobule and the left medial frontal gyrus in AH versus N-AH patients. These results imply that AH is reflecting increased beta frequency oscillations with neural generators localized in speech-related areas.

  20. Quantitative evaluation of the disintegration of orally rapid disintegrating tablets by X-ray computed tomography.

    PubMed

    Otsuka, Makoto; Yamanaka, Azusa; Uchino, Tomohiro; Otsuka, Kuniko; Sadamoto, Kiyomi; Ohshima, Hiroyuki

    2012-01-01

    To measure the rapid disintegration of Oral Disintegrating Tablets (ODT), a new test (XCT) was developed using X-ray computing tomography (X-ray CT). Placebo ODT, rapid disintegration candy (RDC) and Gaster®-D-Tablets (GAS) were used as model samples. All these ODTs were used to measure oral disintegration time (DT) in distilled water at 37±2°C by XCT. DTs were affected by the width of mesh screens, and degree to which the tablet holder vibrated from air bubbles. An in-vivo tablet disintegration test was performed for RDC using 11 volunteers. DT by the in-vivo method was significantly longer than that using the conventional tester. The experimental conditions for XCT such as the width of the mesh screen and degree of vibration were adjusted to be consistent with human DT values. Since DTs by the XCT method were almost the same as the human data, this method was able to quantitatively evaluate the rapid disintegration of ODT under the same conditions as inside the oral cavity. The DTs of four commercially available ODTs were comparatively evaluated by the XCT method, conventional tablet disintegration test and in-vivo method.

  1. Quantitative computed tomography features and clinical manifestations associated with the extent of bronchiectasis in patients with moderate-to-severe COPD

    PubMed Central

    Bak, So Hyeon; Kim, Soohyun; Hong, Yoonki; Heo, Jeongwon; Lim, Myoung-Nam; Kim, Woo Jin

    2018-01-01

    Background Few studies have investigated the quantitative computed tomography (CT) features associated with the severity of bronchiectasis in COPD patients. The purpose of this study was to identify the quantitative CT features and clinical values to determine the extent of bronchiectasis in moderate-to-severe COPD patients. Methods A total of 127 moderate-to-severe COPD patients were selected from the cohort of COPD in Dusty Areas (CODA). The study subjects were classified into three groups according to the extent of bronchiectasis on CT: no bronchiectasis, mild bronchiectasis, and moderate-to-severe bronchiectasis. The three groups were compared with respect to demographic data, symptoms, medical history, serum inflammatory markers, pulmonary function, and quantitative CT values. Results Among 127 moderate-to-severe COPD subjects, 73 patients (57.5%) were detected to have bronchiectasis, 51 patients (40.2%) to have mild bronchiectasis, and 22 patients (17.3%) to have moderate-to-severe bronchiectasis. Compared with COPD patients without bronchiectasis, those with bronchiectasis were older and had higher frequency of prior tuberculosis, lower prevalence of bronchodilator reversibility (BDR), and more severe air trapping (P < 0.05). Moderate-to-severe bronchiectasis patients had lower body mass index (BMI), higher frequency of prior tuberculosis, lower prevalence of BDR, worse pulmonary function, and more severe air trapping (P < 0.05) than those in the mild bronchiectasis group. Conclusion Moderate-to-severe bronchiectasis was associated with a history of pulmonary tuberculosis, lower BMI, severe airflow obstruction, and lower BDR in moderate-to-severe COPD patients. Quantitative analysis of CT showed that severe air trapping was associated with the extent of bronchiectasis in these patients. PMID:29750028

  2. Speckle contrast optical tomography: A new method for deep tissue three-dimensional tomography of blood flow

    PubMed Central

    Varma, Hari M.; Valdes, Claudia P.; Kristoffersen, Anna K.; Culver, Joseph P.; Durduran, Turgut

    2014-01-01

    A novel tomographic method based on the laser speckle contrast, speckle contrast optical tomography (SCOT) is introduced that allows us to reconstruct three dimensional distribution of blood flow in deep tissues. This method is analogous to the diffuse optical tomography (DOT) but for deep tissue blood flow. We develop a reconstruction algorithm based on first Born approximation to generate three dimensional distribution of flow using the experimental data obtained from tissue simulating phantoms. PMID:24761306

  3. Allan Cormack, Computerized Axial Tomography (CAT), and Magnetic Resonance

    Science.gov Websites

    Radiopharmaceuticals, DOE Technical Report, 1977 Emission Computed Tomography: A New Technique for the Quantitative Extending the Power of Nuclear Magnetic Resonance Techniques Magnetic Resonance Imaging Research Top Some

  4. SedCT: MATLAB™ tools for standardized and quantitative processing of sediment core computed tomography (CT) data collected using a medical CT scanner

    NASA Astrophysics Data System (ADS)

    Reilly, B. T.; Stoner, J. S.; Wiest, J.

    2017-08-01

    Computed tomography (CT) of sediment cores allows for high-resolution images, three-dimensional volumes, and down core profiles. These quantitative data are generated through the attenuation of X-rays, which are sensitive to sediment density and atomic number, and are stored in pixels as relative gray scale values or Hounsfield units (HU). We present a suite of MATLAB™ tools specifically designed for routine sediment core analysis as a means to standardize and better quantify the products of CT data collected on medical CT scanners. SedCT uses a graphical interface to process Digital Imaging and Communications in Medicine (DICOM) files, stitch overlapping scanned intervals, and create down core HU profiles in a manner robust to normal coring imperfections. Utilizing a random sampling technique, SedCT reduces data size and allows for quick processing on typical laptop computers. SedCTimage uses a graphical interface to create quality tiff files of CT slices that are scaled to a user-defined HU range, preserving the quantitative nature of CT images and easily allowing for comparison between sediment cores with different HU means and variance. These tools are presented along with examples from lacustrine and marine sediment cores to highlight the robustness and quantitative nature of this method.

  5. 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.

  6. 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

  7. Validation of electrical impedance tomography qualitative and quantitative values and comparison of the numeric pain distress score against mammography.

    PubMed

    Juliana, Norsham; Shahar, Suzana; Chelliah, Kanaga Kumari; Ghazali, Ahmad Rohi; Osman, Fazilah; Sahar, Mohd Azmani

    2014-01-01

    Electrical impedance tomography (EIT) is a potential supplement for mammogram screening. This study aimed to evaluate and feasibility of EIT as opposed to mammography and to determine pain perception with both imaging methods. Women undergoing screening mammography at the Radiology Department of National University of Malaysia Medical Centre were randomly selected for EIT imaging. All women were requested to give a pain score after each imaging session. Two independent raters were chosen to define the image findings of EIT. A total of 164 women in the age range from 40 to 65-year-old participated and were divided into two groups; normal and abnormal. EIT sensitivity and specificity for rater 1 were 69.4% and 63.3, whereas for rater 2 they were 55.3% and 57.0% respectively. The reliability for each rater ranged between good to very good (p<0.05). Quantitative values of EIT showed there were significant differences in all values between groups (ANCOVA, p<0.05). Interestingly, EIT scored a median pain score of 1.51±0.75 whereas mammography scored 4.15±0.87 (Mann Whitney U test, p<0.05). From these quantitative values, EIT has the potential as a health discriminating index. Its ability to replace image findings from mammography needs further investigation.

  8. Practical no-gold-standard evaluation framework for quantitative imaging methods: application to lesion segmentation in positron emission tomography

    PubMed Central

    Jha, Abhinav K.; Mena, Esther; Caffo, Brian; Ashrafinia, Saeed; Rahmim, Arman; Frey, Eric; Subramaniam, Rathan M.

    2017-01-01

    Abstract. Recently, a class of no-gold-standard (NGS) techniques have been proposed to evaluate quantitative imaging methods using patient data. These techniques provide figures of merit (FoMs) quantifying the precision of the estimated quantitative value without requiring repeated measurements and without requiring a gold standard. However, applying these techniques to patient data presents several practical difficulties including assessing the underlying assumptions, accounting for patient-sampling-related uncertainty, and assessing the reliability of the estimated FoMs. To address these issues, we propose statistical tests that provide confidence in the underlying assumptions and in the reliability of the estimated FoMs. Furthermore, the NGS technique is integrated within a bootstrap-based methodology to account for patient-sampling-related uncertainty. The developed NGS framework was applied to evaluate four methods for segmenting lesions from F-Fluoro-2-deoxyglucose positron emission tomography images of patients with head-and-neck cancer on the task of precisely measuring the metabolic tumor volume. The NGS technique consistently predicted the same segmentation method as the most precise method. The proposed framework provided confidence in these results, even when gold-standard data were not available. The bootstrap-based methodology indicated improved performance of the NGS technique with larger numbers of patient studies, as was expected, and yielded consistent results as long as data from more than 80 lesions were available for the analysis. PMID:28331883

  9. 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

  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. Quantitative contrast-enhanced optical coherence tomography

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Winetraub, Yonatan; SoRelle, Elliott D.; Bio-X Program, Stanford University, 299 Campus Drive, Stanford, California 94305

    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 amore » 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.« less

  12. Optimisation of quantitative lung SPECT applied to mild COPD: a software phantom simulation study.

    PubMed

    Norberg, Pernilla; Olsson, Anna; Alm Carlsson, Gudrun; Sandborg, Michael; Gustafsson, Agnetha

    2015-01-01

    The amount of inhomogeneities in a (99m)Tc Technegas single-photon emission computed tomography (SPECT) lung image, caused by reduced ventilation in lung regions affected by chronic obstructive pulmonary disease (COPD), is correlated to disease advancement. A quantitative analysis method, the CVT method, measuring these inhomogeneities was proposed in earlier work. To detect mild COPD, which is a difficult task, optimised parameter values are needed. In this work, the CVT method was optimised with respect to the parameter values of acquisition, reconstruction and analysis. The ordered subset expectation maximisation (OSEM) algorithm was used for reconstructing the lung SPECT images. As a first step towards clinical application of the CVT method in detecting mild COPD, this study was based on simulated SPECT images of an advanced anthropomorphic lung software phantom including respiratory and cardiac motion, where the mild COPD lung had an overall ventilation reduction of 5%. The best separation between healthy and mild COPD lung images as determined using the CVT measure of ventilation inhomogeneity and 125 MBq (99m)Tc was obtained using a low-energy high-resolution collimator (LEHR) and a power 6 Butterworth post-filter with a cutoff frequency of 0.6 to 0.7 cm(-1). Sixty-four reconstruction updates and a small kernel size should be used when the whole lung is analysed, and for the reduced lung a greater number of updates and a larger kernel size are needed. A LEHR collimator and 125 (99m)Tc MBq together with an optimal combination of cutoff frequency, number of updates and kernel size, gave the best result. Suboptimal selections of either cutoff frequency, number of updates and kernel size will reduce the imaging system's ability to detect mild COPD in the lung phantom.

  13. Effects of calibration methods on quantitative material decomposition in photon-counting spectral computed tomography using a maximum a posteriori estimator.

    PubMed

    Curtis, Tyler E; Roeder, Ryan K

    2017-10-01

    Advances in photon-counting detectors have enabled quantitative material decomposition using multi-energy or spectral computed tomography (CT). Supervised methods for material decomposition utilize an estimated attenuation for each material of interest at each photon energy level, which must be calibrated based upon calculated or measured values for known compositions. Measurements using a calibration phantom can advantageously account for system-specific noise, but the effect of calibration methods on the material basis matrix and subsequent quantitative material decomposition has not been experimentally investigated. Therefore, the objective of this study was to investigate the influence of the range and number of contrast agent concentrations within a modular calibration phantom on the accuracy of quantitative material decomposition in the image domain. Gadolinium was chosen as a model contrast agent in imaging phantoms, which also contained bone tissue and water as negative controls. The maximum gadolinium concentration (30, 60, and 90 mM) and total number of concentrations (2, 4, and 7) were independently varied to systematically investigate effects of the material basis matrix and scaling factor calibration on the quantitative (root mean squared error, RMSE) and spatial (sensitivity and specificity) accuracy of material decomposition. Images of calibration and sample phantoms were acquired using a commercially available photon-counting spectral micro-CT system with five energy bins selected to normalize photon counts and leverage the contrast agent k-edge. Material decomposition of gadolinium, calcium, and water was performed for each calibration method using a maximum a posteriori estimator. Both the quantitative and spatial accuracy of material decomposition were most improved by using an increased maximum gadolinium concentration (range) in the basis matrix calibration; the effects of using a greater number of concentrations were relatively small in

  14. Quantitative Assessment of Transportation Network Vulnerability with Dynamic Traffic Simulation Methods

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Shekar, Venkateswaran; Fiondella, Lance; Chatterjee, Samrat

    Transportation networks are critical to the social and economic function of nations. Given the continuing increase in the populations of cities throughout the world, the criticality of transportation infrastructure is expected to increase. Thus, it is ever more important to mitigate congestion as well as to assess the impact disruptions would have on individuals who depend on transportation for their work and livelihood. Moreover, several government organizations are responsible for ensuring transportation networks are available despite the constant threat of natural disasters and terrorist activities. Most of the previous transportation network vulnerability research has been performed in the context ofmore » static traffic models, many of which are formulated as traditional optimization problems. However, transportation networks are dynamic because their usage varies over time. Thus, more appropriate methods to characterize the vulnerability of transportation networks should consider their dynamic properties. This paper presents a quantitative approach to assess the vulnerability of a transportation network to disruptions with methods from traffic simulation. Our approach can prioritize the critical links over time and is generalizable to the case where both link and node disruptions are of concern. We illustrate the approach through a series of examples. Our results demonstrate that the approach provides quantitative insight into the time varying criticality of links. Such an approach could be used as the objective function of less traditional optimization methods that use simulation and other techniques to evaluate the relative utility of a particular network defense to reduce vulnerability and increase resilience.« less

  15. Massively parallel data processing for quantitative total flow imaging with optical coherence microscopy and tomography

    NASA Astrophysics Data System (ADS)

    Sylwestrzak, Marcin; Szlag, Daniel; Marchand, Paul J.; Kumar, Ashwin S.; Lasser, Theo

    2017-08-01

    We present an application of massively parallel processing of quantitative flow measurements data acquired using spectral optical coherence microscopy (SOCM). The need for massive signal processing of these particular datasets has been a major hurdle for many applications based on SOCM. In view of this difficulty, we implemented and adapted quantitative total flow estimation algorithms on graphics processing units (GPU) and achieved a 150 fold reduction in processing time when compared to a former CPU implementation. As SOCM constitutes the microscopy counterpart to spectral optical coherence tomography (SOCT), the developed processing procedure can be applied to both imaging modalities. We present the developed DLL library integrated in MATLAB (with an example) and have included the source code for adaptations and future improvements. Catalogue identifier: AFBT_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AFBT_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU GPLv3 No. of lines in distributed program, including test data, etc.: 913552 No. of bytes in distributed program, including test data, etc.: 270876249 Distribution format: tar.gz Programming language: CUDA/C, MATLAB. Computer: Intel x64 CPU, GPU supporting CUDA technology. Operating system: 64-bit Windows 7 Professional. Has the code been vectorized or parallelized?: Yes, CPU code has been vectorized in MATLAB, CUDA code has been parallelized. RAM: Dependent on users parameters, typically between several gigabytes and several tens of gigabytes Classification: 6.5, 18. Nature of problem: Speed up of data processing in optical coherence microscopy Solution method: Utilization of GPU for massively parallel data processing Additional comments: Compiled DLL library with source code and documentation, example of utilization (MATLAB script with raw data) Running time: 1,8 s for one B-scan (150 × faster in comparison to the CPU

  16. Quantitative pre-clinical screening of therapeutics for joint diseases using contrast enhanced micro-computed tomography.

    PubMed

    Willett, N J; Thote, T; Hart, M; Moran, S; Guldberg, R E; Kamath, R V

    2016-09-01

    The development of effective therapies for cartilage protection has been limited by a lack of efficient quantitative cartilage imaging modalities in pre-clinical in vivo models. Our objectives were two-fold: first, to validate a new contrast-enhanced 3D imaging analysis technique, equilibrium partitioning of an ionic contrast agent-micro computed tomography (EPIC-μCT), in a rat medial meniscal transection (MMT) osteoarthritis (OA) model; and second, to quantitatively assess the sensitivity of EPIC-μCT to detect the effects of matrix metalloproteinase inhibitor (MMPi) therapy on cartilage degeneration. Rats underwent MMT surgery and tissues were harvested at 1, 2, and 3 weeks post-surgery or rats received an MMPi or vehicle treatment and tissues harvested 3 weeks post-surgery. Parameters of disease progression were evaluated using histopathology and EPIC-μCT. Correlations and power analyses were performed to compare the techniques. EPIC-μCT was shown to provide simultaneous 3D quantification of multiple parameters, including cartilage degeneration and osteophyte formation. In MMT animals treated with MMPi, OA progression was attenuated, as measured by 3D parameters such as lesion volume and osteophyte size. A post-hoc power analysis showed that 3D parameters for EPIC-μCT were more sensitive than 2D parameters requiring fewer animals to detect a therapeutic effect of MMPi. 2D parameters were comparable between EPIC-μCT and histopathology. This study demonstrated that EPIC-μCT has high sensitivity to provide 3D structural and compositional measurements of cartilage and bone in the joint. EPIC-μCT can be used in combination with histology to provide a comprehensive analysis to screen new potential therapies. Copyright © 2016 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights reserved.

  17. BPF-type region-of-interest reconstruction for parallel translational computed tomography.

    PubMed

    Wu, Weiwen; Yu, Hengyong; Wang, Shaoyu; Liu, Fenglin

    2017-01-01

    The objective of this study is to present and test a new ultra-low-cost linear scan based tomography architecture. Similar to linear tomosynthesis, the source and detector are translated in opposite directions and the data acquisition system targets on a region-of-interest (ROI) to acquire data for image reconstruction. This kind of tomographic architecture was named parallel translational computed tomography (PTCT). In previous studies, filtered backprojection (FBP)-type algorithms were developed to reconstruct images from PTCT. However, the reconstructed ROI images from truncated projections have severe truncation artefact. In order to overcome this limitation, we in this study proposed two backprojection filtering (BPF)-type algorithms named MP-BPF and MZ-BPF to reconstruct ROI images from truncated PTCT data. A weight function is constructed to deal with data redundancy for multi-linear translations modes. Extensive numerical simulations are performed to evaluate the proposed MP-BPF and MZ-BPF algorithms for PTCT in fan-beam geometry. Qualitative and quantitative results demonstrate that the proposed BPF-type algorithms cannot only more accurately reconstruct ROI images from truncated projections but also generate high-quality images for the entire image support in some circumstances.

  18. Gold Nanoparticle Quantitation by Whole Cell Tomography.

    PubMed

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

    2015-12-22

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

  19. The measurement of liver fat from single-energy quantitative computed tomography scans

    PubMed Central

    Cheng, Xiaoguang; Brown, J. Keenan; Guo, Zhe; Zhou, Jun; Wang, Fengzhe; Yang, Liqiang; Wang, Xiaohong; Xu, Li

    2017-01-01

    Background Studies of soft tissue composition using computed tomography (CT) scans are often semi-quantitative and based on Hounsfield units (HU) measurements that have not been calibrated with a quantitative CT (QCT) phantom. We describe a study to establish the water (H2O) and dipotassium hydrogen phosphate (K2HPO4) basis set equivalent densities of fat and fat-free liver tissue. With this information liver fat can be accurately measured from any abdominal CT scan calibrated with a suitable phantom. Methods Liver fat content was measured by comparing single-energy QCT (SEQCT) HU measurements of the liver with predicted HU values for fat and fat-free liver tissue calculated from their H2O and K2HPO4 equivalent densities and calibration data from a QCT phantom. The equivalent densities of fat were derived from a listing of its constituent fatty acids, and those of fat-free liver tissue from a dual-energy QCT (DEQCT) study performed in 14 healthy Chinese subjects. This information was used to calculate liver fat from abdominal SEQCT scans performed in a further 541 healthy Chinese subjects (mean age 62 years; range, 31–95 years) enrolled in the Prospective Urban Rural Epidemiology (PURE) Study. Results The equivalent densities of fat were 941.75 mg/cm3 H2O and –43.72 mg/cm3 K2HPO4, and for fat-free liver tissue 1,040.13 mg/cm3 H2O and 21.34 mg/cm3 K2HPO4. Liver fat in the 14 subjects in the DEQCT study varied from 0–17.9% [median: 4.5%; interquartile range (IQR): 3.0–7.9%]. Liver fat in the 541 PURE study subjects varied from –0.3–29.9% (median: 4.9%; IQR: 3.4–6.9%). Conclusions We have established H2O and K2HPO4 equivalent densities for fat and fat-free liver tissue that allow a measurement of liver fat to be obtained from any abdominal CT scan acquired with a QCT phantom. Although radiation dose considerations preclude the routine use of QCT to measure liver fat, the method described here facilitates its measurement in patients having CT scans

  20. Quantitative Computed Tomography Ventriculography for Assessment and Monitoring of Hydrocephalus: A Pilot Study and Description of Method in Subarachnoid Hemorrhage.

    PubMed

    Multani, Jasjit Singh; Oermann, Eric Karl; Titano, Joseph; Mascitelli, Justin; Nicol, Kelly; Feng, Rui; Skovrlj, Branko; Pain, Margaret; Mocco, J D; Bederson, Joshua B; Costa, Anthony; Shrivastava, Raj

    2017-08-01

    There is no facile quantitative method for monitoring hydrocephalus (HCP). We propose quantitative computed tomography (CT) ventriculography (qCTV) as a novel computer vision tool for empirically assessing HCP in patients with subarachnoid hemorrhage (SAH). Twenty patients with SAH who were evaluated for ventriculoperitoneal shunt (VPS) placement were selected for inclusion. Ten patients with normal head computed tomography (CTH) findings were analyzed as negative controls. CTH scans were segmented both manually and automatically (by qCTV) to generate measures of ventricular volume. The median manually calculated ventricular volume was 36.1 cm 3 (interquartile range [IQR], 30-115 cm 3 ), which was similar to the median qCTV measured volume of 37.5 cm 3 (IQR, 32-118 cm 3 ) (P = 0.796). Patients undergoing VPS placement demonstrated an increase in median ventricular volume on qCTV from 21 cm 3 to 40 cm 3 on day T-2 and to 51 cm 3 by day 0, a change of 144%. This is in contrast to patients who did not require shunting, in whom median ventricular volume decreased from 16 cm 3 to 14 cm 3 on day T-2 and to 13 cm 3 by day 0, with an average overall volume decrease 19% (P = 0.001). The average change in ventricular volume predicted which patients would require VPS placement, successfully identifying 7 of 10 patients (P = 0.004). Using an optimized cutoff of a change in ventricular volume of 2.5 cm 3 identified all patients who went on to require VPS placement (10 of 10; P = 0.011). qCTV is a reliable means of quantifying ventricular volume and hydrocephalus. This technique offers a new tool for monitoring neurosurgical patients for hydrocephalus, and may be beneficial for use in future research studies, as well as in the routine care of patients with hydrocephalus. Copyright © 2017 Elsevier Inc. All rights reserved.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Lee, Choonsik; Kim, Kwang Pyo; Long, Daniel

    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 malemore » 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

  2. Efficient tomography of a quantum many-body system

    NASA Astrophysics Data System (ADS)

    Lanyon, B. P.; Maier, C.; Holzäpfel, M.; Baumgratz, T.; Hempel, C.; Jurcevic, P.; Dhand, I.; Buyskikh, A. S.; Daley, A. J.; Cramer, M.; Plenio, M. B.; Blatt, R.; Roos, C. F.

    2017-12-01

    Quantum state tomography is the standard technique for estimating the quantum state of small systems. But its application to larger systems soon becomes impractical as the required resources scale exponentially with the size. Therefore, considerable effort is dedicated to the development of new characterization tools for quantum many-body states. Here we demonstrate matrix product state tomography, which is theoretically proven to allow for the efficient and accurate estimation of a broad class of quantum states. We use this technique to reconstruct the dynamical state of a trapped-ion quantum simulator comprising up to 14 entangled and individually controlled spins: a size far beyond the practical limits of quantum state tomography. Our results reveal the dynamical growth of entanglement and describe its complexity as correlations spread out during a quench: a necessary condition for future demonstrations of better-than-classical performance. Matrix product state tomography should therefore find widespread use in the study of large quantum many-body systems and the benchmarking and verification of quantum simulators and computers.

  3. The influence of Stochastic perturbation of Geotechnical media On Electromagnetic tomography

    NASA Astrophysics Data System (ADS)

    Song, Lei; Yang, Weihao; Huangsonglei, Jiahui; Li, HaiPeng

    2015-04-01

    Electromagnetic tomography (CT) are commonly utilized in Civil engineering to detect the structure defects or geological anomalies. CT are generally recognized as a high precision geophysical method and the accuracy of CT are expected to be several centimeters and even to be several millimeters. Then, high frequency antenna with short wavelength are utilized commonly in Civil Engineering. As to the geotechnical media, stochastic perturbation of the EM parameters are inevitably exist in geological scales, in structure scales and in local scales, et al. In those cases, the geometric dimensionings of the target body, the EM wavelength and the accuracy expected might be of the same order. When the high frequency EM wave propagated in the stochastic geotechnical media, the GPR signal would be reflected not only from the target bodies but also from the stochastic perturbation of the background media. To detect the karst caves in dissolution fracture rock, one need to assess the influence of the stochastic distributed dissolution holes and fractures; to detect the void in a concrete structure, one should master the influence of the stochastic distributed stones, et al. In this paper, on the base of stochastic media discrete realizations, the authors try to evaluate quantificationally the influence of the stochastic perturbation of Geotechnical media by Radon/Iradon Transfer through full-combined Monte Carlo numerical simulation. It is found the stochastic noise is related with transfer angle, perturbing strength, angle interval, autocorrelation length, et al. And the quantitative formula of the accuracy of the electromagnetic tomography is also established, which could help on the precision estimation of GPR tomography in stochastic perturbation Geotechnical media. Key words: Stochastic Geotechnical Media; Electromagnetic Tomography; Radon/Iradon Transfer.

  4. 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.

  5. Selection of stationary phase particle geometry using X-ray computed tomography and computational fluid dynamics simulations.

    PubMed

    Schmidt, Irma; Minceva, Mirjana; Arlt, Wolfgang

    2012-02-17

    The X-ray computed tomography (CT) is used to determine local parameters related to the column packing homogeneity and hydrodynamics in columns packed with spherically and irregularly shaped particles of same size. The results showed that the variation of porosity and axial dispersion coefficient along the column axis is insignificant, compared to their radial distribution. The methodology of using the data attained by CT measurements to perform a CFD simulation of a batch separation of model binary mixtures, with different concentration and separation factors is demonstrated. The results of the CFD simulation study show that columns packed with spherically shaped particles provide higher yield in comparison to columns packed with irregularly shaped particles only below a certain value of the separation factor. The presented methodology can be used for selecting a suited packing material for a particular separation task. Copyright © 2012 Elsevier B.V. All rights reserved.

  6. Quantitative assessment of cervical vertebral maturation using cone beam computed tomography in Korean girls.

    PubMed

    Byun, Bo-Ram; Kim, Yong-Il; Yamaguchi, Tetsutaro; 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 R (2) 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.

  7. 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 R 2 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

  8. A Direct, Quantitative Connection between Molecular Dynamics Simulations and Vibrational Probe Line Shapes.

    PubMed

    Xu, Rosalind J; Blasiak, Bartosz; Cho, Minhaeng; Layfield, Joshua P; Londergan, Casey H

    2018-05-17

    A quantitative connection between molecular dynamics simulations and vibrational spectroscopy of probe-labeled systems would enable direct translation of experimental data into structural and dynamical information. To constitute this connection, all-atom molecular dynamics (MD) simulations were performed for two SCN probe sites (solvent-exposed and buried) in a calmodulin-target peptide complex. Two frequency calculation approaches with substantial nonelectrostatic components, a quantum mechanics/molecular mechanics (QM/MM)-based technique and a solvatochromic fragment potential (SolEFP) approach, were used to simulate the infrared probe line shapes. While QM/MM results disagreed with experiment, SolEFP results matched experimental frequencies and line shapes and revealed the physical and dynamic bases for the observed spectroscopic behavior. The main determinant of the CN probe frequency is the exchange repulsion between the probe and its local structural neighbors, and there is a clear dynamic explanation for the relatively broad probe line shape observed at the "buried" probe site. This methodology should be widely applicable to vibrational probes in many environments.

  9. Visualization of subcutaneous insulin injections by x-ray computed tomography

    NASA Astrophysics Data System (ADS)

    Thomsen, M.; Poulsen, M.; Bech, M.; Velroyen, A.; Herzen, J.; Beckmann, F.; Feidenhans'l, R.; Pfeiffer, F.

    2012-11-01

    We report how the three-dimensional structure of subcutaneous injections of soluble insulin can be visualized by x-ray computed tomography using an iodine based contrast agent. The injections investigated are performed ex vivo in porcine adipose tissue. Full tomography scans carried out at a laboratory x-ray source with a total acquisition time of about 1 min yield CT-images with an effective pixel size of 109 × 109 μm2. The depots are segmented using a modified Chan-Vese algorithm and we are able to observe differences in the shape of the injection depot and the position of the depot in the skin among equally performed injections. To overcome the beam hardening artefacts, which affect the quantitative prediction of the volume injected, we additionally present results concerning the visualization of two injections using synchrotron radiation. The spatial concentration distribution of iodine is calculated to show the dilution of the insulin drug inside the depot. Characterisation of the shape of the depot and the spatial concentration profile of the injected fluid is important knowledge when improving the clinical formulation of an insulin drug, the performance of injection devices and when predicting the effect of the drug through biomedical simulations.

  10. X-ray luminescence computed tomography imaging via multiple intensity weighted narrow beam irradiation

    NASA Astrophysics Data System (ADS)

    Feng, Bo; Gao, Feng; Zhao, Huijuan; Zhang, Limin; Li, Jiao; Zhou, Zhongxing

    2018-02-01

    The purpose of this work is to introduce and study a novel x-ray beam irradiation pattern for X-ray Luminescence Computed Tomography (XLCT), termed multiple intensity-weighted narrow-beam irradiation. The proposed XLCT imaging method is studied through simulations of x-ray and diffuse lights propagation. The emitted optical photons from X-ray excitable nanophosphors were collected by optical fiber bundles from the right-side surface of the phantom. The implementation of image reconstruction is based on the simulated measurements from 6 or 12 angular projections in terms of 3 or 5 x-ray beams scanning mode. The proposed XLCT imaging method is compared against the constant intensity weighted narrow-beam XLCT. From the reconstructed XLCT images, we found that the Dice similarity and quantitative ratio of targets have a certain degree of improvement. The results demonstrated that the proposed method can offer simultaneously high image quality and fast image acquisition.

  11. Frequency Domain Ultrasound Waveform Tomography: Breast Imaging Using a Ring Transducer

    PubMed Central

    Sandhu, G Y; Li, C; Roy, O; Schmidt, S; Duric, N

    2016-01-01

    Application of the frequency domain acoustic wave equation on data acquired from ultrasound tomography scans is shown to yield high resolution sound speed images on the order of the wavelength of the highest reconstructed frequency. Using a signal bandwidth of 0.4–1 MHz and an average sound speed of 1500 m/s, the resolution is approximately 1.5 mm. The quantitative sound speed values and morphology provided by these images have the potential to inform diagnosis and classification of breast disease. In this study, we present the formalism, practical application, and in vivo results of waveform tomography applied to breast data gathered by two different ultrasound tomography scanners that utilize ring transducers. The formalism includes a review of frequency domain modeling of the wave equation using finite difference operators as well as a review of the gradient descent method for the iterative reconstruction scheme. It is shown that the practical application of waveform tomography requires an accurate starting model, careful data processing, and a method to gradually incorporate higher frequency information into the sound speed reconstruction. Following these steps resulted in high resolution quantitative sound speed images of the breast. These images show marked improvement relative to commonly used ray tomography reconstruction methods. The robustness of the method is demonstrated by obtaining similar results from two different ultrasound tomography devices. We also compare our method to MRI to demonstrate concordant findings. The clinical data used in this work was obtained from a HIPAA compliant clinical study (IRB 040912M1F). PMID:26110909

  12. Evaluation of simulation-based scatter correction for 3-D PET cardiac imaging

    NASA Astrophysics Data System (ADS)

    Watson, C. C.; Newport, D.; Casey, M. E.; deKemp, R. A.; Beanlands, R. S.; Schmand, M.

    1997-02-01

    Quantitative imaging of the human thorax poses one of the most difficult challenges for three-dimensional (3-D) (septaless) positron emission tomography (PET), due to the strong attenuation of the annihilation radiation and the large contribution of scattered photons to the data. In [/sup 18/F] fluorodeoxyglucose (FDG) studies of the heart with the patient's arms in the field of view, the contribution of scattered events can exceed 50% of the total detected coincidences. Accurate correction for this scatter component is necessary for meaningful quantitative image analysis and tracer kinetic modeling. For this reason, the authors have implemented a single-scatter simulation technique for scatter correction in positron volume imaging. Here, they describe this algorithm and present scatter correction results from human and chest phantom studies.

  13. Simulation of photoacoustic tomography (PAT) system in COMSOL and comparison of two popular reconstruction techniques

    NASA Astrophysics Data System (ADS)

    Sowmiya, C.; Thittai, Arun K.

    2017-03-01

    Photoacoustic imaging is a molecular cum functional imaging modality based on differential optical absorption of the incident laser pulse by the endogeneous tissue chromophores. Several numerical simulations and finite element models have been developed in the past to describe and study Photoacoustic (PA) signal generation principles and study the effect of variation in PA parameters. Most of these simulation work concentrate on analyzing extracted 1D PA signals and each of them mostly describe only few of the building blocks of a Photoacoustic Tomography (PAT) imaging system. Papers describing simulation of the entire PAT system in one simulation platform, along with reconstruction is seemingly rare. This study attempts to describe how a commercially available Finite Element software (COMSOL(R)), can serve as a single platform for simulating PAT that couples the electromagnetic, thermodynamic and acoustic pressure physics involved in PA phenomena. Further, an array of detector elements placed at the boundary in the FE model can provide acoustic pressure data that can be exported to Matlab(R) to perform tomographic image reconstruction. The performance of two most commonly used image reconstruction techniques; namely, Filtered Backprojection (FBP) and Synthetic Aperture (SA) beamforming are compared. Results obtained showed that the lateral resolution obtained using FBP vs. SA largely depends on the aperture parameters. FBP reconstruction was able to provide a slightly better lateral resolution for smaller aperture while SA worked better for larger aperture. This interesting effect is currently being investigated further. Computationally FBP was faster, but it had artifacts along the spherical shell on which the data is projected.

  14. MOEMS optical delay line for optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Choudhary, Om P.; Chouksey, S.; Sen, P. K.; Sen, P.; Solanki, J.; Andrews, J. T.

    2014-09-01

    Micro-Opto-Electro-Mechanical optical coherence tomography, a lab-on-chip for biomedical applications is designed, studied, fabricated and characterized. To fabricate the device standard PolyMUMPS processes is adopted. We report the utilization of electro-optic modulator for a fast scanning optical delay line for time domain optical coherence tomography. Design optimization are performed using Tanner EDA while simulations are performed using COMSOL. The paper summarizes various results and fabrication methodology adopted. The success of the device promises a future hand-held or endoscopic optical coherence tomography for biomedical applications.

  15. Simulation tools for scattering corrections in spectrally resolved x-ray computed tomography using McXtrace

    NASA Astrophysics Data System (ADS)

    Busi, Matteo; Olsen, Ulrik L.; Knudsen, Erik B.; Frisvad, Jeppe R.; Kehres, Jan; Dreier, Erik S.; Khalil, Mohamad; Haldrup, Kristoffer

    2018-03-01

    Spectral computed tomography is an emerging imaging method that involves using recently developed energy discriminating photon-counting detectors (PCDs). This technique enables measurements at isolated high-energy ranges, in which the dominating undergoing interaction between the x-ray and the sample is the incoherent scattering. The scattered radiation causes a loss of contrast in the results, and its correction has proven to be a complex problem, due to its dependence on energy, material composition, and geometry. Monte Carlo simulations can utilize a physical model to estimate the scattering contribution to the signal, at the cost of high computational time. We present a fast Monte Carlo simulation tool, based on McXtrace, to predict the energy resolved radiation being scattered and absorbed by objects of complex shapes. We validate the tool through measurements using a CdTe single PCD (Multix ME-100) and use it for scattering correction in a simulation of a spectral CT. We found the correction to account for up to 7% relative amplification in the reconstructed linear attenuation. It is a useful tool for x-ray CT to obtain a more accurate material discrimination, especially in the high-energy range, where the incoherent scattering interactions become prevailing (>50 keV).

  16. 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

  17. A Computer-Aided Analysis Method of SPECT Brain Images for Quantitative Treatment Monitoring: Performance Evaluations and Clinical Applications.

    PubMed

    Zheng, Xiujuan; Wei, Wentao; Huang, Qiu; Song, Shaoli; Wan, Jieqing; Huang, Gang

    2017-01-01

    The objective and quantitative analysis of longitudinal single photon emission computed tomography (SPECT) images are significant for the treatment monitoring of brain disorders. Therefore, a computer aided analysis (CAA) method is introduced to extract a change-rate map (CRM) as a parametric image for quantifying the changes of regional cerebral blood flow (rCBF) in longitudinal SPECT brain images. The performances of the CAA-CRM approach in treatment monitoring are evaluated by the computer simulations and clinical applications. The results of computer simulations show that the derived CRMs have high similarities with their ground truths when the lesion size is larger than system spatial resolution and the change rate is higher than 20%. In clinical applications, the CAA-CRM approach is used to assess the treatment of 50 patients with brain ischemia. The results demonstrate that CAA-CRM approach has a 93.4% accuracy of recovered region's localization. Moreover, the quantitative indexes of recovered regions derived from CRM are all significantly different among the groups and highly correlated with the experienced clinical diagnosis. In conclusion, the proposed CAA-CRM approach provides a convenient solution to generate a parametric image and derive the quantitative indexes from the longitudinal SPECT brain images for treatment monitoring.

  18. Understanding Atom Probe Tomography of Oxide-Supported Metal Nanoparticles by Correlation with Atomic Resolution Electron Microscopy and Field Evaporation Simulation

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Devaraj, Arun; Colby, Robert J.; Vurpillot, F.

    2014-03-26

    Metal-dielectric composite materials, specifically metal nanoparticles supported on or embedded in metal oxides, are widely used in catalysis. The accurate optimization of such nanostructures warrants the need for detailed three-dimensional characterization. Atom probe tomography is uniquely capable of generating sub-nanometer structural and compositional data with part-per-million mass sensitivity, but there are reconstruction artifacts for composites containing materials with strongly differing fields of evaporation, as for oxide-supported metal nanoparticles. By correlating atom probe tomography with scanning transmission electron microscopy for Au nanoparticles embedded in an MgO support, deviations from an ideal topography during evaporation are demonstrated directly, and correlated with compositionalmore » errors in the reconstructed data. Finite element simulations of the field evaporation process confirm that protruding Au nanoparticles will evolve on the tip surface, and that evaporation field variations lead to an inaccurate assessment of the local composition, effectively lowering the spatial resolution of the final reconstructed dataset. Cross-correlating the experimental data with simulations results in a more detailed understanding of local evaporation aberrations during APT analysis of metal-oxide composites, paving the way towards a more accurate three-dimensional characterization of this technologically important class of materials.« less

  19. Quantitative analysis of pulmonary pathophysiology using postmortem computed tomography with regard to the cause of death.

    PubMed

    Michiue, Tomomi; Sakurai, Terumi; Ishikawa, Takaki; Oritani, Shigeki; Maeda, Hitoshi

    2012-07-10

    Radiological lung transparency depends on the air contents involved in respiratory function. The present study quantitatively investigated postmortem lung air distribution in forensic autopsy cases (n=135) using computed tomography (CT) to analyze cardiopulmonary pathophysiology in the death process, involving emphysema, congestion and edema. Combined analyses of the CT morphology and attenuation value (Hounsfield unit, HU) of the bilateral lungs, with reference to histopathology, could categorize CT findings (10-90 percentile mode/mean HU values) with regard to the causes of death as follows: (I) hyperaeration (mode/mean HU below -760/-560: emphysema) for obstructive pulmonary disease, starvation and hypothermia (cold exposure); (II) mostly normal aeration with partial ground glass opacification (mode/mean HU, -850 to -360/-700 to -380: partial congestion and edema), consisting of subtype II-a with peri-bronchial/-vascular opacity for mechanical asphyxia, drowning and fire fatality, and subtype II-b with decreased vascularity for gunshot head injury, cerebrovascular disease and hemopericardium; (III) hypoaeration to airless with predominant hypostatic ground glass opacification (mode/mean HU, -870 to 0/-720 to -200: mottled hypostatic congestion and edema) for blunt head/neck injury, intoxication, hyperthermia (heat stroke) and congestive heart failure; (IV) hypoaeration to airless with predominant hypostatic consolidation (mode/mean HU, -790 to 0/-520 to -70: intense hypostatic congestion with edema) for acute ischemic heart disease; and (V) airless to consolidated (mode/mean HU over -420/-370: segmental or multiple patchy consolidations with edema) for pneumonia. Mode HU represents the major alveolar status, while the mean HU reflects the whole lung air contents. CT data analysis is useful for quantitative evaluation of pulmonary pathology as a supplementary procedure. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  20. Advanced Instrumentation for Positron Emission Tomography [PET

    DOE R&D Accomplishments Database

    Derenzo, S. E.; Budinger, T. F.

    1985-04-01

    This paper summarizes the physical processes and medical science goals that underlay modern instrumentation design for Positron Emission Tomography. The paper discusses design factors such as detector material, crystalphototube coupling, shielding geometry, sampling motion, electronics design, time-of-flight, and the interrelationships with quantitative accuracy, spatial resolution, temporal resolution, maximum data rates, and cost.

  1. 3D frequency-domain ultrasound waveform tomography breast imaging

    NASA Astrophysics Data System (ADS)

    Sandhu, Gursharan Yash; West, Erik; Li, Cuiping; Roy, Olivier; Duric, Neb

    2017-03-01

    Frequency-domain ultrasound waveform tomography is a promising method for the visualization and characterization of breast disease. It has previously been shown to accurately reconstruct the sound speed distributions of breasts of varying densities. The reconstructed images show detailed morphological and quantitative information that can help differentiate different types of breast disease including benign and malignant lesions. The attenuation properties of an ex vivo phantom have also been assessed. However, the reconstruction algorithms assumed a 2D geometry while the actual data acquisition process was not. Although clinically useful sound speed images can be reconstructed assuming this mismatched geometry, artifacts from the reconstruction process exist within the reconstructed images. This is especially true for registration across different modalities and when the 2D assumption is violated. For example, this happens when a patient's breast is rapidly sloping. It is also true for attenuation imaging where energy lost or gained out of the plane gets transformed into artifacts within the image space. In this paper, we will briefly review ultrasound waveform tomography techniques, give motivation for pursuing the 3D method, discuss the 3D reconstruction algorithm, present the results of 3D forward modeling, show the mismatch that is induced by the violation of 3D modeling via numerical simulations, and present a 3D inversion of a numerical phantom.

  2. Does peripheral quantitative computed tomography ignore tissue density of cancellous bone?

    PubMed

    Banse, X; Devogelaer, J P

    2002-01-01

    The purpose of this work was to determine the capacity of peripheral quantitative computed tomography (pQCT) to accurately measure the true physical properties of vertebral cancellous bone samples and to predict their stiffness. pQCT bone mineral density (BMD) was first measured in ideal conditions. Ten cubic specimens of vertebral cancellous bone (10 x 10 x 10 mm) were washed with a water jet, defatted, and scanned in saline after elimination of air bubbles; thirteen slices were obtained. Seventy-one unprepared cylindrical samples were scanned in more realistic conditions, which allow further biomechanical testing. After extraction from the vertebral body, the samples were pushed into a plastic tube (no effort was made to remove the marrow or air bubbles), and only four slices were obtained to reduce the duration of scan. For the 81 samples, the true bone volume fraction (BV/TV, %), true apparent density (rho(app), g/cm(3)), and tissue density (rho(tiss), g/cm(3)) (an indicator of the degree of mineralization of the matrix) were then measured using Archimedes principle. rho(app) was closely correlated to BV/TV (r(2) = 0.97). rho(tiss) (1.58 +/- 0.08 g/cm(2)) was almost constant but had some influence on rho(app) (r(2) = 0.03, p < 0.001). The pQCT BMD predicted accurately rho(app) (r(2) = 0.96) and BV/TV (r(2) = 0.93) for the cylinders. For the cubes, in ideal conditions, the same correlations were even better (r(2) > 0.99, both). Analysis of covariance indicated no difference (p > 0.05) in the regressions due to preparation of the samples. The stiffness was better predicted by the true rho(app) (r(2) = 0.87) than by BV/TV (r(2) = 0.83), indicating that stiffness was influenced by small differences in the tissue density. Consequently, the correlation between pQCT BMD and stiffness was excellent (r(2) = 0.84). The fact that pQCT did not ignore this tissue density information compensated for the inaccuracies linked to realistic scanning conditions of the cylinder.

  3. Sex- and Age-Related Differences in Bone Microarchitecture in Men Relative to Women Assessed by High-Resolution Peripheral Quantitative Computed Tomography

    PubMed Central

    Amin, Shreyasee; Khosla, Sundeep

    2012-01-01

    The trabecular and cortical compartments of bone each contributes to bone strength. Until recently, assessment of trabecular and cortical microstructure has required a bone biopsy. Now, trabecular and cortical microstructure of peripheral bone sites can be determined noninvasively using high-resolution peripheral quantitative computed tomography (HR-pQCT). Studies that have used HR-pQCT to evaluate cohorts of both men and women have provided novel insights into the changes in bone microarchitecture that occur with age between the sexes, which may help to explain the lower fracture incidence in older men relative to women. This review will highlight observations from these studies on both the sex- and age-related differences in trabecular and cortical microstructure that may underlie the differences in bone strength, and thereby fracture risk, between men and women. PMID:22496983

  4. Internet Tomography in Support of Internet and Network Simulation and Emulation Modelling

    NASA Astrophysics Data System (ADS)

    Moloisane, A.; Ganchev, I.; O'Droma, M.

    Internet performance measurement data extracted through Internet Tomography techniques and metrics and how it may be used to enhance the capacity of network simulation and emulation modelling is addressed in this paper. The advantages of network simulation and emulation as a means to aid design and develop the component networks, which make up the Internet and are fundamental to its ongoing evolution, are highlighted. The Internet's rapid growth has spurred development of new protocols and algorithms to meet changing operational requirements such as security, multicast delivery, mobile networking, policy management, and quality of service (QoS) support. Both the development and evaluation of these operational tools requires the answering of many design and operational questions. Creating the technical support required by network engineers and managers in their efforts to seek answers to these questions is in itself a major challenge. Within the Internet the number and range of services supported continues to grow exponentially, from legacy and client/server applications to VoIP, multimedia streaming services and interactive multimedia services. Services have their own distinctive requirements and idiosyncrasies. They respond differently to bandwidth limitations, latency and jitter problems. They generate different types of “conversations” between end-user terminals, back-end resources and middle-tier servers. To add to the complexity, each new or enhanced service introduced onto the network contends for available bandwidth with every other service. In an effort to ensure networking products and resources being designed and developed handling diverse conditions encountered in real Internet environments, network simulation and emulation modelling is a valuable tool, and becoming a critical element, in networking product and application design and development. The better these laboratory tools reflect real-world environment and conditions the more helpful to

  5. Progress and opportunities in EELS and EDS tomography.

    PubMed

    Collins, Sean M; Midgley, Paul A

    2017-09-01

    Electron tomography using energy loss and X-ray spectroscopy in the electron microscope continues to develop in rapidly evolving and diverse directions, enabling new insight into the three-dimensional chemistry and physics of nanoscale volumes. Progress has been made recently in improving reconstructions from EELS and EDS signals in electron tomography by applying compressed sensing methods, characterizing new detector technologies in detail, deriving improved models of signal generation, and exploring machine learning approaches to signal processing. These disparate threads can be brought together in a cohesive framework in terms of a model-based approach to analytical electron tomography. Models incorporate information on signal generation and detection as well as prior knowledge of structures in the spectrum image data. Many recent examples illustrate the flexibility of this approach and its feasibility for addressing challenges in non-linear or limited signals in EELS and EDS tomography. Further work in combining multiple imaging and spectroscopy modalities, developing synergistic data acquisition, processing, and reconstruction approaches, and improving the precision of quantitative spectroscopic tomography will expand the frontiers of spatial resolution, dose limits, and maximal information recovery. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. Quantitative Evaluation of Adult Subglottic Stenosis Using Intraoperative Long-range Optical Coherence Tomography

    PubMed Central

    Sharma, Giriraj K.; Loy, Anthony Chin; Su, Erica; Jing, Joe; Chen, Zhongping; Wong, Brian J-F.; Verma, Sunil

    2016-01-01

    Objectives To determine the feasibility of long-range optical coherence tomography (LR-OCT) as a tool to intraoperatively image and measure the subglottis and trachea during suspension microlaryngoscopy before and after endoscopic treatment of subglottic stenosis (SGS). Methods Long-range optical coherence tomography of the adult subglottis and trachea was performed during suspension microlaryngoscopy before and after endoscopic treatment for SGS. The anteroposterior and transverse diameters, cross-sectional area (CSA), distance from the vocal cords, and length of the SGS were measured using a MATLAB software. Pre-intervention and postintervention airway dimensions were compared. Three-dimensional volumetric airway reconstructions were generated using medical image processing software (MIMICS). Results Intraoperative LR-OCT imaging was performed in 3 patients undergoing endoscopic management of SGS. Statistically significant differences in mean anteroposterior diameter (P < .01), transverse diameter (P < .001), and CSA (P < .001) were noted between pre-intervention and postintervention data. Three-dimensional airway models were viewed in cross-sectional format and via virtual “fly through” bronchoscopy. Conclusions This is the first report of intraoperative LR-OCT of the subglottic and tracheal airway before and after surgical management of SGS in humans. Long-range optical coherence tomography offers a practical means to measure the dimensions of SGS and acquire objective data on the response to endoscopic treatment of SGS. PMID:27354215

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

    PubMed

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

    2015-01-01

    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. 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.

  9. Developing a denoising filter for electron microscopy and tomography data in the cloud.

    PubMed

    Starosolski, Zbigniew; Szczepanski, Marek; Wahle, Manuel; Rusu, Mirabela; Wriggers, Willy

    2012-09-01

    The low radiation conditions and the predominantly phase-object image formation of cryo-electron microscopy (cryo-EM) result in extremely high noise levels and low contrast in the recorded micrographs. The process of single particle or tomographic 3D reconstruction does not completely eliminate this noise and is even capable of introducing new sources of noise during alignment or when correcting for instrument parameters. The recently developed Digital Paths Supervised Variance (DPSV) denoising filter uses local variance information to control regional noise in a robust and adaptive manner. The performance of the DPSV filter was evaluated in this review qualitatively and quantitatively using simulated and experimental data from cryo-EM and tomography in two and three dimensions. We also assessed the benefit of filtering experimental reconstructions for visualization purposes and for enhancing the accuracy of feature detection. The DPSV filter eliminates high-frequency noise artifacts (density gaps), which would normally preclude the accurate segmentation of tomography reconstructions or the detection of alpha-helices in single-particle reconstructions. This collaborative software development project was carried out entirely by virtual interactions among the authors using publicly available development and file sharing tools.

  10. Positron Emission Tomography - Computed Tomography (PET/CT)

    MedlinePlus

    ... A-Z Positron Emission Tomography - Computed Tomography (PET/CT) Positron emission tomography (PET) uses small amounts of ... What is Positron Emission Tomography – Computed Tomography (PET/CT) Scanning? Positron emission tomography, also called PET imaging ...

  11. Imaging performance of a hybrid x-ray computed tomography-fluorescence molecular tomography system using priors.

    PubMed

    Ale, Angelique; Schulz, Ralf B; Sarantopoulos, Athanasios; Ntziachristos, Vasilis

    2010-05-01

    The performance is studied of two newly introduced and previously suggested methods that incorporate priors into inversion schemes associated with data from a recently developed hybrid x-ray computed tomography and fluorescence molecular tomography system, the latter based on CCD camera photon detection. The unique data set studied attains accurately registered data of high spatially sampled photon fields propagating through tissue along 360 degrees projections. Approaches that incorporate structural prior information were included in the inverse problem by adding a penalty term to the minimization function utilized for image reconstructions. Results were compared as to their performance with simulated and experimental data from a lung inflammation animal model and against the inversions achieved when not using priors. The importance of using priors over stand-alone inversions is also showcased with high spatial sampling simulated and experimental data. The approach of optimal performance in resolving fluorescent biodistribution in small animals is also discussed. Inclusion of prior information from x-ray CT data in the reconstruction of the fluorescence biodistribution leads to improved agreement between the reconstruction and validation images for both simulated and experimental data.

  12. Development of quantitative parameters to assess in-vivo optical coherence tomography images of late oral radiation toxicity patients

    NASA Astrophysics Data System (ADS)

    Davoudi, Bahar; Damodaran, Vani; Bizheva, Kostadinka; Yang, Victor; Dinniwell, Robert; Levin, Wilfred; Vitkin, Alex

    2013-03-01

    Late oral radiation toxicity is a common condition occurring in a considerable percentage of head and neck cancer patients after radiation therapy which reduces their quality of life. The current examination of these patients is based on a visual inspection of the surface of the oral cavity; however, it is well known that many of the complications start in the subsurface layers before any superficial manifestation. Considering the currently suboptimal examination techniques, we address this clinical problem by using optical coherence tomography (OCT) to monitor the subsurface oral layers with micron-scale resolution images. A spectral-domain OCT system and a specialized oral imaging probe were designed and built for a clinical study to image late oral radiation toxicity patients. In addition to providing qualitative 2D and 3D images of the subsurface oral layers, quantitative metrics were developed to assess the back-scattering and thickness properties of different layers. Metric derivations are explained and preliminary results from late radiation toxicity patients and healthy volunteers are presented and discussed.

  13. 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

  14. Longitudinal spatial coherence gated high-resolution tomography and quantitative phase microscopy of biological cells and tissues with uniform illumination

    NASA Astrophysics Data System (ADS)

    Mehta, Dalip Singh; Ahmad, Azeem; Dubey, Vishesh; Singh, Veena; Butola, Ankit; Mohanty, Tonmoy; Nandi, Sreyankar

    2018-02-01

    We report longitudinal spatial coherence (LSC) gated high-resolution tomography and quantitative phase microscopy of biological cells and tissues with uniform illumination using laser as a light source. To accomplish this a pseudo thermal light source was synthesized by passing laser beams through an optical system, which is basically a speckle reduction system with combined effect of spatial, temporal, angular and polarisation diversity. The longitudinal spatial coherence length of such light was significantly reduced by synthesizing a pseudo thermal source with the combined effect of spatial, angular and temporal diversity. This results in a low spatially coherent (i.e., broad angular frequency spectrum) light source with narrow temporal frequency spectrum. Light from such a pseudo thermal light source was passed through an interference microscope with varying magnification, such as, 10X and 50X. The interference microscope was used for full-field OCT imaging of multilayer objects and topography of industrial objects. Experimental results of optical sectioning of multilayer biological objects with high axial-resolution less than 10μm was achieved which is comparable to broadband white light source. The synthesized light source with reduced speckles having uniform illumination on the sample, which can be very useful for fluorescence microscopy as well as quantitative phase microscopy with less phase noise. The present system does not require any dispersion compensation optical system for biological samples as a highly monochromatic light source is used.

  15. Waste inspection tomography (WIT)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Bernardi, R.T.

    1996-12-31

    WIT is a self-sufficient mobile semitrailer for nondestructive evaluation and nondestructive assay of nuclear waste drums using x-ray and gamma-ray tomography. The recently completed Phase I included the design, fabrication, and initial testing of all WIT subsystems installed on-board the trailer. Initial test results include 2 MeV digital radiography, computed tomography, Anger camera imaging, single photon emission computed tomography, gamma-ray spectroscopy, collimated gamma scanning, and active and passive computed tomography using a 1.4 mCi source of {sup 166}Ho. These techniques were initially demonstrated on a 55-gallon phantom drum with 3 simulated waste matrices of combustibles, heterogeneous metals, and cement usingmore » check sources of gamma active isotopes such as {sup 137}Cs and {sup 133}Ba with 9-250 {mu}Ci activities. Waste matrix identification, isotopic identification, and attenuation-corrected gamma activity determination were demonstrated nondestructively and noninvasively in Phase I. Currently ongoing Phase II involves DOE site field test demonstrations at LLNL, RFETS, and INEL with real nuclear waste drums. Current WIT experience includes 55 gallon drums of cement, graphite, sludge, glass, metals, and combustibles. Thus far WIT has inspected drums with 0-20 gms of {sup 239}Pu.« less

  16. Early Assessment of Treatment Responses During Radiation Therapy for Lung Cancer Using Quantitative Analysis of Daily Computed Tomography

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Paul, Jijo; Yang, Cungeng; Wu, Hui

    Purpose: To investigate early tumor and normal tissue responses during the course of radiation therapy (RT) for lung cancer using quantitative analysis of daily computed tomography (CT) scans. Methods and Materials: Daily diagnostic-quality CT scans acquired using CT-on-rails during CT-guided RT for 20 lung cancer patients were quantitatively analyzed. On each daily CT set, the contours of the gross tumor volume (GTV) and lungs were generated and the radiation dose delivered was reconstructed. The changes in CT image intensity (Hounsfield unit [HU]) features in the GTV and the multiple normal lung tissue shells around the GTV were extracted from themore » daily CT scans. The associations between the changes in the mean HUs, GTV, accumulated dose during RT delivery, and patient survival rate were analyzed. Results: During the RT course, radiation can induce substantial changes in the HU histogram features on the daily CT scans, with reductions in the GTV mean HUs (dH) observed in the range of 11 to 48 HU (median 30). The dH is statistically related to the accumulated GTV dose (R{sup 2} > 0.99) and correlates weakly with the change in GTV (R{sup 2} = 0.3481). Statistically significant increases in patient survival rates (P=.038) were observed for patients with a higher dH in the GTV. In the normal lung, the 4 regions proximal to the GTV showed statistically significant (P<.001) HU reductions from the first to last fraction. Conclusion: Quantitative analysis of the daily CT scans indicated that the mean HUs in lung tumor and surrounding normal tissue were reduced during RT delivery. This reduction was observed in the early phase of the treatment, is patient specific, and correlated with the delivered dose. A larger HU reduction in the GTV correlated significantly with greater patient survival. The changes in daily CT features, such as the mean HU, can be used for early assessment of the radiation response during RT delivery for lung cancer.« less

  17. Early Assessment of Treatment Responses During Radiation Therapy for Lung Cancer Using Quantitative Analysis of Daily Computed Tomography.

    PubMed

    Paul, Jijo; Yang, Cungeng; Wu, Hui; Tai, An; Dalah, Entesar; Zheng, Cheng; Johnstone, Candice; Kong, Feng-Ming; Gore, Elizabeth; Li, X Allen

    2017-06-01

    To investigate early tumor and normal tissue responses during the course of radiation therapy (RT) for lung cancer using quantitative analysis of daily computed tomography (CT) scans. Daily diagnostic-quality CT scans acquired using CT-on-rails during CT-guided RT for 20 lung cancer patients were quantitatively analyzed. On each daily CT set, the contours of the gross tumor volume (GTV) and lungs were generated and the radiation dose delivered was reconstructed. The changes in CT image intensity (Hounsfield unit [HU]) features in the GTV and the multiple normal lung tissue shells around the GTV were extracted from the daily CT scans. The associations between the changes in the mean HUs, GTV, accumulated dose during RT delivery, and patient survival rate were analyzed. During the RT course, radiation can induce substantial changes in the HU histogram features on the daily CT scans, with reductions in the GTV mean HUs (dH) observed in the range of 11 to 48 HU (median 30). The dH is statistically related to the accumulated GTV dose (R 2  > 0.99) and correlates weakly with the change in GTV (R 2  = 0.3481). Statistically significant increases in patient survival rates (P=.038) were observed for patients with a higher dH in the GTV. In the normal lung, the 4 regions proximal to the GTV showed statistically significant (P<.001) HU reductions from the first to last fraction. Quantitative analysis of the daily CT scans indicated that the mean HUs in lung tumor and surrounding normal tissue were reduced during RT delivery. This reduction was observed in the early phase of the treatment, is patient specific, and correlated with the delivered dose. A larger HU reduction in the GTV correlated significantly with greater patient survival. The changes in daily CT features, such as the mean HU, can be used for early assessment of the radiation response during RT delivery for lung cancer. Copyright © 2017 Elsevier Inc. All rights reserved.

  18. Intraprocedural yttrium-90 positron emission tomography/CT for treatment optimization of yttrium-90 radioembolization.

    PubMed

    Bourgeois, Austin C; Chang, Ted T; Bradley, Yong C; Acuff, Shelley N; Pasciak, Alexander S

    2014-02-01

    Radioembolization with yttrium-90 ((90)Y) microspheres relies on delivery of appropriate treatment activity to ensure patient safety and optimize treatment efficacy. We report a case in which (90)Y positron emission tomography (PET)/computed tomography (CT) was performed to optimize treatment planning during a same-day, three-part treatment session. This treatment consisted of (i) an initial (90)Y infusion with a dosage determined using an empiric treatment planning model, (ii) quantitative (90)Y PET/CT imaging, and (iii) a secondary infusion with treatment planning based on quantitative imaging data with the goal of delivering a specific total tumor absorbed dose. © 2014 SIR Published by SIR All rights reserved.

  19. Quantitative computed tomography of the lungs and airways in healthy nonsmoking adults.

    PubMed

    Zach, Jordan Alexander; Newell, John D; Schroeder, Joyce; Murphy, James R; Curran-Everett, Douglas; Hoffman, Eric A; Westgate, Philip M; Han, MeiLan K; Silverman, Edwin K; Crapo, James D; Lynch, David A

    2012-10-01

    The purposes of this study were to evaluate the reference range of quantitative computed tomography (QCT) measures of lung attenuation and airway parameter measurements in healthy nonsmoking adults and to identify sources of variation in those measures and possible means to adjust for them. Within the COPDGene study, 92 healthy non-Hispanic white nonsmokers (29 men, 63 women; mean [SD] age, 62.7 [9.0] years; mean [SD] body mass index [BMI], 28.1 [5.1] kg/m(2)) underwent volumetric computed tomography (CT) at full inspiration and at the end of a normal expiration. On QCT analysis (Pulmonary Workstation 2, VIDA Diagnostics), inspiratory low-attenuation areas were defined as lung tissue with attenuation values -950 Hounsfield units or less on inspiratory CT (LAA(I-950)). Expiratory low-attenuation areas were defined as lung tissue -856 Hounsfield units or less on expiratory CT (LAA(E-856)). We used simple linear regression to determine the impact of age and sex on QCT parameters and multiple regression to assess the additional impact of total lung capacity and functional residual capacity measured by CT (TLC(CT) and FRC(CT)), scanner type, and mean tracheal air attenuation. Airways were evaluated using measures of airway wall thickness, inner luminal area, wall area percentage (WA%), and standardized thickness of an airway with inner perimeter of 10 mm (Pi10). Mean (SD) %LAA(I-950) was 2.0% (2.7%), and mean (SD) %LAA(E-856) was 9.2% (6.8%). Mean (SD) %LAA(I-950) was 3.6% (3.2%) in men, compared with 1.3% (2.0%) in women (P < 0.001). The %LAA(I-950) did not change significantly with age (P = 0.08) or BMI (P = 0.52). %LAA(E-856) did not show any independent relationship with age (P = 0.33), sex (P = 0.70), or BMI (P = 0.32). On multivariate analysis, %LAA(I-950) showed a direct relationship to TLC(CT) (P = 0.002) and an inverse relationship to mean tracheal air attenuation (P = 0.003), and %LAA(E-856) was related to age (P = 0.001), FRC(CT) (P = 0.007), and scanner type

  20. Studies on muon tomography for archaeological internal structures scanning

    NASA Astrophysics Data System (ADS)

    Gómez, H.; Carloganu, C.; Gibert, D.; Jacquemier, J.; Karyotakis, Y.; Marteau, J.; Niess, V.; Katsanevas, S.; Tonazzo, A.

    2016-05-01

    Muon tomography is a potential non-invasive technique for internal structure scanning. It has already interesting applications in geophysics and can be used for archaeological purposes. Muon tomography is based on the measurement of the muon flux after crossing the structure studied. Differences on the mean density of these structures imply differences on the detected muon rate for a given direction. Based on this principle, Monte Carlo simulations represent a useful tool to provide a model of the expected muon rate and angular distribution depending on the composition of the studied object, being useful to estimate the expected detected muons and to better understand the experimental results. These simulations are mainly dependent on the geometry and composition of the studied object and on the modelling of the initial muon flux at surface. In this work, the potential of muon tomography in archaeology is presented and evaluated with Monte Carlo simulations by estimating the differences on the muon rate due to the presence of internal structures and its composition. The influence of the chosen muon model at surface in terms of energy and angular distributions in the final result has been also studied.

  1. Bayesian seismic tomography by parallel interacting Markov chains

    NASA Astrophysics Data System (ADS)

    Gesret, Alexandrine; Bottero, Alexis; Romary, Thomas; Noble, Mark; Desassis, Nicolas

    2014-05-01

    The velocity field estimated by first arrival traveltime tomography is commonly used as a starting point for further seismological, mineralogical, tectonic or similar analysis. In order to interpret quantitatively the results, the tomography uncertainty values as well as their spatial distribution are required. The estimated velocity model is obtained through inverse modeling by minimizing an objective function that compares observed and computed traveltimes. This step is often performed by gradient-based optimization algorithms. The major drawback of such local optimization schemes, beyond the possibility of being trapped in a local minimum, is that they do not account for the multiple possible solutions of the inverse problem. They are therefore unable to assess the uncertainties linked to the solution. Within a Bayesian (probabilistic) framework, solving the tomography inverse problem aims at estimating the posterior probability density function of velocity model using a global sampling algorithm. Markov chains Monte-Carlo (MCMC) methods are known to produce samples of virtually any distribution. In such a Bayesian inversion, the total number of simulations we can afford is highly related to the computational cost of the forward model. Although fast algorithms have been recently developed for computing first arrival traveltimes of seismic waves, the complete browsing of the posterior distribution of velocity model is hardly performed, especially when it is high dimensional and/or multimodal. In the latter case, the chain may even stay stuck in one of the modes. In order to improve the mixing properties of classical single MCMC, we propose to make interact several Markov chains at different temperatures. This method can make efficient use of large CPU clusters, without increasing the global computational cost with respect to classical MCMC and is therefore particularly suited for Bayesian inversion. The exchanges between the chains allow a precise sampling of the

  2. 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.

  3. Atom probe tomography of lithium-doped network glasses.

    PubMed

    Greiwe, Gerd-Hendrik; Balogh, Zoltan; Schmitz, Guido

    2014-06-01

    Li-doped silicate and borate glasses are electronically insulating, but provide considerable ionic conductivity. Under measurement conditions of laser-assisted atom probe tomography, mobile Li ions are redistributed in response to high electric fields. In consequence, the direct interpretation of measured composition profiles is prevented. It is demonstrated that composition profiles are nevertheless well understood by a complex model taking into account the electronic structure of dielectric materials, ionic mobility and field screening. Quantitative data on band bending and field penetration during measurement are derived which are important in understanding laser-assisted atom probe tomography of dielectric materials. Copyright © 2014 Elsevier B.V. All rights reserved.

  4. 3D Imaging with Holographic Tomography

    NASA Astrophysics Data System (ADS)

    Sheppard, Colin J. R.; Kou, Shan Shan

    2010-04-01

    There are two main types of tomography that enable the 3D internal structures of objects to be reconstructed from scattered data. The commonly known computerized tomography (CT) give good results in the x-ray wavelength range where the filtered back-projection theorem and Radon transform can be used. These techniques rely on the Fourier projection-slice theorem where rays are considered to propagate straight through the object. Another type of tomography called `diffraction tomography' applies in applications in optics and acoustics where diffraction and scattering effects must be taken into account. The latter proves to be a more difficult problem, as light no longer travels straight through the sample. Holographic tomography is a popular way of performing diffraction tomography and there has been active experimental research on reconstructing complex refractive index data using this approach recently. However, there are two distinct ways of doing tomography: either by rotation of the object or by rotation of the illumination while fixing the detector. The difference between these two setups is intuitive but needs to be quantified. From Fourier optics and information transformation point of view, we use 3D transfer function analysis to quantitatively describe how spatial frequencies of the object are mapped to the Fourier domain. We first employ a paraxial treatment by calculating the Fourier transform of the defocused OTF. The shape of the calculated 3D CTF for tomography, by scanning the illumination in one direction only, takes on a form that we might call a 'peanut,' compared to the case of object rotation, where a diablo is formed, the peanut exhibiting significant differences and non-isotropy. In particular, there is a line singularity along one transverse direction. Under high numerical aperture conditions, the paraxial treatment is not accurate, and so we make use of 3D analytical geometry to calculate the behaviour in the non-paraxial case. This time, we

  5. Systematic calibration of an integrated x-ray and optical tomography system for preclinical radiation research

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Yang, Yidong, E-mail: yidongyang@med.miami.edu; Wang, Ken Kang-Hsin; Wong, John W.

    2015-04-15

    Purpose: The cone beam computed tomography (CBCT) guided small animal radiation research platform (SARRP) has been developed for focal tumor irradiation, allowing laboratory researchers to test basic biological hypotheses that can modify radiotherapy outcomes in ways that were not feasible previously. CBCT provides excellent bone to soft tissue contrast, but is incapable of differentiating tumors from surrounding soft tissue. Bioluminescence tomography (BLT), in contrast, allows direct visualization of even subpalpable tumors and quantitative evaluation of tumor response. Integration of BLT with CBCT offers complementary image information, with CBCT delineating anatomic structures and BLT differentiating luminescent tumors. This study is tomore » develop a systematic method to calibrate an integrated CBCT and BLT imaging system which can be adopted onboard the SARRP to guide focal tumor irradiation. Methods: The integrated imaging system consists of CBCT, diffuse optical tomography (DOT), and BLT. The anatomy acquired from CBCT and optical properties acquired from DOT serve as a priori information for the subsequent BLT reconstruction. Phantoms were designed and procedures were developed to calibrate the CBCT, DOT/BLT, and the entire integrated system. Geometrical calibration was performed to calibrate the CBCT system. Flat field correction was performed to correct the nonuniform response of the optical imaging system. Absolute emittance calibration was performed to convert the camera readout to the emittance at the phantom or animal surface, which enabled the direct reconstruction of the bioluminescence source strength. Phantom and mouse imaging were performed to validate the calibration. Results: All calibration procedures were successfully performed. Both CBCT of a thin wire and a euthanized mouse revealed no spatial artifact, validating the accuracy of the CBCT calibration. The absolute emittance calibration was validated with a 650 nm laser source, resulting

  6. Systematic calibration of an integrated x-ray and optical tomography system for preclinical radiation research

    PubMed Central

    Yang, Yidong; Wang, Ken Kang-Hsin; Eslami, Sohrab; Iordachita, Iulian I.; Patterson, Michael S.; Wong, John W.

    2015-01-01

    Purpose: The cone beam computed tomography (CBCT) guided small animal radiation research platform (SARRP) has been developed for focal tumor irradiation, allowing laboratory researchers to test basic biological hypotheses that can modify radiotherapy outcomes in ways that were not feasible previously. CBCT provides excellent bone to soft tissue contrast, but is incapable of differentiating tumors from surrounding soft tissue. Bioluminescence tomography (BLT), in contrast, allows direct visualization of even subpalpable tumors and quantitative evaluation of tumor response. Integration of BLT with CBCT offers complementary image information, with CBCT delineating anatomic structures and BLT differentiating luminescent tumors. This study is to develop a systematic method to calibrate an integrated CBCT and BLT imaging system which can be adopted onboard the SARRP to guide focal tumor irradiation. Methods: The integrated imaging system consists of CBCT, diffuse optical tomography (DOT), and BLT. The anatomy acquired from CBCT and optical properties acquired from DOT serve as a priori information for the subsequent BLT reconstruction. Phantoms were designed and procedures were developed to calibrate the CBCT, DOT/BLT, and the entire integrated system. Geometrical calibration was performed to calibrate the CBCT system. Flat field correction was performed to correct the nonuniform response of the optical imaging system. Absolute emittance calibration was performed to convert the camera readout to the emittance at the phantom or animal surface, which enabled the direct reconstruction of the bioluminescence source strength. Phantom and mouse imaging were performed to validate the calibration. Results: All calibration procedures were successfully performed. Both CBCT of a thin wire and a euthanized mouse revealed no spatial artifact, validating the accuracy of the CBCT calibration. The absolute emittance calibration was validated with a 650 nm laser source, resulting in a 3

  7. 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

  8. Three dimensional computed tomography lung modeling is useful in simulation and navigation of lung cancer surgery.

    PubMed

    Ikeda, Norihiko; Yoshimura, Akinobu; Hagiwara, Masaru; Akata, Soichi; Saji, Hisashi

    2013-01-01

    The number of minimally invasive operations, such as video-assisted thoracoscopic surgery (VATS) lobectomy or segmentectomy, has enormously increased in recent years. These operations require extreme knowledge of the anatomy of pulmonary vessels and bronchi in each patient, and surgeons must carefully dissect the branches of pulmonary vessels during operation. Thus, foreknowledge of the anatomy of each patient would greatly contribute to the safety and accuracy of the operation. The development of multi-detector computed tomography (MDCT) has promoted three dimensional (3D) images of lung structures. It is possible to see the vascular and bronchial structures from the view of the operator; therefore, it is employed for preoperative simulation as well as navigation during operation. Due to advances in software, even small vessels can be accurately imaged, which is useful in performing segmentectomy. Surgical simulation and navigation systems based on high quality 3D lung modeling, including vascular and bronchial structures, can be used routinely to enhance the safety operation, education of junior staff, as well as providing a greater sense of security to the operators.

  9. Molecular Optical Simulation Environment (MOSE): A Platform for the Simulation of Light Propagation in Turbid Media

    PubMed Central

    Ren, Shenghan; Chen, Xueli; Wang, Hailong; Qu, Xiaochao; Wang, Ge; Liang, Jimin; Tian, Jie

    2013-01-01

    The study of light propagation in turbid media has attracted extensive attention in the field of biomedical optical molecular imaging. In this paper, we present a software platform for the simulation of light propagation in turbid media named the “Molecular Optical Simulation Environment (MOSE)”. Based on the gold standard of the Monte Carlo method, MOSE simulates light propagation both in tissues with complicated structures and through free-space. In particular, MOSE synthesizes realistic data for bioluminescence tomography (BLT), fluorescence molecular tomography (FMT), and diffuse optical tomography (DOT). The user-friendly interface and powerful visualization tools facilitate data analysis and system evaluation. As a major measure for resource sharing and reproducible research, MOSE aims to provide freeware for research and educational institutions, which can be downloaded at http://www.mosetm.net. PMID:23577215

  10. Characterization of dynamic physiology of the bladder by optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Yuan, Zhijia; Keng, Kerri; Pan, Rubin; Ren, Hugang; Du, Congwu; Kim, Jason; Pan, Yingtian

    2012-03-01

    Because of its high spatial resolution and noninvasive imaging capabilities, optical coherence tomography has been used to characterize the morphological details of various biological tissues including urinary bladder and to diagnose their alternations (e.g., cancers). In addition to static morphology, the dynamic features of tissue morphology can provide important information that can be used to diagnose the physiological and functional characteristics of biological tissues. Here, we present the imaging studies based on optical coherence tomography to characterize motion related physiology and functions of rat bladder detrusor muscles and compared the results with traditional biomechanical measurements. Our results suggest that optical coherence tomography is capable of providing quantitative evaluation of contractile functions of intact bladder (without removing bladder epithelium and connective tissue), which is potentially of more clinical relevance for future clinical diagnosis - if incorporated with cystoscopic optical coherence tomography.

  11. Photoacoustic tomography guided diffuse optical tomography for small-animal model

    NASA Astrophysics Data System (ADS)

    Wang, Yihan; Gao, Feng; Wan, Wenbo; Zhang, Yan; Li, Jiao

    2015-03-01

    Diffuse optical tomography (DOT) is a biomedical imaging technology for noninvasive visualization of spatial variation about the optical properties of tissue, which can be applied to in vivo small-animal disease model. However, traditional DOT suffers low spatial resolution due to tissue scattering. To overcome this intrinsic shortcoming, multi-modal approaches that incorporate DOT with other imaging techniques have been intensively investigated, where a priori information provided by the other modalities is normally used to reasonably regularize the inverse problem of DOT. Nevertheless, these approaches usually consider the anatomical structure, which is different from the optical structure. Photoacoustic tomography (PAT) is an emerging imaging modality that is particularly useful for visualizing lightabsorbing structures embedded in soft tissue with higher spatial resolution compared with pure optical imaging. Thus, we present a PAT-guided DOT approach, to obtain the location a priori information of optical structure provided by PAT first, and then guide DOT to reconstruct the optical parameters quantitatively. The results of reconstruction of phantom experiments demonstrate that both quantification and spatial resolution of DOT could be highly improved by the regularization of feasible-region information provided by PAT.

  12. Distinct quantitative computed tomography emphysema patterns are associated with physiology and function in smokers.

    PubMed

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

    2013-11-01

    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. To study the epidemiologic associations of distinct emphysema patterns with measures of lung-related physiology, function, and health care use in smokers. 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. 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). 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.

  13. Characterization of human oral tissues based on quantitative analysis of optical coherence tomography images

    NASA Astrophysics Data System (ADS)

    Salehi, Hassan S.; Kosa, Ali; Mahdian, Mina; Moslehpour, Saeid; Alnajjar, Hisham; Tadinada, Aditya

    2017-02-01

    In this paper, five types of tissues, human enamel, human cortical bone, human trabecular bone, muscular tissue, and fatty tissue were imaged ex vivo using optical coherence tomography (OCT). The specimens were prepared in blocks of 5 x 5 x 3 mm (width x length x height). The OCT imaging system was a swept source OCT system operating at wavelengths ranging between 1250 nm and 1360 nm with an average power of 18 mW and a scan rate of 50 to 100 kHz. The imaging probe was placed on top of a 2 x 2 cm stabilizing device to maintain a standard distance from the samples. Ten image samples from each type of tissue were obtained. To acquire images with minimum inhomogeneity, imaging was performed multiple times at different points. Based on the observed texture differences between OCT images of soft and hard tissues, spatial and spectral features were quantitatively extracted from the OCT images. The Radon transform from angles of 0 deg to 90 deg was computed, averaged over all the angles, normalized to peak at unity, and then fitted with Gaussian function. The mean absolute values of the spatial frequency components of the OCT image were considered as a feature, where 2-D fast Fourier transform (FFT) was done to OCT images. These OCT features can reliably differentiate between a range of hard and soft tissues, and could be extremely valuable in assisting dentists for in vivo evaluation of oral tissues and early detection of pathologic changes in tissues.

  14. 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.

  15. 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

  16. Integration of SimSET photon history generator in GATE for efficient Monte Carlo simulations of pinhole SPECT.

    PubMed

    Chen, Chia-Lin; Wang, Yuchuan; Lee, Jason J S; Tsui, Benjamin M W

    2008-07-01

    The authors developed and validated an efficient Monte Carlo simulation (MCS) workflow to facilitate small animal pinhole SPECT imaging research. This workflow seamlessly integrates two existing MCS tools: simulation system for emission tomography (SimSET) and GEANT4 application for emission tomography (GATE). Specifically, we retained the strength of GATE in describing complex collimator/detector configurations to meet the anticipated needs for studying advanced pinhole collimation (e.g., multipinhole) geometry, while inserting the fast SimSET photon history generator (PHG) to circumvent the relatively slow GEANT4 MCS code used by GATE in simulating photon interactions inside voxelized phantoms. For validation, data generated from this new SimSET-GATE workflow were compared with those from GATE-only simulations as well as experimental measurements obtained using a commercial small animal pinhole SPECT system. Our results showed excellent agreement (e.g., in system point response functions and energy spectra) between SimSET-GATE and GATE-only simulations, and, more importantly, a significant computational speedup (up to approximately 10-fold) provided by the new workflow. Satisfactory agreement between MCS results and experimental data were also observed. In conclusion, the authors have successfully integrated SimSET photon history generator in GATE for fast and realistic pinhole SPECT simulations, which can facilitate research in, for example, the development and application of quantitative pinhole and multipinhole SPECT for small animal imaging. This integrated simulation tool can also be adapted for studying other preclinical and clinical SPECT techniques.

  17. Reduced ventilation-perfusion (V/Q) mismatch following endobronchial valve insertion demonstrated by Gallium-68 V/Q photon emission tomography/computed tomography.

    PubMed

    Leong, Paul; Le Roux, Pierre-Yves; Callahan, Jason; Siva, Shankar; Hofman, Michael S; Steinfort, Daniel P

    2017-09-01

    Endobronchial valves (EBVs) are increasingly deployed in the management of severe emphysema. Initial studies focussed on volume reduction as the mechanism, with subsequent improvement in forced expiratory volume in 1 s (FEV 1 ). More recent studies have emphasized importance of perfusion on predicting outcomes, though findings have been inconsistent. Gallium-68 ventilation-perfusion (V/Q) photon emission tomography (PET)/computed tomography (CT) is a novel imaging modality with advantages in spatial resolution, quantitation, and speed over conventional V/Q scintigraphy. We report a pilot case in which V/Q-PET/CT demonstrated discordant findings compared with quantitative CT analysis, and directed left lower lobe EBV placement. The patient experienced a significant improvement in 6-min walk distance (6MWD) without change in spirometry. Post-EBV V/Q-PET/CT demonstrated a marked decrease in unmatched (detrimental) V/Q areas and improvement in overall V/Q matching on post-EBV V/Q-PET/CT. These preliminary novel findings suggest that EBVs improve V/Q matching and may explain the observed functional improvements.

  18. Quantitative imaging methods in osteoporosis.

    PubMed

    Oei, Ling; Koromani, Fjorda; Rivadeneira, Fernando; Zillikens, M Carola; Oei, Edwin H G

    2016-12-01

    Osteoporosis is characterized by a decreased bone mass and quality resulting in an increased fracture risk. Quantitative imaging methods are critical in the diagnosis and follow-up of treatment effects in osteoporosis. Prior radiographic vertebral fractures and bone mineral density (BMD) as a quantitative parameter derived from dual-energy X-ray absorptiometry (DXA) are among the strongest known predictors of future osteoporotic fractures. Therefore, current clinical decision making relies heavily on accurate assessment of these imaging features. Further, novel quantitative techniques are being developed to appraise additional characteristics of osteoporosis including three-dimensional bone architecture with quantitative computed tomography (QCT). Dedicated high-resolution (HR) CT equipment is available to enhance image quality. At the other end of the spectrum, by utilizing post-processing techniques such as the trabecular bone score (TBS) information on three-dimensional architecture can be derived from DXA images. Further developments in magnetic resonance imaging (MRI) seem promising to not only capture bone micro-architecture but also characterize processes at the molecular level. This review provides an overview of various quantitative imaging techniques based on different radiological modalities utilized in clinical osteoporosis care and research.

  19. Calibration methods influence quantitative material decomposition in photon-counting spectral CT

    NASA Astrophysics Data System (ADS)

    Curtis, Tyler E.; Roeder, Ryan K.

    2017-03-01

    Photon-counting detectors and nanoparticle contrast agents can potentially enable molecular imaging and material decomposition in computed tomography (CT). Material decomposition has been investigated using both simulated and acquired data sets. However, the effect of calibration methods on material decomposition has not been systematically investigated. Therefore, the objective of this study was to investigate the influence of the range and number of contrast agent concentrations within a modular calibration phantom on quantitative material decomposition. A commerciallyavailable photon-counting spectral micro-CT (MARS Bioimaging) was used to acquire images with five energy bins selected to normalize photon counts and leverage the contrast agent k-edge. Material basis matrix values were determined using multiple linear regression models and material decomposition was performed using a maximum a posteriori estimator. The accuracy of quantitative material decomposition was evaluated by the root mean squared error (RMSE), specificity, sensitivity, and area under the curve (AUC). An increased maximum concentration (range) in the calibration significantly improved RMSE, specificity and AUC. The effects of an increased number of concentrations in the calibration were not statistically significant for the conditions in this study. The overall results demonstrated that the accuracy of quantitative material decomposition in spectral CT is significantly influenced by calibration methods, which must therefore be carefully considered for the intended diagnostic imaging application.

  20. CLASSIFICATION AND QUANTITATIVE ANALYSIS OF GEOGRAPHIC ATROPHY JUNCTIONAL ZONE USING SPECTRAL DOMAIN OPTICAL COHERENCE TOMOGRAPHY.

    PubMed

    Qu, Jinfeng; Velaga, Swetha Bindu; Hariri, Amir H; Nittala, Muneeswar Gupta; Sadda, Srinivas

    2017-08-22

    The junctional zone at the border of areas of geographic atrophy (GA) in eyes with nonneovascular age-related macular degeneration is an important target region for future therapeutic strategies. The goal of this study was to perform a detailed classification and quantitative characterization of the junctional zone using spectral domain optical coherence tomography. Spectral domain optical coherence tomography volume cube scans (Spectralis OCT, 1024 × 37, Automatic Real Time > 9) were obtained from 15 eyes of 11 patients with GA because of nonneovascular age-related macular degeneration. Volume optical coherence tomography data were imported into previously described validated grading software (3D-OCTOR), and manual segmentation of the retinal pigment epithelium (RPE) and photoreceptor layers was performed on all B-scans (total of 555). Retinal pigment epithelium and photoreceptor defect maps were produced for each case. The borders of the photoreceptor defect area and RPE defect area were delineated individually on separate annotation layers. The two outlines were then superimposed to compare the areas of overlap and nonoverlap. The perimeter of the RPE defect area was calculated by the software in pixels. The superimposed outline of the photoreceptor defect area and the RPE defect area was scrutinized to classify the overlap configuration of the junctional zone into one of three categories: Type 0, exact correspondence between the edge of the RPE defect and photoreceptor defect; Type 1, loss of photoreceptors outside and beyond the edge of the RPE defect; Type 2, preservation of photoreceptors beyond the edge of the RPE defect. The relative proportion of the various border configurations was expressed as a percentage of the perimeter of the RPE defect. Each configuration was then classified into four subgroups according to irregularity of the RPE band and the presence of debris. Fifteen eyes of 11 patients (mean age: 79.3 ± 4.3 years; range: 79-94 years) were

  1. Influence of Cone-Beam Computed Tomography filters on diagnosis of simulated endodontic complications.

    PubMed

    Verner, F S; D'Addazio, P S; Campos, C N; Devito, K L; Almeida, S M; Junqueira, R B

    2017-11-01

    To evaluate the influence of cone-beam computed tomography (CBCT) filters on diagnosis of simulated endodontic complications. Sixteen human teeth, in three mandibles, were submitted to the following simulated endodontic complications: (G1) fractured file, (G2) perforations in the canal walls, (G3) deviated cast post, and (G4) external root resorption. The mandibles were submitted to CBCT examination (I-Cat ® Next Generation). Five oral radiologists evaluated the images independently with and without XoranCat ® software filters. Accuracy, sensitivity and specificity were determined. ROC curves were calculated for each group with the filters, and the areas under the curves were compared using anova (one-way) test. McNemar test was applied for pair-wise agreement between all images versus the gold standard and original images versus images with filters (P < 0.05). G1 was the most difficult endodontic complication to diagnosis, followed by G2, G4 and G3. There were no differences between areas under the ROC curves for the filters in all groups; however, Sharpen Super Mild filter had the best results for G1 (0.47), Angio Sharpen Low 3 × 3 for G2 (0.93), Angio Sharpen Low 3 × 3, S9, Shadow and Sharpen for G3 (1.00) and Sharpen 3 × 3 for G4 (1.00). The McNemar test revealed significant differences between all filters with the gold standard (P = 0.00 for all filters) and the originals images (P = 0.00 for all filters) only in G1 group. There were no differences in the other groups. The filters did not improve the diagnosis of the simulated endodontic complications evaluated. Their diagnosis remains a major challenge in clinical practice. © 2016 International Endodontic Journal. Published by John Wiley & Sons Ltd.

  2. 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.

  3. Processing of next generation weather radar-multisensor precipitation estimates and quantitative precipitation forecast data for the DuPage County streamflow simulation system

    USGS Publications Warehouse

    Bera, Maitreyee; Ortel, Terry W.

    2018-01-12

    The U.S. Geological Survey, in cooperation with DuPage County Stormwater Management Department, is testing a near real-time streamflow simulation system that assists in the management and operation of reservoirs and other flood-control structures in the Salt Creek and West Branch DuPage River drainage basins in DuPage County, Illinois. As part of this effort, the U.S. Geological Survey maintains a database of hourly meteorological and hydrologic data for use in this near real-time streamflow simulation system. Among these data are next generation weather radar-multisensor precipitation estimates and quantitative precipitation forecast data, which are retrieved from the North Central River Forecasting Center of the National Weather Service. The DuPage County streamflow simulation system uses these quantitative precipitation forecast data to create streamflow predictions for the two simulated drainage basins. This report discusses in detail how these data are processed for inclusion in the Watershed Data Management files used in the streamflow simulation system for the Salt Creek and West Branch DuPage River drainage basins.

  4. Quantitative colorectal cancer perfusion measurement using dynamic contrast-enhanced multidetector-row computed tomography: effect of acquisition time and implications for protocols.

    PubMed

    Goh, Vicky; Halligan, Steve; Hugill, Jo-Ann; Gartner, Louise; Bartram, Clive I

    2005-01-01

    To determine the effect of acquisition time on quantitative colorectal cancer perfusion measurement. Dynamic contrast-enhanced computed tomography (CT) was performed prospectively in 10 patients with histologically proven colorectal cancer using 4-detector row CT (Lightspeed Plus; GE Healthcare Technologies, Waukesha, WI). Tumor blood flow, blood volume, mean transit time, and permeability were assessed for 3 acquisition times (45, 65, and 130 seconds). Mean values for all 4 perfusion parameters for each acquisition time were compared using the paired t test. Significant differences in permeability values were noted between acquisitions of 45 seconds and 65 and 130 seconds, respectively (P=0.02, P=0.007). There was no significant difference for values of blood volume, blood flow, and mean transit time between any of the acquisition times. Scan acquisitions of 45 seconds are too short for reliable permeability measurement in the abdomen. Longer acquisition times are required.

  5. Quantitative Analysis of {sup 18}F-Fluorodeoxyglucose Positron Emission Tomography Identifies Novel Prognostic Imaging Biomarkers in Locally Advanced Pancreatic Cancer Patients Treated With Stereotactic Body Radiation Therapy

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Cui, Yi; Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo; Song, Jie

    Purpose: To identify prognostic biomarkers in pancreatic cancer using high-throughput quantitative image analysis. Methods and Materials: In this institutional review board–approved study, we retrospectively analyzed images and outcomes for 139 locally advanced pancreatic cancer patients treated with stereotactic body radiation therapy (SBRT). The overall population was split into a training cohort (n=90) and a validation cohort (n=49) according to the time of treatment. We extracted quantitative imaging characteristics from pre-SBRT {sup 18}F-fluorodeoxyglucose positron emission tomography, including statistical, morphologic, and texture features. A Cox proportional hazard regression model was built to predict overall survival (OS) in the training cohort using 162more » robust image features. To avoid over-fitting, we applied the elastic net to obtain a sparse set of image features, whose linear combination constitutes a prognostic imaging signature. Univariate and multivariate Cox regression analyses were used to evaluate the association with OS, and concordance index (CI) was used to evaluate the survival prediction accuracy. Results: The prognostic imaging signature included 7 features characterizing different tumor phenotypes, including shape, intensity, and texture. On the validation cohort, univariate analysis showed that this prognostic signature was significantly associated with OS (P=.002, hazard ratio 2.74), which improved upon conventional imaging predictors including tumor volume, maximum standardized uptake value, and total legion glycolysis (P=.018-.028, hazard ratio 1.51-1.57). On multivariate analysis, the proposed signature was the only significant prognostic index (P=.037, hazard ratio 3.72) when adjusted for conventional imaging and clinical factors (P=.123-.870, hazard ratio 0.53-1.30). In terms of CI, the proposed signature scored 0.66 and was significantly better than competing prognostic indices (CI 0.48-0.64, Wilcoxon rank sum test P<1e

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

    PubMed Central

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

    2011-01-01

    Presbyopia is an age related, gradual loss of accommodation, mainly due to changes in the crystalline lens. As part of research efforts to understand and cure this condition, ex vivo, cross-sectional optical coherence tomography images of crystalline lenses were obtained by using the Ex-Vivo Accommodation Simulator (EVAS II) instrument and analyzed to extract their physical and optical properties. Various filters and edge detection methods were applied to isolate the edge contour. An ellipse is fitted to the lens outline to obtain central reference point for transforming the pixel data into the analysis coordinate system. This allows for the fitting of a high order equation to obtain a mathematical description of the edge contour, which obeys constraints of continuity as well as zero to infinite surface slopes from apex to equator. Geometrical parameters of the lens were determined for the lens images captured at different accommodative states. Various curve fitting functions were developed to mathematically describe the anterior and posterior surfaces of the lens. Their differences were evaluated and their suitability for extracting optical performance of the lens was assessed. The robustness of these algorithms was tested by analyzing the same images repeated times. PMID:21639571

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

    PubMed

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

    2011-05-01

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

  8. 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

  9. Global Seismic Imaging Based on Adjoint Tomography

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

    Our aim is to perform adjoint tomography at the scale of globe to image the entire planet. We have started elastic inversions with a global data set of 253 CMT earthquakes with moment magnitudes in the range 5.8 ≤ Mw ≤ 7 and used GSN stations as well as some local networks such as USArray, European stations, etc. Using an iterative pre-conditioned conjugate gradient scheme, we initially set the aim to obtain a global crustal and mantle model with confined transverse isotropy in the upper mantle. Global adjoint tomography has so far remained a challenge mainly due to computational limitations. Recent improvements in our 3D solvers (e.g., a GPU version) and access to high-performance computational centers (e.g., ORNL's Cray XK7 "Titan" system) now enable us to perform iterations with higher-resolution (T > 9 s) and longer-duration (200 min) simulations to accommodate high-frequency body waves and major-arc surface waves, respectively, which help improve data coverage. The remaining challenge is the heavy I/O traffic caused by the numerous files generated during the forward/adjoint simulations and the pre- and post-processing stages of our workflow. We improve the global adjoint tomography workflow by adopting the ADIOS file format for our seismic data as well as models, kernels, etc., to improve efficiency on high-performance clusters. Our ultimate aim is to use data from all available networks and earthquakes within the magnitude range of our interest (5.5 ≤ Mw ≤ 7) which requires a solid framework to manage big data in our global adjoint tomography workflow. We discuss the current status and future of global adjoint tomography based on our initial results as well as practical issues such as handling big data in inversions and on high-performance computing systems.

  10. Imaging and modeling of flow in porous media using clinical nuclear emission tomography systems and computational fluid dynamics

    NASA Astrophysics Data System (ADS)

    Boutchko, Rostyslav; Rayz, Vitaliy L.; Vandehey, Nicholas T.; O'Neil, James P.; Budinger, Thomas F.; Nico, Peter S.; Druhan, Jennifer L.; Saloner, David A.; Gullberg, Grant T.; Moses, William W.

    2012-01-01

    This paper presents experimental and modeling aspects of applying nuclear emission tomography to study fluid flow in laboratory packed porous media columns of the type frequently used in geophysics, geochemistry and hydrology research. Positron emission tomography (PET) and single photon emission computed tomography (SPECT) are used as non-invasive tools to obtain dynamic 3D images of radioactive tracer concentrations. Dynamic sequences obtained using 18F-FDG PET are used to trace flow through a 5 cm diameter × 20 cm tall sand packed column with and without an impermeable obstacle. In addition, a custom-made rotating column setup placed in a clinical two-headed SPECT camera is used to image 99mTc-DTPA tracer propagation in a through-flowing column (10 cm diameter × 30 cm tall) packed with recovered aquifer sediments. A computational fluid dynamics software package FLUENT is used to model the observed flow dynamics. Tracer distributions obtained in the simulations in the smaller column uniformly packed with sand and in the column with an obstacle are remarkably similar to the reconstructed images in the PET experiments. SPECT results demonstrate strongly non-uniform flow patterns for the larger column slurry-packed with sub-surface sediment and slow upward flow. In the numerical simulation of the SPECT study, two symmetric channels with increased permeability are prescribed along the column walls, which result in the emergence of two well-defined preferential flow paths. Methods and results of this work provide new opportunities in hydrologic and biogeochemical research. The primary target application for developed technologies is non-destructive, non-perturbing, quantitative imaging of flow dynamics within laboratory scale porous media systems.

  11. Imaging and modeling of flow in porous media using clinical nuclear emission tomography systems and computational fluid dynamics.

    PubMed

    Boutchko, Rostyslav; Rayz, Vitaliy L; Vandehey, Nicholas T; O'Neil, James P; Budinger, Thomas F; Nico, Peter S; Druhan, Jennifer L; Saloner, David A; Gullberg, Grant T; Moses, William W

    2012-01-01

    This paper presents experimental and modeling aspects of applying nuclear emission tomography to study fluid flow in laboratory packed porous media columns of the type frequently used in geophysics, geochemistry and hydrology research. Positron emission tomography (PET) and single photon emission computed tomography (SPECT) are used as non-invasive tools to obtain dynamic 3D images of radioactive tracer concentrations. Dynamic sequences obtained using 18 F-FDG PET are used to trace flow through a 5 cm diameter × 20 cm tall sand packed column with and without an impermeable obstacle. In addition, a custom-made rotating column setup placed in a clinical two-headed SPECT camera is used to image 99m Tc-DTPA tracer propagation in a through-flowing column (10 cm diameter × 30 cm tall) packed with recovered aquifer sediments. A computational fluid dynamics software package FLUENT is used to model the observed flow dynamics. Tracer distributions obtained in the simulations in the smaller column uniformly packed with sand and in the column with an obstacle are remarkably similar to the reconstructed images in the PET experiments. SPECT results demonstrate strongly non-uniform flow patterns for the larger column slurry-packed with sub-surface sediment and slow upward flow. In the numerical simulation of the SPECT study, two symmetric channels with increased permeability are prescribed along the column walls, which result in the emergence of two well-defined preferential flow paths. Methods and results of this work provide new opportunities in hydrologic and biogeochemical research. The primary target application for developed technologies is non-destructive, non-perturbing, quantitative imaging of flow dynamics within laboratory scale porous media systems.

  12. Multiple methods for multiple futures: Integrating qualitative scenario planning and quantitative simulation modeling for natural resource decision making

    USGS Publications Warehouse

    Symstad, Amy J.; Fisichelli, Nicholas A.; Miller, Brian W.; Rowland, Erika; Schuurman, Gregor W.

    2017-01-01

    Scenario planning helps managers incorporate climate change into their natural resource decision making through a structured “what-if” process of identifying key uncertainties and potential impacts and responses. Although qualitative scenarios, in which ecosystem responses to climate change are derived via expert opinion, often suffice for managers to begin addressing climate change in their planning, this approach may face limits in resolving the responses of complex systems to altered climate conditions. In addition, this approach may fall short of the scientific credibility managers often require to take actions that differ from current practice. Quantitative simulation modeling of ecosystem response to climate conditions and management actions can provide this credibility, but its utility is limited unless the modeling addresses the most impactful and management-relevant uncertainties and incorporates realistic management actions. We use a case study to compare and contrast management implications derived from qualitative scenario narratives and from scenarios supported by quantitative simulations. We then describe an analytical framework that refines the case study’s integrated approach in order to improve applicability of results to management decisions. The case study illustrates the value of an integrated approach for identifying counterintuitive system dynamics, refining understanding of complex relationships, clarifying the magnitude and timing of changes, identifying and checking the validity of assumptions about resource responses to climate, and refining management directions. Our proposed analytical framework retains qualitative scenario planning as a core element because its participatory approach builds understanding for both managers and scientists, lays the groundwork to focus quantitative simulations on key system dynamics, and clarifies the challenges that subsequent decision making must address.

  13. Stereo-tomography in triangulated models

    NASA Astrophysics Data System (ADS)

    Yang, Kai; Shao, Wei-Dong; Xing, Feng-yuan; Xiong, Kai

    2018-04-01

    Stereo-tomography is a distinctive tomographic method. It is capable of estimating the scatterer position, the local dip of scatterer and the background velocity simultaneously. Building a geologically consistent velocity model is always appealing for applied and earthquake seismologists. Differing from the previous work to incorporate various regularization techniques into the cost function of stereo-tomography, we think extending stereo-tomography to the triangulated model will be the most straightforward way to achieve this goal. In this paper, we provided all the Fréchet derivatives of stereo-tomographic data components with respect to model components for slowness-squared triangulated model (or sloth model) in 2D Cartesian coordinate based on the ray perturbation theory for interfaces. A sloth model representation means a sparser model representation when compared with conventional B-spline model representation. A sparser model representation leads to a smaller scale of stereo-tomographic (Fréchet) matrix, a higher-accuracy solution when solving linear equations, a faster convergence rate and a lower requirement for quantity of data space. Moreover, a quantitative representation of interface strengthens the relationships among different model components, which makes the cross regularizations among these model components, such as node coordinates, scatterer coordinates and scattering angles, etc., more straightforward and easier to be implemented. The sensitivity analysis, the model resolution matrix analysis and a series of synthetic data examples demonstrate the correctness of the Fréchet derivatives, the applicability of the regularization terms and the robustness of the stereo-tomography in triangulated model. It provides a solid theoretical foundation for the real applications in the future.

  14. Survival outcomes after radiation therapy for stage III non-small-cell lung cancer after adoption of computed tomography-based simulation.

    PubMed

    Chen, Aileen B; Neville, Bridget A; Sher, David J; Chen, Kun; Schrag, Deborah

    2011-06-10

    Technical studies suggest that computed tomography (CT) -based simulation improves the therapeutic ratio for thoracic radiation therapy (TRT), although few studies have evaluated its use or impact on outcomes. We used the Surveillance, Epidemiology and End Results (SEER) -Medicare linked data to identify CT-based simulation for TRT among Medicare beneficiaries diagnosed with stage III non-small-cell lung cancer (NSCLC) between 2000 and 2005. Demographic and clinical factors associated with use of CT simulation were identified, and the impact of CT simulation on survival was analyzed by using Cox models and propensity score analysis. The proportion of patients treated with TRT who had CT simulation increased from 2.4% in 1994 to 34.0% in 2000 to 77.6% in 2005. Of the 5,540 patients treated with TRT from 2000 to 2005, 60.1% had CT simulation. Geographic variation was seen in rates of CT simulation, with lower rates in rural areas and in the South and West compared with those in the Northeast and Midwest. Patients treated with chemotherapy were more likely to have CT simulation (65.2% v 51.2%; adjusted odds ratio, 1.67; 95% CI, 1.48 to 1.88; P < .01), although there was no significant association between use of surgery and CT simulation. Controlling for demographic and clinical characteristics, CT simulation was associated with lower risk of death (adjusted hazard ratio, 0.77; 95% CI, 0.73 to 0.82; P < .01) compared with conventional simulation. CT-based simulation has been widely, although not uniformly, adopted for the treatment of stage III NSCLC and is associated with higher survival among patients receiving TRT.

  15. Quantitative breast tissue characterization using grating-based x-ray phase-contrast imaging

    NASA Astrophysics Data System (ADS)

    Willner, M.; Herzen, J.; Grandl, S.; Auweter, S.; Mayr, D.; Hipp, A.; Chabior, M.; Sarapata, A.; Achterhold, K.; Zanette, I.; Weitkamp, T.; Sztrókay, A.; Hellerhoff, K.; Reiser, M.; Pfeiffer, F.

    2014-04-01

    X-ray phase-contrast imaging has received growing interest in recent years due to its high capability in visualizing soft tissue. Breast imaging became the focus of particular attention as it is considered the most promising candidate for a first clinical application of this contrast modality. In this study, we investigate quantitative breast tissue characterization using grating-based phase-contrast computed tomography (CT) at conventional polychromatic x-ray sources. Different breast specimens have been scanned at a laboratory phase-contrast imaging setup and were correlated to histopathology. Ascertained tumor types include phylloides tumor, fibroadenoma and infiltrating lobular carcinoma. Identified tissue types comprising adipose, fibroglandular and tumor tissue have been analyzed in terms of phase-contrast Hounsfield units and are compared to high-quality, high-resolution data obtained with monochromatic synchrotron radiation, as well as calculated values based on tabulated tissue properties. The results give a good impression of the method’s prospects and limitations for potential tumor detection and the associated demands on such a phase-contrast breast CT system. Furthermore, the evaluated quantitative tissue values serve as a reference for simulations and the design of dedicated phantoms for phase-contrast mammography.

  16. Simulation of FIB-SEM images for analysis of porous microstructures.

    PubMed

    Prill, Torben; Schladitz, Katja

    2013-01-01

    Focused ion beam nanotomography-scanning electron microscopy tomography yields high-quality three-dimensional images of materials microstructures at the nanometer scale combining serial sectioning using a focused ion beam with SEM. However, FIB-SEM tomography of highly porous media leads to shine-through artifacts preventing automatic segmentation of the solid component. We simulate the SEM process in order to generate synthetic FIB-SEM image data for developing and validating segmentation methods. Monte-Carlo techniques yield accurate results, but are too slow for the simulation of FIB-SEM tomography requiring hundreds of SEM images for one dataset alone. Nevertheless, a quasi-analytic description of the specimen and various acceleration techniques, including a track compression algorithm and an acceleration for the simulation of secondary electrons, cut down the computing time by orders of magnitude, allowing for the first time to simulate FIB-SEM tomography. © Wiley Periodicals, Inc.

  17. Effect of task-related extracerebral circulation on diffuse optical tomography: experimental data and simulations on the forehead.

    PubMed

    Näsi, Tiina; Mäki, Hanna; Hiltunen, Petri; Heiskala, Juha; Nissilä, Ilkka; Kotilahti, Kalle; Ilmoniemi, Risto J

    2013-03-01

    The effect of task-related extracerebral circulatory changes on diffuse optical tomography (DOT) of brain activation was evaluated using experimental data from 14 healthy human subjects and computer simulations. Total hemoglobin responses to weekday-recitation, verbal-fluency, and hand-motor tasks were measured with a high-density optode grid placed on the forehead. The tasks caused varying levels of mental and physical stress, eliciting extracerebral circulatory changes that the reconstruction algorithm was unable to fully distinguish from cerebral hemodynamic changes, resulting in artifacts in the brain activation images. Crosstalk between intra- and extracranial layers was confirmed by the simulations. The extracerebral effects were attenuated by superficial signal regression and depended to some extent on the heart rate, thus allowing identification of hemodynamic changes related to brain activation during the verbal-fluency task. During the hand-motor task, the extracerebral component was stronger, making the separation less clear. DOT provides a tool for distinguishing extracerebral components from signals of cerebral origin. Especially in the case of strong task-related extracerebral circulatory changes, however, sophisticated reconstruction methods are needed to eliminate crosstalk artifacts.

  18. 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

  19. A method for evaluating the murine pulmonary vasculature using micro-computed tomography.

    PubMed

    Phillips, Michael R; Moore, Scott M; Shah, Mansi; Lee, Clara; Lee, Yueh Z; Faber, James E; McLean, Sean E

    2017-01-01

    Significant mortality and morbidity are associated with alterations in the pulmonary vasculature. While techniques have been described for quantitative morphometry of whole-lung arterial trees in larger animals, no methods have been described in mice. We report a method for the quantitative assessment of murine pulmonary arterial vasculature using high-resolution computed tomography scanning. Mice were harvested at 2 weeks, 4 weeks, and 3 months of age. The pulmonary artery vascular tree was pressure perfused to maximal dilation with a radio-opaque casting material with viscosity and pressure set to prevent capillary transit and venous filling. The lungs were fixed and scanned on a specimen computed tomography scanner at 8-μm resolution, and the vessels were segmented. Vessels were grouped into categories based on lumen diameter and branch generation. Robust high-resolution segmentation was achieved, permitting detailed quantitation of pulmonary vascular morphometrics. As expected, postnatal lung development was associated with progressive increase in small-vessel number and arterial branching complexity. These methods for quantitative analysis of the pulmonary vasculature in postnatal and adult mice provide a useful tool for the evaluation of mouse models of disease that affect the pulmonary vasculature. Copyright © 2016 Elsevier Inc. All rights reserved.

  20. Simulation tools for two-dimensional experiments in x-ray computed tomography using the FORBILD head phantom

    PubMed Central

    Yu, Zhicong; Noo, Frédéric; Dennerlein, Frank; Wunderlich, Adam; Lauritsch, Günter; Hornegger, Joachim

    2012-01-01

    Mathematical phantoms are essential for the development and early-stage evaluation of image reconstruction algorithms in x-ray computed tomography (CT). This note offers tools for computer simulations using a two-dimensional (2D) phantom that models the central axial slice through the FORBILD head phantom. Introduced in 1999, in response to a need for a more robust test, the FORBILD head phantom is now seen by many as the gold standard. However, the simple Shepp-Logan phantom is still heavily used by researchers working on 2D image reconstruction. Universal acceptance of the FORBILD head phantom may have been prevented by its significantly-higher complexity: software that allows computer simulations with the Shepp-Logan phantom is not readily applicable to the FORBILD head phantom. The tools offered here address this problem. They are designed for use with Matlab®, as well as open-source variants, such as FreeMat and Octave, which are all widely used in both academia and industry. To get started, the interested user can simply copy and paste the codes from this PDF document into Matlab® M-files. PMID:22713335

  1. Simulation tools for two-dimensional experiments in x-ray computed tomography using the FORBILD head phantom.

    PubMed

    Yu, Zhicong; Noo, Frédéric; Dennerlein, Frank; Wunderlich, Adam; Lauritsch, Günter; Hornegger, Joachim

    2012-07-07

    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.

  2. A no-gold-standard technique for objective assessment of quantitative nuclear-medicine imaging methods

    PubMed Central

    Jha, Abhinav K; Caffo, Brian; Frey, Eric C

    2016-01-01

    The objective optimization and evaluation of nuclear-medicine quantitative imaging methods using patient data is highly desirable but often hindered by the lack of a gold standard. Previously, a regression-without-truth (RWT) approach has been proposed for evaluating quantitative imaging methods in the absence of a gold standard, but this approach implicitly assumes that bounds on the distribution of true values are known. Several quantitative imaging methods in nuclear-medicine imaging measure parameters where these bounds are not known, such as the activity concentration in an organ or the volume of a tumor. We extended upon the RWT approach to develop a no-gold-standard (NGS) technique for objectively evaluating such quantitative nuclear-medicine imaging methods with patient data in the absence of any ground truth. Using the parameters estimated with the NGS technique, a figure of merit, the noise-to-slope ratio (NSR), can be computed, which can rank the methods on the basis of precision. An issue with NGS evaluation techniques is the requirement of a large number of patient studies. To reduce this requirement, the proposed method explored the use of multiple quantitative measurements from the same patient, such as the activity concentration values from different organs in the same patient. The proposed technique was evaluated using rigorous numerical experiments and using data from realistic simulation studies. The numerical experiments demonstrated that the NSR was estimated accurately using the proposed NGS technique when the bounds on the distribution of true values were not precisely known, thus serving as a very reliable metric for ranking the methods on the basis of precision. In the realistic simulation study, the NGS technique was used to rank reconstruction methods for quantitative single-photon emission computed tomography (SPECT) based on their performance on the task of estimating the mean activity concentration within a known volume of interest

  3. A no-gold-standard technique for objective assessment of quantitative nuclear-medicine imaging methods.

    PubMed

    Jha, Abhinav K; Caffo, Brian; Frey, Eric C

    2016-04-07

    The objective optimization and evaluation of nuclear-medicine quantitative imaging methods using patient data is highly desirable but often hindered by the lack of a gold standard. Previously, a regression-without-truth (RWT) approach has been proposed for evaluating quantitative imaging methods in the absence of a gold standard, but this approach implicitly assumes that bounds on the distribution of true values are known. Several quantitative imaging methods in nuclear-medicine imaging measure parameters where these bounds are not known, such as the activity concentration in an organ or the volume of a tumor. We extended upon the RWT approach to develop a no-gold-standard (NGS) technique for objectively evaluating such quantitative nuclear-medicine imaging methods with patient data in the absence of any ground truth. Using the parameters estimated with the NGS technique, a figure of merit, the noise-to-slope ratio (NSR), can be computed, which can rank the methods on the basis of precision. An issue with NGS evaluation techniques is the requirement of a large number of patient studies. To reduce this requirement, the proposed method explored the use of multiple quantitative measurements from the same patient, such as the activity concentration values from different organs in the same patient. The proposed technique was evaluated using rigorous numerical experiments and using data from realistic simulation studies. The numerical experiments demonstrated that the NSR was estimated accurately using the proposed NGS technique when the bounds on the distribution of true values were not precisely known, thus serving as a very reliable metric for ranking the methods on the basis of precision. In the realistic simulation study, the NGS technique was used to rank reconstruction methods for quantitative single-photon emission computed tomography (SPECT) based on their performance on the task of estimating the mean activity concentration within a known volume of interest

  4. How Well Does Dual-Energy Computed Tomography With Metal Artifact Reduction Software Improve Image Quality and Quantify Computed Tomography Number and Iodine Concentration?

    PubMed

    Ohira, Shingo; Kanayama, Naoyuki; Wada, Kentaro; Karino, Tsukasa; Nitta, Yuya; Ueda, Yoshihiro; Miyazaki, Masayoshi; Koizumi, Masahiko; Teshima, Teruki

    2018-04-02

    The objective of this study was to assess the accuracy of the quantitative measurements obtained using dual-energy computed tomography with metal artifact reduction software (MARS). Dual-energy computed tomography scans (fast kV-switching) are performed on a phantom, by varying the number of metal rods (Ti and Pb) and reference iodine materials. Objective and subjective image analyses are performed on retroreconstructed virtual monochromatic images (VMIs) (VMI at 70 keV). The maximum artifact indices for VMI-Ti and VMI-Pb (5 metal rods) with MARS (without MARS) were 17.4 (166.7) and 34.6 (810.6), respectively; MARS significantly improved the mean subjective 5-point score (P < 0.05). The maximum differences between the measured Hounsfield unit and theoretical values for 5 mg/mL iodine and 2-mm core rods were -42.2% and -68.5%, for VMI-Ti and VMI-Pb (5 metal rods), respectively, and the corresponding differences in the iodine concentration were -64.7% and -73.0%, respectively. Metal artifact reduction software improved the objective and subjective image quality; however, the quantitative values were underestimated.

  5. Accuracy of lung nodule density on HRCT: analysis by PSF-based image simulation.

    PubMed

    Ohno, Ken; Ohkubo, Masaki; Marasinghe, Janaka C; Murao, Kohei; Matsumoto, Toru; Wada, Shinichi

    2012-11-08

    A computed tomography (CT) image simulation technique based on the point spread function (PSF) was applied to analyze the accuracy of CT-based clinical evaluations of lung nodule density. The PSF of the CT system was measured and used to perform the lung nodule image simulation. Then, the simulated image was resampled at intervals equal to the pixel size and the slice interval found in clinical high-resolution CT (HRCT) images. On those images, the nodule density was measured by placing a region of interest (ROI) commonly used for routine clinical practice, and comparing the measured value with the true value (a known density of object function used in the image simulation). It was quantitatively determined that the measured nodule density depended on the nodule diameter and the image reconstruction parameters (kernel and slice thickness). In addition, the measured density fluctuated, depending on the offset between the nodule center and the image voxel center. This fluctuation was reduced by decreasing the slice interval (i.e., with the use of overlapping reconstruction), leading to a stable density evaluation. Our proposed method of PSF-based image simulation accompanied with resampling enables a quantitative analysis of the accuracy of CT-based evaluations of lung nodule density. These results could potentially reveal clinical misreadings in diagnosis, and lead to more accurate and precise density evaluations. They would also be of value for determining the optimum scan and reconstruction parameters, such as image reconstruction kernels and slice thicknesses/intervals.

  6. Quantitative Computed Tomography (QCT) derived Bone Mineral Density (BMD) in finite element studies: a review of the literature.

    PubMed

    Knowles, Nikolas K; Reeves, Jacob M; Ferreira, Louis M

    2016-12-01

    Finite element modeling of human bone provides a powerful tool to evaluate a wide variety of outcomes in a highly repeatable and parametric manner. These models are most often derived from computed tomography data, with mechanical properties related to bone mineral density (BMD) from the x-ray energy attenuation provided from this data. To increase accuracy, many researchers report the use of quantitative computed tomography (QCT), in which a calibration phantom is used during image acquisition to improve the estimation of BMD. Since model accuracy is dependent on the methods used in the calculation of BMD and density-mechanical property relationships, it is important to use relationships developed for the same anatomical location and using the same scanner settings, as these may impact model accuracy. The purpose of this literature review is to report the relationships used in the conversion of QCT equivalent density measures to ash, apparent, and/or tissue densities in recent finite element (FE) studies used in common density-modulus relationships. For studies reporting experimental validation, the validation metrics and results are presented. Of the studies reviewed, 29% reported the use of a dipotassium phosphate (K 2 HPO 4 ) phantom, 47% a hydroxyapatite (HA) phantom, 13% did not report phantom type, 7% reported use of both K 2 HPO 4 and HA phantoms, and 4% alternate phantom types. Scanner type and/or settings were omitted or partially reported in 31% of studies. The majority of studies used densitometric and/or density-modulus relationships derived from different anatomical locations scanned in different scanners with different scanner settings. The methods used to derive various densitometric relationships are reported and recommendations are provided toward the standardization of reporting metrics. This review assessed the current state of QCT-based FE modeling with use of clinical scanners. It was found that previously developed densitometric relationships

  7. Validation of the Monte Carlo simulator GATE for indium-111 imaging.

    PubMed

    Assié, K; Gardin, I; Véra, P; Buvat, I

    2005-07-07

    Monte Carlo simulations are useful for optimizing and assessing single photon emission computed tomography (SPECT) protocols, especially when aiming at measuring quantitative parameters from SPECT images. Before Monte Carlo simulated data can be trusted, the simulation model must be validated. The purpose of this work was to validate the use of GATE, a new Monte Carlo simulation platform based on GEANT4, for modelling indium-111 SPECT data, the quantification of which is of foremost importance for dosimetric studies. To that end, acquisitions of (111)In line sources in air and in water and of a cylindrical phantom were performed, together with the corresponding simulations. The simulation model included Monte Carlo modelling of the camera collimator and of a back-compartment accounting for photomultiplier tubes and associated electronics. Energy spectra, spatial resolution, sensitivity values, images and count profiles obtained for experimental and simulated data were compared. An excellent agreement was found between experimental and simulated energy spectra. For source-to-collimator distances varying from 0 to 20 cm, simulated and experimental spatial resolution differed by less than 2% in air, while the simulated sensitivity values were within 4% of the experimental values. The simulation of the cylindrical phantom closely reproduced the experimental data. These results suggest that GATE enables accurate simulation of (111)In SPECT acquisitions.

  8. Positron Emission Tomography: Principles, Technology, and Recent Developments

    NASA Astrophysics Data System (ADS)

    Ziegler, Sibylle I.

    2005-04-01

    Positron emission tomography (PET) is a nuclear medical imaging technique for quantitative measurement of physiologic parameters in vivo (an overview of principles and applications can be found in [P.E. Valk, et al., eds. Positron Emission Tomography. Basic Science and Clinical Practice. 2003, Springer: Heidelberg]), based on the detection of small amounts of posi-tron-emitter-labelled biologic molecules. Various radiotracers are available for neuro-logical, cardiological, and oncological applications in the clinic and in research proto-cols. This overview describes the basic principles, technology, and recent develop-ments in PET, followed by a section on the development of a tomograph with ava-lanche photodiodes dedicated for small animal imaging as an example of efforts in the domain of high resolution tomographs.

  9. Effects of detector dead-time on quantitative analyses involving boron and multi-hit detection events in atom probe tomography.

    PubMed

    Meisenkothen, Frederick; Steel, Eric B; Prosa, Ty J; Henry, Karen T; Prakash Kolli, R

    2015-12-01

    In atom probe tomography (APT), some elements tend to field evaporate preferentially in multi-hit detection events. Boron (B) is one such element. It is thought that a large fraction of the B signal may be lost during data acquisition and is not reported in the mass spectrum or in the 3-D APT reconstruction. Understanding the relationship between the field evaporation behavior of B and the limitations for detecting multi-hit events can provide insight into the signal loss mechanism for B and may suggest ways to improve B detection accuracy. The present work reports data for nominally pure B and for B-implanted silicon (Si) (NIST-SRM2137) at dose levels two-orders of magnitude lower than previously studied by Da Costa, et al. in 2012. Boron concentration profiles collected from SRM2137 specimens qualitatively confirmed a signal loss mechanism is at work in laser pulsed atom probe measurements of B in Si. Ion correlation analysis was used to graphically demonstrate that the detector dead-time results in few same isotope, same charge-state (SISCS) ion pairs being properly recorded in the multi-hit data, explaining why B is consistently under-represented in quantitative analyses. Given the important role of detector dead-time as a signal loss mechanism, the results from three different methods of estimating the detector dead-time are presented. The findings of this study apply to all quantitative analyses that involve multi-hit data, but the dead-time will have the greatest effect on the elements that have a significant quantity of ions detected in multi-hit events. Published by Elsevier B.V.

  10. Quantitative Imaging Biomarkers of NAFLD

    PubMed Central

    Kinner, Sonja; Reeder, Scott B.

    2016-01-01

    Conventional imaging modalities, including ultrasonography (US), computed tomography (CT), and magnetic resonance (MR), play an important role in the diagnosis and management of patients with nonalcoholic fatty liver disease (NAFLD) by allowing noninvasive diagnosis of hepatic steatosis. However, conventional imaging modalities are limited as biomarkers of NAFLD for various reasons. Multi-parametric quantitative MRI techniques overcome many of the shortcomings of conventional imaging and allow comprehensive and objective evaluation of NAFLD. MRI can provide unconfounded biomarkers of hepatic fat, iron, and fibrosis in a single examination—a virtual biopsy has become a clinical reality. In this article, we will review the utility and limitation of conventional US, CT, and MR imaging for the diagnosis NAFLD. Recent advances in imaging biomarkers of NAFLD are also discussed with an emphasis in multi-parametric quantitative MRI. PMID:26848588

  11. Retroperitoneal tumour radiotherapy: clinical improvements using kilovoltage cone beam computed tomography.

    PubMed

    Juan-Senabre, Xavier J; Ferrer-Albiach, Carlos; Rodríguez-Cordón, Marta; Santos-Serra, Agustín; López-Tarjuelo, Juan; Calzada-Feliu, Salvador

    2009-04-01

    We present a clinical case of a patient diagnosed with a retroperitoneal sarcoma, which received preoperative treatment with daily verification via computed tomography obtained with kilovoltage cone beam. We compare the benefit of this treatment compared to other conventional treatment without image guiding, reporting quantitative results.

  12. Spent nuclear fuel assembly inspection using neutron computed tomography

    NASA Astrophysics Data System (ADS)

    Pope, Chad Lee

    The research presented here focuses on spent nuclear fuel assembly inspection using neutron computed tomography. Experimental measurements involving neutron beam transmission through a spent nuclear fuel assembly serve as benchmark measurements for an MCNP simulation model. Comparison of measured results to simulation results shows good agreement. Generation of tomography images from MCNP tally results was accomplished using adapted versions of built in MATLAB algorithms. Multiple fuel assembly models were examined to provide a broad set of conclusions. Tomography images revealing assembly geometric information including the fuel element lattice structure and missing elements can be obtained using high energy neutrons. A projection difference technique was developed which reveals the substitution of unirradiated fuel elements for irradiated fuel elements, using high energy neutrons. More subtle material differences such as altering the burnup of individual elements can be identified with lower energy neutrons provided the scattered neutron contribution to the image is limited. The research results show that neutron computed tomography can be used to inspect spent nuclear fuel assemblies for the purpose of identifying anomalies such as missing elements or substituted elements. The ability to identify anomalies in spent fuel assemblies can be used to deter diversion of material by increasing the risk of early detection as well as improve reprocessing facility operations by confirming the spent fuel configuration is as expected or allowing segregation if anomalies are detected.

  13. Use of quantitative SPECT/CT reconstruction in 99mTc-sestamibi imaging of patients with renal masses.

    PubMed

    Jones, Krystyna M; Solnes, Lilja B; Rowe, Steven P; Gorin, Michael A; Sheikhbahaei, Sara; Fung, George; Frey, Eric C; Allaf, Mohamad E; Du, Yong; Javadi, Mehrbod S

    2018-02-01

    Technetium-99m ( 99m Tc)-sestamibi single-photon emission computed tomography/computed tomography (SPECT/CT) has previously been shown to allow for the accurate differentiation of benign renal oncocytomas and hybrid oncocytic/chromophobe tumors (HOCTs) apart from other malignant renal tumor histologies, with oncocytomas/HOCTs showing high uptake and renal cell carcinoma (RCC) showing low uptake based on uptake ratios from non-quantitative single-photon emission computed tomography (SPECT) reconstructions. However, in this study, several tumors fell close to the uptake ratio cutoff, likely due to limitations in conventional SPECT/CT reconstruction methods. We hypothesized that application of quantitative SPECT/CT (QSPECT) reconstruction methods developed by our group would provide more robust separation of hot and cold lesions, serving as an imaging framework on which quantitative biomarkers can be validated for evaluation of renal masses with 99m Tc-sestamibi. Single-photon emission computed tomography data were reconstructed using the clinical Flash 3D reconstruction and QSPECT methods. Two blinded readers then characterized each tumor as hot or cold. Semi-quantitative uptake ratios were calculated by dividing lesion activity by background renal activity for both Flash 3D and QSPECT reconstructions. The difference between median (mean) hot and cold tumor uptake ratios measured 0.655 (0.73) with the QSPECT method and 0.624 (0.67) with the conventional method, resulting in increased separation between hot and cold tumors. Sub-analysis of 7 lesions near the separation point showed a higher absolute difference (0.16) between QPSECT and Flash 3D mean uptake ratios compared to the remaining lesions. Our finding of improved separation between uptake ratios of hot and cold lesions using QSPECT reconstruction lays the foundation for additional quantitative SPECT techniques such as SPECT-UV in the setting of renal 99m Tc-sestamibi and other SPECT/CT exams. With robust

  14. Seismic imaging: From classical to adjoint tomography

    NASA Astrophysics Data System (ADS)

    Liu, Q.; Gu, Y. J.

    2012-09-01

    Seismic tomography has been a vital tool in probing the Earth's internal structure and enhancing our knowledge of dynamical processes in the Earth's crust and mantle. While various tomographic techniques differ in data types utilized (e.g., body vs. surface waves), data sensitivity (ray vs. finite-frequency approximations), and choices of model parameterization and regularization, most global mantle tomographic models agree well at long wavelengths, owing to the presence and typical dimensions of cold subducted oceanic lithospheres and hot, ascending mantle plumes (e.g., in central Pacific and Africa). Structures at relatively small length scales remain controversial, though, as will be discussed in this paper, they are becoming increasingly resolvable with the fast expanding global and regional seismic networks and improved forward modeling and inversion techniques. This review paper aims to provide an overview of classical tomography methods, key debates pertaining to the resolution of mantle tomographic models, as well as to highlight recent theoretical and computational advances in forward-modeling methods that spearheaded the developments in accurate computation of sensitivity kernels and adjoint tomography. The first part of the paper is devoted to traditional traveltime and waveform tomography. While these approaches established a firm foundation for global and regional seismic tomography, data coverage and the use of approximate sensitivity kernels remained as key limiting factors in the resolution of the targeted structures. In comparison to classical tomography, adjoint tomography takes advantage of full 3D numerical simulations in forward modeling and, in many ways, revolutionizes the seismic imaging of heterogeneous structures with strong velocity contrasts. For this reason, this review provides details of the implementation, resolution and potential challenges of adjoint tomography. Further discussions of techniques that are presently popular in

  15. 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.

  16. Simulation of field-induced molecular dissociation in atom-probe tomography: Identification of a neutral emission channel

    NASA Astrophysics Data System (ADS)

    Zanuttini, David; Blum, Ivan; Rigutti, Lorenzo; Vurpillot, François; Douady, Julie; Jacquet, Emmanuelle; Anglade, Pierre-Matthieu; Gervais, Benoit

    2017-06-01

    We investigate the dynamics of dicationic metal-oxide molecules under large electric-field conditions, on the basis of ab initio calculations coupled to molecular dynamics. Applied to the case of ZnO2 + in the field of atom probe tomography (APT), our simulation reveals the dissociation into three distinct exit channels. The proportions of these channels depend critically on the field strength and on the initial molecular orientation with respect to the field. For typical field strength used in APT experiments, an efficient dissociation channel leads to emission of neutral oxygen atoms, which escape detection. The calculated composition biases and their dependence on the field strength show remarkable consistency with recent APT experiments on ZnO crystals. Our work shows that bond breaking in strong static fields may lead to significant neutral atom production, and therefore to severe elemental composition biases in measurements.

  17. X-ray fast tomography and its applications in dynamical phenomena studies in geosciences at Advanced Photon Source

    NASA Astrophysics Data System (ADS)

    Xiao, Xianghui; Fusseis, Florian; De Carlo, Francesco

    2012-10-01

    State-of-art synchrotron radiation based micro-computed tomography provides high spatial and temporal resolution. This matches the needs of many research problems in geosciences. In this letter we report the current capabilities in microtomography at sector 2BM at the Advanced Photon Source (APS) of Argonne National Laboratory. The beamline is well suited to routinely acquire three-dimensional data of excellent quality with sub-micron resolution. Fast cameras in combination with a polychromatic beam allow time-lapse experiments with temporal resolutions of down to 200 ms. Data processing utilizes quantitative phase retrieval to optimize contrast in phase contrast tomographic data. The combination of these capabilities with purpose-designed experimental cells allows for a wide range of dynamic studies on geoscientific topics, two of which are summarized here. In the near future, new experimental cells capable of simulating conditions in most geological reservoirs will be available for general use. Ultimately, these advances will be matched by a new wide-field imaging beam line, which will be constructed as part of the APS upgrade. It is expected that even faster tomography with larger field of view can be conducted at this beam line, creating new opportunities for geoscientific studies.

  18. From Tomography to Material Properties of Thermal Protection Systems

    NASA Technical Reports Server (NTRS)

    Mansour, Nagi N.; Panerai, Francesco; Ferguson, Joseph C.; Borner, Arnaud; Barnhardt, Michael; Wright, Michael

    2017-01-01

    A NASA Ames Research Center (ARC) effort, under the Entry Systems Modeling (ESM) project, aims at developing micro-tomography (micro-CT) experiments and simulations for studying materials used in hypersonic entry systems. X-ray micro-tomography allows for non-destructive 3D imaging of a materials micro-structure at the sub-micron scale, providing fiber-scale representations of porous thermal protection systems (TPS) materials. The technique has also allowed for In-situ experiments that can resolve response phenomena under realistic environmental conditions such as high temperature, mechanical loads, and oxidizing atmospheres. Simulation tools have been developed at the NASA Ames Research Center to determine material properties and material response from the high-fidelity tomographic representations of the porous materials with the goal of informing macroscopic TPS response models and guiding future TPS design.

  19. Cortical neuron activation induced by electromagnetic stimulation: a quantitative analysis via modelling and simulation.

    PubMed

    Wu, Tiecheng; Fan, Jie; Lee, Kim Seng; Li, Xiaoping

    2016-02-01

    Previous simulation works concerned with the mechanism of non-invasive neuromodulation has isolated many of the factors that can influence stimulation potency, but an inclusive account of the interplay between these factors on realistic neurons is still lacking. To give a comprehensive investigation on the stimulation-evoked neuronal activation, we developed a simulation scheme which incorporates highly detailed physiological and morphological properties of pyramidal cells. The model was implemented on a multitude of neurons; their thresholds and corresponding activation points with respect to various field directions and pulse waveforms were recorded. The results showed that the simulated thresholds had a minor anisotropy and reached minimum when the field direction was parallel to the dendritic-somatic axis; the layer 5 pyramidal cells always had lower thresholds but substantial variances were also observed within layers; reducing pulse length could magnify the threshold values as well as the variance; tortuosity and arborization of axonal segments could obstruct action potential initiation. The dependence of the initiation sites on both the orientation and the duration of the stimulus implies that the cellular excitability might represent the result of the competition between various firing-capable axonal components, each with a unique susceptibility determined by the local geometry. Moreover, the measurements obtained in simulation intimately resemble recordings in physiological and clinical studies, which seems to suggest that, with minimum simplification of the neuron model, the cable theory-based simulation approach can have sufficient verisimilitude to give quantitatively accurate evaluation of cell activities in response to the externally applied field.

  20. Three-dimensional quantitative flow diagnostics

    NASA Technical Reports Server (NTRS)

    Miles, Richard B.; Nosenchuck, Daniel M.

    1989-01-01

    The principles, capabilities, and practical implementation of advanced measurement techniques for the quantitative characterization of three-dimensional flows are reviewed. Consideration is given to particle, Rayleigh, and Raman scattering; fluorescence; flow marking by H2 bubbles, photochromism, photodissociation, and vibrationally excited molecules; light-sheet volume imaging; and stereo imaging. Also discussed are stereo schlieren methods, holographic particle imaging, optical tomography, acoustic and magnetic-resonance imaging, and the display of space-filling data. Extensive diagrams, graphs, photographs, sample images, and tables of numerical data are provided.

  1. The Quantitative Measurements of Vascular Density and Flow Area of Optic Nerve Head Using Optical Coherence Tomography Angiography.

    PubMed

    Bazvand, Fatemeh; Mirshahi, Reza; Fadakar, Kaveh; Faghihi, Houshangh; Sabour, Siamak; Ghassemi, Fariba

    2017-08-01

    The purpose of this study was to evaluate the vascular density (VD) and the flow area on optic nerve head (ONH) and peripapillary area, and the impact of age and sex using optical coherence tomography angiography (OCTA) in healthy human subjects. Both eyes of each volunteer were scanned by an RTVue XR Avanti; Optovue with OCTA using the split-spectrum amplitude-decorrelation angiography algorithm technique. Masked graders evaluated enface angiodisc OCTA data. The flow area of ONH and the VD were automatically calculated. A total of 79 eyes of patients with a mean age of 37.03±11.27 were examined. The total ONH (papillary and peripapillary) area VD was 56.03%±4.55%. The flow area of the ONH was 1.74±0.10 mm/1.34 mm. The temporal and inferotemporal peripapillary VD was different between male and female patients. Increasing age causes some changes in the flow area of the ONH and the papillary VD from the third to the fourth decade (analysis of variance test; P<0.05). A normal quantitative database of the flow area and VD of the papillary and peripapillary area, obtained by RTVue XR with OCT angiography technique, is presented here.

  2. Accuracy in contouring of small and low contrast lesions: Comparison between diagnostic quality computed tomography scanner and computed tomography simulation scanner-A phantom study

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Ho, Yick Wing, E-mail: mpr@hksh.com; Wong, Wing Kei Rebecca; Yu, Siu Ki

    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 inmore » 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

  3. Diagnostic accuracy of semi-automatic quantitative metrics as an alternative to expert reading of CT myocardial perfusion in the CORE320 study.

    PubMed

    Ostovaneh, Mohammad R; Vavere, Andrea L; Mehra, Vishal C; Kofoed, Klaus F; Matheson, Matthew B; Arbab-Zadeh, Armin; Fujisawa, Yasuko; Schuijf, Joanne D; Rochitte, Carlos E; Scholte, Arthur J; Kitagawa, Kakuya; Dewey, Marc; Cox, Christopher; DiCarli, Marcelo F; George, Richard T; Lima, Joao A C

    To determine the diagnostic accuracy of semi-automatic quantitative metrics compared to expert reading for interpretation of computed tomography perfusion (CTP) imaging. The CORE320 multicenter diagnostic accuracy clinical study enrolled patients between 45 and 85 years of age who were clinically referred for invasive coronary angiography (ICA). Computed tomography angiography (CTA), CTP, single photon emission computed tomography (SPECT), and ICA images were interpreted manually in blinded core laboratories by two experienced readers. Additionally, eight quantitative CTP metrics as continuous values were computed semi-automatically from myocardial and blood attenuation and were combined using logistic regression to derive a final quantitative CTP metric score. For the reference standard, hemodynamically significant coronary artery disease (CAD) was defined as a quantitative ICA stenosis of 50% or greater and a corresponding perfusion defect by SPECT. Diagnostic accuracy was determined by area under the receiver operating characteristic curve (AUC). Of the total 377 included patients, 66% were male, median age was 62 (IQR: 56, 68) years, and 27% had prior myocardial infarction. In patient based analysis, the AUC (95% CI) for combined CTA-CTP expert reading and combined CTA-CTP semi-automatic quantitative metrics was 0.87(0.84-0.91) and 0.86 (0.83-0.9), respectively. In vessel based analyses the AUC's were 0.85 (0.82-0.88) and 0.84 (0.81-0.87), respectively. No significant difference in AUC was found between combined CTA-CTP expert reading and CTA-CTP semi-automatic quantitative metrics in patient based or vessel based analyses(p > 0.05 for all). Combined CTA-CTP semi-automatic quantitative metrics is as accurate as CTA-CTP expert reading to detect hemodynamically significant CAD. Copyright © 2018 Society of Cardiovascular Computed Tomography. Published by Elsevier Inc. All rights reserved.

  4. Evaluation of breeding strategies for polledness in dairy cattle using a newly developed simulation framework for quantitative and Mendelian traits.

    PubMed

    Scheper, Carsten; Wensch-Dorendorf, Monika; Yin, Tong; Dressel, Holger; Swalve, Herrmann; König, Sven

    2016-06-29

    Intensified selection of polled individuals has recently gained importance in predominantly horned dairy cattle breeds as an alternative to routine dehorning. The status quo of the current polled breeding pool of genetically-closely related artificial insemination sires with lower breeding values for performance traits raises questions regarding the effects of intensified selection based on this founder pool. We developed a stochastic simulation framework that combines the stochastic simulation software QMSim and a self-designed R program named QUALsim that acts as an external extension. Two traits were simulated in a dairy cattle population for 25 generations: one quantitative (QMSim) and one qualitative trait with Mendelian inheritance (i.e. polledness, QUALsim). The assignment scheme for qualitative trait genotypes initiated realistic initial breeding situations regarding allele frequencies, true breeding values for the quantitative trait and genetic relatedness. Intensified selection for polled cattle was achieved using an approach that weights estimated breeding values in the animal best linear unbiased prediction model for the quantitative trait depending on genotypes or phenotypes for the polled trait with a user-defined weighting factor. Selection response for the polled trait was highest in the selection scheme based on genotypes. Selection based on phenotypes led to significantly lower allele frequencies for polled. The male selection path played a significantly greater role for a fast dissemination of polled alleles compared to female selection strategies. Fixation of the polled allele implies selection based on polled genotypes among males. In comparison to a base breeding scenario that does not take polledness into account, intensive selection for polled substantially reduced genetic gain for this quantitative trait after 25 generations. Reducing selection intensity for polled males while maintaining strong selection intensity among females

  5. Image characterization metrics for muon tomography

    NASA Astrophysics Data System (ADS)

    Luo, Weidong; Lehovich, Andre; Anashkin, Edward; Bai, Chuanyong; Kindem, Joel; Sossong, Michael; Steiger, Matt

    2014-05-01

    Muon tomography uses naturally occurring cosmic rays to detect nuclear threats in containers. Currently there are no systematic image characterization metrics for muon tomography. We propose a set of image characterization methods to quantify the imaging performance of muon tomography. These methods include tests of spatial resolution, uniformity, contrast, signal to noise ratio (SNR) and vertical smearing. Simulated phantom data and analysis methods were developed to evaluate metric applicability. Spatial resolution was determined as the FWHM of the point spread functions in X, Y and Z axis for 2.5cm tungsten cubes. Uniformity was measured by drawing a volume of interest (VOI) within a large water phantom and defined as the standard deviation of voxel values divided by the mean voxel value. Contrast was defined as the peak signals of a set of tungsten cubes divided by the mean voxel value of the water background. SNR was defined as the peak signals of cubes divided by the standard deviation (noise) of the water background. Vertical smearing, i.e. vertical thickness blurring along the zenith axis for a set of 2 cm thick tungsten plates, was defined as the FWHM of vertical spread function for the plate. These image metrics provided a useful tool to quantify the basic imaging properties for muon tomography.

  6. Quantitative NDE of Composite Structures at NASA

    NASA Technical Reports Server (NTRS)

    Cramer, K. Elliott; Leckey, Cara A. C.; Howell, Patricia A.; Johnston, Patrick H.; Burke, Eric R.; Zalameda, Joseph N.; Winfree, William P.; Seebo, Jeffery P.

    2015-01-01

    The use of composite materials continues to increase in the aerospace community due to the potential benefits of reduced weight, increased strength, and manufacturability. Ongoing work at NASA involves the use of the large-scale composite structures for spacecraft (payload shrouds, cryotanks, crew modules, etc). NASA is also working to enable the use and certification of composites in aircraft structures through the Advanced Composites Project (ACP). The rapid, in situ characterization of a wide range of the composite materials and structures has become a critical concern for the industry. In many applications it is necessary to monitor changes in these materials over a long time. The quantitative characterization of composite defects such as fiber waviness, reduced bond strength, delamination damage, and microcracking are of particular interest. The research approaches of NASA's Nondestructive Evaluation Sciences Branch include investigation of conventional, guided wave, and phase sensitive ultrasonic methods, infrared thermography and x-ray computed tomography techniques. The use of simulation tools for optimizing and developing these methods is also an active area of research. This paper will focus on current research activities related to large area NDE for rapidly characterizing aerospace composites.

  7. Breast ultrasound tomography with two parallel transducer arrays: preliminary clinical results

    NASA Astrophysics Data System (ADS)

    Huang, Lianjie; Shin, Junseob; Chen, Ting; Lin, Youzuo; Intrator, Miranda; Hanson, Kenneth; Epstein, Katherine; Sandoval, Daniel; Williamson, Michael

    2015-03-01

    Ultrasound tomography has great potential to provide quantitative estimations of physical properties of breast tumors for accurate characterization of breast cancer. We design and manufacture a new synthetic-aperture breast ultrasound tomography system with two parallel transducer arrays. The distance of these two transducer arrays is adjustable for scanning breasts with different sizes. The ultrasound transducer arrays are translated vertically to scan the entire breast slice by slice and acquires ultrasound transmission and reflection data for whole-breast ultrasound imaging and tomographic reconstructions. We use the system to acquire patient data at the University of New Mexico Hospital for clinical studies. We present some preliminary imaging results of in vivo patient ultrasound data. Our preliminary clinical imaging results show promising of our breast ultrasound tomography system with two parallel transducer arrays for breast cancer imaging and characterization.

  8. Entrance surface dose distribution and organ dose assessment for cone-beam computed tomography using measurements and Monte Carlo simulations with voxel phantoms

    NASA Astrophysics Data System (ADS)

    Baptista, M.; Di Maria, S.; Vieira, S.; Vaz, P.

    2017-11-01

    Cone-Beam Computed Tomography (CBCT) enables high-resolution volumetric scanning of the bone and soft tissue anatomy under investigation at the treatment accelerator. This technique is extensively used in Image Guided Radiation Therapy (IGRT) for pre-treatment verification of patient position and target volume localization. When employed daily and several times per patient, CBCT imaging may lead to high cumulative imaging doses to the healthy tissues surrounding the exposed organs. This work aims at (1) evaluating the dose distribution during a CBCT scan and (2) calculating the organ doses involved in this image guiding procedure for clinically available scanning protocols. Both Monte Carlo (MC) simulations and measurements were performed. To model and simulate the kV imaging system mounted on a linear accelerator (Edge™, Varian Medical Systems) the state-of-the-art MC radiation transport program MCNPX 2.7.0 was used. In order to validate the simulation results, measurements of the Computed Tomography Dose Index (CTDI) were performed, using standard PMMA head and body phantoms, with 150 mm length and a standard pencil ionizing chamber (IC) 100 mm long. Measurements for head and pelvis scanning protocols, usually adopted in clinical environment were acquired, using two acquisition modes (full-fan and half fan). To calculate the organ doses, the implemented MC model of the CBCT scanner together with a male voxel phantom ("Golem") was used. The good agreement between the MCNPX simulations and the CTDIw measurements (differences up to 17%) presented in this work reveals that the CBCT MC model was successfully validated, taking into account the several uncertainties. The adequacy of the computational model to map dose distributions during a CBCT scan is discussed in order to identify ways to reduce the total CBCT imaging dose. The organ dose assessment highlights the need to evaluate the therapeutic and the CBCT imaging doses, in a more balanced approach, and the

  9. 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.

  10. Quantitative EEG analysis using error reduction ratio-causality test; validation on simulated and real EEG data.

    PubMed

    Sarrigiannis, Ptolemaios G; Zhao, Yifan; Wei, Hua-Liang; Billings, Stephen A; Fotheringham, Jayne; Hadjivassiliou, Marios

    2014-01-01

    To introduce a new method of quantitative EEG analysis in the time domain, the error reduction ratio (ERR)-causality test. To compare performance against cross-correlation and coherence with phase measures. A simulation example was used as a gold standard to assess the performance of ERR-causality, against cross-correlation and coherence. The methods were then applied to real EEG data. Analysis of both simulated and real EEG data demonstrates that ERR-causality successfully detects dynamically evolving changes between two signals, with very high time resolution, dependent on the sampling rate of the data. Our method can properly detect both linear and non-linear effects, encountered during analysis of focal and generalised seizures. We introduce a new quantitative EEG method of analysis. It detects real time levels of synchronisation in the linear and non-linear domains. It computes directionality of information flow with corresponding time lags. This novel dynamic real time EEG signal analysis unveils hidden neural network interactions with a very high time resolution. These interactions cannot be adequately resolved by the traditional methods of coherence and cross-correlation, which provide limited results in the presence of non-linear effects and lack fidelity for changes appearing over small periods of time. Copyright © 2013 International Federation of Clinical Neurophysiology. Published by Elsevier Ireland Ltd. All rights reserved.

  11. The Neural Correlates of Driving Performance Identified Using Positron Emission Tomography

    ERIC Educational Resources Information Center

    Horikawa, E.; Okamura, N.; Tashiro, M.; Sakurada, Y.; Maruyama, M.; Arai, H.; Yamaguchi, K.; Sasaki, H.; Yanai, K.; Itoh, M.

    2005-01-01

    Driving is a complex behavior involving multiple cognitive domains. To identify neural correlates of driving performance, [^1^5O]H"2O positron emission tomography was performed using a simulated driving task. Compared with the resting condition, simulated driving increased regional cerebral blood flow (rCBF) in the cerebellum, occipital, and…

  12. Quantitative tomographic measurements of opaque multiphase flows

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    GEORGE,DARIN L.; TORCZYNSKI,JOHN R.; SHOLLENBERGER,KIM ANN

    2000-03-01

    An electrical-impedance tomography (EIT) system has been developed for quantitative measurements of radial phase distribution profiles in two-phase and three-phase vertical column flows. The EIT system is described along with the computer algorithm used for reconstructing phase volume fraction profiles. EIT measurements were validated by comparison with a gamma-densitometry tomography (GDT) system. The EIT system was used to accurately measure average solid volume fractions up to 0.05 in solid-liquid flows, and radial gas volume fraction profiles in gas-liquid flows with gas volume fractions up to 0.15. In both flows, average phase volume fractions and radial volume fraction profiles from GDTmore » and EIT were in good agreement. A minor modification to the formula used to relate conductivity data to phase volume fractions was found to improve agreement between the methods. GDT and EIT were then applied together to simultaneously measure the solid, liquid, and gas radial distributions within several vertical three-phase flows. For average solid volume fractions up to 0.30, the gas distribution for each gas flow rate was approximately independent of the amount of solids in the column. Measurements made with this EIT system demonstrate that EIT may be used successfully for noninvasive, quantitative measurements of dispersed multiphase flows.« less

  13. A collimator optimization method for quantitative imaging: application to Y-90 bremsstrahlung SPECT.

    PubMed

    Rong, Xing; Frey, Eric C

    2013-08-01

    Post-therapy quantitative 90Y bremsstrahlung single photon emission computed tomography (SPECT) has shown great potential to provide reliable activity estimates, which are essential for dose verification. Typically 90Y imaging is performed with high- or medium-energy collimators. However, the energy spectrum of 90Y bremsstrahlung photons is substantially different than typical for these collimators. In addition, dosimetry requires quantitative images, and collimators are not typically optimized for such tasks. Optimizing a collimator for 90Y imaging is both novel and potentially important. Conventional optimization methods are not appropriate for 90Y bremsstrahlung photons, which have a continuous and broad energy distribution. In this work, the authors developed a parallel-hole collimator optimization method for quantitative tasks that is particularly applicable to radionuclides with complex emission energy spectra. The authors applied the proposed method to develop an optimal collimator for quantitative 90Y bremsstrahlung SPECT in the context of microsphere radioembolization. To account for the effects of the collimator on both the bias and the variance of the activity estimates, the authors used the root mean squared error (RMSE) of the volume of interest activity estimates as the figure of merit (FOM). In the FOM, the bias due to the null space of the image formation process was taken in account. The RMSE was weighted by the inverse mass to reflect the application to dosimetry; for a different application, more relevant weighting could easily be adopted. The authors proposed a parameterization for the collimator that facilitates the incorporation of the important factors (geometric sensitivity, geometric resolution, and septal penetration fraction) determining collimator performance, while keeping the number of free parameters describing the collimator small (i.e., two parameters). To make the optimization results for quantitative 90Y bremsstrahlung SPECT more

  14. Morphometric analysis - Cone beam computed tomography to predict bone quality and quantity.

    PubMed

    Hohlweg-Majert, B; Metzger, M C; Kummer, T; Schulze, D

    2011-07-01

    Modified quantitative computed tomography is a method used to predict bone quality and quantify the bone mass of the jaw. The aim of this study was to determine whether bone quantity or quality was detected by cone beam computed tomography (CBCT) combined with image analysis. MATERIALS AND PROCEDURES: Different measurements recorded on two phantoms (Siemens phantom, Comac phantom) were evaluated on images taken with the Somatom VolumeZoom (Siemens Medical Solutions, Erlangen, Germany) and the NewTom 9000 (NIM s.r.l., Verona, Italy) in order to calculate a calibration curve. The spatial relationships of six sample cylinders and the repositioning from four pig skull halves relative to adjacent defined anatomical structures were assessed by means of three-dimensional visualization software. The calibration curves for computer tomography (CT) and cone beam computer tomography (CBCT) using the Siemens phantom showed linear correlation in both modalities between the Hounsfield Units (HU) and bone morphology. A correction factor for CBCT was calculated. Exact information about the micromorphology of the bone cylinders was only available using of micro computer tomography. Cone-beam computer tomography is a suitable choice for analysing bone mass, but, it does not give any information about bone quality. 2010 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights reserved.

  15. Optical coherence tomography angiography in age-related macular degeneration: The game changer.

    PubMed

    Lupidi, Marco; Cerquaglia, Alessio; Chhablani, Jay; Fiore, Tito; Singh, Sumit Randhir; Cardillo Piccolino, Felice; Corbucci, Roberta; Coscas, Florence; Coscas, Gabriel; Cagini, Carlo

    2018-04-01

    Optical coherence tomography angiography is one of the biggest advances in ophthalmic imaging. It enables a depth-resolved assessment of the retinal and choroidal blood flow, far exceeding the levels of detail commonly obtained with dye angiographies. One of the first applications of optical coherence tomography angiography was in detecting the presence of choroidal neovascularization in age-related macular degeneration and establishing its position in relation to the retinal pigmented epithelium and Bruch's membrane, and thereby classifying the CNV as type 1, type 2, type 3, or mixed lesions. Optical coherence tomography angiograms, due to the longer wavelength used by optical coherence tomography, showed a more distinct choroidal neovascularization vascular pattern than fluorescein angiography, since there is less suffering from light scattering or is less obscured by overlying subretinal hemorrhages or exudation. Qualitative and quantitative assessments of optical coherence tomography angiography findings in exudative and nonexudative age-related macular degeneration have been largely investigated within the past 3 years both in clinical and experimental settings. This review constitutes an up-to-date of all the potential applications of optical coherence tomography angiography in age-related macular degeneration in order to better understand how to translate its theoretical usefulness into the current clinical practice.

  16. Reduction of variable-truncation artifacts from beam occlusion during in situ x-ray tomography

    NASA Astrophysics Data System (ADS)

    Borg, Leise; Jørgensen, Jakob S.; Frikel, Jürgen; Sporring, Jon

    2017-12-01

    Many in situ x-ray tomography studies require experimental rigs which may partially occlude the beam and cause parts of the projection data to be missing. In a study of fluid flow in porous chalk using a percolation cell with four metal bars drastic streak artifacts arise in the filtered backprojection (FBP) reconstruction at certain orientations. Projections with non-trivial variable truncation caused by the metal bars are the source of these variable-truncation artifacts. To understand the artifacts a mathematical model of variable-truncation data as a function of metal bar radius and distance to sample is derived and verified numerically and with experimental data. The model accurately describes the arising variable-truncation artifacts across simulated variations of the experimental setup. Three variable-truncation artifact-reduction methods are proposed, all aimed at addressing sinogram discontinuities that are shown to be the source of the streaks. The ‘reduction to limited angle’ (RLA) method simply keeps only non-truncated projections; the ‘detector-directed smoothing’ (DDS) method smooths the discontinuities; while the ‘reflexive boundary condition’ (RBC) method enforces a zero derivative at the discontinuities. Experimental results using both simulated and real data show that the proposed methods effectively reduce variable-truncation artifacts. The RBC method is found to provide the best artifact reduction and preservation of image features using both visual and quantitative assessment. The analysis and artifact-reduction methods are designed in context of FBP reconstruction motivated by computational efficiency practical for large, real synchrotron data. While a specific variable-truncation case is considered, the proposed methods can be applied to general data cut-offs arising in different in situ x-ray tomography experiments.

  17. Multi-component Cu-Strengthened Steel Welding Simulations: Atom Probe Tomography and Synchrotron X-ray Diffraction Analyses

    NASA Astrophysics Data System (ADS)

    Hunter, Allen H.; Farren, Jeffrey D.; DuPont, John N.; Seidman, David N.

    2015-07-01

    An experimental steel with the composition Fe-1.39Cu-2.70Ni-0.58Al-0.48Mn-0.48Si-0.065Nb-0.05C (wt pct) or alternatively Fe-1.43Cu-2.61Ni-1.21Al-0.48Mn-0.98Si-0.039Nb-0.23C (at. pct) has been developed at Northwestern University, which has both high toughness and high strength after quenching and aging treatments. Simulated heat-affected zone (HAZ) samples are utilized to analyze the microstructures typically obtained after gas metal arc welding (GMAW). Dissolution within the HAZ of cementite (Fe3C) and NbC (F.C.C.) is revealed using synchrotron X-ray diffraction, while dissolution of Cu precipitates is measured employing local electrode atom probe tomography. The results are compared to Thermo-Calc equilibrium calculations. Comparison of measured Cu precipitate radii, number density, and volume fraction with similar measurements from a GMAW sample suggests that the cooling rate in the simulations is faster than in the experimental GMAW sample, resulting in significantly less Cu precipitate nucleation and growth during the cooling part of the weld thermal cycle. The few Cu precipitates detected in the simulated samples are primarily located on grain boundaries resulting from heterogeneous nucleation. The dissolution of NbC precipitates and the resultant austenite coarsening in the highest-temperature sample, coupled with a rapid cooling rate, results in the growth of bainite, and an increase in the strength of the matrix in the absence of significant Cu precipitation.

  18. Depth-resolved imaging of colon tumor using optical coherence tomography and fluorescence laminar optical tomography (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Tang, Qinggong; Frank, Aaron; Wang, Jianting; Chen, Chao-wei; Jin, Lily; Lin, Jon; Chan, Joanne M.; Chen, Yu

    2016-03-01

    Early detection of neoplastic changes remains a critical challenge in clinical cancer diagnosis and treatment. Many cancers arise from epithelial layers such as those of the gastrointestinal (GI) tract. Current standard endoscopic technology is unable to detect those subsurface lesions. Since cancer development is associated with both morphological and molecular alterations, imaging technologies that can quantitative image tissue's morphological and molecular biomarkers and assess the depth extent of a lesion in real time, without the need for tissue excision, would be a major advance in GI cancer diagnostics and therapy. In this research, we investigated the feasibility of multi-modal optical imaging including high-resolution optical coherence tomography (OCT) and depth-resolved high-sensitivity fluorescence laminar optical tomography (FLOT) for structural and molecular imaging. APC (adenomatous polyposis coli) mice model were imaged using OCT and FLOT and the correlated histopathological diagnosis was obtained. Quantitative structural (the scattering coefficient) and molecular imaging parameters (fluorescence intensity) from OCT and FLOT images were developed for multi-parametric analysis. This multi-modal imaging method has demonstrated the feasibility for more accurate diagnosis with 87.4% (87.3%) for sensitivity (specificity) which gives the most optimal diagnosis (the largest area under receiver operating characteristic (ROC) curve). This project results in a new non-invasive multi-modal imaging platform for improved GI cancer detection, which is expected to have a major impact on detection, diagnosis, and characterization of GI cancers, as well as a wide range of epithelial cancers.

  19. Objective evaluation of reconstruction methods for quantitative SPECT imaging in the absence of ground truth.

    PubMed

    Jha, Abhinav K; Song, Na; Caffo, Brian; Frey, Eric C

    2015-04-13

    Quantitative single-photon emission computed tomography (SPECT) imaging is emerging as an important tool in clinical studies and biomedical research. There is thus a need for optimization and evaluation of systems and algorithms that are being developed for quantitative SPECT imaging. An appropriate objective method to evaluate these systems is by comparing their performance in the end task that is required in quantitative SPECT imaging, such as estimating the mean activity concentration in a volume of interest (VOI) in a patient image. This objective evaluation can be performed if the true value of the estimated parameter is known, i.e. we have a gold standard. However, very rarely is this gold standard known in human studies. Thus, no-gold-standard techniques to optimize and evaluate systems and algorithms in the absence of gold standard are required. In this work, we developed a no-gold-standard technique to objectively evaluate reconstruction methods used in quantitative SPECT when the parameter to be estimated is the mean activity concentration in a VOI. We studied the performance of the technique with realistic simulated image data generated from an object database consisting of five phantom anatomies with all possible combinations of five sets of organ uptakes, where each anatomy consisted of eight different organ VOIs. Results indicate that the method provided accurate ranking of the reconstruction methods. We also demonstrated the application of consistency checks to test the no-gold-standard output.

  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. Detection of extracellular matrix modification in cancer models with inverse spectroscopic optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Spicer, Graham L. C.; Azarin, Samira M.; Yi, Ji; Young, Scott T.; Ellis, Ronald; Bauer, Greta M.; Shea, Lonnie D.; Backman, Vadim

    2016-10-01

    In cancer biology, there has been a recent effort to understand tumor formation in the context of the tissue microenvironment. In particular, recent progress has explored the mechanisms behind how changes in the cell-extracellular matrix ensemble influence progression of the disease. The extensive use of in vitro tissue culture models in simulant matrix has proven effective at studying such interactions, but modalities for non-invasively quantifying aspects of these systems are scant. We present the novel application of an imaging technique, Inverse Spectroscopic Optical Coherence Tomography, for the non-destructive measurement of in vitro biological samples during matrix remodeling. Our findings indicate that the nanoscale-sensitive mass density correlation shape factor D of cancer cells increases in response to a more crosslinked matrix. We present a facile technique for the non-invasive, quantitative study of the micro- and nano-scale structure of the extracellular matrix and its host cells.

  2. GEANT4 simulation of a scintillating-fibre tracker for the cosmic-ray muon tomography of legacy nuclear waste containers

    NASA Astrophysics Data System (ADS)

    Clarkson, A.; Hamilton, D. J.; Hoek, M.; Ireland, D. G.; Johnstone, J. R.; Kaiser, R.; Keri, T.; Lumsden, S.; Mahon, D. F.; McKinnon, B.; Murray, M.; Nutbeam-Tuffs, S.; Shearer, C.; Staines, C.; Yang, G.; Zimmerman, C.

    2014-05-01

    Cosmic-ray muons are highly penetrative charged particles that are observed at the sea level with a flux of approximately one per square centimetre per minute. They interact with matter primarily through Coulomb scattering, which is exploited in the field of muon tomography to image shielded objects in a wide range of applications. In this paper, simulation studies are presented that assess the feasibility of a scintillating-fibre tracker system for use in the identification and characterisation of nuclear materials stored within industrial legacy waste containers. A system consisting of a pair of tracking modules above and a pair below the volume to be assayed is simulated within the GEANT4 framework using a range of potential fibre pitches and module separations. Each module comprises two orthogonal planes of fibres that allow the reconstruction of the initial and Coulomb-scattered muon trajectories. A likelihood-based image reconstruction algorithm has been developed that allows the container content to be determined with respect to the scattering density λ, a parameter which is related to the atomic number Z of the scattering material. Images reconstructed from this simulation are presented for a range of anticipated scenarios that highlight the expected image resolution and the potential of this system for the identification of high-Z materials within a shielded, concrete-filled container. First results from a constructed prototype system are presented in comparison with those from a detailed simulation. Excellent agreement between experimental data and simulation is observed showing clear discrimination between the different materials assayed throughout.

  3. Two-dimensional imaging of gas temperature and concentration based on hyperspectral tomography

    NASA Astrophysics Data System (ADS)

    Xin, Ming-yuan; Jin, Xing; Wang, Guang-yu; Song, Junling

    2016-10-01

    Two-dimensional imaging of gas temperature and concentration is realized by hyperspectral tomography, which has the characteristics of using multi-wavelengths absorption spectral information, so that the imaging could be accomplished in a small number of projections and viewing angles. A temperature and concentration model is established to simulate the combustion conditions and a total number of 10 near-infrared absorption spectral information of H2O is used. An improved simulated annealing algorithm by adjusting search step is performed the main search algorithm for the tomography. By adding random errors into the absorption area information, the stability of the algorithm is tested, and the results are compared with the reconstructions provided by algebraic reconstruction technique which takes advantage of 2 spectral information contents in imaging. The results show that the two methods perform equivalent in low-level noise environment, but at high-level, hyperspectral tomography turns out to be more stable.

  4. Please Don't Move-Evaluating Motion Artifact From Peripheral Quantitative Computed Tomography Scans Using Textural Features.

    PubMed

    Rantalainen, Timo; Chivers, Paola; Beck, Belinda R; Robertson, Sam; Hart, Nicolas H; Nimphius, Sophia; Weeks, Benjamin K; McIntyre, Fleur; Hands, Beth; Siafarikas, Aris

    Most imaging methods, including peripheral quantitative computed tomography (pQCT), are susceptible to motion artifacts particularly in fidgety pediatric populations. Methods currently used to address motion artifact include manual screening (visual inspection) and objective assessments of the scans. However, previously reported objective methods either cannot be applied on the reconstructed image or have not been tested for distal bone sites. Therefore, the purpose of the present study was to develop and validate motion artifact classifiers to quantify motion artifact in pQCT scans. Whether textural features could provide adequate motion artifact classification performance in 2 adolescent datasets with pQCT scans from tibial and radial diaphyses and epiphyses was tested. The first dataset was split into training (66% of sample) and validation (33% of sample) datasets. Visual classification was used as the ground truth. Moderate to substantial classification performance (J48 classifier, kappa coefficients from 0.57 to 0.80) was observed in the validation dataset with the novel texture-based classifier. In applying the same classifier to the second cross-sectional dataset, a slight-to-fair (κ = 0.01-0.39) classification performance was observed. Overall, this novel textural analysis-based classifier provided a moderate-to-substantial classification of motion artifact when the classifier was specifically trained for the measurement device and population. Classification based on textural features may be used to prescreen obviously acceptable and unacceptable scans, with a subsequent human-operated visual classification of any remaining scans. Copyright © 2017 The International Society for Clinical Densitometry. Published by Elsevier Inc. All rights reserved.

  5. Fourier domain preconditioned conjugate gradient algorithm for atmospheric tomography.

    PubMed

    Yang, Qiang; Vogel, Curtis R; Ellerbroek, Brent L

    2006-07-20

    By 'atmospheric tomography' we mean the estimation of a layered atmospheric turbulence profile from measurements of the pupil-plane phase (or phase gradients) corresponding to several different guide star directions. We introduce what we believe to be a new Fourier domain preconditioned conjugate gradient (FD-PCG) algorithm for atmospheric tomography, and we compare its performance against an existing multigrid preconditioned conjugate gradient (MG-PCG) approach. Numerical results indicate that on conventional serial computers, FD-PCG is as accurate and robust as MG-PCG, but it is from one to two orders of magnitude faster for atmospheric tomography on 30 m class telescopes. Simulations are carried out for both natural guide stars and for a combination of finite-altitude laser guide stars and natural guide stars to resolve tip-tilt uncertainty.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Budzevich, M; Grove, O; Balagurunathan, Y

    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,more » 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

  7. Quantitative Pulmonary Imaging Using Computed Tomography and Magnetic Resonance Imaging

    PubMed Central

    Washko, George R.; Parraga, Grace; Coxson, Harvey O.

    2011-01-01

    Measurements of lung function, including spirometry and body plethesmography, are easy to perform and are the current clinical standard for assessing disease severity. However, these lung functional techniques do not adequately explain the observed variability in clinical manifestations of disease and offer little insight into the relationship of lung structure and function. Lung imaging and the image based assessment of lung disease has matured to the extent that it is common for clinical, epidemiologic, and genetic investigation to have a component dedicated to image analysis. There are several exciting imaging modalities currently being used for the non-invasive study of lung anatomy and function. In this review we will focus on two of them, x-ray computed tomography and magnetic resonance imaging. Following a brief introduction of each method we detail some of the most recent work being done to characterize smoking-related lung disease and the clinical applications of such knowledge. PMID:22142490

  8. 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.

  9. Tibial Geometry in Individuals with Neurofibromatosis Type 1 without Anterolateral Bowing of the Lower Leg Using Peripheral Quantitative Computed Tomography

    PubMed Central

    Stevenson, David A.; Viskochil, David H.; Carey, John C.; Slater, Hillarie; Murray, Mary; Sheng, Xiaoming; D’Astous, Jacques; Hanson, Heather; Schorry, Elizabeth; Moyer-Mileur, Laurie J.

    2008-01-01

    Introduction Lower leg bowing with tibial pseudarthrosis is associated with neurofibromatosis type 1 (NF1). The objective of the study is to determine if the geometry of the lower limb in individuals with neurofibromatosis type 1 (NF1) differs from controls, and to characterize the osseous components of the tibia in NF1. Methods Peripheral quantitative computed tomography (pQCT) of the lower limb was performed (90 individuals with NF1 without tibial and/or fibular dysplasia: 474 healthy individuals without NF1). Subjects were 4–18 years of age. Individuals with NF1 were compared to controls using an analysis-of-covariance with a fixed set of covariates (age, weight, height, Tanner stage, and gender). Results Using pQCT, NF1 individuals without bowing of the lower leg have smaller periosteal circumferences (p<0.0001), smaller cortical area (p<0.0001), and decreased tibial cortical and trabecular bone mineral content (BMC) (p<0.0001) compared to controls. Discussion Individuals with NF1 have a different geometry of the lower leg compared to healthy controls suggesting that NF1 haploinsufficiency impacts bone homeostasis although not resulting in overt anterolateral bowing of the lower leg. PMID:19118659

  10. Validation of a Monte Carlo model used for simulating tube current modulation in computed tomography over a wide range of phantom conditions/challenges

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Bostani, Maryam, E-mail: mbostani@mednet.ucla.edu; McMillan, Kyle; Cagnon, Chris H.

    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 purposemore » 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

  11. Quantitative analysis of packed and compacted granular systems by x-ray microtomography

    NASA Astrophysics Data System (ADS)

    Fu, Xiaowei; Milroy, Georgina E.; Dutt, Meenakshi; Bentham, A. Craig; Hancock, Bruno C.; Elliott, James A.

    2005-04-01

    The packing and compaction of powders are general processes in pharmaceutical, food, ceramic and powder metallurgy industries. Understanding how particles pack in a confined space and how powders behave during compaction is crucial for producing high quality products. This paper outlines a new technique, based on modern desktop X-ray tomography and image processing, to quantitatively investigate the packing of particles in the process of powder compaction and provide great insights on how powder densify during powder compaction, which relate in terms of materials properties and processing conditions to tablet manufacture by compaction. A variety of powder systems were considered, which include glass, sugar, NaCl, with a typical particle size of 200-300 mm and binary mixtures of NaCl-Glass Spheres. The results are new and have been validated by SEM observation and numerical simulations using discrete element methods (DEM). The research demonstrates that XMT technique has the potential in further investigating of pharmaceutical processing and even verifying other physical models on complex packing.

  12. Dose fractionation theorem in 3-D reconstruction (tomography)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Glaeser, R.M.

    It is commonly assumed that the large number of projections for single-axis tomography precludes its application to most beam-labile specimens. However, Hegerl and Hoppe have pointed out that the total dose required to achieve statistical significance for each voxel of a computed 3-D reconstruction is the same as that required to obtain a single 2-D image of that isolated voxel, at the same level of statistical significance. Thus a statistically significant 3-D image can be computed from statistically insignificant projections, as along as the total dosage that is distributed among these projections is high enough that it would have resultedmore » in a statistically significant projection, if applied to only one image. We have tested this critical theorem by simulating the tomographic reconstruction of a realistic 3-D model created from an electron micrograph. The simulations verify the basic conclusions of high absorption, signal-dependent noise, varying specimen contrast and missing angular range. Furthermore, the simulations demonstrate that individual projections in the series of fractionated-dose images can be aligned by cross-correlation because they contain significant information derived from the summation of features from different depths in the structure. This latter information is generally not useful for structural interpretation prior to 3-D reconstruction, owing to the complexity of most specimens investigated by single-axis tomography. These results, in combination with dose estimates for imaging single voxels and measurements of radiation damage in the electron microscope, demonstrate that it is feasible to use single-axis tomography with soft X-ray microscopy of frozen-hydrated specimens.« less

  13. 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

  14. Global Adjoint Tomography: Next-Generation Models

    NASA Astrophysics Data System (ADS)

    Bozdag, Ebru; Lefebvre, Matthieu; Lei, Wenjie; Orsvuran, Ridvan; Peter, Daniel; Ruan, Youyi; Smith, James; Komatitsch, Dimitri; Tromp, Jeroen

    2017-04-01

    The first-generation global adjoint tomography model GLAD-M15 (Bozdag et al. 2016) is the result of 15 conjugate-gradient iterations based on GPU-accelerated spectral-element simulations of 3D wave propagation and Fréchet kernels. For simplicity, GLAD-M15 was constructed as an elastic model with transverse isotropy confined to the upper mantle. However, Earth's mantle and crust show significant evidence of anisotropy as a result of its composition and deformation. There may be different sources of seismic anisotropy affecting both body and surface waves. As a first attempt, we initially tackle with surface-wave anisotropy and proceed iterations using the same 253 earthquake data set used in GLAD-M15 with an emphasize on upper-mantle. Furthermore, we explore new misfits, such as double-difference measurements (Yuan et al. 2016), to better deal with the possible artifacts of the uneven distribution of seismic stations globally and minimize source uncertainties in structural inversions. We will present our observations with the initial results of azimuthally anisotropic inversions and also discuss the next generation global models with various parametrizations. Meanwhile our goal is to use all available seismic data in imaging. This however requires a solid framework to perform iterative adjoint tomography workflows with big data on supercomputers. We will talk about developments in adjoint tomography workflow from the need of defining new seismic and computational data formats (e.g., ASDF by Krischer et al. 2016, ADIOS by Liu et al. 2011) to developing new pre- and post-processing tools together with experimenting workflow management tools, such as Pegasus (Deelman et al. 2015). All our simulations are performed on Oak Ridge National Laboratory's Cray XK7 "Titan" system. Our ultimate aim is to get ready to harness ORNL's next-generation supercomputer "Summit", an IBM with Power-9 CPUs and NVIDIA Volta GPU accelerators, to be ready by 2018 which will enable us to

  15. Detecting cell death with optical coherence tomography and envelope statistics

    NASA Astrophysics Data System (ADS)

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

    2011-02-01

    Currently no standard clinical or preclinical noninvasive method exists to monitor cell death based on morphological changes at the cellular level. In our past work we have demonstrated that quantitative high frequency ultrasound imaging can detect cell death in vitro and in vivo. In this study we apply quantitative methods previously used with high frequency ultrasound to optical coherence tomography (OCT) to detect cell death. The ultimate goal of this work is to use these methods for optically-based clinical and preclinical cancer treatment monitoring. Optical coherence tomography data were acquired from acute myeloid leukemia cells undergoing three modes of cell death. Significant increases in integrated backscatter were observed for cells undergoing apoptosis and mitotic arrest, while necrotic cells induced a decrease. These changes appear to be linked to structural changes observed in histology obtained from the cell samples. Signal envelope statistics were analyzed from fittings of the generalized gamma distribution to histograms of envelope intensities. The parameters from this distribution demonstrated sensitivities to morphological changes in the cell samples. These results indicate that OCT integrated backscatter and first order envelope statistics can be used to detect and potentially differentiate between modes of cell death in vitro.

  16. Feasibility study of archaeological structures scanning by muon tomography

    NASA Astrophysics Data System (ADS)

    Gómez, H.; Carloganu, C.; Gibert, D.; Marteau, J.; Niess, V.; Katsanevas, S.; Tonazzo, A.

    2015-08-01

    One of the main concerns in archaeology is to find of a method to study precisely archaeological structures in the least invasive way possible to avoid damage. The requirement of preserving the structures integrity prevents, in the case of pyramids or tumuli, the study of any internal structure (halls or tombs) which are not reachable by existing corridors. One non-invasive method is the muon tomography. By placing a detector which allows to register the muon direction after the structure, it is possible to have an idea of its composition based on the attenuation of the muon flux, which depends on the material length and density that muons have crossed. This technique, alone or together with other exploration techniques as seismic tomography or electrical resistivity tomography, can provide useful information about the internal structure of the archaeological form that can not be obtained by conventional archaeological methods. In this work, the time measurement necessary to obtain a significant result about the composition of an archaeological structure is estimated. To do that, a Monte Carlo simulation framework based on the MUSIC software, properly tuned for this study, has been developed. The particular case of the Kastas Amfipoli Macedonian tumulus has been considered to perform the simulations.

  17. 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.

  18. Using Contaminant Transport Simulations to Optimize Electrical Resistivity Tomography Survey Design for Improved Contaminant Detection at Lined Ponds

    NASA Astrophysics Data System (ADS)

    Herring, T.; Pidlisecky, A.

    2015-12-01

    The saline flowback water produced during hydraulic fracturing is often stored in lined surface ponds. Leakage from these ponds poses a significant environmental threat and there is a need for a reliable and economical long term monitoring strategy. Electrical resistivity tomography (ERT), being sensitive to changes in groundwater salinity, is therefore well suited to such a problem. The goal of this work is to compare the leak detection capabilities of a surface ERT array and a downhole ERT array. In this study several plausible 3D electrical conductivity models were created that simulated a contaminant plume evolving over time, using realistic contaminant concentrations, plume geometries, water saturation profiles, and seasonal temperature profiles. The forward modeled data were used to identify the advantages and drawbacks of using each ERT array orientation.

  19. Use of cone beam computed tomography in identifying postmenopausal women with osteoporosis.

    PubMed

    Brasileiro, C B; Chalub, L L F H; Abreu, M H N G; Barreiros, I D; Amaral, T M P; Kakehasi, A M; Mesquita, R A

    2017-12-01

    The aim of this study is to correlate radiometric indices from cone beam computed tomography (CBCT) images and bone mineral density (BMD) in postmenopausal women. Quantitative CBCT indices can be used to screen for women with low BMD. Osteoporosis is a disease characterized by the deterioration of bone tissue and the consequent decrease in BMD and increase in bone fragility. Several studies have been performed to assess radiometric indices in panoramic images as low-BMD predictors. The aim of this study is to correlate radiometric indices from CBCT images and BMD in postmenopausal women. Sixty postmenopausal women with indications for dental implants and CBCT evaluation were selected. Dual-energy X-ray absorptiometry (DXA) was performed, and the patients were divided into normal, osteopenia, and osteoporosis groups, according to the World Health Organization (WHO) criteria. Cross-sectional images were used to evaluate the computed tomography mandibular index (CTMI), the computed tomography index (inferior) (CTI (I)) and computed tomography index (superior) (CTI (S)). Student's t test was used to compare the differences between the indices of the groups' intraclass correlation coefficient (ICC). Statistical analysis showed a high degree of interobserver and intraobserver agreement for all measurements (ICC > 0.80). The mean values of CTMI, CTI (S), and CTI (I) were lower in the osteoporosis group than in osteopenia and normal patients (p < 0.05). In comparing normal patients and women with osteopenia, there was no statistically significant difference in the mean value of CTI (I) (p = 0.075). Quantitative CBCT indices may help dentists to screen for women with low spinal and femoral bone mineral density so that they can refer postmenopausal women for bone densitometry.

  20. A relative quantitative assessment of myocardial perfusion by first-pass technique: animal study

    NASA Astrophysics Data System (ADS)

    Chen, Jun; Zhang, Zhang; Yu, Xuefang; Zhou, Kenneth J.

    2015-03-01

    The purpose of this study is to quantitatively assess the myocardial perfusion by first-pass technique in swine model. Numerous techniques based on the analysis of Computed Tomography (CT) Hounsfield Unit (HU) density have emerged. Although these methods proposed to be able to assess haemodynamically significant coronary artery stenosis, their limitations are noticed. There are still needs to develop some new techniques. Experiments were performed upon five (5) closed-chest swine. Balloon catheters were placed into the coronary artery to simulate different degrees of luminal stenosis. Myocardial Blood Flow (MBF) was measured using color microsphere technique. Fractional Flow Reserve (FFR) was measured using pressure wire. CT examinations were performed twice during First-pass phase under adenosine-stress condition. CT HU Density (HUDCT) and CT HU Density Ratio (HUDRCT) were calculated using the acquired CT images. Our study presents that HUDRCT shows a good (y=0.07245+0.09963x, r2=0.898) correlation with MBF and FFR. In receiver operating characteristic (ROC) curve analyses, HUDRCT provides excellent diagnostic performance for the detection of significant ischemia during adenosine-stress as defined by FFR indicated by the value of Area Under the Curve (AUC) of 0.927. HUDRCT has the potential to be developed as a useful indicator of quantitative assessment of myocardial perfusion.

  1. Study on feasibility of laser reflective tomography with satellite-accompany

    NASA Astrophysics Data System (ADS)

    Gu, Yu; Hu, Yi-hua; Hao, Shi-qi; Gu, You-lin; Zhao, Nan-xiang; Wang, Yang-yang

    2015-10-01

    Laser reflective tomography is a long-range, high-resolution active detection technology, whose advantage is that the spatial resolution is unrelated with the imaging distance. Accompany satellite is a specific satellite around the target spacecraft with encircling movement. When using the accompany satellite to detect the target aircraft, multi-angle echo data can be obtained with the application of reflective tomography imaging. The feasibility of such detection working mode was studied in this article. Accompany orbit model was established with horizontal circular fleet and the parameters of accompany flight was defined. The simulation of satellite-to-satellite reflective tomography imaging with satellite-accompany was carried out. The operating mode of reflective tomographic data acquisition from monostatic laser radar was discussed and designed. The flight period, which equals to the all direction received data consuming time, is one of the important accompany flight parameters. The azimuth angle determines the plane of image formation while the elevation angle determines the projection direction. Both of the azimuth and elevation angles guide the satellite attitude stability controller in order to point the laser radar spot on the target. The influences of distance between accompany satellite and target satellite on tomographic imaging consuming time was analyzed. The influences of flight period, azimuth angle and elevation angle on tomographic imaging were analyzed as well. Simulation results showed that the satellite-accompany laser reflective tomography is a feasible and effective method to the satellite-to-satellite detection.

  2. 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. Copyright © 2014 Elsevier B.V. All rights reserved.

  3. Research on ionospheric tomography based on variable pixel height

    NASA Astrophysics Data System (ADS)

    Zheng, Dunyong; Li, Peiqing; He, Jie; Hu, Wusheng; Li, Chaokui

    2016-05-01

    A novel ionospheric tomography technique based on variable pixel height was developed for the tomographic reconstruction of the ionospheric electron density distribution. The method considers the height of each pixel as an unknown variable, which is retrieved during the inversion process together with the electron density values. In contrast to conventional computerized ionospheric tomography (CIT), which parameterizes the model with a fixed pixel height, the variable-pixel-height computerized ionospheric tomography (VHCIT) model applies a disturbance to the height of each pixel. In comparison with conventional CIT models, the VHCIT technique achieved superior results in a numerical simulation. A careful validation of the reliability and superiority of VHCIT was performed. According to the results of the statistical analysis of the average root mean square errors, the proposed model offers an improvement by 15% compared with conventional CIT models.

  4. Comparison of different numerical treatments for x-ray phase tomography of soft tissue from differential phase projections

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Pelliccia, Daniele; Vaz, Raquel; Svalbe, Imants

    X-ray imaging of soft tissue is made difficult by their low absorbance. The use of x-ray phase imaging and tomography can significantly enhance the detection of these tissues and several approaches have been proposed to this end. Methods such as analyzer-based imaging or grating interferometry produce differential phase projections that can be used to reconstruct the 3D distribution of the sample refractive index. We report on the quantitative comparison of three different methods to obtain x-ray phase tomography with filtered back-projection from differential phase projections in the presence of noise. The three procedures represent different numerical approaches to solve themore » same mathematical problem, namely phase retrieval and filtered back-projection. It is found that obtaining individual phase projections and subsequently applying a conventional filtered back-projection algorithm produces the best results for noisy experimental data, when compared with other procedures based on the Hilbert transform. The algorithms are tested on simulated phantom data with added noise and the predictions are confirmed by experimental data acquired using a grating interferometer. The experiment is performed on unstained adult zebrafish, an important model organism for biomedical studies. The method optimization described here allows resolution of weak soft tissue features, such as muscle fibers.« less

  5. Quantitative analysis of image quality for acceptance and commissioning of an MRI simulator with a semiautomatic method.

    PubMed

    Chen, Xinyuan; Dai, Jianrong

    2018-05-01

    Magnetic Resonance Imaging (MRI) simulation differs from diagnostic MRI in purpose, technical requirements, and implementation. We propose a semiautomatic method for image acceptance and commissioning for the scanner, the radiofrequency (RF) coils, and pulse sequences for an MRI simulator. The ACR MRI accreditation large phantom was used for image quality analysis with seven parameters. Standard ACR sequences with a split head coil were adopted to examine the scanner's basic performance. The performance of simulation RF coils were measured and compared using the standard sequence with different clinical diagnostic coils. We used simulation sequences with simulation coils to test the quality of image and advanced performance of the scanner. Codes and procedures were developed for semiautomatic image quality analysis. When using standard ACR sequences with a split head coil, image quality passed all ACR recommended criteria. The image intensity uniformity with a simulation RF coil decreased about 34% compared with the eight-channel diagnostic head coil, while the other six image quality parameters were acceptable. Those two image quality parameters could be improved to more than 85% by built-in intensity calibration methods. In the simulation sequences test, the contrast resolution was sensitive to the FOV and matrix settings. The geometric distortion of simulation sequences such as T1-weighted and T2-weighted images was well-controlled in the isocenter and 10 cm off-center within a range of ±1% (2 mm). We developed a semiautomatic image quality analysis method for quantitative evaluation of images and commissioning of an MRI simulator. The baseline performances of simulation RF coils and pulse sequences have been established for routine QA. © 2018 The Authors. Journal of Applied Clinical Medical Physics published by Wiley Periodicals, Inc. on behalf of American Association of Physicists in Medicine.

  6. Cosmic Ray Inspection and Passive Tomography for SNM Detection

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Armitage, John; Oakham, Gerald; Bryman, Douglas

    2009-12-02

    The Cosmic Ray Inspection and Passive Tomography (CRIPT) project has recently started investigating the detection of illicit Special Nuclear Material in cargo using cosmic ray muon tomography and complementary neutron detectors. We are currently performing simulation studies to help with the design of small scale prototypes. Based on the prototype tests and refined simulations, we will determine whether the muon tracking system for the full scale prototype will be based on drift chambers or extruded scintillator trackers. An analysis of the operations of the Port of Montreal has determined how long muon scan times should take if all or amore » subset of the cargo is to be screened. As long as the throughput of the muon system(s) is equal to the rate at which containers are unloaded from ships, the impact on port operations would not be great if a muon scanning stage were required for all cargo. We also show preliminary simulation results indicating that excellent separation between Al, Fe and Pb is possible under ideal conditions. The discrimination power is reduced but still significant when realistic momentum resolution measurements are considered.« less

  7. Cosmic Ray Inspection and Passive Tomography for SNM Detection

    NASA Astrophysics Data System (ADS)

    Armitage, John; Bryman, Douglas; Cousins, Thomas; Gallant, Grant; Jason, Andrew; Jonkmans, Guy; Noël, Scott; Oakham, Gerald; Stocki, Trevor J.; Waller, David

    2009-12-01

    The Cosmic Ray Inspection and Passive Tomography (CRIPT) project has recently started investigating the detection of illicit Special Nuclear Material in cargo using cosmic ray muon tomography and complementary neutron detectors. We are currently performing simulation studies to help with the design of small scale prototypes. Based on the prototype tests and refined simulations, we will determine whether the muon tracking system for the full scale prototype will be based on drift chambers or extruded scintillator trackers. An analysis of the operations of the Port of Montreal has determined how long muon scan times should take if all or a subset of the cargo is to be screened. As long as the throughput of the muon system(s) is equal to the rate at which containers are unloaded from ships, the impact on port operations would not be great if a muon scanning stage were required for all cargo. We also show preliminary simulation results indicating that excellent separation between Al, Fe and Pb is possible under ideal conditions. The discrimination power is reduced but still significant when realistic momentum resolution measurements are considered.

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

    PubMed Central

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

    2015-01-01

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

  9. Cone-beam computed tomography-based diagnosis and treatment simulation for a patient with a protrusive profile and a gummy smile

    PubMed Central

    Imamura, Toshihiro; Kokai, Satoshi; Ono, Takashi

    2018-01-01

    For patients with bimaxillary protrusion, significant retraction and intrusion of the anterior teeth are sometimes essential to improve the facial profile. However, severe root resorption of the maxillary incisors occasionally occurs after treatment because of various factors. For instance, it has been reported that approximation or invasion of the incisive canal by the anterior tooth roots during retraction may cause apical root damage. Thus, determination of the position of the maxillary incisors is key for orthodontic diagnosis and treatment planning in such cases. Cone-beam computed tomography (CBCT) may be useful for simulating the post-treatment position of the maxillary incisors and surrounding structures in order to ensure safe teeth movement. Here, we present a case of Class II malocclusion with bimaxillary protrusion, wherein apical root damage due to treatment was minimized by pretreatment evaluation of the anatomical structures and simulation of the maxillary central incisor movement using CBCT. Considerable retraction and intrusion of the maxillary incisors, which resulted in a significant improvement in the facial profile and smile, were achieved without severe root resorption. Our findings suggest that CBCT-based diagnosis and treatment simulation may facilitate safe and dynamic orthodontic tooth movement, particularly in patients requiring maximum anterior tooth retraction. PMID:29732305

  10. 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

  11. ODTbrain: a Python library for full-view, dense diffraction tomography.

    PubMed

    Müller, Paul; Schürmann, Mirjam; Guck, Jochen

    2015-11-04

    Analyzing the three-dimensional (3D) refractive index distribution of a single cell makes it possible to describe and characterize its inner structure in a marker-free manner. A dense, full-view tomographic data set is a set of images of a cell acquired for multiple rotational positions, densely distributed from 0 to 360 degrees. The reconstruction is commonly realized by projection tomography, which is based on the inversion of the Radon transform. The reconstruction quality of projection tomography is greatly improved when first order scattering, which becomes relevant when the imaging wavelength is comparable to the characteristic object size, is taken into account. This advanced reconstruction technique is called diffraction tomography. While many implementations of projection tomography are available today, there is no publicly available implementation of diffraction tomography so far. We present a Python library that implements the backpropagation algorithm for diffraction tomography in 3D. By establishing benchmarks based on finite-difference time-domain (FDTD) simulations, we showcase the superiority of the backpropagation algorithm over the backprojection algorithm. Furthermore, we discuss how measurment parameters influence the reconstructed refractive index distribution and we also give insights into the applicability of diffraction tomography to biological cells. The present software library contains a robust implementation of the backpropagation algorithm. The algorithm is ideally suited for the application to biological cells. Furthermore, the implementation is a drop-in replacement for the classical backprojection algorithm and is made available to the large user community of the Python programming language.

  12. Evaluation of patients with painful total hip arthroplasty using combined single photon emission tomography and conventional computerized tomography (SPECT/CT) - a comparison of semi-quantitative versus 3D volumetric quantitative measurements.

    PubMed

    Barthassat, Emilienne; Afifi, Faik; Konala, Praveen; Rasch, Helmut; Hirschmann, Michael T

    2017-05-08

    It was the primary purpose of our study to evaluate the inter- and intra-observer reliability of a standardized SPECT/CT algorithm for evaluating patients with painful primary total hip arthroplasty (THA). The secondary purpose was a comparison of semi-quantitative and 3D volumetric quantification method for assessment of bone tracer uptake (BTU) in those patients. A novel SPECT/CT localization scheme consisting of 14 femoral and 4 acetabular regions on standardized axial and coronal slices was introduced and evaluated in terms of inter- and intra-observer reliability in 37 consecutive patients with hip pain after THA. BTU for each anatomical region was assessed semi-quantitatively using a color-coded Likert type scale (0-10) and volumetrically quantified using a validated software. Two observers interpreted the SPECT/CT findings in all patients two times with six weeks interval between interpretations in random order. Semi-quantitative and quantitative measurements were compared in terms of reliability. In addition, the values were correlated using Pearson`s correlation. A factorial cluster analysis of BTU was performed to identify clinically relevant regions, which should be grouped and analysed together. The localization scheme showed high inter- and intra-observer reliabilities for all femoral and acetabular regions independent of the measurement method used (semiquantitative versus 3D volumetric quantitative measurements). A high to moderate correlation between both measurement methods was shown for the distal femur, the proximal femur and the acetabular cup. The factorial cluster analysis showed that the anatomical regions might be summarized into three distinct anatomical regions. These were the proximal femur, the distal femur and the acetabular cup region. The SPECT/CT algorithm for assessment of patients with pain after THA is highly reliable independent from the measurement method used. Three clinically relevant anatomical regions (proximal femoral

  13. 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

  14. Estimation of whole body fat from appendicular soft tissue from peripheral quantitative computed tomography in adolescent girls

    PubMed Central

    Lee, Vinson R.; Blew, Rob M.; Farr, Josh N.; Tomas, Rita; Lohman, Timothy G.; Going, Scott B.

    2013-01-01

    Objective Assess the utility of peripheral quantitative computed tomography (pQCT) for estimating whole body fat in adolescent girls. Research Methods and Procedures Our sample included 458 girls (aged 10.7 ± 1.1y, mean BMI = 18.5 ± 3.3 kg/m2) who had DXA scans for whole body percent fat (DXA %Fat). Soft tissue analysis of pQCT scans provided thigh and calf subcutaneous percent fat and thigh and calf muscle density (muscle fat content surrogates). Anthropometric variables included weight, height and BMI. Indices of maturity included age and maturity offset. The total sample was split into validation (VS; n = 304) and cross-validation (CS; n = 154) samples. Linear regression was used to develop prediction equations for estimating DXA %Fat from anthropometric variables and pQCT-derived soft tissue components in VS and the best prediction equation was applied to CS. Results Thigh and calf SFA %Fat were positively correlated with DXA %Fat (r = 0.84 to 0.85; p <0.001) and thigh and calf muscle densities were inversely related to DXA %Fat (r = −0.30 to −0.44; p < 0.001). The best equation for estimating %Fat included thigh and calf SFA %Fat and thigh and calf muscle density (adj. R2 = 0.90; SEE = 2.7%). Bland-Altman analysis in CS showed accurate estimates of percent fat (adj. R2 = 0.89; SEE = 2.7%) with no bias. Discussion Peripheral QCT derived indices of adiposity can be used to accurately estimate whole body percent fat in adolescent girls. PMID:25147482

  15. Quantifying the vascular response to ischemia with speckle variance optical coherence tomography

    PubMed Central

    Poole, Kristin M.; McCormack, Devin R.; Patil, Chetan A.; Duvall, Craig L.; Skala, Melissa C.

    2014-01-01

    Longitudinal monitoring techniques for preclinical models of vascular remodeling are critical to the development of new therapies for pathological conditions such as ischemia and cancer. In models of skeletal muscle ischemia in particular, there is a lack of quantitative, non-invasive and long term assessment of vessel morphology. Here, we have applied speckle variance optical coherence tomography (OCT) methods to quantitatively assess vascular remodeling and growth in a mouse model of peripheral arterial disease. This approach was validated on two different mouse strains known to have disparate rates and abilities of recovering following induction of hind limb ischemia. These results establish the potential for speckle variance OCT as a tool for quantitative, preclinical screening of pro- and anti-angiogenic therapies. PMID:25574425

  16. [Impact of point spread function correction in standardized uptake value quantitation for positron emission tomography images: a study based on phantom experiments and clinical images].

    PubMed

    Nakamura, Akihiro; Tanizaki, Yasuo; Takeuchi, Miho; Ito, Shigeru; Sano, Yoshitaka; Sato, Mayumi; Kanno, Toshihiko; Okada, Hiroyuki; Torizuka, Tatsuo; Nishizawa, Sadahiko

    2014-06-01

    While point spread function (PSF)-based positron emission tomography (PET) reconstruction effectively improves the spatial resolution and image quality of PET, it may damage its quantitative properties by producing edge artifacts, or Gibbs artifacts, which appear to cause overestimation of regional radioactivity concentration. In this report, we investigated how edge artifacts produce negative effects on the quantitative properties of PET. Experiments with a National Electrical Manufacturers Association (NEMA) phantom, containing radioactive spheres of a variety of sizes and background filled with cold air or water, or radioactive solutions, showed that profiles modified by edge artifacts were reproducible regardless of background μ values, and the effects of edge artifacts increased with increasing sphere-to-background radioactivity concentration ratio (S/B ratio). Profiles were also affected by edge artifacts in complex fashion in response to variable combinations of sphere sizes and S/B ratios; and central single-peak overestimation up to 50% was occasionally noted in relatively small spheres with high S/B ratios. Effects of edge artifacts were obscured in spheres with low S/B ratios. In patient images with a variety of focal lesions, areas of higher radioactivity accumulation were generally more enhanced by edge artifacts, but the effects were variable depending on the size of and accumulation in the lesion. PET images generated using PSF-based reconstruction are therefore not appropriate for the evaluation of SUV.

  17. Image Reconstruction Under Contact Impedance Effect in Micro Electrical Impedance Tomography Sensors.

    PubMed

    Liu, Xiayi; Yao, Jiafeng; Zhao, Tong; Obara, Hiromichi; Cui, Yahui; Takei, Masahiro

    2018-06-01

    Contact impedance has an important effect on micro electrical impedance tomography (EIT) sensors compared to conventional macro sensors. In the present work, a complex contact impedance effect ratio ξ is defined to quantitatively evaluate the effect of the contact impedance on the accuracy of the reconstructed images by micro EIT. Quality of the reconstructed image under various ξ is estimated by the phantom simulation to find the optimum algorithm. The generalized vector sampled pattern matching (GVSPM) method reveals the best image quality and the best tolerance to ξ. Moreover, the images of yeast cells sedimentary distribution in a multilayered microchannel are reconstructed by the GVSPM method under various mean magnitudes of contact impedance effect ratio |ξ|. The result shows that the best image quality that has the smallest voltage error U E = 0.581 is achieved with measurement frequency f = 1 MHz and mean magnitude |ξ| = 26. In addition, the reconstructed images of cells distribution become improper while f < 10 kHz and mean value of |ξ| > 2400.

  18. A Comparison of Ultrasound Tomography Methods in Circular Geometry

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Leach, R R; Azevedo, S G; Berryman, J G

    2002-01-24

    Extremely high quality data was acquired using an experimental ultrasound scanner developed at Lawrence Livermore National Laboratory using a 2D ring geometry with up to 720 transmitter/receiver transducer positions. This unique geometry allows reflection and transmission modes and transmission imaging and quantification of a 3D volume using 2D slice data. Standard image reconstruction methods were applied to the data including straight-ray filtered back projection, reflection tomography, and diffraction tomography. Newer approaches were also tested such as full wave, full wave adjoint method, bent-ray filtered back projection, and full-aperture tomography. A variety of data sets were collected including a formalin-fixed humanmore » breast tissue sample, a commercial ultrasound complex breast phantom, and cylindrical objects with and without inclusions. The resulting reconstruction quality of the images ranges from poor to excellent. The method and results of this study are described including like-data reconstructions produced by different algorithms with side-by-side image comparisons. Comparisons to medical B-scan and x-ray CT scan images are also shown. Reconstruction methods with respect to image quality using resolution, noise, and quantitative accuracy, and computational efficiency metrics will also be discussed.« less

  19. Review of progress in quantitative NDE. [Nondestructive Evaluation (NDE)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Not Available

    1991-01-01

    This booklet is composed of abstracts from papers submitted at a meeting on quantitative NDE. A multitude of topics are discussed including analysis of composite materials, NMR uses, x-ray instruments and techniques, manufacturing uses, neural networks, eddy currents, stress measurements, magnetic materials, adhesive bonds, signal processing, NDE of mechanical structures, tomography,defect sizing, NDE of plastics and ceramics, new techniques, optical and electromagnetic techniques, and nonlinear techniques. (GHH)

  20. 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.

  1. Quantitative analysis of a reconstruction method for fully three-dimensional PET.

    PubMed

    Suckling, J; Ott, R J; Deehan, B J

    1992-03-01

    The major advantage of positron emission tomography (PET) using large area planar detectors over scintillator-based commercial ring systems is the potentially larger (by a factor of two or three) axial field-of-view (FOV). However, to achieve the space invariance of the point spread function necessary for Fourier filtering a polar angle rejection criterion is applied to the data during backprojection resulting in a trade-off between FOV size and sensitivity. A new algorithm due to Defrise and co-workers developed for list-mode data overcomes this problem with a solution involving the division of the image into several subregions. A comparison between the existing backprojection-then-filter algorithm and the new method (with three subregions) has been made using both simulated and real data collected from the MUP-PET positron camera. Signal-to-noise analysis reveals that improvements of up to a factor of 1.4 are possible resulting from an increased data usage of up to a factor of 2.5 depending on the axial extent of the imaged object. Quantitation is also improved.

  2. Coagulation monitoring based on blood elastic measurement using optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Xu, Xiangqun; Zhu, Jiang; Chen, Zhongping

    2017-02-01

    Blood coagulation monitoring is important to diagnose hematological diseases and cardiovascular diseases and to predict the risk of bleeding and excessive clotting. In this study, we developed a system to dynamically monitor blood coagulation and quantitatively determine the coagulation function by blood elastic measurement. When blood forms a clot from a liquid, ultrasonic force induces a shear wave, which is detected by optical coherence tomography (OCT). The coagulation of porcine whole blood recalcified by calcium chloride is assessed using the metrics of reaction time, clot formation kinetics and maximum shear modulus. The OCE system can noninvasively monitor the blood coagulation and quantitatively determine the coagulation function.

  3. Simultaneous fast scanning XRF, dark field, phase-, and absorption contrast tomography

    NASA Astrophysics Data System (ADS)

    Medjoubi, Kadda; Bonissent, Alain; Leclercq, Nicolas; Langlois, Florent; Mercère, Pascal; Somogyi, Andrea

    2013-09-01

    Scanning hard X-ray nanoprobe imaging provides a unique tool for probing specimens with high sensitivity and large penetration depth. Moreover, the combination of complementary techniques such as X-ray fluorescence, absorption, phase contrast and dark field imaging gives complete quantitative information on the sample structure, composition and chemistry. The multi-technique "FLYSCAN" data acquisition scheme developed at Synchrotron SOLEIL permits to perform fast continuous scanning imaging and as such makes scanning tomography techniques feasible in a time-frame well-adapted to typical user experiments. Here we present the recent results of simultaneous fast scanning multi-technique tomography performed at Soleil. This fast scanning scheme will be implemented at the Nanoscopium beamline for large field of view 2D and 3D multimodal imaging.

  4. Computed tomography measurement of gaseous fuel concentration by infrared laser light absorption

    NASA Astrophysics Data System (ADS)

    Kawazoe, Hiromitsu; Inagaki, Kazuhisa; Emi, Y.; Yoshino, Fumio

    1997-11-01

    A system to measure gaseous hydrocarbon distributions was devised, which is based on IR light absorption by C-H stretch mode of vibration and computed tomography method. It is called IR-CT method in the paper. Affection of laser light power fluctuation was diminished by monitoring source light intensity by the second IR light detector. Calibration test for methane fuel was carried out to convert spatial data of line absorption coefficient into quantitative methane concentration. This system was applied to three flow fields. The first is methane flow with lifted flame which is generated by a gourd-shaped fuel nozzle. Feasibility of the IR-CT method was confirmed through the measurement. The second application is combustion field with diffusion flame. Calibration to determine absorptivity was undertaken, and measured line absorption coefficient was converted spatial fuel concentration using corresponding temperature data. The last case is modeled in cylinder gas flow of internal combustion engine, where gaseous methane was led to the intake valve in steady flow state. The fuel gas flow simulates behavior of gaseous gasoline which is evaporated at intake valve tulip. Computed tomography measurement of inner flow is essentially difficult because of existence of surrounding wall. In this experiment, IR laser beam was led to planed portion by IR light fiber. It is found that fuel convection by airflow takes great part in air-fuel mixture formation and the developed IR-CT system to measure fuel concentration is useful to analyze air-fuel mixture formation process and to develop new combustors.

  5. X-ray phase contrast tomography from whole organ down to single cells

    NASA Astrophysics Data System (ADS)

    Krenkel, Martin; Töpperwien, Mareike; Bartels, Matthias; Lingor, Paul; Schild, Detlev; Salditt, Tim

    2014-09-01

    We use propagation based hard x-ray phase contrast tomography to explore the three dimensional structure of neuronal tissues from the organ down to sub-cellular level, based on combinations of synchrotron radiation and laboratory sources. To this end a laboratory based microfocus tomography setup has been built in which the geometry was optimized for phase contrast imaging and tomography. By utilizing phase retrieval algorithms, quantitative reconstructions can be obtained that enable automatic renderings without edge artifacts. A high brightness liquid metal microfocus x-ray source in combination with a high resolution detector yielding a resolution down to 1.5 μm. To extend the method to nanoscale resolution we use a divergent x-ray waveguide beam geometry at the synchrotron. Thus, the magnification can be easily tuned by placing the sample at different defocus distances. Due to the small Fresnel numbers in this geometry the measured images are of holographic nature which poses a challenge in phase retrieval.

  6. Computed Tomography

    NASA Astrophysics Data System (ADS)

    Castellano, Isabel; Geleijns, Jacob

    After its clinical introduction in 1973, computed tomography developed from an x-ray modality for axial imaging in neuroradiology into a versatile three dimensional imaging modality for a wide range of applications in for example oncology, vascular radiology, cardiology, traumatology and even in interventional radiology. Computed tomography is applied for diagnosis, follow-up studies and screening of healthy subpopulations with specific risk factors. This chapter provides a general introduction in computed tomography, covering a short history of computed tomography, technology, image quality, dosimetry, room shielding, quality control and quality criteria.

  7. One step linear reconstruction method for continuous wave diffuse optical tomography

    NASA Astrophysics Data System (ADS)

    Ukhrowiyah, N.; Yasin, M.

    2017-09-01

    The method one step linear reconstruction method for continuous wave diffuse optical tomography is proposed and demonstrated for polyvinyl chloride based material and breast phantom. Approximation which used in this method is selecting regulation coefficient and evaluating the difference between two states that corresponding to the data acquired without and with a change in optical properties. This method is used to recovery of optical parameters from measured boundary data of light propagation in the object. The research is demonstrated by simulation and experimental data. Numerical object is used to produce simulation data. Chloride based material and breast phantom sample is used to produce experimental data. Comparisons of results between experiment and simulation data are conducted to validate the proposed method. The results of the reconstruction image which is produced by the one step linear reconstruction method show that the image reconstruction almost same as the original object. This approach provides a means of imaging that is sensitive to changes in optical properties, which may be particularly useful for functional imaging used continuous wave diffuse optical tomography of early diagnosis of breast cancer.

  8. Multi-observation PET image analysis for patient follow-up quantitation and therapy assessment

    NASA Astrophysics Data System (ADS)

    David, S.; Visvikis, D.; Roux, C.; Hatt, M.

    2011-09-01

    In positron emission tomography (PET) imaging, an early therapeutic response is usually characterized by variations of semi-quantitative parameters restricted to maximum SUV measured in PET scans during the treatment. Such measurements do not reflect overall tumor volume and radiotracer uptake variations. The proposed approach is based on multi-observation image analysis for merging several PET acquisitions to assess tumor metabolic volume and uptake variations. The fusion algorithm is based on iterative estimation using a stochastic expectation maximization (SEM) algorithm. The proposed method was applied to simulated and clinical follow-up PET images. We compared the multi-observation fusion performance to threshold-based methods, proposed for the assessment of the therapeutic response based on functional volumes. On simulated datasets the adaptive threshold applied independently on both images led to higher errors than the ASEM fusion and on clinical datasets it failed to provide coherent measurements for four patients out of seven due to aberrant delineations. The ASEM method demonstrated improved and more robust estimation of the evaluation leading to more pertinent measurements. Future work will consist in extending the methodology and applying it to clinical multi-tracer datasets in order to evaluate its potential impact on the biological tumor volume definition for radiotherapy applications.

  9. Quantification of pericardial effusions by echocardiography and computed tomography.

    PubMed

    Leibowitz, David; Perlman, Gidon; Planer, David; Gilon, Dan; Berman, Philip; Bogot, Naama

    2011-01-15

    Echocardiography is a well-accepted tool for the diagnosis and quantification of pericardial effusion (PEff). Given the increasing use of computed tomographic (CT) scanning, more PEffs are being initially diagnosed by computed tomography. No study has compared quantification of PEff by computed tomography and echocardiography. The objective of this study was to assess the accuracy of quantification of PEff by 2-dimensional echocardiography and computed tomography compared to the amount of pericardial fluid drained at pericardiocentesis. We retrospectively reviewed an institutional database to identify patients who underwent chest computed tomography and echocardiography before percutaneous pericardiocentesis with documentation of the amount of fluid withdrawn. Digital 2-dimensional echocardiographic and CT images were retrieved and quantification of PEff volume was performed by applying the formula for the volume of a prolate ellipse, π × 4/3 × maximal long-axis dimension/2 × maximal transverse dimension/2 × maximal anteroposterior dimension/2, to the pericardial sac and to the heart. Nineteen patients meeting study qualifications were entered into the study. The amount of PEff drained was 200 to 1,700 ml (mean 674 ± 340). Echocardiographically calculated pericardial effusion volume correlated relatively well with PEff volume (r = 0.73, p <0.001, mean difference -41 ± 225 ml). There was only moderate correlation between CT volume quantification and actual volume drained (r = 0.4, p = 0.004, mean difference 158 ± 379 ml). In conclusion, echocardiography appears a more accurate imaging technique than computed tomography in quantitative assessment of nonloculated PEffs and should continue to be the primary imaging in these patients. Copyright © 2011 Elsevier Inc. All rights reserved.

  10. X-ray-induced acoustic computed tomography for 3D breast imaging: A simulation study.

    PubMed

    Tang, Shanshan; Yang, Kai; Chen, Yong; Xiang, Liangzhong

    2018-04-01

    The objective of this study is to demonstrate the feasibility of x-ray-induced acoustic computed tomography (XACT) for early breast un-palpable microcalcification (μCa) detection in three dimensions (3D). The proposed technique provides the true 3D imaging for breast volume which overcomes the disadvantage of the tissue superposition in mammography. A 3D breast digital phantom was rendered from two-dimensional (2D) breast CT slices. Three different tissue types, including the skin, adipose tissue, and glandular tissue, were labeled in the 3D breast phantom. μCas were manually embedded in different locations inside the breast phantom. For each tissue type, the initial pressure rise caused by the x-ray-induced acoustic (XA) effect was calculated according to its themoacoustic properties. The XA wave's propagation from the point of generation and its detection by ultrasound detector array were simulated by Matlab K-Wave toolbox. The 3D breast XACT volume with μCa was acquired without tissue superposition, and the system was characterized by μCas placed at different locations. The simulation results illustrated that the proposed breast XACT system has the ability to show the μCa cluster in 3D without any tissue superposition. Meanwhile, μCa as small as 100 μm in size can be detected with high imaging contrast, high signal to noise ratio (SNR), and high contrast to noise ratio (CNR). The dose required by the proposed XACT configuration was calculated to be 0.4 mGy for a 4.5 cm-thick compressed breast. This is one-tenth of the dose level of a typical two-view mammography for a breast with the same compression thickness. The initial exploration for the feasibility of 3D breast XACT has been conducted in this study. The system feasibility and characterization were illustrated through a 3D breast phantom and simulation works. The 3D breast XACT with the proposed system configuration has great potential to be applied as a low-dose screening and diagnostic technique

  11. Detection of brain tumor margins using optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Juarez-Chambi, Ronald M.; Kut, Carmen; Rico-Jimenez, Jesus; Campos-Delgado, Daniel U.; Quinones-Hinojosa, Alfredo; Li, Xingde; Jo, Javier

    2018-02-01

    In brain cancer surgery, it is critical to achieve extensive resection without compromising adjacent healthy, noncancerous regions. Various technological advances have made major contributions in imaging, including intraoperative magnetic imaging (MRI) and computed tomography (CT). However, these technologies have pros and cons in providing quantitative, real-time and three-dimensional (3D) continuous guidance in brain cancer detection. Optical Coherence Tomography (OCT) is a non-invasive, label-free, cost-effective technique capable of imaging tissue in three dimensions and real time. The purpose of this study is to reliably and efficiently discriminate between non-cancer and cancerinfiltrated brain regions using OCT images. To this end, a mathematical model for quantitative evaluation known as the Blind End-Member and Abundances Extraction method (BEAE). This BEAE method is a constrained optimization technique which extracts spatial information from volumetric OCT images. Using this novel method, we are able to discriminate between cancerous and non-cancerous tissues and using logistic regression as a classifier for automatic brain tumor margin detection. Using this technique, we are able to achieve excellent performance using an extensive cross-validation of the training dataset (sensitivity 92.91% and specificity 98.15%) and again using an independent, blinded validation dataset (sensitivity 92.91% and specificity 86.36%). In summary, BEAE is well-suited to differentiate brain tissue which could support the guiding surgery process for tissue resection.

  12. Detection of brain tumor margins using optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Juarez-Chambi, Ronald M.; Kut, Carmen; Rico-Jimenez, Jesus; Campos-Delgado, Daniel U.; Quinones-Hinojosa, Alfredo; Li, Xingde; Jo, Javier

    2018-02-01

    In brain cancer surgery, it is critical to achieve extensive resection without compromising adjacent healthy, non-cancerous regions. Various technological advances have made major contributions in imaging, including intraoperative magnetic imaging (MRI) and computed tomography (CT). However, these technologies have pros and cons in providing quantitative, real-time and three-dimensional (3D) continuous guidance in brain cancer detection. Optical Coherence Tomography (OCT) is a non-invasive, label-free, cost-effective technique capable of imaging tissue in three dimensions and real time. The purpose of this study is to reliably and efficiently discriminate between non-cancer and cancer-infiltrated brain regions using OCT images. To this end, a mathematical model for quantitative evaluation known as the Blind End- Member and Abundances Extraction method (BEAE). This BEAE method is a constrained optimization technique which extracts spatial information from volumetric OCT images. Using this novel method, we are able to discriminate between cancerous and non-cancerous tissues and using logistic regression as a classifier for automatic brain tumor margin detection. Using this technique, we are able to achieve excellent performance using an extensive cross-validation of the training dataset (sensitivity 92.91% and specificity 98.15%) and again using an independent, blinded validation dataset (sensitivity 92.91% and specificity 86.36%). In summary, BEAE is well-suited to differentiate brain tissue which could support the guiding surgery process for tissue resection.

  13. 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.

  14. Application of Neutron Tomography in Culture Heritage research.

    PubMed

    Mongy, T

    2014-02-01

    Neutron Tomography (NT) investigation of Culture Heritages (CH) is an efficient tool for understanding the culture of ancient civilizations. Neutron imaging (NI) is a-state-of-the-art non-destructive tool in the area of CH and plays an important role in the modern archeology. The NI technology can be widely utilized in the field of elemental analysis. At Egypt Second Research Reactor (ETRR-2), a collimated Neutron Radiography (NR) beam is employed for neutron imaging purposes. A digital CCD camera is utilized for recording the beam attenuation in the sample. This helps for the detection of hidden objects and characterization of material properties. Research activity can be extended to use computer software for quantitative neutron measurement. Development of image processing algorithms can be used to obtain high quality images. In this work, full description of ETRR-2 was introduced with up to date neutron imaging system as well. Tomographic investigation of a clay forged artifact represents CH object was studied by neutron imaging methods in order to obtain some hidden information and highlight some attractive quantitative measurements. Computer software was used for imaging processing and enhancement. Also the Astra Image 3.0 Pro software was employed for high precise measurements and imaging enhancement using advanced algorithms. This work increased the effective utilization of the ETRR-2 Neutron Radiography/Tomography (NR/T) technique in Culture Heritages activities. © 2013 Elsevier Ltd. All rights reserved.

  15. Reduction of Metal Artifact in Single Photon-Counting Computed Tomography by Spectral-Driven Iterative Reconstruction Technique

    PubMed Central

    Nasirudin, Radin A.; Mei, Kai; Panchev, Petar; Fehringer, Andreas; Pfeiffer, Franz; Rummeny, Ernst J.; Fiebich, Martin; Noël, Peter B.

    2015-01-01

    Purpose The exciting prospect of Spectral CT (SCT) using photon-counting detectors (PCD) will lead to new techniques in computed tomography (CT) that take advantage of the additional spectral information provided. We introduce a method to reduce metal artifact in X-ray tomography by incorporating knowledge obtained from SCT into a statistical iterative reconstruction scheme. We call our method Spectral-driven Iterative Reconstruction (SPIR). Method The proposed algorithm consists of two main components: material decomposition and penalized maximum likelihood iterative reconstruction. In this study, the spectral data acquisitions with an energy-resolving PCD were simulated using a Monte-Carlo simulator based on EGSnrc C++ class library. A jaw phantom with a dental implant made of gold was used as an object in this study. A total of three dental implant shapes were simulated separately to test the influence of prior knowledge on the overall performance of the algorithm. The generated projection data was first decomposed into three basis functions: photoelectric absorption, Compton scattering and attenuation of gold. A pseudo-monochromatic sinogram was calculated and used as input in the reconstruction, while the spatial information of the gold implant was used as a prior. The results from the algorithm were assessed and benchmarked with state-of-the-art reconstruction methods. Results Decomposition results illustrate that gold implant of any shape can be distinguished from other components of the phantom. Additionally, the result from the penalized maximum likelihood iterative reconstruction shows that artifacts are significantly reduced in SPIR reconstructed slices in comparison to other known techniques, while at the same time details around the implant are preserved. Quantitatively, the SPIR algorithm best reflects the true attenuation value in comparison to other algorithms. Conclusion It is demonstrated that the combination of the additional information from

  16. Electrical Capacitance Volume Tomography: Design and Applications

    PubMed Central

    Wang, Fei; Marashdeh, Qussai; Fan, Liang-Shih; Warsito, Warsito

    2010-01-01

    This article reports recent advances and progress in the field of electrical capacitance volume tomography (ECVT). ECVT, developed from the two-dimensional electrical capacitance tomography (ECT), is a promising non-intrusive imaging technology that can provide real-time three-dimensional images of the sensing domain. Images are reconstructed from capacitance measurements acquired by electrodes placed on the outside boundary of the testing vessel. In this article, a review of progress on capacitance sensor design and applications to multi-phase flows is presented. The sensor shape, electrode configuration, and the number of electrodes that comprise three key elements of three-dimensional capacitance sensors are illustrated. The article also highlights applications of ECVT sensors on vessels of various sizes from 1 to 60 inches with complex geometries. Case studies are used to show the capability and validity of ECVT. The studies provide qualitative and quantitative real-time three-dimensional information of the measuring domain under study. Advantages of ECVT render it a favorable tool to be utilized for industrial applications and fundamental multi-phase flow research. PMID:22294905

  17. In vivo fluorescence lifetime optical projection tomography

    PubMed Central

    McGinty, James; Taylor, Harriet B.; Chen, Lingling; Bugeon, Laurence; Lamb, Jonathan R.; Dallman, Margaret J.; French, Paul M. W.

    2011-01-01

    We demonstrate the application of fluorescence lifetime optical projection tomography (FLIM-OPT) to in vivo imaging of lysC:GFP transgenic zebrafish embryos (Danio rerio). This method has been applied to unambiguously distinguish between the fluorescent protein (GFP) signal in myeloid cells from background autofluorescence based on the fluorescence lifetime. The combination of FLIM, an inherently ratiometric method, in conjunction with OPT results in a quantitative 3-D tomographic technique that could be used as a robust method for in vivo biological and pharmaceutical research, for example as a readout of Förster resonance energy transfer based interactions. PMID:21559145

  18. Bringing Standardized Processes in Atom-Probe Tomography: I Establishing Standardized Terminology

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Anderson, Ian M; Danoix, F; Forbes, Richard

    2011-01-01

    Defining standardized methods requires careful consideration of the entire field and its applications. The International Field Emission Society (IFES) has elected a Standards Committee, whose task is to determine the needed steps to establish atom-probe tomography as an accepted metrology technique. Specific tasks include developing protocols or standards for: terminology and nomenclature; metrology and instrumentation, including specifications for reference materials; test methodologies; modeling and simulations; and science-based health, safety, and environmental practices. The Committee is currently working on defining terminology related to atom-probe tomography with the goal to include terms into a document published by the International Organization for Standardsmore » (ISO). A lot of terms also used in other disciplines have already been defined) and will be discussed for adoption in the context of atom-probe tomography.« less

  19. 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.

  20. Quantitative angle-insensitive flow measurement using relative standard deviation OCT

    NASA Astrophysics Data System (ADS)

    Zhu, Jiang; Zhang, Buyun; Qi, Li; Wang, Ling; Yang, Qiang; Zhu, Zhuqing; Huo, Tiancheng; Chen, Zhongping

    2017-10-01

    Incorporating different data processing methods, optical coherence tomography (OCT) has the ability for high-resolution angiography and quantitative flow velocity measurements. However, OCT angiography cannot provide quantitative information of flow velocities, and the velocity measurement based on Doppler OCT requires the determination of Doppler angles, which is a challenge in a complex vascular network. In this study, we report on a relative standard deviation OCT (RSD-OCT) method which provides both vascular network mapping and quantitative information for flow velocities within a wide range of Doppler angles. The RSD values are angle-insensitive within a wide range of angles, and a nearly linear relationship was found between the RSD values and the flow velocities. The RSD-OCT measurement in a rat cortex shows that it can quantify the blood flow velocities as well as map the vascular network in vivo.

  1. Quantitative angle-insensitive flow measurement using relative standard deviation OCT.

    PubMed

    Zhu, Jiang; Zhang, Buyun; Qi, Li; Wang, Ling; Yang, Qiang; Zhu, Zhuqing; Huo, Tiancheng; Chen, Zhongping

    2017-10-30

    Incorporating different data processing methods, optical coherence tomography (OCT) has the ability for high-resolution angiography and quantitative flow velocity measurements. However, OCT angiography cannot provide quantitative information of flow velocities, and the velocity measurement based on Doppler OCT requires the determination of Doppler angles, which is a challenge in a complex vascular network. In this study, we report on a relative standard deviation OCT (RSD-OCT) method which provides both vascular network mapping and quantitative information for flow velocities within a wide range of Doppler angles. The RSD values are angle-insensitive within a wide range of angles, and a nearly linear relationship was found between the RSD values and the flow velocities. The RSD-OCT measurement in a rat cortex shows that it can quantify the blood flow velocities as well as map the vascular network in vivo .

  2. Correction of motion artifacts in endoscopic optical coherence tomography and autofluorescence images based on azimuthal en face image registration.

    PubMed

    Abouei, Elham; Lee, Anthony M D; Pahlevaninezhad, Hamid; Hohert, Geoffrey; Cua, Michelle; Lane, Pierre; Lam, Stephen; MacAulay, Calum

    2018-01-01

    We present a method for the correction of motion artifacts present in two- and three-dimensional in vivo endoscopic images produced by rotary-pullback catheters. This method can correct for cardiac/breathing-based motion artifacts and catheter-based motion artifacts such as nonuniform rotational distortion (NURD). This method assumes that en face tissue imaging contains slowly varying structures that are roughly parallel to the pullback axis. The method reduces motion artifacts using a dynamic time warping solution through a cost matrix that measures similarities between adjacent frames in en face images. We optimize and demonstrate the suitability of this method using a real and simulated NURD phantom and in vivo endoscopic pulmonary optical coherence tomography and autofluorescence images. Qualitative and quantitative evaluations of the method show an enhancement of the image quality. (2018) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE).

  3. Design and characterization of a small muon tomography system

    NASA Astrophysics Data System (ADS)

    Jo, Woo Jin; An, Su Jung; Kim, Hyun-Il; Lee, Chae Young; Chung, Heejun; Chung, Yong Hyun

    2015-02-01

    Muon tomography is a useful method for monitoring special nuclear materials (SNMs) because it can provide effective information on the presence of high-Z materials, has a high enough energy to deeply penetrate large amounts of shielding, and does not lead to any health risks and danger above background. We developed a 2-D muon detector and designed a muon tomography system employing four detector modules. Two top and two bottom detectors are, respectively, employed to record the incident and the scattered muon trajectories. The detector module for the muon tomography system consists of a plastic scintillator, wavelength-shifting (WLS) fiber arrays placed orthogonally on the top and the bottom of the scintillator, and a position-sensitive photomultiplier (PSPMT). The WLS fiber arrays absorb light photons emitted by the plastic scintillator and re-emit green lights guided to the PSPMT. The light distribution among the WLS fiber arrays determines the position of the muon interaction; consequently, 3-D tomographic images can be obtained by extracting the crossing points of the individual muon trajectories by using a point-of-closest-approach algorithm. The goal of this study is to optimize the design parameters of a muon tomography system by using the Geant4 code and to experimentally evaluate the performance of the prototype detector. Images obtained by the prototype detector with a 420-nm laser light source showed good agreement with the simulation results. This indicates that the proposed detector is feasible for use in a muon tomography system and can be used to verify the Z-discrimination capability of the muon tomography system.

  4. A three-step reconstruction method for fluorescence molecular tomography based on compressive sensing

    NASA Astrophysics Data System (ADS)

    Zhu, Yansong; Jha, Abhinav K.; Dreyer, Jakob K.; Le, Hanh N. D.; Kang, Jin U.; Roland, Per E.; Wong, Dean F.; Rahmim, Arman

    2017-02-01

    Fluorescence molecular tomography (FMT) is a promising tool for real time in vivo quantification of neurotransmission (NT) as we pursue in our BRAIN initiative effort. However, the acquired image data are noisy and the reconstruction problem is ill-posed. Further, while spatial sparsity of the NT effects could be exploited, traditional compressive-sensing methods cannot be directly applied as the system matrix in FMT is highly coherent. To overcome these issues, we propose and assess a three-step reconstruction method. First, truncated singular value decomposition is applied on the data to reduce matrix coherence. The resultant image data are input to a homotopy-based reconstruction strategy that exploits sparsity via l1 regularization. The reconstructed image is then input to a maximum-likelihood expectation maximization (MLEM) algorithm that retains the sparseness of the input estimate and improves upon the quantitation by accurate Poisson noise modeling. The proposed reconstruction method was evaluated in a three-dimensional simulated setup with fluorescent sources in a cuboidal scattering medium with optical properties simulating human brain cortex (reduced scattering coefficient: 9.2 cm-1, absorption coefficient: 0.1 cm-1 and tomographic measurements made using pixelated detectors. In different experiments, fluorescent sources of varying size and intensity were simulated. The proposed reconstruction method provided accurate estimates of the fluorescent source intensity, with a 20% lower root mean square error on average compared to the pure-homotopy method for all considered source intensities and sizes. Further, compared with conventional l2 regularized algorithm, overall, the proposed method reconstructed substantially more accurate fluorescence distribution. The proposed method shows considerable promise and will be tested using more realistic simulations and experimental setups.

  5. A spectral X-ray CT simulation study for quantitative determination of iron

    NASA Astrophysics Data System (ADS)

    Su, Ting; Kaftandjian, Valérie; Duvauchelle, Philippe; Zhu, Yuemin

    2018-06-01

    Iron is an essential element in the human body and disorders in iron such as iron deficiency or overload can cause serious diseases. This paper aims to explore the ability of spectral X-ray CT to quantitatively separate iron from calcium and potassium and to investigate the influence of different acquisition parameters on material decomposition performance. We simulated spectral X-ray CT imaging of a PMMA phantom filled with iron, calcium, and potassium solutions at various concentrations (15-200 mg/cc). Different acquisition parameters were considered, such as the number of energy bins (6, 10, 15, 20, 30, 60) and exposure factor per projection (0.025, 0.1, 1, 10, 100 mA s). Based on the simulation data, we investigated the performance of two regularized material decomposition approaches: projection domain method and image domain method. It was found that the former method discriminated iron from calcium, potassium and water in all cases and tended to benefit from lower number of energy bins for lower exposure factor acquisition. The latter method succeeded in iron determination only when the number of energy bins equals 60, and in this case, the contrast-to-noise ratios of the decomposed iron images are higher than those obtained using the projection domain method. The results demonstrate that both methods are able to discriminate and quantify iron from calcium, potassium and water under certain conditions. Their performances vary with the acquisition parameters of spectral CT. One can use one method or the other to benefit better performance according to the data available.

  6. APPLICATION OF 3D COMPUTER-AIDED TOMOGRAPHY TO THE QUANTIFICATION OF MARINE SEDIMENT COMMUNITIES IN POLLUTION GRADIENTS

    EPA Science Inventory

    Computer-Aided Tomography (CT) has been demonstrated to be a cost efficient tool for the qualitative and quantitative study of estuarine benthic communities along pollution gradients.
    Now we have advanced this technology to successfully visualize and discriminate three dimen...

  7. The dynamic micro computed tomography at SSRF

    NASA Astrophysics Data System (ADS)

    Chen, R.; Xu, L.; Du, G.; Deng, B.; Xie, H.; Xiao, T.

    2018-05-01

    Synchrotron radiation micro-computed tomography (SR-μCT) is a critical technique for quantitative characterizing the 3D internal structure of samples, recently the dynamic SR-μCT has been attracting vast attention since it can evaluate the three-dimensional structure evolution of a sample. A dynamic μCT method, which is based on monochromatic beam, was developed at the X-ray Imaging and Biomedical Application Beamline at Shanghai Synchrotron Radiation Facility, by combining the compressed sensing based CT reconstruction algorithm and hardware upgrade. The monochromatic beam based method can achieve quantitative information, and lower dose than the white beam base method in which the lower energy beam is absorbed by the sample rather than contribute to the final imaging signal. The developed method is successfully used to investigate the compression of the air sac during respiration in a bell cricket, providing new knowledge for further research on the insect respiratory system.

  8. An image filtering technique for SPIDER visible tomography

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Fonnesu, N., E-mail: nicola.fonnesu@igi.cnr.it; Agostini, M.; Brombin, M.

    2014-02-15

    The tomographic diagnostic developed for the beam generated in the SPIDER facility (100 keV, 50 A prototype negative ion source of ITER neutral beam injector) will characterize the two-dimensional particle density distribution of the beam. The simulations described in the paper show that instrumental noise has a large influence on the maximum achievable resolution of the diagnostic. To reduce its impact on beam pattern reconstruction, a filtering technique has been adapted and implemented in the tomography code. This technique is applied to the simulated tomographic reconstruction of the SPIDER beam, and the main results are reported.

  9. A heuristic statistical stopping rule for iterative reconstruction in emission tomography.

    PubMed

    Ben Bouallègue, F; Crouzet, J F; Mariano-Goulart, D

    2013-01-01

    We propose a statistical stopping criterion for iterative reconstruction in emission tomography based on a heuristic statistical description of the reconstruction process. The method was assessed for MLEM reconstruction. Based on Monte-Carlo numerical simulations and using a perfectly modeled system matrix, our method was compared with classical iterative reconstruction followed by low-pass filtering in terms of Euclidian distance to the exact object, noise, and resolution. The stopping criterion was then evaluated with realistic PET data of a Hoffman brain phantom produced using the GATE platform for different count levels. The numerical experiments showed that compared with the classical method, our technique yielded significant improvement of the noise-resolution tradeoff for a wide range of counting statistics compatible with routine clinical settings. When working with realistic data, the stopping rule allowed a qualitatively and quantitatively efficient determination of the optimal image. Our method appears to give a reliable estimation of the optimal stopping point for iterative reconstruction. It should thus be of practical interest as it produces images with similar or better quality than classical post-filtered iterative reconstruction with a mastered computation time.

  10. Living specimen tomography by digital holographic microscopy: morphometry of testate amoeba

    NASA Astrophysics Data System (ADS)

    Charrière, Florian; Pavillon, Nicolas; Colomb, Tristan; Depeursinge, Christian; Heger, Thierry J.; Mitchell, Edward A. D.; Marquet, Pierre; Rappaz, Benjamin

    2006-08-01

    This paper presents an optical diffraction tomography technique based on digital holographic microscopy. Quantitative 2-dimensional phase images are acquired for regularly-spaced angular positions of the specimen covering a total angle of π, allowing to built 3-dimensional quantitative refractive index distributions by an inverse Radon transform. A 20x magnification allows a resolution better than 3 μm in all three dimensions, with accuracy better than 0.01 for the refractive index measurements. This technique is for the first time to our knowledge applied to living specimen (testate amoeba, Protista). Morphometric measurements are extracted from the tomographic reconstructions, showing that the commonly used method for testate amoeba biovolume evaluation leads to systematic under evaluations by about 50%.

  11. Imaging complex objects using learning tomography

    NASA Astrophysics Data System (ADS)

    Lim, JooWon; Goy, Alexandre; Shoreh, Morteza Hasani; Unser, Michael; Psaltis, Demetri

    2018-02-01

    Optical diffraction tomography (ODT) can be described using the scattering process through an inhomogeneous media. An inherent nonlinearity exists relating the scattering medium and the scattered field due to multiple scattering. Multiple scattering is often assumed to be negligible in weakly scattering media. This assumption becomes invalid as the sample gets more complex resulting in distorted image reconstructions. This issue becomes very critical when we image a complex sample. Multiple scattering can be simulated using the beam propagation method (BPM) as the forward model of ODT combined with an iterative reconstruction scheme. The iterative error reduction scheme and the multi-layer structure of BPM are similar to neural networks. Therefore we refer to our imaging method as learning tomography (LT). To fairly assess the performance of LT in imaging complex samples, we compared LT with the conventional iterative linear scheme using Mie theory which provides the ground truth. We also demonstrate the capacity of LT to image complex samples using experimental data of a biological cell.

  12. Quantitative computed tomography and cranial burr holes: a model to evaluate the quality of cranial reconstruction in humans.

    PubMed

    Worm, Paulo Valdeci; Ferreira, Nelson Pires; Ferreira, Marcelo Paglioli; Kraemer, Jorge Luiz; Lenhardt, Rene; Alves, Ronnie Peterson Marcondes; Wunderlich, Ricardo Castilho; Collares, Marcus Vinicius Martins

    2012-05-01

    Current methods to evaluate the biologic development of bone grafts in human beings do not quantify results accurately. Cranial burr holes are standardized critical bone defects, and the differences between bone powder and bone grafts have been determined in numerous experimental studies. This study evaluated quantitative computed tomography (QCT) as a method to objectively measure cranial bone density after cranial reconstruction with autografts. In each of 8 patients, 2 of 4 surgical burr holes were reconstructed with autogenous wet bone powder collected during skull trephination, and the other 2 holes, with a circular cortical bone fragment removed from the inner table of the cranial bone flap. After 12 months, the reconstructed areas and a sample of normal bone were studied using three-dimensional QCT; bone density was measured in Hounsfield units (HU). Mean (SD) bone density was 1535.89 (141) HU for normal bone (P < 0.0001), 964 (176) HU for bone fragments, and 453 (241) HU for bone powder (P < 0.001). As expected, the density of the bone fragment graft was consistently greater than that of bone powder. Results confirm the accuracy and reproducibility of QCT, already demonstrated for bone in other locations, and suggest that it is an adequate tool to evaluate cranial reconstructions. The combination of QCT and cranial burr holes is an excellent model to accurately measure the quality of new bone in cranial reconstructions and also seems to be an appropriate choice of experimental model to clinically test any cranial bone or bone substitute reconstruction.

  13. Electron Tomography and Simulation of Baculovirus Actin Comet Tails Support a Tethered Filament Model of Pathogen Propulsion

    PubMed Central

    Mueller, Jan; Pfanzelter, Julia; Winkler, Christoph; Narita, Akihiro; Le Clainche, Christophe; Nemethova, Maria; Carlier, Marie-France; Maeda, Yuichiro; Welch, Matthew D.; Ohkawa, Taro; Schmeiser, Christian; Resch, Guenter P.; Small, J. Victor

    2014-01-01

    Several pathogens induce propulsive actin comet tails in cells they invade to disseminate their infection. They achieve this by recruiting factors for actin nucleation, the Arp2/3 complex, and polymerization regulators from the host cytoplasm. Owing to limited information on the structural organization of actin comets and in particular the spatial arrangement of filaments engaged in propulsion, the underlying mechanism of pathogen movement is currently speculative and controversial. Using electron tomography we have resolved the three-dimensional architecture of actin comet tails propelling baculovirus, the smallest pathogen yet known to hijack the actin motile machinery. Comet tail geometry was also mimicked in mixtures of virus capsids with purified actin and a minimal inventory of actin regulators. We demonstrate that propulsion is based on the assembly of a fishbone-like array of actin filaments organized in subsets linked by branch junctions, with an average of four filaments pushing the virus at any one time. Using an energy-minimizing function we have simulated the structure of actin comet tails as well as the tracks adopted by baculovirus in infected cells in vivo. The results from the simulations rule out gel squeezing models of propulsion and support those in which actin filaments are continuously tethered during branch nucleation and polymerization. Since Listeria monocytogenes, Shigella flexneri, and Vaccinia virus among other pathogens use the same common toolbox of components as baculovirus to move, we suggest they share the same principles of actin organization and mode of propulsion. PMID:24453943

  14. Electron tomography and simulation of baculovirus actin comet tails support a tethered filament model of pathogen propulsion.

    PubMed

    Mueller, Jan; Pfanzelter, Julia; Winkler, Christoph; Narita, Akihiro; Le Clainche, Christophe; Nemethova, Maria; Carlier, Marie-France; Maeda, Yuichiro; Welch, Matthew D; Ohkawa, Taro; Schmeiser, Christian; Resch, Guenter P; Small, J Victor

    2014-01-01

    Several pathogens induce propulsive actin comet tails in cells they invade to disseminate their infection. They achieve this by recruiting factors for actin nucleation, the Arp2/3 complex, and polymerization regulators from the host cytoplasm. Owing to limited information on the structural organization of actin comets and in particular the spatial arrangement of filaments engaged in propulsion, the underlying mechanism of pathogen movement is currently speculative and controversial. Using electron tomography we have resolved the three-dimensional architecture of actin comet tails propelling baculovirus, the smallest pathogen yet known to hijack the actin motile machinery. Comet tail geometry was also mimicked in mixtures of virus capsids with purified actin and a minimal inventory of actin regulators. We demonstrate that propulsion is based on the assembly of a fishbone-like array of actin filaments organized in subsets linked by branch junctions, with an average of four filaments pushing the virus at any one time. Using an energy-minimizing function we have simulated the structure of actin comet tails as well as the tracks adopted by baculovirus in infected cells in vivo. The results from the simulations rule out gel squeezing models of propulsion and support those in which actin filaments are continuously tethered during branch nucleation and polymerization. Since Listeria monocytogenes, Shigella flexneri, and Vaccinia virus among other pathogens use the same common toolbox of components as baculovirus to move, we suggest they share the same principles of actin organization and mode of propulsion.

  15. Discrimination of correlated and entangling quantum channels with selective process tomography

    DOE PAGES

    Dumitrescu, Eugene; Humble, Travis S.

    2016-10-10

    The accurate and reliable characterization of quantum dynamical processes underlies efforts to validate quantum technologies, where discrimination between competing models of observed behaviors inform efforts to fabricate and operate qubit devices. We present a protocol for quantum channel discrimination that leverages advances in direct characterization of quantum dynamics (DCQD) codes. We demonstrate that DCQD codes enable selective process tomography to improve discrimination between entangling and correlated quantum dynamics. Numerical simulations show selective process tomography requires only a few measurement configurations to achieve a low false alarm rate and that the DCQD encoding improves the resilience of the protocol to hiddenmore » sources of noise. Lastly, our results show that selective process tomography with DCQD codes is useful for efficiently distinguishing sources of correlated crosstalk from uncorrelated noise in current and future experimental platforms.« less

  16. [Contribution of X-ray computed tomography in the evaluation of kidney performance].

    PubMed

    Lemoine, Sandrine; Rognant, Nicolas; Collet-Benzaquen, Diane; Juillard, Laurent

    2012-07-01

    X-ray computer assisted tomography scanner is an imaging method based on the use of X-ray attenuation in tissue. This attenuation is proportional to the density of the tissue (without or after contrast media injection) in each pixel image of the image. Spiral scanner, the electron beam computed tomography (EBCT) scanner and multidetector computed tomography scanner allow renal anatomical measurements, such as cortical and medullary volume, but also the measurement of renal functional parameters, such as regional renal perfusion, renal blood flow and glomerular filtration rate. These functional parameters are extracted from the modeling of the kinetics of the contrast media concentration in the vascular space and the renal tissue, using two main mathematical models (the gamma variate model and the Patlak model). Renal functional imaging allows measuring quantitative parameters on each kidney separately, in a non-invasive manner, providing significant opportunities in nephrology, both for experimental and clinical studies. However, this method uses contrast media that may alter renal function, thus limiting its use in patients with chronic renal failure. Moreover, the increase irradiation delivered to the patient with multi detector computed tomography (MDCT) should be considered. Copyright © 2011 Association Société de néphrologie. Published by Elsevier SAS. All rights reserved.

  17. Chirp optical coherence tomography of layered scattering media.

    PubMed

    Haberland, U H; Blazek, V; Schmitt, H J

    1998-07-01

    A new noninvasive technique that reveals cross sectional images of scattering media is presented. It is based on a continuous wave frequency modulated radar, but uses a tunable laser in the near infrared. As the full width at half maximum resolution of 16 μm is demonstrated with an external cavity laser, the chirp optical coherence tomography becomes an alternative to conventional short coherence tomography with the advantage of a simplified optical setup. The analysis of two-layer solid phantoms shows that the backscattered light gets stronger with decreasing anisotropic factor and increasing scattering coefficient, as predicted by Monte Carlo simulations. By introducing a two-phase chirp sequence, the combination of lateral resolved perfusion and depth resolved structure is shown. © 1998 Society of Photo-Optical Instrumentation Engineers.

  18. Bilateral filtering using the full noise covariance matrix applied to x-ray phase-contrast computed tomography.

    PubMed

    Allner, S; Koehler, T; Fehringer, A; Birnbacher, L; Willner, M; Pfeiffer, F; Noël, P B

    2016-05-21

    The purpose of this work is to develop an image-based de-noising algorithm that exploits complementary information and noise statistics from multi-modal images, as they emerge in x-ray tomography techniques, for instance grating-based phase-contrast CT and spectral CT. Among the noise reduction methods, image-based de-noising is one popular approach and the so-called bilateral filter is a well known algorithm for edge-preserving filtering. We developed a generalization of the bilateral filter for the case where the imaging system provides two or more perfectly aligned images. The proposed generalization is statistically motivated and takes the full second order noise statistics of these images into account. In particular, it includes a noise correlation between the images and spatial noise correlation within the same image. The novel generalized three-dimensional bilateral filter is applied to the attenuation and phase images created with filtered backprojection reconstructions from grating-based phase-contrast tomography. In comparison to established bilateral filters, we obtain improved noise reduction and at the same time a better preservation of edges in the images on the examples of a simulated soft-tissue phantom, a human cerebellum and a human artery sample. The applied full noise covariance is determined via cross-correlation of the image noise. The filter results yield an improved feature recovery based on enhanced noise suppression and edge preservation as shown here on the example of attenuation and phase images captured with grating-based phase-contrast computed tomography. This is supported by quantitative image analysis. Without being bound to phase-contrast imaging, this generalized filter is applicable to any kind of noise-afflicted image data with or without noise correlation. Therefore, it can be utilized in various imaging applications and fields.

  19. Probing myocardium biomechanics using quantitative optical coherence elastography

    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

    We present a quantitative optical coherence elastographic method for noncontact assessment of the myocardium elasticity. The method is based on shear wave imaging optical coherence tomography (SWI-OCT), where a focused air-puff system is used to induce localized tissue deformation through a low-pressure short-duration air stream and a phase-sensitive OCT system is utilized to monitor the propagation of the induced tissue displacement with nanoscale sensitivity. The 1-D scanning of M-mode OCT imaging and the application of optical phase retrieval and mapping techniques enable the reconstruction and visualization of 2-D depth-resolved shear wave propagation in tissue with ultra-high frame rate. The feasibility of this method in quantitative elasticity measurement is demonstrated on tissue-mimicking phantoms with the estimated Young's modulus compared with uniaxial compression tests. We also performed pilot experiments on ex vivo mouse cardiac muscle tissues with normal and genetically altered cardiomyocytes. Our results indicate this noncontact quantitative optical coherence elastographic method can be a useful tool for the cardiac muscle research and studies.

  20. 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

  1. VIBA-Lab 3.0: Computer program for simulation and semi-quantitative analysis of PIXE and RBS spectra and 2D elemental maps

    NASA Astrophysics Data System (ADS)

    Orlić, Ivica; Mekterović, Darko; Mekterović, Igor; Ivošević, Tatjana

    2015-11-01

    VIBA-Lab is a computer program originally developed by the author and co-workers at the National University of Singapore (NUS) as an interactive software package for simulation of Particle Induced X-ray Emission and Rutherford Backscattering Spectra. The original program is redeveloped to a VIBA-Lab 3.0 in which the user can perform semi-quantitative analysis by comparing simulated and measured spectra as well as simulate 2D elemental maps for a given 3D sample composition. The latest version has a new and more versatile user interface. It also has the latest data set of fundamental parameters such as Coster-Kronig transition rates, fluorescence yields, mass absorption coefficients and ionization cross sections for K and L lines in a wider energy range than the original program. Our short-term plan is to introduce routine for quantitative analysis for multiple PIXE and XRF excitations. VIBA-Lab is an excellent teaching tool for students and researchers in using PIXE and RBS techniques. At the same time the program helps when planning an experiment and when optimizing experimental parameters such as incident ions, their energy, detector specifications, filters, geometry, etc. By "running" a virtual experiment the user can test various scenarios until the optimal PIXE and BS spectra are obtained and in this way save a lot of expensive machine time.

  2. Synchronization Tomography: Modeling and Exploring Complex Brain Dynamics

    NASA Astrophysics Data System (ADS)

    Fieseler, Thomas

    2002-03-01

    Phase synchronization (PS) plays an important role both under physiological and pathological conditions. With standard averaging techniques of MEG data, it is difficult to reliably detect cortico-cortical and cortico-muscular PS processes that are not time-locked to an external stimulus. For this reason, novel synchronization analysis techniques were developed and directly applied to MEG signals. Of course, due to the lack of an inverse modeling (i.e. source localization), the spatial resolution of this approach was limited. To detect and localize cerebral PS, we here present the synchronization tomography (ST): For this, we first estimate the cerebral current source density by means of the magnetic field tomography (MFT). We then apply the single-run PS analysis to the current source density in each voxel of the reconstruction space. In this way we study simulated PS, voxel by voxel in order to determine the spatio-temporal resolution of the ST. To this end different generators of ongoing rhythmic cerebral activity are simulated by current dipoles at different locations and directions, which are modeled by slightly detuned chaotic oscillators. MEG signals for these generators are simulated for a spherical head model and a whole-head MEG system. MFT current density solutions are calculated from these simulated signals within a hemispherical source space. We compare the spatial resolution of the ST with that of the MFT. Our results show that adjacent sources which are indistinguishable for the MFT, can nevertheless be separated with the ST, provided they are not strongly phase synchronized. This clearly demonstrates the potential of combining spatial information (i.e. source localization) with temporal information for the anatomical localization of phase synchronization in the human brain.

  3. Computer system for definition of the quantitative geometry of musculature from CT images.

    PubMed

    Daniel, Matej; Iglic, Ales; Kralj-Iglic, Veronika; Konvicková, Svatava

    2005-02-01

    The computer system for quantitative determination of musculoskeletal geometry from computer tomography (CT) images has been developed. The computer system processes series of CT images to obtain three-dimensional (3D) model of bony structures where the effective muscle fibres can be interactively defined. Presented computer system has flexible modular structure and is suitable also for educational purposes.

  4. Quantitative simulation of extraterrestrial engineering devices

    NASA Technical Reports Server (NTRS)

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

    1991-01-01

    This is a multicomponent, multidisciplinary project whose overall objective is to build an integrated database, simulation, visualization, and optimization system for the proposed oxygen manufacturing plant on Mars. Specifically, the system allows users to enter physical description, engineering, and connectivity data through a uniform, user-friendly interface and stores the data in formats compatible with other software also developed as part of this project. These latter components include: (1) programs to simulate the behavior of various parts of the plant in Martian conditions; (2) an animation program which, in different modes, provides visual feedback to designers and researchers about the location of and temperature distribution among components as well as heat, mass, and data flow through the plant as it operates in different scenarios; (3) a control program to investigate the stability and response of the system under different disturbance conditions; and (4) an optimization program to maximize or minimize various criteria as the system evolves into its final design. All components of the system are interconnected so that changes entered through one component are reflected in the others.

  5. Bayesian image reconstruction for improving detection performance of muon tomography.

    PubMed

    Wang, Guobao; Schultz, Larry J; Qi, Jinyi

    2009-05-01

    Muon tomography is a novel technology that is being developed for detecting high-Z materials in vehicles or cargo containers. Maximum likelihood methods have been developed for reconstructing the scattering density image from muon measurements. However, the instability of maximum likelihood estimation often results in noisy images and low detectability of high-Z targets. In this paper, we propose using regularization to improve the image quality of muon tomography. We formulate the muon reconstruction problem in a Bayesian framework by introducing a prior distribution on scattering density images. An iterative shrinkage algorithm is derived to maximize the log posterior distribution. At each iteration, the algorithm obtains the maximum a posteriori update by shrinking an unregularized maximum likelihood update. Inverse quadratic shrinkage functions are derived for generalized Laplacian priors and inverse cubic shrinkage functions are derived for generalized Gaussian priors. Receiver operating characteristic studies using simulated data demonstrate that the Bayesian reconstruction can greatly improve the detection performance of muon tomography.

  6. The use of optical coherence tomography to analyze the efficacy of skin care products

    NASA Astrophysics Data System (ADS)

    Irani, Sarosh; Turani, Zahra; Fotouhi, Audrey; Daveluy, Steven; Mehregan, Darius; Chen, Wei; Gelovani, Juri; Nasiriavanaki, Mohammadreza

    2018-02-01

    In this study, we assess the applicability of optical coherence tomography (OCT) for non-invasive imaging of skin morphology for the assessment of efficacy of cosmetic skin wrinkle-reduction products in humans. Evaluation of skin care products for reduction of facial wrinkles is largely limited to photographic (non-quantitative) comparison of skin surface texture before and after either single or prolonged application of skin care product. OCT could be a technique for monitoring changes in cross-sectional skin morphology. An optical attenuation coefficient analysis is also carried out to quantitatively study the changes in different layers of the skin.

  7. Dipyridamole stress myocardial perfusion by computed tomography in patients with left bundle branch block.

    PubMed

    Cabeda, Estêvan Vieira; Falcão, Andréa Maria Gomes; Soares, José; Rochitte, Carlos Eduardo; Nomura, César Higa; Ávila, Luiz Francisco Rodrigues; Parga, José Rodrigues

    2015-12-01

    Functional tests have limited accuracy for identifying myocardial ischemia in patients with left bundle branch block (LBBB). To assess the diagnostic accuracy of dipyridamole-stress myocardial computed tomography perfusion (CTP) by 320-detector CT in patients with LBBB using invasive quantitative coronary angiography (QCA) (stenosis ≥ 70%) as reference; to investigate the advantage of adding CTP to coronary computed tomography angiography (CTA) and compare the results with those of single photon emission computed tomography (SPECT) myocardial perfusion scintigraphy. Thirty patients with LBBB who had undergone SPECT for the investigation of coronary artery disease were referred for stress tomography. Independent examiners performed per-patient and per-coronary territory assessments. All patients gave written informed consent to participate in the study that was approved by the institution's ethics committee. The patients' mean age was 62 ± 10 years. The mean dose of radiation for the tomography protocol was 9.3 ± 4.6 mSv. With regard to CTP, the per-patient values for sensitivity, specificity, positive and negative predictive values, and accuracy were 86%, 81%, 80%, 87%, and 83%, respectively (p = 0.001). The per-territory values were 63%, 86%, 65%, 84%, and 79%, respectively (p < 0.001). In both analyses, the addition of CTP to CTA achieved higher diagnostic accuracy for detecting myocardial ischemia than SPECT (p < 0.001). The use of the stress tomography protocol is feasible and has good diagnostic accuracy for assessing myocardial ischemia in patients with LBBB.

  8. Non-Conventional Applications of Computerized Tomography: Analysis of Solid Dosage Forms Produced by Pharmaceutical Industry

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Martins de Oliveira, Jose Jr.; Germano Martins, Antonio Cesar

    X-ray computed tomography (CT) refers to the cross-sectional imaging of an object measuring the transmitted radiation at different directions. In this work, we describe a non-conventional application of computerized tomography: visualization and improvements in the understanding of some internal structural features of solid dosage forms. A micro-CT X-ray scanner, with a minimum resolution of 30 mum was used to characterize some pharmaceutical tablets, granules, controlled-release osmotic tablet and liquid-filled soft-gelatin capsules. The analysis presented in this work are essentially qualitative, but quantitative parameters, such as porosity, density distribution, tablets dimensions, etc. could also be obtained using the related CT techniques.

  9. Anatomic and Quantitative Temporal Bone CT for Preoperative Assessment of Branchio-Oto-Renal Syndrome.

    PubMed

    Ginat, D T; Ferro, L; Gluth, M B

    2016-12-01

    We describe the temporal bone computed tomography (CT) findings of an unusual case of branchio-oto-renal syndrome with ectopic ossicles that are partially located in the middle cranial fossa. We also describe quantitative temporal bone CT assessment pertaining to cochlear implantation in the setting of anomalous cochlear anatomy associated with this syndrome.

  10. Linearization improves the repeatability of quantitative dynamic contrast-enhanced MRI.

    PubMed

    Jones, Kyle M; Pagel, Mark D; Cárdenas-Rodríguez, Julio

    2018-04-01

    The purpose of this study was to compare the repeatabilities of the linear and nonlinear Tofts and reference region models (RRM) for dynamic contrast-enhanced MRI (DCE-MRI). Simulated and experimental DCE-MRI data from 12 rats with a flank tumor of C6 glioma acquired over three consecutive days were analyzed using four quantitative and semi-quantitative DCE-MRI metrics. The quantitative methods used were: 1) linear Tofts model (LTM), 2) non-linear Tofts model (NTM), 3) linear RRM (LRRM), and 4) non-linear RRM (NRRM). The following semi-quantitative metrics were used: 1) maximum enhancement ratio (MER), 2) time to peak (TTP), 3) initial area under the curve (iauc64), and 4) slope. LTM and NTM were used to estimate K trans , while LRRM and NRRM were used to estimate K trans relative to muscle (R Ktrans ). Repeatability was assessed by calculating the within-subject coefficient of variation (wSCV) and the percent intra-subject variation (iSV) determined with the Gage R&R analysis. The iSV for R Ktrans using LRRM was two-fold lower compared to NRRM at all simulated and experimental conditions. A similar trend was observed for the Tofts model, where LTM was at least 50% more repeatable than the NTM under all experimental and simulated conditions. The semi-quantitative metrics iauc64 and MER were as equally repeatable as K trans and R Ktrans estimated by LTM and LRRM respectively. The iSV for iauc64 and MER were significantly lower than the iSV for slope and TTP. In simulations and experimental results, linearization improves the repeatability of quantitative DCE-MRI by at least 30%, making it as repeatable as semi-quantitative metrics. Copyright © 2017 Elsevier Inc. All rights reserved.

  11. Quantitative comparison of electron temperature fluctuations to nonlinear gyrokinetic simulations in C-Mod Ohmic L-mode discharges

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Sung, C., E-mail: csung@physics.ucla.edu; White, A. E.; Greenwald, M.

    2016-04-15

    Long wavelength turbulent electron temperature fluctuations (k{sub y}ρ{sub s} < 0.3) are measured in the outer core region (r/a > 0.8) of Ohmic L-mode plasmas at Alcator C-Mod [E. S. Marmar et al., Nucl. Fusion 49, 104014 (2009)] with a correlation electron cyclotron emission diagnostic. The relative amplitude and frequency spectrum of the fluctuations are compared quantitatively with nonlinear gyrokinetic simulations using the GYRO code [J. Candy and R. E. Waltz, J. Comput. Phys. 186, 545 (2003)] in two different confinement regimes: linear Ohmic confinement (LOC) regime and saturated Ohmic confinement (SOC) regime. When comparing experiment with nonlinear simulations, it is found that local,more » electrostatic ion-scale simulations (k{sub y}ρ{sub s} ≲ 1.7) performed at r/a ∼ 0.85 reproduce the experimental ion heat flux levels, electron temperature fluctuation levels, and frequency spectra within experimental error bars. In contrast, the electron heat flux is robustly under-predicted and cannot be recovered by using scans of the simulation inputs within error bars or by using global simulations. If both the ion heat flux and the measured temperature fluctuations are attributed predominantly to long-wavelength turbulence, then under-prediction of electron heat flux strongly suggests that electron scale turbulence is important for transport in C-Mod Ohmic L-mode discharges. In addition, no evidence is found from linear or nonlinear simulations for a clear transition from trapped electron mode to ion temperature gradient turbulence across the LOC/SOC transition, and also there is no evidence in these Ohmic L-mode plasmas of the “Transport Shortfall” [C. Holland et al., Phys. Plasmas 16, 052301 (2009)].« less

  12. Magnetic Resonance Based Electrical Properties Tomography: A Review

    PubMed Central

    Zhang, Xiaotong; Liu, Jiaen

    2014-01-01

    Frequency-dependent electrical properties (EPs; conductivity and permittivity) of biological tissues provide important diagnostic information (e.g. tumor characterization), and also play an important role in quantifying radiofrequency (RF) coil induced Specific Absorption Rate (SAR) which is a major safety concern in high- and ultrahigh-field Magnetic Resonance Imaging (MRI) applications. Cross-sectional imaging of EPs has been pursued for decades. Recently introduced Electrical Properties Tomography (EPT) approaches utilize the measurable RF magnetic field induced by the RF coil in an MRI system to quantitatively reconstruct the EP distribution in vivo and non-invasively with a spatial resolution of a few millimeters or less. This paper reviews the Electrical Properties Tomography approach from its basic theory in electromagnetism to the state of the art research outcomes. Emphasizing on the imaging reconstruction methods rather than experimentation techniques, we review the developed imaging algorithms, validation results in physical phantoms and biological tissues, as well as their applications in in vivo tumor detection and subject-specific SAR prediction. Challenges for future research are also discussed. PMID:24803104

  13. 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.

  14. Bone-marrow densitometry: Assessment of marrow space of human vertebrae by single energy high resolution-quantitative computed tomography

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Peña, Jaime A.; Damm, Timo; Bastgen, Jan

    Purpose: Accurate noninvasive assessment of vertebral bone marrow fat fraction is important for diagnostic assessment of a variety of disorders and therapies known to affect marrow composition. Moreover, it provides a means to correct fat-induced bias of single energy quantitative computed tomography (QCT) based bone mineral density (BMD) measurements. The authors developed new segmentation and calibration methods to obtain quantitative surrogate measures of marrow-fat density in the axial skeleton. Methods: The authors developed and tested two high resolution-QCT (HR-QCT) based methods which permit segmentation of bone voids in between trabeculae hypothesizing that they are representative of bone marrow space. Themore » methods permit calculation of marrow content in units of mineral equivalent marrow density (MeMD). The first method is based on global thresholding and peeling (GTP) to define a volume of interest away from the transition between trabecular bone and marrow. The second method, morphological filtering (MF), uses spherical elements of different radii (0.1–1.2 mm) and automatically places them in between trabeculae to identify regions with large trabecular interspace, the bone-void space. To determine their performance, data were compared ex vivo to high-resolution peripheral CT (HR-pQCT) images as the gold-standard. The performance of the methods was tested on a set of excised human vertebrae with intact bone marrow tissue representative of an elderly population with low BMD. Results: 86% (GTP) and 87% (MF) of the voxels identified as true marrow space on HR-pQCT images were correctly identified on HR-QCT images and thus these volumes of interest can be considered to be representative of true marrow space. Within this volume, MeMD was estimated with residual errors of 4.8 mg/cm{sup 3} corresponding to accuracy errors in fat fraction on the order of 5% both for GTP and MF methods. Conclusions: The GTP and MF methods on HR-QCT images permit

  15. Quantitative computed tomography applied to interstitial lung diseases.

    PubMed

    Obert, Martin; Kampschulte, Marian; Limburg, Rebekka; Barańczuk, Stefan; Krombach, Gabriele A

    2018-03-01

    To evaluate a new image marker that retrieves information from computed tomography (CT) density histograms, with respect to classification properties between different lung parenchyma groups. Furthermore, to conduct a comparison of the new image marker with conventional markers. Density histograms from 220 different subjects (normal = 71; emphysema = 73; fibrotic = 76) were used to compare the conventionally applied emphysema index (EI), 15 th percentile value (PV), mean value (MV), variance (V), skewness (S), kurtosis (K), with a new histogram's functional shape (HFS) method. Multinomial logistic regression (MLR) analyses was performed to calculate predictions of different lung parenchyma group membership using the individual methods, as well as combinations thereof, as covariates. Overall correct assigned subjects (OCA), sensitivity (sens), specificity (spec), and Nagelkerke's pseudo R 2 (NR 2 ) effect size were estimated. NR 2 was used to set up a ranking list of the different methods. MLR indicates the highest classification power (OCA of 92%; sens 0.95; spec 0.89; NR 2 0.95) when all histogram analyses methods were applied together in the MLR. Highest classification power among individually applied methods was found using the HFS concept (OCA 86%; sens 0.93; spec 0.79; NR 2 0.80). Conventional methods achieved lower classification potential on their own: EI (OCA 69%; sens 0.95; spec 0.26; NR 2 0.52); PV (OCA 69%; sens 0.90; spec 0.37; NR 2 0.57); MV (OCA 65%; sens 0.71; spec 0.58; NR 2 0.61); V (OCA 66%; sens 0.72; spec 0.53; NR 2 0.66); S (OCA 65%; sens 0.88; spec 0.26; NR 2 0.55); and K (OCA 63%; sens 0.90; spec 0.16; NR 2 0.48). The HFS method, which was so far applied to a CT bone density curve analysis, is also a remarkable information extraction tool for lung density histograms. Presumably, being a principle mathematical approach, the HFS method can extract valuable health related information also from histograms from complete different areas

  16. 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

  17. TU-H-CAMPUS-IeP1-04: Combined Organ Dose for Digital Subtraction Angiography and Computed Tomography Using Monte Carlo Simulation

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Sakabe, D; Ohno, T; Araki, F

    Purpose: The purpose of this study was to evaluate the combined organ dose of digital subtraction angiography (DSA) and computed tomography (CT) using a Monte Carlo (MC) simulation on the abdominal intervention. Methods: The organ doses for DSA and CT were obtained with MC simulation and actual measurements using fluorescent-glass dosimeters at 7 abdominal portions in an Alderson-Rando phantom. DSA was performed from three directions: posterior anterior (PA), right anterior oblique (RAO), and left anterior oblique (LAO). The organ dose with MC simulation was compared with actual radiation dose measurements. Calculations for the MC simulation were carried out with themore » GMctdospp (IMPS, Germany) software based on the EGSnrc MC code. Finally, the combined organ dose for DSA and CT was calculated from the MC simulation using the X-ray conditions of a patient with a diagnosis of hepatocellular carcinoma. Results: For DSA from the PA direction, the organ doses for the actual measurements and MC simulation were 2.2 and 2.4 mGy/100 mAs at the liver, respectively, and 3.0 and 3.1 mGy/100 mAs at the spinal cord, while for CT, the organ doses were 15.2 and 15.1 mGy/100 mAs at the liver, and 14.6 and 13.5 mGy/100 mAs at the spinal cord. The maximum difference in organ dose between the actual measurements and the MC simulation was 11.0% of the spleen at PA, 8.2% of the spinal cord at RAO, and 6.1% of left kidney at LAO with DSA and 9.3% of the stomach with CT. The combined organ dose (4 DSAs and 6 CT scans) with the use of actual patient conditions was found to be 197.4 mGy for the liver and 205.1 mGy for the spinal cord. Conclusion: Our method makes it possible to accurately assess the organ dose to patients for abdominal intervention with combined DSA and CT.« less

  18. Gate Set Tomography on two qubits

    NASA Astrophysics Data System (ADS)

    Nielsen, Erik; Blume-Kohout, Robin; Gamble, John; Rudinger, Kenneth

    Gate set tomography (GST) is a method for characterizing quantum gates that does not require pre-calibrated operations, and has been used to both certify and improve the operation of single qubits. We analyze the performance of GST applied to a simulated two-qubit system, and show that Heisenberg scaling is achieved in this case. We present a GST analysis of preliminary two-qubit experimental data, and draw comparisons with the simulated data case. Finally, we will discuss recent theoretical developments that have improved the efficiency of GST estimation procedures, and which are particularly beneficial when characterizing two qubit systems. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under Contract DE-AC04-94AL85000.

  19. Ultralow dose computed tomography attenuation correction for pediatric PET CT using adaptive statistical iterative reconstruction

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Brady, Samuel L., E-mail: samuel.brady@stjude.org; Shulkin, Barry L.

    2015-02-15

    Purpose: To develop ultralow dose computed tomography (CT) attenuation correction (CTAC) acquisition protocols for pediatric positron emission tomography CT (PET CT). Methods: A GE Discovery 690 PET CT hybrid scanner was used to investigate the change to quantitative PET and CT measurements when operated at ultralow doses (10–35 mA s). CT quantitation: noise, low-contrast resolution, and CT numbers for 11 tissue substitutes were analyzed in-phantom. CT quantitation was analyzed to a reduction of 90% volume computed tomography dose index (0.39/3.64; mGy) from baseline. To minimize noise infiltration, 100% adaptive statistical iterative reconstruction (ASiR) was used for CT reconstruction. PET imagesmore » were reconstructed with the lower-dose CTAC iterations and analyzed for: maximum body weight standardized uptake value (SUV{sub bw}) of various diameter targets (range 8–37 mm), background uniformity, and spatial resolution. Radiation dose and CTAC noise magnitude were compared for 140 patient examinations (76 post-ASiR implementation) to determine relative dose reduction and noise control. Results: CT numbers were constant to within 10% from the nondose reduced CTAC image for 90% dose reduction. No change in SUV{sub bw}, background percent uniformity, or spatial resolution for PET images reconstructed with CTAC protocols was found down to 90% dose reduction. Patient population effective dose analysis demonstrated relative CTAC dose reductions between 62% and 86% (3.2/8.3–0.9/6.2). Noise magnitude in dose-reduced patient images increased but was not statistically different from predose-reduced patient images. Conclusions: Using ASiR allowed for aggressive reduction in CT dose with no change in PET reconstructed images while maintaining sufficient image quality for colocalization of hybrid CT anatomy and PET radioisotope uptake.« less

  20. Tropospheric wet refractivity tomography using multiplicative algebraic reconstruction technique

    NASA Astrophysics Data System (ADS)

    Xiaoying, Wang; Ziqiang, Dai; Enhong, Zhang; Fuyang, K. E.; Yunchang, Cao; Lianchun, Song

    2014-01-01

    Algebraic reconstruction techniques (ART) have been successfully used to reconstruct the total electron content (TEC) of the ionosphere and in recent years be tentatively used in tropospheric wet refractivity and water vapor tomography in the ground-based GNSS technology. The previous research on ART used in tropospheric water vapor tomography focused on the convergence and relaxation parameters for various algebraic reconstruction techniques and rarely discussed the impact of Gaussian constraints and initial field on the iteration results. The existing accuracy evaluation parameters calculated from slant wet delay can only evaluate the resultant precision of the voxels penetrated by slant paths and cannot evaluate that of the voxels not penetrated by any slant path. The paper proposes two new statistical parameters Bias and RMS, calculated from wet refractivity of the total voxels, to improve the deficiencies of existing evaluation parameters and then discusses the effect of the Gaussian constraints and initial field on the convergence and tomography results in multiplicative algebraic reconstruction technique (MART) to reconstruct the 4D tropospheric wet refractivity field using simulation method.

  1. Quantitative radiomics: impact of stochastic effects on textural feature analysis implies the need for standards

    PubMed Central

    Nyflot, Matthew J.; Yang, Fei; Byrd, Darrin; Bowen, Stephen R.; Sandison, George A.; Kinahan, Paul E.

    2015-01-01

    Abstract. Image heterogeneity metrics such as textural features are an active area of research for evaluating clinical outcomes with positron emission tomography (PET) imaging and other modalities. However, the effects of stochastic image acquisition noise on these metrics are poorly understood. We performed a simulation study by generating 50 statistically independent PET images of the NEMA IQ phantom with realistic noise and resolution properties. Heterogeneity metrics based on gray-level intensity histograms, co-occurrence matrices, neighborhood difference matrices, and zone size matrices were evaluated within regions of interest surrounding the lesions. The impact of stochastic variability was evaluated with percent difference from the mean of the 50 realizations, coefficient of variation and estimated sample size for clinical trials. Additionally, sensitivity studies were performed to simulate the effects of patient size and image reconstruction method on the quantitative performance of these metrics. Complex trends in variability were revealed as a function of textural feature, lesion size, patient size, and reconstruction parameters. In conclusion, the sensitivity of PET textural features to normal stochastic image variation and imaging parameters can be large and is feature-dependent. Standards are needed to ensure that prospective studies that incorporate textural features are properly designed to measure true effects that may impact clinical outcomes. PMID:26251842

  2. Quantitative radiomics: impact of stochastic effects on textural feature analysis implies the need for standards.

    PubMed

    Nyflot, Matthew J; Yang, Fei; Byrd, Darrin; Bowen, Stephen R; Sandison, George A; Kinahan, Paul E

    2015-10-01

    Image heterogeneity metrics such as textural features are an active area of research for evaluating clinical outcomes with positron emission tomography (PET) imaging and other modalities. However, the effects of stochastic image acquisition noise on these metrics are poorly understood. We performed a simulation study by generating 50 statistically independent PET images of the NEMA IQ phantom with realistic noise and resolution properties. Heterogeneity metrics based on gray-level intensity histograms, co-occurrence matrices, neighborhood difference matrices, and zone size matrices were evaluated within regions of interest surrounding the lesions. The impact of stochastic variability was evaluated with percent difference from the mean of the 50 realizations, coefficient of variation and estimated sample size for clinical trials. Additionally, sensitivity studies were performed to simulate the effects of patient size and image reconstruction method on the quantitative performance of these metrics. Complex trends in variability were revealed as a function of textural feature, lesion size, patient size, and reconstruction parameters. In conclusion, the sensitivity of PET textural features to normal stochastic image variation and imaging parameters can be large and is feature-dependent. Standards are needed to ensure that prospective studies that incorporate textural features are properly designed to measure true effects that may impact clinical outcomes.

  3. Recent developments in guided wave travel time tomography

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Zon, Tim van; Volker, Arno

    The concept of predictive maintenance using permanent sensors that monitor the integrity of an installation is an interesting addition to the current method of periodic inspections. Guided wave tomography had been developed to create a map of the wall thickness using the travel times of guided waves. It can be used for both monitoring and for inspection of pipe-segments that are difficult to access, for instance at the location of pipe-supports. An important outcome of the tomography is the minimum remaining wall thickness, as this is critical in the scheduling of a replacement of the pipe-segment. In order to improvemore » the sizing accuracy we have improved the tomography scheme. A number of major improvements have been realized allowing to extend the application envelope to pipes with a larger wall thickness and to larger distances between the transducer rings. Simulation results indicate that the sizing accuracy has improved and that is now possible to have a spacing of 8 meter between the source-ring and the receiver-ring. Additionally a reduction of the number of sensors required might be possible as well.« less

  4. Assessment of radiation exposure in dental cone-beam computerized tomography with the use of metal-oxide semiconductor field-effect transistor (MOSFET) dosimeters and Monte Carlo simulations.

    PubMed

    Koivisto, J; Kiljunen, T; Tapiovaara, M; Wolff, J; Kortesniemi, M

    2012-09-01

    The aims of this study were to assess the organ and effective dose (International Commission on Radiological Protection (ICRP) 103) resulting from dental cone-beam computerized tomography (CBCT) imaging using a novel metal-oxide semiconductor field-effect transistor (MOSFET) dosimeter device, and to assess the reliability of the MOSFET measurements by comparing the results with Monte Carlo PCXMC simulations. Organ dose measurements were performed using 20 MOSFET dosimeters that were embedded in the 8 most radiosensitive organs in the maxillofacial and neck area. The dose-area product (DAP) values attained from CBCT scans were used for PCXMC simulations. The acquired MOSFET doses were then compared with the Monte Carlo simulations. The effective dose measurements using MOSFET dosimeters yielded, using 0.5-cm steps, a value of 153 μSv and the PCXMC simulations resulted in a value of 136 μSv. The MOSFET dosimeters placed in a head phantom gave results similar to Monte Carlo simulations. Minor vertical changes in the positioning of the phantom had a substantial affect on the overall effective dose. Therefore, the MOSFET dosimeters constitute a feasible method for dose assessment of CBCT units in the maxillofacial region. Copyright © 2012 Elsevier Inc. All rights reserved.

  5. Analysis and an image recovery algorithm for ultrasonic tomography system

    NASA Technical Reports Server (NTRS)

    Jin, Michael Y.

    1994-01-01

    The problem of an ultrasonic reflectivity tomography is similar to that of a spotlight-mode aircraft Synthetic Aperture Radar (SAR) system. The analysis for a circular path spotlight mode SAR in this paper leads to the insight of the system characteristics. It indicates that such a system when operated in a wide bandwidth is capable of achieving the ultimate resolution; one quarter of the wavelength of the carrier frequency. An efficient processing algorithm based on the exact two dimensional spectrum is presented. The results of simulation indicate that the impulse responses meet the predicted resolution performance. Compared to an algorithm previously developed for the ultrasonic reflectivity tomography, the throughput rate of this algorithm is about ten times higher.

  6. Testing the Proterozoic GAD Hypothesis with Reconstructed Tomography Dynamo Models

    NASA Astrophysics Data System (ADS)

    Panzik, J. E.; Driscoll, P. E.; Rudolph, M. L.

    2014-12-01

    Pre-Mesozoic continental reconstructions and paleoclimatic inferences from paleomagnetism rely critically upon the assumption of a time-averaged geocentric axial dipole (GAD) magnetic field. Though the geomagnetic field of the past 5 myr has been extensively studied and small geometric variations are being refined (e.g., Johnson et al., 2008, GGG 9), the pre-Mesozoic geomagnetic field geometry remains unresolved and is suggested to have large, non-dipolar contributions (e.g. Kent and Smethurst, 1998, EPSL 160, 391-402). We address the paleo-morphology by looking at inclination versus paleolatitude histograms derived from numerical geodynamo simulations with spatially variable CMB heat flux, similar to the method used by Bloxham (2000, Nature 405, 63-65). We will be using homogeneous heat flux simulations as a standard and compare the results to those of a present day tomography and a reconstracted 200 Ma tomography CMB heat flux. By comparing the relative contribution of non-dipolar components to the dipole field, we find that strong CMB heat flux heterogeneity is necessary to create the large non-dipolar contributions inferred for the paleomagnetic field.

  7. Representation of photon limited data in emission tomography using origin ensembles

    NASA Astrophysics Data System (ADS)

    Sitek, A.

    2008-06-01

    Representation and reconstruction of data obtained by emission tomography scanners are challenging due to high noise levels in the data. Typically, images obtained using tomographic measurements are represented using grids. In this work, we define images as sets of origins of events detected during tomographic measurements; we call these origin ensembles (OEs). A state in the ensemble is characterized by a vector of 3N parameters Y, where the parameters are the coordinates of origins of detected events in a three-dimensional space and N is the number of detected events. The 3N-dimensional probability density function (PDF) for that ensemble is derived, and we present an algorithm for OE image estimation from tomographic measurements. A displayable image (e.g. grid based image) is derived from the OE formulation by calculating ensemble expectations based on the PDF using the Markov chain Monte Carlo method. The approach was applied to computer-simulated 3D list-mode positron emission tomography data. The reconstruction errors for a 10 000 000 event acquisition for simulated ranged from 0.1 to 34.8%, depending on object size and sampling density. The method was also applied to experimental data and the results of the OE method were consistent with those obtained by a standard maximum-likelihood approach. The method is a new approach to representation and reconstruction of data obtained by photon-limited emission tomography measurements.

  8. Early Dose Response to Yttrium-90 Microsphere Treatment of Metastatic Liver Cancer by a Patient-Specific Method Using Single Photon Emission Computed Tomography and Positron Emission Tomography

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Campbell, Janice M.; Department of Radiation Oncology, Wayne State University, Detroit, MI; Wong, C. Oliver

    2009-05-01

    Purpose: To evaluate a patient-specific single photon emission computed tomography (SPECT)-based method of dose calculation for treatment planning of yttrium-90 ({sup 90}Y) microsphere selective internal radiotherapy (SIRT). Methods and Materials: Fourteen consecutive {sup 90}Y SIRTs for colorectal liver metastasis were retrospectively analyzed. Absorbed dose to tumor and normal liver tissue was calculated by partition methods with two different tumor/normal liver vascularity ratios: an average 3:1 and a patient-specific ratio derived from pretreatment technetium-99m macroaggregated albumin SPECT. Tumor response was quantitatively evaluated from fluorine-18 fluoro-2-deoxy-D-glucose positron emission tomography scans. Results: Positron emission tomography showed a significant decrease in total tumor standardizedmore » uptake value (average, 52%). There was a significant difference in the tumor absorbed dose between the average and specific methods (p = 0.009). Response vs. dose curves fit by linear and linear-quadratic modeling showed similar results. Linear fit r values increased for all tumor response parameters with the specific method (+0.20 for mean standardized uptake value). Conclusion: Tumor dose calculated with the patient-specific method was more predictive of response in liver-directed {sup 90}Y SIRT.« less

  9. Extinction measurement of dense media by an optical coherence tomography technique

    NASA Astrophysics Data System (ADS)

    Ago, Tomoki; Iwai, Toshiaki; Yokota, Ryoko

    2016-10-01

    The optical coherence tomography will make progress as the next stage toward a spectroscopic analysis technique. The spectroscopic analysis is based on the Beer-Lambert law. The absorption and scattering coefficients even for the dense medium can be measured by the Beer-Lambert law because the OCT can detect only the light keeping the coherency which propagated rectilinearly and retro-reflected from scatters. This study is concerned with the quantitative verification of Beer-Lambert law in the OCT imaging.

  10. 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.

  11. Quantitative wood–adhesive penetration with X-ray computed tomography

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Paris, Jesse L.; Kamke, Frederick A.

    Micro X-ray computed tomography (XCT) was used to analyze the 3D adhesive penetration behavior of different wood–adhesive bondlines. Three adhesives, a phenol formaldehyde (PF), a polymeric diphenylmethane diisocyanate (pMDI), and a hybrid polyvinyl acetate (PVA), all tagged with iodine for enhanced X-ray attenuation, were used to prepare single-bondline laminates in two softwoods, Douglas-fir and loblolly pine, and one hardwood, a hybrid polar. Adhesive penetration depth was measured with two separate calculations, and results were compared with 2D fluorescent micrographs. A total of 54 XCT scans were collected, representing six replicates of each treatment type; each replicate, however, consisted of approximatelymore » 1500 individual, cross-section slices stacked along the specimen length. As these adhesives were highly modified, the presented results do not indicate typical behavior for their broader adhesive classes. Still, clear penetration differences were observed between each adhesive type, and between wood species bonded with both the PF and pMDI adhesives. Furthermore, penetration results depended on the calculation method used. Two adhesive types with noticeably different resin distributions in the cured bondline, showed relatively similar penetration depths when calculated with a traditional effective penetration equation. However, when the same data was calculated with a weighted penetration calculation, which accounts for both adhesive area and depth, the results appeared to better represent the different distributions depicted in the photomicrographs and tomograms. Additionally, individual replicate comparisons showed variation due to specimen anatomy, not easily observed or interpreted from 2D images. Finally, 3D views of segmented 3D adhesive phases offered unique, in-situ views of the cured adhesive structures. In particular, voids formed by CO 2 bubbles generated during pMDI cure were clearly visible in penetrated columns of the solidified

  12. Quantitative analysis of skeletal muscle mass in patients with rheumatic diseases under glucocorticoid therapy--comparison among bioelectrical impedance analysis, computed tomography, and magnetic resonance imaging.

    PubMed

    Hosono, Osamu; Yoshikawa, Noritada; Shimizu, Noriaki; Kiryu, Shigeru; Uehara, Masaaki; Kobayashi, Hiroshi; Matsumiya, Ryo; Kuribara, Akiko; Maruyama, Takako; Tanaka, Hirotoshi

    2015-03-01

    To determine the availability of bioelectrical impedance analysis (BIA), computed tomography (CT), and magnetic resonance imaging (MRI) for measurement of skeletal muscle mass in patients with rheumatic diseases and quantitatively assess skeletal muscle loss after glucocorticoid (GC) treatment. The data from 22 patients with rheumatic diseases were retrospectively obtained. The muscle mass of body segments was measured with a BIA device in terms of skeletal muscle mass index (SMI). Cross-sectional area (CSA) was obtained from CT and MRI scans at the mid-thigh level using the image analysis program. We further assessed the data of three different measurements before and after GC treatment in 7 patients with rheumatic diseases. SMI of whole body was significantly correlated with estimated muscle volume and mid-thigh muscle CSA with CT and MRI (p < 0.01). Significant correlations between SMI and mid-thigh muscle CSA of each leg were also found (p < 0.01). All the three measurements were negatively correlated with GC dosage (p < 0.01). Significant decline in mid-thigh muscle CSA with CT and MRI was found after GC treatment in 7 patients (p < 0.02). Those patients showed significant decline in SMI of whole body after GC treatment, but not in SMI of each leg. On the other hand, significant correlations between mid-thigh muscle CSA with CT and MRI were found before and after GC treatment (p < 0.01). GC-related skeletal muscle loss could be quantitatively assessed with BIA, CT, or MRI in patients with rheumatic diseases, and CT and MRI appeared to be more accurate than BIA.

  13. Tomography and generative training with quantum Boltzmann machines

    NASA Astrophysics Data System (ADS)

    Kieferová, Mária; Wiebe, Nathan

    2017-12-01

    The promise of quantum neural nets, which utilize quantum effects to model complex data sets, has made their development an aspirational goal for quantum machine learning and quantum computing in general. Here we provide methods of training quantum Boltzmann machines. Our work generalizes existing methods and provides additional approaches for training quantum neural networks that compare favorably to existing methods. We further demonstrate that quantum Boltzmann machines enable a form of partial quantum state tomography that further provides a generative model for the input quantum state. Classical Boltzmann machines are incapable of this. This verifies the long-conjectured connection between tomography and quantum machine learning. Finally, we prove that classical computers cannot simulate our training process in general unless BQP=BPP , provide lower bounds on the complexity of the training procedures and numerically investigate training for small nonstoquastic Hamiltonians.

  14. Deterministic absorbed dose estimation in computed tomography using a discrete ordinates method

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Norris, Edward T.; Liu, Xin, E-mail: xinliu@mst.edu; Hsieh, Jiang

    Purpose: Organ dose estimation for a patient undergoing computed tomography (CT) scanning is very important. Although Monte Carlo methods are considered gold-standard in patient dose estimation, the computation time required is formidable for routine clinical calculations. Here, the authors instigate a deterministic method for estimating an absorbed dose more efficiently. Methods: Compared with current Monte Carlo methods, a more efficient approach to estimating the absorbed dose is to solve the linear Boltzmann equation numerically. In this study, an axial CT scan was modeled with a software package, Denovo, which solved the linear Boltzmann equation using the discrete ordinates method. Themore » CT scanning configuration included 16 x-ray source positions, beam collimators, flat filters, and bowtie filters. The phantom was the standard 32 cm CT dose index (CTDI) phantom. Four different Denovo simulations were performed with different simulation parameters, including the number of quadrature sets and the order of Legendre polynomial expansions. A Monte Carlo simulation was also performed for benchmarking the Denovo simulations. A quantitative comparison was made of the simulation results obtained by the Denovo and the Monte Carlo methods. Results: The difference in the simulation results of the discrete ordinates method and those of the Monte Carlo methods was found to be small, with a root-mean-square difference of around 2.4%. It was found that the discrete ordinates method, with a higher order of Legendre polynomial expansions, underestimated the absorbed dose near the center of the phantom (i.e., low dose region). Simulations of the quadrature set 8 and the first order of the Legendre polynomial expansions proved to be the most efficient computation method in the authors’ study. The single-thread computation time of the deterministic simulation of the quadrature set 8 and the first order of the Legendre polynomial expansions was 21 min on a personal

  15. Robust membrane detection based on tensor voting for electron tomography.

    PubMed

    Martinez-Sanchez, Antonio; Garcia, Inmaculada; Asano, Shoh; Lucic, Vladan; Fernandez, Jose-Jesus

    2014-04-01

    Electron tomography enables three-dimensional (3D) visualization and analysis of the subcellular architecture at a resolution of a few nanometers. Segmentation of structural components present in 3D images (tomograms) is often necessary for their interpretation. However, it is severely hampered by a number of factors that are inherent to electron tomography (e.g. noise, low contrast, distortion). Thus, there is a need for new and improved computational methods to facilitate this challenging task. In this work, we present a new method for membrane segmentation that is based on anisotropic propagation of the local structural information using the tensor voting algorithm. The local structure at each voxel is then refined according to the information received from other voxels. Because voxels belonging to the same membrane have coherent structural information, the underlying global structure is strengthened. In this way, local information is easily integrated at a global scale to yield segmented structures. This method performs well under low signal-to-noise ratio typically found in tomograms of vitrified samples under cryo-tomography conditions and can bridge gaps present on membranes. The performance of the method is demonstrated by applications to tomograms of different biological samples and by quantitative comparison with standard template matching procedure. Copyright © 2014 Elsevier Inc. All rights reserved.

  16. Quantitative computed tomography determined regional lung mechanics in normal nonsmokers, normal smokers and metastatic sarcoma subjects.

    PubMed

    Choi, Jiwoong; Hoffman, Eric A; Lin, Ching-Long; Milhem, Mohammed M; Tessier, Jean; Newell, John D

    2017-01-01

    Extra-thoracic tumors send out pilot cells that attach to the pulmonary endothelium. We hypothesized that this could alter regional lung mechanics (tissue stiffening or accumulation of fluid and inflammatory cells) through interactions with host cells. We explored this with serial inspiratory computed tomography (CT) and image matching to assess regional changes in lung expansion. We retrospectively assessed 44 pairs of two serial CT scans on 21 sarcoma patients: 12 without lung metastases and 9 with lung metastases. For each subject, two or more serial inspiratory clinically-derived CT scans were retrospectively collected. Two research-derived control groups were included: 7 normal nonsmokers and 12 asymptomatic smokers with two inspiratory scans taken the same day or one year apart respectively. We performed image registration for local-to-local matching scans to baseline, and derived local expansion and density changes at an acinar scale. Welch two sample t test was used for comparison between groups. Statistical significance was determined with a p value < 0.05. Lung regions of metastatic sarcoma patients (but not the normal control group) demonstrated an increased proportion of normalized lung expansion between the first and second CT. These hyper-expanded regions were associated with, but not limited to, visible metastatic lung lesions. Compared with the normal control group, the percent of increased normalized hyper-expanded lung in sarcoma subjects was significantly increased (p < 0.05). There was also evidence of increased lung "tissue" volume (non-air components) in the hyper-expanded regions of the cancer subjects relative to non-hyper-expanded regions. "Tissue" volume increase was present in the hyper-expanded regions of metastatic and non-metastatic sarcoma subjects. This putatively could represent regional inflammation related to the presence of tumor pilot cell-host related interactions. This new quantitative CT (QCT) method for linking serial

  17. Muon Tomography for Geological Repositories.

    NASA Astrophysics Data System (ADS)

    Woodward, D.; Kudryavtsev, V.; Gluyas, J.; Clark, S. J.; Thompson, L. F.; Klinger, J.; Spooner, N. J.; Blackwell, T. B.; Pal, S.; Lincoln, D. L.; Paling, S. M.; Mitchell, C. N.; Benton, C.; Coleman, M. L.; Telfer, S.; Cole, A.; Nolan, S.; Chadwick, P.

    2015-12-01

    Cosmic-ray muons are subatomic particles produced in the upper atmosphere in collisions of primary cosmic rays with atoms in air. Due to their high penetrating power these muons can be used to image the content (primarily density) of matter they pass through. They have already been used to image the structure of pyramids, volcanoes and other objects. Their applications can be extended to investigating the structure of, and monitoring changes in geological formations and repositories, in particular deep subsurface sites with stored CO2. Current methods of monitoring subsurface CO2, such as repeat seismic surveys, are episodic and require highly skilled personnel to operate. Our simulations based on simplified models have previously shown that muon tomography could be used to continuously monitor CO2 injection and migration and complement existing technologies. Here we present a simulation of the monitoring of CO2 plume evolution in a geological reservoir using muon tomography. The stratigraphy in the vicinity of the reservoir is modelled using geological data, and a numerical fluid flow model is used to describe the time evolution of the CO2 plume. A planar detection region with a surface area of 1000 m2 is considered, at a vertical depth of 776 m below the seabed. We find that one year of constant CO2 injection leads to changes in the column density of about 1%, and that the CO2 plume is already resolvable with an exposure time of less than 50 days. The attached figure show a map of CO2 plume in angular coordinates as reconstructed from observed muons. In parallel with simulation efforts, a small prototype muon detector has been designed, built and tested in a deep subsurface laboratory. Initial calibrations of the detector have shown that it can reach the required angular resolution for muon detection. Stable operation in a small borehole within a few months has been demonstrated.

  18. On the use of GPS tomography to investigate water vapor variability during a Mistral/sea breeze event in southeastern France

    NASA Astrophysics Data System (ADS)

    Bastin, Sophie; Champollion, Cédric; Bock, Olivier; Drobinski, Philippe; Masson, Frédéric

    2005-03-01

    Global Positioning System (GPS) tomography analyses of water vapor, complemented by high-resolution numerical simulations are used to investigate a Mistral/sea breeze event in the region of Marseille, France, during the ESCOMPTE experiment. This is the first time GPS tomography has been used to validate the three-dimensional water vapor concentration from numerical simulation, and to analyze a small-scale meteorological event. The high spatial and temporal resolution of GPS analyses provides a unique insight into the evolution of the vertical and horizontal distribution of water vapor during the Mistral/sea-breeze transition.

  19. Diffuse optical correlation tomography of cerebral blood flow during cortical spreading depression in rat brain

    NASA Astrophysics Data System (ADS)

    Zhou, Chao; Yu, Guoqiang; Furuya, Daisuke; Greenberg, Joel; Yodh, Arjun; Durduran, Turgut

    2006-02-01

    Diffuse optical correlation methods were adapted for three-dimensional (3D) tomography of cerebral blood flow (CBF) in small animal models. The image reconstruction was optimized using a noise model for diffuse correlation tomography which enabled better data selection and regularization. The tomographic approach was demonstrated with simulated data and during in-vivo cortical spreading depression (CSD) in rat brain. Three-dimensional images of CBF were obtained through intact skull in tissues(~4mm) deep below the cortex.

  20. Anthropomorphic thorax phantom for cardio-respiratory motion simulation in tomographic imaging

    NASA Astrophysics Data System (ADS)

    Bolwin, Konstantin; Czekalla, Björn; Frohwein, Lynn J.; Büther, Florian; Schäfers, Klaus P.

    2018-02-01

    Patient motion during medical imaging using techniques such as computed tomography (CT), magnetic resonance imaging (MRI), positron emission tomography (PET), or single emission computed tomography (SPECT) is well known to degrade images, leading to blurring effects or severe artifacts. Motion correction methods try to overcome these degrading effects. However, they need to be validated under realistic conditions. In this work, a sophisticated anthropomorphic thorax phantom is presented that combines several aspects of a simulator for cardio-respiratory motion. The phantom allows us to simulate various types of cardio-respiratory motions inside a human-like thorax, including features such as inflatable lungs, beating left ventricular myocardium, respiration-induced motion of the left ventricle, moving lung lesions, and moving coronary artery plaques. The phantom is constructed to be MR-compatible. This means that we can not only perform studies in PET, SPECT and CT, but also inside an MRI system. The technical features of the anthropomorphic thorax phantom Wilhelm are presented with regard to simulating motion effects in hybrid emission tomography and radiotherapy. This is supplemented by a study on the detectability of small coronary plaque lesions in PET/CT under the influence of cardio-respiratory motion, and a study on the accuracy of left ventricular blood volumes.

  1. Application of X-ray phase contrast micro-tomography to the identification of traditional Chinese medicines

    NASA Astrophysics Data System (ADS)

    Ye, L. L.; Xue, Y. L.; Ni, L. H.; Tan, H.; Wang, Y. D.; Xiao, T. Q.

    2013-07-01

    Nondestructive and in situ investigation to the characteristic microstructures are important to the identification of traditional Chinese medicines (TCMs), especially for precious specimens and samples with oil contains. X-ray phase contrast micro-tomography (XPCMT) could be a practical solution for this kind of investigation. Fructus Foeniculi, a fruit kind of TCMs, is selected as the test sample. Experimental results show that the characteristic microstructures of Fructus Foeniculi, including vittae, vascular bundles, embryo, endosperm and the mesocarp reticulate cells around the vittae can be clearly distinguished and the integrated dissepiments microstructure in the vittae was observed successfully. Especially, for the first time, with virtual slice technique, it can investigate the liquid contains inside the TCMs. The results show that the vittae filled with volatile oil in the oil chamber were observed with this nondestructive and in situ 3-dimensional imaging technique. Furthermore, taking the advantage of micro-computed tomography, we can obtain the characteristic microstructures' quantitative information of the volume in liquid state. The volume of the oil chambers and the volatile oil, which are contained inside the vittae, was quantitatively analyzed. Accordingly, it can calculate the volume ratio of the volatile oil easily and accurately. As a result, we could conclude that XPCMT could be a useful tool for the nondestructive identification and quantitative analysis to TCMs.

  2. Measurement of tracer gas distributions using an open-path FTIR system coupled with computed tomography

    NASA Astrophysics Data System (ADS)

    Drescher, Anushka C.; Yost, Michael G.; Park, Doo Y.; Levine, Steven P.; Gadgil, Ashok J.; Fischer, Marc L.; Nazaroff, William W.

    1995-05-01

    Optical remote sensing and iterative computed tomography (CT) can be combined to measure the spatial distribution of gaseous pollutant concentrations in a plane. We have conducted chamber experiments to test this combination of techniques using an Open Path Fourier Transform Infrared Spectrometer (OP-FTIR) and a standard algebraic reconstruction technique (ART). ART was found to converge to solutions that showed excellent agreement with the ray integral concentrations measured by the FTIR but were inconsistent with simultaneously gathered point sample concentration measurements. A new CT method was developed based on (a) the superposition of bivariate Gaussians to model the concentration distribution and (b) a simulated annealing minimization routine to find the parameters of the Gaussians that resulted in the best fit to the ray integral concentration data. This new method, named smooth basis function minimization (SBFM) generated reconstructions that agreed well, both qualitatively and quantitatively, with the concentration profiles generated from point sampling. We present one set of illustrative experimental data to compare the performance of ART and SBFM.

  3. Simulated lumbar minimally invasive surgery educational model with didactic and technical components.

    PubMed

    Chitale, Rohan; Ghobrial, George M; Lobel, Darlene; Harrop, James

    2013-10-01

    The learning and development of technical skills are paramount for neurosurgical trainees. External influences and a need for maximizing efficiency and proficiency have encouraged advancements in simulator-based learning models. To confirm the importance of establishing an educational curriculum for teaching minimally invasive techniques of pedicle screw placement using a computer-enhanced physical model of percutaneous pedicle screw placement with simultaneous didactic and technical components. A 2-hour educational curriculum was created to educate neurosurgical residents on anatomy, pathophysiology, and technical aspects associated with image-guided pedicle screw placement. Predidactic and postdidactic practical and written scores were analyzed and compared. Scores were calculated for each participant on the basis of the optimal pedicle screw starting point and trajectory for both fluoroscopy and computed tomographic navigation. Eight trainees participated in this module. Average mean scores on the written didactic test improved from 78% to 100%. The technical component scores for fluoroscopic guidance improved from 58.8 to 52.9. Technical score for computed tomography-navigated guidance also improved from 28.3 to 26.6. Didactic and technical quantitative scores with a simulator-based educational curriculum improved objectively measured resident performance. A minimally invasive spine simulation model and curriculum may serve a valuable function in the education of neurosurgical residents and outcomes for patients.

  4. Effects of Scan Resolutions and Element Sizes on Bovine Vertebral Mechanical Parameters from Quantitative Computed Tomography-Based Finite Element Analysis

    PubMed Central

    Zhang, Meng; Gao, Jiazi; Huang, Xu; Zhang, Min; Liu, Bei

    2017-01-01

    Quantitative computed tomography-based finite element analysis (QCT/FEA) has been developed to predict vertebral strength. However, QCT/FEA models may be different with scan resolutions and element sizes. The aim of this study was to explore the effects of scan resolutions and element sizes on QCT/FEA outcomes. Nine bovine vertebral bodies were scanned using the clinical CT scanner and reconstructed from datasets with the two-slice thickness, that is, 0.6 mm (PA resolution) and 1 mm (PB resolution). There were significantly linear correlations between the predicted and measured principal strains (R2 > 0.7, P < 0.0001), and the predicted vertebral strength and stiffness were modestly correlated with the experimental values (R2 > 0.6, P < 0.05). Two different resolutions and six different element sizes were combined in pairs, and finite element (FE) models of bovine vertebral cancellous bones in the 12 cases were obtained. It showed that the mechanical parameters of FE models with the PB resolution were similar to those with the PA resolution. The computational accuracy of FE models with the element sizes of 0.41 × 0.41 × 0.6 mm3 and 0.41 × 0.41 × 1 mm3 was higher by comparing the apparent elastic modulus and yield strength. Therefore, scan resolution and element size should be chosen optimally to improve the accuracy of QCT/FEA. PMID:29065624

  5. Quantitative analysis of computed tomography images and early detection of cerebral edema for pediatric traumatic brain injury patients: retrospective study.

    PubMed

    Kim, Hakseung; Kim, Gwang-dong; Yoon, Byung C; Kim, Keewon; Kim, Byung-Jo; Choi, Young Hun; Czosnyka, Marek; Oh, Byung-Mo; Kim, Dong-Joo

    2014-10-22

    The purpose of this study was to identify whether the distribution of Hounsfield Unit (HU) values across the intracranial area in computed tomography (CT) images can be used as an effective diagnostic tool for determining the severity of cerebral edema in pediatric traumatic brain injury (TBI) patients. CT images, medical records and radiology reports on 70 pediatric patients were collected. Based on radiology reports and the Marshall classification, the patients were grouped as mild edema patients (n=37) or severe edema patients (n=33). Automated quantitative analysis using unenhanced CT images was applied to eliminate artifacts and identify the difference in HU value distribution across the intracranial area between these groups. The proportion of pixels with HU=17 to 24 was highly correlated with the existence of severe cerebral edema (P<0.01). This proportion was also able to differentiate patients who developed delayed cerebral edema from mild TBI patients. A significant difference between deceased patients and surviving patients in terms of the HU distribution came from the proportion of pixels with HU=19 to HU=23 (P<0.01). The proportion of pixels with an HU value of 17 to 24 in the entire cerebral area of a non-enhanced CT image can be an effective basis for evaluating the severity of cerebral edema. Based on this result, we propose a novel approach for the early detection of severe cerebral edema.

  6. Improving image segmentation performance and quantitative analysis via a computer-aided grading methodology for optical coherence tomography retinal image analysis.

    PubMed

    Debuc, Delia Cabrera; Salinas, Harry M; Ranganathan, Sudarshan; Tátrai, Erika; Gao, Wei; Shen, Meixiao; Wang, Jianhua; Somfai, Gábor M; Puliafito, Carmen A

    2010-01-01

    We demonstrate quantitative analysis and error correction of optical coherence tomography (OCT) retinal images by using a custom-built, computer-aided grading methodology. A total of 60 Stratus OCT (Carl Zeiss Meditec, Dublin, California) B-scans collected from ten normal healthy eyes are analyzed by two independent graders. The average retinal thickness per macular region is compared with the automated Stratus OCT results. Intergrader and intragrader reproducibility is calculated by Bland-Altman plots of the mean difference between both gradings and by Pearson correlation coefficients. In addition, the correlation between Stratus OCT and our methodology-derived thickness is also presented. The mean thickness difference between Stratus OCT and our methodology is 6.53 microm and 26.71 microm when using the inner segment/outer segment (IS/OS) junction and outer segment/retinal pigment epithelium (OS/RPE) junction as the outer retinal border, respectively. Overall, the median of the thickness differences as a percentage of the mean thickness is less than 1% and 2% for the intragrader and intergrader reproducibility test, respectively. The measurement accuracy range of the OCT retinal image analysis (OCTRIMA) algorithm is between 0.27 and 1.47 microm and 0.6 and 1.76 microm for the intragrader and intergrader reproducibility tests, respectively. Pearson correlation coefficients demonstrate R(2)>0.98 for all Early Treatment Diabetic Retinopathy Study (ETDRS) regions. Our methodology facilitates a more robust and localized quantification of the retinal structure in normal healthy controls and patients with clinically significant intraretinal features.

  7. Diagnosis and evaluation of gastric cancer by positron emission tomography

    PubMed Central

    Wu, Chen-Xi; Zhu, Zhao-Hui

    2014-01-01

    Gastric cancer is the second leading cause of cancer mortality worldwide. The diagnosis of gastric cancer has been significantly improved with the broad availability of gastrointestinal endoscopy. Effective technologies for accurate staging and quantitative evaluation are still in demand to merit reasonable treatment and better prognosis for the patients presented with advanced disease. Preoperative staging using conventional imaging tools, such as computed tomography (CT) and endoscopic ultrasonography, is inadequate. Positron emission tomography (PET), using 18F-fluorodeoxyglucose (FDG) as a tracer and integrating CT for anatomic localization, holds a promise to detect unsuspected metastasis and has been extensively used in a variety of malignancies. However, the value of FDG PET/CT in diagnosis and evaluation of gastric cancer is still controversial. This article reviews the current literature in diagnosis, staging, response evaluation, and relapse monitoring of gastric cancer, and discusses the current understanding, improvement, and future prospects in this area. PMID:24782610

  8. Charged-particle emission tomography

    PubMed Central

    Ding, Yijun; Caucci, Luca; Barrett, Harrison H.

    2018-01-01

    Purpose Conventional charged-particle imaging techniques —such as autoradiography —provide only two-dimensional (2D) black ex vivo images of thin tissue slices. In order to get volumetric information, images of multiple thin slices are stacked. This process is time consuming and prone to distortions, as registration of 2D images is required. We propose a direct three-dimensional (3D) autoradiography technique, which we call charged-particle emission tomography (CPET). This 3D imaging technique enables imaging of thick tissue sections, thus increasing laboratory throughput and eliminating distortions due to registration. CPET also has the potential to enable in vivo charged-particle imaging with a window chamber or an endoscope. Methods Our approach to charged-particle emission tomography uses particle-processing detectors (PPDs) to estimate attributes of each detected particle. The attributes we estimate include location, direction of propagation, and/or the energy deposited in the detector. Estimated attributes are then fed into a reconstruction algorithm to reconstruct the 3D distribution of charged-particle-emitting radionuclides. Several setups to realize PPDs are designed. Reconstruction algorithms for CPET are developed. Results Reconstruction results from simulated data showed that a PPD enables CPET if the PPD measures more attributes than just the position from each detected particle. Experiments showed that a two-foil charged-particle detector is able to measure the position and direction of incident alpha particles. Conclusions We proposed a new volumetric imaging technique for charged-particle-emitting radionuclides, which we have called charged-particle emission tomography (CPET). We also proposed a new class of charged-particle detectors, which we have called particle-processing detectors (PPDs). When a PPD is used to measure the direction and/or energy attributes along with the position attributes, CPET is feasible. PMID:28370094

  9. Charged-particle emission tomography.

    PubMed

    Ding, Yijun; Caucci, Luca; Barrett, Harrison H

    2017-06-01

    Conventional charged-particle imaging techniques - such as autoradiography - provide only two-dimensional (2D) black ex vivo images of thin tissue slices. In order to get volumetric information, images of multiple thin slices are stacked. This process is time consuming and prone to distortions, as registration of 2D images is required. We propose a direct three-dimensional (3D) autoradiography technique, which we call charged-particle emission tomography (CPET). This 3D imaging technique enables imaging of thick tissue sections, thus increasing laboratory throughput and eliminating distortions due to registration. CPET also has the potential to enable in vivo charged-particle imaging with a window chamber or an endoscope. Our approach to charged-particle emission tomography uses particle-processing detectors (PPDs) to estimate attributes of each detected particle. The attributes we estimate include location, direction of propagation, and/or the energy deposited in the detector. Estimated attributes are then fed into a reconstruction algorithm to reconstruct the 3D distribution of charged-particle-emitting radionuclides. Several setups to realize PPDs are designed. Reconstruction algorithms for CPET are developed. Reconstruction results from simulated data showed that a PPD enables CPET if the PPD measures more attributes than just the position from each detected particle. Experiments showed that a two-foil charged-particle detector is able to measure the position and direction of incident alpha particles. We proposed a new volumetric imaging technique for charged-particle-emitting radionuclides, which we have called charged-particle emission tomography (CPET). We also proposed a new class of charged-particle detectors, which we have called particle-processing detectors (PPDs). When a PPD is used to measure the direction and/or energy attributes along with the position attributes, CPET is feasible. © 2017 The Authors. Medical Physics published by Wiley Periodicals

  10. Retinal status analysis method based on feature extraction and quantitative grading in OCT images.

    PubMed

    Fu, Dongmei; Tong, Hejun; Zheng, Shuang; Luo, Ling; Gao, Fulin; Minar, Jiri

    2016-07-22

    Optical coherence tomography (OCT) is widely used in ophthalmology for viewing the morphology of the retina, which is important for disease detection and assessing therapeutic effect. The diagnosis of retinal diseases is based primarily on the subjective analysis of OCT images by trained ophthalmologists. This paper describes an OCT images automatic analysis method for computer-aided disease diagnosis and it is a critical part of the eye fundus diagnosis. This study analyzed 300 OCT images acquired by Optovue Avanti RTVue XR (Optovue Corp., Fremont, CA). Firstly, the normal retinal reference model based on retinal boundaries was presented. Subsequently, two kinds of quantitative methods based on geometric features and morphological features were proposed. This paper put forward a retinal abnormal grading decision-making method which was used in actual analysis and evaluation of multiple OCT images. This paper showed detailed analysis process by four retinal OCT images with different abnormal degrees. The final grading results verified that the analysis method can distinguish abnormal severity and lesion regions. This paper presented the simulation of the 150 test images, where the results of analysis of retinal status showed that the sensitivity was 0.94 and specificity was 0.92.The proposed method can speed up diagnostic process and objectively evaluate the retinal status. This paper aims on studies of retinal status automatic analysis method based on feature extraction and quantitative grading in OCT images. The proposed method can obtain the parameters and the features that are associated with retinal morphology. Quantitative analysis and evaluation of these features are combined with reference model which can realize the target image abnormal judgment and provide a reference for disease diagnosis.

  11. Low-dose CT for quantitative analysis in acute respiratory distress syndrome

    PubMed Central

    2013-01-01

    Introduction The clinical use of serial quantitative computed tomography (CT) to characterize lung disease and guide the optimization of mechanical ventilation in patients with acute respiratory distress syndrome (ARDS) is limited by the risk of cumulative radiation exposure and by the difficulties and risks related to transferring patients to the CT room. We evaluated the effects of tube current-time product (mAs) variations on quantitative results in healthy lungs and in experimental ARDS in order to support the use of low-dose CT for quantitative analysis. Methods In 14 sheep chest CT was performed at baseline and after the induction of ARDS via intravenous oleic acid injection. For each CT session, two consecutive scans were obtained applying two different mAs: 60 mAs was paired with 140, 15 or 7.5 mAs. All other CT parameters were kept unaltered (tube voltage 120 kVp, collimation 32 × 0.5 mm, pitch 0.85, matrix 512 × 512, pixel size 0.625 × 0.625 mm). Quantitative results obtained at different mAs were compared via Bland-Altman analysis. Results Good agreement was observed between 60 mAs and 140 mAs and between 60 mAs and 15 mAs (all biases less than 1%). A further reduction of mAs to 7.5 mAs caused an increase in the bias of poorly aerated and nonaerated tissue (-2.9% and 2.4%, respectively) and determined a significant widening of the limits of agreement for the same compartments (-10.5% to 4.8% for poorly aerated tissue and -5.9% to 10.8% for nonaerated tissue). Estimated mean effective dose at 140, 60, 15 and 7.5 mAs corresponded to 17.8, 7.4, 2.0 and 0.9 mSv, respectively. Image noise of scans performed at 140, 60, 15 and 7.5 mAs corresponded to 10, 16, 38 and 74 Hounsfield units, respectively. Conclusions A reduction of effective dose up to 70% has been achieved with minimal effects on lung quantitative results. Low-dose computed tomography provides accurate quantitative results and could be used to characterize lung compartment distribution and

  12. Computed Tomography (CT) - Spine

    MedlinePlus

    ... Resources Professions Site Index A-Z Computed Tomography (CT) - Spine Computed tomography (CT) of the spine is ... of CT Scanning of the Spine? What is CT Scanning of the Spine? Computed tomography, more commonly ...

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  14. Mspire-Simulator: LC-MS shotgun proteomic simulator for creating realistic gold standard data.

    PubMed

    Noyce, Andrew B; Smith, Rob; Dalgleish, James; Taylor, Ryan M; Erb, K C; Okuda, Nozomu; Prince, John T

    2013-12-06

    The most important step in any quantitative proteomic pipeline is feature detection (aka peak picking). However, generating quality hand-annotated data sets to validate the algorithms, especially for lower abundance peaks, is nearly impossible. An alternative for creating gold standard data is to simulate it with features closely mimicking real data. We present Mspire-Simulator, a free, open-source shotgun proteomic simulator that goes beyond previous simulation attempts by generating LC-MS features with realistic m/z and intensity variance along with other noise components. It also includes machine-learned models for retention time and peak intensity prediction and a genetic algorithm to custom fit model parameters for experimental data sets. We show that these methods are applicable to data from three different mass spectrometers, including two fundamentally different types, and show visually and analytically that simulated peaks are nearly indistinguishable from actual data. Researchers can use simulated data to rigorously test quantitation software, and proteomic researchers may benefit from overlaying simulated data on actual data sets.

  15. Time Dependent Tomography of the Solar Corona in Three Spatial Dimensions

    NASA Astrophysics Data System (ADS)

    Butala, M. D.; Frazin, R. A.; Kamalabadi, F.

    2006-12-01

    The combination of the soon to be launched STEREO mission with SOHO will provide scientists with three simultaneous space-borne views of the Sun. The increase in available measurements will reduce the data acquisition time necessary to obtain 3D coronal electron density (N_e) estimates from coronagraph images using a technique called solar rotational tomography (SRT). However, the data acquisition period will still be long enough for the corona to dynamically evolve, requiring time dependent solar tomography. The Kalman filter (KF) would seem to be an ideal computational method for time dependent SRT. Unfortunately, the KF scales poorly with problem size and is, as a result, inapplicable. A Monte Carlo approximation to the KF called the localized ensemble Kalman filter was developed for massive applications and has the promise of making the time dependent estimation of the 3D coronal N_e possible. We present simulations showing that this method will make time dependent tomography in three spatial dimensions computationally feasible.

  16. Diagnostic Yield of Transbronchial Biopsy in Comparison to High Resolution Computerized Tomography in Sarcoidosis Cases

    PubMed

    Akten, H Serpil; Kilic, Hatice; Celik, Bulent; Erbas, Gonca; Isikdogan, Zeynep; Turktas, Haluk; Kokturk, Nurdan

    2018-04-25

    This study aimed to evaluate the diagnostic yield of fiberoptic bronchoscopic (FOB) transbronchial biopsy and its relation with quantitative findings of high resolution computerized tomography (HRCT). A total of 83 patients, 19 males and 64 females with a mean age of 45.1 years diagnosed with sarcoidosis with complete records of high resolution computerized tomography were retrospectively recruited during the time period from Feb 2005 to Jan 2015. High resolution computerized tomography scans were retrospectively assessed in random order by an experienced observer without knowledge of the bronchoscopic results or lung function tests. According to the radiological staging with HRCT, 2.4% of the patients (n=2) were stage 0, 19.3% (n=16) were stage 1, 72.3% (n=60) were stage 2 and 6.0% (n=5) were stage 3. This study showed that transbronchial lung biopsy showed positive results in 39.7% of the stage I or II sarcoidosis patients who were diagnosed by bronchoscopy. Different high resolution computerized tomography patterns and different scores of involvement did make a difference in the diagnostic accuracy of transbronchial biopsy (p=0.007). Creative Commons Attribution License

  17. Optical coherence tomography for diagnosing periodontal disease

    NASA Astrophysics Data System (ADS)

    Colston, Bill W., Jr.; Everett, Matthew J.; Da Silva, Luiz B.; Otis, Linda L.; Nathel, Howard

    1997-05-01

    We have, in this preliminary study, investigated the use of optical coherence tomography for diagnosis of periodontal disease. We took in vitro OCT images of the dental and periodontal tissues from a young pig and compared them to histological sections. These images distinguish tooth and soft tissue relationships that are important in diagnosing and assessing periodontal disease. We have imaged the attachment of gingiva to the tooth surface and located the cemento-enamel junction. This junction is an important reference point for defining attachment level in the diagnosis of periodontal disease. the boundary between enamel and dentin is also visible for most of the length of the anatomical crown, allowing quantitation of enamel thickness and character.

  18. Quantitative Analysis Of Three-dimensional Branching Systems From X-ray Computed Microtomography Data

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    McKinney, Adriana L.; Varga, Tamas

    Branching structures such as lungs, blood vessels and plant roots play a critical role in life. Growth, structure, and function of these branching structures have an immense effect on our lives. Therefore, quantitative size information on such structures in their native environment is invaluable for studying their growth and the effect of the environment on them. X-ray computed tomography (XCT) has been an effective tool for in situ imaging and analysis of branching structures. We developed a costless tool that approximates the surface and volume of branching structures. Our methodology of noninvasive imaging, segmentation and extraction of quantitative information ismore » demonstrated through the analysis of a plant root in its soil medium from 3D tomography data. XCT data collected on a grass specimen was used to visualize its root structure. A suite of open-source software was employed to segment the root from the soil and determine its isosurface, which was used to calculate its volume and surface. This methodology of processing 3D data is applicable to other branching structures even when the structure of interest is of similar x-ray attenuation to its environment and difficulties arise with sample segmentation.« less

  19. Correlation of quantitative computed tomographic subchondral bone density and ash density in horses.

    PubMed

    Drum, M G; Les, C M; Park, R D; Norrdin, R W; McIlwraith, C W; Kawcak, C E

    2009-02-01

    The purpose of this study was to compare subchondral bone density obtained using quantitative computed tomography with ash density values from intact equine joints, and to determine if there are measurable anatomic variations in mean subchondral bone density. Five adult equine metacarpophalangeal joints were scanned with computed tomography (CT), disarticulated, and four 1-cm(3) regions of interest (ROI) cut from the distal third metacarpal bone. Bone cubes were ashed, and percent mineralization and ash density were recorded. Three-dimensional models were created of the distal third metacarpal bone from CT images. Four ROIs were measured on the distal aspect of the third metacarpal bone at axial and abaxial sites of the medial and lateral condyles for correlation with ash samples. Overall correlations of mean quantitative CT (QCT) density with ash density (r=0.82) and percent mineralization (r=0.93) were strong. There were significant differences between abaxial and axial ROIs for mean QCT density, percent bone mineralization and ash density (p<0.05). QCT appears to be a good measure of bone density in equine subchondral bone. Additionally, differences existed between axial and abaxial subchondral bone density in the equine distal third metacarpal bone.

  20. [Image reconstruction of conductivity on magnetoacoustic tomography with magnetic induction].

    PubMed

    Li, Jingyu; Yin, Tao; Liu, Zhipeng; Xu, Guohui

    2010-04-01

    The electric characteristics such as impedance and conductivity of the organization will change in the case where pathological changes occurred in the biological tissue. The change in electric characteristics usually took place before the change in the density of tissues, and also, the difference in electric characteristics such as conductivity between normal tissue and pathological tissue is obvious. The method of magneto-acoustic tomography with magnetic induction is based on the theory of magnetic eddy current induction, the principle of vibration generation and acoustic transmission to get the boundary of the pathological tissue. The pathological change could be inspected by electricity characteristic imaging which is invasive to the tissue. In this study, a two-layer concentric spherical model is established to simulate the malignant tumor tissue surrounded by normal tissue mutual relations of the magneto-sound coupling effect and the coupling equations in the magnetic field are used to get the algorithms for reconstructing the conductivity. Simulation study is conducted to test the proposed model and validate the performance of the reconstructed algorithms. The result indicates that the use of signal processing method in this paper can image the conductivity boundaries of the sample in the scanning cross section. The computer simulating results validate the feasibility of applying the method of magneto-acoustic tomography with magnetic induction for malignant tumor imaging.

  1. 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. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  2. Lensless transport-of-intensity phase microscopy and tomography with a color LED matrix

    NASA Astrophysics Data System (ADS)

    Zuo, Chao; Sun, Jiasong; Zhang, Jialin; Hu, Yan; Chen, Qian

    2015-07-01

    We demonstrate lens-less quantitative phase microscopy and diffraction tomography based on a compact on-chip platform, using only a CMOS image sensor and a programmable color LED array. Based on multi-wavelength transport-of- intensity phase retrieval and multi-angle illumination diffraction tomography, this platform offers high quality, depth resolved images with a lateral resolution of ˜3.7μm and an axial resolution of ˜5μm, over wide large imaging FOV of 24mm2. The resolution and FOV can be further improved by using a larger image sensors with small pixels straightforwardly. This compact, low-cost, robust, portable platform with a decent imaging performance may offer a cost-effective tool for telemedicine needs, or for reducing health care costs for point-of-care diagnostics in resource-limited environments.

  3. Image change detection using paradoxical theory for patient follow-up quantitation and therapy assessment.

    PubMed

    David, Simon; Visvikis, Dimitris; Quellec, Gwénolé; Le Rest, Catherine Cheze; Fernandez, Philippe; Allard, Michèle; Roux, Christian; Hatt, Mathieu

    2012-09-01

    In clinical oncology, positron emission tomography (PET) imaging can be used to assess therapeutic response by quantifying the evolution of semi-quantitative values such as standardized uptake value, early during treatment or after treatment. Current guidelines do not include metabolically active tumor volume (MATV) measurements and derived parameters such as total lesion glycolysis (TLG) to characterize the response to the treatment. To achieve automatic MATV variation estimation during treatment, we propose an approach based on the change detection principle using the recent paradoxical theory, which models imprecision, uncertainty, and conflict between sources. It was applied here simultaneously to pre- and post-treatment PET scans. The proposed method was applied to both simulated and clinical datasets, and its performance was compared to adaptive thresholding applied separately on pre- and post-treatment PET scans. On simulated datasets, the adaptive threshold was associated with significantly higher classification errors than the developed approach. On clinical datasets, the proposed method led to results more consistent with the known partial responder status of these patients. The method requires accurate rigid registration of both scans which can be obtained only in specific body regions and does not explicitly model uptake heterogeneity. In further investigations, the change detection of intra-MATV tracer uptake heterogeneity will be developed by incorporating textural features into the proposed approach.

  4. Joint reconstruction of x-ray fluorescence and transmission tomography

    DOE PAGES

    Di, Zichao; Chen, Si; Hong, Young Pyo; ...

    2017-05-30

    X-ray fluorescence tomography is based on the detection of fluorescence x-ray photons produced following x-ray absorption while a specimen is rotated; it provides information on the 3D distribution of selected elements within a sample. One limitation in the quality of sample recovery is the separation of elemental signals due to the finite energy resolution of the detector. Another limitation is the effect of self-absorption, which can lead to inaccurate results with dense samples. To recover a higher quality elemental map, we combine x-ray fluorescence detection with a second data modality: conventional x-ray transmission tomography using absorption. By using these combinedmore » signals in a nonlinear optimization-based approach, we demonstrate the benefit of our algorithm on real experimental data and obtain an improved quantitative reconstruction of the spatial distribution of dominant elements in the sample. Furthermore, compared with single-modality inversion based on x-ray fluorescence alone, this joint inversion approach reduces ill-posedness and should result in improved elemental quantification and better correction of self-absorption.« less

  5. Joint reconstruction of x-ray fluorescence and transmission tomography

    PubMed Central

    Di, Zichao Wendy; Chen, Si; Hong, Young Pyo; Jacobsen, Chris; Leyffer, Sven; Wild, Stefan M.

    2017-01-01

    X-ray fluorescence tomography is based on the detection of fluorescence x-ray photons produced following x-ray absorption while a specimen is rotated; it provides information on the 3D distribution of selected elements within a sample. One limitation in the quality of sample recovery is the separation of elemental signals due to the finite energy resolution of the detector. Another limitation is the effect of self-absorption, which can lead to inaccurate results with dense samples. To recover a higher quality elemental map, we combine x-ray fluorescence detection with a second data modality: conventional x-ray transmission tomography using absorption. By using these combined signals in a nonlinear optimization-based approach, we demonstrate the benefit of our algorithm on real experimental data and obtain an improved quantitative reconstruction of the spatial distribution of dominant elements in the sample. Compared with single-modality inversion based on x-ray fluorescence alone, this joint inversion approach reduces ill-posedness and should result in improved elemental quantification and better correction of self-absorption. PMID:28788848

  6. Direct conversion semiconductor detectors in positron emission tomography

    NASA Astrophysics Data System (ADS)

    Cates, Joshua W.; Gu, Yi; Levin, Craig S.

    2015-05-01

    Semiconductor detectors are playing an increasing role in ongoing research to improve image resolution, contrast, and quantitative accuracy in preclinical applications of positron emission tomography (PET). These detectors serve as a medium for direct detection of annihilation photons. Early clinical translation of this technology has shown improvements in image quality and tumor delineation for head and neck cancers, relative to conventional scintillator-based systems. After a brief outline of the basics of PET imaging and the physical detection mechanisms for semiconductor detectors, an overview of ongoing detector development work is presented. The capabilities of semiconductor-based PET systems and the current state of these devices are discussed.

  7. Automated choroidal neovascularization detection algorithm for optical coherence tomography angiography.

    PubMed

    Liu, Li; Gao, Simon S; Bailey, Steven T; Huang, David; Li, Dengwang; Jia, Yali

    2015-09-01

    Optical coherence tomography angiography has recently been used to visualize choroidal neovascularization (CNV) in participants with age-related macular degeneration. Identification and quantification of CNV area is important clinically for disease assessment. An automated algorithm for CNV area detection is presented in this article. It relies on denoising and a saliency detection model to overcome issues such as projection artifacts and the heterogeneity of CNV. Qualitative and quantitative evaluations were performed on scans of 7 participants. Results from the algorithm agreed well with manual delineation of CNV area.

  8. 3D quantitative photoacoustic image reconstruction using Monte Carlo method and linearization

    NASA Astrophysics Data System (ADS)

    Okawa, Shinpei; Hirasawa, Takeshi; Tsujita, Kazuhiro; Kushibiki, Toshihiro; Ishihara, Miya

    2018-02-01

    To quantify the functional and structural information of peripheral blood vessels for diagnoses of diseases which affects peripheral blood vessels such as diabetes and peripheral vascular disease, a 3D quantitative photoacoustic tomography (QPAT) reconstructing the optical properties such as the absorption coefficient reflecting microvascular structures and hemoglobin concentration and oxygenation saturation is studied. QPAT image reconstruction algorithms based on radiative transfer equation (RTE) and photon diffusion equation (PDE) have been proposed. However, it is not easy to use RTE in the clinical practice because of the huge computational load and long calculation time. On the other hand, it is always considered problematic to use PDE, because it does not approximate RTE well near the illuminating position. In this study, we developed the 3D QPAT image reconstruction using Monte Carlo (MC) method which approximates RTE better than PDE to reconstruct the optical properties in the region near the illuminating surface. To reduce the calculation time, we applied linearization. The QPAT image reconstruction algorithm with MC method and linearization was examined in numerical simulations and phantom experiment by use of a scanning system with a single probe consisting of P(VDF-TrFE) piezo electric film and optical fiber.

  9. A dual-PIXE tomography setup for reconstruction of Germanium in ICF target

    NASA Astrophysics Data System (ADS)

    Guo, N.; Lu, H. Y.; Wang, Q.; Meng, J.; Gao, D. Z.; Zhang, Y. J.; Liang, X. X.; Zhang, W.; Li, J.; Ma, X. J.; Shen, H.

    2017-08-01

    Inertial Confinement Fusion (ICF) is one type of fusion energy research which could initiate nuclear fusion reactions through heating and compressing thermonuclear fuel. Compared to a pure plastic target, Germanium doping into the CH ablator layer by Glow Discharge Polymer (GDP) technique can increase the ablation velocity and the standoff distance between the ablation front and laser-deposition region. During target fabrication process, quantitative doping of Ge should be accurately controlled. Particle Induced X-ray Emission Tomography (PIXE-T) can make not only quantification of the concentration, but also reconstruction of the spatial distribution of doped element. The Si (Li) detector for PIXE tomography technique had a disadvantage of low counting rate. To make up this deficiency, another detector of Si (Li) with the same configuration positioned at the opposite side with the same detective angle 135° have been implemented. Simultaneously acquired elemental maps of Ge obtained using two detectors may be different because of the X-ray absorption along the X-ray exit route in the target. In this paper, the X-ray detection efficiency is drastically improved by this dual-PIXE tomography system.

  10. Polarization sensitive optical coherence tomography – a review [Invited

    PubMed Central

    de Boer, Johannes F.; Hitzenberger, Christoph K.; Yasuno, Yoshiaki

    2017-01-01

    Optical coherence tomography (OCT) is now a well-established modality for high-resolution cross-sectional and three-dimensional imaging of transparent and translucent samples and tissues. Conventional, intensity based OCT, however, does not provide a tissue-specific contrast, causing an ambiguity with image interpretation in several cases. Polarization sensitive (PS) OCT draws advantage from the fact that several materials and tissues can change the light’s polarization state, adding an additional contrast channel and providing quantitative information. In this paper, we review basic and advanced methods of PS-OCT and demonstrate its use in selected biomedical applications. PMID:28663869

  11. Introducing Seismic Tomography with Computational Modeling

    NASA Astrophysics Data System (ADS)

    Neves, R.; Neves, M. L.; Teodoro, V.

    2011-12-01

    Learning seismic tomography principles and techniques involves advanced physical and computational knowledge. In depth learning of such computational skills is a difficult cognitive process that requires a strong background in physics, mathematics and computer programming. The corresponding learning environments and pedagogic methodologies should then involve sets of computational modelling activities with computer software systems which allow students the possibility to improve their mathematical or programming knowledge and simultaneously focus on the learning of seismic wave propagation and inverse theory. To reduce the level of cognitive opacity associated with mathematical or programming knowledge, several computer modelling systems have already been developed (Neves & Teodoro, 2010). Among such systems, Modellus is particularly well suited to achieve this goal because it is a domain general environment for explorative and expressive modelling with the following main advantages: 1) an easy and intuitive creation of mathematical models using just standard mathematical notation; 2) the simultaneous exploration of images, tables, graphs and object animations; 3) the attribution of mathematical properties expressed in the models to animated objects; and finally 4) the computation and display of mathematical quantities obtained from the analysis of images and graphs. Here we describe virtual simulations and educational exercises which enable students an easy grasp of the fundamental of seismic tomography. The simulations make the lecture more interactive and allow students the possibility to overcome their lack of advanced mathematical or programming knowledge and focus on the learning of seismological concepts and processes taking advantage of basic scientific computation methods and tools.

  12. Predicted cancer risks induced by computed tomography examinations during childhood, by a quantitative risk assessment approach.

    PubMed

    Journy, Neige; Ancelet, Sophie; Rehel, Jean-Luc; Mezzarobba, Myriam; Aubert, Bernard; Laurier, Dominique; Bernier, Marie-Odile

    2014-03-01

    The potential adverse effects associated with exposure to ionizing radiation from computed tomography (CT) in pediatrics must be characterized in relation to their expected clinical benefits. Additional epidemiological data are, however, still awaited for providing a lifelong overview of potential cancer risks. This paper gives predictions of potential lifetime risks of cancer incidence that would be induced by CT examinations during childhood in French routine practices in pediatrics. Organ doses were estimated from standard radiological protocols in 15 hospitals. Excess risks of leukemia, brain/central nervous system, breast and thyroid cancers were predicted from dose-response models estimated in the Japanese atomic bomb survivors' dataset and studies of medical exposures. Uncertainty in predictions was quantified using Monte Carlo simulations. This approach predicts that 100,000 skull/brain scans in 5-year-old children would result in eight (90 % uncertainty interval (UI) 1-55) brain/CNS cancers and four (90 % UI 1-14) cases of leukemia and that 100,000 chest scans would lead to 31 (90 % UI 9-101) thyroid cancers, 55 (90 % UI 20-158) breast cancers, and one (90 % UI <0.1-4) leukemia case (all in excess of risks without exposure). Compared to background risks, radiation-induced risks would be low for individuals throughout life, but relative risks would be highest in the first decades of life. Heterogeneity in the radiological protocols across the hospitals implies that 5-10 % of CT examinations would be related to risks 1.4-3.6 times higher than those for the median doses. Overall excess relative risks in exposed populations would be 1-10 % depending on the site of cancer and the duration of follow-up. The results emphasize the potential risks of cancer specifically from standard CT examinations in pediatrics and underline the necessity of optimization of radiological protocols.

  13. Single-Photon Computed Tomography With Large Position-Sensitive Phototubes*

    NASA Astrophysics Data System (ADS)

    Feldmann, John; Ranck, Amoreena; Saunders, Robert S.; Welsh, Robert E.; Bradley, Eric L.; Saha, Margaret S.; Kross, Brian; Majewski, Stan; Popov, Vladimir; Weisenberger, Andrew G.; Wojcik, Randolph

    2000-10-01

    Position-sensitive photomultiplier tubes (PSPMTs) coupled to pixelated CsI(Tl) scintillators have been used with parallel-hole collimators to view the metabolism in small animals of radiopharmaceuticals tagged with ^125I. We report here our preliminary results analyzed using a tomography program^1 written in IDL programming language. The PSPMTs are mounted on a rotating gantry so as to view the subject animal from any azimuth. Preliminary results to test the tomography algorithm have been obtained by placing a variety of plastic mouse-brain phantoms (loaded with Na^125I) in front of one of the detectors and rotating the phantom in steps through 360 degrees. Results of this simulation taken with a variety of collimator hole sizes will be compared and discussed. Extentions of this technique to the use of very small PSPMTs (Hamamatsu M-64) which are capable of a very close approach to those parts of the animal of greatest interest will be described. *Supported in part by The Department of Energy, The National Science Foundation, The American Diabetes Association, The Howard Hughes Foundation and The Jeffress Trust. 1. Tomography algorithm kindly provided by Dr. S. Meikle of The Royal Prince Albert Hospital, Sydney, Australia

  14. A modified discrete algebraic reconstruction technique for multiple grey image reconstruction for limited angle range tomography.

    PubMed

    Liang, Zhiting; Guan, Yong; Liu, Gang; Chen, Xiangyu; Li, Fahu; Guo, Pengfei; Tian, Yangchao

    2016-03-01

    The `missing wedge', which is due to a restricted rotation range, is a major challenge for quantitative analysis of an object using tomography. With prior knowledge of the grey levels, the discrete algebraic reconstruction technique (DART) is able to reconstruct objects accurately with projections in a limited angle range. However, the quality of the reconstructions declines as the number of grey levels increases. In this paper, a modified DART (MDART) was proposed, in which each independent region of homogeneous material was chosen as a research object, instead of the grey values. The grey values of each discrete region were estimated according to the solution of the linear projection equations. The iterative process of boundary pixels updating and correcting the grey values of each region was executed alternately. Simulation experiments of binary phantoms as well as multiple grey phantoms show that MDART is capable of achieving high-quality reconstructions with projections in a limited angle range. The interesting advancement of MDART is that neither prior knowledge of the grey values nor the number of grey levels is necessary.

  15. Coupling of in-situ X-ray Microtomography Observations with Discrete Element Simulations-Application to Powder Sintering

    NASA Astrophysics Data System (ADS)

    Olmos, L.; Bouvard, D.; Martin, C. L.; Bellet, D.; Di Michiel, M.

    2009-06-01

    The sintering of both a powder with a wide particle size distribution (0-63 μm) and of a powder with artificially created pores is investigated by coupling in situ X-ray microtomography observations with Discrete Element simulations. The micro structure evolution of the copper particles is observed by microtomography all along a typical sintering cycle at 1050° C at the European Synchrotron Research Facilities (ESRF, Grenoble, France). A quantitative analysis of the 3D images provides original data on interparticle indentation, coordination and particle displacements throughout sintering. In parallel, the sintering of similar powder systems has been simulated with a discrete element code which incorporates appropriate sintering contact laws from the literature. The initial numerical packing is generated directly from the 3D microtomography images or alternatively from a random set of particles with the same size distribution. The comparison between the information drawn from the simulations and the one obtained by tomography leads to the conclusion that the first method is not satisfactory because real particles are not perfectly spherical as the numerical ones. On the opposite the packings built with the second method show sintering behaviors close to the behaviors of real materials, although particle rearrangement is underestimated by DEM simulations.

  16. Acoustic vector tomography and its application to magnetoacoustic tomography with magnetic induction (MAT-MI).

    PubMed

    Li, Xu; Xia, Rongmin; He, Bin

    2008-01-01

    A new tomographic algorithm for reconstructing a curl-free vector field, whose divergence serves as acoustic source is proposed. It is shown that under certain conditions, the scalar acoustic measurements obtained from a surface enclosing the source area can be vectorized according to the known measurement geometry and then be used to reconstruct the vector field. The proposed method is validated by numerical experiments. This method can be easily applied to magnetoacoustic tomography with magnetic induction (MAT-MI). A simulation study of applying this method to MAT-MI shows that compared to existing methods, the proposed method can give an accurate estimation of the induced current distribution and a better reconstruction of electrical conductivity within an object.

  17. Differentiating malignant from benign gastric mucosal lesions with quantitative analysis in dual energy spectral computed tomography: Initial experience.

    PubMed

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

    2017-01-01

    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 less than

  18. Comparison of Visual and Quantitative Florbetapir F 18 Positron Emission Tomography Analysis in Predicting Mild Cognitive Impairment Outcomes.

    PubMed

    Schreiber, Stefanie; Landau, Susan M; Fero, Allison; Schreiber, Frank; Jagust, William J

    2015-10-01

    The applicability of β-amyloid peptide (Aβ) positron emission tomography (PET) as a biomarker in clinical settings to aid in selection of individuals at preclinical and prodromal Alzheimer disease (AD) will depend on the practicality of PET image analysis. In this context, visual-based Aβ PET assessment seems to be the most feasible approach. To determine the agreement between visual and quantitative Aβ PET analysis and to assess the ability of both techniques to predict conversion from mild cognitive impairment (MCI) to AD. A longitudinal study was conducted among the Alzheimer's Disease Neuroimaging Initiative (ADNI) sites in the United States and Canada during a 1.6-year mean follow-up period. The study was performed from September 21, 2010, to August 11, 2014; data analysis was conducted from September 21, 2014, to May 26, 2015. Participants included 401 individuals with MCI receiving care at a specialty clinic (219 [54.6%] men; mean [SD] age, 71.6 [7.5] years; 16.2 [2.7] years of education). All participants were studied with florbetapir F 18 [18F] PET. The standardized uptake value ratio (SUVR) positivity threshold was 1.11, and one reader rated all images, with a subset of 125 scans rated by a second reader. Sensitivity and specificity of positive and negative [18F] florbetapir PET categorization, which was estimated with cerebrospinal fluid Aβ1-42 as the reference standard. Risk for conversion to AD was assessed using Cox proportional hazards regression models. The frequency of Aβ positivity was 48.9% (196 patients; visual analysis), 55.1% (221 patients; SUVR), and 64.8% (166 patients; cerebrospinal fluid), yielding substantial agreement between visual and SUVR data (κ = 0.74) and between all methods (Fleiss κ = 0.71). For approximately 10% of the 401 participants in whom visual and SUVR data disagreed, interrater reliability was moderate (κ = 0.44), but it was very high if visual and quantitative results agreed (κ = 0.92). Visual

  19. Dual-energy computed tomography for the detection of focal liver lesions.

    PubMed

    Lago, K N; Vallejos, J; Capuñay, C; Salas, E; Reynoso, E; Carpio, J B; Carrascosa, P M

    To qualitatively and quantitatively explore the spectral study of focal liver lesions, comparing it with the usual polychromatic assessment with single-energy computed tomography. We prospectively studied 50 patients with at least one focal liver lesion who were referred for abdominal multidetector computed tomography with intravenous contrast material. The portal phase was acquired with dual energy sources. The density of the lesions and of the surrounding liver parenchyma was measured both in the baseline polychromatic acquisition and in the posterior monochromatic reconstructions at 40 keV, 70 keV, and 140 keV. Spectral curves were traced and the dual-energy indices and contrast-to-noise ratio were calculated. Lastly, the quality of the images and the detectability of the lesions were assessed qualitatively. Densitometric differences between the different types of lesions (avascular and vascularized) and the liver were greater at low energy levels (left side of the spectral curve) than in the polychromatic evaluation. In the subjective assessment, the 40keV energy level had the greatest lesion detectability. Monochromatic spectral study with dual-energy computed tomography provides better lesion detectability at 40keV compared to that provided by the ordinary polychromatic evaluation. Copyright © 2017 SERAM. Publicado por Elsevier España, S.L.U. All rights reserved.

  20. Solving the forward problem of magnetoacoustic tomography with magnetic induction by means of the finite element method

    NASA Astrophysics Data System (ADS)

    Li, Xun; Li, Xu; Zhu, Shanan; He, Bin

    2009-05-01

    Magnetoacoustic tomography with magnetic induction (MAT-MI) is a recently proposed imaging modality to image the electrical impedance of biological tissue. It combines the good contrast of electrical impedance tomography with the high spatial resolution of sonography. In this paper, a three-dimensional MAT-MI forward problem was investigated using the finite element method (FEM). The corresponding FEM formulae describing the forward problem are introduced. In the finite element analysis, magnetic induction in an object with conductivity values close to biological tissues was first carried out. The stimulating magnetic field was simulated as that generated from a three-dimensional coil. The corresponding acoustic source and field were then simulated. Computer simulation studies were conducted using both concentric and eccentric spherical conductivity models with different geometric specifications. In addition, the grid size for finite element analysis was evaluated for the model calibration and evaluation of the corresponding acoustic field.