Evaluation of a Multicore-Optimized Implementation for Tomographic Reconstruction

PubMed Central

Agulleiro, Jose-Ignacio; Fernández, José Jesús

2012-01-01

Tomography allows elucidation of the three-dimensional structure of an object from a set of projection images. In life sciences, electron microscope tomography is providing invaluable information about the cell structure at a resolution of a few nanometres. Here, large images are required to combine wide fields of view with high resolution requirements. The computational complexity of the algorithms along with the large image size then turns tomographic reconstruction into a computationally demanding problem. Traditionally, high-performance computing techniques have been applied to cope with such demands on supercomputers, distributed systems and computer clusters. In the last few years, the trend has turned towards graphics processing units (GPUs). Here we present a detailed description and a thorough evaluation of an alternative approach that relies on exploitation of the power available in modern multicore computers. The combination of single-core code optimization, vector processing, multithreading and efficient disk I/O operations succeeds in providing fast tomographic reconstructions on standard computers. The approach turns out to be competitive with the fastest GPU-based solutions thus far. PMID:23139768

Volume Segmentation and Ghost Particles

NASA Astrophysics Data System (ADS)

Ziskin, Isaac; Adrian, Ronald

2011-11-01

Volume Segmentation Tomographic PIV (VS-TPIV) is a type of tomographic PIV in which images of particles in a relatively thick volume are segmented into images on a set of much thinner volumes that may be approximated as planes, as in 2D planar PIV. The planes of images can be analysed by standard mono-PIV, and the volume of flow vectors can be recreated by assembling the planes of vectors. The interrogation process is similar to a Holographic PIV analysis, except that the planes of image data are extracted from two-dimensional camera images of the volume of particles instead of three-dimensional holographic images. Like the tomographic PIV method using the MART algorithm, Volume Segmentation requires at least two cameras and works best with three or four. Unlike the MART method, Volume Segmentation does not require reconstruction of individual particle images one pixel at a time and it does not require an iterative process, so it operates much faster. As in all tomographic reconstruction strategies, ambiguities known as ghost particles are produced in the segmentation process. The effect of these ghost particles on the PIV measurement is discussed. This research was supported by Contract 79419-001-09, Los Alamos National Laboratory.

Trace: a high-throughput tomographic reconstruction engine for large-scale datasets

DOE PAGES

Bicer, Tekin; Gursoy, Doga; Andrade, Vincent De; ...

2017-01-28

Here, synchrotron light source and detector technologies enable scientists to perform advanced experiments. These scientific instruments and experiments produce data at such scale and complexity that large-scale computation is required to unleash their full power. One of the widely used data acquisition technique at light sources is Computed Tomography, which can generate tens of GB/s depending on x-ray range. A large-scale tomographic dataset, such as mouse brain, may require hours of computation time with a medium size workstation. In this paper, we present Trace, a data-intensive computing middleware we developed for implementation and parallelization of iterative tomographic reconstruction algorithms. Tracemore » provides fine-grained reconstruction of tomography datasets using both (thread level) shared memory and (process level) distributed memory parallelization. Trace utilizes a special data structure called replicated reconstruction object to maximize application performance. We also present the optimizations we have done on the replicated reconstruction objects and evaluate them using a shale and a mouse brain sinogram. Our experimental evaluations show that the applied optimizations and parallelization techniques can provide 158x speedup (using 32 compute nodes) over single core configuration, which decreases the reconstruction time of a sinogram (with 4501 projections and 22400 detector resolution) from 12.5 hours to less than 5 minutes per iteration.« less

Trace: a high-throughput tomographic reconstruction engine for large-scale datasets

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

Bicer, Tekin; Gursoy, Doga; Andrade, Vincent De

Here, synchrotron light source and detector technologies enable scientists to perform advanced experiments. These scientific instruments and experiments produce data at such scale and complexity that large-scale computation is required to unleash their full power. One of the widely used data acquisition technique at light sources is Computed Tomography, which can generate tens of GB/s depending on x-ray range. A large-scale tomographic dataset, such as mouse brain, may require hours of computation time with a medium size workstation. In this paper, we present Trace, a data-intensive computing middleware we developed for implementation and parallelization of iterative tomographic reconstruction algorithms. Tracemore » provides fine-grained reconstruction of tomography datasets using both (thread level) shared memory and (process level) distributed memory parallelization. Trace utilizes a special data structure called replicated reconstruction object to maximize application performance. We also present the optimizations we have done on the replicated reconstruction objects and evaluate them using a shale and a mouse brain sinogram. Our experimental evaluations show that the applied optimizations and parallelization techniques can provide 158x speedup (using 32 compute nodes) over single core configuration, which decreases the reconstruction time of a sinogram (with 4501 projections and 22400 detector resolution) from 12.5 hours to less than 5 minutes per iteration.« less

String-averaging incremental subgradients for constrained convex optimization with applications to reconstruction of tomographic images

NASA Astrophysics Data System (ADS)

Massambone de Oliveira, Rafael; Salomão Helou, Elias; Fontoura Costa, Eduardo

2016-11-01

We present a method for non-smooth convex minimization which is based on subgradient directions and string-averaging techniques. In this approach, the set of available data is split into sequences (strings) and a given iterate is processed independently along each string, possibly in parallel, by an incremental subgradient method (ISM). The end-points of all strings are averaged to form the next iterate. The method is useful to solve sparse and large-scale non-smooth convex optimization problems, such as those arising in tomographic imaging. A convergence analysis is provided under realistic, standard conditions. Numerical tests are performed in a tomographic image reconstruction application, showing good performance for the convergence speed when measured as the decrease ratio of the objective function, in comparison to classical ISM.

TomoBank: a tomographic data repository for computational x-ray science

NASA Astrophysics Data System (ADS)

De Carlo, Francesco; Gürsoy, Doğa; Ching, Daniel J.; Joost Batenburg, K.; Ludwig, Wolfgang; Mancini, Lucia; Marone, Federica; Mokso, Rajmund; Pelt, Daniël M.; Sijbers, Jan; Rivers, Mark

2018-03-01

There is a widening gap between the fast advancement of computational methods for tomographic reconstruction and their successful implementation in production software at various synchrotron facilities. This is due in part to the lack of readily available instrument datasets and phantoms representative of real materials for validation and comparison of new numerical methods. Recent advancements in detector technology have made sub-second and multi-energy tomographic data collection possible (Gibbs et al 2015 Sci. Rep. 5 11824), but have also increased the demand to develop new reconstruction methods able to handle in situ (Pelt and Batenburg 2013 IEEE Trans. Image Process. 22 5238-51) and dynamic systems (Mohan et al 2015 IEEE Trans. Comput. Imaging 1 96-111) that can be quickly incorporated in beamline production software (Gürsoy et al 2014 J. Synchrotron Radiat. 21 1188-93). The x-ray tomography data bank, tomoBank, provides a repository of experimental and simulated datasets with the aim to foster collaboration among computational scientists, beamline scientists, and experimentalists and to accelerate the development and implementation of tomographic reconstruction methods for synchrotron facility production software by providing easy access to challenging datasets and their descriptors.

Application Of Iterative Reconstruction Techniques To Conventional Circular Tomography

NASA Astrophysics Data System (ADS)

Ghosh Roy, D. N.; Kruger, R. A.; Yih, B. C.; Del Rio, S. P.; Power, R. L.

1985-06-01

Two "point-by-point" iteration procedures, namely, Iterative Least Square Technique (ILST) and Simultaneous Iterative Reconstructive Technique (SIRT) were applied to classical circular tomographic reconstruction. The technique of tomosynthetic DSA was used in forming the tomographic images. Reconstructions of a dog's renal and neck anatomy are presented.

Tomographic Reconstruction from a Few Views: A Multi-Marginal Optimal Transport Approach

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

Abraham, I., E-mail: isabelle.abraham@cea.fr; Abraham, R., E-mail: romain.abraham@univ-orleans.fr; Bergounioux, M., E-mail: maitine.bergounioux@univ-orleans.fr

2017-02-15

In this article, we focus on tomographic reconstruction. The problem is to determine the shape of the interior interface using a tomographic approach while very few X-ray radiographs are performed. We use a multi-marginal optimal transport approach. Preliminary numerical results are presented.

Tomographic imaging of OH laser-induced fluorescence in laminar and turbulent jet flames

NASA Astrophysics Data System (ADS)

Li, Tao; Pareja, Jhon; Fuest, Frederik; Schütte, Manuel; Zhou, Yihui; Dreizler, Andreas; Böhm, Benjamin

2018-01-01

In this paper a new approach for 3D flame structure diagnostics using tomographic laser-induced fluorescence (Tomo-LIF) of the OH radical was evaluated. The approach combined volumetric illumination with a multi-camera detection system of eight views. Single-shot measurements were performed in a methane/air premixed laminar flame and in a non-premixed turbulent methane jet flame. 3D OH fluorescence distributions in the flames were reconstructed using the simultaneous multiplicative algebraic reconstruction technique. The tomographic measurements were compared and validated against results of OH-PLIF in the laminar flame. The effects of the experimental setup of the detection system and the size of the volumetric illumination on the quality of the tomographic reconstructions were evaluated. Results revealed that the Tomo-LIF is suitable for volumetric reconstruction of flame structures with acceptable spatial resolution and uncertainty. It was found that the number of views and their angular orientation have a strong influence on the quality and accuracy of the tomographic reconstruction while the illumination volume thickness influences mainly the spatial resolution.

A cost-utility analysis of the use of preoperative computed tomographic angiography in abdomen-based perforator flap breast reconstruction.

PubMed

Offodile, Anaeze C; Chatterjee, Abhishek; Vallejo, Sergio; Fisher, Carla S; Tchou, Julia C; Guo, Lifei

2015-04-01

Computed tomographic angiography is a diagnostic tool increasingly used for preoperative vascular mapping in abdomen-based perforator flap breast reconstruction. This study compared the use of computed tomographic angiography and the conventional practice of Doppler ultrasonography only in postmastectomy reconstruction using a cost-utility model. Following a comprehensive literature review, a decision analytic model was created using the three most clinically relevant health outcomes in free autologous breast reconstruction with computed tomographic angiography versus Doppler ultrasonography only. Cost and utility estimates for each health outcome were used to derive the quality-adjusted life-years and incremental cost-utility ratio. One-way sensitivity analysis was performed to scrutinize the robustness of the authors' results. Six studies and 782 patients were identified. Cost-utility analysis revealed a baseline cost savings of $3179, a gain in quality-adjusted life-years of 0.25. This yielded an incremental cost-utility ratio of -$12,716, implying a dominant choice favoring preoperative computed tomographic angiography. Sensitivity analysis revealed that computed tomographic angiography was costlier when the operative time difference between the two techniques was less than 21.3 minutes. However, the clinical advantage of computed tomographic angiography over Doppler ultrasonography only showed that computed tomographic angiography would still remain the cost-effective option even if it offered no additional operating time advantage. The authors' results show that computed tomographic angiography is a cost-effective technology for identifying lower abdominal perforators for autologous breast reconstruction. Although the perfect study would be a randomized controlled trial of the two approaches with true cost accrual, the authors' results represent the best available evidence.

Efficient volumetric estimation from plenoptic data

NASA Astrophysics Data System (ADS)

Anglin, Paul; Reeves, Stanley J.; Thurow, Brian S.

2013-03-01

The commercial release of the Lytro camera, and greater availability of plenoptic imaging systems in general, have given the image processing community cost-effective tools for light-field imaging. While this data is most commonly used to generate planar images at arbitrary focal depths, reconstruction of volumetric fields is also possible. Similarly, deconvolution is a technique that is conventionally used in planar image reconstruction, or deblurring, algorithms. However, when leveraged with the ability of a light-field camera to quickly reproduce multiple focal planes within an imaged volume, deconvolution offers a computationally efficient method of volumetric reconstruction. Related research has shown than light-field imaging systems in conjunction with tomographic reconstruction techniques are also capable of estimating the imaged volume and have been successfully applied to particle image velocimetry (PIV). However, while tomographic volumetric estimation through algorithms such as multiplicative algebraic reconstruction techniques (MART) have proven to be highly accurate, they are computationally intensive. In this paper, the reconstruction problem is shown to be solvable by deconvolution. Deconvolution offers significant improvement in computational efficiency through the use of fast Fourier transforms (FFTs) when compared to other tomographic methods. This work describes a deconvolution algorithm designed to reconstruct a 3-D particle field from simulated plenoptic data. A 3-D extension of existing 2-D FFT-based refocusing techniques is presented to further improve efficiency when computing object focal stacks and system point spread functions (PSF). Reconstruction artifacts are identified; their underlying source and methods of mitigation are explored where possible, and reconstructions of simulated particle fields are provided.

Real-Space x-ray tomographic reconstruction of randomly oriented objects with sparse data frames.

PubMed

Ayyer, Kartik; Philipp, Hugh T; Tate, Mark W; Elser, Veit; Gruner, Sol M

2014-02-10

Schemes for X-ray imaging single protein molecules using new x-ray sources, like x-ray free electron lasers (XFELs), require processing many frames of data that are obtained by taking temporally short snapshots of identical molecules, each with a random and unknown orientation. Due to the small size of the molecules and short exposure times, average signal levels of much less than 1 photon/pixel/frame are expected, much too low to be processed using standard methods. One approach to process the data is to use statistical methods developed in the EMC algorithm (Loh & Elser, Phys. Rev. E, 2009) which processes the data set as a whole. In this paper we apply this method to a real-space tomographic reconstruction using sparse frames of data (below 10(-2) photons/pixel/frame) obtained by performing x-ray transmission measurements of a low-contrast, randomly-oriented object. This extends the work by Philipp et al. (Optics Express, 2012) to three dimensions and is one step closer to the single molecule reconstruction problem.

Tomography with energy dispersive diffraction

NASA Astrophysics Data System (ADS)

Stock, S. R.; Okasinski, J. S.; Woods, R.; Baldwin, J.; Madden, T.; Quaranta, O.; Rumaiz, A.; Kuczewski, T.; Mead, J.; Krings, T.; Siddons, P.; Miceli, A.; Almer, J. D.

2017-09-01

X-ray diffraction can be used as the signal for tomographic reconstruction and provides a cross-sectional map of the crystallographic phases and related quantities. Diffraction tomography has been developed over the last decade using monochromatic x-radiation and an area detector. This paper reports tomographic reconstruction with polychromatic radiation and an energy sensitive detector array. The energy dispersive diffraction (EDD) geometry, the instrumentation and the reconstruction process are described and related to the expected resolution. Results of EDD tomography are presented for two samples containing hydroxyapatite (hAp). The first is a 3D-printed sample with an elliptical crosssection and contains synthetic hAp. The second is a human second metacarpal bone from the Roman-era cemetery at Ancaster, UK and contains bio-hAp which may have been altered by diagenesis. Reconstructions with different diffraction peaks are compared. Prospects for future EDD tomography are also discussed.

A maximum entropy reconstruction technique for tomographic particle image velocimetry

NASA Astrophysics Data System (ADS)

Bilsky, A. V.; Lozhkin, V. A.; Markovich, D. M.; Tokarev, M. P.

2013-04-01

This paper studies a novel approach for reducing tomographic PIV computational complexity. The proposed approach is an algebraic reconstruction technique, termed MENT (maximum entropy). This technique computes the three-dimensional light intensity distribution several times faster than SMART, using at least ten times less memory. Additionally, the reconstruction quality remains nearly the same as with SMART. This paper presents the theoretical computation performance comparison for MENT, SMART and MART, followed by validation using synthetic particle images. Both the theoretical assessment and validation of synthetic images demonstrate significant computational time reduction. The data processing accuracy of MENT was compared to that of SMART in a slot jet experiment. A comparison of the average velocity profiles shows a high level of agreement between the results obtained with MENT and those obtained with SMART.

Linear information retrieval method in X-ray grating-based phase contrast imaging and its interchangeability with tomographic reconstruction

NASA Astrophysics Data System (ADS)

Wu, Z.; Gao, K.; Wang, Z. L.; Shao, Q. G.; Hu, R. F.; Wei, C. X.; Zan, G. B.; Wali, F.; Luo, R. H.; Zhu, P. P.; Tian, Y. C.

2017-06-01

In X-ray grating-based phase contrast imaging, information retrieval is necessary for quantitative research, especially for phase tomography. However, numerous and repetitive processes have to be performed for tomographic reconstruction. In this paper, we report a novel information retrieval method, which enables retrieving phase and absorption information by means of a linear combination of two mutually conjugate images. Thanks to the distributive law of the multiplication as well as the commutative law and associative law of the addition, the information retrieval can be performed after tomographic reconstruction, thus simplifying the information retrieval procedure dramatically. The theoretical model of this method is established in both parallel beam geometry for Talbot interferometer and fan beam geometry for Talbot-Lau interferometer. Numerical experiments are also performed to confirm the feasibility and validity of the proposed method. In addition, we discuss its possibility in cone beam geometry and its advantages compared with other methods. Moreover, this method can also be employed in other differential phase contrast imaging methods, such as diffraction enhanced imaging, non-interferometric imaging, and edge illumination.

AOF LTAO mode: reconstruction strategy and first test results

NASA Astrophysics Data System (ADS)

Oberti, Sylvain; Kolb, Johann; Le Louarn, Miska; La Penna, Paolo; Madec, Pierre-Yves; Neichel, Benoit; Sauvage, Jean-François; Fusco, Thierry; Donaldson, Robert; Soenke, Christian; Suárez Valles, Marcos; Arsenault, Robin

2016-07-01

GALACSI is the Adaptive Optics (AO) system serving the instrument MUSE in the framework of the Adaptive Optics Facility (AOF) project. Its Narrow Field Mode (NFM) is a Laser Tomography AO (LTAO) mode delivering high resolution in the visible across a small Field of View (FoV) of 7.5" diameter around the optical axis. From a reconstruction standpoint, GALACSI NFM intends to optimize the correction on axis by estimating the turbulence in volume via a tomographic process, then projecting the turbulence profile onto one single Deformable Mirror (DM) located in the pupil, close to the ground. In this paper, the laser tomographic reconstruction process is described. Several methods (virtual DM, virtual layer projection) are studied, under the constraint of a single matrix vector multiplication. The pseudo-synthetic interaction matrix model and the LTAO reconstructor design are analysed. Moreover, the reconstruction parameter space is explored, in particular the regularization terms. Furthermore, we present here the strategy to define the modal control basis and split the reconstruction between the Low Order (LO) loop and the High Order (HO) loop. Finally, closed loop performance obtained with a 3D turbulence generator will be analysed with respect to the most relevant system parameters to be tuned.

Looking for the Signal: A guide to iterative noise and artefact removal in X-ray tomographic reconstructions of porous geomaterials

NASA Astrophysics Data System (ADS)

Bruns, S.; Stipp, S. L. S.; Sørensen, H. O.

2017-07-01

X-ray micro- and nanotomography has evolved into a quantitative analysis tool rather than a mere qualitative visualization technique for the study of porous natural materials. Tomographic reconstructions are subject to noise that has to be handled by image filters prior to quantitative analysis. Typically, denoising filters are designed to handle random noise, such as Gaussian or Poisson noise. In tomographic reconstructions, noise has been projected from Radon space to Euclidean space, i.e. post reconstruction noise cannot be expected to be random but to be correlated. Reconstruction artefacts, such as streak or ring artefacts, aggravate the filtering process so algorithms performing well with random noise are not guaranteed to provide satisfactory results for X-ray tomography reconstructions. With sufficient image resolution, the crystalline origin of most geomaterials results in tomography images of objects that are untextured. We developed a denoising framework for these kinds of samples that combines a noise level estimate with iterative nonlocal means denoising. This allows splitting the denoising task into several weak denoising subtasks where the later filtering steps provide a controlled level of texture removal. We describe a hands-on explanation for the use of this iterative denoising approach and the validity and quality of the image enhancement filter was evaluated in a benchmarking experiment with noise footprints of a varying level of correlation and residual artefacts. They were extracted from real tomography reconstructions. We found that our denoising solutions were superior to other denoising algorithms, over a broad range of contrast-to-noise ratios on artificial piecewise constant signals.

Robust statistical reconstruction for charged particle tomography

DOEpatents

Schultz, Larry Joe; Klimenko, Alexei Vasilievich; Fraser, Andrew Mcleod; Morris, Christopher; Orum, John Christopher; Borozdin, Konstantin N; Sossong, Michael James; Hengartner, Nicolas W

2013-10-08

Systems and methods for charged particle detection including statistical reconstruction of object volume scattering density profiles from charged particle tomographic data to determine the probability distribution of charged particle scattering using a statistical multiple scattering model and determine a substantially maximum likelihood estimate of object volume scattering density using expectation maximization (ML/EM) algorithm to reconstruct the object volume scattering density. The presence of and/or type of object occupying the volume of interest can be identified from the reconstructed volume scattering density profile. The charged particle tomographic data can be cosmic ray muon tomographic data from a muon tracker for scanning packages, containers, vehicles or cargo. The method can be implemented using a computer program which is executable on a computer.

Breathing motion compensated reconstruction for C-arm cone beam CT imaging: initial experience based on animal data

NASA Astrophysics Data System (ADS)

Schäfer, D.; Lin, M.; Rao, P. P.; Loffroy, R.; Liapi, E.; Noordhoek, N.; Eshuis, P.; Radaelli, A.; Grass, M.; Geschwind, J.-F. H.

2012-03-01

C-arm based tomographic 3D imaging is applied in an increasing number of minimal invasive procedures. Due to the limited acquisition speed for a complete projection data set required for tomographic reconstruction, breathing motion is a potential source of artifacts. This is the case for patients who cannot comply breathing commands (e.g. due to anesthesia). Intra-scan motion estimation and compensation is required. Here, a scheme for projection based local breathing motion estimation is combined with an anatomy adapted interpolation strategy and subsequent motion compensated filtered back projection. The breathing motion vector is measured as a displacement vector on the projections of a tomographic short scan acquisition using the diaphragm as a landmark. Scaling of the displacement to the acquisition iso-center and anatomy adapted volumetric motion vector field interpolation delivers a 3D motion vector per voxel. Motion compensated filtered back projection incorporates this motion vector field in the image reconstruction process. This approach is applied in animal experiments on a flat panel C-arm system delivering improved image quality (lower artifact levels, improved tumor delineation) in 3D liver tumor imaging.

GPS Tomography: Water Vapour Monitoring for Germany

NASA Astrophysics Data System (ADS)

Bender, Michael; Dick, Galina; Wickert, Jens; Raabe, Armin

2010-05-01

Ground based GPS atmosphere sounding provides numerous atmospheric quantities with a high temporal resolution for all weather conditions. The spatial resolution of the GPS observations is mainly given by the number of GNSS satellites and GPS ground stations. The latter could considerably be increased in the last few years leading to more reliable and better resolved GPS products. New techniques such as the GPS water vapour tomography gain increased significance as data from large and dense GPS networks become available. The GPS tomography has the potential to provide spatially resolved fields of different quantities operationally, i. e. the humidity or wet refractivity as required for meteorological applications or the refraction index which is important for several space based observations or for precise positioning. The number of German GPS stations operationally processed by the GFZ in Potsdam was recently enlarged to more than 300. About 28000 IWV observations and more than 1.4 millions of slant total delay data are now available per day with a temporal resolution of 15 min and 2.5 min, respectively. The extended network leads not only to a higher spatial resolution of the tomographically reconstructed 3D fields but also to a much higher stability of the inversion process and with that to an increased quality of the results. Under these improved conditions the GPS tomography can operate continuously over several days or weeks without applying too tight constraints. Time series of tomographically reconstructed humidity fields will be shown and different initialisation strategies will be discussed: Initialisation with a simple exponential profile, with a 3D humidity field extrapolated from synoptic observations and with the result of the preceeding reconstruction. The results are compared to tomographic reconstructions initialised with COSMO-DE analyses and to the corresponding model fields. The inversion can be further stabilised by making use of independent adequately weighted observations, such as synoptic observations or IWV data. The impact of such observations on the quality of the tomographic reconstruction will be discussed together with different alternatives for weighting different types of observations.

Label-free tomographic reconstruction of optically thick structures using GLIM (Conference Presentation)

NASA Astrophysics Data System (ADS)

Kandel, Mikhail E.; Kouzehgarani, Ghazal N.; Ngyuen, Tan H.; Gillette, Martha U.; Popescu, Gabriel

2017-02-01

Although the contrast generated in transmitted light microscopy is due to the elastic scattering of light, multiple scattering scrambles the image and reduces overall visibility. To image both thin and thick samples, we turn to gradient light interference microscopy (GLIM) to simultaneously measure morphological parameters such as cell mass, volume, and surfaces as they change through time. Because GLIM combines multiple intensity images corresponding to controlled phase offsets between laterally sheared beams, incoherent contributions from multiple scattering are implicitly cancelled during the phase reconstruction procedure. As the interfering beams traverse near identical paths, they remain comparable in power and interfere with optimal contrast. This key property lets us obtain tomographic parameters from wide field z-scans after simple numerical processing. Here we show our results on reconstructing tomograms of bovine embryos, characterizing the time-lapse growth of HeLa cells in 3D, and preliminary results on imaging much larger specimen such as brain slices.

Effect of Shot Noise on Simultaneous Sensing in Frequency Division Multiplexed Diffuse Optical Tomographic Imaging Process.

PubMed

Jang, Hansol; Lim, Gukbin; Hong, Keum-Shik; Cho, Jaedu; Gulsen, Gultekin; Kim, Chang-Seok

2017-11-28

Diffuse optical tomography (DOT) has been studied for use in the detection of breast cancer, cerebral oxygenation, and cognitive brain signals. As optical imaging studies have increased significantly, acquiring imaging data in real time has become increasingly important. We have developed frequency-division multiplexing (FDM) DOT systems to analyze their performance with respect to acquisition time and imaging quality, in comparison with the conventional time-division multiplexing (TDM) DOT. A large tomographic area of a cylindrical phantom 60 mm in diameter could be successfully reconstructed using both TDM DOT and FDM DOT systems. In our experiment with 6 source-detector (S-D) pairs, the TDM DOT and FDM DOT systems required 6.18 and 1 s, respectively, to obtain a single tomographic data set. While the absorption coefficient of the reconstruction image was underestimated in the case of the FDM DOT, we experimentally confirmed that the abnormal region can be clearly distinguished from the background phantom using both methods.

Tomographic determination of the power distribution in electron beams

DOEpatents

Teruya, Alan T.; Elmer, John W.

1996-01-01

A tomographic technique for determining the power distribution of an electron beam using electron beam profile data acquired from a modified Faraday cup to create an image of the current density in high and low power beams. A refractory metal disk with a number of radially extending slits is placed above a Faraday cup. The beam is swept in a circular pattern so that its path crosses each slit in a perpendicular manner, thus acquiring all the data needed for a reconstruction in one circular sweep. Also, a single computer is used to generate the signals actuating the sweep, to acquire that data, and to do the reconstruction, thus reducing the time and equipment necessary to complete the process.

Tomographic determination of the power distribution in electron beams

DOEpatents

Teruya, A.T.; Elmer, J.W.

1996-12-10

A tomographic technique for determining the power distribution of an electron beam using electron beam profile data acquired from a modified Faraday cup to create an image of the current density in high and low power beams is disclosed. A refractory metal disk with a number of radially extending slits is placed above a Faraday cup. The beam is swept in a circular pattern so that its path crosses each slit in a perpendicular manner, thus acquiring all the data needed for a reconstruction in one circular sweep. Also, a single computer is used to generate the signals actuating the sweep, to acquire that data, and to do the reconstruction, thus reducing the time and equipment necessary to complete the process. 4 figs.

On the feasibility of tomographic-PIV with low pulse energy illumination in a lifted turbulent jet flame

NASA Astrophysics Data System (ADS)

Boxx, I.; Carter, C. D.; Meier, W.

2014-08-01

Tomographic particle image velocimetry (tomographic-PIV) is a recently developed measurement technique used to acquire volumetric velocity field data in liquid and gaseous flows. The technique relies on line-of-sight reconstruction of the rays between a 3D particle distribution and a multi-camera imaging system. In a turbulent flame, however, index-of-refraction variations resulting from local heat-release may inhibit reconstruction and thereby render the technique infeasible. The objective of this study was to test the efficacy of tomographic-PIV in a turbulent flame. An additional goal was to determine the feasibility of acquiring usable tomographic-PIV measurements in a turbulent flame at multi-kHz acquisition rates with current-generation laser and camera technology. To this end, a setup consisting of four complementary metal oxide semiconductor cameras and a dual-cavity Nd:YAG laser was implemented to test the technique in a lifted turbulent jet flame. While the cameras were capable of kHz-rate image acquisition, the laser operated at a pulse repetition rate of only 10 Hz. However, use of this laser allowed exploration of the required pulse energy and thus power for a kHz-rate system. The imaged region was 29 × 28 × 2.7 mm in size. The tomographic reconstruction of the 3D particle distributions was accomplished using the multiplicative algebraic reconstruction technique. The results indicate that volumetric velocimetry via tomographic-PIV is feasible with pulse energies of 25 mJ, which is within the capability of current-generation kHz-rate diode-pumped solid-state lasers.

Multislice spiral CT simulator for dynamic cardiopulmonary studies

NASA Astrophysics Data System (ADS)

De Francesco, Silvia; Ferreira da Silva, Augusto M.

2002-04-01

We've developed a Multi-slice Spiral CT Simulator modeling the acquisition process of a real tomograph over a 4-dimensional phantom (4D MCAT) of the human thorax. The simulator allows us to visually characterize artifacts due to insufficient temporal sampling and a priori evaluate the quality of the images obtained in cardio-pulmonary studies (both with single-/multi-slice and ECG gated acquisition processes). The simulating environment allows both for conventional and spiral scanning modes and includes a model of noise in the acquisition process. In case of spiral scanning, reconstruction facilities include longitudinal interpolation methods (360LI and 180LI both for single and multi-slice). Then, the reconstruction of the section is performed through FBP. The reconstructed images/volumes are affected by distortion due to insufficient temporal sampling of the moving object. The developed simulating environment allows us to investigate the nature of the distortion characterizing it qualitatively and quantitatively (using, for example, Herman's measures). Much of our work is focused on the determination of adequate temporal sampling and sinogram regularization techniques. At the moment, the simulator model is limited to the case of multi-slice tomograph, being planned as a next step of development the extension to cone beam or area detectors.

Tomographic imaging using poissonian detector data

DOEpatents

Aspelmeier, Timo; Ebel, Gernot; Hoeschen, Christoph

2013-10-15

An image reconstruction method for reconstructing a tomographic image (f.sub.j) of a region of investigation within an object (1), comprises the steps of providing detector data (y.sub.i) comprising Poisson random values measured at an i-th of a plurality of different positions, e.g. i=(k,l) with pixel index k on a detector device and angular index l referring to both the angular position (.alpha..sub.l) and the rotation radius (r.sub.l) of the detector device (10) relative to the object (1), providing a predetermined system matrix A.sub.ij assigning a j-th voxel of the object (1) to the i-th detector data (y.sub.i), and reconstructing the tomographic image (f.sub.j) based on the detector data (y.sub.i), said reconstructing step including a procedure of minimizing a functional F(f) depending on the detector data (y.sub.i) and the system matrix A.sub.ij and additionally including a sparse or compressive representation of the object (1) in an orthobasis T, wherein the tomographic image (f.sub.j) represents the global minimum of the functional F(f). Furthermore, an imaging method and an imaging device using the image reconstruction method are described.

Tomographic reconstruction of heat release rate perturbations induced by helical modes in turbulent swirl flames

NASA Astrophysics Data System (ADS)

Moeck, Jonas P.; Bourgouin, Jean-François; Durox, Daniel; Schuller, Thierry; Candel, Sébastien

2013-04-01

Swirl flows with vortex breakdown are widely used in industrial combustion systems for flame stabilization. This type of flow is known to sustain a hydrodynamic instability with a rotating helical structure, one common manifestation of it being the precessing vortex core. The role of this unsteady flow mode in combustion is not well understood, and its interaction with combustion instabilities and flame stabilization remains unclear. It is therefore important to assess the structure of the perturbation in the flame that is induced by this helical mode. Based on principles of tomographic reconstruction, a method is presented to determine the 3-D distribution of the heat release rate perturbation associated with the helical mode. Since this flow instability is rotating, a phase-resolved sequence of projection images of light emitted from the flame is identical to the Radon transform of the light intensity distribution in the combustor volume and thus can be used for tomographic reconstruction. This is achieved with one stationary camera only, a vast reduction in experimental and hardware requirements compared to a multi-camera setup or camera repositioning, which is typically required for tomographic reconstruction. Different approaches to extract the coherent part of the oscillation from the images are discussed. Two novel tomographic reconstruction algorithms specifically tailored to the structure of the heat release rate perturbations related to the helical mode are derived. The reconstruction techniques are first applied to an artificial field to illustrate the accuracy. High-speed imaging data acquired in a turbulent swirl-stabilized combustor setup with strong helical mode oscillations are then used to reconstruct the 3-D structure of the associated perturbation in the flame.

Tomographic phase microscopy: principles and applications in bioimaging [Invited

PubMed Central

Jin, Di; Zhou, Renjie; Yaqoob, Zahid; So, Peter T. C.

2017-01-01

Tomographic phase microscopy (TPM) is an emerging optical microscopic technique for bioimaging. TPM uses digital holographic measurements of complex scattered fields to reconstruct three-dimensional refractive index (RI) maps of cells with diffraction-limited resolution by solving inverse scattering problems. In this paper, we review the developments of TPM from the fundamental physics to its applications in bioimaging. We first provide a comprehensive description of the tomographic reconstruction physical models used in TPM. The RI map reconstruction algorithms and various regularization methods are discussed. Selected TPM applications for cellular imaging, particularly in hematology, are reviewed. Finally, we examine the limitations of current TPM systems, propose future solutions, and envision promising directions in biomedical research. PMID:29386746

Optical tomographic memories: algorithms for the efficient information readout

NASA Astrophysics Data System (ADS)

Pantelic, Dejan V.

1990-07-01

Tomographic alogithms are modified in order to reconstruct the inf ormation previously stored by focusing laser radiation in a volume of photosensitive media. Apriori information about the position of bits of inf ormation is used. 1. THE PRINCIPLES OF TOMOGRAPHIC MEMORIES Tomographic principles can be used to store and reconstruct the inf ormation artificially stored in a bulk of a photosensitive media 1 The information is stored by changing some characteristics of a memory material (e. g. refractive index). Radiation from the two independent light sources (e. g. lasers) is f ocused inside the memory material. In this way the intensity of the light is above the threshold only in the localized point where the light rays intersect. By scanning the material the information can be stored in binary or nary format. When the information is stored it can be read by tomographic methods. However the situation is quite different from the classical tomographic problem. Here a lot of apriori information is present regarding the p0- sitions of the bits of information profile representing single bit and a mode of operation (binary or n-ary). 2. ALGORITHMS FOR THE READOUT OF THE TOMOGRAPHIC MEMORIES Apriori information enables efficient reconstruction of the memory contents. In this paper a few methods for the information readout together with the simulation results will be presented. Special attention will be given to the noise considerations. Two different

GPU acceleration towards real-time image reconstruction in 3D tomographic diffractive microscopy

NASA Astrophysics Data System (ADS)

Bailleul, J.; Simon, B.; Debailleul, M.; Liu, H.; Haeberlé, O.

2012-06-01

Phase microscopy techniques regained interest in allowing for the observation of unprepared specimens with excellent temporal resolution. Tomographic diffractive microscopy is an extension of holographic microscopy which permits 3D observations with a finer resolution than incoherent light microscopes. Specimens are imaged by a series of 2D holograms: their accumulation progressively fills the range of frequencies of the specimen in Fourier space. A 3D inverse FFT eventually provides a spatial image of the specimen. Consequently, acquisition then reconstruction are mandatory to produce an image that could prelude real-time control of the observed specimen. The MIPS Laboratory has built a tomographic diffractive microscope with an unsurpassed 130nm resolution but a low imaging speed - no less than one minute. Afterwards, a high-end PC reconstructs the 3D image in 20 seconds. We now expect an interactive system providing preview images during the acquisition for monitoring purposes. We first present a prototype implementing this solution on CPU: acquisition and reconstruction are tied in a producer-consumer scheme, sharing common data into CPU memory. Then we present a prototype dispatching some reconstruction tasks to GPU in order to take advantage of SIMDparallelization for FFT and higher bandwidth for filtering operations. The CPU scheme takes 6 seconds for a 3D image update while the GPU scheme can go down to 2 or > 1 seconds depending on the GPU class. This opens opportunities for 4D imaging of living organisms or crystallization processes. We also consider the relevance of GPU for 3D image interaction in our specific conditions.

TomoPhantom, a software package to generate 2D-4D analytical phantoms for CT image reconstruction algorithm benchmarks

NASA Astrophysics Data System (ADS)

Kazantsev, Daniil; Pickalov, Valery; Nagella, Srikanth; Pasca, Edoardo; Withers, Philip J.

2018-01-01

In the field of computerized tomographic imaging, many novel reconstruction techniques are routinely tested using simplistic numerical phantoms, e.g. the well-known Shepp-Logan phantom. These phantoms cannot sufficiently cover the broad spectrum of applications in CT imaging where, for instance, smooth or piecewise-smooth 3D objects are common. TomoPhantom provides quick access to an external library of modular analytical 2D/3D phantoms with temporal extensions. In TomoPhantom, quite complex phantoms can be built using additive combinations of geometrical objects, such as, Gaussians, parabolas, cones, ellipses, rectangles and volumetric extensions of them. Newly designed phantoms are better suited for benchmarking and testing of different image processing techniques. Specifically, tomographic reconstruction algorithms which employ 2D and 3D scanning geometries, can be rigorously analyzed using the software. TomoPhantom also provides a capability of obtaining analytical tomographic projections which further extends the applicability of software towards more realistic, free from the "inverse crime" testing. All core modules of the package are written in the C-OpenMP language and wrappers for Python and MATLAB are provided to enable easy access. Due to C-based multi-threaded implementation, volumetric phantoms of high spatial resolution can be obtained with computational efficiency.

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

Raymund, T.D.

Recently, several tomographic techniques for ionospheric electron density imaging have been proposed. These techniques reconstruct a vertical slice image of electron density using total electron content data. The data are measured between a low orbit beacon satellite and fixed receivers located along the projected orbital path of the satellite. By using such tomographic techniques, it may be possible to inexpensively (relative to incoherent scatter techniques) image the ionospheric electron density in a vertical plane several times per day. The satellite and receiver geometry used to measure the total electron content data causes the data to be incomplete; that is, themore » measured data do not contain enough information to completely specify the ionospheric electron density distribution in the region between the satellite and the receivers. A new algorithm is proposed which allows the incorporation of other complementary measurements, such as those from ionosondes, and also includes ways to include a priori information about the unknown electron density distribution in the reconstruction process. The algorithm makes use of two-dimensional basis functions. Illustrative application of this algorithm is made to simulated cases with good results. The technique is also applied to real total electron content (TEC) records collected in Scandinavia in conjunction with the EISCAT incoherent scatter radar. The tomographic reconstructions are compared with the incoherent scatter electron density images of the same region of the ionosphere.« less

Tuning the cache memory usage in tomographic reconstruction on standard computers with Advanced Vector eXtensions (AVX)

PubMed Central

Agulleiro, Jose-Ignacio; Fernandez, Jose-Jesus

2015-01-01

Cache blocking is a technique widely used in scientific computing to minimize the exchange of information with main memory by reusing the data kept in cache memory. In tomographic reconstruction on standard computers using vector instructions, cache blocking turns out to be central to optimize performance. To this end, sinograms of the tilt-series and slices of the volumes to be reconstructed have to be divided into small blocks that fit into the different levels of cache memory. The code is then reorganized so as to operate with a block as much as possible before proceeding with another one. This data article is related to the research article titled Tomo3D 2.0 – Exploitation of Advanced Vector eXtensions (AVX) for 3D reconstruction (Agulleiro and Fernandez, 2015) [1]. Here we present data of a thorough study of the performance of tomographic reconstruction by varying cache block sizes, which allows derivation of expressions for their automatic quasi-optimal tuning. PMID:26217710

Tuning the cache memory usage in tomographic reconstruction on standard computers with Advanced Vector eXtensions (AVX).

PubMed

Agulleiro, Jose-Ignacio; Fernandez, Jose-Jesus

2015-06-01

Cache blocking is a technique widely used in scientific computing to minimize the exchange of information with main memory by reusing the data kept in cache memory. In tomographic reconstruction on standard computers using vector instructions, cache blocking turns out to be central to optimize performance. To this end, sinograms of the tilt-series and slices of the volumes to be reconstructed have to be divided into small blocks that fit into the different levels of cache memory. The code is then reorganized so as to operate with a block as much as possible before proceeding with another one. This data article is related to the research article titled Tomo3D 2.0 - Exploitation of Advanced Vector eXtensions (AVX) for 3D reconstruction (Agulleiro and Fernandez, 2015) [1]. Here we present data of a thorough study of the performance of tomographic reconstruction by varying cache block sizes, which allows derivation of expressions for their automatic quasi-optimal tuning.

Phillips-Tikhonov regularization with a priori information for neutron emission tomographic reconstruction on Joint European Torus

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

Bielecki, J.; Scholz, M.; Drozdowicz, K.

A method of tomographic reconstruction of the neutron emissivity in the poloidal cross section of the Joint European Torus (JET, Culham, UK) tokamak was developed. Due to very limited data set (two projection angles, 19 lines of sight only) provided by the neutron emission profile monitor (KN3 neutron camera), the reconstruction is an ill-posed inverse problem. The aim of this work consists in making a contribution to the development of reliable plasma tomography reconstruction methods that could be routinely used at JET tokamak. The proposed method is based on Phillips-Tikhonov regularization and incorporates a priori knowledge of the shape ofmore » normalized neutron emissivity profile. For the purpose of the optimal selection of the regularization parameters, the shape of normalized neutron emissivity profile is approximated by the shape of normalized electron density profile measured by LIDAR or high resolution Thomson scattering JET diagnostics. In contrast with some previously developed methods of ill-posed plasma tomography reconstruction problem, the developed algorithms do not include any post-processing of the obtained solution and the physical constrains on the solution are imposed during the regularization process. The accuracy of the method is at first evaluated by several tests with synthetic data based on various plasma neutron emissivity models (phantoms). Then, the method is applied to the neutron emissivity reconstruction for JET D plasma discharge #85100. It is demonstrated that this method shows good performance and reliability and it can be routinely used for plasma neutron emissivity reconstruction on JET.« less

Optimal reconstruction of the states in qutrit systems

NASA Astrophysics Data System (ADS)

Yan, Fei; Yang, Ming; Cao, Zhuo-Liang

2010-10-01

Based on mutually unbiased measurements, an optimal tomographic scheme for the multiqutrit states is presented explicitly. Because the reconstruction process of states based on mutually unbiased states is free of information waste, we refer to our scheme as the optimal scheme. By optimal we mean that the number of the required conditional operations reaches the minimum in this tomographic scheme for the states of qutrit systems. Special attention will be paid to how those different mutually unbiased measurements are realized; that is, how to decompose each transformation that connects each mutually unbiased basis with the standard computational basis. It is found that all those transformations can be decomposed into several basic implementable single- and two-qutrit unitary operations. For the three-qutrit system, there exist five different mutually unbiased-bases structures with different entanglement properties, so we introduce the concept of physical complexity to minimize the number of nonlocal operations needed over the five different structures. This scheme is helpful for experimental scientists to realize the most economical reconstruction of quantum states in qutrit systems.

High-efficiency tomographic reconstruction of quantum states by quantum nondemolition measurements

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

Huang, J. S.; Centre for Quantum Technologies and Department of Physics, National University of Singapore, 3 Science Drive 2, Singapore 117542; Wei, L. F.

We propose a high-efficiency scheme to tomographically reconstruct an unknown quantum state by using a series of quantum nondemolition (QND) measurements. The proposed QND measurements of the qubits are implemented by probing the stationary transmissions through a driven dispersively coupled resonator. It is shown that only one kind of QND measurement is sufficient to determine all the diagonal elements of the density matrix of the detected quantum state. The remaining nondiagonal elements can be similarly determined by transferring them to the diagonal locations after a series of unitary operations. Compared with the tomographic reconstructions based on the usual destructive projectivemore » measurements (wherein one such measurement can determine only one diagonal element of the density matrix), the present reconstructive approach exhibits significantly high efficiency. Specifically, our generic proposal is demonstrated by the experimental circuit quantum electrodynamics systems with a few Josephson charge qubits.« less

Rapid tomographic reconstruction based on machine learning for time-resolved combustion diagnostics

NASA Astrophysics Data System (ADS)

Yu, Tao; Cai, Weiwei; Liu, Yingzheng

2018-04-01

Optical tomography has attracted surged research efforts recently due to the progress in both the imaging concepts and the sensor and laser technologies. The high spatial and temporal resolutions achievable by these methods provide unprecedented opportunity for diagnosis of complicated turbulent combustion. However, due to the high data throughput and the inefficiency of the prevailing iterative methods, the tomographic reconstructions which are typically conducted off-line are computationally formidable. In this work, we propose an efficient inversion method based on a machine learning algorithm, which can extract useful information from the previous reconstructions and build efficient neural networks to serve as a surrogate model to rapidly predict the reconstructions. Extreme learning machine is cited here as an example for demonstrative purpose simply due to its ease of implementation, fast learning speed, and good generalization performance. Extensive numerical studies were performed, and the results show that the new method can dramatically reduce the computational time compared with the classical iterative methods. This technique is expected to be an alternative to existing methods when sufficient training data are available. Although this work is discussed under the context of tomographic absorption spectroscopy, we expect it to be useful also to other high speed tomographic modalities such as volumetric laser-induced fluorescence and tomographic laser-induced incandescence which have been demonstrated for combustion diagnostics.

Rapid tomographic reconstruction based on machine learning for time-resolved combustion diagnostics.

PubMed

Yu, Tao; Cai, Weiwei; Liu, Yingzheng

2018-04-01

Optical tomography has attracted surged research efforts recently due to the progress in both the imaging concepts and the sensor and laser technologies. The high spatial and temporal resolutions achievable by these methods provide unprecedented opportunity for diagnosis of complicated turbulent combustion. However, due to the high data throughput and the inefficiency of the prevailing iterative methods, the tomographic reconstructions which are typically conducted off-line are computationally formidable. In this work, we propose an efficient inversion method based on a machine learning algorithm, which can extract useful information from the previous reconstructions and build efficient neural networks to serve as a surrogate model to rapidly predict the reconstructions. Extreme learning machine is cited here as an example for demonstrative purpose simply due to its ease of implementation, fast learning speed, and good generalization performance. Extensive numerical studies were performed, and the results show that the new method can dramatically reduce the computational time compared with the classical iterative methods. This technique is expected to be an alternative to existing methods when sufficient training data are available. Although this work is discussed under the context of tomographic absorption spectroscopy, we expect it to be useful also to other high speed tomographic modalities such as volumetric laser-induced fluorescence and tomographic laser-induced incandescence which have been demonstrated for combustion diagnostics.

Three-dimensional reconstructions from computed tomographic scans on smartphones and tablets: a simple tutorial for the ward and operating room using public domain software.

PubMed

Ketoff, Serge; Khonsari, Roman Hossein; Schouman, Thomas; Bertolus, Chloé

2014-11-01

Handling 3-dimensional reconstructions of computed tomographic scans on portable devices is problematic because of the size of the Digital Imaging and Communications in Medicine (DICOM) stacks. The authors provide a user-friendly method allowing the production, transfer, and sharing of good-quality 3-dimensional reconstructions on smartphones and tablets. Copyright © 2014 American Association of Oral and Maxillofacial Surgeons. Published by Elsevier Inc. All rights reserved.

TomoBank: a tomographic data repository for computational x-ray science

DOE PAGES

De Carlo, Francesco; Gürsoy, Doğa; Ching, Daniel J.; ...

2018-02-08

There is a widening gap between the fast advancement of computational methods for tomographic reconstruction and their successful implementation in production software at various synchrotron facilities. This is due in part to the lack of readily available instrument datasets and phantoms representative of real materials for validation and comparison of new numerical methods. Recent advancements in detector technology made sub-second and multi-energy tomographic data collection possible [1], but also increased the demand to develop new reconstruction methods able to handle in-situ [2] and dynamic systems [3] that can be quickly incorporated in beamline production software [4]. The X-ray Tomography Datamore » Bank, tomoBank, provides a repository of experimental and simulated datasets with the aim to foster collaboration among computational scientists, beamline scientists, and experimentalists and to accelerate the development and implementation of tomographic reconstruction methods for synchrotron facility production software by providing easy access to challenging dataset and their descriptors.« less

Tomographic image reconstruction using the cell broadband engine (CBE) general purpose hardware

NASA Astrophysics Data System (ADS)

Knaup, Michael; Steckmann, Sven; Bockenbach, Olivier; Kachelrieß, Marc

2007-02-01

Tomographic image reconstruction, such as the reconstruction of CT projection values, of tomosynthesis data, PET or SPECT events, is computational very demanding. In filtered backprojection as well as in iterative reconstruction schemes, the most time-consuming steps are forward- and backprojection which are often limited by the memory bandwidth. Recently, a novel general purpose architecture optimized for distributed computing became available: the Cell Broadband Engine (CBE). Its eight synergistic processing elements (SPEs) currently allow for a theoretical performance of 192 GFlops (3 GHz, 8 units, 4 floats per vector, 2 instructions, multiply and add, per clock). To maximize image reconstruction speed we modified our parallel-beam and perspective backprojection algorithms which are highly optimized for standard PCs, and optimized the code for the CBE processor. 1-3 In addition, we implemented an optimized perspective forwardprojection on the CBE which allows us to perform statistical image reconstructions like the ordered subset convex (OSC) algorithm. 4 Performance was measured using simulated data with 512 projections per rotation and 5122 detector elements. The data were backprojected into an image of 512 3 voxels using our PC-based approaches and the new CBE- based algorithms. Both the PC and the CBE timings were scaled to a 3 GHz clock frequency. On the CBE, we obtain total reconstruction times of 4.04 s for the parallel backprojection, 13.6 s for the perspective backprojection and 192 s for a complete OSC reconstruction, consisting of one initial Feldkamp reconstruction, followed by 4 OSC iterations.

Acoustic representation of tomographic data

NASA Astrophysics Data System (ADS)

Wampler, Cheryl; Zahrt, John D.; Hotchkiss, Robert S.; Zahrt, Rebecca; Kust, Mark

1993-04-01

Tomographic data and tomographic reconstructions are naturally periodic in the angle of rotation of the turntable and the polar angel of the coordinates in the object, respectively. Similarly, acoustic waves are periodic and have amplitude and wavelength as free parameters that can be fit to another representation. Work has been in progress for some time in bringing the acoustic senses to bear on large data sets rather than just the visual sense. We will provide several different acoustic representations of both raw data and density maps. Rather than graphical portrayal of the data and reconstructions, you will be presented various 'tone poems.'

Evaluation of a 3D point cloud tetrahedral tomographic reconstruction method

PubMed Central

Pereira, N F; Sitek, A

2011-01-01

Tomographic reconstruction on an irregular grid may be superior to reconstruction on a regular grid. This is achieved through an appropriate choice of the image space model, the selection of an optimal set of points and the use of any available prior information during the reconstruction process. Accordingly, a number of reconstruction-related parameters must be optimized for best performance. In this work, a 3D point cloud tetrahedral mesh reconstruction method is evaluated for quantitative tasks. A linear image model is employed to obtain the reconstruction system matrix and five point generation strategies are studied. The evaluation is performed using the recovery coefficient, as well as voxel- and template-based estimates of bias and variance measures, computed over specific regions in the reconstructed image. A similar analysis is performed for regular grid reconstructions that use voxel basis functions. The maximum likelihood expectation maximization reconstruction algorithm is used. For the tetrahedral reconstructions, of the five point generation methods that are evaluated, three use image priors. For evaluation purposes, an object consisting of overlapping spheres with varying activity is simulated. The exact parallel projection data of this object are obtained analytically using a parallel projector, and multiple Poisson noise realizations of these exact data are generated and reconstructed using the different point generation strategies. The unconstrained nature of point placement in some of the irregular mesh-based reconstruction strategies has superior activity recovery for small, low-contrast image regions. The results show that, with an appropriately generated set of mesh points, the irregular grid reconstruction methods can out-perform reconstructions on a regular grid for mathematical phantoms, in terms of the performance measures evaluated. PMID:20736496

Evaluation of a 3D point cloud tetrahedral tomographic reconstruction method

NASA Astrophysics Data System (ADS)

Pereira, N. F.; Sitek, A.

2010-09-01

Tomographic reconstruction on an irregular grid may be superior to reconstruction on a regular grid. This is achieved through an appropriate choice of the image space model, the selection of an optimal set of points and the use of any available prior information during the reconstruction process. Accordingly, a number of reconstruction-related parameters must be optimized for best performance. In this work, a 3D point cloud tetrahedral mesh reconstruction method is evaluated for quantitative tasks. A linear image model is employed to obtain the reconstruction system matrix and five point generation strategies are studied. The evaluation is performed using the recovery coefficient, as well as voxel- and template-based estimates of bias and variance measures, computed over specific regions in the reconstructed image. A similar analysis is performed for regular grid reconstructions that use voxel basis functions. The maximum likelihood expectation maximization reconstruction algorithm is used. For the tetrahedral reconstructions, of the five point generation methods that are evaluated, three use image priors. For evaluation purposes, an object consisting of overlapping spheres with varying activity is simulated. The exact parallel projection data of this object are obtained analytically using a parallel projector, and multiple Poisson noise realizations of these exact data are generated and reconstructed using the different point generation strategies. The unconstrained nature of point placement in some of the irregular mesh-based reconstruction strategies has superior activity recovery for small, low-contrast image regions. The results show that, with an appropriately generated set of mesh points, the irregular grid reconstruction methods can out-perform reconstructions on a regular grid for mathematical phantoms, in terms of the performance measures evaluated.

Iterative Reconstruction of Volumetric Particle Distribution for 3D Velocimetry

NASA Astrophysics Data System (ADS)

Wieneke, Bernhard; Neal, Douglas

2011-11-01

A number of different volumetric flow measurement techniques exist for following the motion of illuminated particles. For experiments that have lower seeding densities, 3D-PTV uses recorded images from typically 3-4 cameras and then tracks the individual particles in space and time. This technique is effective in flows that have lower seeding densities. For flows that have a higher seeding density, tomographic PIV uses a tomographic reconstruction algorithm (e.g. MART) to reconstruct voxel intensities of the recorded volume followed by the cross-correlation of subvolumes to provide the instantaneous 3D vector fields on a regular grid. A new hybrid algorithm is presented which iteratively reconstructs the 3D-particle distribution directly using particles with certain imaging properties instead of voxels as base functions. It is shown with synthetic data that this method is capable of reconstructing densely seeded flows up to 0.05 particles per pixel (ppp) with the same or higher accuracy than 3D-PTV and tomographic PIV. Finally, this new method is validated using experimental data on a turbulent jet.

Simulation of Tomographic Reconstruction of Magnetosphere Plasma Distribution By Multi-spacecraft Systems.

NASA Astrophysics Data System (ADS)

Kunitsyn, V.; Nesterov, I.; Andreeva, E.; Zelenyi, L.; Veselov, M.; Galperin, Y.; Buchner, J.

A satellite radiotomography method for electron density distributions was recently proposed for closely-space multi-spacecraft group of high-altitude satellites to study the physics of reconnection process. The original idea of the ROY project is to use a constellation of spacecrafts (one main and several sub-satellites) in order to carry out closely-spaced multipoint measurements and 2D tomographic reconstruction of elec- tron density in the space between the main satellite and the subsatellites. The distances between the satellites were chosen to vary from dozens to few hundreds of kilometers. The easiest data interpretation is achieved when the subsatellites are placed along the plasma streamline. Then, whenever a plasma density irregularity moves between the main satellite and the subsatellites it will be scanned in different directions and we can get 2D distribution of plasma using these projections. However in general sub- satellites are not placed exactly along the plasma streamline. The method of plasma velocity determination relative to multi-spacecraft systems is considered. Possibilities of 3D tomographic imaging using multi-spacecraft systems are analyzed. The model- ing has shown that efficient scheme for 3D tomographic imaging would be to place spacecrafts in different planes so that the angle between the planes would make not more then ten degrees. Work is supported by INTAS PROJECT 2000-465.

Image reconstruction of muon tomographic data using a density-based clustering method

NASA Astrophysics Data System (ADS)

Perry, Kimberly B.

Muons are subatomic particles capable of reaching the Earth's surface before decaying. When these particles collide with an object that has a high atomic number (Z), their path of travel changes substantially. Tracking muon movement through shielded containers can indicate what types of materials lie inside. This thesis proposes using a density-based clustering algorithm called OPTICS to perform image reconstructions using muon tomographic data. The results show that this method is capable of detecting high-Z materials quickly, and can also produce detailed reconstructions with large amounts of data.

Scanning transmission electron microscopy through-focal tilt-series on biological specimens.

PubMed

Trepout, Sylvain; Messaoudi, Cédric; Perrot, Sylvie; Bastin, Philippe; Marco, Sergio

2015-10-01

Since scanning transmission electron microscopy can produce high signal-to-noise ratio bright-field images of thick (≥500 nm) specimens, this tool is emerging as the method of choice to study thick biological samples via tomographic approaches. However, in a convergent-beam configuration, the depth of field is limited because only a thin portion of the specimen (from a few nanometres to tens of nanometres depending on the convergence angle) can be imaged in focus. A method known as through-focal imaging enables recovery of the full depth of information by combining images acquired at different levels of focus. In this work, we compare tomographic reconstruction with the through-focal tilt-series approach (a multifocal series of images per tilt angle) with reconstruction with the classic tilt-series acquisition scheme (one single-focus image per tilt angle). We visualised the base of the flagellum in the protist Trypanosoma brucei via an acquisition and image-processing method tailored to obtain quantitative and qualitative descriptors of reconstruction volumes. Reconstructions using through-focal imaging contained more contrast and more details for thick (≥500 nm) biological samples. Copyright © 2015 Elsevier Ltd. All rights reserved.

Sodankylä ionospheric tomography dataset 2003-2014

NASA Astrophysics Data System (ADS)

Norberg, J.; Roininen, L.; Kero, A.; Raita, T.; Ulich, T.; Markkanen, M.; Juusola, L.; Kauristie, K.

2015-12-01

Sodankylä Geophysical Observatory has been operating a tomographic receiver network and collecting the produced data since 2003. The collected dataset consists of phase difference curves measured from Russian COSMOS dual-frequency (150/400 MHz) low-Earth-orbit satellite signals, and tomographic electron density reconstructions obtained from these measurements. In this study vertical total electron content (VTEC) values are integrated from the reconstructed electron densities to make a qualitative and quantitative analysis to validate the long-term performance of the tomographic system. During the observation period, 2003-2014, there were three-to-five operational stations at the Fenno-Scandinavian sector. Altogether the analysis consists of around 66 000 overflights, but to ensure the quality of the reconstructions, the examination is limited to cases with descending (north to south) overflights and maximum elevation over 60°. These constraints limit the number of overflights to around 10 000. Based on this dataset, one solar cycle of ionospheric vertical total electron content estimates is constructed. The measurements are compared against International Reference Ionosphere IRI-2012 model, F10.7 solar flux index and sunspot number data. Qualitatively the tomographic VTEC estimate corresponds to reference data very well, but the IRI-2012 model are on average 40 % higher of that of the tomographic results.

SSULI/SSUSI UV Tomographic Images of Large-Scale Plasma Structuring

NASA Astrophysics Data System (ADS)

Hei, M. A.; Budzien, S. A.; Dymond, K.; Paxton, L. J.; Schaefer, R. K.; Groves, K. M.

2015-12-01

We present a new technique that creates tomographic reconstructions of atmospheric ultraviolet emission based on data from the Special Sensor Ultraviolet Limb Imager (SSULI) and the Special Sensor Ultraviolet Spectrographic Imager (SSUSI), both flown on the Defense Meteorological Satellite Program (DMSP) Block 5D3 series satellites. Until now, the data from these two instruments have been used independently of each other. The new algorithm combines SSULI/SSUSI measurements of 135.6 nm emission using the tomographic technique; the resultant data product - whole-orbit reconstructions of atmospheric volume emission within the satellite orbital plane - is substantially improved over the original data sets. Tests using simulated atmospheric emission verify that the algorithm performs well in a variety of situations, including daytime, nighttime, and even in the challenging terminator regions. A comparison with ALTAIR radar data validates that the volume emission reconstructions can be inverted to yield maps of electron density. The algorithm incorporates several innovative new features, including the use of both SSULI and SSUSI data to create tomographic reconstructions, the use of an inversion algorithm (Richardson-Lucy; RL) that explicitly accounts for the Poisson statistics inherent in optical measurements, and a pseudo-diffusion based regularization scheme implemented between iterations of the RL code. The algorithm also explicitly accounts for extinction due to absorption by molecular oxygen.

Total variation iterative constraint algorithm for limited-angle tomographic reconstruction of non-piecewise-constant structures

NASA Astrophysics Data System (ADS)

Krauze, W.; Makowski, P.; Kujawińska, M.

2015-06-01

Standard tomographic algorithms applied to optical limited-angle tomography result in the reconstructions that have highly anisotropic resolution and thus special algorithms are developed. State of the art approaches utilize the Total Variation (TV) minimization technique. These methods give very good results but are applicable to piecewise constant structures only. In this paper, we propose a novel algorithm for 3D limited-angle tomography - Total Variation Iterative Constraint method (TVIC) which enhances the applicability of the TV regularization to non-piecewise constant samples, like biological cells. This approach consists of two parts. First, the TV minimization is used as a strong regularizer to create a sharp-edged image converted to a 3D binary mask which is then iteratively applied in the tomographic reconstruction as a constraint in the object domain. In the present work we test the method on a synthetic object designed to mimic basic structures of a living cell. For simplicity, the test reconstructions were performed within the straight-line propagation model (SIRT3D solver from the ASTRA Tomography Toolbox), but the strategy is general enough to supplement any algorithm for tomographic reconstruction that supports arbitrary geometries of plane-wave projection acquisition. This includes optical diffraction tomography solvers. The obtained reconstructions present resolution uniformity and general shape accuracy expected from the TV regularization based solvers, but keeping the smooth internal structures of the object at the same time. Comparison between three different patterns of object illumination arrangement show very small impact of the projection acquisition geometry on the image quality.

Vectorization with SIMD extensions speeds up reconstruction in electron tomography.

PubMed

Agulleiro, J I; Garzón, E M; García, I; Fernández, J J

2010-06-01

Electron tomography allows structural studies of cellular structures at molecular detail. Large 3D reconstructions are needed to meet the resolution requirements. The processing time to compute these large volumes may be considerable and so, high performance computing techniques have been used traditionally. This work presents a vector approach to tomographic reconstruction that relies on the exploitation of the SIMD extensions available in modern processors in combination to other single processor optimization techniques. This approach succeeds in producing full resolution tomograms with an important reduction in processing time, as evaluated with the most common reconstruction algorithms, namely WBP and SIRT. The main advantage stems from the fact that this approach is to be run on standard computers without the need of specialized hardware, which facilitates the development, use and management of programs. Future trends in processor design open excellent opportunities for vector processing with processor's SIMD extensions in the field of 3D electron microscopy.

Impact of time-of-flight on indirect 3D and direct 4D parametric image reconstruction in the presence of inconsistent dynamic PET data.

PubMed

Kotasidis, F A; Mehranian, A; Zaidi, H

2016-05-07

Kinetic parameter estimation in dynamic PET suffers from reduced accuracy and precision when parametric maps are estimated using kinetic modelling following image reconstruction of the dynamic data. Direct approaches to parameter estimation attempt to directly estimate the kinetic parameters from the measured dynamic data within a unified framework. Such image reconstruction methods have been shown to generate parametric maps of improved precision and accuracy in dynamic PET. However, due to the interleaving between the tomographic and kinetic modelling steps, any tomographic or kinetic modelling errors in certain regions or frames, tend to spatially or temporally propagate. This results in biased kinetic parameters and thus limits the benefits of such direct methods. Kinetic modelling errors originate from the inability to construct a common single kinetic model for the entire field-of-view, and such errors in erroneously modelled regions could spatially propagate. Adaptive models have been used within 4D image reconstruction to mitigate the problem, though they are complex and difficult to optimize. Tomographic errors in dynamic imaging on the other hand, can originate from involuntary patient motion between dynamic frames, as well as from emission/transmission mismatch. Motion correction schemes can be used, however, if residual errors exist or motion correction is not included in the study protocol, errors in the affected dynamic frames could potentially propagate either temporally, to other frames during the kinetic modelling step or spatially, during the tomographic step. In this work, we demonstrate a new strategy to minimize such error propagation in direct 4D image reconstruction, focusing on the tomographic step rather than the kinetic modelling step, by incorporating time-of-flight (TOF) within a direct 4D reconstruction framework. Using ever improving TOF resolutions (580 ps, 440 ps, 300 ps and 160 ps), we demonstrate that direct 4D TOF image reconstruction can substantially prevent kinetic parameter error propagation either from erroneous kinetic modelling, inter-frame motion or emission/transmission mismatch. Furthermore, we demonstrate the benefits of TOF in parameter estimation when conventional post-reconstruction (3D) methods are used and compare the potential improvements to direct 4D methods. Further improvements could possibly be achieved in the future by combining TOF direct 4D image reconstruction with adaptive kinetic models and inter-frame motion correction schemes.

Impact of time-of-flight on indirect 3D and direct 4D parametric image reconstruction in the presence of inconsistent dynamic PET data

NASA Astrophysics Data System (ADS)

Kotasidis, F. A.; Mehranian, A.; Zaidi, H.

2016-05-01

Kinetic parameter estimation in dynamic PET suffers from reduced accuracy and precision when parametric maps are estimated using kinetic modelling following image reconstruction of the dynamic data. Direct approaches to parameter estimation attempt to directly estimate the kinetic parameters from the measured dynamic data within a unified framework. Such image reconstruction methods have been shown to generate parametric maps of improved precision and accuracy in dynamic PET. However, due to the interleaving between the tomographic and kinetic modelling steps, any tomographic or kinetic modelling errors in certain regions or frames, tend to spatially or temporally propagate. This results in biased kinetic parameters and thus limits the benefits of such direct methods. Kinetic modelling errors originate from the inability to construct a common single kinetic model for the entire field-of-view, and such errors in erroneously modelled regions could spatially propagate. Adaptive models have been used within 4D image reconstruction to mitigate the problem, though they are complex and difficult to optimize. Tomographic errors in dynamic imaging on the other hand, can originate from involuntary patient motion between dynamic frames, as well as from emission/transmission mismatch. Motion correction schemes can be used, however, if residual errors exist or motion correction is not included in the study protocol, errors in the affected dynamic frames could potentially propagate either temporally, to other frames during the kinetic modelling step or spatially, during the tomographic step. In this work, we demonstrate a new strategy to minimize such error propagation in direct 4D image reconstruction, focusing on the tomographic step rather than the kinetic modelling step, by incorporating time-of-flight (TOF) within a direct 4D reconstruction framework. Using ever improving TOF resolutions (580 ps, 440 ps, 300 ps and 160 ps), we demonstrate that direct 4D TOF image reconstruction can substantially prevent kinetic parameter error propagation either from erroneous kinetic modelling, inter-frame motion or emission/transmission mismatch. Furthermore, we demonstrate the benefits of TOF in parameter estimation when conventional post-reconstruction (3D) methods are used and compare the potential improvements to direct 4D methods. Further improvements could possibly be achieved in the future by combining TOF direct 4D image reconstruction with adaptive kinetic models and inter-frame motion correction schemes.

A review of GPU-based medical image reconstruction.

PubMed

Després, Philippe; Jia, Xun

2017-10-01

Tomographic image reconstruction is a computationally demanding task, even more so when advanced models are used to describe a more complete and accurate picture of the image formation process. Such advanced modeling and reconstruction algorithms can lead to better images, often with less dose, but at the price of long calculation times that are hardly compatible with clinical workflows. Fortunately, reconstruction tasks can often be executed advantageously on Graphics Processing Units (GPUs), which are exploited as massively parallel computational engines. This review paper focuses on recent developments made in GPU-based medical image reconstruction, from a CT, PET, SPECT, MRI and US perspective. Strategies and approaches to get the most out of GPUs in image reconstruction are presented as well as innovative applications arising from an increased computing capacity. The future of GPU-based image reconstruction is also envisioned, based on current trends in high-performance computing. Copyright © 2017 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Multi-modal molecular diffuse optical tomography system for small animal imaging

PubMed Central

Guggenheim, James A.; Basevi, Hector R. A.; Frampton, Jon; Styles, Iain B.; Dehghani, Hamid

2013-01-01

A multi-modal optical imaging system for quantitative 3D bioluminescence and functional diffuse imaging is presented, which has no moving parts and uses mirrors to provide multi-view tomographic data for image reconstruction. It is demonstrated that through the use of trans-illuminated spectral near infrared measurements and spectrally constrained tomographic reconstruction, recovered concentrations of absorbing agents can be used as prior knowledge for bioluminescence imaging within the visible spectrum. Additionally, the first use of a recently developed multi-view optical surface capture technique is shown and its application to model-based image reconstruction and free-space light modelling is demonstrated. The benefits of model-based tomographic image recovery as compared to 2D planar imaging are highlighted in a number of scenarios where the internal luminescence source is not visible or is confounding in 2D images. The results presented show that the luminescence tomographic imaging method produces 3D reconstructions of individual light sources within a mouse-sized solid phantom that are accurately localised to within 1.5mm for a range of target locations and depths indicating sensitivity and accurate imaging throughout the phantom volume. Additionally the total reconstructed luminescence source intensity is consistent to within 15% which is a dramatic improvement upon standard bioluminescence imaging. Finally, results from a heterogeneous phantom with an absorbing anomaly are presented demonstrating the use and benefits of a multi-view, spectrally constrained coupled imaging system that provides accurate 3D luminescence images. PMID:24954977

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

De Carlo, Francesco; Gürsoy, Doğa; Ching, Daniel J.

There is a widening gap between the fast advancement of computational methods for tomographic reconstruction and their successful implementation in production software at various synchrotron facilities. This is due in part to the lack of readily available instrument datasets and phantoms representative of real materials for validation and comparison of new numerical methods. Recent advancements in detector technology made sub-second and multi-energy tomographic data collection possible [1], but also increased the demand to develop new reconstruction methods able to handle in-situ [2] and dynamic systems [3] that can be quickly incorporated in beamline production software [4]. The X-ray Tomography Datamore » Bank, tomoBank, provides a repository of experimental and simulated datasets with the aim to foster collaboration among computational scientists, beamline scientists, and experimentalists and to accelerate the development and implementation of tomographic reconstruction methods for synchrotron facility production software by providing easy access to challenging dataset and their descriptors.« less

Fast projection/backprojection and incremental methods applied to synchrotron light tomographic reconstruction.

PubMed

de Lima, Camila; Salomão Helou, Elias

2018-01-01

Iterative methods for tomographic image reconstruction have the computational cost of each iteration dominated by the computation of the (back)projection operator, which take roughly O(N 3 ) floating point operations (flops) for N × N pixels images. Furthermore, classical iterative algorithms may take too many iterations in order to achieve acceptable images, thereby making the use of these techniques unpractical for high-resolution images. Techniques have been developed in the literature in order to reduce the computational cost of the (back)projection operator to O(N 2 logN) flops. Also, incremental algorithms have been devised that reduce by an order of magnitude the number of iterations required to achieve acceptable images. The present paper introduces an incremental algorithm with a cost of O(N 2 logN) flops per iteration and applies it to the reconstruction of very large tomographic images obtained from synchrotron light illuminated data.

Tensor-based Dictionary Learning for Dynamic Tomographic Reconstruction

PubMed Central

Tan, Shengqi; Zhang, Yanbo; Wang, Ge; Mou, Xuanqin; Cao, Guohua; Wu, Zhifang; Yu, Hengyong

2015-01-01

In dynamic computed tomography (CT) reconstruction, the data acquisition speed limits the spatio-temporal resolution. Recently, compressed sensing theory has been instrumental in improving CT reconstruction from far few-view projections. In this paper, we present an adaptive method to train a tensor-based spatio-temporal dictionary for sparse representation of an image sequence during the reconstruction process. The correlations among atoms and across phases are considered to capture the characteristics of an object. The reconstruction problem is solved by the alternating direction method of multipliers. To recover fine or sharp structures such as edges, the nonlocal total variation is incorporated into the algorithmic framework. Preclinical examples including a sheep lung perfusion study and a dynamic mouse cardiac imaging demonstrate that the proposed approach outperforms the vectorized dictionary-based CT reconstruction in the case of few-view reconstruction. PMID:25779991

Tomographic diffractive microscopy with a wavefront sensor.

PubMed

Ruan, Y; Bon, P; Mudry, E; Maire, G; Chaumet, P C; Giovannini, H; Belkebir, K; Talneau, A; Wattellier, B; Monneret, S; Sentenac, A

2012-05-15

Tomographic diffractive microscopy is a recent imaging technique that reconstructs quantitatively the three-dimensional permittivity map of a sample with a resolution better than that of conventional wide-field microscopy. Its main drawbacks lie in the complexity of the setup and in the slowness of the image recording as both the amplitude and the phase of the field scattered by the sample need to be measured for hundreds of successive illumination angles. In this Letter, we show that, using a wavefront sensor, tomographic diffractive microscopy can be implemented easily on a conventional microscope. Moreover, the number of illuminations can be dramatically decreased if a constrained reconstruction algorithm is used to recover the sample map of permittivity.

Tomographic and analog 3-D simulations using NORA. [Non-Overlapping Redundant Image Array formed by multiple pinholes

NASA Technical Reports Server (NTRS)

Yin, L. I.; Trombka, J. I.; Bielefeld, M. J.; Seltzer, S. M.

1984-01-01

The results of two computer simulations demonstrate the feasibility of using the nonoverlapping redundant array (NORA) to form three-dimensional images of objects with X-rays. Pinholes admit the X-rays to nonoverlapping points on a detector. The object is reconstructed in the analog mode by optical correlation and in the digital mode by tomographic computations. Trials were run with a stick-figure pyramid and extended objects with out-of-focus backgrounds. Substitution of spherical optical lenses for the pinholes increased the light transmission sufficiently that objects could be easily viewed in a dark room. Out-of-focus aberrations in tomographic reconstruction could be eliminated using Chang's (1976) algorithm.

3D reconstruction of the magnetic vector potential using model based iterative reconstruction

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

Prabhat, K. C.; Aditya Mohan, K.; Phatak, Charudatta

Lorentz transmission electron microscopy (TEM) observations of magnetic nanoparticles contain information on the magnetic and electrostatic potentials. Vector field electron tomography (VFET) can be used to reconstruct electromagnetic potentials of the nanoparticles from their corresponding LTEM images. The VFET approach is based on the conventional filtered back projection approach to tomographic reconstructions and the availability of an incomplete set of measurements due to experimental limitations means that the reconstructed vector fields exhibit significant artifacts. In this paper, we outline a model-based iterative reconstruction (MBIR) algorithm to reconstruct the magnetic vector potential of magnetic nanoparticles. We combine a forward model formore » image formation in TEM experiments with a prior model to formulate the tomographic problem as a maximum a-posteriori probability estimation problem (MAP). The MAP cost function is minimized iteratively to determine the vector potential. Here, a comparative reconstruction study of simulated as well as experimental data sets show that the MBIR approach yields quantifiably better reconstructions than the VFET approach.« less

3D reconstruction of the magnetic vector potential using model based iterative reconstruction.

PubMed

Prabhat, K C; Aditya Mohan, K; Phatak, Charudatta; Bouman, Charles; De Graef, Marc

2017-11-01

Lorentz transmission electron microscopy (TEM) observations of magnetic nanoparticles contain information on the magnetic and electrostatic potentials. Vector field electron tomography (VFET) can be used to reconstruct electromagnetic potentials of the nanoparticles from their corresponding LTEM images. The VFET approach is based on the conventional filtered back projection approach to tomographic reconstructions and the availability of an incomplete set of measurements due to experimental limitations means that the reconstructed vector fields exhibit significant artifacts. In this paper, we outline a model-based iterative reconstruction (MBIR) algorithm to reconstruct the magnetic vector potential of magnetic nanoparticles. We combine a forward model for image formation in TEM experiments with a prior model to formulate the tomographic problem as a maximum a-posteriori probability estimation problem (MAP). The MAP cost function is minimized iteratively to determine the vector potential. A comparative reconstruction study of simulated as well as experimental data sets show that the MBIR approach yields quantifiably better reconstructions than the VFET approach. Copyright © 2017 Elsevier B.V. All rights reserved.

3D reconstruction of the magnetic vector potential using model based iterative reconstruction

DOE PAGES

Prabhat, K. C.; Aditya Mohan, K.; Phatak, Charudatta; ...

2017-07-03

Lorentz transmission electron microscopy (TEM) observations of magnetic nanoparticles contain information on the magnetic and electrostatic potentials. Vector field electron tomography (VFET) can be used to reconstruct electromagnetic potentials of the nanoparticles from their corresponding LTEM images. The VFET approach is based on the conventional filtered back projection approach to tomographic reconstructions and the availability of an incomplete set of measurements due to experimental limitations means that the reconstructed vector fields exhibit significant artifacts. In this paper, we outline a model-based iterative reconstruction (MBIR) algorithm to reconstruct the magnetic vector potential of magnetic nanoparticles. We combine a forward model formore » image formation in TEM experiments with a prior model to formulate the tomographic problem as a maximum a-posteriori probability estimation problem (MAP). The MAP cost function is minimized iteratively to determine the vector potential. Here, a comparative reconstruction study of simulated as well as experimental data sets show that the MBIR approach yields quantifiably better reconstructions than the VFET approach.« less

The accuracy of tomographic particle image velocimetry for measurements of a turbulent boundary layer

NASA Astrophysics Data System (ADS)

Atkinson, Callum; Coudert, Sebastien; Foucaut, Jean-Marc; Stanislas, Michel; Soria, Julio

2011-04-01

To investigate the accuracy of tomographic particle image velocimetry (Tomo-PIV) for turbulent boundary layer measurements, a series of synthetic image-based simulations and practical experiments are performed on a high Reynolds number turbulent boundary layer at Reθ = 7,800. Two different approaches to Tomo-PIV are examined using a full-volume slab measurement and a thin-volume "fat" light sheet approach. Tomographic reconstruction is performed using both the standard MART technique and the more efficient MLOS-SMART approach, showing a 10-time increase in processing speed. Random and bias errors are quantified under the influence of the near-wall velocity gradient, reconstruction method, ghost particles, seeding density and volume thickness, using synthetic images. Experimental Tomo-PIV results are compared with hot-wire measurements and errors are examined in terms of the measured mean and fluctuating profiles, probability density functions of the fluctuations, distributions of fluctuating divergence through the volume and velocity power spectra. Velocity gradients have a large effect on errors near the wall and also increase the errors associated with ghost particles, which convect at mean velocities through the volume thickness. Tomo-PIV provides accurate experimental measurements at low wave numbers; however, reconstruction introduces high noise levels that reduces the effective spatial resolution. A thinner volume is shown to provide a higher measurement accuracy at the expense of the measurement domain, albeit still at a lower effective spatial resolution than planar and Stereo-PIV.

Subsurface PpIX imaging in vivo with ultrasound-guided tomographic spectroscopy: reconstruction vs. born-normalized data

NASA Astrophysics Data System (ADS)

Flynn, Brendan P.; D'Souza, Alisha V.; Kanick, Stephen C.; Maytin, Edward; Hasan, Tayyaba; Pogue, Brian W.

2013-03-01

Aminolevulinic acid (ALA)-induced Protoporphyrin IX (PpIX)-based photodynamic therapy (PDT) is an effective treatment for skin cancers including basal cell carcinoma (BCC). Topically applied ALA promotes PpIX production preferentially in tumors, and many strategies have been developed to increase PpIX distribution and PDT treatment efficacy at depths > 1mm is not fully understood. While surface imaging techniques provide useful diagnosis, dosimetry, and efficacy information for superficial tumors, these methods cannot interrogate deeper tumors to provide in situ insight into spatial PpIX distributions. We have developed an ultrasound-guided, white-light-informed, tomographics spectroscopy system for the spatial measurement of subsurface PpIX. Detailed imaging system specifications, methodology, and optical-phantom-based characterization will be presented separately. Here we evaluate preliminary in vivo results using both full tomographic reconstruction and by plotting individual tomographic source-detector pair data against US images.

Compressive sensing reconstruction of 3D wet refractivity based on GNSS and InSAR observations

NASA Astrophysics Data System (ADS)

Heublein, Marion; Alshawaf, Fadwa; Erdnüß, Bastian; Zhu, Xiao Xiang; Hinz, Stefan

2018-06-01

In this work, the reconstruction quality of an approach for neutrospheric water vapor tomography based on Slant Wet Delays (SWDs) obtained from Global Navigation Satellite Systems (GNSS) and Interferometric Synthetic Aperture Radar (InSAR) is investigated. The novelties of this approach are (1) the use of both absolute GNSS and absolute InSAR SWDs for tomography and (2) the solution of the tomographic system by means of compressive sensing (CS). The tomographic reconstruction is performed based on (i) a synthetic SWD dataset generated using wet refractivity information from the Weather Research and Forecasting (WRF) model and (ii) a real dataset using GNSS and InSAR SWDs. Thus, the validation of the achieved results focuses (i) on a comparison of the refractivity estimates with the input WRF refractivities and (ii) on radiosonde profiles. In case of the synthetic dataset, the results show that the CS approach yields a more accurate and more precise solution than least squares (LSQ). In addition, the benefit of adding synthetic InSAR SWDs into the tomographic system is analyzed. When applying CS, adding synthetic InSAR SWDs into the tomographic system improves the solution both in magnitude and in scattering. When solving the tomographic system by means of LSQ, no clear behavior is observed. In case of the real dataset, the estimated refractivities of both methodologies show a consistent behavior although the LSQ and CS solution strategies differ.

Investigating Gravity Waves in Polar Mesospheric Clouds Using Tomographic Reconstructions of AIM Satellite Imagery

NASA Astrophysics Data System (ADS)

Hart, V. P.; Taylor, M. J.; Doyle, T. E.; Zhao, Y.; Pautet, P.-D.; Carruth, B. L.; Rusch, D. W.; Russell, J. M.

2018-01-01

This research presents the first application of tomographic techniques for investigating gravity wave structures in polar mesospheric clouds (PMCs) imaged by the Cloud Imaging and Particle Size instrument on the NASA AIM satellite. Albedo data comprising consecutive PMC scenes were used to tomographically reconstruct a 3-D layer using the Partially Constrained Algebraic Reconstruction Technique algorithm and a previously developed "fanning" technique. For this pilot study, a large region (760 × 148 km) of the PMC layer (altitude 83 km) was sampled with a 2 km horizontal resolution, and an intensity weighted centroid technique was developed to create novel 2-D surface maps, characterizing the individual gravity waves as well as their altitude variability. Spectral analysis of seven selected wave events observed during the Northern Hemisphere 2007 PMC season exhibited dominant horizontal wavelengths of 60-90 km, consistent with previous studies. These tomographic analyses have enabled a broad range of new investigations. For example, a clear spatial anticorrelation was observed between the PMC albedo and wave-induced altitude changes, with higher-albedo structures aligning well with wave troughs, while low-intensity regions aligned with wave crests. This result appears to be consistent with current theories of PMC development in the mesopause region. This new tomographic imaging technique also provides valuable wave amplitude information enabling further mesospheric gravity wave investigations, including quantitative analysis of their hemispheric and interannual characteristics and variations.

Characterization and MCNP simulation of neutron energy spectrum shift after transmission through strong absorbing materials and its impact on tomography reconstructed image.

PubMed

Hachouf, N; Kharfi, F; Boucenna, A

2012-10-01

An ideal neutron radiograph, for quantification and 3D tomographic image reconstruction, should be a transmission image which exactly obeys to the exponential attenuation law of a monochromatic neutron beam. There are many reasons for which this assumption does not hold for high neutron absorbing materials. The main deviations from the ideal are due essentially to neutron beam hardening effect. The main challenges of this work are the characterization of neutron transmission through boron enriched steel materials and the observation of beam hardening. Then, in our work, the influence of beam hardening effect on neutron tomographic image, for samples based on these materials, is studied. MCNP and FBP simulation are performed to adjust linear attenuation coefficients data and to perform 2D tomographic image reconstruction with and without beam hardening corrections. A beam hardening correction procedure is developed and applied based on qualitative and quantitative analyses of the projections data. Results from original and corrected 2D reconstructed images obtained shows the efficiency of the proposed correction procedure. Copyright © 2012 Elsevier Ltd. All rights reserved.

Phase contrast X-ray microtomography of the Rhodnius prolixus head: Comparison of direct reconstruction and phase retrieval approach

NASA Astrophysics Data System (ADS)

Almeida, A. P.; Braz, D.; Nogueira, L. P.; Colaço, M. V.; Soares, J.; Cardoso, S. C.; Garcia, E. S.; Azambuja, P.; Gonzalez, M. S.; Mohammadi, S.; Tromba, G.; Barroso, R. C.

2014-02-01

We have used phase-contrast X-ray microtomography (PPC-μCT) to study the head of the blood-feeding bug, Rhodnius prolixus, which is one of the most important insect vector of Trypanosoma cruzi, ethiologic agent of Chagas disease in Latin America. Images reconstructed from phase-retrieved projections processed by ANKA phase are compared to those obtained through direct tomographic reconstruction of the flat-field-corrected transmission radiographs. It should be noted that the relative locations of the important morphological internal structures are observable with a precision that is difficult to obtain without the phase retrieval approach.

A Survey of the Use of Iterative Reconstruction Algorithms in Electron Microscopy

PubMed Central

Otón, J.; Vilas, J. L.; Kazemi, M.; Melero, R.; del Caño, L.; Cuenca, J.; Conesa, P.; Gómez-Blanco, J.; Marabini, R.; Carazo, J. M.

2017-01-01

One of the key steps in Electron Microscopy is the tomographic reconstruction of a three-dimensional (3D) map of the specimen being studied from a set of two-dimensional (2D) projections acquired at the microscope. This tomographic reconstruction may be performed with different reconstruction algorithms that can be grouped into several large families: direct Fourier inversion methods, back-projection methods, Radon methods, or iterative algorithms. In this review, we focus on the latter family of algorithms, explaining the mathematical rationale behind the different algorithms in this family as they have been introduced in the field of Electron Microscopy. We cover their use in Single Particle Analysis (SPA) as well as in Electron Tomography (ET). PMID:29312997

A 3D gantry single photon emission tomograph with hemispherical coverage for dedicated breast imaging

NASA Astrophysics Data System (ADS)

Tornai, Martin P.; Bowsher, James E.; Archer, Caryl N.; Peter, Jörg; Jaszczak, Ronald J.; MacDonald, Lawrence R.; Patt, Bradley E.; Iwanczyk, Jan S.

2003-01-01

A novel tomographic gantry was designed, built and initially evaluated for single photon emission imaging of metabolically active lesions in the pendant breast and near chest wall. Initial emission imaging measurements with breast lesions of various uptake ratios are presented. Methods: A prototype tomograph was constructed utilizing a compact gamma camera having a field-of-view of <13×13 cm 2 with arrays of 2×2×6 mm 3 quantized NaI(Tl) scintillators coupled to position sensitive PMTs. The camera was mounted on a radially oriented support with 6 cm variable radius-of-rotation. This unit is further mounted on a goniometric cradle providing polar motion, and in turn mounted on an azimuthal rotation stage capable of indefinite vertical axis-of-rotation about the central rotation axis (RA). Initial measurements with isotopic Tc-99 m (140 keV) to evaluate the system include acquisitions with various polar tilt angles about the RA. Tomographic measurements were made of a frequency and resolution cold-rod phantom filled with aqueous Tc-99 m. Tomographic and planar measurements of 0.6 and 1.0 cm diameter fillable spheres in an available ˜950 ml hemi-ellipsoidal (uncompressed) breast phantom attached to a life-size anthropomorphic torso phantom with lesion:breast-and-body:cardiac-and-liver activity concentration ratios of 11:1:19 were compared. Various photopeak energy windows from 10-30% widths were obtained, along with a 35% scatter window below a 15% photopeak window from the list mode data. Projections with all photopeak window and camera tilt conditions were reconstructed with an ordered subsets expectation maximization (OSEM) algorithm capable of reconstructing arbitrary tomographic orbits. Results: As iteration number increased for the tomographically measured data at all polar angles, contrasts increased while signal-to-noise ratios (SNRs) decreased in the expected way with OSEM reconstruction. The rollover between contrast improvement and SNR degradation of the lesion occurred at two to three iterations. The reconstructed tomographic data yielded SNRs with or without scatter correction that were >9 times better than the planar scans. There was up to a factor of ˜2.5 increase in total primary and scatter contamination in the photopeak window with increasing tilt angle from 15° to 45°, consistent with more direct line-of-sight of myocardial and liver activity with increased camera polar angle. Conclusion: This new, ultra-compact, dedicated tomographic imaging system has the potential of providing valuable, fully 3D functional information about small, otherwise indeterminate breast lesions as an adjunct to diagnostic mammography.

Markov chain Monte Carlo estimation of quantum states

NASA Astrophysics Data System (ADS)

Diguglielmo, James; Messenger, Chris; Fiurášek, Jaromír; Hage, Boris; Samblowski, Aiko; Schmidt, Tabea; Schnabel, Roman

2009-03-01

We apply a Bayesian data analysis scheme known as the Markov chain Monte Carlo to the tomographic reconstruction of quantum states. This method yields a vector, known as the Markov chain, which contains the full statistical information concerning all reconstruction parameters including their statistical correlations with no a priori assumptions as to the form of the distribution from which it has been obtained. From this vector we can derive, e.g., the marginal distributions and uncertainties of all model parameters, and also of other quantities such as the purity of the reconstructed state. We demonstrate the utility of this scheme by reconstructing the Wigner function of phase-diffused squeezed states. These states possess non-Gaussian statistics and therefore represent a nontrivial case of tomographic reconstruction. We compare our results to those obtained through pure maximum-likelihood and Fisher information approaches.

Synthetic Incoherence via Scanned Gaussian Beams

PubMed Central

Levine, Zachary H.

2006-01-01

Tomography, in most formulations, requires an incoherent signal. For a conventional transmission electron microscope, the coherence of the beam often results in diffraction effects that limit the ability to perform a 3D reconstruction from a tilt series with conventional tomographic reconstruction algorithms. In this paper, an analytic solution is given to a scanned Gaussian beam, which reduces the beam coherence to be effectively incoherent for medium-size (of order 100 voxels thick) tomographic applications. The scanned Gaussian beam leads to more incoherence than hollow-cone illumination. PMID:27274945

Equation for wave processes in inhomogeneous moving media and functional solution of the acoustic tomography problem based on it

NASA Astrophysics Data System (ADS)

Rumyantseva, O. D.; Shurup, A. S.

2017-01-01

The paper considers the derivation of the wave equation and Helmholtz equation for solving the tomographic problem of reconstruction combined scalar-vector inhomogeneities describing perturbations of the sound velocity and absorption, the vector field of flows, and perturbations of the density of the medium. Restrictive conditions under which the obtained equations are meaningful are analyzed. Results of numerical simulation of the two-dimensional functional-analytical Novikov-Agaltsov algorithm for reconstructing the flow velocity using the the obtained Helmholtz equation are presented.

3D tomographic imaging with the γ-eye planar scintigraphic gamma camera

NASA Astrophysics Data System (ADS)

Tunnicliffe, H.; Georgiou, M.; Loudos, G. K.; Simcox, A.; Tsoumpas, C.

2017-11-01

γ-eye is a desktop planar scintigraphic gamma camera (100 mm × 50 mm field of view) designed by BET Solutions as an affordable tool for dynamic, whole body, small-animal imaging. This investigation tests the viability of using γ-eye for the collection of tomographic data for 3D SPECT reconstruction. Two software packages, QSPECT and STIR (software for tomographic image reconstruction), have been compared. Reconstructions have been performed using QSPECT’s implementation of the OSEM algorithm and STIR’s OSMAPOSL (Ordered Subset Maximum A Posteriori One Step Late) and OSSPS (Ordered Subsets Separable Paraboloidal Surrogate) algorithms. Reconstructed images of phantom and mouse data have been assessed in terms of spatial resolution, sensitivity to varying activity levels and uniformity. The effect of varying the number of iterations, the voxel size (1.25 mm default voxel size reduced to 0.625 mm and 0.3125 mm), the point spread function correction and the weight of prior terms were explored. While QSPECT demonstrated faster reconstructions, STIR outperformed it in terms of resolution (as low as 1 mm versus 3 mm), particularly when smaller voxel sizes were used, and in terms of uniformity, particularly when prior terms were used. Little difference in terms of sensitivity was seen throughout.

Computed Tomography Angiography in Microsurgery: Indications, Clinical Utility, and Pitfalls

PubMed Central

Lee, Gordon K.; Fox, Paige M.; Riboh, Jonathan; Hsu, Charles; Saber, Sepideh; Rubin, Geoffrey D.; Chang, James

2013-01-01

Objective: Computed tomographic angiography (CTA) can be used to obtain 3-dimensional vascular images and soft-tissue definition. The goal of this study was to evaluate the reliability, usefulness, and pitfalls of CTA in preoperative planning of microvascular reconstructive surgery. Methods: A retrospective review of patients who obtained preoperative CTA in preparation for planned microvascular reconstruction was performed over a 5-year period (2001–2005). The influence of CTA on the original operative plan was assessed for each patient, and CTA results were correlated to the operative findings. Results: Computed tomographic angiography was performed on 94 patients in preparation for microvascular reconstruction. In 48 patients (51%), vascular abnormalities were noted on CTA. Intraoperative findings correlated with CTA results in 97% of cases. In 42 patients (45%), abnormal CTA findings influenced the original operative plan, such as the choice of vessels, side of harvest, or nature of the reconstruction (local flap instead of free tissue transfer). Technical difficulties in performing CTA were encountered in 5 patients (5%) in whom interference from external fixation devices was the main cause. Conclusions: This large study of CTA obtained for preoperative planning of reconstructive microsurgery at both donor and recipient sites study demonstrates that CTA is safe and highly accurate. Computed tomographic angiography can alter the surgeon's reconstructive plan when abnormalities are noted preoperatively and consequently improve results by decreasing vascular complication rates. The use of CTA should be considered for cases of microsurgical reconstruction where the vascular anatomy may be questionable. PMID:24023972

Development of a high-performance noise-reduction filter for tomographic reconstruction

NASA Astrophysics Data System (ADS)

Kao, Chien-Min; Pan, Xiaochuan

2001-07-01

We propose a new noise-reduction method for tomographic reconstruction. The method incorporates a priori information on the source image for allowing the derivation of the energy spectrum of its ideal sinogram. In combination with the energy spectrum of the Poisson noise in the measured sinogram, we are able to derive a Wiener-like filter for effective suppression of the sinogram noise. The filtered backprojection (FBP) algorithm, with a ramp filter, is then applied to the filtered sinogram to produce tomographic images. The resulting filter has a closed-form expression in the frequency space and contains a single user-adjustable regularization parameter. The proposed method is hence simple to implement and easy to use. In contrast to the ad hoc apodizing windows, such as Hanning and Butterworth filters, that are commonly used in the conventional FBP reconstruction, the proposed filter is theoretically more rigorous as it is derived by basing upon an optimization criterion, subject to a known class of source image intensity distributions.

First results from the ionospheric tomography experiment using beacon TEC data obtained by means of a network along a longitude of 136°E over Japan

NASA Astrophysics Data System (ADS)

Thampi, Smitha V.; Yamamoto, Mamoru

2010-03-01

A chain of newly designed GNU (GNU is not UNIX) Radio Beacon Receivers (GRBR) has recently been established over Japan, primarily for tomographic imaging of the ionosphere over this region. Receivers installed at Shionomisaki (33.45°N, 135.8°E), Shigaraki (34.8°N, 136.1°E), and Fukui (36°N, 136°E) continuously track low earth orbiting satellites (LEOS), mainly OSCAR, Cosmos, and FORMOSAT-3/COSMIC, to obtain simultaneous total electron content (TEC) data from these three locations, which are then used for the tomographic reconstruction of ionospheric electron densities. This is the first GRBR network established for TEC observations, and the first beacon-based tomographic imaging in Japanese longitudes. The first tomographic images revealed the temporal evolution with all of the major features in the ionospheric electron density distribution over Japan. A comparison of the tomographically reconstructed electron densities with the ƒ o F 2 data from Kokubunji (35°N, 139°E) revealed that there was good agreement between the datasets. These first results show the potential of GRBR and its network for making continuous, unattended ionospheric TEC measurements and for tomographic imaging of the ionosphere.

Automated tilt series alignment and tomographic reconstruction in IMOD.

PubMed

Mastronarde, David N; Held, Susannah R

2017-02-01

Automated tomographic reconstruction is now possible in the IMOD software package, including the merging of tomograms taken around two orthogonal axes. Several developments enable the production of high-quality tomograms. When using fiducial markers for alignment, the markers to be tracked through the series are chosen automatically; if there is an excess of markers available, a well-distributed subset is selected that is most likely to track well. Marker positions are refined by applying an edge-enhancing Sobel filter, which results in a 20% improvement in alignment error for plastic-embedded samples and 10% for frozen-hydrated samples. Robust fitting, in which outlying points are given less or no weight in computing the fitting error, is used to obtain an alignment solution, so that aberrant points from the automated tracking can have little effect on the alignment. When merging two dual-axis tomograms, the alignment between them is refined from correlations between local patches; a measure of structure was developed so that patches with insufficient structure to give accurate correlations can now be excluded automatically. We have also developed a script for running all steps in the reconstruction process with a flexible mechanism for setting parameters, and we have added a user interface for batch processing of tilt series to the Etomo program in IMOD. Batch processing is fully compatible with interactive processing and can increase efficiency even when the automation is not fully successful, because users can focus their effort on the steps that require manual intervention. Copyright © 2016 Elsevier Inc. All rights reserved.

Tomographic imaging of flourescence resonance energy transfer in highly light scattering media

NASA Astrophysics Data System (ADS)

Soloviev, Vadim Y.; McGinty, James; Tahir, Khadija B.; Laine, Romain; Stuckey, Daniel W.; Mohan, P. Surya; Hajnal, Joseph V.; Sardini, Alessandro; French, Paul M. W.; Arridge, Simon R.

2010-02-01

Three-dimensional localization of protein conformation changes in turbid media using Förster Resonance Energy Transfer (FRET) was investigated by tomographic fluorescence lifetime imaging (FLIM). FRET occurs when a donor fluorophore, initially in its electronic excited state, transfers energy to an acceptor fluorophore in close proximity through non-radiative dipole-dipole coupling. An acceptor effectively behaves as a quencher of the donor's fluorescence. The quenching process is accompanied by a reduction in the quantum yield and lifetime of the donor fluorophore. Therefore, FRET can be localized by imaging changes in the quantum yield and the fluorescence lifetime of the donor fluorophore. Extending FRET to diffuse optical tomography has potentially important applications such as in vivo studies in small animal. We show that FRET can be localized by reconstructing the quantum yield and lifetime distribution from time-resolved non-invasive boundary measurements of fluorescence and transmitted excitation radiation. Image reconstruction was obtained by an inverse scattering algorithm. Thus we report, to the best of our knowledge, the first tomographic FLIM-FRET imaging in turbid media. The approach is demonstrated by imaging a highly scattering cylindrical phantom concealing two thin wells containing cytosol preparations of HEK293 cells expressing TN-L15, a cytosolic genetically-encoded calcium FRET sensor. A 10mM calcium chloride solution was added to one of the wells to induce a protein conformation change upon binding to TN-L15, resulting in FRET and a corresponding decrease in the donor fluorescence lifetime. The resulting fluorescence lifetime distribution, the quantum efficiency, absorption and scattering coefficients were reconstructed.

A resolution-enhancing image reconstruction method for few-view differential phase-contrast tomography

NASA Astrophysics Data System (ADS)

Guan, Huifeng; Anastasio, Mark A.

2017-03-01

It is well-known that properly designed image reconstruction methods can facilitate reductions in imaging doses and data-acquisition times in tomographic imaging. The ability to do so is particularly important for emerging modalities such as differential X-ray phase-contrast tomography (D-XPCT), which are currently limited by these factors. An important application of D-XPCT is high-resolution imaging of biomedical samples. However, reconstructing high-resolution images from few-view tomographic measurements remains a challenging task. In this work, a two-step sub-space reconstruction strategy is proposed and investigated for use in few-view D-XPCT image reconstruction. It is demonstrated that the resulting iterative algorithm can mitigate the high-frequency information loss caused by data incompleteness and produce images that have better preserved high spatial frequency content than those produced by use of a conventional penalized least squares (PLS) estimator.

Acceleration of image-based resolution modelling reconstruction using an expectation maximization nested algorithm.

PubMed

Angelis, G I; Reader, A J; Markiewicz, P J; Kotasidis, F A; Lionheart, W R; Matthews, J C

2013-08-07

Recent studies have demonstrated the benefits of a resolution model within iterative reconstruction algorithms in an attempt to account for effects that degrade the spatial resolution of the reconstructed images. However, these algorithms suffer from slower convergence rates, compared to algorithms where no resolution model is used, due to the additional need to solve an image deconvolution problem. In this paper, a recently proposed algorithm, which decouples the tomographic and image deconvolution problems within an image-based expectation maximization (EM) framework, was evaluated. This separation is convenient, because more computational effort can be placed on the image deconvolution problem and therefore accelerate convergence. Since the computational cost of solving the image deconvolution problem is relatively small, multiple image-based EM iterations do not significantly increase the overall reconstruction time. The proposed algorithm was evaluated using 2D simulations, as well as measured 3D data acquired on the high-resolution research tomograph. Results showed that bias reduction can be accelerated by interleaving multiple iterations of the image-based EM algorithm solving the resolution model problem, with a single EM iteration solving the tomographic problem. Significant improvements were observed particularly for voxels that were located on the boundaries between regions of high contrast within the object being imaged and for small regions of interest, where resolution recovery is usually more challenging. Minor differences were observed using the proposed nested algorithm, compared to the single iteration normally performed, when an optimal number of iterations are performed for each algorithm. However, using the proposed nested approach convergence is significantly accelerated enabling reconstruction using far fewer tomographic iterations (up to 70% fewer iterations for small regions). Nevertheless, the optimal number of nested image-based EM iterations is hard to be defined and it should be selected according to the given application.

Sodankylä ionospheric tomography data set 2003-2014

NASA Astrophysics Data System (ADS)

Norberg, Johannes; Roininen, Lassi; Kero, Antti; Raita, Tero; Ulich, Thomas; Markkanen, Markku; Juusola, Liisa; Kauristie, Kirsti

2016-07-01

Sodankylä Geophysical Observatory has been operating a receiver network for ionospheric tomography and collecting the produced data since 2003. The collected data set consists of phase difference curves measured from COSMOS navigation satellites from the Russian Parus network (Wood and Perry, 1980) and tomographic electron density reconstructions obtained from these measurements. In this study vertical total electron content (VTEC) values are integrated from the reconstructed electron densities to make a qualitative and quantitative analysis to validate the long-term performance of the tomographic system. During the observation period, 2003-2014, there were three to five operational stations at the Fennoscandia sector. Altogether the analysis consists of around 66 000 overflights, but to ensure the quality of the reconstructions, the examination is limited to cases with descending (north to south) overflights and maximum elevation over 60°. These constraints limit the number of overflights to around 10 000. Based on this data set, one solar cycle of ionospheric VTEC estimates is constructed. The measurements are compared against the International Reference Ionosphere (IRI)-2012 model, F10.7 solar flux index and sunspot number data. Qualitatively the tomographic VTEC estimate corresponds to reference data very well, but the IRI-2012 model results are on average 40 % higher than that of the tomographic results.

DART, a platform for the creation and registration of cone beam digital tomosynthesis datasets.

PubMed

Sarkar, Vikren; Shi, Chengyu; Papanikolaou, Niko

2011-04-01

Digital tomosynthesis is an imaging modality that allows for tomographic reconstructions using only a fraction of the images needed for CT reconstruction. Since it offers the advantages of tomographic images with a smaller imaging dose delivered to the patient, the technique offers much promise for use in patient positioning prior to radiation delivery. This paper describes a software environment developed to help in the creation of digital tomosynthesis image sets from digital portal images using three different reconstruction algorithms. The software then allows for use of the tomograms for patient positioning or for dose recalculation if shifts are not applied, possibly as part of an adaptive radiotherapy regimen.

Muon tomography imaging algorithms for nuclear threat detection inside large volume containers with the Muon Portal detector

NASA Astrophysics Data System (ADS)

Riggi, S.; Antonuccio-Delogu, V.; Bandieramonte, M.; Becciani, U.; Costa, A.; La Rocca, P.; Massimino, P.; Petta, C.; Pistagna, C.; Riggi, F.; Sciacca, E.; Vitello, F.

2013-11-01

Muon tomographic visualization techniques try to reconstruct a 3D image as close as possible to the real localization of the objects being probed. Statistical algorithms under test for the reconstruction of muon tomographic images in the Muon Portal Project are discussed here. Autocorrelation analysis and clustering algorithms have been employed within the context of methods based on the Point Of Closest Approach (POCA) reconstruction tool. An iterative method based on the log-likelihood approach was also implemented. Relative merits of all such methods are discussed, with reference to full GEANT4 simulations of different scenarios, incorporating medium and high-Z objects inside a container.

Initial evaluation of discrete orthogonal basis reconstruction of ECT images

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

Moody, E.B.; Donohue, K.D.

1996-12-31

Discrete orthogonal basis restoration (DOBR) is a linear, non-iterative, and robust method for solving inverse problems for systems characterized by shift-variant transfer functions. This simulation study evaluates the feasibility of using DOBR for reconstructing emission computed tomographic (ECT) images. The imaging system model uses typical SPECT parameters and incorporates the effects of attenuation, spatially-variant PSF, and Poisson noise in the projection process. Sample reconstructions and statistical error analyses for a class of digital phantoms compare the DOBR performance for Hartley and Walsh basis functions. Test results confirm that DOBR with either basis set produces images with good statistical properties. Nomore » problems were encountered with reconstruction instability. The flexibility of the DOBR method and its consistent performance warrants further investigation of DOBR as a means of ECT image reconstruction.« less

Hybrid-dual-fourier tomographic algorithm for a fast three-dimensionial optical image reconstruction in turbid media

NASA Technical Reports Server (NTRS)

Alfano, Robert R. (Inventor); Cai, Wei (Inventor)

2007-01-01

A reconstruction technique for reducing computation burden in the 3D image processes, wherein the reconstruction procedure comprises an inverse and a forward model. The inverse model uses a hybrid dual Fourier algorithm that combines a 2D Fourier inversion with a 1D matrix inversion to thereby provide high-speed inverse computations. The inverse algorithm uses a hybrid transfer to provide fast Fourier inversion for data of multiple sources and multiple detectors. The forward model is based on an analytical cumulant solution of a radiative transfer equation. The accurate analytical form of the solution to the radiative transfer equation provides an efficient formalism for fast computation of the forward model.

3D ion velocity distribution function measurement in an electric thruster using laser induced fluorescence tomography

NASA Astrophysics Data System (ADS)

Elias, P. Q.; Jarrige, J.; Cucchetti, E.; Cannat, F.; Packan, D.

2017-09-01

Measuring the full ion velocity distribution function (IVDF) by non-intrusive techniques can improve our understanding of the ionization processes and beam dynamics at work in electric thrusters. In this paper, a Laser-Induced Fluorescence (LIF) tomographic reconstruction technique is applied to the measurement of the IVDF in the plume of a miniature Hall effect thruster. A setup is developed to move the laser axis along two rotation axes around the measurement volume. The fluorescence spectra taken from different viewing angles are combined using a tomographic reconstruction algorithm to build the complete 3D (in phase space) time-averaged distribution function. For the first time, this technique is used in the plume of a miniature Hall effect thruster to measure the full distribution function of the xenon ions. Two examples of reconstructions are provided, in front of the thruster nose-cone and in front of the anode channel. The reconstruction reveals the features of the ion beam, in particular on the thruster axis where a toroidal distribution function is observed. These findings are consistent with the thruster shape and operation. This technique, which can be used with other LIF schemes, could be helpful in revealing the details of the ion production regions and the beam dynamics. Using a more powerful laser source, the current implementation of the technique could be improved to reduce the measurement time and also to reconstruct the temporal evolution of the distribution function.

Automatic alignment for three-dimensional tomographic reconstruction

NASA Astrophysics Data System (ADS)

van Leeuwen, Tristan; Maretzke, Simon; Joost Batenburg, K.

2018-02-01

In tomographic reconstruction, the goal is to reconstruct an unknown object from a collection of line integrals. Given a complete sampling of such line integrals for various angles and directions, explicit inverse formulas exist to reconstruct the object. Given noisy and incomplete measurements, the inverse problem is typically solved through a regularized least-squares approach. A challenge for both approaches is that in practice the exact directions and offsets of the x-rays are only known approximately due to, e.g. calibration errors. Such errors lead to artifacts in the reconstructed image. In the case of sufficient sampling and geometrically simple misalignment, the measurements can be corrected by exploiting so-called consistency conditions. In other cases, such conditions may not apply and we have to solve an additional inverse problem to retrieve the angles and shifts. In this paper we propose a general algorithmic framework for retrieving these parameters in conjunction with an algebraic reconstruction technique. The proposed approach is illustrated by numerical examples for both simulated data and an electron tomography dataset.

Two-step tomographic reconstructions of temperature and species concentration in a flame based on laser absorption measurements with a rotation platform

NASA Astrophysics Data System (ADS)

Xia, Huihui; Kan, Ruifeng; Xu, Zhenyu; He, Yabai; Liu, Jianguo; Chen, Bing; Yang, Chenguang; Yao, Lu; Wei, Min; Zhang, Guangle

2017-03-01

We present a system for accurate tomographic reconstruction of the combustion temperature and H2O vapor concentration of a flame based on laser absorption measurements, in combination with an innovative two-step algebraic reconstruction technique. A total of 11 collimated laser beams generated from outputs of fiber-coupled diode lasers formed a two-dimensional 5 × 6 orthogonal beam grids and measured at two H2O absorption transitions (7154.354/7154.353 cm-1 and 7467.769 cm-1). The measurement system was designed on a rotation platform to achieve a two-folder improvement in spatial resolution. Numerical simulation showed that the proposed two-step algebraic reconstruction technique for temperature and concentration, respectively, greatly improved the reconstruction accuracy of species concentration when compared with a traditional calculation. Experimental results demonstrated the good performances of the measurement system and the two-step reconstruction technique for applications such as flame monitoring and combustion diagnosis.

Reconstruction of spatial distributions of sound velocity and absorption in soft biological tissues using model ultrasonic tomographic data

NASA Astrophysics Data System (ADS)

Burov, V. A.; Zotov, D. I.; Rumyantseva, O. D.

2014-07-01

A two-step algorithm is used to reconstruct the spatial distributions of the acoustic characteristics of soft biological tissues-the sound velocity and absorption coefficient. Knowing these distributions is urgent for early detection of benign and malignant neoplasms in biological tissues, primarily in the breast. At the first stage, large-scale distributions are estimated; at the second step, they are refined with a high resolution. Results of reconstruction on the base of model initial data are presented. The principal necessity of preliminary reconstruction of large-scale distributions followed by their being taken into account at the second step is illustrated. The use of CUDA technology for processing makes it possible to obtain final images of 1024 × 1024 samples in only a few minutes.

'tomo_display' and 'vol_tools': IDL VM Packages for Tomography Data Reconstruction, Processing, and Visualization

NASA Astrophysics Data System (ADS)

Rivers, M. L.; Gualda, G. A.

2009-05-01

One of the challenges in tomography is the availability of suitable software for image processing and analysis in 3D. We present here 'tomo_display' and 'vol_tools', two packages created in IDL that enable reconstruction, processing, and visualization of tomographic data. They complement in many ways the capabilities offered by Blob3D (Ketcham 2005 - Geosphere, 1: 32-41, DOI: 10.1130/GES00001.1) and, in combination, allow users without programming knowledge to perform all steps necessary to obtain qualitative and quantitative information using tomographic data. The package 'tomo_display' was created and is maintained by Mark Rivers. It allows the user to: (1) preprocess and reconstruct parallel beam tomographic data, including removal of anomalous pixels, ring artifact reduction, and automated determination of the rotation center, (2) visualization of both raw and reconstructed data, either as individual frames, or as a series of sequential frames. The package 'vol_tools' consists of a series of small programs created and maintained by Guilherme Gualda to perform specific tasks not included in other packages. Existing modules include simple tools for cropping volumes, generating histograms of intensity, sample volume measurement (useful for porous samples like pumice), and computation of volume differences (for differential absorption tomography). The module 'vol_animate' can be used to generate 3D animations using rendered isosurfaces around objects. Both packages use the same NetCDF format '.volume' files created using code written by Mark Rivers. Currently, only 16-bit integer volumes are created and read by the packages, but floating point and 8-bit data can easily be stored in the NetCDF format as well. A simple GUI to convert sequences of tiffs into '.volume' files is available within 'vol_tools'. Both 'tomo_display' and 'vol_tools' include options to (1) generate onscreen output that allows for dynamic visualization in 3D, (2) save sequences of tiffs to disk, and (3) generate MPEG movies for inclusion in presentations, publications, websites, etc. Both are freely available as run-time ('.sav') versions that can be run using the free IDL Virtual Machine TM, available from ITT Visual Information Solutions: http://www.ittvis.com/ProductServices/IDL/VirtualMachine.aspx The run-time versions of 'tomo_display' and 'vol_tools' can be downloaded from: http://cars.uchicago.edu/software/idl/tomography.html http://sites.google.com/site/voltools/

Ultrasonic guided wave tomography of pipes: A development of new techniques for the nondestructive evaluation of cylindrical geometries and guided wave multi-mode analysis

NASA Astrophysics Data System (ADS)

Leonard, Kevin Raymond

This dissertation concentrates on the development of two new tomographic techniques that enable wide-area inspection of pipe-like structures. By envisioning a pipe as a plate wrapped around upon itself, the previous Lamb Wave Tomography (LWT) techniques are adapted to cylindrical structures. Helical Ultrasound Tomography (HUT) uses Lamb-like guided wave modes transmitted and received by two circumferential arrays in a single crosshole geometry. Meridional Ultrasound Tomography (MUT) creates the same crosshole geometry with a linear array of transducers along the axis of the cylinder. However, even though these new scanning geometries are similar to plates, additional complexities arise because they are cylindrical structures. First, because it is a single crosshole geometry, the wave vector coverage is poorer than in the full LWT system. Second, since waves can travel in both directions around the circumference of the pipe, modes can also constructively and destructively interfere with each other. These complexities necessitate improved signal processing algorithms to produce accurate and unambiguous tomographic reconstructions. Consequently, this work also describes a new algorithm for improving the extraction of multi-mode arrivals from guided wave signals. Previous work has relied solely on the first arriving mode for the time-of-flight measurements. In order to improve the LWT, HUT and MUT systems reconstructions, improved signal processing methods are needed to extract information about the arrival times of the later arriving modes. Because each mode has different through-thickness displacement values, they are sensitive to different types of flaws, and the information gained from the multi-mode analysis improves understanding of the structural integrity of the inspected material. Both tomographic frequency compounding and mode sorting algorithms are introduced. It is also shown that each of these methods improve the reconstructed images both qualitatively and quantitatively.

Digital Longitudinal Tomosynthesis

NASA Astrophysics Data System (ADS)

Rimkus, Daniel Steven

1985-12-01

The purpose of this dissertation was to investigate the clinical utility of digital longitudinal tomosynthesis in radiology. By acquiring a finite group of digital images during a longitudinal tomographic exposure, and processing these images, tomographic planes, other than the fulcrum plane, can be reconstructed. This process is now termed "tomosynthesis". A prototype system utilizing this technique was developed. Both phantom and patient studies were done with this system. The phantom studies were evaluated by subjective, visual criterion and by quantitative analysis of edge sharpness and noise in the reconstructions. Two groups of patients and one volunteer were studied. The first patient group consisted of 8 patients undergoing intravenous urography (IVU). These patients had digital tomography and film tomography of the abdomen. The second patient group consisted of 4 patients with lung cancer admitted to the hospital for laser resection of endobronchial tumor. These patients had mediastinal digital tomograms to evaluate the trachea and mainstem bronchi. The knee of one volunteer was imaged by film tomography and digital tomography. The results of the phantom studies showed that the digital reconstructions accurately produced images of the desired planes. The edge sharpness of the reconstructions approached that of the acquired images. Adequate reconstructions were achieved with as few as 5 images acquired during the exposure, with the quality of the reconstructions improving as the number of images acquired increased. The IVU patients' digital studies had less contrast and spatial resolution than the film tomograms. The single renal lesion visible on the film tomograms was also visible in the digital images. The digital mediastinal studies were felt by several radiologists to be superior to a standard chest xray in evaluating the airways. The digital images of the volunteer's knee showed many of the same anatomic features as the film tomogram, but the digital images had less spatial and contrast resolution. With the equipment improvements discussed in the thesis, digital tomography may have an important role in radiology.

Quantitative proton imaging from multiple physics processes: a proof of concept

NASA Astrophysics Data System (ADS)

Bopp, C.; Rescigno, R.; Rousseau, M.; Brasse, D.

2015-07-01

Proton imaging is developed in order to improve the accuracy of charged particle therapy treatment planning. It makes it possible to directly map the relative stopping powers of the materials using the information on the energy loss of the protons. In order to reach a satisfactory spatial resolution in the reconstructed images, the position and direction of each particle is recorded upstream and downstream from the patient. As a consequence of individual proton detection, information on the transmission rate and scattering of the protons is available. Image reconstruction processes are proposed to make use of this information. A proton tomographic acquisition of an anthropomorphic head phantom was simulated. The transmission rate of the particles was used to reconstruct a map of the macroscopic cross section for nuclear interactions of the materials. A two-step iterative reconstruction process was implemented to reconstruct a map of the inverse scattering length of the materials using the scattering of the protons. Results indicate that, while the reconstruction processes should be optimized, it is possible to extract quantitative information from the transmission rate and scattering of the protons. This suggests that proton imaging could provide additional knowledge on the materials that may be of use to further improve treatment planning.

Quantitative proton imaging from multiple physics processes: a proof of concept.

PubMed

Bopp, C; Rescigno, R; Rousseau, M; Brasse, D

2015-07-07

Proton imaging is developed in order to improve the accuracy of charged particle therapy treatment planning. It makes it possible to directly map the relative stopping powers of the materials using the information on the energy loss of the protons. In order to reach a satisfactory spatial resolution in the reconstructed images, the position and direction of each particle is recorded upstream and downstream from the patient. As a consequence of individual proton detection, information on the transmission rate and scattering of the protons is available. Image reconstruction processes are proposed to make use of this information. A proton tomographic acquisition of an anthropomorphic head phantom was simulated. The transmission rate of the particles was used to reconstruct a map of the macroscopic cross section for nuclear interactions of the materials. A two-step iterative reconstruction process was implemented to reconstruct a map of the inverse scattering length of the materials using the scattering of the protons. Results indicate that, while the reconstruction processes should be optimized, it is possible to extract quantitative information from the transmission rate and scattering of the protons. This suggests that proton imaging could provide additional knowledge on the materials that may be of use to further improve treatment planning.

Metric on the space of quantum states from relative entropy. Tomographic reconstruction

NASA Astrophysics Data System (ADS)

Man'ko, Vladimir I.; Marmo, Giuseppe; Ventriglia, Franco; Vitale, Patrizia

2017-08-01

In the framework of quantum information geometry, we derive, from quantum relative Tsallis entropy, a family of quantum metrics on the space of full rank, N level quantum states, by means of a suitably defined coordinate free differential calculus. The cases N=2, N=3 are discussed in detail and notable limits are analyzed. The radial limit procedure has been used to recover quantum metrics for lower rank states, such as pure states. By using the tomographic picture of quantum mechanics we have obtained the Fisher-Rao metric for the space of quantum tomograms and derived a reconstruction formula of the quantum metric of density states out of the tomographic one. A new inequality obtained for probabilities of three spin-1/2 projections in three perpendicular directions is proposed to be checked in experiments with superconducting circuits.

GPU-based prompt gamma ray imaging from boron neutron capture therapy.

PubMed

Yoon, Do-Kun; Jung, Joo-Young; Jo Hong, Key; Sil Lee, Keum; Suk Suh, Tae

2015-01-01

The purpose of this research is to perform the fast reconstruction of a prompt gamma ray image using a graphics processing unit (GPU) computation from boron neutron capture therapy (BNCT) simulations. To evaluate the accuracy of the reconstructed image, a phantom including four boron uptake regions (BURs) was used in the simulation. After the Monte Carlo simulation of the BNCT, the modified ordered subset expectation maximization reconstruction algorithm using the GPU computation was used to reconstruct the images with fewer projections. The computation times for image reconstruction were compared between the GPU and the central processing unit (CPU). Also, the accuracy of the reconstructed image was evaluated by a receiver operating characteristic (ROC) curve analysis. The image reconstruction time using the GPU was 196 times faster than the conventional reconstruction time using the CPU. For the four BURs, the area under curve values from the ROC curve were 0.6726 (A-region), 0.6890 (B-region), 0.7384 (C-region), and 0.8009 (D-region). The tomographic image using the prompt gamma ray event from the BNCT simulation was acquired using the GPU computation in order to perform a fast reconstruction during treatment. The authors verified the feasibility of the prompt gamma ray image reconstruction using the GPU computation for BNCT simulations.

Feasibility of track-based multiple scattering tomography

NASA Astrophysics Data System (ADS)

Jansen, H.; Schütze, P.

2018-04-01

We present a tomographic technique making use of a gigaelectronvolt electron beam for the determination of the material budget distribution of centimeter-sized objects by means of simulations and measurements. In both cases, the trajectory of electrons traversing a sample under test is reconstructed using a pixel beam-telescope. The width of the deflection angle distribution of electrons undergoing multiple Coulomb scattering at the sample is estimated. Basing the sinogram on position-resolved estimators enables the reconstruction of the original sample using an inverse radon transform. We exemplify the feasibility of this tomographic technique via simulations of two structured cubes—made of aluminium and lead—and via an in-beam measured coaxial adapter. The simulations yield images with FWHM edge resolutions of (177 ± 13) μm and a contrast-to-noise ratio of 5.6 ± 0.2 (7.8 ± 0.3) for aluminium (lead) compared to air. The tomographic reconstruction of a coaxial adapter serves as experimental evidence of the technique and yields a contrast-to-noise ratio of 15.3 ± 1.0 and a FWHM edge resolution of (117 ± 4) μm.

Lq -Lp optimization for multigrid fluorescence tomography of small animals using simplified spherical harmonics

NASA Astrophysics Data System (ADS)

Edjlali, Ehsan; Bérubé-Lauzière, Yves

2018-01-01

We present the first Lq -Lp optimization scheme for fluorescence tomographic imaging. This is then applied to small animal imaging. Fluorescence tomography is an ill-posed, and in full generality, a nonlinear problem that seeks to image the 3D concentration distribution of a fluorescent agent inside a biological tissue. Standard candidates for regularization to deal with the ill-posedness of the image reconstruction problem include L1 and L2 regularization. In this work, a general Lq -Lp regularization framework (Lq discrepancy function - Lp regularization term) is introduced for fluorescence tomographic imaging. A method to calculate the gradient for this general framework is developed which allows evaluating the performance of different cost functions/regularization schemes in solving the fluorescence tomographic problem. The simplified spherical harmonics approximation is used to accurately model light propagation inside the tissue. Furthermore, a multigrid mesh is utilized to decrease the dimension of the inverse problem and reduce the computational cost of the solution. The inverse problem is solved iteratively using an lm-BFGS quasi-Newton optimization method. The simulations are performed under different scenarios of noisy measurements. These are carried out on the Digimouse numerical mouse model with the kidney being the target organ. The evaluation of the reconstructed images is performed both qualitatively and quantitatively using several metrics including QR, RMSE, CNR, and TVE under rigorous conditions. The best reconstruction results under different scenarios are obtained with an L1.5 -L1 scheme with premature termination of the optimization process. This is in contrast to approaches commonly found in the literature relying on L2 -L2 schemes.

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.

Three-dimensional study of the vector potential of magnetic structures.

PubMed

Phatak, Charudatta; Petford-Long, Amanda K; De Graef, Marc

2010-06-25

The vector potential is central to a number of areas of condensed matter physics, such as superconductivity and magnetism. We have used a combination of electron wave phase reconstruction and electron tomographic reconstruction to experimentally measure and visualize the three-dimensional vector potential in and around a magnetic Permalloy structure. The method can probe the vector potential of the patterned structures with a resolution of about 13 nm. A transmission electron microscope operated in the Lorentz mode is used to record four tomographic tilt series. Measurements for a square Permalloy structure with an internal closure domain configuration are presented.

Creating three-dimensional tooth models from tomographic images.

PubMed

Lima da Silva, Isaac Newton; Barbosa, Gustavo Frainer; Soares, Rodrigo Borowski Grecco; Beltrao, Maria Cecilia Gomes; Spohr, Ana Maria; Mota, Eduardo Golcalves; Oshima, Hugo Mitsuo Silva; Burnett, Luiz Henrique

2008-01-01

The use of Finite Element Analysis (FEA) is becoming very frequent in Dentistry. However, most of the three-dimensional models presented by the literature for teeth are limited in terms of geometry. Discrepancy in shape and dimensions can cause wrong results to occur. Sharp cusps and faceted contour can produce stress concentrations, which are incoherent with the reality. The aim of this study was the processing of tomographic images in order to develop an advanced three-dimensional reconstruction of the anatomy of a molar tooth and the integration of the resulting solid with commercially available CAD/CAE software. Computed tomographic images were obtained from 0.5 mm thick slices of mandibular molar and transferred to commercial cad software. Once the point cloud data have been generated, the work on these points started to get to the solid model of the tooth with Pro/Engineer software. The obtained tooth model showed very accurate shape and dimensions, as it was obtained from real tooth data with error of 0.0 to -0.8 mm. The methodology presented was efficient for creating a biomodel of a tooth from tomographic images that realistically represented its anatomy.

RF tomography of metallic objects in free space: preliminary results

NASA Astrophysics Data System (ADS)

Li, Jia; Ewing, Robert L.; Berdanier, Charles; Baker, Christopher

2015-05-01

RF tomography has great potential in defense and homeland security applications. A distributed sensing research facility is under development at Air Force Research Lab. To develop a RF tomographic imaging system for the facility, preliminary experiments have been performed in an indoor range with 12 radar sensors distributed on a circle of 3m radius. Ultra-wideband pulses are used to illuminate single and multiple metallic targets. The echoes received by distributed sensors were processed and combined for tomography reconstruction. Traditional matched filter algorithm and truncated singular value decomposition (SVD) algorithm are compared in terms of their complexity, accuracy, and suitability for distributed processing. A new algorithm is proposed for shape reconstruction, which jointly estimates the object boundary and scatter points on the waveform's propagation path. The results show that the new algorithm allows accurate reconstruction of object shape, which is not available through the matched filter and truncated SVD algorithms.

Shrink-wrapped isosurface from cross sectional images

PubMed Central

Choi, Y. K.; Hahn, J. K.

2010-01-01

Summary This paper addresses a new surface reconstruction scheme for approximating the isosurface from a set of tomographic cross sectional images. Differently from the novel Marching Cubes (MC) algorithm, our method does not extract the iso-density surface (isosurface) directly from the voxel data but calculates the iso-density point (isopoint) first. After building a coarse initial mesh approximating the ideal isosurface by the cell-boundary representation, it metamorphoses the mesh into the final isosurface by a relaxation scheme, called shrink-wrapping process. Compared with the MC algorithm, our method is robust and does not make any cracks on surface. Furthermore, since it is possible to utilize lots of additional isopoints during the surface reconstruction process by extending the adjacency definition, theoretically the resulting surface can be better in quality than the MC algorithm. According to experiments, it is proved to be very robust and efficient for isosurface reconstruction from cross sectional images. PMID:20703361

X-ray tomography system to investigate granular materials during mechanical loading

NASA Astrophysics Data System (ADS)

Athanassiadis, Athanasios G.; La Rivière, Patrick J.; Sidky, Emil; Pelizzari, Charles; Pan, Xiaochuan; Jaeger, Heinrich M.

2014-08-01

We integrate a small and portable medical x-ray device with mechanical testing equipment to enable in situ, non-invasive measurements of a granular material's response to mechanical loading. We employ an orthopedic C-arm as the x-ray source and detector to image samples mounted in the materials tester. We discuss the design of a custom rotation stage, which allows for sample rotation and tomographic reconstruction under applied compressive stress. We then discuss the calibration of the system for 3D computed tomography, as well as the subsequent image reconstruction process. Using this system to reconstruct packings of 3D-printed particles, we resolve packing features with 0.52 mm resolution in a (60 mm)3 field of view. By analyzing the performance bounds of the system, we demonstrate that the reconstructions exhibit only moderate noise.

Statistical reconstruction for cosmic ray muon tomography.

PubMed

Schultz, Larry J; Blanpied, Gary S; Borozdin, Konstantin N; Fraser, Andrew M; Hengartner, Nicolas W; Klimenko, Alexei V; Morris, Christopher L; Orum, Chris; Sossong, Michael J

2007-08-01

Highly penetrating cosmic ray muons constantly shower the earth at a rate of about 1 muon per cm2 per minute. We have developed a technique which exploits the multiple Coulomb scattering of these particles to perform nondestructive inspection without the use of artificial radiation. In prior work [1]-[3], we have described heuristic methods for processing muon data to create reconstructed images. In this paper, we present a maximum likelihood/expectation maximization tomographic reconstruction algorithm designed for the technique. This algorithm borrows much from techniques used in medical imaging, particularly emission tomography, but the statistics of muon scattering dictates differences. We describe the statistical model for multiple scattering, derive the reconstruction algorithm, and present simulated examples. We also propose methods to improve the robustness of the algorithm to experimental errors and events departing from the statistical model.

Simultaneous determination of sample thickness, tilt, and electron mean free path using tomographic tilt images based on Beer-Lambert law

PubMed Central

Yan, Rui; Edwards, Thomas J.; Pankratz, Logan M.; Kuhn, Richard J.; Lanman, Jason K.; Liu, Jun; Jiang, Wen

2015-01-01

Cryo-electron tomography (cryo-ET) is an emerging technique that can elucidate the architecture of macromolecular complexes and cellular ultrastructure in a near-native state. Some important sample parameters, such as thickness and tilt, are needed for 3-D reconstruction. However, these parameters can currently only be determined using trial 3-D reconstructions. Accurate electron mean free path plays a significant role in modeling image formation process essential for simulation of electron microscopy images and model-based iterative 3-D reconstruction methods; however, their values are voltage and sample dependent and have only been experimentally measured for a limited number of sample conditions. Here, we report a computational method, tomoThickness, based on the Beer-Lambert law, to simultaneously determine the sample thickness, tilt and electron inelastic mean free path by solving an overdetermined nonlinear least square optimization problem utilizing the strong constraints of tilt relationships. The method has been extensively tested with both stained and cryo datasets. The fitted electron mean free paths are consistent with reported experimental measurements. The accurate thickness estimation eliminates the need for a generous assignment of Z-dimension size of the tomogram. Interestingly, we have also found that nearly all samples are a few degrees tilted relative to the electron beam. Compensation of the intrinsic sample tilt can result in horizontal structure and reduced Z-dimension of tomograms. Our fast, pre-reconstruction method can thus provide important sample parameters that can help improve performance of tomographic reconstruction of a wide range of samples. PMID:26433027

Simultaneous determination of sample thickness, tilt, and electron mean free path using tomographic tilt images based on Beer-Lambert law.

PubMed

Yan, Rui; Edwards, Thomas J; Pankratz, Logan M; Kuhn, Richard J; Lanman, Jason K; Liu, Jun; Jiang, Wen

2015-11-01

Cryo-electron tomography (cryo-ET) is an emerging technique that can elucidate the architecture of macromolecular complexes and cellular ultrastructure in a near-native state. Some important sample parameters, such as thickness and tilt, are needed for 3-D reconstruction. However, these parameters can currently only be determined using trial 3-D reconstructions. Accurate electron mean free path plays a significant role in modeling image formation process essential for simulation of electron microscopy images and model-based iterative 3-D reconstruction methods; however, their values are voltage and sample dependent and have only been experimentally measured for a limited number of sample conditions. Here, we report a computational method, tomoThickness, based on the Beer-Lambert law, to simultaneously determine the sample thickness, tilt and electron inelastic mean free path by solving an overdetermined nonlinear least square optimization problem utilizing the strong constraints of tilt relationships. The method has been extensively tested with both stained and cryo datasets. The fitted electron mean free paths are consistent with reported experimental measurements. The accurate thickness estimation eliminates the need for a generous assignment of Z-dimension size of the tomogram. Interestingly, we have also found that nearly all samples are a few degrees tilted relative to the electron beam. Compensation of the intrinsic sample tilt can result in horizontal structure and reduced Z-dimension of tomograms. Our fast, pre-reconstruction method can thus provide important sample parameters that can help improve performance of tomographic reconstruction of a wide range of samples. Copyright © 2015 Elsevier Inc. All rights reserved.

3D multimodal cardiac data reconstruction using angiography and computerized tomographic angiography registration.

PubMed

Moosavi Tayebi, Rohollah; Wirza, Rahmita; Sulaiman, Puteri S B; Dimon, Mohd Zamrin; Khalid, Fatimah; Al-Surmi, Aqeel; Mazaheri, Samaneh

2015-04-22

Computerized tomographic angiography (3D data representing the coronary arteries) and X-ray angiography (2D X-ray image sequences providing information about coronary arteries and their stenosis) are standard and popular assessment tools utilized for medical diagnosis of coronary artery diseases. At present, the results of both modalities are individually analyzed by specialists and it is difficult for them to mentally connect the details of these two techniques. The aim of this work is to assist medical diagnosis by providing specialists with the relationship between computerized tomographic angiography and X-ray angiography. In this study, coronary arteries from two modalities are registered in order to create a 3D reconstruction of the stenosis position. The proposed method starts with coronary artery segmentation and labeling for both modalities. Then, stenosis and relevant labeled artery in X-ray angiography image are marked by a specialist. Proper control points for the marked artery in both modalities are automatically detected and normalized. Then, a geometrical transformation function is computed using these control points. Finally, this function is utilized to register the marked artery from the X-ray angiography image on the computerized tomographic angiography and get the 3D position of the stenosis lesion. The result is a 3D informative model consisting of stenosis and coronary arteries' information from the X-ray angiography and computerized tomographic angiography modalities. The results of the proposed method for coronary artery segmentation, labeling and 3D reconstruction are evaluated and validated on the dataset containing both modalities. The advantage of this method is to aid specialists to determine a visual relationship between the correspondent coronary arteries from two modalities and also set up a connection between stenosis points from an X-ray angiography along with their 3D positions on the coronary arteries from computerized tomographic angiography. Moreover, another benefit of this work is that the medical acquisition standards remain unchanged, which means that no calibration in the acquisition devices is required. It can be applied on most computerized tomographic angiography and angiography devices.

Quantitative tomographic imaging of intermolecular FRET in small animals

PubMed Central

Venugopal, Vivek; Chen, Jin; Barroso, Margarida; Intes, Xavier

2012-01-01

Forster resonance energy transfer (FRET) is a nonradiative transfer of energy between two fluorescent molecules (a donor and an acceptor) in nanometer range proximity. FRET imaging methods have been applied to proteomic studies and drug discovery applications based on intermolecular FRET efficiency measurements and stoichiometric measurements of FRET interaction as quantitative parameters of interest. Importantly, FRET provides information about biomolecular interactions at a molecular level, well beyond the diffraction limits of standard microscopy techniques. The application of FRET to small animal imaging will allow biomedical researchers to investigate physiological processes occurring at nanometer range in vivo as well as in situ. In this work a new method for the quantitative reconstruction of FRET measurements in small animals, incorporating a full-field tomographic acquisition system with a Monte Carlo based hierarchical reconstruction scheme, is described and validated in murine models. Our main objective is to estimate the relative concentration of two forms of donor species, i.e., a donor molecule involved in FRETing to an acceptor close by and a nonFRETing donor molecule. PMID:23243567

Tomographic capabilities of the new GEM based SXR diagnostic of WEST

NASA Astrophysics Data System (ADS)

Jardin, A.; Mazon, D.; O'Mullane, M.; Mlynar, J.; Loffelmann, V.; Imrisek, M.; Chernyshova, M.; Czarski, T.; Kasprowicz, G.; Wojenski, A.; Bourdelle, C.; Malard, P.

2016-07-01

The tokamak WEST (Tungsten Environment in Steady-State Tokamak) will start operating by the end of 2016 as a test bed for the ITER divertor components in long pulse operation. In this context, radiative cooling of heavy impurities like tungsten (W) in the Soft X-ray (SXR) range [0.1 keV; 20 keV] is a critical issue for the plasma core performances. Thus reliable tools are required to monitor the local impurity density and avoid W accumulation. The WEST SXR diagnostic will be equipped with two new GEM (Gas Electron Multiplier) based poloidal cameras allowing to perform 2D tomographic reconstructions in tunable energy bands. In this paper tomographic capabilities of the Minimum Fisher Information (MFI) algorithm developed for Tore Supra and upgraded for WEST are investigated, in particular through a set of emissivity phantoms and the standard WEST scenario including reconstruction errors, influence of noise as well as computational time.

Two-dimensional tomographic terahertz imaging by homodyne self-mixing.

PubMed

Mohr, Till; Breuer, Stefan; Giuliani, G; Elsäßer, Wolfgang

2015-10-19

We realize a compact two-dimensional tomographic terahertz imaging experiment involving only one photoconductive antenna (PCA) simultaneously serving as a transmitter and receiver of the terahertz radiation. A hollow-core Teflon cylinder filled with α-Lactose monohydrate powder is studied at two terahertz frequencies, far away and at a specific absorption line of the powder. This sample is placed between the antenna and a chopper wheel, which serves as back reflector of the terahertz radiation into the PCA. Amplitude and phase information of the continuous-wave (CW) terahertz radiation are extracted from the measured homodyne self-mixing (HSM) signal after interaction with the cylinder. The influence of refraction is studied by modeling the set-up utilizing ZEMAX and is discussed by means of the measured 1D projections. The tomographic reconstruction by using the Simultaneous Algebraic Reconstruction Technique (SART) allows to identify both object geometry and α-Lactose filling.

Evaluation of sample holders designed for long-lasting X-ray micro-tomographic scans of ex-vivo soft tissue samples

NASA Astrophysics Data System (ADS)

Dudak, J.; Zemlicka, J.; Krejci, F.; Karch, J.; Patzelt, M.; Zach, P.; Sykora, V.; Mrzilkova, J.

2016-03-01

X-ray microradiography and microtomography are imaging techniques with increasing applicability in the field of biomedical and preclinical research. Application of hybrid pixel detector Timepix enables to obtain very high contrast of low attenuating materials such as soft biological tissue. However X-ray imaging of ex-vivo soft tissue samples is a difficult task due to its structural instability. Ex-vivo biological tissue is prone to fast drying-out which is connected with undesired changes of sample size and shape producing later on artefacts within the tomographic reconstruction. In this work we present the optimization of our Timepix equipped micro-CT system aiming to maintain soft tissue sample in stable condition. Thanks to the suggested approach higher contrast of tomographic reconstructions can be achieved while also large samples that require detector scanning can be easily measured.

Imaging open-path Fourier transform infrared spectrometer for 3D cloud profiling

NASA Astrophysics Data System (ADS)

Rentz Dupuis, Julia; Mansur, David J.; Vaillancourt, Robert; Carlson, David; Evans, Thomas; Schundler, Elizabeth; Todd, Lori; Mottus, Kathleen

2010-04-01

OPTRA has developed an imaging open-path Fourier transform infrared (I-OP-FTIR) spectrometer for 3D profiling of chemical and biological agent simulant plumes released into test ranges and chambers. An array of I-OP-FTIR instruments positioned around the perimeter of the test site, in concert with advanced spectroscopic algorithms, enables real time tomographic reconstruction of the plume. The approach is intended as a referee measurement for test ranges and chambers. This Small Business Technology Transfer (STTR) effort combines the instrumentation and spectroscopic capabilities of OPTRA, Inc. with the computed tomographic expertise of the University of North Carolina, Chapel Hill. In this paper, we summarize the design and build and detail system characterization and test of a prototype I-OP-FTIR instrument. System characterization includes radiometric performance and spectral resolution. Results from a series of tomographic reconstructions of sulfur hexafluoride plumes in a laboratory setting are also presented.

Imaging open-path Fourier transform infrared spectrometer for 3D cloud profiling

NASA Astrophysics Data System (ADS)

Rentz Dupuis, Julia; Mansur, David J.; Engel, James R.; Vaillancourt, Robert; Todd, Lori; Mottus, Kathleen

2008-04-01

OPTRA and University of North Carolina are developing an imaging open-path Fourier transform infrared (I-OP-FTIR) spectrometer for 3D profiling of chemical and biological agent simulant plumes released into test ranges and chambers. An array of I-OP-FTIR instruments positioned around the perimeter of the test site, in concert with advanced spectroscopic algorithms, enables real time tomographic reconstruction of the plume. The approach will be considered as a candidate referee measurement for test ranges and chambers. This Small Business Technology Transfer (STTR) effort combines the instrumentation and spectroscopic capabilities of OPTRA, Inc. with the computed tomographic expertise of the University of North Carolina, Chapel Hill. In this paper, we summarize progress to date and overall system performance projections based on the instrument, spectroscopy, and tomographic reconstruction accuracy. We then present a preliminary optical design of the I-OP-FTIR.

Limited-angle tomography for analyzer-based phase-contrast X-ray imaging

PubMed Central

Majidi, Keivan; Wernick, Miles N; Li, Jun; Muehleman, Carol; Brankov, Jovan G

2014-01-01

Multiple-Image Radiography (MIR) is an analyzer-based phase-contrast X-ray imaging method (ABI), which is emerging as a potential alternative to conventional radiography. MIR simultaneously generates three planar parametric images containing information about scattering, refraction and attenuation properties of the object. The MIR planar images are linear tomographic projections of the corresponding object properties, which allows reconstruction of volumetric images using computed tomography (CT) methods. However, when acquiring a full range of linear projections around the tissue of interest is not feasible or the scanning time is limited, limited-angle tomography techniques can be used to reconstruct these volumetric images near the central plane, which is the plane that contains the pivot point of the tomographic movement. In this work, we use computer simulations to explore the applicability of limited-angle tomography to MIR. We also investigate the accuracy of reconstructions as a function of number of tomographic angles for a fixed total radiation exposure. We use this function to find an optimal range of angles over which data should be acquired for limited-angle tomography MIR (LAT-MIR). Next, we apply the LAT-MIR technique to experimentally acquired MIR projections obtained in a cadaveric human thumb study. We compare the reconstructed slices near the central plane to the same slices reconstructed by CT-MIR using the full angular view around the object. Finally, we perform a task-based evaluation of LAT-MIR performance for different numbers of angular views, and use template matching to detect cartilage in the refraction image near the central plane. We use the signal-to-noise ratio of this test as the detectability metric to investigate an optimum range of tomographic angles for detecting soft tissues in LAT-MIR. Both results show that there is an optimum range of angular view for data acquisition where LAT-MIR yields the best performance, comparable to CT-MIR only if one considers volumetric images near the central plane and not the whole volume. PMID:24898008

Limited-angle tomography for analyzer-based phase-contrast x-ray imaging

NASA Astrophysics Data System (ADS)

Majidi, Keivan; Wernick, Miles N.; Li, Jun; Muehleman, Carol; Brankov, Jovan G.

2014-07-01

Multiple-image radiography (MIR) is an analyzer-based phase-contrast x-ray imaging method, which is emerging as a potential alternative to conventional radiography. MIR simultaneously generates three planar parametric images containing information about scattering, refraction and attenuation properties of the object. The MIR planar images are linear tomographic projections of the corresponding object properties, which allows reconstruction of volumetric images using computed tomography (CT) methods. However, when acquiring a full range of linear projections around the tissue of interest is not feasible or the scanning time is limited, limited-angle tomography techniques can be used to reconstruct these volumetric images near the central plane, which is the plane that contains the pivot point of the tomographic movement. In this work, we use computer simulations to explore the applicability of limited-angle tomography to MIR. We also investigate the accuracy of reconstructions as a function of number of tomographic angles for a fixed total radiation exposure. We use this function to find an optimal range of angles over which data should be acquired for limited-angle tomography MIR (LAT-MIR). Next, we apply the LAT-MIR technique to experimentally acquired MIR projections obtained in a cadaveric human thumb study. We compare the reconstructed slices near the central plane to the same slices reconstructed by CT-MIR using the full angular view around the object. Finally, we perform a task-based evaluation of LAT-MIR performance for different numbers of angular views, and use template matching to detect cartilage in the refraction image near the central plane. We use the signal-to-noise ratio of this test as the detectability metric to investigate an optimum range of tomographic angles for detecting soft tissues in LAT-MIR. Both results show that there is an optimum range of angular view for data acquisition where LAT-MIR yields the best performance, comparable to CT-MIR only if one considers volumetric images near the central plane and not the whole volume.

Volume reconstruction optimization for tomo-PIV algorithms applied to experimental data

NASA Astrophysics Data System (ADS)

Martins, Fabio J. W. A.; Foucaut, Jean-Marc; Thomas, Lionel; Azevedo, Luis F. A.; Stanislas, Michel

2015-08-01

Tomographic PIV is a three-component volumetric velocity measurement technique based on the tomographic reconstruction of a particle distribution imaged by multiple camera views. In essence, the performance and accuracy of this technique is highly dependent on the parametric adjustment and the reconstruction algorithm used. Although synthetic data have been widely employed to optimize experiments, the resulting reconstructed volumes might not have optimal quality. The purpose of the present study is to offer quality indicators that can be applied to data samples in order to improve the quality of velocity results obtained by the tomo-PIV technique. The methodology proposed can potentially lead to significantly reduction in the time required to optimize a tomo-PIV reconstruction, also leading to better quality velocity results. Tomo-PIV data provided by a six-camera turbulent boundary-layer experiment were used to optimize the reconstruction algorithms according to this methodology. Velocity statistics measurements obtained by optimized BIMART, SMART and MART algorithms were compared with hot-wire anemometer data and velocity measurement uncertainties were computed. Results indicated that BIMART and SMART algorithms produced reconstructed volumes with equivalent quality as the standard MART with the benefit of reduced computational time.

GPU-based prompt gamma ray imaging from boron neutron capture therapy

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

Yoon, Do-Kun; Jung, Joo-Young; Suk Suh, Tae, E-mail: suhsanta@catholic.ac.kr

Purpose: The purpose of this research is to perform the fast reconstruction of a prompt gamma ray image using a graphics processing unit (GPU) computation from boron neutron capture therapy (BNCT) simulations. Methods: To evaluate the accuracy of the reconstructed image, a phantom including four boron uptake regions (BURs) was used in the simulation. After the Monte Carlo simulation of the BNCT, the modified ordered subset expectation maximization reconstruction algorithm using the GPU computation was used to reconstruct the images with fewer projections. The computation times for image reconstruction were compared between the GPU and the central processing unit (CPU).more » Also, the accuracy of the reconstructed image was evaluated by a receiver operating characteristic (ROC) curve analysis. Results: The image reconstruction time using the GPU was 196 times faster than the conventional reconstruction time using the CPU. For the four BURs, the area under curve values from the ROC curve were 0.6726 (A-region), 0.6890 (B-region), 0.7384 (C-region), and 0.8009 (D-region). Conclusions: The tomographic image using the prompt gamma ray event from the BNCT simulation was acquired using the GPU computation in order to perform a fast reconstruction during treatment. The authors verified the feasibility of the prompt gamma ray image reconstruction using the GPU computation for BNCT simulations.« less

TU-FG-BRB-07: GPU-Based Prompt Gamma Ray Imaging From Boron Neutron Capture Therapy

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

Kim, S; Suh, T; Yoon, D

Purpose: The purpose of this research is to perform the fast reconstruction of a prompt gamma ray image using a graphics processing unit (GPU) computation from boron neutron capture therapy (BNCT) simulations. Methods: To evaluate the accuracy of the reconstructed image, a phantom including four boron uptake regions (BURs) was used in the simulation. After the Monte Carlo simulation of the BNCT, the modified ordered subset expectation maximization reconstruction algorithm using the GPU computation was used to reconstruct the images with fewer projections. The computation times for image reconstruction were compared between the GPU and the central processing unit (CPU).more » Also, the accuracy of the reconstructed image was evaluated by a receiver operating characteristic (ROC) curve analysis. Results: The image reconstruction time using the GPU was 196 times faster than the conventional reconstruction time using the CPU. For the four BURs, the area under curve values from the ROC curve were 0.6726 (A-region), 0.6890 (B-region), 0.7384 (C-region), and 0.8009 (D-region). Conclusion: The tomographic image using the prompt gamma ray event from the BNCT simulation was acquired using the GPU computation in order to perform a fast reconstruction during treatment. The authors verified the feasibility of the prompt gamma ray reconstruction using the GPU computation for BNCT simulations.« less

Tomographic diagnostic of the hydrogen beam from a negative ion source

NASA Astrophysics Data System (ADS)

Agostini, M.; Brombin, M.; Serianni, G.; Pasqualotto, R.

2011-10-01

In this paper the tomographic diagnostic developed to characterize the 2D density distribution of a particle beam from a negative ion source is described. In particular, the reliability of this diagnostic has been tested by considering the geometry of the source for the production of ions of deuterium extracted from an rf plasma (SPIDER). SPIDER is a low energy prototype negative ion source for the international thermonuclear experimental reactor (ITER) neutral beam injector, aimed at demonstrating the capability to create and extract a current of D- (H-) ions up to 50 A (60 A) accelerated at 100 kV. The ions are extracted over a wide surface (1.52×0.56m2) with a uniform plasma density which is prescribed to remain within 10% of the mean value. The main target of the tomographic diagnostic is the measurement of the beam uniformity with sufficient spatial resolution and of its evolution throughout the pulse duration. To reach this target, a tomographic algorithm based on the simultaneous algebraic reconstruction technique is developed and the geometry of the lines of sight is optimized so as to cover the whole area of the beam. Phantoms that reproduce different experimental beam configurations are simulated and reconstructed, and the role of the noise in the signals is studied. The simulated phantoms are correctly reconstructed and their two-dimensional spatial nonuniformity is correctly estimated, up to a noise level of 10% with respect to the signal.

Numerical Simulations to Assess ART and MART Performance for Ionospheric Tomography of Chapman Profiles.

PubMed

Prol, Fabricio S; Camargo, Paulo O; Muella, Marcio T A H

2017-01-01

The incomplete geometrical coverage of the Global Navigation Satellite System (GNSS) makes the ionospheric tomographic system an ill-conditioned problem for ionospheric imaging. In order to detect the principal limitations of the ill-conditioned tomographic solutions, numerical simulations of the ionosphere are under constant investigation. In this paper, we show an investigation of the accuracy of Algebraic Reconstruction Technique (ART) and Multiplicative ART (MART) for performing tomographic reconstruction of Chapman profiles using a simulated optimum scenario of GNSS signals tracked by ground-based receivers. Chapman functions were used to represent the ionospheric morphology and a set of analyses was conducted to assess ART and MART performance for estimating the Total Electron Content (TEC) and parameters that describes the Chapman function. The results showed that MART performed better in the reconstruction of the electron density peak and ART gave a better representation for estimating TEC and the shape of the ionosphere. Since we used an optimum scenario of the GNSS signals, the analyses indicate the intrinsic problems that may occur with ART and MART to recover valuable information for many applications of Telecommunication, Spatial Geodesy and Space Weather.

X-ray tomography system to investigate granular materials during mechanical loading

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

Athanassiadis, Athanasios G.; Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139; La Rivière, Patrick J.

2014-08-15

We integrate a small and portable medical x-ray device with mechanical testing equipment to enable in situ, non-invasive measurements of a granular material's response to mechanical loading. We employ an orthopedic C-arm as the x-ray source and detector to image samples mounted in the materials tester. We discuss the design of a custom rotation stage, which allows for sample rotation and tomographic reconstruction under applied compressive stress. We then discuss the calibration of the system for 3D computed tomography, as well as the subsequent image reconstruction process. Using this system to reconstruct packings of 3D-printed particles, we resolve packing featuresmore » with 0.52 mm resolution in a (60 mm){sup 3} field of view. By analyzing the performance bounds of the system, we demonstrate that the reconstructions exhibit only moderate noise.« less

Bidirectional reflectance distribution function effects in ladar-based reflection tomography.

PubMed

Jin, Xuemin; Levine, Robert Y

2009-07-20

Light reflection from a surface is described by the bidirectional reflectance distribution function (BRDF). In this paper, BRDF effects in reflection tomography are studied using modeled range-resolved reflection from well-characterized geometrical surfaces. It is demonstrated that BRDF effects can cause a darkening at the interior boundary of the reconstructed surface analogous to the well-known beam hardening artifact in x-ray transmission computed tomography (CT). This artifact arises from reduced reflection at glancing incidence angles to the surface. It is shown that a purely Lambertian surface without shadowed components is perfectly reconstructed from range-resolved measurements. This result is relevant to newly fabricated carbon nanotube materials. Shadowing is shown to cause crossed streak artifacts similar to limited-angle effects in CT reconstruction. In tomographic reconstruction, these effects can overwhelm highly diffuse components in proximity to specularly reflecting elements. Diffuse components can be recovered by specialized processing, such as reducing glints via thresholded measurements.

Cryo-Electron Tomography for Structural Characterization of Macromolecular Complexes

PubMed Central

Cope, Julia; Heumann, John; Hoenger, Andreas

2011-01-01

Cryo-electron tomography (cryo-ET) is an emerging 3-D reconstruction technology that combines the principles of tomographic 3-D reconstruction with the unmatched structural preservation of biological material embedded in vitreous ice. Cryo-ET is particularly suited to investigating cell-biological samples and large macromolecular structures that are too polymorphic to be reconstructed by classical averaging-based 3-D reconstruction procedures. This unit aims to make cryo-ET accessible to newcomers and discusses the specialized equipment required, as well as the relevant advantages and hurdles associated with sample preparation by vitrification and cryo-ET. Protocols describe specimen preparation, data recording and 3-D data reconstruction for cryo-ET, with a special focus on macromolecular complexes. A step-by-step procedure for specimen vitrification by plunge freezing is provided, followed by the general practicalities of tilt-series acquisition for cryo-ET, including advice on how to select an area appropriate for acquiring a tilt series. A brief introduction to the underlying computational reconstruction principles applied in tomography is described, along with instructions for reconstructing a tomogram from cryo-tilt series data. Finally, a method is detailed for extracting small subvolumes containing identical macromolecular structures from tomograms for alignment and averaging as a means to increase the signal-to-noise ratio and eliminate missing wedge effects inherent in tomographic reconstructions. PMID:21842467

Jini service to reconstruct tomographic data

NASA Astrophysics Data System (ADS)

Knoll, Peter; Mirzaei, S.; Koriska, K.; Koehn, H.

2002-06-01

A number of imaging systems rely on the reconstruction of a 3- dimensional model from its projections through the process of computed tomography (CT). In medical imaging, for example magnetic resonance imaging (MRI), positron emission tomography (PET), and Single Computer Tomography (SPECT) acquire two-dimensional projections of a three dimensional projections of a three dimensional object. In order to calculate the 3-dimensional representation of the object, i.e. its voxel distribution, several reconstruction algorithms have been developed. Currently, mainly two reconstruct use: the filtered back projection(FBP) and iterative methods. Although the quality of iterative reconstructed SPECT slices is better than that of FBP slices, such iterative algorithms are rarely used for clinical routine studies because of their low availability and increased reconstruction time. We used Jini and a self-developed iterative reconstructions algorithm to design and implement a Jini reconstruction service. With this service, the physician selects the patient study from a database and a Jini client automatically discovers the registered Jini reconstruction services in the department's Intranet. After downloading the proxy object the this Jini service, the SPECT acquisition data are reconstructed. The resulting transaxial slices are visualized using a Jini slice viewer, which can be used for various imaging modalities.

Natural pixel decomposition for computational tomographic reconstruction from interferometric projection: algorithms and comparison

NASA Astrophysics Data System (ADS)

Cha, Don J.; Cha, Soyoung S.

1995-09-01

A computational tomographic technique, termed the variable grid method (VGM), has been developed for improving interferometric reconstruction of flow fields under ill-posed data conditions of restricted scanning and incomplete projection. The technique is based on natural pixel decomposition, that is, division of a field into variable grid elements. The performances of two algorithms, that is, original and revised versions, are compared to investigate the effects of the data redundancy criteria and seed element forming schemes. Tests of the VGMs are conducted through computer simulation of experiments and reconstruction of fields with a limited view angel of 90 degree(s). The temperature fields at two horizontal sections of a thermal plume of two interacting isothermal cubes, produced by a finite numerical code, are analyzed as test fields. The computer simulation demonstrates the superiority of the revised VGM to either the conventional fixed grid method or the original VGM. Both the maximum and average reconstruction errors are reduced appreciably. The reconstruction shows substantial improvement in the regions with dense scanning by probing rays. These regions are usually of interest in engineering applications.

Optimization-Based Approach for Joint X-Ray Fluorescence and Transmission Tomographic Inversion

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

Di, Zichao; Leyffer, Sven; Wild, Stefan M.

2016-01-01

Fluorescence tomographic reconstruction, based on the detection of photons coming from fluorescent emission, can be used for revealing the internal elemental composition of a sample. On the other hand, conventional X-ray transmission tomography can be used for reconstructing the spatial distribution of the absorption coefficient inside a sample. In this work, we integrate both X-ray fluorescence and X-ray transmission data modalities and formulate a nonlinear optimization-based approach for reconstruction of the elemental composition of a given object. This model provides a simultaneous reconstruction of both the quantitative spatial distribution of all elements and the absorption effect in the sample. Mathematicallymore » speaking, we show that compared with the single-modality inversion (i.e., the X-ray transmission or fluorescence alone), the joint inversion provides a better-posed problem, which implies a better recovery. Therefore, the challenges in X-ray fluorescence tomography arising mainly from the effects of self-absorption in the sample are partially mitigated. The use of this technique is demonstrated on the reconstruction of several synthetic samples.« less

Intensity-enhanced MART for tomographic PIV

NASA Astrophysics Data System (ADS)

Wang, HongPing; Gao, Qi; Wei, RunJie; Wang, JinJun

2016-05-01

A novel technique to shrink the elongated particles and suppress the ghost particles in particle reconstruction of tomographic particle image velocimetry is presented. This method, named as intensity-enhanced multiplicative algebraic reconstruction technique (IntE-MART), utilizes an inverse diffusion function and an intensity suppressing factor to improve the quality of particle reconstruction and consequently the precision of velocimetry. A numerical assessment about vortex ring motion with and without image noise is performed to evaluate the new algorithm in terms of reconstruction, particle elongation and velocimetry. The simulation is performed at seven different seeding densities. The comparison of spatial filter MART and IntE-MART on the probability density function of particle peak intensity suggests that one of the local minima of the distribution can be used to separate the ghosts and actual particles. Thus, ghost removal based on IntE-MART is also introduced. To verify the application of IntE-MART, a real plate turbulent boundary layer experiment is performed. The result indicates that ghost reduction can increase the accuracy of RMS of velocity field.

Iterative reconstruction of volumetric particle distribution

NASA Astrophysics Data System (ADS)

Wieneke, Bernhard

2013-02-01

For tracking the motion of illuminated particles in space and time several volumetric flow measurement techniques are available like 3D-particle tracking velocimetry (3D-PTV) recording images from typically three to four viewing directions. For higher seeding densities and the same experimental setup, tomographic PIV (Tomo-PIV) reconstructs voxel intensities using an iterative tomographic reconstruction algorithm (e.g. multiplicative algebraic reconstruction technique, MART) followed by cross-correlation of sub-volumes computing instantaneous 3D flow fields on a regular grid. A novel hybrid algorithm is proposed here that similar to MART iteratively reconstructs 3D-particle locations by comparing the recorded images with the projections calculated from the particle distribution in the volume. But like 3D-PTV, particles are represented by 3D-positions instead of voxel-based intensity blobs as in MART. Detailed knowledge of the optical transfer function and the particle image shape is mandatory, which may differ for different positions in the volume and for each camera. Using synthetic data it is shown that this method is capable of reconstructing densely seeded flows up to about 0.05 ppp with similar accuracy as Tomo-PIV. Finally the method is validated with experimental data.

Semi-Tomographic Gamma Scanning Technique for Non-Destructive Assay of Radioactive Waste Drums

NASA Astrophysics Data System (ADS)

Gu, Weiguo; Rao, Kaiyuan; Wang, Dezhong; Xiong, Jiemei

2016-12-01

Segmented gamma scanning (SGS) and tomographic gamma scanning (TGS) are two traditional detection techniques for low and intermediate level radioactive waste drum. This paper proposes one detection method named semi-tomographic gamma scanning (STGS) to avoid the poor detection accuracy of SGS and shorten detection time of TGS. This method and its algorithm synthesize the principles of SGS and TGS. In this method, each segment is divided into annual voxels and tomography is used in the radiation reconstruction. The accuracy of STGS is verified by experiments and simulations simultaneously for the 208 liter standard waste drums which contains three types of nuclides. The cases of point source or multi-point sources, uniform or nonuniform materials are employed for comparison. The results show that STGS exhibits a large improvement in the detection performance, and the reconstruction error and statistical bias are reduced by one quarter to one third or less for most cases if compared with SGS.

Optical tomograph optimized for tumor detection inside highly absorbent organs

NASA Astrophysics Data System (ADS)

Boutet, Jérôme; Koenig, Anne; Hervé, Lionel; Berger, Michel; Dinten, Jean-Marc; Josserand, Véronique; Coll, Jean-Luc

2011-05-01

This paper presents a tomograph for small animal fluorescence imaging. The compact and cost-effective system described in this article was designed to address the problem of tumor detection inside highly absorbent heterogeneous organs, such as lungs. To validate the tomograph's ability to detect cancerous nodules inside lungs, in vivo tumor growth was studied on seven cancerous mice bearing murine mammary tumors marked with Alexa Fluor 700. They were successively imaged 10, 12, and 14 days after the primary tumor implantation. The fluorescence maps were compared over this time period. As expected, the reconstructed fluorescence increases with the tumor growth stage.

Lamb wave tomographic imaging system for aircraft structural health assessment

NASA Astrophysics Data System (ADS)

Schwarz, Willi G.; Read, Michael E.; Kremer, Matthew J.; Hinders, Mark K.; Smith, Barry T.

1999-01-01

A tomographic imaging system using ultrasonic Lamb waves for the nondestructive inspection of aircraft components such as wings and fuselage is being developed. The computer-based system provides large-area inspection capability by electronically scanning an array of transducers that can be easily attached to flat and curved surface without moving parts. Images of the inspected area are produced in near real time employing a tomographic reconstruction method adapted from seismological applications. Changes in material properties caused by structural flaws such as disbonds, corrosion, and fatigue cracks can be effectively detected and characterized utilizing this fast NDE technique.

Development of a GNSS water vapour tomography system using algebraic reconstruction techniques

NASA Astrophysics Data System (ADS)

Bender, Michael; Dick, Galina; Ge, Maorong; Deng, Zhiguo; Wickert, Jens; Kahle, Hans-Gert; Raabe, Armin; Tetzlaff, Gerd

2011-05-01

A GNSS water vapour tomography system developed to reconstruct spatially resolved humidity fields in the troposphere is described. The tomography system was designed to process the slant path delays of about 270 German GNSS stations in near real-time with a temporal resolution of 30 min, a horizontal resolution of 40 km and a vertical resolution of 500 m or better. After a short introduction to the GPS slant delay processing the framework of the GNSS tomography is described in detail. Different implementations of the iterative algebraic reconstruction techniques (ART) used to invert the linear inverse problem are discussed. It was found that the multiplicative techniques (MART) provide the best results with least processing time, i.e., a tomographic reconstruction of about 26,000 slant delays on a 8280 cell grid can be obtained in less than 10 min. Different iterative reconstruction techniques are compared with respect to their convergence behaviour and some numerical parameters. The inversion can be considerably stabilized by using additional non-GNSS observations and implementing various constraints. Different strategies for initialising the tomography and utilizing extra information are discussed. At last an example of a reconstructed field of the wet refractivity is presented and compared to the corresponding distribution of the integrated water vapour, an analysis of a numerical weather model (COSMO-DE) and some radiosonde profiles.

A new art code for tomographic interferometry

NASA Technical Reports Server (NTRS)

Tan, H.; Modarress, D.

1987-01-01

A new algebraic reconstruction technique (ART) code based on the iterative refinement method of least squares solution for tomographic reconstruction is presented. Accuracy and the convergence of the technique is evaluated through the application of numerically generated interferometric data. It was found that, in general, the accuracy of the results was superior to other reported techniques. The iterative method unconditionally converged to a solution for which the residual was minimum. The effects of increased data were studied. The inversion error was found to be a function of the input data error only. The convergence rate, on the other hand, was affected by all three parameters. Finally, the technique was applied to experimental data, and the results are reported.

Microstructural Quantification, Property Prediction, and Stochastic Reconstruction of Heterogeneous Materials Using Limited X-Ray Tomography Data

NASA Astrophysics Data System (ADS)

Li, Hechao

An accurate knowledge of the complex microstructure of a heterogeneous material is crucial for quantitative structure-property relations establishment and its performance prediction and optimization. X-ray tomography has provided a non-destructive means for microstructure characterization in both 3D and 4D (i.e., structural evolution over time). Traditional reconstruction algorithms like filtered-back-projection (FBP) method or algebraic reconstruction techniques (ART) require huge number of tomographic projections and segmentation process before conducting microstructural quantification. This can be quite time consuming and computationally intensive. In this thesis, a novel procedure is first presented that allows one to directly extract key structural information in forms of spatial correlation functions from limited x-ray tomography data. The key component of the procedure is the computation of a "probability map", which provides the probability of an arbitrary point in the material system belonging to specific phase. The correlation functions of interest are then readily computed from the probability map. Using effective medium theory, accurate predictions of physical properties (e.g., elastic moduli) can be obtained. Secondly, a stochastic optimization procedure that enables one to accurately reconstruct material microstructure from a small number of x-ray tomographic projections (e.g., 20 - 40) is presented. Moreover, a stochastic procedure for multi-modal data fusion is proposed, where both X-ray projections and correlation functions computed from limited 2D optical images are fused to accurately reconstruct complex heterogeneous materials in 3D. This multi-modal reconstruction algorithm is proved to be able to integrate the complementary data to perform an excellent optimization procedure, which indicates its high efficiency in using limited structural information. Finally, the accuracy of the stochastic reconstruction procedure using limited X-ray projection data is ascertained by analyzing the microstructural degeneracy and the roughness of energy landscape associated with different number of projections. Ground-state degeneracy of a microstructure is found to decrease with increasing number of projections, which indicates a higher probability that the reconstructed configurations match the actual microstructure. The roughness of energy landscape can also provide information about the complexity and convergence behavior of the reconstruction for given microstructures and projection number.

Configuration optimization of laser guide stars and wavefront correctors for multi-conjugation adaptive optics

NASA Astrophysics Data System (ADS)

Xuan, Li; He, Bin; Hu, Li-Fa; Li, Da-Yu; Xu, Huan-Yu; Zhang, Xing-Yun; Wang, Shao-Xin; Wang, Yu-Kun; Yang, Cheng-Liang; Cao, Zhao-Liang; Mu, Quan-Quan; Lu, Xing-Hai

2016-09-01

Multi-conjugation adaptive optics (MCAOs) have been investigated and used in the large aperture optical telescopes for high-resolution imaging with large field of view (FOV). The atmospheric tomographic phase reconstruction and projection of three-dimensional turbulence volume onto wavefront correctors, such as deformable mirrors (DMs) or liquid crystal wavefront correctors (LCWCs), is a very important step in the data processing of an MCAO’s controller. In this paper, a method according to the wavefront reconstruction performance of MCAO is presented to evaluate the optimized configuration of multi laser guide stars (LGSs) and the reasonable conjugation heights of LCWCs. Analytical formulations are derived for the different configurations and are used to generate optimized parameters for MCAO. Several examples are given to demonstrate our LGSs configuration optimization method. Compared with traditional methods, our method has minimum wavefront tomographic error, which will be helpful to get higher imaging resolution at large FOV in MCAO. Project supported by the National Natural Science Foundation of China (Grant Nos. 11174274, 11174279, 61205021, 11204299, 61475152, and 61405194) and the State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences.

Tomographic reconstruction of an aerosol plume using passive multiangle observations from the MISR satellite instrument

NASA Astrophysics Data System (ADS)

Garay, Michael J.; Davis, Anthony B.; Diner, David J.

2016-12-01

We present initial results using computed tomography to reconstruct the three-dimensional structure of an aerosol plume from passive observations made by the Multi-angle Imaging SpectroRadiometer (MISR) instrument on NASA's Terra satellite. MISR views the Earth from nine different angles at four visible and near-infrared wavelengths. Adopting the 672 nm channel, we treat each view as an independent measure of aerosol optical thickness along the line of sight at 1.1 km resolution. A smoke plume over dark water is selected as it provides a more tractable lower boundary condition for the retrieval. A tomographic algorithm is used to reconstruct the horizontal and vertical aerosol extinction field for one along-track slice from the path of all camera rays passing through a regular grid. The results compare well with ground-based lidar observations from a nearby Micropulse Lidar Network site.

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

Levin, Barnaby D. A.; Padgett, Elliot; Chen, Chien-Chun

Electron tomography in materials science has flourished with the demand to characterize nanoscale materials in three dimensions (3D). Access to experimental data is vital for developing and validating reconstruction methods that improve resolution and reduce radiation dose requirements. This work presents five high-quality scanning transmission electron microscope (STEM) tomography datasets in order to address the critical need for open access data in this field. The datasets represent the current limits of experimental technique, are of high quality, and contain materials with structural complexity. Included are tomographic series of a hyperbranched Co 2 P nanocrystal, platinum nanoparticles on a carbonmore » nanofibre imaged over the complete 180° tilt range, a platinum nanoparticle and a tungsten needle both imaged at atomic resolution by equal slope tomography, and a through-focal tilt series of PtCu nanoparticles. A volumetric reconstruction from every dataset is provided for comparison and development of post-processing and visualization techniques. Researchers interested in creating novel data processing and reconstruction algorithms will now have access to state of the art experimental test data.« less

Refraction-based X-ray Computed Tomography for Biomedical Purpose Using Dark Field Imaging Method

NASA Astrophysics Data System (ADS)

Sunaguchi, Naoki; Yuasa, Tetsuya; Huo, Qingkai; Ichihara, Shu; Ando, Masami

We have proposed a tomographic x-ray imaging system using DFI (dark field imaging) optics along with a data-processing method to extract information on refraction from the measured intensities, and a reconstruction algorithm to reconstruct a refractive-index field from the projections generated from the extracted refraction information. The DFI imaging system consists of a tandem optical system of Bragg- and Laue-case crystals, a positioning device system for a sample, and two CCD (charge coupled device) cameras. Then, we developed a software code to simulate the data-acquisition, data-processing, and reconstruction methods to investigate the feasibility of the proposed methods. Finally, in order to demonstrate its efficacy, we imaged a sample with DCIS (ductal carcinoma in situ) excised from a breast cancer patient using a system constructed at the vertical wiggler beamline BL-14C in KEK-PF. Its CT images depicted a variety of fine histological structures, such as milk ducts, duct walls, secretions, adipose and fibrous tissue. They correlate well with histological sections.

Global Distribution of Mercury's Neutrals from MESSENGER Measurements Combined with a Tomographic Method

NASA Technical Reports Server (NTRS)

Sarantos, Menelaos; McClintock, Bill; Vervack, Ron, Jr.; Killen, Rosemary; Merkel, Aimee; Slavin, James; Solomon, Sean C.

2011-01-01

The MErcury Surface, Space ENvironment, GEochemistry, and Ranging (MESSENGER) spacecraft entered orbit about Mercury on March 18, 2011. Since then, the Ultraviolet and Visible Spectrometer (UVVS) onboard this spacecraft has been observing Mercury's collisionless exosphere. We present measurements by MESSENGER UVVS of the sodium, calcium, and magnesium distributions that were obtained during multiple passes through the tail over a period of one month. Global maps of the exosphere were constructed daily from such measurements using a recently developed tomographic technique. During this period, Mercury moved towards the Sun from being about 0.44 astronomical units (AU) to approximately 0.32 AU from the Sun. Hence, our reconstructions provide information about the three-dimensional structure of the exosphere, the source processes for these species, and their dependence with orbital distance during the entire in-leg of Mercury's orbit.

MIMO nonlinear ultrasonic tomography by propagation and backpropagation method.

PubMed

Dong, Chengdong; Jin, Yuanwei

2013-03-01

This paper develops a fast ultrasonic tomographic imaging method in a multiple-input multiple-output (MIMO) configuration using the propagation and backpropagation (PBP) method. By this method, ultrasonic excitation signals from multiple sources are transmitted simultaneously to probe the objects immersed in the medium. The scattering signals are recorded by multiple receivers. Utilizing the nonlinear ultrasonic wave propagation equation and the received time domain scattered signals, the objects are to be reconstructed iteratively in three steps. First, the propagation step calculates the predicted acoustic potential data at the receivers using an initial guess. Second, the difference signal between the predicted value and the measured data is calculated. Third, the backpropagation step computes updated acoustical potential data by backpropagating the difference signal to the same medium computationally. Unlike the conventional PBP method for tomographic imaging where each source takes turns to excite the acoustical field until all the sources are used, the developed MIMO-PBP method achieves faster image reconstruction by utilizing multiple source simultaneous excitation. Furthermore, we develop an orthogonal waveform signaling method using a waveform delay scheme to reduce the impact of speckle patterns in the reconstructed images. By numerical experiments we demonstrate that the proposed MIMO-PBP tomographic imaging method results in faster convergence and achieves superior imaging quality.

An efficient and accurate approach to MTE-MART for time-resolved tomographic PIV

NASA Astrophysics Data System (ADS)

Lynch, K. P.; Scarano, F.

2015-03-01

The motion-tracking-enhanced MART (MTE-MART; Novara et al. in Meas Sci Technol 21:035401, 2010) has demonstrated the potential to increase the accuracy of tomographic PIV by the combined use of a short sequence of non-simultaneous recordings. A clear bottleneck of the MTE-MART technique has been its computational cost. For large datasets comprising time-resolved sequences, MTE-MART becomes unaffordable and has been barely applied even for the analysis of densely seeded tomographic PIV datasets. A novel implementation is proposed for tomographic PIV image sequences, which strongly reduces the computational burden of MTE-MART, possibly below that of regular MART. The method is a sequential algorithm that produces a time-marching estimation of the object intensity field based on an enhanced guess, which is built upon the object reconstructed at the previous time instant. As the method becomes effective after a number of snapshots (typically 5-10), the sequential MTE-MART (SMTE) is most suited for time-resolved sequences. The computational cost reduction due to SMTE simply stems from the fewer MART iterations required for each time instant. Moreover, the method yields superior reconstruction quality and higher velocity field measurement precision when compared with both MART and MTE-MART. The working principle is assessed in terms of computational effort, reconstruction quality and velocity field accuracy with both synthetic time-resolved tomographic images of a turbulent boundary layer and two experimental databases documented in the literature. The first is the time-resolved data of flow past an airfoil trailing edge used in the study of Novara and Scarano (Exp Fluids 52:1027-1041, 2012); the second is a swirling jet in a water flow. In both cases, the effective elimination of ghost particles is demonstrated in number and intensity within a short temporal transient of 5-10 frames, depending on the seeding density. The increased value of the velocity space-time correlation coefficient demonstrates the increased velocity field accuracy of SMTE compared with MART.

DIRECT OBSERVATION OF SOLAR CORONAL MAGNETIC FIELDS BY VECTOR TOMOGRAPHY OF THE CORONAL EMISSION LINE POLARIZATIONS

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

Kramar, M.; Lin, H.; Tomczyk, S., E-mail: kramar@cua.edu, E-mail: lin@ifa.hawaii.edu, E-mail: tomczyk@ucar.edu

We present the first direct “observation” of the global-scale, 3D coronal magnetic fields of Carrington Rotation (CR) Cycle 2112 using vector tomographic inversion techniques. The vector tomographic inversion uses measurements of the Fe xiii 10747 Å Hanle effect polarization signals by the Coronal Multichannel Polarimeter (CoMP) and 3D coronal density and temperature derived from scalar tomographic inversion of Solar Terrestrial Relations Observatory (STEREO)/Extreme Ultraviolet Imager (EUVI) coronal emission lines (CELs) intensity images as inputs to derive a coronal magnetic field model that best reproduces the observed polarization signals. While independent verifications of the vector tomography results cannot be performed, wemore » compared the tomography inverted coronal magnetic fields with those constructed by magnetohydrodynamic (MHD) simulations based on observed photospheric magnetic fields of CR 2112 and 2113. We found that the MHD model for CR 2112 is qualitatively consistent with the tomography inverted result for most of the reconstruction domain except for several regions. Particularly, for one of the most noticeable regions, we found that the MHD simulation for CR 2113 predicted a model that more closely resembles the vector tomography inverted magnetic fields. In another case, our tomographic reconstruction predicted an open magnetic field at a region where a coronal hole can be seen directly from a STEREO-B/EUVI image. We discuss the utilities and limitations of the tomographic inversion technique, and present ideas for future developments.« less

On the regularization for nonlinear tomographic absorption spectroscopy

NASA Astrophysics Data System (ADS)

Dai, Jinghang; Yu, Tao; Xu, Lijun; Cai, Weiwei

2018-02-01

Tomographic absorption spectroscopy (TAS) has attracted increased research efforts recently due to the development in both hardware and new imaging concepts such as nonlinear tomography and compressed sensing. Nonlinear TAS is one of the emerging modality that bases on the concept of nonlinear tomography and has been successfully demonstrated both numerically and experimentally. However, all the previous demonstrations were realized using only two orthogonal projections simply for ease of implementation. In this work, we examine the performance of nonlinear TAS using other beam arrangements and test the effectiveness of the beam optimization technique that has been developed for linear TAS. In addition, so far only smoothness prior has been adopted and applied in nonlinear TAS. Nevertheless, there are also other useful priors such as sparseness and model-based prior which have not been investigated yet. This work aims to show how these priors can be implemented and included in the reconstruction process. Regularization through Bayesian formulation will be introduced specifically for this purpose, and a method for the determination of a proper regularization factor will be proposed. The comparative studies performed with different beam arrangements and regularization schemes on a few representative phantoms suggest that the beam optimization method developed for linear TAS also works for the nonlinear counterpart and the regularization scheme should be selected properly according to the available a priori information under specific application scenarios so as to achieve the best reconstruction fidelity. Though this work is conducted under the context of nonlinear TAS, it can also provide useful insights for other tomographic modalities.

Tomographic Validation of the AWSoM Model of the Inner Corona During Solar Minima

NASA Astrophysics Data System (ADS)

Manchester, W.; Vásquez, A. M.; Lloveras, D. G.; Mac Cormack, C.; Nuevo, F.; Lopez-Fuentes, M.; Frazin, R. A.; van der Holst, B.; Landi, E.; Gombosi, T. I.

2017-12-01

Continuous improvement of MHD three-dimensional (3D) models of the global solar corona, such as the Alfven Wave Solar Model (AWSoM) of the Space Weather Modeling Framework (SWMF), requires testing their ability to reproduce observational constraints at a global scale. To that end, solar rotational tomography based on EUV image time-series can be used to reconstruct the 3D distribution of the electron density and temperature in the inner solar corona (r < 1.25 Rsun). The tomographic results, combined with a global coronal magnetic model, can further provide constraints on the energy input flux required at the coronal base to maintain stable structures. In this work, tomographic reconstructions are used to validate steady-state 3D MHD simulations of the inner corona using the latest version of the AWSoM model. We perform the study for selected rotations representative of solar minimum conditions, when the global structure of the corona is more axisymmetric. We analyse in particular the ability of the MHD simulation to match the tomographic results across the boundary region between the equatorial streamer belt and the surrounding coronal holes. The region is of particular interest as the plasma flow from that zone is thought to be related to the origin of the slow component of the solar wind.

Optimal joule heating of the subsurface

DOEpatents

Berryman, James G.; Daily, William D.

1994-01-01

A method for simultaneously heating the subsurface and imaging the effects of the heating. This method combines the use of tomographic imaging (electrical resistance tomography or ERT) to image electrical resistivity distribution underground, with joule heating by electrical currents injected in the ground. A potential distribution is established on a series of buried electrodes resulting in energy deposition underground which is a function of the resistivity and injection current density. Measurement of the voltages and currents also permits a tomographic reconstruction of the resistivity distribution. Using this tomographic information, the current injection pattern on the driving electrodes can be adjusted to change the current density distribution and thus optimize the heating. As the heating changes conditions, the applied current pattern can be repeatedly adjusted (based on updated resistivity tomographs) to affect real time control of the heating.

Three-Dimensional Characterization of Buried Metallic Targets via a Tomographic Algorithm Applied to GPR Synthetic Data

NASA Astrophysics Data System (ADS)

Comite, Davide; Galli, Alessandro; Catapano, Ilaria; Soldovieri, Francesco; Pettinelli, Elena

2013-04-01

This work is focused on the three-dimensional (3-D) imaging of buried metallic targets achievable by processing GPR (ground penetrating radar) simulation data via a tomographic inversion algorithm. The direct scattering problem has been analysed by means of a recently-developed numerical setup based on an electromagnetic time-domain CAD tool (CST Microwave Studio), which enables us to efficiently explore different GPR scenarios of interest [1]. The investigated 3D domain considers here two media, representing, e.g., an air/soil environment in which variously-shaped metallic (PEC) scatterers can be buried. The GPR system is simulated with Tx/Rx antennas placed in a bistatic configuration at the soil interface. In the implementation, the characteristics of the antennas may suitably be chosen in terms of topology, offset, radiative features, frequency ranges, etc. Arbitrary time-domain waveforms can be used as the input GPR signal (e.g., a Gaussian-like pulse having the frequency spectrum in the microwave range). The gathered signal at the output port includes the backscattered wave from the objects to be reconstructed, and the relevant data may be displayed in canonical radargram forms [1]. The GPR system sweeps along one main rectilinear direction, and the scanning process is here repeated along different close parallel lines to acquire data for a full 3-D analysis. Starting from the processing of the synthetic GPR data, a microwave tomographic approach is used to tackle the imaging, which is based on the Kirchhoff approximation to linearize the inverse scattering problem [2]. The target reconstruction is given in terms of the amplitude of the 'object function' (normalized with respect to its maximum inside the 3-D investigation domain). The data of the scattered field are collected considering a multi-frequency step process inside the fixed range of the signal spectrum, under a multi-bistatic configuration where the Tx and Rx antennas are separated by an offset distance and move at the interface over rectilinear observation domains. Analyses have been performed for some canonical scatterer shapes (e.g., sphere and cylinder, cube and parallelepiped, cone and wedge) in order to specifically highlight the influence of all the three dimensions (length, depth, and width) in the reconstruction of the targets. The roles of both size and location of the objects are also addressed in terms of the probing signal wavelengths and of the antenna offset. The results show to what extent it is possible to achieve a correct spatial localization of the targets, in conjunction with a generally satisfactory prediction of their 3-D size and shape. It should anyway be noted that the tomographic reconstructions here manage challenging cases of non-penetrable objects with data gathered under a reflection configuration, hence most of the information achievable is expected relating to the upper illuminated parts of the reflectors that give rise to the main scattering effects. The limits in the identification of fine geometrical details are discussed further in connection with the critical aspects of GPR operation, which include the adopted detection configuration and the frequency spectrum of the employed signals. [1] G. Valerio, A. Galli, P. M. Barone, S. E. Lauro, E. Mattei, and E. Pettinelli, "GPR detectability of rocks in a Martian-like shallow subsoil: a numerical approach," Planet. Space Sci., Vol. 62, pp. 31-40, 2012. [2] R. Solimene, A. Buonanno, F. Soldovieri, and R. Pierri, "Physical optics imaging of 3D PEC objects: vector and multipolarized approaches," IEEE Trans. Geosci. Remote Sens., Vol. 48, pp. 1799-1808, Apr. 2010.

Validation of Ionosonde Electron Density Reconstruction Algorithms with IONOLAB-RAY in Central Europe

NASA Astrophysics Data System (ADS)

Gok, Gokhan; Mosna, Zbysek; Arikan, Feza; Arikan, Orhan; Erdem, Esra

2016-07-01

Ionospheric observation is essentially accomplished by specialized radar systems called ionosondes. The time delay between the transmitted and received signals versus frequency is measured by the ionosondes and the received signals are processed to generate ionogram plots, which show the time delay or reflection height of signals with respect to transmitted frequency. The critical frequencies of ionospheric layers and virtual heights, that provide useful information about ionospheric structurecan be extracted from ionograms . Ionograms also indicate the amount of variability or disturbances in the ionosphere. With special inversion algorithms and tomographical methods, electron density profiles can also be estimated from the ionograms. Although structural pictures of ionosphere in the vertical direction can be observed from ionosonde measurements, some errors may arise due to inaccuracies that arise from signal propagation, modeling, data processing and tomographic reconstruction algorithms. Recently IONOLAB group (www.ionolab.org) developed a new algorithm for effective and accurate extraction of ionospheric parameters and reconstruction of electron density profile from ionograms. The electron density reconstruction algorithm applies advanced optimization techniques to calculate parameters of any existing analytical function which defines electron density with respect to height using ionogram measurement data. The process of reconstructing electron density with respect to height is known as the ionogram scaling or true height analysis. IONOLAB-RAY algorithm is a tool to investigate the propagation path and parameters of HF wave in the ionosphere. The algorithm models the wave propagation using ray representation under geometrical optics approximation. In the algorithm , the structural ionospheric characteristics arerepresented as realistically as possible including anisotropicity, inhomogenity and time dependence in 3-D voxel structure. The algorithm is also used for various purposes including calculation of actual height and generation of ionograms. In this study, the performance of electron density reconstruction algorithm of IONOLAB group and standard electron density profile algorithms of ionosondes are compared with IONOLAB-RAY wave propagation simulation in near vertical incidence. The electron density reconstruction and parameter extraction algorithms of ionosondes are validated with the IONOLAB-RAY results both for quiet anddisturbed ionospheric states in Central Europe using ionosonde stations such as Pruhonice and Juliusruh . It is observed that IONOLAB ionosonde parameter extraction and electron density reconstruction algorithm performs significantly better compared to standard algorithms especially for disturbed ionospheric conditions. IONOLAB-RAY provides an efficient and reliable tool to investigate and validate ionosonde electron density reconstruction algorithms, especially in determination of reflection height (true height) of signals and critical parameters of ionosphere. This study is supported by TUBITAK 114E541, 115E915 and Joint TUBITAK 114E092 and AS CR 14/001 projects.

Performance of different reflectance and diffuse optical imaging tomographic approaches in fluorescence molecular imaging of small animals

NASA Astrophysics Data System (ADS)

Dinten, Jean-Marc; Petié, Philippe; da Silva, Anabela; Boutet, Jérôme; Koenig, Anne; Hervé, Lionel; Berger, Michel; Laidevant, Aurélie; Rizo, Philippe

2006-03-01

Optical imaging of fluorescent probes is an essential tool for investigation of molecular events in small animals for drug developments. In order to get localization and quantification information of fluorescent labels, CEA-LETI has developed efficient approaches in classical reflectance imaging as well as in diffuse optical tomographic imaging with continuous and temporal signals. This paper presents an overview of the different approaches investigated and their performances. High quality fluorescence reflectance imaging is obtained thanks to the development of an original "multiple wavelengths" system. The uniformity of the excitation light surface area is better than 15%. Combined with the use of adapted fluorescent probes, this system enables an accurate detection of pathological tissues, such as nodules, beneath the animal's observed area. Performances for the detection of ovarian nodules on a nude mouse are shown. In order to investigate deeper inside animals and get 3D localization, diffuse optical tomography systems are being developed for both slab and cylindrical geometries. For these two geometries, our reconstruction algorithms are based on analytical expression of light diffusion. Thanks to an accurate introduction of light/matter interaction process in the algorithms, high quality reconstructions of tumors in mice have been obtained. Reconstruction of lung tumors on mice are presented. By the use of temporal diffuse optical imaging, localization and quantification performances can be improved at the price of a more sophisticated acquisition system and more elaborate information processing methods. Such a system based on a pulsed laser diode and a time correlated single photon counting system has been set up. Performances of this system for localization and quantification of fluorescent probes are presented.

GENFIRE: A generalized Fourier iterative reconstruction algorithm for high-resolution 3D imaging

DOE PAGES

Pryor, Alan; Yang, Yongsoo; Rana, Arjun; ...

2017-09-05

Tomography has made a radical impact on diverse fields ranging from the study of 3D atomic arrangements in matter to the study of human health in medicine. Despite its very diverse applications, the core of tomography remains the same, that is, a mathematical method must be implemented to reconstruct the 3D structure of an object from a number of 2D projections. Here, we present the mathematical implementation of a tomographic algorithm, termed GENeralized Fourier Iterative REconstruction (GENFIRE), for high-resolution 3D reconstruction from a limited number of 2D projections. GENFIRE first assembles a 3D Fourier grid with oversampling and then iteratesmore » between real and reciprocal space to search for a global solution that is concurrently consistent with the measured data and general physical constraints. The algorithm requires minimal human intervention and also incorporates angular refinement to reduce the tilt angle error. We demonstrate that GENFIRE can produce superior results relative to several other popular tomographic reconstruction techniques through numerical simulations and by experimentally reconstructing the 3D structure of a porous material and a frozen-hydrated marine cyanobacterium. As a result, equipped with a graphical user interface, GENFIRE is freely available from our website and is expected to find broad applications across different disciplines.« less

GENFIRE: A generalized Fourier iterative reconstruction algorithm for high-resolution 3D imaging

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

Pryor, Alan; Yang, Yongsoo; Rana, Arjun

Tomography has made a radical impact on diverse fields ranging from the study of 3D atomic arrangements in matter to the study of human health in medicine. Despite its very diverse applications, the core of tomography remains the same, that is, a mathematical method must be implemented to reconstruct the 3D structure of an object from a number of 2D projections. Here, we present the mathematical implementation of a tomographic algorithm, termed GENeralized Fourier Iterative REconstruction (GENFIRE), for high-resolution 3D reconstruction from a limited number of 2D projections. GENFIRE first assembles a 3D Fourier grid with oversampling and then iteratesmore » between real and reciprocal space to search for a global solution that is concurrently consistent with the measured data and general physical constraints. The algorithm requires minimal human intervention and also incorporates angular refinement to reduce the tilt angle error. We demonstrate that GENFIRE can produce superior results relative to several other popular tomographic reconstruction techniques through numerical simulations and by experimentally reconstructing the 3D structure of a porous material and a frozen-hydrated marine cyanobacterium. As a result, equipped with a graphical user interface, GENFIRE is freely available from our website and is expected to find broad applications across different disciplines.« less

Image intensifier-based volume tomographic angiography imaging system: system evaluation

NASA Astrophysics Data System (ADS)

Ning, Ruola; Wang, Xiaohui; Shen, Jianjun; Conover, David L.

1995-05-01

An image intensifier-based rotational volume tomographic angiography imaging system has been constructed. The system consists of an x-ray tube and an image intensifier that are separately mounted on a gantry. This system uses an image intensifier coupled to a TV camera as a two-dimensional detector so that a set of two-dimensional projections can be acquired for a direct three-dimensional reconstruction (3D). This system has been evaluated with two phantoms: a vascular phantom and a monkey head cadaver. One hundred eighty projections of each phantom were acquired with the system. A set of three-dimensional images were directly reconstructed from the projection data. The experimental results indicate that good imaging quality can be obtained with this system.

Model studies of laser absorption computed tomography for remote air pollution measurement

NASA Technical Reports Server (NTRS)

Wolfe, D. C., Jr.; Byer, R. L.

1982-01-01

Model studies of the potential of laser absorption-computed tomography are presented which demonstrate the possibility of sensitive remote atmospheric pollutant measurements, over kilometer-sized areas, with two-dimensional resolution, at modest laser source powers. An analysis of this tomographic reconstruction process as a function of measurement SNR, laser power, range, and system geometry, shows that the system is able to yield two-dimensional maps of pollutant concentrations at ranges and resolutions superior to those attainable with existing, direct-detection laser radars.

DEVELOPMENTAL PALEOBIOLOGY OF THE VERTEBRATE SKELETON.

PubMed

Rücklin, Martin; Donoghue, Philip C J; Cunningham, John A; Marone, Federica; Stampanoni, Marco

2014-07-01

Studies of the development of organisms can reveal crucial information on homology of structures. Developmental data are not peculiar to living organisms, and they are routinely preserved in the mineralized tissues that comprise the vertebrate skeleton, allowing us to obtain direct insight into the developmental evolution of this most formative of vertebrate innovations. The pattern of developmental processes is recorded in fossils as successive stages inferred from the gross morphology of multiple specimens and, more reliably and routinely, through the ontogenetic stages of development seen in the skeletal histology of individuals. Traditional techniques are destructive and restricted to a 2-D plane with the third dimension inferred. Effective non-invasive methods of visualizing paleohistology to reconstruct developmental stages of the skeleton are necessary. In a brief survey of paleohistological techniques we discuss the pros and cons of these methods. The use of tomographic methods to reconstruct development of organs is exemplified by the study of the placoderm dentition. Testing evidence for the presence of teeth in placoderms, the first jawed vertebrates, we compare the methods that have been used. These include inferring the development from morphology, and using serial sectioning, microCT or synchrotron X-ray tomographic microscopy (SRXTM) to reconstruct growth stages and directions of growth. The ensuing developmental interpretations are biased by the methods and degree of inference. The most direct and reliable method is using SRXTM data to trace sclerochronology. The resulting developmental data can be used to resolve homology and test hypotheses on the origin of evolutionary novelties.

Computer-aided design and rapid prototyping-assisted contouring of costal cartilage graft for facial reconstructive surgery.

PubMed

Lee, Shu Jin; Lee, Heow Pueh; Tse, Kwong Ming; Cheong, Ee Cherk; Lim, Siak Piang

2012-06-01

Complex 3-D defects of the facial skeleton are difficult to reconstruct with freehand carving of autogenous bone grafts. Onlay bone grafts are hard to carve and are associated with imprecise graft-bone interface contact and bony resorption. Autologous cartilage is well established in ear reconstruction as it is easy to carve and is associated with minimal resorption. In the present study, we aimed to reconstruct the hypoplastic orbitozygomatic region in a patient with left hemifacial microsomia using computer-aided design and rapid prototyping to facilitate costal cartilage carving and grafting. A three-step process of (1) 3-D reconstruction of the computed tomographic image, (2) mirroring the facial skeleton, and (3) modeling and rapid prototyping of the left orbitozygomaticomalar region and reconstruction template was performed. The template aided in donor site selection and extracorporeal contouring of the rib cartilage graft to allow for an accurate fit of the graft to the bony model prior to final fixation in the patient. We are able to refine the existing computer-aided design and rapid prototyping methods to allow for extracorporeal contouring of grafts and present rib cartilage as a good alternative to bone for autologous reconstruction.

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.

Using additive manufacturing in accuracy evaluation of reconstructions from computed tomography.

PubMed

Smith, Erin J; Anstey, Joseph A; Venne, Gabriel; Ellis, Randy E

2013-05-01

Bone models derived from patient imaging and fabricated using additive manufacturing technology have many potential uses including surgical planning, training, and research. This study evaluated the accuracy of bone surface reconstruction of two diarthrodial joints, the hip and shoulder, from computed tomography. Image segmentation of the tomographic series was used to develop a three-dimensional virtual model, which was fabricated using fused deposition modelling. Laser scanning was used to compare cadaver bones, printed models, and intermediate segmentations. The overall bone reconstruction process had a reproducibility of 0.3 ± 0.4 mm. Production of the model had an accuracy of 0.1 ± 0.1 mm, while the segmentation had an accuracy of 0.3 ± 0.4 mm, indicating that segmentation accuracy was the key factor in reconstruction. Generally, the shape of the articular surfaces was reproduced accurately, with poorer accuracy near the periphery of the articular surfaces, particularly in regions with periosteum covering and where osteophytes were apparent.

Tomographic imaging of transparent biological samples using the pyramid phase microscope

PubMed Central

Iglesias, Ignacio

2016-01-01

We show how a pyramid phase microscope can be used to obtain tomographic information of the spatial variation of refractive index in biological samples using the Radon transform. A method that uses the information provided by the phase microscope for axial and lateral repositioning of the sample when it rotates is also described. Its application to the reconstruction of mouse embryos in the blastocyst stage is demonstrated. PMID:27570696

Medical ultrasonic tomographic system

NASA Technical Reports Server (NTRS)

Heyser, R. C.; Lecroissette, D. H.; Nathan, R.; Wilson, R. L.

1977-01-01

An electro-mechanical scanning assembly was designed and fabricated for the purpose of generating an ultrasound tomogram. A low cost modality was demonstrated in which analog instrumentation methods formed a tomogram on photographic film. Successful tomogram reconstructions were obtained on in vitro test objects by using the attenuation of the fist path ultrasound signal as it passed through the test object. The nearly half century tomographic methods of X-ray analysis were verified as being useful for ultrasound imaging.

Imaging of turbulent structures and tomographic reconstruction of TORPEX plasma emissivity

NASA Astrophysics Data System (ADS)

Iraji, D.; Furno, I.; Fasoli, A.; Theiler, C.

2010-12-01

In the TORPEX [A. Fasoli et al., Phys. Plasmas 13, 055902 (2006)], a simple magnetized plasma device, low frequency electrostatic fluctuations associated with interchange waves, are routinely measured by means of extensive sets of Langmuir probes. To complement the electrostatic probe measurements of plasma turbulence and study of plasma structures smaller than the spatial resolution of probes array, a nonperturbative direct imaging system has been developed on TORPEX, including a fast framing Photron-APX-RS camera and an image intensifier unit. From the line-integrated camera images, we compute the poloidal emissivity profile of the plasma by applying a tomographic reconstruction technique using a pixel method and solving an overdetermined set of equations by singular value decomposition. This allows comparing statistical, spectral, and spatial properties of visible light radiation with electrostatic fluctuations. The shape and position of the time-averaged reconstructed plasma emissivity are observed to be similar to those of the ion saturation current profile. In the core plasma, excluding the electron cyclotron and upper hybrid resonant layers, the mean value of the plasma emissivity is observed to vary with (Te)α(ne)β, in which α =0.25-0.7 and β =0.8-1.4, in agreement with collisional radiative model. The tomographic reconstruction is applied to the fast camera movie acquired with 50 kframes/s rate and 2 μs of exposure time to obtain the temporal evolutions of the emissivity fluctuations. Conditional average sampling is also applied to visualize and measure sizes of structures associated with the interchange mode. The ω-time and the two-dimensional k-space Fourier analysis of the reconstructed emissivity fluctuations show the same interchange mode that is detected in the ω and k spectra of the ion saturation current fluctuations measured by probes. Small scale turbulent plasma structures can be detected and tracked in the reconstructed emissivity movies with the spatial resolution down to 2 cm, well beyond the spatial resolution of the probe array.

Blob-enhanced reconstruction technique

NASA Astrophysics Data System (ADS)

Castrillo, Giusy; Cafiero, Gioacchino; Discetti, Stefano; Astarita, Tommaso

2016-09-01

A method to enhance the quality of the tomographic reconstruction and, consequently, the 3D velocity measurement accuracy, is presented. The technique is based on integrating information on the objects to be reconstructed within the algebraic reconstruction process. A first guess intensity distribution is produced with a standard algebraic method, then the distribution is rebuilt as a sum of Gaussian blobs, based on location, intensity and size of agglomerates of light intensity surrounding local maxima. The blobs substitution regularizes the particle shape allowing a reduction of the particles discretization errors and of their elongation in the depth direction. The performances of the blob-enhanced reconstruction technique (BERT) are assessed with a 3D synthetic experiment. The results have been compared with those obtained by applying the standard camera simultaneous multiplicative reconstruction technique (CSMART) to the same volume. Several blob-enhanced reconstruction processes, both substituting the blobs at the end of the CSMART algorithm and during the iterations (i.e. using the blob-enhanced reconstruction as predictor for the following iterations), have been tested. The results confirm the enhancement in the velocity measurements accuracy, demonstrating a reduction of the bias error due to the ghost particles. The improvement is more remarkable at the largest tested seeding densities. Additionally, using the blobs distributions as a predictor enables further improvement of the convergence of the reconstruction algorithm, with the improvement being more considerable when substituting the blobs more than once during the process. The BERT process is also applied to multi resolution (MR) CSMART reconstructions, permitting simultaneously to achieve remarkable improvements in the flow field measurements and to benefit from the reduction in computational time due to the MR approach. Finally, BERT is also tested on experimental data, obtaining an increase of the signal-to-noise ratio in the reconstructed flow field and a higher value of the correlation factor in the velocity measurements with respect to the volume to which the particles are not replaced.

1975 Memorial Award Paper. Image generation and display techniques for CT scan data. Thin transverse and reconstructed coronal and sagittal planes.

PubMed

Glenn, W V; Johnston, R J; Morton, P E; Dwyer, S J

1975-01-01

The various limitations to computerized axial tomographic (CT) interpretation are due in part to the 8-13 mm standard tissue plane thickness and in part to the absence of alternative planes of view, such as coronal or sagittal images. This paper describes a method for gathering multiple overlapped 8 mm transverse sections, subjecting these data to a deconvolution process, and then displaying thin (1 mm) transverse as well as reconstructed coronal and sagittal CT images. Verification of the deconvolution technique with phantom experiments is described. Application of the phantom results to human post mortem CT scan data illustrates this method's faithful reconstruction of coronal and sagittal tissue densities when correlated with actual specimen photographs of a sectioned brain. A special CT procedure, limited basal overlap scanning, is proposed for use on current first generation CT scanners without hardware modification.

The Ettention software package.

PubMed

Dahmen, Tim; Marsalek, Lukas; Marniok, Nico; Turoňová, Beata; Bogachev, Sviatoslav; Trampert, Patrick; Nickels, Stefan; Slusallek, Philipp

2016-02-01

We present a novel software package for the problem "reconstruction from projections" in electron microscopy. The Ettention framework consists of a set of modular building-blocks for tomographic reconstruction algorithms. The well-known block iterative reconstruction method based on Kaczmarz algorithm is implemented using these building-blocks, including adaptations specific to electron tomography. Ettention simultaneously features (1) a modular, object-oriented software design, (2) optimized access to high-performance computing (HPC) platforms such as graphic processing units (GPU) or many-core architectures like Xeon Phi, and (3) accessibility to microscopy end-users via integration in the IMOD package and eTomo user interface. We also provide developers with a clean and well-structured application programming interface (API) that allows for extending the software easily and thus makes it an ideal platform for algorithmic research while hiding most of the technical details of high-performance computing. Copyright © 2015 Elsevier B.V. All rights reserved.

Ghost hunting—an assessment of ghost particle detection and removal methods for tomographic-PIV

NASA Astrophysics Data System (ADS)

Elsinga, G. E.; Tokgoz, S.

2014-08-01

This paper discusses and compares several methods, which aim to remove spurious peaks, i.e. ghost particles, from the volume intensity reconstruction in tomographic-PIV. The assessment is based on numerical simulations of time-resolved tomographic-PIV experiments in linear shear flows. Within the reconstructed volumes, intensity peaks are detected and tracked over time. These peaks are associated with particles (either ghosts or actual particles) and are characterized by their peak intensity, size and track length. Peak intensity and track length are found to be effective in discriminating between most ghosts and the actual particles, although not all ghosts can be detected using only a single threshold. The size of the reconstructed particles does not reveal an important difference between ghosts and actual particles. The joint distribution of peak intensity and track length however does, under certain conditions, allow a complete separation of ghosts and actual particles. The ghosts can have either a high intensity or a long track length, but not both combined, like all the actual particles. Removing the detected ghosts from the reconstructed volume and performing additional MART iterations can decrease the particle position error at low to moderate seeding densities, but increases the position error, velocity error and tracking errors at higher densities. The observed trends in the joint distribution of peak intensity and track length are confirmed by results from a real experiment in laminar Taylor-Couette flow. This diagnostic plot allows an estimate of the number of ghosts that are indistinguishable from the actual particles.

Comparative assessment of pressure field reconstructions from particle image velocimetry measurements and Lagrangian particle tracking

NASA Astrophysics Data System (ADS)

van Gent, P. L.; Michaelis, D.; van Oudheusden, B. W.; Weiss, P.-É.; de Kat, R.; Laskari, A.; Jeon, Y. J.; David, L.; Schanz, D.; Huhn, F.; Gesemann, S.; Novara, M.; McPhaden, C.; Neeteson, N. J.; Rival, D. E.; Schneiders, J. F. G.; Schrijer, F. F. J.

2017-04-01

A test case for pressure field reconstruction from particle image velocimetry (PIV) and Lagrangian particle tracking (LPT) has been developed by constructing a simulated experiment from a zonal detached eddy simulation for an axisymmetric base flow at Mach 0.7. The test case comprises sequences of four subsequent particle images (representing multi-pulse data) as well as continuous time-resolved data which can realistically only be obtained for low-speed flows. Particle images were processed using tomographic PIV processing as well as the LPT algorithm `Shake-The-Box' (STB). Multiple pressure field reconstruction techniques have subsequently been applied to the PIV results (Eulerian approach, iterative least-square pseudo-tracking, Taylor's hypothesis approach, and instantaneous Vortex-in-Cell) and LPT results (FlowFit, Vortex-in-Cell-plus, Voronoi-based pressure evaluation, and iterative least-square pseudo-tracking). All methods were able to reconstruct the main features of the instantaneous pressure fields, including methods that reconstruct pressure from a single PIV velocity snapshot. Highly accurate reconstructed pressure fields could be obtained using LPT approaches in combination with more advanced techniques. In general, the use of longer series of time-resolved input data, when available, allows more accurate pressure field reconstruction. Noise in the input data typically reduces the accuracy of the reconstructed pressure fields, but none of the techniques proved to be critically sensitive to the amount of noise added in the present test case.

Optimal joule heating of the subsurface

DOEpatents

Berryman, J.G.; Daily, W.D.

1994-07-05

A method for simultaneously heating the subsurface and imaging the effects of the heating is disclosed. This method combines the use of tomographic imaging (electrical resistance tomography or ERT) to image electrical resistivity distribution underground, with joule heating by electrical currents injected in the ground. A potential distribution is established on a series of buried electrodes resulting in energy deposition underground which is a function of the resistivity and injection current density. Measurement of the voltages and currents also permits a tomographic reconstruction of the resistivity distribution. Using this tomographic information, the current injection pattern on the driving electrodes can be adjusted to change the current density distribution and thus optimize the heating. As the heating changes conditions, the applied current pattern can be repeatedly adjusted (based on updated resistivity tomographs) to affect real time control of the heating.

Lamb-Wave-Based Tomographic Imaging Techniques for Hole-Edge Corrosion Monitoring in Plate Structures

PubMed Central

Wang, Dengjiang; Zhang, Weifang; Wang, Xiangyu; Sun, Bo

2016-01-01

This study presents a novel monitoring method for hole-edge corrosion damage in plate structures based on Lamb wave tomographic imaging techniques. An experimental procedure with a cross-hole layout using 16 piezoelectric transducers (PZTs) was designed. The A0 mode of the Lamb wave was selected, which is sensitive to thickness-loss damage. The iterative algebraic reconstruction technique (ART) method was used to locate and quantify the corrosion damage at the edge of the hole. Hydrofluoric acid with a concentration of 20% was used to corrode the specimen artificially. To estimate the effectiveness of the proposed method, the real corrosion damage was compared with the predicted corrosion damage based on the tomographic method. The results show that the Lamb-wave-based tomographic method can be used to monitor the hole-edge corrosion damage accurately. PMID:28774041

On the retrieval of crystallographic information from atom probe microscopy data via signal mapping from the detector coordinate space.

PubMed

Wallace, Nathan D; Ceguerra, Anna V; Breen, Andrew J; Ringer, Simon P

2018-06-01

Atom probe tomography is a powerful microscopy technique capable of reconstructing the 3D position and chemical identity of millions of atoms within engineering materials, at the atomic level. Crystallographic information contained within the data is particularly valuable for the purposes of reconstruction calibration and grain boundary analysis. Typically, analysing this data is a manual, time-consuming and error prone process. In many cases, the crystallographic signal is so weak that it is difficult to detect at all. In this study, a new automated signal processing methodology is demonstrated. We use the affine properties of the detector coordinate space, or the 'detector stack', as the basis for our calculations. The methodological framework and the visualisation tools are shown to be superior to the standard method of crystallographic pole visualisation directly from field evaporation images and there is no requirement for iterations between a full real-space initial tomographic reconstruction and the detector stack. The mapping approaches are demonstrated for aluminium, tungsten, magnesium and molybdenum. Implications for reconstruction calibration, accuracy of crystallographic measurements, reliability and repeatability are discussed. Copyright © 2018 Elsevier B.V. All rights reserved.

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.

Bright-field electron tomography of individual inorganic fullerene-like structures

NASA Astrophysics Data System (ADS)

Bar Sadan, Maya; Wolf, Sharon G.; Houben, Lothar

2010-03-01

Nanotubes and fullerene-like nanoparticles of various inorganic layered compounds have been studied extensively in recent years. Their characterisation on the atomic scale has proven essential for progress in synthesis as well as for the theoretical modelling of their physical properties. We show that with electron tomography it is possible to achieve a reliable reconstruction of the 3D structure of nested WS2 or MoS2 fullerene-like and nanotube structures with sub-nanometre resolution using electron microscopes that are not aberration-corrected. Model-based simulations were used to identify imaging parameters, under which structural features such as the shell structure can be retained in the tomogram reconstructed from bright-field micrographs. The isolation of a particle out of an agglomerate for the analysis of a single structure and its interconnection with other particles is facilitated through the tomograms. The internal structure of the layers within the particle alongside the shape and content of its internal void are reconstructed. The tomographic reconstruction yields insights regarding the growth process as well as structural defects, such as non-continuous layers, which relate to the lubrication properties.Nanotubes and fullerene-like nanoparticles of various inorganic layered compounds have been studied extensively in recent years. Their characterisation on the atomic scale has proven essential for progress in synthesis as well as for the theoretical modelling of their physical properties. We show that with electron tomography it is possible to achieve a reliable reconstruction of the 3D structure of nested WS2 or MoS2 fullerene-like and nanotube structures with sub-nanometre resolution using electron microscopes that are not aberration-corrected. Model-based simulations were used to identify imaging parameters, under which structural features such as the shell structure can be retained in the tomogram reconstructed from bright-field micrographs. The isolation of a particle out of an agglomerate for the analysis of a single structure and its interconnection with other particles is facilitated through the tomograms. The internal structure of the layers within the particle alongside the shape and content of its internal void are reconstructed. The tomographic reconstruction yields insights regarding the growth process as well as structural defects, such as non-continuous layers, which relate to the lubrication properties. Electronic supplementary information (ESI) available: Figs. S1 and S2 and movies S1-S6. See DOI: 10.1039/b9nr00251k

LASER APPLICATIONS IN MEDICINE: Analysis of distortions in the velocity profiles of suspension flows inside a light-scattering medium upon their reconstruction from the optical coherence Doppler tomograph signal

NASA Astrophysics Data System (ADS)

Bykov, A. V.; Kirillin, M. Yu; Priezzhev, A. V.

2005-11-01

Model signals from one and two plane flows of a particle suspension are obtained for an optical coherence Doppler tomograph (OCDT) by the Monte-Carlo method. The optical properties of particles mimic the properties of non-aggregating erythrocytes. The flows are considered in a stationary scattering medium with optical properties close to those of the skin. It is shown that, as the flow position depth increases, the flow velocity determined from the OCDT signal becomes smaller than the specified velocity and the reconstructed profile extends in the direction of the distant boundary, which is accompanied by the shift of its maximum. In the case of two flows, an increase in the velocity of the near-surface flow leads to the overestimated values of velocity of the reconstructed profile of the second flow. Numerical simulations were performed by using a multiprocessor parallel-architecture computer.

Tomographic Neutron Imaging using SIRT

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

Gregor, Jens; FINNEY, Charles E A; Toops, Todd J

2013-01-01

Neutron imaging is complementary to x-ray imaging in that materials such as water and plastic are highly attenuating while material such as metal is nearly transparent. We showcase tomographic imaging of a diesel particulate filter. Reconstruction is done using a modified version of SIRT called PSIRT. We expand on previous work and introduce Tikhonov regularization. We show that near-optimal relaxation can still be achieved. The algorithmic ideas apply to cone beam x-ray CT and other inverse problems.

A synchrotron radiation microtomography system for the analysis of trabecular bone samples.

PubMed

Salomé, M; Peyrin, F; Cloetens, P; Odet, C; Laval-Jeantet, A M; Baruchel, J; Spanne, P

1999-10-01

X-ray computed microtomography is particularly well suited for studying trabecular bone architecture, which requires three-dimensional (3-D) images with high spatial resolution. For this purpose, we describe a three-dimensional computed microtomography (microCT) system using synchrotron radiation, developed at ESRF. Since synchrotron radiation provides a monochromatic and high photon flux x-ray beam, it allows high resolution and a high signal-to-noise ratio imaging. The principle of the system is based on truly three-dimensional parallel tomographic acquisition. It uses a two-dimensional (2-D) CCD-based detector to record 2-D radiographs of the transmitted beam through the sample under different angles of view. The 3-D tomographic reconstruction, performed by an exact 3-D filtered backprojection algorithm, yields 3-D images with cubic voxels. The spatial resolution of the detector was experimentally measured. For the application to bone investigation, the voxel size was set to 6.65 microm, and the experimental spatial resolution was found to be 11 microm. The reconstructed linear attenuation coefficient was calibrated from hydroxyapatite phantoms. Image processing tools are being developed to extract structural parameters quantifying trabecular bone architecture from the 3-D microCT images. First results on human trabecular bone samples are presented.

Improved tomographic reconstructions using adaptive time-dependent intensity normalization.

PubMed

Titarenko, Valeriy; Titarenko, Sofya; Withers, Philip J; De Carlo, Francesco; Xiao, Xianghui

2010-09-01

The first processing step in synchrotron-based micro-tomography is the normalization of the projection images against the background, also referred to as a white field. Owing to time-dependent variations in illumination and defects in detection sensitivity, the white field is different from the projection background. In this case standard normalization methods introduce ring and wave artefacts into the resulting three-dimensional reconstruction. In this paper the authors propose a new adaptive technique accounting for these variations and allowing one to obtain cleaner normalized data and to suppress ring and wave artefacts. The background is modelled by the product of two time-dependent terms representing the illumination and detection stages. These terms are written as unknown functions, one scaled and shifted along a fixed direction (describing the illumination term) and one translated by an unknown two-dimensional vector (describing the detection term). The proposed method is applied to two sets (a stem Salix variegata and a zebrafish Danio rerio) acquired at the parallel beam of the micro-tomography station 2-BM at the Advanced Photon Source showing significant reductions in both ring and wave artefacts. In principle the method could be used to correct for time-dependent phenomena that affect other tomographic imaging geometries such as cone beam laboratory X-ray computed tomography.

Longitudinal phase space tomography using a booster cavity at PITZ

NASA Astrophysics Data System (ADS)

Malyutin, D.; Gross, M.; Isaev, I.; Khojoyan, M.; Kourkafas, G.; Krasilnikov, M.; Marchetti, B.; Otevrel, M.; Stephan, F.; Vashchenko, G.

2017-11-01

The knowledge of the longitudinal phase space (LPS) of electron beams is of great importance for optimizing the performance of high brightness photo injectors. To get the longitudinal phase space of an electron bunch in a linear accelerator a tomographic technique can be used. The method is based on measurements of the bunch momentum spectra while varying the bunch energy chirp. The energy chirp can be varied by one of the RF accelerating structures in the accelerator and the resulting momentum distribution can be measured with a dipole spectrometer further downstream. As a result, the longitudinal phase space can be reconstructed. Application of the tomographic technique for reconstruction of the longitudinal phase space is introduced in detail in this paper. Measurement results from the PITZ facility are shown and analyzed.

Three-dimensional Image Reconstruction in J-PET Using Filtered Back-projection Method

NASA Astrophysics Data System (ADS)

Shopa, R. Y.; Klimaszewski, K.; Kowalski, P.; Krzemień, W.; Raczyński, L.; Wiślicki, W.; Białas, P.; Curceanu, C.; Czerwiński, E.; Dulski, K.; Gajos, A.; Głowacz, B.; Gorgol, M.; Hiesmayr, B.; Jasińska, B.; Kisielewska-Kamińska, D.; Korcyl, G.; Kozik, T.; Krawczyk, N.; Kubicz, E.; Mohammed, M.; Pawlik-Niedźwiecka, M.; Niedźwiecki, S.; Pałka, M.; Rudy, Z.; Sharma, N. G.; Sharma, S.; Silarski, M.; Skurzok, M.; Wieczorek, A.; Zgardzińska, B.; Zieliński, M.; Moskal, P.

We present a method and preliminary results of the image reconstruction in the Jagiellonian PET tomograph. Using GATE (Geant4 Application for Tomographic Emission), interactions of the 511 keV photons with a cylindrical detector were generated. Pairs of such photons, flying back-to-back, originate from e+e- annihilations inside a 1-mm spherical source. Spatial and temporal coordinates of hits were smeared using experimental resolutions of the detector. We incorporated the algorithm of the 3D Filtered Back Projection, implemented in the STIR and TomoPy software packages, which differ in approximation methods. Consistent results for the Point Spread Functions of ~5/7,mm and ~9/20, mm were obtained, using STIR, for transverse and longitudinal directions, respectively, with no time of flight information included.

Portable imaging system method and apparatus

DOEpatents

Freifeld, Barry M.; Kneafsley, Timothy J.; Pruess, Jacob; Tomutsa, Liviu; Reiter, Paul A.; deCastro, Ted M.

2006-07-25

An operator shielded X-ray imaging system has sufficiently low mass (less than 300 kg) and is compact enough to enable portability by reducing operator shielding requirements to a minimum shielded volume. The resultant shielded volume may require a relatively small mass of shielding in addition to the already integrally shielded X-ray source, intensifier, and detector. The system is suitable for portable imaging of well cores at remotely located well drilling sites. The system accommodates either small samples, or small cross-sectioned objects of unlimited length. By rotating samples relative to the imaging device, the information required for computer aided tomographic reconstruction may be obtained. By further translating the samples relative to the imaging system, fully three dimensional (3D) tomographic reconstructions may be obtained of samples having arbitrary length.

Tunable diode laser absorption spectroscopy-based tomography system for on-line monitoring of two-dimensional distributions of temperature and H2O mole fraction.

PubMed

Xu, Lijun; Liu, Chang; Jing, Wenyang; Cao, Zhang; Xue, Xin; Lin, Yuzhen

2016-01-01

To monitor two-dimensional (2D) distributions of temperature and H2O mole fraction, an on-line tomography system based on tunable diode laser absorption spectroscopy (TDLAS) was developed. To the best of the authors' knowledge, this is the first report on a multi-view TDLAS-based system for simultaneous tomographic visualization of temperature and H2O mole fraction in real time. The system consists of two distributed feedback (DFB) laser diodes, a tomographic sensor, electronic circuits, and a computer. The central frequencies of the two DFB laser diodes are at 7444.36 cm(-1) (1343.3 nm) and 7185.6 cm(-1) (1391.67 nm), respectively. The tomographic sensor is used to generate fan-beam illumination from five views and to produce 60 ray measurements. The electronic circuits not only provide stable temperature and precise current controlling signals for the laser diodes but also can accurately sample the transmitted laser intensities and extract integrated absorbances in real time. Finally, the integrated absorbances are transferred to the computer, in which the 2D distributions of temperature and H2O mole fraction are reconstructed by using a modified Landweber algorithm. In the experiments, the TDLAS-based tomography system was validated by using asymmetric premixed flames with fixed and time-varying equivalent ratios, respectively. The results demonstrate that the system is able to reconstruct the profiles of the 2D distributions of temperature and H2O mole fraction of the flame and effectively capture the dynamics of the combustion process, which exhibits good potential for flame monitoring and on-line combustion diagnosis.

Tunable diode laser absorption spectroscopy-based tomography system for on-line monitoring of two-dimensional distributions of temperature and H2O mole fraction

NASA Astrophysics Data System (ADS)

Xu, Lijun; Liu, Chang; Jing, Wenyang; Cao, Zhang; Xue, Xin; Lin, Yuzhen

2016-01-01

To monitor two-dimensional (2D) distributions of temperature and H2O mole fraction, an on-line tomography system based on tunable diode laser absorption spectroscopy (TDLAS) was developed. To the best of the authors' knowledge, this is the first report on a multi-view TDLAS-based system for simultaneous tomographic visualization of temperature and H2O mole fraction in real time. The system consists of two distributed feedback (DFB) laser diodes, a tomographic sensor, electronic circuits, and a computer. The central frequencies of the two DFB laser diodes are at 7444.36 cm-1 (1343.3 nm) and 7185.6 cm-1 (1391.67 nm), respectively. The tomographic sensor is used to generate fan-beam illumination from five views and to produce 60 ray measurements. The electronic circuits not only provide stable temperature and precise current controlling signals for the laser diodes but also can accurately sample the transmitted laser intensities and extract integrated absorbances in real time. Finally, the integrated absorbances are transferred to the computer, in which the 2D distributions of temperature and H2O mole fraction are reconstructed by using a modified Landweber algorithm. In the experiments, the TDLAS-based tomography system was validated by using asymmetric premixed flames with fixed and time-varying equivalent ratios, respectively. The results demonstrate that the system is able to reconstruct the profiles of the 2D distributions of temperature and H2O mole fraction of the flame and effectively capture the dynamics of the combustion process, which exhibits good potential for flame monitoring and on-line combustion diagnosis.

Nanomaterial datasets to advance tomography in scanning transmission electron microscopy

DOE PAGES

Levin, Barnaby D. A.; Padgett, Elliot; Chen, Chien-Chun; ...

2016-06-07

Electron tomography in materials science has flourished with the demand to characterize nanoscale materials in three dimensions (3D). Access to experimental data is vital for developing and validating reconstruction methods that improve resolution and reduce radiation dose requirements. This work presents five high-quality scanning transmission electron microscope (STEM) tomography datasets in order to address the critical need for open access data in this field. The datasets represent the current limits of experimental technique, are of high quality, and contain materials with structural complexity. Included are tomographic series of a hyperbranched Co 2 P nanocrystal, platinum nanoparticles on a carbonmore » nanofibre imaged over the complete 180° tilt range, a platinum nanoparticle and a tungsten needle both imaged at atomic resolution by equal slope tomography, and a through-focal tilt series of PtCu nanoparticles. A volumetric reconstruction from every dataset is provided for comparison and development of post-processing and visualization techniques. Researchers interested in creating novel data processing and reconstruction algorithms will now have access to state of the art experimental test data.« less

Nanomaterial datasets to advance tomography in scanning transmission electron microscopy.

PubMed

Levin, Barnaby D A; Padgett, Elliot; Chen, Chien-Chun; Scott, M C; Xu, Rui; Theis, Wolfgang; Jiang, Yi; Yang, Yongsoo; Ophus, Colin; Zhang, Haitao; Ha, Don-Hyung; Wang, Deli; Yu, Yingchao; Abruña, Hector D; Robinson, Richard D; Ercius, Peter; Kourkoutis, Lena F; Miao, Jianwei; Muller, David A; Hovden, Robert

2016-06-07

Electron tomography in materials science has flourished with the demand to characterize nanoscale materials in three dimensions (3D). Access to experimental data is vital for developing and validating reconstruction methods that improve resolution and reduce radiation dose requirements. This work presents five high-quality scanning transmission electron microscope (STEM) tomography datasets in order to address the critical need for open access data in this field. The datasets represent the current limits of experimental technique, are of high quality, and contain materials with structural complexity. Included are tomographic series of a hyperbranched Co2P nanocrystal, platinum nanoparticles on a carbon nanofibre imaged over the complete 180° tilt range, a platinum nanoparticle and a tungsten needle both imaged at atomic resolution by equal slope tomography, and a through-focal tilt series of PtCu nanoparticles. A volumetric reconstruction from every dataset is provided for comparison and development of post-processing and visualization techniques. Researchers interested in creating novel data processing and reconstruction algorithms will now have access to state of the art experimental test data.

Nanomaterial datasets to advance tomography in scanning transmission electron microscopy

PubMed Central

Levin, Barnaby D.A.; Padgett, Elliot; Chen, Chien-Chun; Scott, M.C.; Xu, Rui; Theis, Wolfgang; Jiang, Yi; Yang, Yongsoo; Ophus, Colin; Zhang, Haitao; Ha, Don-Hyung; Wang, Deli; Yu, Yingchao; Abruña, Hector D.; Robinson, Richard D.; Ercius, Peter; Kourkoutis, Lena F.; Miao, Jianwei; Muller, David A.; Hovden, Robert

2016-01-01

Electron tomography in materials science has flourished with the demand to characterize nanoscale materials in three dimensions (3D). Access to experimental data is vital for developing and validating reconstruction methods that improve resolution and reduce radiation dose requirements. This work presents five high-quality scanning transmission electron microscope (STEM) tomography datasets in order to address the critical need for open access data in this field. The datasets represent the current limits of experimental technique, are of high quality, and contain materials with structural complexity. Included are tomographic series of a hyperbranched Co2P nanocrystal, platinum nanoparticles on a carbon nanofibre imaged over the complete 180° tilt range, a platinum nanoparticle and a tungsten needle both imaged at atomic resolution by equal slope tomography, and a through-focal tilt series of PtCu nanoparticles. A volumetric reconstruction from every dataset is provided for comparison and development of post-processing and visualization techniques. Researchers interested in creating novel data processing and reconstruction algorithms will now have access to state of the art experimental test data. PMID:27272459

Space-Based Three-Dimensional Imaging of Equatorial Plasma Bubbles: Advancing the Understanding of Ionospheric Density Depletions and Scintillation

DTIC Science & Technology

2012-03-28

Scintillation 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER Comberiate, Joseph M. 5e. TASK NUMBER 5f. WORK...bubble climatology. A tomographic reconstruction technique was modified and applied to SSUSI data to reconstruct three-dimensional cubes of ionospheric... modified and applied to SSUSI data to reconstruct three-dimensional cubes of ionospheric electron density. These data cubes allowed for 3-D imaging of

Survival of a pedicled latissimus dorsi flap in breast reconstruction without a thoracodorsal pedicle.

PubMed

Hartmann, C E A; Branford, O A; Malhotra, A; Chana, J S

2013-07-01

The latissimus dorsi flap, first performed by Tansini in 1892, was popularised for use by Olivari in 1976. The successful transfer of a latissimus dorsi flap during breast reconstruction has previously been thought to be dependent on having an intact thoracodorsal pedicle to ensure flap survival. It is well documented that the flap may also survive on the serratus branch in thoracodorsal pedicle division. We report a case of a 52-year-old female patient who underwent successful delayed breast reconstruction with a latissimus dorsi flap following previous mastectomy and axillary node clearance. Intraoperatively, the thoracodorsal pedicle and serratus branch were found to have been previously divided. On postoperative computer tomographic angiography the thoracodorsal pedicle was shown to be divided together with the serratus branch. The flap was seen to be supplied by the lateral thoracic artery. To our knowledge survival of a pedicled latissimus dorsi flap in breast reconstruction with a vascular supply from this vessel following thoracodorsal pedicle division has not previously been described. Previous thoracodorsal pedicle and serratus branch division may not be an absolute contraindication for the use of the latissimus dorsi flap in breast reconstruction, depending on the results of preoperative Doppler or computer tomographic angiography studies. Copyright © 2012 British Association of Plastic, Reconstructive and Aesthetic Surgeons. Published by Elsevier Ltd. All rights reserved.

Complex facial deformity reconstruction with a surgical guide incorporating a built-in occlusal stent as the positioning reference.

PubMed

Fang, Jing-Jing; Liu, Jia-Kuang; Wu, Tzu-Chieh; Lee, Jing-Wei; Kuo, Tai-Hong

2013-05-01

Computer-aided design has gained increasing popularity in clinical practice, and the advent of rapid prototyping technology has further enhanced the quality and predictability of surgical outcomes. It provides target guides for complex bony reconstruction during surgery. Therefore, surgeons can efficiently and precisely target fracture restorations. Based on three-dimensional models generated from a computed tomographic scan, precise preoperative planning simulation on a computer is possible. Combining the interdisciplinary knowledge of surgeons and engineers, this study proposes a novel surgical guidance method that incorporates a built-in occlusal wafer that serves as the positioning reference.Two patients with complex facial deformity suffering from severe facial asymmetry problems were recruited. In vitro facial reconstruction was first rehearsed on physical models, where a customized surgical guide incorporating a built-in occlusal stent as the positioning reference was designed to implement the surgery plan. This study is intended to present the authors' preliminary experience in a complex facial reconstruction procedure. It suggests that in regions with less information, where intraoperative computed tomographic scans or navigation systems are not available, our approach could be an effective, expedient, straightforward aid to enhance surgical outcome in a complex facial repair.

Novel edge treatment method for improving the transmission reconstruction quality in Tomographic Gamma Scanning.

PubMed

Han, Miaomiao; Guo, Zhirong; Liu, Haifeng; Li, Qinghua

2018-05-01

Tomographic Gamma Scanning (TGS) is a method used for the nondestructive assay of radioactive wastes. In TGS, the actual irregular edge voxels are regarded as regular cubic voxels in the traditional treatment method. In this study, in order to improve the performance of TGS, a novel edge treatment method is proposed that considers the actual shapes of these voxels. The two different edge voxel treatment methods were compared by computing the pixel-level relative errors and normalized mean square errors (NMSEs) between the reconstructed transmission images and the ideal images. Both methods were coupled with two different interative algorithms comprising Algebraic Reconstruction Technique (ART) with a non-negativity constraint and Maximum Likelihood Expectation Maximization (MLEM). The results demonstrated that the traditional method for edge voxel treatment can introduce significant error and that the real irregular edge voxel treatment method can improve the performance of TGS by obtaining better transmission reconstruction images. With the real irregular edge voxel treatment method, MLEM algorithm and ART algorithm can be comparable when assaying homogenous matrices, but MLEM algorithm is superior to ART algorithm when assaying heterogeneous matrices. Copyright © 2018 Elsevier Ltd. All rights reserved.

Temporal sparsity exploiting nonlocal regularization for 4D computed tomography reconstruction

PubMed Central

Kazantsev, Daniil; Guo, Enyu; Kaestner, Anders; Lionheart, William R. B.; Bent, Julian; Withers, Philip J.; Lee, Peter D.

2016-01-01

X-ray imaging applications in medical and material sciences are frequently limited by the number of tomographic projections collected. The inversion of the limited projection data is an ill-posed problem and needs regularization. Traditional spatial regularization is not well adapted to the dynamic nature of time-lapse tomography since it discards the redundancy of the temporal information. In this paper, we propose a novel iterative reconstruction algorithm with a nonlocal regularization term to account for time-evolving datasets. The aim of the proposed nonlocal penalty is to collect the maximum relevant information in the spatial and temporal domains. With the proposed sparsity seeking approach in the temporal space, the computational complexity of the classical nonlocal regularizer is substantially reduced (at least by one order of magnitude). The presented reconstruction method can be directly applied to various big data 4D (x, y, z+time) tomographic experiments in many fields. We apply the proposed technique to modelled data and to real dynamic X-ray microtomography (XMT) data of high resolution. Compared to the classical spatio-temporal nonlocal regularization approach, the proposed method delivers reconstructed images of improved resolution and higher contrast while remaining significantly less computationally demanding. PMID:27002902

Tomographic wavefront retrieval by combined use of geometric and plenoptic sensors

NASA Astrophysics Data System (ADS)

Trujillo-Sevilla, J. M.; Rodríguez-Ramos, L. F.; Fernández-Valdivia, Juan J.; Marichal-Hernández, José G.; Rodríguez-Ramos, J. M.

2014-05-01

Modern astronomic telescopes take advantage of multi-conjugate adaptive optics, in which wavefront sensors play a key role. A single sensor capable of measuring wavefront phases at any angle of observation would be helpful when improving atmospheric tomographic reconstruction. A new sensor combining both geometric and plenoptic arrangements is proposed, and a simulation demonstrating its working principle is also shown. Results show that this sensor is feasible, and also that single extended objects can be used to perform tomography of atmospheric turbulence.

A 3D tomographic reconstruction method to analyze Jupiter's electron-belt emission observations

NASA Astrophysics Data System (ADS)

Santos-Costa, Daniel; Girard, Julien; Tasse, Cyril; Zarka, Philippe; Kita, Hajime; Tsuchiya, Fuminori; Misawa, Hiroaki; Clark, George; Bagenal, Fran; Imai, Masafumi; Becker, Heidi N.; Janssen, Michael A.; Bolton, Scott J.; Levin, Steve M.; Connerney, John E. P.

2017-04-01

Multi-dimensional reconstruction techniques of Jupiter's synchrotron radiation from radio-interferometric observations were first developed by Sault et al. [Astron. Astrophys., 324, 1190-1196, 1997]. The tomographic-like technique introduced 20 years ago had permitted the first 3-dimensional mapping of the brightness distribution around the planet. This technique has demonstrated the advantage to be weakly dependent on planetary field models. It also does not require any knowledge on the energy and spatial distributions of the radiating electrons. On the downside, it is assumed that the volume emissivity of any punctual point source around the planet is isotropic. This assumption becomes incorrect when mapping the brightness distribution for non-equatorial point sources or any point sources from Juno's perspective. In this paper, we present our modeling effort to bypass the isotropy issue. Our approach is to use radio-interferometric observations and determine the 3-D brightness distribution in a cylindrical coordinate system. For each set (z, r), we constrain the longitudinal distribution with a Fourier series and the anisotropy is addressed with a simple periodic function when possible. We develop this new method over a wide range of frequencies using past VLA and LOFAR observations of Jupiter. We plan to test this reconstruction method with observations of Jupiter that are currently being carried out with LOFAR and GMRT in support to the Juno mission. We describe how this new 3D tomographic reconstruction method provides new model constraints on the energy and spatial distributions of Jupiter's ultra-relativistic electrons close to the planet and be used to interpret Juno MWR observations of Jupiter's electron-belt emission and assist in evaluating the background noise from the radiation environment in the atmospheric measurements.

GPS tomographic experiment on water vapour dynamics in the troposphere over Lisbon

NASA Astrophysics Data System (ADS)

Benevides, Pedro; Catalao, Joao; Miranda, Pedro

2015-04-01

Quantification of the water vapour variability on the atmosphere remains a difficult task, affecting the weather prediction. Coarse water vapour resolution measurements in space and time affect the numerical weather prediction solution models causing artifacts in the prediction of severe weather phenomena. The GNSS atmospheric processing has been developed in the past years providing integrated water vapour estimates comparable with the meteorological sensor measurements, with studies registering 1 to 2 kg/m2 bias, but lack a vertical determination of the atmospheric processes. The GNSS tomography in the troposphere is one of the most promising techniques for sensing the three-dimensional water vapour state of the atmosphere. The determination of the integrated water vapour profile by means of the widely accepted GNSS meteorology techniques, allows the reconstruction of several slant path delay rays in the satellite line of view, providing an opportunity to sense the troposphere at tree-dimensions plus time. The tomographic system can estimate an image solution of the water vapour but impositions have to be introduced to the system of equations inversion because of the non-optimal GNSS observation geometry. Application of this technique on atmospheric processes like large convective precipitation or mesoscale water vapour circulation have been able to describe its local dynamic vertical variation. A 3D tomographic experiment was developed over an area of 60x60 km2 around Lisbon (Portugal). The GNSS network available composed by 9 receivers was used for an experiment of densification of the permanent network using 8 temporarily installed GPS receivers (totalling 17 stations). This study was performed during several weeks in July 2013, where a radiosonde campaign was also held in order to validate the tomographic inversion solution. 2D integrated water vapour maps directly obtained from the GNSS processing were also evaluated and local coastal breeze circulation patterns were identified. Preliminary results show good agreement between radiosonde vertical profiles of water vapour and the correspondent grid columnar profile of the tomographic solution. This study aims for a preliminary characterization of the 3D water vapour field over this region, investigating its potential for monitor small scale air circulation on coastal areas like sea breeze meteorological phenomenon. This study was funded by the Portuguese Science Foundation FCT, under project SMOG PTDC/CTE-ATM/119922/2010 and PhD grant SFRH/BD/80288/2011.

Ambient Noise Interferometry and Surface Wave Array Tomography: Promises and Problems

NASA Astrophysics Data System (ADS)

van der Hilst, R. D.; Yao, H.; de Hoop, M. V.; Campman, X.; Solna, K.

2008-12-01

In the late 1990ies most seismologists would have frowned at the possibility of doing high-resolution surface wave tomography with noise instead of with signal associated with ballistic source-receiver propagation. Some may still do, but surface wave tomography with Green's functions estimated through ambient noise interferometry ('sourceless tomography') has transformed from a curiosity into one of the (almost) standard tools for analysis of data from dense seismograph arrays. Indeed, spectacular applications of ambient noise surface wave tomography have recently been published. For example, application to data from arrays in SE Tibet revealed structures in the crust beneath the Tibetan plateau that could not be resolved by traditional tomography (Yao et al., GJI, 2006, 2008). While the approach is conceptually simple, in application the proverbial devil is in the detail. Full reconstruction of the Green's function requires that the wavefields used are diffusive and that ambient noise energy is evenly distributed in the spatial dimensions of interest. In the field, these conditions are not usually met, and (frequency dependent) non-uniformity of the noise sources may lead to incomplete reconstruction of the Green's function. Furthermore, ambient noise distributions can be time-dependent, and seasonal variations have been documented. Naive use of empirical Green's functions may produce (unknown) bias in the tomographic models. The degrading effect on EGFs of the directionality of noise distribution forms particular challenges for applications beyond isotropic surface wave inversions, such as inversions for (azimuthal) anisotropy and attempts to use higher modes (or body waves). Incomplete Green's function reconstruction can (probably) not be prevented, but it may be possible to reduce the problem and - at least - understand the degree of incomplete reconstruction and prevent it from degrading the tomographic model. We will present examples of Rayleigh wave inversions and discuss strategies to mitigate effects of incomplete Green's function reconstruction on tomographic images.

Full characterization of a three-photon Greenberger-Horne-Zeilinger state using quantum state tomography.

PubMed

Resch, K J; Walther, P; Zeilinger, A

2005-02-25

We have performed the first experimental tomographic reconstruction of a three-photon polarization state. Quantum state tomography is a powerful tool for fully describing the density matrix of a quantum system. We measured 64 three-photon polarization correlations and used a "maximum-likelihood" reconstruction method to reconstruct the Greenberger-Horne-Zeilinger state. The entanglement class has been characterized using an entanglement witness operator and the maximum predicted values for the Mermin inequality were extracted.

Real-time plasma control based on the ISTTOK tomography diagnostica)

NASA Astrophysics Data System (ADS)

Carvalho, P. J.; Carvalho, B. B.; Neto, A.; Coelho, R.; Fernandes, H.; Sousa, J.; Varandas, C.; Chávez-Alarcón, E.; Herrera-Velázquez, J. J. E.

2008-10-01

The presently available processing power in generic processing units (GPUs) combined with state-of-the-art programmable logic devices benefits the implementation of complex, real-time driven, data processing algorithms for plasma diagnostics. A tomographic reconstruction diagnostic has been developed for the ISTTOK tokamak, based on three linear pinhole cameras each with ten lines of sight. The plasma emissivity in a poloidal cross section is computed locally on a submillisecond time scale, using a Fourier-Bessel algorithm, allowing the use of the output signals for active plasma position control. The data acquisition and reconstruction (DAR) system is based on ATCA technology and consists of one acquisition board with integrated field programmable gate array (FPGA) capabilities and a dual-core Pentium module running real-time application interface (RTAI) Linux. In this paper, the DAR real-time firmware/software implementation is presented, based on (i) front-end digital processing in the FPGA; (ii) a device driver specially developed for the board which enables streaming data acquisition to the host GPU; and (iii) a fast reconstruction algorithm running in Linux RTAI. This system behaves as a module of the central ISTTOK control and data acquisition system (FIRESIGNAL). Preliminary results of the above experimental setup are presented and a performance benchmarking against the magnetic coil diagnostic is shown.

High-Latitude Ionospheric Imaging using Canadian High Arctic Ionospheric Network (CHAIN)

NASA Astrophysics Data System (ADS)

Meziane, K.; Jayachandran, P. T.; Hamza, A. M.; MacDougall, J. W.

2013-12-01

Understanding the polar cap dynamics is a fundamental problem in solar-terrestrial physics; any breakthroughs would have to take into account the interactions that take place at the interfaces between the Solar Wind and the Magnetosphere and between the latter and the ionosphere, respectively. Over the past decade a significant number of ground-based GPS receivers and digital ionosondes have been deployed in the polar cap and auroral region. This deployment has allowed the harvest of much needed data, otherwise not available, which in turn helps understand the dynamics of the polar ionospheric regions. A technique, used consistently by researchers in the field, consists of inverting the Total Electron Content (TEC) along the ray path obtained from a system of GPS receivers. In the present study, a combination of tomography and ionosonde data from the CHAIN network is used to examine the dynamics of polar cap patches. First, the TEC derived from GPS receivers through tomographic reconstruction is directly compared with ionosonde data. The comparison includes periods of quite and disturbed geomagnetic activity. We then use the vertical density profiles derived from the CHAIN ionosondes as initial seeds for the reconstruction of the tomographic images of the polar cap regions. Precise electron density peaks obtained through the tomographic reconstruction fall within a range that is consistent with direct CHAIN measurements when certain conditions are met. An assessment of the performance of the resulting combination of GPS and ionosonde data is performed, and conclusions are presented.

Infrared laser transillumination CT imaging system using parallel fiber arrays and optical switches for finger joint imaging

NASA Astrophysics Data System (ADS)

Sasaki, Yoshiaki; Emori, Ryota; Inage, Hiroki; Goto, Masaki; Takahashi, Ryo; Yuasa, Tetsuya; Taniguchi, Hiroshi; Devaraj, Balasigamani; Akatsuka, Takao

2004-05-01

The heterodyne detection technique, on which the coherent detection imaging (CDI) method founds, can discriminate and select very weak, highly directional forward scattered, and coherence retaining photons that emerge from scattering media in spite of their complex and highly scattering nature. That property enables us to reconstruct tomographic images using the same reconstruction technique as that of X-Ray CT, i.e., the filtered backprojection method. Our group had so far developed a transillumination laser CT imaging method based on the CDI method in the visible and near-infrared regions and reconstruction from projections, and reported a variety of tomographic images both in vitro and in vivo of biological objects to demonstrate the effectiveness to biomedical use. Since the previous system was not optimized, it took several hours to obtain a single image. For a practical use, we developed a prototype CDI-based imaging system using parallel fiber array and optical switches to reduce the measurement time significantly. Here, we describe a prototype transillumination laser CT imaging system using fiber-optic based on optical heterodyne detection for early diagnosis of rheumatoid arthritis (RA), by demonstrating the tomographic imaging of acrylic phantom as well as the fundamental imaging properties. We expect that further refinements of the fiber-optic-based laser CT imaging system could lead to a novel and practical diagnostic tool for rheumatoid arthritis and other joint- and bone-related diseases in human finger.

Interdisciplinary Study of Egyptian Mummies from the Pushkin State Museum of Fine Arts Collection at the National Research Centre ``Kurchatov Institute''

NASA Astrophysics Data System (ADS)

Yatsishina, E. B.; Kovalchuk, M. V.; Loshak, M. D.; Vasilyev, S. V.; Vasilieva, O. A.; Dyuzheva, O. P.; Pojidaev, V. M.; Ushakov, V. L.

2018-05-01

Nine ancient Egyptian mummies (dated preliminarily to the period from the 1st mill. BCE to the first centuries CE) from the collection of the State Pushkin Museum of Fine Arts have been studied at the National Research Centre "Kurchatov Institute" (NRC KI) on the base of the complex of NBICS technologies. Tomographic scanning is performed using a magneto-resonance tomograph (3 T) and a hybrid positron emission tomography/computed tomography (PET-CT) scanner. Three-dimensional reconstructions of mummies and their anthropological measurements are carried out. Some medical conclusions are drawn based on the tomographic data. In addition, the embalming composition and tissue of one of the mummies are preliminarily analyzed.

Lumbar artery perforators: an anatomical study based on computed tomographic angiography imaging.

PubMed

Sommeling, Casper Emile; Colebunders, Britt; Pardon, Heleen E; Stillaert, Filip B; Blondeel, Phillip N; van Landuyt, Koenraad

2017-08-01

The free lumbar artery perforator flap has recently been introduced as a potentially valuable option for autologous breast reconstruction in a subset of patients. Up to date, few anatomical studies, exploring the lumbar region as a donor site for perforator- based flaps, have been conducted. An anatomical study of the position of the dominant lumbar artery perforator was performed, using the preoperative computed tomographic angiography images of 24 autologous breast reconstruction patients. In total, 61 dominant perforators were determined, 28 on the left and 33 on the right side. A radiologist defined the position of the perforator as coordinates in an xy-grid. Dominant perforators were shown to originate from the lumbar arteries at the level of lumbar vertebrae three or four. Remarkably, approximately 85% of these lumbar artery perforators enter the skin at 7-10 cm lateral from the midline (mean left 8.6 cm, right 8.2 cm). This study concludes a rather constant position of the dominant perforator. Therefore, preoperative-computed tomographic angiography is not always essential to find this perforator and Doppler ultrasound could be considered as an alternative, thereby carefully assessing all advantages and disadvantages inherent to either of these imaging methods.

3D homogeneity study in PMMA layers using a Fourier domain OCT system

NASA Astrophysics Data System (ADS)

Briones-R., Manuel de J.; Torre-Ibarra, Manuel H. De La; Tavera, Cesar G.; Luna H., Juan M.; Mendoza-Santoyo, Fernando

2016-11-01

Micro-metallic particles embedded in polymers are now widely used in several industrial applications in order to modify the mechanical properties of the bulk. A uniform distribution of these particles inside the polymers is highly desired for instance, when a biological backscattering is simulated or a bio-framework is designed. A 3D Fourier domain optical coherence tomography system to detect the polymer's internal homogeneity is proposed. This optical system has a 2D camera sensor array that records a fringe pattern used to reconstruct with a single shot the tomographic image of the sample. The system gathers the full 3D tomographic and optical phase information during a controlled deformation by means of a motion linear stage. This stage avoids the use of expensive tilting stages, which in addition are commonly controlled by piezo drivers. As proof of principle, a series of different deformations were proposed to detect the uniform or non-uniform internal deposition of copper micro particles. The results are presented as images coming from the 3D tomographic micro reconstruction of the samples, and the 3D optical phase information that identifies the in-homogeneity regions within the Poly methyl methacrylate (PMMA) volume.

A software tool of digital tomosynthesis application for patient positioning in radiotherapy.

PubMed

Yan, Hui; Dai, Jian-Rong

2016-03-08

Digital Tomosynthesis (DTS) is an image modality in reconstructing tomographic images from two-dimensional kV projections covering a narrow scan angles. Comparing with conventional cone-beam CT (CBCT), it requires less time and radiation dose in data acquisition. It is feasible to apply this technique in patient positioning in radiotherapy. To facilitate its clinical application, a software tool was developed and the reconstruction processes were accelerated by graphic process-ing unit (GPU). Two reconstruction and two registration processes are required for DTS application which is different from conventional CBCT application which requires one image reconstruction process and one image registration process. The reconstruction stage consists of productions of two types of DTS. One type of DTS is reconstructed from cone-beam (CB) projections covering a narrow scan angle and is named onboard DTS (ODTS), which represents the real patient position in treatment room. Another type of DTS is reconstructed from digitally reconstructed radiography (DRR) and is named reference DTS (RDTS), which represents the ideal patient position in treatment room. Prior to the reconstruction of RDTS, The DRRs are reconstructed from planning CT using the same acquisition setting of CB projections. The registration stage consists of two matching processes between ODTS and RDTS. The target shift in lateral and longitudinal axes are obtained from the matching between ODTS and RDTS in coronal view, while the target shift in longitudinal and vertical axes are obtained from the matching between ODTS and RDTS in sagittal view. In this software, both DRR and DTS reconstruction algorithms were implemented on GPU environments for acceleration purpose. The comprehensive evaluation of this software tool was performed including geometric accuracy, image quality, registration accuracy, and reconstruction efficiency. The average correlation coefficient between DRR/DTS generated by GPU-based algorithm and CPU-based algorithm is 0.99. Based on the measurements of cube phantom on DTS, the geometric errors are within 0.5 mm in three axes. For both cube phantom and pelvic phantom, the registration errors are within 0.5 mm in three axes. Compared with reconstruction performance of CPU-based algorithms, the performances of DRR and DTS reconstructions are improved by a factor of 15 to 20. A GPU-based software tool was developed for DTS application for patient positioning of radiotherapy. The geometric and registration accuracy met the clinical requirement in patient setup of radiotherapy. The high performance of DRR and DTS reconstruction algorithms was achieved by the GPU-based computation environments. It is a useful software tool for researcher and clinician in evaluating DTS application in patient positioning of radiotherapy.

Tomographic reconstruction of tracer gas concentration profiles in a room with the use of a single OP-FTIR and two iterative algorithms: ART and PWLS.

PubMed

Park, D Y; Fessler, J A; Yost, M G; Levine, S P

2000-03-01

Computed tomographic (CT) reconstructions of air contaminant concentration fields were conducted in a room-sized chamber employing a single open-path Fourier transform infrared (OP-FTIR) instrument and a combination of 52 flat mirrors and 4 retroreflectors. A total of 56 beam path data were repeatedly collected for around 1 hr while maintaining a stable concentration gradient. The plane of the room was divided into 195 pixels (13 x 15) for reconstruction. The algebraic reconstruction technique (ART) failed to reconstruct the original concentration gradient patterns for most cases. These poor results were caused by the "highly underdetermined condition" in which the number of unknown values (156 pixels) exceeds that of known data (56 path integral concentrations) in the experimental setting. A new CT algorithm, called the penalized weighted least-squares (PWLS), was applied to remedy this condition. The peak locations were correctly positioned in the PWLS-CT reconstructions. A notable feature of the PWLS-CT reconstructions was a significant reduction of highly irregular noise peaks found in the ART-CT reconstructions. However, the peak heights were slightly reduced in the PWLS-CT reconstructions due to the nature of the PWLS algorithm. PWLS could converge on the original concentration gradient even when a fairly high error was embedded into some experimentally measured path integral concentrations. It was also found in the simulation tests that the PWLS algorithm was very robust with respect to random errors in the path integral concentrations. This beam geometry and the use of a single OP-FTIR scanning system, in combination with the PWLS algorithm, is a system applicable to both environmental and industrial settings.

Tomographic Reconstruction of Tracer Gas Concentration Profiles in a Room with the Use of a Single OP-FTIR and Two Iterative Algorithms: ART and PWLS.

PubMed

Park, Doo Y; Fessier, Jeffrey A; Yost, Michael G; Levine, Steven P

2000-03-01

Computed tomographic (CT) reconstructions of air contaminant concentration fields were conducted in a room-sized chamber employing a single open-path Fourier transform infrared (OP-FTIR) instrument and a combination of 52 flat mirrors and 4 retroreflectors. A total of 56 beam path data were repeatedly collected for around 1 hr while maintaining a stable concentration gradient. The plane of the room was divided into 195 pixels (13 × 15) for reconstruction. The algebraic reconstruction technique (ART) failed to reconstruct the original concentration gradient patterns for most cases. These poor results were caused by the "highly underdetermined condition" in which the number of unknown values (156 pixels) exceeds that of known data (56 path integral concentrations) in the experimental setting. A new CT algorithm, called the penalized weighted least-squares (PWLS), was applied to remedy this condition. The peak locations were correctly positioned in the PWLS-CT reconstructions. A notable feature of the PWLS-CT reconstructions was a significant reduction of highly irregular noise peaks found in the ART-CT reconstructions. However, the peak heights were slightly reduced in the PWLS-CT reconstructions due to the nature of the PWLS algorithm. PWLS could converge on the original concentration gradient even when a fairly high error was embedded into some experimentally measured path integral concentrations. It was also found in the simulation tests that the PWLS algorithm was very robust with respect to random errors in the path integral concentrations. This beam geometry and the use of a single OP-FTIR scanning system, in combination with the PWLS algorithm, is a system applicable to both environmental and industrial settings.

On a novel low cost high accuracy experimental setup for tomographic particle image velocimetry

NASA Astrophysics Data System (ADS)

Discetti, Stefano; Ianiro, Andrea; Astarita, Tommaso; Cardone, Gennaro

2013-07-01

This work deals with the critical aspects related to cost reduction of a Tomo PIV setup and to the bias errors introduced in the velocity measurements by the coherent motion of the ghost particles. The proposed solution consists of using two independent imaging systems composed of three (or more) low speed single frame cameras, which can be up to ten times cheaper than double shutter cameras with the same image quality. Each imaging system is used to reconstruct a particle distribution in the same measurement region, relative to the first and the second exposure, respectively. The reconstructed volumes are then interrogated by cross-correlation in order to obtain the measured velocity field, as in the standard tomographic PIV implementation. Moreover, differently from tomographic PIV, the ghost particle distributions of the two exposures are uncorrelated, since their spatial distribution is camera orientation dependent. For this reason, the proposed solution promises more accurate results, without the bias effect of the coherent ghost particles motion. Guidelines for the implementation and the application of the present method are proposed. The performances are assessed with a parametric study on synthetic experiments. The proposed low cost system produces a much lower modulation with respect to an equivalent three-camera system. Furthermore, the potential accuracy improvement using the Motion Tracking Enhanced MART (Novara et al 2010 Meas. Sci. Technol. 21 035401) is much higher than in the case of the standard implementation of tomographic PIV.

CCD-camera-based diffuse optical tomography to study ischemic stroke in preclinical rat models

NASA Astrophysics Data System (ADS)

Lin, Zi-Jing; Niu, Haijing; Liu, Yueming; Su, Jianzhong; Liu, Hanli

2011-02-01

Stroke, due to ischemia or hemorrhage, is the neurological deficit of cerebrovasculature and is the third leading cause of death in the United States. More than 80 percent of stroke patients are ischemic stroke due to blockage of artery in the brain by thrombosis or arterial embolism. Hence, development of an imaging technique to image or monitor the cerebral ischemia and effect of anti-stoke therapy is more than necessary. Near infrared (NIR) optical tomographic technique has a great potential to be utilized as a non-invasive image tool (due to its low cost and portability) to image the embedded abnormal tissue, such as a dysfunctional area caused by ischemia. Moreover, NIR tomographic techniques have been successively demonstrated in the studies of cerebro-vascular hemodynamics and brain injury. As compared to a fiberbased diffuse optical tomographic system, a CCD-camera-based system is more suitable for pre-clinical animal studies due to its simpler setup and lower cost. In this study, we have utilized the CCD-camera-based technique to image the embedded inclusions based on tissue-phantom experimental data. Then, we are able to obtain good reconstructed images by two recently developed algorithms: (1) depth compensation algorithm (DCA) and (2) globally convergent method (GCM). In this study, we will demonstrate the volumetric tomographic reconstructed results taken from tissuephantom; the latter has a great potential to determine and monitor the effect of anti-stroke therapies.

Bright-field electron tomography of individual inorganic fullerene-like structures.

PubMed

Bar Sadan, Maya; Wolf, Sharon G; Houben, Lothar

2010-03-01

Nanotubes and fullerene-like nanoparticles of various inorganic layered compounds have been studied extensively in recent years. Their characterisation on the atomic scale has proven essential for progress in synthesis as well as for the theoretical modelling of their physical properties. We show that with electron tomography it is possible to achieve a reliable reconstruction of the 3D structure of nested WS(2) or MoS(2) fullerene-like and nanotube structures with sub-nanometre resolution using electron microscopes that are not aberration-corrected. Model-based simulations were used to identify imaging parameters, under which structural features such as the shell structure can be retained in the tomogram reconstructed from bright-field micrographs. The isolation of a particle out of an agglomerate for the analysis of a single structure and its interconnection with other particles is facilitated through the tomograms. The internal structure of the layers within the particle alongside the shape and content of its internal void are reconstructed. The tomographic reconstruction yields insights regarding the growth process as well as structural defects, such as non-continuous layers, which relate to the lubrication properties.

A novel fully automatic scheme for fiducial marker-based alignment in electron tomography.

PubMed

Han, Renmin; Wang, Liansan; Liu, Zhiyong; Sun, Fei; Zhang, Fa

2015-12-01

Although the topic of fiducial marker-based alignment in electron tomography (ET) has been widely discussed for decades, alignment without human intervention remains a difficult problem. Specifically, the emergence of subtomogram averaging has increased the demand for batch processing during tomographic reconstruction; fully automatic fiducial marker-based alignment is the main technique in this process. However, the lack of an accurate method for detecting and tracking fiducial markers precludes fully automatic alignment. In this paper, we present a novel, fully automatic alignment scheme for ET. Our scheme has two main contributions: First, we present a series of algorithms to ensure a high recognition rate and precise localization during the detection of fiducial markers. Our proposed solution reduces fiducial marker detection to a sampling and classification problem and further introduces an algorithm to solve the parameter dependence of marker diameter and marker number. Second, we propose a novel algorithm to solve the tracking of fiducial markers by reducing the tracking problem to an incomplete point set registration problem. Because a global optimization of a point set registration occurs, the result of our tracking is independent of the initial image position in the tilt series, allowing for the robust tracking of fiducial markers without pre-alignment. The experimental results indicate that our method can achieve an accurate tracking, almost identical to the current best one in IMOD with half automatic scheme. Furthermore, our scheme is fully automatic, depends on fewer parameters (only requires a gross value of the marker diameter) and does not require any manual interaction, providing the possibility of automatic batch processing of electron tomographic reconstruction. Copyright © 2015 Elsevier Inc. All rights reserved.

Interferometric tomography of fuel cells for monitoring membrane water content.

PubMed

Waller, Laura; Kim, Jungik; Shao-Horn, Yang; Barbastathis, George

2009-08-17

We have developed a system that uses two 1D interferometric phase projections for reconstruction of 2D water content changes over time in situ in a proton exchange membrane (PEM) fuel cell system. By modifying the filtered backprojection tomographic algorithm, we are able to incorporate a priori information about the object distribution into a fast reconstruction algorithm which is suitable for real-time monitoring.

Imaging of turbulent structures and tomographic reconstruction of TORPEX plasma emissivity

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

Iraji, D.; Furno, I.; Fasoli, A.

In the TORPEX [A. Fasoli et al., Phys. Plasmas 13, 055902 (2006)], a simple magnetized plasma device, low frequency electrostatic fluctuations associated with interchange waves, are routinely measured by means of extensive sets of Langmuir probes. To complement the electrostatic probe measurements of plasma turbulence and study of plasma structures smaller than the spatial resolution of probes array, a nonperturbative direct imaging system has been developed on TORPEX, including a fast framing Photron-APX-RS camera and an image intensifier unit. From the line-integrated camera images, we compute the poloidal emissivity profile of the plasma by applying a tomographic reconstruction technique usingmore » a pixel method and solving an overdetermined set of equations by singular value decomposition. This allows comparing statistical, spectral, and spatial properties of visible light radiation with electrostatic fluctuations. The shape and position of the time-averaged reconstructed plasma emissivity are observed to be similar to those of the ion saturation current profile. In the core plasma, excluding the electron cyclotron and upper hybrid resonant layers, the mean value of the plasma emissivity is observed to vary with (T{sub e}){sup {alpha}}(n{sub e}){sup {beta}}, in which {alpha}=0.25-0.7 and {beta}=0.8-1.4, in agreement with collisional radiative model. The tomographic reconstruction is applied to the fast camera movie acquired with 50 kframes/s rate and 2 {mu}s of exposure time to obtain the temporal evolutions of the emissivity fluctuations. Conditional average sampling is also applied to visualize and measure sizes of structures associated with the interchange mode. The {omega}-time and the two-dimensional k-space Fourier analysis of the reconstructed emissivity fluctuations show the same interchange mode that is detected in the {omega} and k spectra of the ion saturation current fluctuations measured by probes. Small scale turbulent plasma structures can be detected and tracked in the reconstructed emissivity movies with the spatial resolution down to 2 cm, well beyond the spatial resolution of the probe array.« less

TV-based conjugate gradient method and discrete L-curve for few-view CT reconstruction of X-ray in vivo data.

PubMed

Yang, Xiaoli; Hofmann, Ralf; Dapp, Robin; van de Kamp, Thomas; dos Santos Rolo, Tomy; Xiao, Xianghui; Moosmann, Julian; Kashef, Jubin; Stotzka, Rainer

2015-03-09

High-resolution, three-dimensional (3D) imaging of soft tissues requires the solution of two inverse problems: phase retrieval and the reconstruction of the 3D image from a tomographic stack of two-dimensional (2D) projections. The number of projections per stack should be small to accommodate fast tomography of rapid processes and to constrain X-ray radiation dose to optimal levels to either increase the duration of in vivo time-lapse series at a given goal for spatial resolution and/or the conservation of structure under X-ray irradiation. In pursuing the 3D reconstruction problem in the sense of compressive sampling theory, we propose to reduce the number of projections by applying an advanced algebraic technique subject to the minimisation of the total variation (TV) in the reconstructed slice. This problem is formulated in a Lagrangian multiplier fashion with the parameter value determined by appealing to a discrete L-curve in conjunction with a conjugate gradient method. The usefulness of this reconstruction modality is demonstrated for simulated and in vivo data, the latter acquired in parallel-beam imaging experiments using synchrotron radiation.

TV-based conjugate gradient method and discrete L-curve for few-view CT reconstruction of X-ray in vivo data

DOE PAGES

Yang, Xiaoli; Hofmann, Ralf; Dapp, Robin; ...

2015-01-01

High-resolution, three-dimensional (3D) imaging of soft tissues requires the solution of two inverse problems: phase retrieval and the reconstruction of the 3D image from a tomographic stack of two-dimensional (2D) projections. The number of projections per stack should be small to accommodate fast tomography of rapid processes and to constrain X-ray radiation dose to optimal levels to either increase the duration o f in vivo time-lapse series at a given goal for spatial resolution and/or the conservation of structure under X-ray irradiation. In pursuing the 3D reconstruction problem in the sense of compressive sampling theory, we propose to reduce themore » number of projections by applying an advanced algebraic technique subject to the minimisation of the total variation (TV) in the reconstructed slice. This problem is formulated in a Lagrangian multiplier fashion with the parameter value determined by appealing to a discrete L-curve in conjunction with a conjugate gradient method. The usefulness of this reconstruction modality is demonstrated for simulated and in vivo data, the latter acquired in parallel-beam imaging experiments using synchrotron radiation.« less

Dense velocity reconstruction from tomographic PTV with material derivatives

NASA Astrophysics Data System (ADS)

Schneiders, Jan F. G.; Scarano, Fulvio

2016-09-01

A method is proposed to reconstruct the instantaneous velocity field from time-resolved volumetric particle tracking velocimetry (PTV, e.g., 3D-PTV, tomographic PTV and Shake-the-Box), employing both the instantaneous velocity and the velocity material derivative of the sparse tracer particles. The constraint to the measured temporal derivative of the PTV particle tracks improves the consistency of the reconstructed velocity field. The method is christened as pouring time into space, as it leverages temporal information to increase the spatial resolution of volumetric PTV measurements. This approach becomes relevant in cases where the spatial resolution is limited by the seeding concentration. The method solves an optimization problem to find the vorticity and velocity fields that minimize a cost function, which includes next to instantaneous velocity, also the velocity material derivative. The velocity and its material derivative are related through the vorticity transport equation, and the cost function is minimized using the limited-memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS) algorithm. The procedure is assessed numerically with a simulated PTV experiment in a turbulent boundary layer from a direct numerical simulation (DNS). The experimental validation considers a tomographic particle image velocimetry (PIV) experiment in a similar turbulent boundary layer and the additional case of a jet flow. The proposed technique (`vortex-in-cell plus', VIC+) is compared to tomographic PIV analysis (3D iterative cross-correlation), PTV interpolation methods (linear and adaptive Gaussian windowing) and to vortex-in-cell (VIC) interpolation without the material derivative. A visible increase in resolved details in the turbulent structures is obtained with the VIC+ approach, both in numerical simulations and experiments. This results in a more accurate determination of the turbulent stresses distribution in turbulent boundary layer investigations. Data from a jet experiment, where the vortex topology is retrieved with a small number of tracers indicate the potential utilization of VIC+ in low-concentration experiments as for instance occurring in large-scale volumetric PTV measurements.

Intravenous volume tomographic pulmonary angiography imaging

NASA Astrophysics Data System (ADS)

Ning, Ruola; Strang, John G.; Chen, Biao; Conover, David L.; Yu, Rongfeng

1999-05-01

This study presents a new intravenous (IV) tomographic angiography imaging technique, called intravenous volume tomographic digital angiography (VTDA) for cross sectional pulmonary angiography. While the advantages of IV-VTDA over spiral CT in terms of volume scanning time and resolution have been validated and reported in our previous papers for head and neck vascular imaging, the superiority of IV-VTDA over spiral CT for cross sectional pulmonary angiography has not been explored yet. The purpose of this study is to demonstrate the advantage of isotropic resolution of IV-VTDA in the x, y and z directions through phantom and animal studies, and to explore its clinical application for detecting clots in pulmonary angiography. A prototype image intensifier-based VTDA imaging system has been designed and constructed by modifying a GE 8800 CT scanner. This system was used for a series of phantom and dog studies. A pulmonary vascular phantom was designed and constructed. The phantom was scanned using the prototype VTDA system for direct 3D reconstruction. Then the same phantom was scanned using a GE CT/i spiral CT scanner using the routine pulmonary CT angiography protocols. IV contrast injection and volume scanning protocols were developed during the dog studies. Both VTDA reconstructed images and spiral CT images of the specially designed phantom were analyzed and compared. The detectability of simulated vessels and clots was assessed as the function of iodine concentration levels, oriented angles, and diameters of the vessels and clots. A set of 3D VTDA reconstruction images of dog pulmonary arteries was obtained with different IV injection rates and isotropic resolution in the x, y and z directions. The results of clot detection studies in dog pulmonary arteries have also been shown. This study presents a new tomographic IV angiography imaging technique for cross sectional pulmonary angiography. The results of phantom and animal studies indicate that IV-VTDA is superior to spiral CT for cross sectional pulmonary angiography.

Interior tomographic imaging for x-ray coherent scattering (Conference Presentation)

NASA Astrophysics Data System (ADS)

Pang, Sean; Zhu, Zheyuan

2017-05-01

Conventional computed tomography reconstructs the attenuation only high-dimensional images. Coherent scatter computed tomography, which reconstructs the angular dependent scattering profiles of 3D objects, can provide molecular signatures that improves the accuracy of material identification and classification. Coherent scatter tomography are traditionally acquired by setups similar to x-ray powder diffraction machine; a collimated source in combination with 2D or 1D detector collimation in order to localize the scattering point. In addition, the coherent scatter cross-section is often 3 orders of magnitude lower than that of the absorption cross-section for the same material. Coded aperture and structured illumination approaches has been shown to greatly improve the collection efficiency. In many applications, especially in security imaging and medical diagnosis, fast and accurate identification of the material composition of a small volume within the whole object would lead to an accelerated imaging procedure and reduced radiation dose. Here, we report an imaging method to reconstruct the material coherent scatter profile within a small volume. The reconstruction along one radial direction can reconstruct a scalar coherent scattering tomographic image. Our methods takes advantage of the finite support of the scattering profile in small angle regime. Our system uses a pencil beam setup without using any detector side collimation. Coherent scatter profile of a 10 mm scattering sample embedded in a 30 mm diameter phantom was reconstructed. The setup has small form factor and is suitable for various portable non-destructive detection applications.

Contribution of computed tomography to the investigation of La Tene culture iron artefacts

NASA Astrophysics Data System (ADS)

Vopálenský, M.; Sankot, P.; Fořt, M.; Kumpová, I.; Vavřík, D.

2017-07-01

The X-ray tomographic study was realized in addition to the standard X-ray radiography for the purpose of the new conservation work upon the La Tene culture iron artifacts from the collections of the National Museum in Prague. These artifacts are heavily damaged by the corrosion, avoiding thus an effective visual exploration. The work shows that even details, which are shallow compared to the artifact thickness and therefore not detectable in standard radiographic images, can be made visible in 3D models obtained tomografically. The tomographic data acquisition was performed utilizing the unique TORATOM device, equipped with a large area X-ray detector with Gadox scintillator. The tomographic reconstruction revealed insufficiencies in the earlier conservation processes of the La Tene culture swords, as well as so-far unknown details, such as the exact sword shapes and their decoration. These new findings allowed better classifying of the artifacts. Tomography also helped in visualizing details of iron clips that are completely hidden under the rust, making thus the technology of the clip formation clearly observable. With this work, it has been proven that tomography can bear valuable new information compared to the standard X-ray radiography commonly used in the investigation of iron archeological artifacts.

Tomographic PIV: particles versus blobs

NASA Astrophysics Data System (ADS)

Champagnat, Frédéric; Cornic, Philippe; Cheminet, Adam; Leclaire, Benjamin; Le Besnerais, Guy; Plyer, Aurélien

2014-08-01

We present an alternative approach to tomographic particle image velocimetry (tomo-PIV) that seeks to recover nearly single voxel particles rather than blobs of extended size. The baseline of our approach is a particle-based representation of image data. An appropriate discretization of this representation yields an original linear forward model with a weight matrix built with specific samples of the system’s point spread function (PSF). Such an approach requires only a few voxels to explain the image appearance, therefore it favors much more sparsely reconstructed volumes than classic tomo-PIV. The proposed forward model is general and flexible and can be embedded in a classical multiplicative algebraic reconstruction technique (MART) or a simultaneous multiplicative algebraic reconstruction technique (SMART) inversion procedure. We show, using synthetic PIV images and by way of a large exploration of the generating conditions and a variety of performance metrics, that the model leads to better results than the classical tomo-PIV approach, in particular in the case of seeding densities greater than 0.06 particles per pixel and of PSFs characterized by a standard deviation larger than 0.8 pixels.

Long-term efficacy of biomodeled polymethyl methacrylate implants for orbitofacial defects.

PubMed

Groth, Michael J; Bhatnagar, Aparna; Clearihue, William J; Goldberg, Robert A; Douglas, Raymond S

2006-01-01

To report the long-term efficacy of custom polymethyl methacrylate implants using high-resolution computed tomographic modeling in the reconstruction of complex orbitofacial defects secondary to trauma. Nine patients with complex orbitofacial bone defects after trauma were evaluated for this retrospective, nonrandomized, noncomparative study. All the patients underwent reconstruction using custom, heat-cured polymethyl methacrylate implants. Patients were followed up postoperatively and evaluated for complications. Nine consecutive patients (5 men and 4 women) aged 28 to 63 years who underwent surgical reconstruction using prefabricated, heat-cured polymethyl methacrylate implants were included in the study. The interval between injury and presentation ranged from 1 month to 40 years. There were no significant complications, including infection, extrusion, or displacement of the implant. In all of the patients, wound healing was uneventful, with antibiotic drugs administered perioperatively. Mean follow-up was 4.3 years from the first visit (range, 6 months to 10 years). Computed tomographic biomodeled, prefabricated, heat-cured polymethyl methacrylate implants are well tolerated in the long term. Their advantages include customized design, long-term biocompatibility, and excellent aesthetic results.

Tomographic iterative reconstruction of a passive scalar in a 3D turbulent flow

NASA Astrophysics Data System (ADS)

Pisso, Ignacio; Kylling, Arve; Cassiani, Massimo; Solveig Dinger, Anne; Stebel, Kerstin; Schmidbauer, Norbert; Stohl, Andreas

2017-04-01

Turbulence in stable planetary boundary layers often encountered in high latitudes influences the exchange fluxes of heat, momentum, water vapor and greenhouse gases between the Earth's surface and the atmosphere. In climate and meteorological models, such effects of turbulence need to be parameterized, ultimately based on experimental data. A novel experimental approach is being developed within the COMTESSA project in order to study turbulence statistics at high resolution. Using controlled tracer releases, high-resolution camera images and estimates of the background radiation, different tomographic algorithms can be applied in order to obtain time series of 3D representations of the scalar dispersion. In this preliminary work, using synthetic data, we investigate different reconstruction algorithms with emphasis on algebraic methods. We study the dependence of the reconstruction quality on the discretization resolution and the geometry of the experimental device in both 2 and 3-D cases. We assess the computational aspects of the iterative algorithms focusing of the phenomenon of semi-convergence applying a variety of stopping rules. We discuss different strategies for error reduction and regularization of the ill-posed problem.

Planning surgical reconstruction in Treacher-Collins syndrome using virtual simulation.

PubMed

Nikkhah, Dariush; Ponniah, Allan; Ruff, Cliff; Dunaway, David

2013-11-01

Treacher-Collins syndrome is a rare autosomal dominant condition of varying phenotypic expression. The surgical correction in this syndrome is difficult, and the approach varies between craniofacial departments worldwide. The authors aimed to design standardized tools for planning orbitozygomatic and mandibular reconstruction in Treacher-Collins syndrome using geometric morphometrics. The Great Ormond Street Hospital database was retrospectively identified for patients with Treacher-Collins syndrome. Thirteen children (aged 2 to 15 years) who had suitable preoperative three-dimensional computed tomographic head scans were included. Six Treacher-Collins syndrome three-dimensional computed tomographic head scans were quantitatively compared using a template of 96 anatomically defined landmarks to 26 age-matched normal dry skulls. Thin-plate spline videos illustrated the characteristic deformities of retromicrognathia and maxillary and orbitozygomatic hypoplasia in the Treacher-Collins syndrome population. Geometric morphometrics was used in the virtual reconstruction of the orbitozygomatic and mandibular region in Treacher-Collins syndrome patients. Intrarater and interrater reliability of the landmarks was acceptable and within a standard deviation of less than 1 mm on 97 percent and 100 percent of 10 repeated scans, respectively. Virtual normalization of the Treacher-Collins syndrome skull effectively describes characteristic skeletal deformities and provides a useful guide to surgical reconstruction. Size-matched stereolithographic templates derived from thin-plate spline warps can provide effective intraoperative templates for zygomatic and mandibular reconstruction in the Treacher-Collins syndrome patient. Diagnostic, V.

Transverse Phase Space Reconstruction and Emittance Measurement of Intense Electron Beams using a Tomography Technique

NASA Astrophysics Data System (ADS)

Stratakis, D.; Kishek, R. A.; Li, H.; Bernal, S.; Walter, M.; Tobin, J.; Quinn, B.; Reiser, M.; O'Shea, P. G.

2006-11-01

Tomography is the technique of reconstructing an image from its projections. It is widely used in the medical community to observe the interior of the human body by processing multiple x-ray images taken at different angles, A few pioneering researchers have adapted tomography to reconstruct detailed phase space maps of charged particle beams. Some questions arise regarding the limitations of tomography technique for space charge dominated beams. For instance is the linear space charge force a valid approximation? Does tomography equally reproduce phase space for complex, experimentally observed, initial particle distributions? Does tomography make any assumptions about the initial distribution? This study explores the use of accurate modeling with the particle-in-cell code WARP to address these questions, using a wide range of different initial distributions in the code. The study also includes a number of experimental results on tomographic phase space mapping performed on the University of Maryland Electron Ring (UMER).

A review of US anthropometric reference data (1971 2000) with comparisons to both stylized and tomographic anatomic models

NASA Astrophysics Data System (ADS)

Huh, C.; Bolch, W. E.

2003-10-01

Two classes of anatomic models currently exist for use in both radiation protection and radiation dose reconstruction: stylized mathematical models and tomographic voxel models. The former utilize 3D surface equations to represent internal organ structure and external body shape, while the latter are based on segmented CT or MR images of a single individual. While tomographic models are clearly more anthropomorphic than stylized models, a given model's characterization as being anthropometric is dependent upon the reference human to which the model is compared. In the present study, data on total body mass, standing/sitting heights and body mass index are collected and reviewed for the US population covering the time interval from 1971 to 2000. These same anthropometric parameters are then assembled for the ORNL series of stylized models, the GSF series of tomographic models (Golem, Helga, Donna, etc), the adult male Zubal tomographic model and the UF newborn tomographic model. The stylized ORNL models of the adult male and female are found to be fairly representative of present-day average US males and females, respectively, in terms of both standing and sitting heights for ages between 20 and 60-80 years. While the ORNL adult male model provides a reasonably close match to the total body mass of the average US 21-year-old male (within ~5%), present-day 40-year-old males have an average total body mass that is ~16% higher. For radiation protection purposes, the use of the larger 73.7 kg adult ORNL stylized hermaphrodite model provides a much closer representation of average present-day US females at ages ranging from 20 to 70 years. In terms of the adult tomographic models from the GSF series, only Donna (40-year-old F) closely matches her age-matched US counterpart in terms of average body mass. Regarding standing heights, the better matches to US age-correlated averages belong to Irene (32-year-old F) for the females and Golem (38-year-old M) for the males. Both Helga (27-year-old F) and Donna, however, provide good matches to average US sitting heights for adult females, while Golem and Otoko (male of unknown age) yield sitting heights that are slightly below US adult male averages. Finally, Helga is seen as the only GSF tomographic female model that yields a body mass index in line with her average US female counterpart at age 26. In terms of dose reconstruction activities, however, all current tomographic voxel models are valuable assets in attempting to cover the broad distribution of individual anthropometric parameters representative of the current US population. It is highly recommended that similar attempts to create a broad library of tomographic models be initiated in the United States and elsewhere to complement and extend the limited number of tomographic models presently available for these efforts.

Metal artifact reduction using a patch-based reconstruction for digital breast tomosynthesis

NASA Astrophysics Data System (ADS)

Borges, Lucas R.; Bakic, Predrag R.; Maidment, Andrew D. A.; Vieira, Marcelo A. C.

2017-03-01

Digital breast tomosynthesis (DBT) is rapidly emerging as the main clinical tool for breast cancer screening. Although several reconstruction methods for DBT are described by the literature, one common issue is the interplane artifacts caused by out-of-focus features. For breasts containing highly attenuating features, such as surgical clips and large calcifications, the artifacts are even more apparent and can limit the detection and characterization of lesions by the radiologist. In this work, we propose a novel method of combining backprojected data into tomographic slices using a patch-based approach, commonly used in denoising. Preliminary tests were performed on a geometry phantom and on an anthropomorphic phantom containing metal inserts. The reconstructed images were compared to a commercial reconstruction solution. Qualitative assessment of the reconstructed images provides evidence that the proposed method reduces artifacts while maintaining low noise levels. Objective assessment supports the visual findings. The artifact spread function shows that the proposed method is capable of suppressing artifacts generated by highly attenuating features. The signal difference to noise ratio shows that the noise levels of the proposed and commercial methods are comparable, even though the commercial method applies post-processing filtering steps, which were not implemented on the proposed method. Thus, the proposed method can produce tomosynthesis reconstructions with reduced artifacts and low noise levels.

Analysis of computer images in the presence of metals

NASA Astrophysics Data System (ADS)

Buzmakov, Alexey; Ingacheva, Anastasia; Prun, Victor; Nikolaev, Dmitry; Chukalina, Marina; Ferrero, Claudio; Asadchikov, Victor

2018-04-01

Artifacts caused by intensely absorbing inclusions are encountered in computed tomography via polychromatic scanning and may obscure or simulate pathologies in medical applications. To improve the quality of reconstruction if high-Z inclusions in presence, previously we proposed and tested with synthetic data an iterative technique with soft penalty mimicking linear inequalities on the photon-starved rays. This note reports a test at the tomographic laboratory set-up at the Institute of Crystallography FSRC "Crystallography and Photonics" RAS in which tomographic scans were successfully made of temporary tooth without inclusion and with Pb inclusion.

Experimental and theoretical analysis for improved microscope design of optical projection tomographic microscopy.

PubMed

Coe, Ryan L; Seibel, Eric J

2013-09-01

We present theoretical and experimental results of axial displacement of objects relative to a fixed condenser focal plane (FP) in optical projection tomographic microscopy (OPTM). OPTM produces three-dimensional, reconstructed images of single cells from two-dimensional projections. The cell rotates in a microcapillary to acquire projections from different perspectives where the objective FP is scanned through the cell while the condenser FP remains fixed at the center of the microcapillary. This work uses a combination of experimental and theoretical methods to improve the OPTM instrument design.

Comment on 'Imaging of prompt gamma rays emitted during delivery of clinical proton beams with a Compton camera: feasibility studies for range verification'.

PubMed

Sitek, Arkadiusz

2016-12-21

The origin ensemble (OE) algorithm is a new method used for image reconstruction from nuclear tomographic data. The main advantage of this algorithm is the ease of implementation for complex tomographic models and the sound statistical theory. In this comment, the author provides the basics of the statistical interpretation of OE and gives suggestions for the improvement of the algorithm in the application to prompt gamma imaging as described in Polf et al (2015 Phys. Med. Biol. 60 7085).

Comment on ‘Imaging of prompt gamma rays emitted during delivery of clinical proton beams with a Compton camera: feasibility studies for range verification’

NASA Astrophysics Data System (ADS)

Sitek, Arkadiusz

2016-12-01

The origin ensemble (OE) algorithm is a new method used for image reconstruction from nuclear tomographic data. The main advantage of this algorithm is the ease of implementation for complex tomographic models and the sound statistical theory. In this comment, the author provides the basics of the statistical interpretation of OE and gives suggestions for the improvement of the algorithm in the application to prompt gamma imaging as described in Polf et al (2015 Phys. Med. Biol. 60 7085).

Nose and Nasal Planum Neoplasia, Reconstruction.

PubMed

Worley, Deanna R

2016-07-01

Most intranasal lesions are best treated with radiation therapy. Computed tomographic imaging with intravenous contrast is critical for treatment planning. Computed tomographic images of the nose will best assess the integrity of the cribriform plate for central nervous system invasion by a nasal tumor. Because of an owner's emotional response to an altered appearance of their dog's face, discussions need to include the entire family before proceeding with nasal planectomy or radical planectomy. With careful case selection, nasal planectomy and radical planectomy surgeries can be locally curative. Copyright © 2016 Elsevier Inc. All rights reserved.

A concept for non-invasive temperature measurement during injection moulding processes

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

Hopmann, Christian; Spekowius, Marcel, E-mail: spekowius@ikv.rwth-aachen.de; Wipperfürth, Jens

2016-03-09

Current models of the injection moulding process insufficiently consider the thermal interactions between melt, solidified material and the mould. A detailed description requires a deep understanding of the underlying processes and a precise observation of the temperature. Because todays measurement concepts do not allow a non-invasive analysis it is necessary to find new measurement techniques for temperature measurements during the manufacturing process. In this work we present the idea of a set up for a tomographic ultrasound measurement of the temperature field inside a plastics melt. The goal is to identify a concept that can be installed on a specializedmore » mould for the injection moulding process. The challenges are discussed and the design of a prototype is shown. Special attention is given to the spatial arrangement of the sensors. Besides the design of a measurement set up a reconstruction strategy for the ultrasound signals is required. We present an approach in which an image processing algorithm can be used to calculate a temperature distribution from the ultrasound scans. We discuss a reconstruction strategy in which the ultrasound signals are converted into a spartial temperature distribution by using pvT curves that are obtained by dilatometer measurements.« less

Fast tomographic methods for the tokamak ISTTOK

NASA Astrophysics Data System (ADS)

Carvalho, P. J.; Thomsen, H.; Gori, S.; Toussaint, U. v.; Weller, A.; Coelho, R.; Neto, A.; Pereira, T.; Silva, C.; Fernandes, H.

2008-04-01

The achievement of long duration, alternating current discharges on the tokamak IST-TOK requires a real-time plasma position control system. The plasma position determination based on magnetic probes system has been found to be inadequate during the current inversion due to the reduced plasma current. A tomography diagnostic has been therefore installed to supply the required feedback to the control system. Several tomographic methods are available for soft X-ray or bolo-metric tomography, among which the Cormack and Neural networks methods stand out due to their inherent speed of up to 1000 reconstructions per second, with currently available technology. This paper discusses the application of these algorithms on fusion devices while comparing performance and reliability of the results. It has been found that although the Cormack based inversion proved to be faster, the neural networks reconstruction has fewer artifacts and is more accurate.

Feasibility of hydrogen density estimation from tomographic sensing of Lyman alpha emission

NASA Astrophysics Data System (ADS)

Waldrop, L.; Kamalabadi, F.; Ren, D.

2015-12-01

In this work, we describe the scientific motivation, basic principles, and feasibility of a new approach to the estimation of neutral hydrogen (H) density in the terrestrial exosphere based on the 3-D tomographic sensing of optically thin H emission at 121.6 nm (Lyman alpha). In contrast to existing techniques, Lyman alpha tomography allows for model-independent reconstruction of the underlying H distribution in support of investigations regarding the origin and time-dependent evolution of exospheric structure. We quantitatively describe the trade-off space between the measurement sampling rate, viewing geometry, and the spatial and temporal resolution of the reconstruction that is supported by the data. We demonstrate that this approach is feasible from either earth-orbiting satellites such as the stereoscopic NASA TWINS mission or from a CubeSat platform along a trans-exosphere trajectory such as that enabled by the upcoming Exploration Mission 1 launch.

Using artificial neural networks (ANN) for open-loop tomography

NASA Astrophysics Data System (ADS)

Osborn, James; De Cos Juez, Francisco Javier; Guzman, Dani; Butterley, Timothy; Myers, Richard; Guesalaga, Andres; Laine, Jesus

2011-09-01

The next generation of adaptive optics (AO) systems require tomographic techniques in order to correct for atmospheric turbulence along lines of sight separated from the guide stars. Multi-object adaptive optics (MOAO) is one such technique. Here, we present a method which uses an artificial neural network (ANN) to reconstruct the target phase given off-axis references sources. This method does not require any input of the turbulence profile and is therefore less susceptible to changing conditions than some existing methods. We compare our ANN method with a standard least squares type matrix multiplication method (MVM) in simulation and find that the tomographic error is similar to the MVM method. In changing conditions the tomographic error increases for MVM but remains constant with the ANN model and no large matrix inversions are required.

Three-dimensional reconstruction for coherent diffraction patterns obtained by XFEL.

PubMed

Nakano, Miki; Miyashita, Osamu; Jonic, Slavica; Song, Changyong; Nam, Daewoong; Joti, Yasumasa; Tama, Florence

2017-07-01

The three-dimensional (3D) structural analysis of single particles using an X-ray free-electron laser (XFEL) is a new structural biology technique that enables observations of molecules that are difficult to crystallize, such as flexible biomolecular complexes and living tissue in the state close to physiological conditions. In order to restore the 3D structure from the diffraction patterns obtained by the XFEL, computational algorithms are necessary as the orientation of the incident beam with respect to the sample needs to be estimated. A program package for XFEL single-particle analysis based on the Xmipp software package, that is commonly used for image processing in 3D cryo-electron microscopy, has been developed. The reconstruction program has been tested using diffraction patterns of an aerosol nanoparticle obtained by tomographic coherent X-ray diffraction microscopy.

Linear Optimization and Image Reconstruction

DTIC Science & Technology

1994-06-01

final example is again a novel one. We formulate the problem of computer assisted tomographic ( CAT ) image reconstruction as a linear optimization...possibility that a patient, Fred, suffers from a brain tumor. Further, the physician opts to make use of the CAT (Computer Aided Tomography) scan device...and examine the inside of Fred’s head without exploratory surgery. The CAT scan machine works by projecting a finite number of X-rays of known

On a gas electron multiplier based synthetic diagnostic for soft x-ray tomography on WEST with focus on impurity transport studies

NASA Astrophysics Data System (ADS)

Jardin, A.; Mazon, D.; Malard, P.; O'Mullane, M.; Chernyshova, M.; Czarski, T.; Malinowski, K.; Kasprowicz, G.; Wojenski, A.; Pozniak, K.

2017-08-01

The tokamak WEST aims at testing ITER divertor high heat flux component technology in long pulse operation. Unfortunately, heavy impurities like tungsten (W) sputtered from the plasma facing components can pollute the plasma core by radiation cooling in the soft x-ray (SXR) range, which is detrimental for the energy confinement and plasma stability. SXR diagnostics give valuable information to monitor impurities and study their transport. The WEST SXR diagnostic is composed of two new cameras based on the Gas Electron Multiplier (GEM) technology. The WEST GEM cameras will be used for impurity transport studies by performing 2D tomographic reconstructions with spectral resolution in tunable energy bands. In this paper, we characterize the GEM spectral response and investigate W density reconstruction thanks to a synthetic diagnostic recently developed and coupled with a tomography algorithm based on the minimum Fisher information (MFI) inversion method. The synthetic diagnostic includes the SXR source from a given plasma scenario, the photoionization, electron cloud transport and avalanche in the detection volume using Magboltz, and tomographic reconstruction of the radiation from the GEM signal. Preliminary studies of the effect of transport on the W ionization equilibrium and on the reconstruction capabilities are also presented.

Digital tomosynthesis (DTS) with a Circular X-ray tube: Its image reconstruction based on total-variation minimization and the image characteristics

NASA Astrophysics Data System (ADS)

Park, Y. O.; Hong, D. K.; Cho, H. S.; Je, U. K.; Oh, J. E.; Lee, M. S.; Kim, H. J.; Lee, S. H.; Jang, W. S.; Cho, H. M.; Choi, S. I.; Koo, Y. S.

2013-09-01

In this paper, we introduce an effective imaging system for digital tomosynthesis (DTS) with a circular X-ray tube, the so-called circular-DTS (CDTS) system, and its image reconstruction algorithm based on the total-variation (TV) minimization method for low-dose, high-accuracy X-ray imaging. Here, the X-ray tube is equipped with a series of cathodes distributed around a rotating anode, and the detector remains stationary throughout the image acquisition. We considered a TV-based reconstruction algorithm that exploited the sparsity of the image with substantially high image accuracy. We implemented the algorithm for the CDTS geometry and successfully reconstructed images of high accuracy. The image characteristics were investigated quantitatively by using some figures of merit, including the universal-quality index (UQI) and the depth resolution. For selected tomographic angles of 20, 40, and 60°, the corresponding UQI values in the tomographic view were estimated to be about 0.94, 0.97, and 0.98, and the depth resolutions were about 4.6, 3.1, and 1.2 voxels in full width at half maximum (FWHM), respectively. We expect the proposed method to be applicable to developing a next-generation dental or breast X-ray imaging system.

Ionization Electron Signal Processing in Single Phase LArTPCs I. Algorithm Description and Quantitative Evaluation with MicroBooNE Simulation

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

Adams, C.; et al.

We describe the concept and procedure of drifted-charge extraction developed in the MicroBooNE experiment, a single-phase liquid argon time projection chamber (LArTPC). This technique converts the raw digitized TPC waveform to the number of ionization electrons passing through a wire plane at a given time. A robust recovery of the number of ionization electrons from both induction and collection anode wire planes will augment the 3D reconstruction, and is particularly important for tomographic reconstruction algorithms. A number of building blocks of the overall procedure are described. The performance of the signal processing is quantitatively evaluated by comparing extracted charge withmore » the true charge through a detailed TPC detector simulation taking into account position-dependent induced current inside a single wire region and across multiple wires. Some areas for further improvement of the performance of the charge extraction procedure are also discussed.« less

Development of a multiperspective optical measuring system for investigating decaying switching arcs at the nozzle exit of circuit breakers.

PubMed

Stoffels, M; Simon, S; Nikolic, P G; Stoller, P; Carstensen, J

2017-03-01

High-voltage gas circuit breakers, which play an important role in the operation and protection of the power grid, function by drawing an arc between two contacts and then extinguishing it by cooling it using a transonic gas flow. Improving the design of circuit breakers requires an understanding of the physical processes in the interruption of the arc, particularly during the zero crossing of the alternating current (the point in time when the arc can be interrupted). Most diagnostic techniques currently available focus on measurement of current, voltage, and gas pressure at defined locations. However, these integral properties do not give sufficient insight into the arc physics. To understand the current interruption process, spatially resolved information about the density, temperature, and conductivity of the arc and surrounding gas flow is needed. Owing to the three-dimensional, unstable nature of the arc in a circuit breaker, especially near current zero, a spatially resolved, tomographic diagnostic technique is required that is capable of freezing the rapid, transient behavior and that is insensitive to the vibrations and electromagnetic interference inherent in the interruption of short-circuit current arcs. Here a new measurement system, based on background-oriented schlieren (BOS) imaging, is presented and assessed. BOS imaging using four beams consisting of white light sources, a background pattern, imaging optics, and a camera permits measurement of the line-of-sight integrated refractive index. Tomographic reconstruction is used to determine the three-dimensional, spatially resolved index of refraction distribution that in turn is used to calculate the density. The quantitative accuracy of a single beam of the BOS setup is verified by using a calibration lens with a known focal length. The ability of the tomographic reconstruction to detect asymmetric features of the arc and surrounding gas flow is assessed semiquantitatively using a nozzle that generates two gas jets, as described in [Exp. Fluids43, 241 (2007)EXFLDU0723-486410.1007/s00348-007-0331-1]. Experiments using a simple model of a circuit breaker, which provides optical access to an ∼1  kA arc that burns between two contacts and is blown through a nozzle system by synthetic air from a high pressure reservoir, are also described. The density in the decaying arc and surrounding gas flow is reconstructed, and the limitations of the technique, which are related to the temporal and spatial resolution, are addressed.

Interval-based reconstruction for uncertainty quantification in PET

NASA Astrophysics Data System (ADS)

Kucharczak, Florentin; Loquin, Kevin; Buvat, Irène; Strauss, Olivier; Mariano-Goulart, Denis

2018-02-01

A new directed interval-based tomographic reconstruction algorithm, called non-additive interval based expectation maximization (NIBEM) is presented. It uses non-additive modeling of the forward operator that provides intervals instead of single-valued projections. The detailed approach is an extension of the maximum likelihood—expectation maximization algorithm based on intervals. The main motivation for this extension is that the resulting intervals have appealing properties for estimating the statistical uncertainty associated with the reconstructed activity values. After reviewing previously published theoretical concepts related to interval-based projectors, this paper describes the NIBEM algorithm and gives examples that highlight the properties and advantages of this interval valued reconstruction.

HeinzelCluster: accelerated reconstruction for FORE and OSEM3D.

PubMed

Vollmar, S; Michel, C; Treffert, J T; Newport, D F; Casey, M; Knöss, C; Wienhard, K; Liu, X; Defrise, M; Heiss, W D

2002-08-07

Using iterative three-dimensional (3D) reconstruction techniques for reconstruction of positron emission tomography (PET) is not feasible on most single-processor machines due to the excessive computing time needed, especially so for the large sinogram sizes of our high-resolution research tomograph (HRRT). In our first approach to speed up reconstruction time we transform the 3D scan into the format of a two-dimensional (2D) scan with sinograms that can be reconstructed independently using Fourier rebinning (FORE) and a fast 2D reconstruction method. On our dedicated reconstruction cluster (seven four-processor systems, Intel PIII@700 MHz, switched fast ethernet and Myrinet, Windows NT Server), we process these 2D sinograms in parallel. We have achieved a speedup > 23 using 26 processors and also compared results for different communication methods (RPC, Syngo, Myrinet GM). The other approach is to parallelize OSEM3D (implementation of C Michel), which has produced the best results for HRRT data so far and is more suitable for an adequate treatment of the sinogram gaps that result from the detector geometry of the HRRT. We have implemented two levels of parallelization for four dedicated cluster (a shared memory fine-grain level on each node utilizing all four processors and a coarse-grain level allowing for 15 nodes) reducing the time for one core iteration from over 7 h to about 35 min.

Parallel Computing for the Computed-Tomography Imaging Spectrometer

NASA Technical Reports Server (NTRS)

Lee, Seungwon

2008-01-01

This software computes the tomographic reconstruction of spatial-spectral data from raw detector images of the Computed-Tomography Imaging Spectrometer (CTIS), which enables transient-level, multi-spectral imaging by capturing spatial and spectral information in a single snapshot.

Synchrotron radiation microtomography of Taylor bubbles in capillary two-phase flow

NASA Astrophysics Data System (ADS)

Boden, Stephan; dos Santos Rolo, Tomy; Baumbach, Tilo; Hampel, Uwe

2014-07-01

We report on a study to measure the three-dimensional shape of Taylor bubbles in capillaries using synchrotron radiation in conjunction with ultrafast radiographic imaging. Moving Taylor bubbles in 2-mm round and square capillaries were radiographically scanned with an ultrahigh frame rate of up to 36,000 fps and 5.6-µm pixel separation. Consecutive images were properly processed to yield 2D transmission radiographs of high contrast-to-noise ratio. Application of 3D tomographic image reconstruction disclosed the 3D bubble shape. The results provide a reference data base for development of sophisticated interface resolving CFD computations.

Maxillary sinusitis and periapical abscess following periodontal therapy: a case report using three-dimensional evaluation.

PubMed

Huang, Chih-Hao; Brunsvold, Michael A

2006-01-01

Maxillary sinusitis may develop from the extension of periodontal disease. In this case, reconstructed three-dimensional images from multidetector spiral computed tomographs were helpful in evaluating periodontal bony defects and their relationship with the maxillary sinus. A 42-year-old woman in good general health presented with a chronic deep periodontal pocket on the palatal and interproximal aspects of tooth #14. Probing depths of the tooth ranged from 2 to 9 mm, and it exhibited a Class 1 mobility. Radiographs revealed a close relationship between the root apex and the maxillary sinus. The patient's periodontal diagnosis was localized severe chronic periodontitis. Treatment of the tooth consisted of cause-related therapy, surgical exploration, and bone grafting. A very deep circumferential bony defect at the palatal root of tooth #14 was noted during surgery. After the operation, the wound healed without incidence, but 10 days later, a maxillary sinusitis and periapical abscess developed. To control the infection, an evaluation of sinus and alveolus using computed tomographs was performed, systemic antibiotics were prescribed, and endodontic treatment was initiated. Two weeks after surgical treatment, the infection was relieved with the help of antibiotics and endodontic treatment. Bilateral bony communications between the maxillary sinus and periodontal bony defect of maxillary first molars were shown on three-dimensional computed tomographs. The digitally reconstructed images added valuable information for evaluating the periodontal defects. Three-dimensional images from spiral computed tomographs (CT) aided in evaluating and treating the close relationship between maxillary sinus disease and adjacent periodontal defects.

A Web simulation of medical image reconstruction and processing as an educational tool.

PubMed

Papamichail, Dimitrios; Pantelis, Evaggelos; Papagiannis, Panagiotis; Karaiskos, Pantelis; Georgiou, Evangelos

2015-02-01

Web educational resources integrating interactive simulation tools provide students with an in-depth understanding of the medical imaging process. The aim of this work was the development of a purely Web-based, open access, interactive application, as an ancillary learning tool in graduate and postgraduate medical imaging education, including a systematic evaluation of learning effectiveness. The pedagogic content of the educational Web portal was designed to cover the basic concepts of medical imaging reconstruction and processing, through the use of active learning and motivation, including learning simulations that closely resemble actual tomographic imaging systems. The user can implement image reconstruction and processing algorithms under a single user interface and manipulate various factors to understand the impact on image appearance. A questionnaire for pre- and post-training self-assessment was developed and integrated in the online application. The developed Web-based educational application introduces the trainee in the basic concepts of imaging through textual and graphical information and proceeds with a learning-by-doing approach. Trainees are encouraged to participate in a pre- and post-training questionnaire to assess their knowledge gain. An initial feedback from a group of graduate medical students showed that the developed course was considered as effective and well structured. An e-learning application on medical imaging integrating interactive simulation tools was developed and assessed in our institution.

Effects of small variations of speed of sound in optoacoustic tomographic imaging

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

Deán-Ben, X. Luís; Ntziachristos, Vasilis; Razansky, Daniel, E-mail: dr@tum.de

2014-07-15

Purpose: Speed of sound difference in the imaged object and surrounding coupling medium may reduce the resolution and overall quality of optoacoustic tomographic reconstructions obtained by assuming a uniform acoustic medium. In this work, the authors investigate the effects of acoustic heterogeneities and discuss potential benefits of accounting for those during the reconstruction procedure. Methods: The time shift of optoacoustic signals in an acoustically heterogeneous medium is studied theoretically by comparing different continuous and discrete wave propagation models. A modification of filtered back-projection reconstruction is subsequently implemented by considering a straight acoustic rays model for ultrasound propagation. The results obtainedmore » with this reconstruction procedure are compared numerically and experimentally to those obtained assuming a heuristically fitted uniform speed of sound in both full-view and limited-view optoacoustic tomography scenarios. Results: The theoretical analysis showcases that the errors in the time-of-flight of the signals predicted by considering the straight acoustic rays model tend to be generally small. When using this model for reconstructing simulated data, the resulting images accurately represent the theoretical ones. On the other hand, significant deviations in the location of the absorbing structures are found when using a uniform speed of sound assumption. The experimental results obtained with tissue-mimicking phantoms and a mouse postmortem are found to be consistent with the numerical simulations. Conclusions: Accurate analysis of effects of small speed of sound variations demonstrates that accounting for differences in the speed of sound allows improving optoacoustic reconstruction results in realistic imaging scenarios involving acoustic heterogeneities in tissues and surrounding media.« less

Evaluation of interpolation methods for surface-based motion compensated tomographic reconstruction for cardiac angiographic C-arm data

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

Mueller, Kerstin; Schwemmer, Chris; Hornegger, Joachim

2013-03-15

Purpose: For interventional cardiac procedures, anatomical and functional information about the cardiac chambers is of major interest. With the technology of angiographic C-arm systems it is possible to reconstruct intraprocedural three-dimensional (3D) images from 2D rotational angiographic projection data (C-arm CT). However, 3D reconstruction of a dynamic object is a fundamental problem in C-arm CT reconstruction. The 2D projections are acquired over a scan time of several seconds, thus the projection data show different states of the heart. A standard FDK reconstruction algorithm would use all acquired data for a filtered backprojection and result in a motion-blurred image. In thismore » approach, a motion compensated reconstruction algorithm requiring knowledge of the 3D heart motion is used. The motion is estimated from a previously presented 3D dynamic surface model. This dynamic surface model results in a sparse motion vector field (MVF) defined at control points. In order to perform a motion compensated reconstruction, a dense motion vector field is required. The dense MVF is generated by interpolation of the sparse MVF. Therefore, the influence of different motion interpolation methods on the reconstructed image quality is evaluated. Methods: Four different interpolation methods, thin-plate splines (TPS), Shepard's method, a smoothed weighting function, and a simple averaging, were evaluated. The reconstruction quality was measured on phantom data, a porcine model as well as on in vivo clinical data sets. As a quality index, the 2D overlap of the forward projected motion compensated reconstructed ventricle and the segmented 2D ventricle blood pool was quantitatively measured with the Dice similarity coefficient and the mean deviation between extracted ventricle contours. For the phantom data set, the normalized root mean square error (nRMSE) and the universal quality index (UQI) were also evaluated in 3D image space. Results: The quantitative evaluation of all experiments showed that TPS interpolation provided the best results. The quantitative results in the phantom experiments showed comparable nRMSE of Almost-Equal-To 0.047 {+-} 0.004 for the TPS and Shepard's method. Only slightly inferior results for the smoothed weighting function and the linear approach were achieved. The UQI resulted in a value of Almost-Equal-To 99% for all four interpolation methods. On clinical human data sets, the best results were clearly obtained with the TPS interpolation. The mean contour deviation between the TPS reconstruction and the standard FDK reconstruction improved in the three human cases by 1.52, 1.34, and 1.55 mm. The Dice coefficient showed less sensitivity with respect to variations in the ventricle boundary. Conclusions: In this work, the influence of different motion interpolation methods on left ventricle motion compensated tomographic reconstructions was investigated. The best quantitative reconstruction results of a phantom, a porcine, and human clinical data sets were achieved with the TPS approach. In general, the framework of motion estimation using a surface model and motion interpolation to a dense MVF provides the ability for tomographic reconstruction using a motion compensation technique.« less

Three-dimensional reconstruction of the peripancreatic vascular system based on computed tomographic angiography images and its clinical application in the surgical management of pancreatic tumors.

PubMed

Fang, Chi-hua; Kong, Deshuai; Wang, Xiaojun; Wang, Huaizhi; Xiang, Nan; Fan, Yingfang; Yang, Jian; Zhong, Shi Zheng

2014-04-01

This study aimed to investigate the clinical significance of 3-dimensional (3D) reconstruction of peripancreatic vessels for patients with suspected pancreatic cancer (PC). A total of 89 patients with PC were included; 60 patients randomly underwent computed tomographic angiography. Based on the findings of 3D reconstruction of peripancreatic vessels, the appropriate method for individualized tumor resection was determined. These patients were compared with 29 conventionally treated patients with PC. The rate of visualization was 100% for great vessels around the pancreas. The detection rates for anterior superior pancreaticoduodenal artery, posterior superior pancreaticoduodenal artery, anterior inferior pancreaticoduodenal artery, posterior inferior pancreaticoduodenal artery, dorsal pancreatic artery, superior marginal arterial branch of the pancreatic head, anterior superior pancreaticoduodenal vein, posterior superior pancreaticoduodenal vein, anterior inferior pancreaticoduodenal vein, and posterior inferior pancreaticoduodenal vein were 86.6%, 85.0%, 76.6%, 71.6%, 91.6%, 53.3%, 61.6%, 55.0%, 43.3%, and 51.6%, respectively. Forty-three patients who had undergone 3D reconstruction underwent surgery. Of the 29 conventionally treated patients, 19 underwent surgery. The operative time, blood loss, length of hospital stay, and complication incidence of the 43 patients were superior to that of the 19 patients. A peripancreatic vascular reconstruction can reveal the vascular anatomy, variations of peripancreatic vascular, and tumor-induced vascular changes; the application of the simulation surgery platform could reduce surgical trauma and decrease operative time.

Seismic tomographic constraints on plate-tectonic reconstructions of Nazca subduction under South America since late Cretaceous (˜80 Ma)

NASA Astrophysics Data System (ADS)

Chen, Y. W.; Wu, J.; Suppe, J.

2017-12-01

Global seismic tomography has provided new and increasingly higher resolution constraints on subducted lithospheric remnants in terms of their position, depth, and volumes. In this study we aim to link tomographic slab anomalies in the mantle under South America to Andean geology using methods to unfold (i.e. structurally restore) slabs back to earth surface and input them to globally consistent plate reconstructions (Wu et al., 2016). The Andean margin of South America has long been interpreted as a classic example of a continuous subduction system since early Jurassic or later. However, significant gaps in Andean plate tectonic reconstructions exist due to missing or incomplete geology from extensive Nazca-South America plate convergence (i.e. >5000 km since 80 Ma). We mapped and unfolded the Nazca slab from global seismic tomography to produce a quantitative plate reconstruction of the Andes back to the late Cretaceous 80 Ma. Our plate model predicts the latest phase of Nazca subduction began in the late Cretaceous subduction after a 100 to 80 Ma plate reorganization, which is supported by Andean geology that indicates a margin-wide compressional event at the mid-late Cretaceous (Tunik et al., 2010). Our Andean plate tectonic reconstructions predict the Andean margin experienced periods of strike-slip/transtensional and even divergent plate tectonics between 80 to 55 Ma. This prediction is roughly consistent with the arc magmatism from northern Chile between 20 to 36°S that resumed at 80 Ma after a magmatic gap. Our model indicates the Andean margin only became fully convergent after 55 Ma. We provide additional constraints on pre-subduction Nazca plate paleogeography by extracting P-wave velocity perturbations within our mapped slab surfaces following Wu et al. (2016). We identified localized slow anomalies within our mapped Nazca slab that apparently show the size and position of the subducted Nazca ridge, Carnegie ridge and the hypothesized Inca plateau within the Nazca slab. These intra-slab velocity anomalies provide the most complete tomographic evidence to date in support the classic, but still controversial hypothesis of subducted, relatively buoyant oceanic lithosphere features along the Andean margin.

Longitudinal Differences of Ionospheric Vertical Density Distribution and Equatorial Electrodynamics

NASA Technical Reports Server (NTRS)

Yizengaw, E.; Zesta, E.; Moldwin, M. B.; Damtie, B.; Mebrahtu, A.; Valledares, C.E.; Pfaff, R. F.

2012-01-01

Accurate estimation of global vertical distribution of ionospheric and plasmaspheric density as a function of local time, season, and magnetic activity is required to improve the operation of space-based navigation and communication systems. The vertical density distribution, especially at low and equatorial latitudes, is governed by the equatorial electrodynamics that produces a vertical driving force. The vertical structure of the equatorial density distribution can be observed by using tomographic reconstruction techniques on ground-based global positioning system (GPS) total electron content (TEC). Similarly, the vertical drift, which is one of the driving mechanisms that govern equatorial electrodynamics and strongly affect the structure and dynamics of the ionosphere in the low/midlatitude region, can be estimated using ground magnetometer observations. We present tomographically reconstructed density distribution and the corresponding vertical drifts at two different longitudes: the East African and west South American sectors. Chains of GPS stations in the east African and west South American longitudinal sectors, covering the equatorial anomaly region of meridian approx. 37 deg and 290 deg E, respectively, are used to reconstruct the vertical density distribution. Similarly, magnetometer sites of African Meridian B-field Education and Research (AMBER) and INTERMAGNET for the east African sector and South American Meridional B-field Array (SAMBA) and Low Latitude Ionospheric Sensor Network (LISN) are used to estimate the vertical drift velocity at two distinct longitudes. The comparison between the reconstructed and Jicamarca Incoherent Scatter Radar (ISR) measured density profiles shows excellent agreement, demonstrating the usefulness of tomographic reconstruction technique in providing the vertical density distribution at different longitudes. Similarly, the comparison between magnetometer estimated vertical drift and other independent drift observation, such as from VEFI onboard Communication/Navigation Outage Forecasting System (C/NOFS) satellite and JULIA radar, is equally promising. The observations at different longitudes suggest that the vertical drift velocities and the vertical density distribution have significant longitudinal differences; especially the equatorial anomaly peaks expand to higher latitudes more in American sector than the African sector, indicating that the vertical drift in the American sector is stronger than the African sector.

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.

CMT for biomedical and other applications

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

Spanne, P.

This session includes two presentations describing applications for x-ray tomography using synchrotron radiation for biomedical uses and fluid flow modeling, and outlines advantages for using monoenergetic x-rays. Contrast mechanisms are briefly described and several graphs of absorbed doses and scattering of x-rays are included. Also presented are schematic diagrams of computerized tomographic instrumentation with camera head. A brief description of goals for a real time tomographic system and expected improvements to the system are described. Color photomicrographs of the Berea Sandstone and human bone are provided, as well as a 3-D microtomographic reconstruction of a human vertebra sample.

Computational modeling of optical projection tomographic microscopy using the finite difference time domain method.

PubMed

Coe, Ryan L; Seibel, Eric J

2012-12-01

We present a method for modeling image formation in optical projection tomographic microscopy (OPTM) using high numerical aperture (NA) condensers and objectives. Similar to techniques used in computed tomography, OPTM produces three-dimensional, reconstructed images of single cells from two-dimensional projections. The model is capable of simulating axial scanning of a microscope objective to produce projections, which are reconstructed using filtered backprojection. Simulation of optical scattering in transmission optical microscopy is designed to analyze all aspects of OPTM image formation, such as degree of specimen staining, refractive-index matching, and objective scanning. In this preliminary work, a set of simulations is performed to examine the effect of changing the condenser NA, objective scan range, and complex refractive index on the final reconstruction of a microshell with an outer radius of 1.5 μm and an inner radius of 0.9 μm. The model lays the groundwork for optimizing OPTM imaging parameters and triaging efforts to further improve the overall system design. As the model is expanded in the future, it will be used to simulate a more realistic cell, which could lead to even greater impact.

Application of optical longitudinal tomography for dental introscopy

NASA Astrophysics Data System (ADS)

Levin, Gennady G.; Burgansky, Alexander A.; Levandovski, Alexei G.

1997-08-01

A new method of dental introscopy in-vitro is suggested by the authors. This method implies the usage of longitudinal tomography techniques and is characterized by non-invasive and non-harmful diagnostics features, as well as interactive regime of image reconstruction which lets an operator (doctor) to control the diagnostics process in real time. He-Ne laser emission is used for obtaining of the projections. By the means of longitudinal tomography, images of different sections of an object (tooth) can be reconstructed. An experiment was held by the authors in which 100 projections of a tooth (premolar) were obtained and images of 10 different sections were reconstructed. These images were later compared to real sections of the tooth. This experiment proved that optical longitudinal tomography can be successfully used for dental introscopy. Authors claim that optical tomographic methods can be used for diagnostics of other biological objects as well. Such objects are characterized by spatial geometrical anisotropy (tubular bones, phalanxes of fingers, penis, etc.). It is especially promising to use this method for children's dentistry. the authors discuss some features of the data acquisition system for optical longitudinal tomography. Reconstruction algorithms are described. The results of experimental reconstruction are presented and advantages of this diagnostics method are discussed.

Optimization of image quality and acquisition time for lab-based X-ray microtomography using an iterative reconstruction algorithm

NASA Astrophysics Data System (ADS)

Lin, Qingyang; Andrew, Matthew; Thompson, William; Blunt, Martin J.; Bijeljic, Branko

2018-05-01

Non-invasive laboratory-based X-ray microtomography has been widely applied in many industrial and research disciplines. However, the main barrier to the use of laboratory systems compared to a synchrotron beamline is its much longer image acquisition time (hours per scan compared to seconds to minutes at a synchrotron), which results in limited application for dynamic in situ processes. Therefore, the majority of existing laboratory X-ray microtomography is limited to static imaging; relatively fast imaging (tens of minutes per scan) can only be achieved by sacrificing imaging quality, e.g. reducing exposure time or number of projections. To alleviate this barrier, we introduce an optimized implementation of a well-known iterative reconstruction algorithm that allows users to reconstruct tomographic images with reasonable image quality, but requires lower X-ray signal counts and fewer projections than conventional methods. Quantitative analysis and comparison between the iterative and the conventional filtered back-projection reconstruction algorithm was performed using a sandstone rock sample with and without liquid phases in the pore space. Overall, by implementing the iterative reconstruction algorithm, the required image acquisition time for samples such as this, with sparse object structure, can be reduced by a factor of up to 4 without measurable loss of sharpness or signal to noise ratio.

TV-based conjugate gradient method and discrete L-curve for few-view CT reconstruction of X-ray in vivo data

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

Yang, Xiaoli; Hofmann, Ralf; Dapp, Robin

2015-01-01

High-resolution, three-dimensional (3D) imaging of soft tissues requires the solution of two inverse problems: phase retrieval and the reconstruction of the 3D image from a tomographic stack of two-dimensional (2D) projections. The number of projections per stack should be small to accommodate fast tomography of rapid processes and to constrain X-ray radiation dose to optimal levels to either increase the duration of in vivo time-lapse series at a given goal for spatial resolution and/or the conservation of structure under X-ray irradiation. In pursuing the 3D reconstruction problem in the sense of compressive sampling theory, we propose to reduce the numbermore » of projections by applying an advanced algebraic technique subject to the minimisation of the total variation (TV) in the reconstructed slice. This problem is formulated in a Lagrangian multiplier fashion with the parameter value determined by appealing to a discrete L-curve in conjunction with a conjugate gradient method. The usefulness of this reconstruction modality is demonstrated for simulated and in vivo data, the latter acquired in parallel-beam imaging experiments using synchrotron radiation. (C) 2015 Optical Society of America« less

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.

Design of 4D x-ray tomography experiments for reconstruction using regularized iterative algorithms

NASA Astrophysics Data System (ADS)

Mohan, K. Aditya

2017-10-01

4D X-ray computed tomography (4D-XCT) is widely used to perform non-destructive characterization of time varying physical processes in various materials. The conventional approach to improving temporal resolution in 4D-XCT involves the development of expensive and complex instrumentation that acquire data faster with reduced noise. It is customary to acquire data with many tomographic views at a high signal to noise ratio. Instead, temporal resolution can be improved using regularized iterative algorithms that are less sensitive to noise and limited views. These algorithms benefit from optimization of other parameters such as the view sampling strategy while improving temporal resolution by reducing the total number of views or the detector exposure time. This paper presents the design principles of 4D-XCT experiments when using regularized iterative algorithms derived using the framework of model-based reconstruction. A strategy for performing 4D-XCT experiments is presented that allows for improving the temporal resolution by progressively reducing the number of views or the detector exposure time. Theoretical analysis of the effect of the data acquisition parameters on the detector signal to noise ratio, spatial reconstruction resolution, and temporal reconstruction resolution is also presented in this paper.

Computed Tomographic Angiographic Perforator Localization for Virtual Surgical Planning of Osteocutaneous Fibular Free Flaps in Head and Neck Reconstruction.

PubMed

Ettinger, Kyle S; Alexander, Amy E; Arce, Kevin

2018-04-10

Virtual surgical planning (VSP), computer-aided design and computer-aided modeling, and 3-dimensional printing are 3 distinct technologies that have become increasingly used in head and neck oncology and microvascular reconstruction. Although each of these technologies has long been used for treatment planning in other surgical disciplines, such as craniofacial surgery, trauma surgery, temporomandibular joint surgery, and orthognathic surgery, its widespread use in head and neck reconstructive surgery remains a much more recent event. In response to the growing trend of VSP being used for the planning of fibular free flaps in head and neck reconstruction, some surgeons have questioned the technology's implementation based on its inadequacy in addressing other reconstructive considerations beyond hard tissue anatomy. Detractors of VSP for head and neck reconstruction highlight its lack of capability in accounting for multiple reconstructive factors, such as recipient vessel selection, vascular pedicle reach, need for dead space obliteration, and skin paddle perforator location. It is with this premise in mind that the authors report on a straightforward technique for anatomically localizing peroneal artery perforators during VSP for osteocutaneous fibular free flaps in which bone and a soft tissue skin paddle are required for ablative reconstruction. The technique allows for anatomic perforator localization during the VSP session based solely on data existent at preoperative computed tomographic angiography (CTA); it does not require any modifications to preoperative clinical workflows. It is the authors' presumption that many surgeons in the field are unaware of this planning capability within the context of modern VSP for head and neck reconstruction. The primary purpose of this report is to introduce and further familiarize surgeons with the technique of CTA perforator localization as a method of improving intraoperative fidelity for VSP of osteocutaneous fibular free flaps. Copyright © 2018. Published by Elsevier Inc.

Model-based tomographic reconstruction

DOEpatents

Chambers, David H; Lehman, Sean K; Goodman, Dennis M

2012-06-26

A model-based approach to estimating wall positions for a building is developed and tested using simulated data. It borrows two techniques from geophysical inversion problems, layer stripping and stacking, and combines them with a model-based estimation algorithm that minimizes the mean-square error between the predicted signal and the data. The technique is designed to process multiple looks from an ultra wideband radar array. The processed signal is time-gated and each section processed to detect the presence of a wall and estimate its position, thickness, and material parameters. The floor plan of a building is determined by moving the array around the outside of the building. In this paper we describe how the stacking and layer stripping algorithms are combined and show the results from a simple numerical example of three parallel walls.

A software tool of digital tomosynthesis application for patient positioning in radiotherapy

PubMed Central

Dai, Jian‐Rong

2016-01-01

Digital Tomosynthesis (DTS) is an image modality in reconstructing tomographic images from two‐dimensional kV projections covering a narrow scan angles. Comparing with conventional cone‐beam CT (CBCT), it requires less time and radiation dose in data acquisition. It is feasible to apply this technique in patient positioning in radiotherapy. To facilitate its clinical application, a software tool was developed and the reconstruction processes were accelerated by graphic processing unit (GPU). Two reconstruction and two registration processes are required for DTS application which is different from conventional CBCT application which requires one image reconstruction process and one image registration process. The reconstruction stage consists of productions of two types of DTS. One type of DTS is reconstructed from cone‐beam (CB) projections covering a narrow scan angle and is named onboard DTS (ODTS), which represents the real patient position in treatment room. Another type of DTS is reconstructed from digitally reconstructed radiography (DRR) and is named reference DTS (RDTS), which represents the ideal patient position in treatment room. Prior to the reconstruction of RDTS, The DRRs are reconstructed from planning CT using the same acquisition setting of CB projections. The registration stage consists of two matching processes between ODTS and RDTS. The target shift in lateral and longitudinal axes are obtained from the matching between ODTS and RDTS in coronal view, while the target shift in longitudinal and vertical axes are obtained from the matching between ODTS and RDTS in sagittal view. In this software, both DRR and DTS reconstruction algorithms were implemented on GPU environments for acceleration purpose. The comprehensive evaluation of this software tool was performed including geometric accuracy, image quality, registration accuracy, and reconstruction efficiency. The average correlation coefficient between DRR/DTS generated by GPU‐based algorithm and CPU‐based algorithm is 0.99. Based on the measurements of cube phantom on DTS, the geometric errors are within 0.5 mm in three axes. For both cube phantom and pelvic phantom, the registration errors are within 0.5 mm in three axes. Compared with reconstruction performance of CPU‐based algorithms, the performances of DRR and DTS reconstructions are improved by a factor of 15 to 20. A GPU‐based software tool was developed for DTS application for patient positioning of radiotherapy. The geometric and registration accuracy met the clinical requirement in patient setup of radiotherapy. The high performance of DRR and DTS reconstruction algorithms was achieved by the GPU‐based computation environments. It is a useful software tool for researcher and clinician in evaluating DTS application in patient positioning of radiotherapy. PACS number(s): 87.57.nf PMID:27074482

Rapidly converging multigrid reconstruction of cone-beam tomographic data

NASA Astrophysics Data System (ADS)

Myers, Glenn R.; Kingston, Andrew M.; Latham, Shane J.; Recur, Benoit; Li, Thomas; Turner, Michael L.; Beeching, Levi; Sheppard, Adrian P.

2016-10-01

In the context of large-angle cone-beam tomography (CBCT), we present a practical iterative reconstruction (IR) scheme designed for rapid convergence as required for large datasets. The robustness of the reconstruction is provided by the "space-filling" source trajectory along which the experimental data is collected. The speed of convergence is achieved by leveraging the highly isotropic nature of this trajectory to design an approximate deconvolution filter that serves as a pre-conditioner in a multi-grid scheme. We demonstrate this IR scheme for CBCT and compare convergence to that of more traditional techniques.

Noise robustness of a combined phase retrieval and reconstruction method for phase-contrast tomography.

PubMed

Kongskov, Rasmus Dalgas; Jørgensen, Jakob Sauer; Poulsen, Henning Friis; Hansen, Per Christian

2016-04-01

Classical reconstruction methods for phase-contrast tomography consist of two stages: phase retrieval and tomographic reconstruction. A novel algebraic method combining the two was suggested by Kostenko et al. [Opt. Express21, 12185 (2013)OPEXFF1094-408710.1364/OE.21.012185], and preliminary results demonstrated improved reconstruction compared with a given two-stage method. Using simulated free-space propagation experiments with a single sample-detector distance, we thoroughly compare the novel method with the two-stage method to address limitations of the preliminary results. We demonstrate that the novel method is substantially more robust toward noise; our simulations point to a possible reduction in counting times by an order of magnitude.

Model-based tomographic reconstruction of objects containing known components.

PubMed

Stayman, J Webster; Otake, Yoshito; Prince, Jerry L; Khanna, A Jay; Siewerdsen, Jeffrey H

2012-10-01

The likelihood of finding manufactured components (surgical tools, implants, etc.) within a tomographic field-of-view has been steadily increasing. One reason is the aging population and proliferation of prosthetic devices, such that more people undergoing diagnostic imaging have existing implants, particularly hip and knee implants. Another reason is that use of intraoperative imaging (e.g., cone-beam CT) for surgical guidance is increasing, wherein surgical tools and devices such as screws and plates are placed within or near to the target anatomy. When these components contain metal, the reconstructed volumes are likely to contain severe artifacts that adversely affect the image quality in tissues both near and far from the component. Because physical models of such components exist, there is a unique opportunity to integrate this knowledge into the reconstruction algorithm to reduce these artifacts. We present a model-based penalized-likelihood estimation approach that explicitly incorporates known information about component geometry and composition. The approach uses an alternating maximization method that jointly estimates the anatomy and the position and pose of each of the known components. We demonstrate that the proposed method can produce nearly artifact-free images even near the boundary of a metal implant in simulated vertebral pedicle screw reconstructions and even under conditions of substantial photon starvation. The simultaneous estimation of device pose also provides quantitative information on device placement that could be valuable to quality assurance and verification of treatment delivery.

Implementation of a cone-beam backprojection algorithm on the cell broadband engine processor

NASA Astrophysics Data System (ADS)

Bockenbach, Olivier; Knaup, Michael; Kachelrieß, Marc

2007-03-01

Tomographic image reconstruction is computationally very demanding. In all cases the backprojection represents the performance bottleneck due to the high operational count and due to the high demand put on the memory subsystem. In the past, solving this problem has lead to the implementation of specific architectures, connecting Application Specific Integrated Circuits (ASICs) or Field Programmable Gate Arrays (FPGAs) to memory through dedicated high speed busses. More recently, there have also been attempt to use Graphic Processing Units (GPUs) to perform the backprojection step. Originally aimed at the gaming market, IBM, Toshiba and Sony have introduced the Cell Broadband Engine (CBE) processor, often considered as a multicomputer on a chip. Clocked at 3 GHz, the Cell allows for a theoretical performance of 192 GFlops and a peak data transfer rate over the internal bus of 200 GB/s. This performance indeed makes the Cell a very attractive architecture for implementing tomographic image reconstruction algorithms. In this study, we investigate the relative performance of a perspective backprojection algorithm when implemented on a standard PC and on the Cell processor. We compare these results to the performance achievable with FPGAs based boards and high end GPUs. The cone-beam backprojection performance was assessed by backprojecting a full circle scan of 512 projections of 1024x1024 pixels into a volume of size 512x512x512 voxels. It took 3.2 minutes on the PC (single CPU) and is as fast as 13.6 seconds on the Cell.

Sparsity-driven tomographic reconstruction of atmospheric water vapor using GNSS and InSAR observations

NASA Astrophysics Data System (ADS)

Heublein, Marion; Alshawaf, Fadwa; Zhu, Xiao Xiang; Hinz, Stefan

2016-04-01

An accurate knowledge of the 3D distribution of water vapor in the atmosphere is a key element for weather forecasting and climate research. On the other hand, as water vapor causes a delay in the microwave signal propagation within the atmosphere, a precise determination of water vapor is required for accurate positioning and deformation monitoring using Global Navigation Satellite Systems (GNSS) and Interferometric Synthetic Aperture Radar (InSAR). However, due to its high variability in time and space, the atmospheric water vapor distribution is difficult to model. Since GNSS meteorology was introduced about twenty years ago, it has increasingly been used as a geodetic technique to generate maps of 2D Precipitable Water Vapor (PWV). Moreover, several approaches for 3D tomographic water vapor reconstruction from GNSS-based estimates using the simple least squares adjustment were presented. In this poster, we present an innovative and sophisticated Compressive Sensing (CS) concept for sparsity-driven tomographic reconstruction of 3D atmospheric wet refractivity fields using data from GNSS and InSAR. The 2D zenith wet delay (ZWD) estimates are obtained by a combination of point-wise estimates of the wet delay using GNSS observations and partial InSAR wet delay maps. These ZWD estimates are aggregated to derive realistic wet delay input data of 100 points as if corresponding to 100 GNSS sites within an area of 100 km × 100 km in the test region of the Upper Rhine Graben. The made-up ZWD values can be mapped into different elevation and azimuth angles. Using the Cosine transform, a sparse representation of the wet refractivity field is obtained. In contrast to existing tomographic approaches, we exploit sparsity as a prior for the regularization of the underdetermined inverse system. The new aspects of this work include both the combination of GNSS and InSAR data for water vapor tomography and the sophisticated CS estimation. The accuracy of the estimated 3D water vapor field is determined by comparing slant integrated wet delays computed from the estimated wet refractivities with real GNSS wet delay estimates. This comparison is performed along different elevation and azimuth angles.

Large-scale tomographic particle image velocimetry using helium-filled soap bubbles

NASA Astrophysics Data System (ADS)

Kühn, Matthias; Ehrenfried, Klaus; Bosbach, Johannes; Wagner, Claus

2011-04-01

To measure large-scale flow structures in air, a tomographic particle image velocimetry (tomographic PIV) system for measurement volumes of the order of one cubic metre is developed, which employs helium-filled soap bubbles (HFSBs) as tracer particles. The technique has several specific characteristics compared to most conventional tomographic PIV systems, which are usually applied to small measurement volumes. One of them is spot lights on the HFSB tracers, which slightly change their position, when the direction of observation is altered. Further issues are the large particle to voxel ratio and the short focal length of the used camera lenses, which result in a noticeable variation of the magnification factor in volume depth direction. Taking the specific characteristics of the HFSBs into account, the feasibility of our large-scale tomographic PIV system is demonstrated by showing that the calibration errors can be reduced down to 0.1 pixels as required. Further, an accurate and fast implementation of the multiplicative algebraic reconstruction technique, which calculates the weighting coefficients when needed instead of storing them, is discussed. The tomographic PIV system is applied to measure forced convection in a convection cell at a Reynolds number of 530 based on the inlet channel height and the mean inlet velocity. The size of the measurement volume and the interrogation volumes amount to 750 mm × 450 mm × 165 mm and 48 mm × 48 mm × 24 mm, respectively. Validation of the tomographic PIV technique employing HFSBs is further provided by comparing profiles of the mean velocity and of the root mean square velocity fluctuations to respective planar PIV data.

Solving ill-posed inverse problems using iterative deep neural networks

NASA Astrophysics Data System (ADS)

Adler, Jonas; Öktem, Ozan

2017-12-01

We propose a partially learned approach for the solution of ill-posed inverse problems with not necessarily linear forward operators. The method builds on ideas from classical regularisation theory and recent advances in deep learning to perform learning while making use of prior information about the inverse problem encoded in the forward operator, noise model and a regularising functional. The method results in a gradient-like iterative scheme, where the ‘gradient’ component is learned using a convolutional network that includes the gradients of the data discrepancy and regulariser as input in each iteration. We present results of such a partially learned gradient scheme on a non-linear tomographic inversion problem with simulated data from both the Sheep-Logan phantom as well as a head CT. The outcome is compared against filtered backprojection and total variation reconstruction and the proposed method provides a 5.4 dB PSNR improvement over the total variation reconstruction while being significantly faster, giving reconstructions of 512 × 512 pixel images in about 0.4 s using a single graphics processing unit (GPU).

Tomographic inversion of satellite photometry

NASA Technical Reports Server (NTRS)

Solomon, S. C.; Hays, P. B.; Abreu, V. J.

1984-01-01

An inversion algorithm capable of reconstructing the volume emission rate of thermospheric airglow features from satellite photometry has been developed. The accuracy and resolution of this technique are investigated using simulated data, and the inversions of several sets of observations taken by the Visible Airglow Experiment are presented.

Prototype of a Muon Tomography Station with GEM detectors for Detection of Shielded Nuclear Contraband

NASA Astrophysics Data System (ADS)

Staib, Michael; Bhopatkar, Vallary; Bittner, William; Hohlmann, Marcus; Locke, Judson; Twigger, Jessie; Gnanvo, Kondo

2012-03-01

Muon tomography for homeland security aims at detecting well-shielded nuclear contraband in cargo and imaging it in 3D. The technique exploits multiple scattering of atmospheric cosmic ray muons, which is stronger in dense, high-Z materials, e.g. enriched uranium, than in low-Z and medium-Z shielding materials. We have constructed and are operating a compact Muon Tomography Station (MTS) that tracks muons with eight 30 cm x 30 cm Triple Gas Electron Multiplier (GEM) detectors placed on the sides of a cubic-foot imaging volume. A point-of-closest-approach algorithm applied to reconstructed incident and exiting tracks is used to create a tomographic reconstruction of the material within the active volume. We discuss the performance of this MTS prototype including characterization and commissioning of the GEM detectors and the data acquisition systems. We also present experimental tomographic images of small high-Z objects including depleted uranium with and without shielding and discuss the performance of material discrimination using this method.

Classification of JET Neutron and Gamma Emissivity Profiles

NASA Astrophysics Data System (ADS)

Craciunescu, T.; Murari, A.; Kiptily, V.; Vega, J.; Contributors, JET

2016-05-01

In thermonuclear plasmas, emission tomography uses integrated measurements along lines of sight (LOS) to determine the two-dimensional (2-D) spatial distribution of the volume emission intensity. Due to the availability of only a limited number views and to the coarse sampling of the LOS, the tomographic inversion is a limited data set problem. Several techniques have been developed for tomographic reconstruction of the 2-D gamma and neutron emissivity on JET. In specific experimental conditions the availability of LOSs is restricted to a single view. In this case an explicit reconstruction of the emissivity profile is no longer possible. However, machine learning classification methods can be used in order to derive the type of the distribution. In the present approach the classification is developed using the theory of belief functions which provide the support to fuse the results of independent clustering and supervised classification. The method allows to represent the uncertainty of the results provided by different independent techniques, to combine them and to manage possible conflicts.

A scanning PIV method for fine-scale turbulence measurements

NASA Astrophysics Data System (ADS)

Lawson, John M.; Dawson, James R.

2014-12-01

A hybrid technique is presented that combines scanning PIV with tomographic reconstruction to make spatially and temporally resolved measurements of the fine-scale motions in turbulent flows. The technique uses one or two high-speed cameras to record particle images as a laser sheet is rapidly traversed across a measurement volume. This is combined with a fast method for tomographic reconstruction of the particle field for use in conjunction with PIV cross-correlation. The method was tested numerically using DNS data and with experiments in a large mixing tank that produces axisymmetric homogeneous turbulence at . A parametric investigation identifies the important parameters for a scanning PIV set-up and provides guidance to the interested experimentalist in achieving the best accuracy. Optimal sheet spacings and thicknesses are reported, and it was found that accurate results could be obtained at quite low scanning speeds. The two-camera method is the most robust to noise, permitting accurate measurements of the velocity gradients and direct determination of the dissipation rate.

Measuring the Autocorrelation Function of Nanoscale Three-Dimensional Density Distribution in Individual Cells Using Scanning Transmission Electron Microscopy, Atomic Force Microscopy, and a New Deconvolution Algorithm.

PubMed

Li, Yue; Zhang, Di; Capoglu, Ilker; Hujsak, Karl A; Damania, Dhwanil; Cherkezyan, Lusik; Roth, Eric; Bleher, Reiner; Wu, Jinsong S; Subramanian, Hariharan; Dravid, Vinayak P; Backman, Vadim

2017-06-01

Essentially all biological processes are highly dependent on the nanoscale architecture of the cellular components where these processes take place. Statistical measures, such as the autocorrelation function (ACF) of the three-dimensional (3D) mass-density distribution, are widely used to characterize cellular nanostructure. However, conventional methods of reconstruction of the deterministic 3D mass-density distribution, from which these statistical measures can be calculated, have been inadequate for thick biological structures, such as whole cells, due to the conflict between the need for nanoscale resolution and its inverse relationship with thickness after conventional tomographic reconstruction. To tackle the problem, we have developed a robust method to calculate the ACF of the 3D mass-density distribution without tomography. Assuming the biological mass distribution is isotropic, our method allows for accurate statistical characterization of the 3D mass-density distribution by ACF with two data sets: a single projection image by scanning transmission electron microscopy and a thickness map by atomic force microscopy. Here we present validation of the ACF reconstruction algorithm, as well as its application to calculate the statistics of the 3D distribution of mass-density in a region containing the nucleus of an entire mammalian cell. This method may provide important insights into architectural changes that accompany cellular processes.

Measuring the Autocorrelation Function of Nanoscale Three-Dimensional Density Distribution in Individual Cells Using Scanning Transmission Electron Microscopy, Atomic Force Microscopy, and a New Deconvolution Algorithm

PubMed Central

Li, Yue; Zhang, Di; Capoglu, Ilker; Hujsak, Karl A.; Damania, Dhwanil; Cherkezyan, Lusik; Roth, Eric; Bleher, Reiner; Wu, Jinsong S.; Subramanian, Hariharan; Dravid, Vinayak P.; Backman, Vadim

2018-01-01

Essentially all biological processes are highly dependent on the nanoscale architecture of the cellular components where these processes take place. Statistical measures, such as the autocorrelation function (ACF) of the three-dimensional (3D) mass–density distribution, are widely used to characterize cellular nanostructure. However, conventional methods of reconstruction of the deterministic 3D mass–density distribution, from which these statistical measures can be calculated, have been inadequate for thick biological structures, such as whole cells, due to the conflict between the need for nanoscale resolution and its inverse relationship with thickness after conventional tomographic reconstruction. To tackle the problem, we have developed a robust method to calculate the ACF of the 3D mass–density distribution without tomography. Assuming the biological mass distribution is isotropic, our method allows for accurate statistical characterization of the 3D mass–density distribution by ACF with two data sets: a single projection image by scanning transmission electron microscopy and a thickness map by atomic force microscopy. Here we present validation of the ACF reconstruction algorithm, as well as its application to calculate the statistics of the 3D distribution of mass–density in a region containing the nucleus of an entire mammalian cell. This method may provide important insights into architectural changes that accompany cellular processes. PMID:28416035

Single-shot ultrafast tomographic imaging by spectral multiplexing

NASA Astrophysics Data System (ADS)

Matlis, N. H.; Axley, A.; Leemans, W. P.

2012-10-01

Computed tomography has profoundly impacted science, medicine and technology by using projection measurements scanned over multiple angles to permit cross-sectional imaging of an object. The application of computed tomography to moving or dynamically varying objects, however, has been limited by the temporal resolution of the technique, which is set by the time required to complete the scan. For objects that vary on ultrafast timescales, traditional scanning methods are not an option. Here we present a non-scanning method capable of resolving structure on femtosecond timescales by using spectral multiplexing of a single laser beam to perform tomographic imaging over a continuous range of angles simultaneously. We use this technique to demonstrate the first single-shot ultrafast computed tomography reconstructions and obtain previously inaccessible structure and position information for laser-induced plasma filaments. This development enables real-time tomographic imaging for ultrafast science, and offers a potential solution to the challenging problem of imaging through scattering surfaces.

Tomographic Reconstruction of Mercury's Exosphere from MESSENGER Flyby Data

NASA Technical Reports Server (NTRS)

Killen, Rosemary M.; McClintock, William E.; Slavin, James A.; Solomon, Sean C.; Vervack, Ronald J., Jr.

2011-01-01

The exosphere of Mercury is among the best-studied examples of a common type of atmosphere, a surface-bounded exosphere. Mercury's exosphere was probed in 2008-2009 with Ultraviolet and Visible Spectrometer (UVVS) measurements obtained during three planetary flybys by the MErcury Surface, Space ENvironment, GEochemistry, and Ranging (MESSENGER) spacecraft [1-3]. The measurements detailed the distribution of two previously known metallic constituents of Mercury's exosphere, Na and Ca, and indicated the presence in the gas phase of yet another metallic species, Mg. Such measurements can answer fundamental scientific questions regarding the relative importance of possible source and loss processes for exospheric species ejected from a surface boundary [4]. The trajectory of MESSENGER during the last of its three flybys provided the best spatial coverage prior to orbit insertion. The measurements by MESSENGER of Na, Ca, and Mg during the third flyby have been analyzed with a novel tomographic method. This approach maximizes the amount of information that can be extracted from line-of-sight measurements because it yields three-dimensional distributions of neutrals consistent with the data.

Markov random field based automatic image alignment for electron tomography.

PubMed

Amat, Fernando; Moussavi, Farshid; Comolli, Luis R; Elidan, Gal; Downing, Kenneth H; Horowitz, Mark

2008-03-01

We present a method for automatic full-precision alignment of the images in a tomographic tilt series. Full-precision automatic alignment of cryo electron microscopy images has remained a difficult challenge to date, due to the limited electron dose and low image contrast. These facts lead to poor signal to noise ratio (SNR) in the images, which causes automatic feature trackers to generate errors, even with high contrast gold particles as fiducial features. To enable fully automatic alignment for full-precision reconstructions, we frame the problem probabilistically as finding the most likely particle tracks given a set of noisy images, using contextual information to make the solution more robust to the noise in each image. To solve this maximum likelihood problem, we use Markov Random Fields (MRF) to establish the correspondence of features in alignment and robust optimization for projection model estimation. The resulting algorithm, called Robust Alignment and Projection Estimation for Tomographic Reconstruction, or RAPTOR, has not needed any manual intervention for the difficult datasets we have tried, and has provided sub-pixel alignment that is as good as the manual approach by an expert user. We are able to automatically map complete and partial marker trajectories and thus obtain highly accurate image alignment. Our method has been applied to challenging cryo electron tomographic datasets with low SNR from intact bacterial cells, as well as several plastic section and X-ray datasets.

Comparison of three‐dimensional analysis and stereological techniques for quantifying lithium‐ion battery electrode microstructures

PubMed Central

TAIWO, OLUWADAMILOLA O.; FINEGAN, DONAL P.; EASTWOOD, DAVID S.; FIFE, JULIE L.; BROWN, LEON D.; DARR, JAWWAD A.; LEE, PETER D.; BRETT, DANIEL J.L.

2016-01-01

Summary Lithium‐ion battery performance is intrinsically linked to electrode microstructure. Quantitative measurement of key structural parameters of lithium‐ion battery electrode microstructures will enable optimization as well as motivate systematic numerical studies for the improvement of battery performance. With the rapid development of 3‐D imaging techniques, quantitative assessment of 3‐D microstructures from 2‐D image sections by stereological methods appears outmoded; however, in spite of the proliferation of tomographic imaging techniques, it remains significantly easier to obtain two‐dimensional (2‐D) data sets. In this study, stereological prediction and three‐dimensional (3‐D) analysis techniques for quantitative assessment of key geometric parameters for characterizing battery electrode microstructures are examined and compared. Lithium‐ion battery electrodes were imaged using synchrotron‐based X‐ray tomographic microscopy. For each electrode sample investigated, stereological analysis was performed on reconstructed 2‐D image sections generated from tomographic imaging, whereas direct 3‐D analysis was performed on reconstructed image volumes. The analysis showed that geometric parameter estimation using 2‐D image sections is bound to be associated with ambiguity and that volume‐based 3‐D characterization of nonconvex, irregular and interconnected particles can be used to more accurately quantify spatially‐dependent parameters, such as tortuosity and pore‐phase connectivity. PMID:26999804

Comparison of three-dimensional analysis and stereological techniques for quantifying lithium-ion battery electrode microstructures.

PubMed

Taiwo, Oluwadamilola O; Finegan, Donal P; Eastwood, David S; Fife, Julie L; Brown, Leon D; Darr, Jawwad A; Lee, Peter D; Brett, Daniel J L; Shearing, Paul R

2016-09-01

Lithium-ion battery performance is intrinsically linked to electrode microstructure. Quantitative measurement of key structural parameters of lithium-ion battery electrode microstructures will enable optimization as well as motivate systematic numerical studies for the improvement of battery performance. With the rapid development of 3-D imaging techniques, quantitative assessment of 3-D microstructures from 2-D image sections by stereological methods appears outmoded; however, in spite of the proliferation of tomographic imaging techniques, it remains significantly easier to obtain two-dimensional (2-D) data sets. In this study, stereological prediction and three-dimensional (3-D) analysis techniques for quantitative assessment of key geometric parameters for characterizing battery electrode microstructures are examined and compared. Lithium-ion battery electrodes were imaged using synchrotron-based X-ray tomographic microscopy. For each electrode sample investigated, stereological analysis was performed on reconstructed 2-D image sections generated from tomographic imaging, whereas direct 3-D analysis was performed on reconstructed image volumes. The analysis showed that geometric parameter estimation using 2-D image sections is bound to be associated with ambiguity and that volume-based 3-D characterization of nonconvex, irregular and interconnected particles can be used to more accurately quantify spatially-dependent parameters, such as tortuosity and pore-phase connectivity. © 2016 The Authors. Journal of Microscopy published by John Wiley & Sons Ltd on behalf of Royal Microscopical Society.

Cone beam tomographic imaging anatomy of the maxillofacial region.

PubMed

Angelopoulos, Christos

2008-10-01

Multiplanar imaging is a fairly new concept in diagnostic imaging available with a number of contemporary imaging modalities such as CT, MR imaging, diagnostic ultrasound, and others. This modality allows reconstruction of images in different planes (flat or curved) from a volume of data that was acquired previously. This concept makes the diagnostic process more interactive, and proper use may increase diagnostic potential. At the same time, the complexity of the anatomical structures on the maxillofacial region may make it harder for these images to be interpreted. This article reviews the anatomy of maxillofacial structures in planar imaging, and more specifically cone-beam CT images.

New signal processing technique for density profile reconstruction using reflectometry.

PubMed

Clairet, F; Ricaud, B; Briolle, F; Heuraux, S; Bottereau, C

2011-08-01

Reflectometry profile measurement requires an accurate determination of the plasma reflected signal. Along with a good resolution and a high signal to noise ratio of the phase measurement, adequate data analysis is required. A new data processing based on time-frequency tomographic representation is used. It provides a clearer separation between multiple components and improves isolation of the relevant signals. In this paper, this data processing technique is applied to two sets of signals coming from two different reflectometer devices used on the Tore Supra tokamak. For the standard density profile reflectometry, it improves the initialization process and its reliability, providing a more accurate profile determination in the far scrape-off layer with density measurements as low as 10(16) m(-1). For a second reflectometer, which provides measurements in front of a lower hybrid launcher, this method improves the separation of the relevant plasma signal from multi-reflection processes due to the proximity of the plasma.

A positron emission tomograph based on LSO-APD modules with a sampling ADC read-out system for a students' advanced laboratory course.

PubMed

Schneider, Florian R; Mann, Alexander B; Konorov, Igor; Delso, Gaspar; Paul, Stephan; Ziegler, Sibylle I

2012-06-01

A one-day laboratory course on positron emission tomography (PET) for the education of physics students and PhD students in medical physics has been set up. In the course, the physical background and the principles of a PET scanner are introduced. Course attendees set the system in operation, calibrate it using a (22)Na point source and reconstruct different source geometries filled with (18)F. The PET scanner features an individual channel read-out of 96 lutetium oxyorthosilicate (LSO) scintillator crystals coupled to avalanche photodiodes (APD). The analog data of each APD are digitized by fast sampling analog to digital converters (SADC) and processed within field programmable gate arrays (FPGA) to extract amplitudes and time stamps. All SADCs are continuously sampling with a precise rate of 80MHz, which is synchronous for the whole system. The data is transmitted via USB to a Linux PC, where further processing and the image reconstruction are performed. The course attendees get an insight into detector techniques, modern read-out electronics, data acquisition and PET image reconstruction. In addition, a short introduction to some common software applications used in particle and high energy physics is part of the course. Copyright © 2011. Published by Elsevier GmbH.

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

Calf Perforator Flaps: A Freestyle Solution for Oral Cavity Reconstruction.

PubMed

Molina, Alexandra R; Citron, Isabelle; Chinaka, Fungayi; Cascarini, Luke; Townley, William A

2017-02-01

Reconstruction of oral cavity defects requires a thin, pliable flap for optimal functional results. Traditional flap choices are imperfect: the anterolateral thigh flap is excessively thick, whereas the radial forearm flap has a poor donor site. The authors therefore favor calf perforator flaps such as the medial sural artery perforator flap to provide thin tissue with an acceptable donor site. This two-part study aims to demonstrate their suitability for intraoral reconstruction. In the radiologic part of the study, the authors compared thigh and calf tissue thickness by examining lower limb computed tomographic scans of 100 legs. For their clinical study, they collected data prospectively on 20 cases of oral cavity reconstruction using calf perforator flaps. The mean thickness of the calf tissue envelope was significantly less than that of the thigh (8.4 mm compared with 17 mm) based on computed tomographic analysis. In the clinical study, a medial sural artery perforator was used in the majority of cases (17 of 20). The mean pedicle length was 10.2 cm and the mean time to raise a flap was 85 minutes. There were no flap losses. One patient was returned to the operating room for management of late hematoma and wound dehiscence. Calf perforator flaps provide ideal tissue for intraoral reconstruction and are significantly thinner than anterolateral thigh flaps. In addition to medial sural artery perforator flaps, the authors raised both sural and soleal artery perforator flaps in this series. Opportunistic use of the calf donor site allows the harvest of thin tissue with minimal donor-site morbidity. Therapeutic, IV.

Imaging open-path Fourier transform infrared spectrometer for 3D cloud profiling

NASA Astrophysics Data System (ADS)

Rentz Dupuis, Julia; Mansur, David J.; Vaillancourt, Robert; Carlson, David; Evans, Thomas; Schundler, Elizabeth; Todd, Lori; Mottus, Kathleen

2009-05-01

OPTRA is developing an imaging open-path Fourier transform infrared (I-OP-FTIR) spectrometer for 3D profiling of chemical and biological agent simulant plumes released into test ranges and chambers. An array of I-OP-FTIR instruments positioned around the perimeter of the test site, in concert with advanced spectroscopic algorithms, enables real time tomographic reconstruction of the plume. The approach is intended as a referee measurement for test ranges and chambers. This Small Business Technology Transfer (STTR) effort combines the instrumentation and spectroscopic capabilities of OPTRA, Inc. with the computed tomographic expertise of the University of North Carolina, Chapel Hill.

Signal processing and general purpose data acquisition system for on-line tomographic measurements

NASA Astrophysics Data System (ADS)

Murari, A.; Martin, P.; Hemming, O.; Manduchi, G.; Marrelli, L.; Taliercio, C.; Hoffmann, A.

1997-01-01

New analog signal conditioning electronics and data acquisition systems have been developed for the soft x-ray and bolometric tomography diagnostic in the reverse field pinch experiment (RFX). For the soft x-ray detectors the analog signal processing includes a fully differential current to voltage conversion, with up to a 200 kHz bandwidth. For the bolometers, a 50 kHz carrier frequency amplifier allows a maximum bandwidth of 10 kHz. In both cases the analog signals are digitized with a 1 MHz sampling rate close to the diagnostic and are transmitted via a transparent asynchronous xmitter/receiver interface (TAXI) link to purpose built Versa Module Europa (VME) modules which perform data acquisition. A software library has been developed for data preprocessing and tomographic reconstruction. It has been written in C language and is self-contained, i.e., no additional mathematical library is required. The package is therefore platform-free: in particular it can perform online analysis in a real-time application, such as continuous display and feedback, and is portable for long duration fusion or other physical experiments. Due to the modular organization of the library, new preprocessing and analysis modules can be easily integrated in the environment. This software is implemented in RFX over three different platforms: open VMS, digital Unix, and VME 68040 CPU.

Alignment Solution for CT Image Reconstruction using Fixed Point and Virtual Rotation Axis.

PubMed

Jun, Kyungtaek; Yoon, Seokhwan

2017-01-25

Since X-ray tomography is now widely adopted in many different areas, it becomes more crucial to find a robust routine of handling tomographic data to get better quality of reconstructions. Though there are several existing techniques, it seems helpful to have a more automated method to remove the possible errors that hinder clearer image reconstruction. Here, we proposed an alternative method and new algorithm using the sinogram and the fixed point. An advanced physical concept of Center of Attenuation (CA) was also introduced to figure out how this fixed point is applied to the reconstruction of image having errors we categorized in this article. Our technique showed a promising performance in restoring images having translation and vertical tilt errors.

Simultaneous measurement of 2-dimensional H2O concentration and temperature distribution in premixed methane/air flame using TDLAS-based tomography technology

NASA Astrophysics Data System (ADS)

Wang, Fei; Wu, Qi; Huang, Qunxing; Zhang, Haidan; Yan, Jianhua; Cen, Kefa

2015-07-01

An innovative tomographic method using tunable diode laser absorption spectroscopy (TDLAS) and algebraic reconstruction technique (ART) is presented in this paper for detecting two-dimensional distribution of H2O concentration and temperature in a premixed flame. The collimated laser beam emitted from a low cost diode laser module was delicately split into 24 sub-beams passing through the flame from different angles and the acquired laser absorption signals were used to retrieve flame temperature and H2O concentration simultaneously. The efficiency of the proposed reconstruction system and the effect of measurement noise were numerically evaluated. The temperature and H2O concentration in flat methane/air premixed flames under three different equivalence ratios were experimentally measured and reconstruction results were compared with model calculations. Numerical assessments indicate that the TDLAS tomographic system is capable for temperature and H2O concentration profiles detecting even the noise strength reaches 3% of absorption signal. Experimental results under different combustion conditions are well demonstrated along the vertical direction and the distribution profiles are in good agreement with model calculation. The proposed method exhibits great potential for 2-D or 3-D combustion diagnostics including non-uniform flames.

Broadband Tomography System: Direct Time-Space Reconstruction Algorithm

NASA Astrophysics Data System (ADS)

Biagi, E.; Capineri, Lorenzo; Castellini, Guido; Masotti, Leonardo F.; Rocchi, Santina

1989-10-01

In this paper a new ultrasound tomographic image algorithm is presented. A complete laboratory system is built up to test the algorithm in experimental conditions. The proposed system is based on a physical model consisting of a bidimensional distribution of single scattering elements. Multiple scattering is neglected, so Born approximation is assumed. This tomographic technique only requires two orthogonal scanning sections. For each rotational position of the object, data are collected by means of the complete data set method in transmission mode. After a numeric envelope detection, the received signals are back-projected in the space-domain through a scalar function. The reconstruction of each scattering element is accomplished by correlating the ultrasound time of flight and attenuation with the points' loci given by the possible positions of the scattering element. The points' locus is represented by an ellipse with the focuses located on the transmitter and receiver positions. In the image matrix the ellipses' contributions are coherently summed in the position of the scattering element. Computer simulations of cylindrical-shaped objects have pointed out the performances of the reconstruction algorithm. Preliminary experimental results show the laboratory system features. On the basis of these results an experimental procedure to test the confidence and repeatability of ultrasonic measurements on human carotid vessel is proposed.

Low-frequency noise effect on terahertz tomography using thermal detectors.

PubMed

Guillet, J P; Recur, B; Balacey, H; Bou Sleiman, J; Darracq, F; Lewis, D; Mounaix, P

2015-08-01

In this paper, the impact of low-frequency noise on terahertz-computed tomography (THz-CT) is analyzed for several measurement configurations and pyroelectric detectors. We acquire real noise data from a continuous millimeter-wave tomographic scanner in order to figure out its impact on reconstructed images. Second, noise characteristics are quantified according to two distinct acquisition methods by (i) extrapolating from experimental acquisitions a sinogram for different noise backgrounds and (ii) reconstructing the corresponding spatial distributions in a slice using a CT reconstruction algorithm. Then we describe the low-frequency noise fingerprint and its influence on reconstructed images. Thanks to the observations, we demonstrate that some experimental choices can dramatically affect the 3D rendering of reconstructions. Thus, we propose some experimental methodologies optimizing the resulting quality and accuracy of the 3D reconstructions, with respect to the low-frequency noise characteristics observed during acquisitions.

Hyperspectral image reconstruction for x-ray fluorescence tomography

DOE PAGES

Gürsoy, Doǧa; Biçer, Tekin; Lanzirotti, Antonio; ...

2015-01-01

A penalized maximum-likelihood estimation is proposed to perform hyperspectral (spatio-spectral) image reconstruction for X-ray fluorescence tomography. The approach minimizes a Poisson-based negative log-likelihood of the observed photon counts, and uses a penalty term that has the effect of encouraging local continuity of model parameter estimates in both spatial and spectral dimensions simultaneously. The performance of the reconstruction method is demonstrated with experimental data acquired from a seed of arabidopsis thaliana collected at the 13-ID-E microprobe beamline at the Advanced Photon Source. The resulting element distribution estimates with the proposed approach show significantly better reconstruction quality than the conventional analytical inversionmore » approaches, and allows for a high data compression factor which can reduce data acquisition times remarkably. In particular, this technique provides the capability to tomographically reconstruct full energy dispersive spectra without compromising reconstruction artifacts that impact the interpretation of results.« less

3D spectral imaging with synchrotron Fourier transform infrared spectro-microtomography

Treesearch

Michael C. Martin; Charlotte Dabat-Blondeau; Miriam Unger; Julia Sedlmair; Dilworth Y. Parkinson; Hans A. Bechtel; Barbara Illman; Jonathan M. Castro; Marco Keiluweit; David Buschke; Brenda Ogle; Michael J. Nasse; Carol J. Hirschmugl

2013-01-01

We report Fourier transform infrared spectro-microtomography, a nondestructive three-dimensional imaging approach that reveals the distribution of distinctive chemical compositions throughout an intact biological or materials sample. The method combines mid-infrared absorption contrast with computed tomographic data acquisition and reconstruction to enhance chemical...

Robust GNSS and InSAR tomography of neutrospheric refractivity using a Compressive Sensing approach

NASA Astrophysics Data System (ADS)

Heublein, Marion; Alshawaf, Fadwa; Zhu, Xiao Xiang; Hinz, Stefan

2017-04-01

Motivation: An accurate knowledge of the 3D distribution of water vapor in the atmosphere is a key element for weather forecasting and climate research. In addition, a precise determination of water vapor is also required for accurate positioning and deformation monitoring using Global Navigation Satellite Systems (GNSS) and Interferometric Synthetic Aperture Radar (InSAR). Several approaches for 3D tomographic water vapor reconstruction from GNSS-based Slant Wet Delay (SWD) estimates using the least squares (LSQ) adjustment exist. However, the tomographic system is in general ill-conditioned and its solution is unstable. Therefore, additional information or constraints need to be added in order to regularize the system. Goal of this work: In this work, we analyze the potential of Compressive Sensing (CS) for robustly reconstructing neutrospheric refractivity from GNSS SWD estimates. Moreover, the benefit of adding InSAR SWD estimates into the tomographic system is studied. Approach: A sparse representation of the refractivity field is obtained using a dictionary composed of Discrete Cosine Transforms (DCT) in longitude and latitude direction and of an Euler transform in height direction. This sparsity of the signal can be used as a prior for regularization and the CS inversion is solved by minimizing the number of non-zero entries of the sparse solution in the DCT-Euler domain. No other regularization constraints or prior knowledge is applied. The tomographic reconstruction relies on total SWD estimates from GNSS Precise Point Positioning (PPP) and Persistent Scatterer (PS) InSAR. On the one hand, GNSS PPP SWD estimates are included into the system of equations. On the other hand, 2D ZWD maps are obtained by a combination of point-wise estimates of the wet delay using GNSS observations and partial InSAR wet delay maps. These ZWD estimates are aggregated to derive realistic wet delay input data at given points as if corresponding to GNSS sites within the study area. The made-up ZWD values can be mapped into different elevation and azimuth angles. Moreover, using the same observation geometry as in the case of the GNSS and InSAR data, a synthetic set of SWD values was generated based on WRF simulations. Results: The CS approach shows particular strength in the case of a small number of SWD estimates. When compared to LSQ, the sparse reconstruction is much more robust. In the case of a low density of GNSS sites, adding InSAR SWD estimates improves the reconstruction accuracy for both LSQ and CS. Based on a synthetic SWD dataset generated using WRF simulations of wet refractivity, the CS based solution of the tomographic system is validated. In the vertical direction, the refractivity distribution deduced from GNSS and InSAR SWD estimates is compared to a tropospheric humidity data set provided by EUMETSAT consisting of daily mean values of specific humidity given on six pressure levels between 1000 hPa and 200 hPa. Study area: The Upper Rhine Graben (URG) characterized by negligible surface deformations is chosen as study area. A network of seven permanent GNSS receivers is used for this study, and a total number of 17 SAR images, acquired by ENVISAT ASAR is available.

3D tomographic reconstruction using geometrical models

NASA Astrophysics Data System (ADS)

Battle, Xavier L.; Cunningham, Gregory S.; Hanson, Kenneth M.

1997-04-01

We address the issue of reconstructing an object of constant interior density in the context of 3D tomography where there is prior knowledge about the unknown shape. We explore the direct estimation of the parameters of a chosen geometrical model from a set of radiographic measurements, rather than performing operations (segmentation for example) on a reconstructed volume. The inverse problem is posed in the Bayesian framework. A triangulated surface describes the unknown shape and the reconstruction is computed with a maximum a posteriori (MAP) estimate. The adjoint differentiation technique computes the derivatives needed for the optimization of the model parameters. We demonstrate the usefulness of the approach and emphasize the techniques of designing forward and adjoint codes. We use the system response of the University of Arizona Fast SPECT imager to illustrate this method by reconstructing the shape of a heart phantom.

Four dimensional material movies: High speed phase-contrast tomography by backprojection along dynamically curved paths.

PubMed

Ruhlandt, A; Töpperwien, M; Krenkel, M; Mokso, R; Salditt, T

2017-07-26

We present an approach towards four dimensional (4d) movies of materials, showing dynamic processes within the entire 3d structure. The method is based on tomographic reconstruction on dynamically curved paths using a motion model estimated by optical flow techniques, considerably reducing the typical motion artefacts of dynamic tomography. At the same time we exploit x-ray phase contrast based on free propagation to enhance the signal from micron scale structure recorded with illumination times down to a millisecond (ms). The concept is demonstrated by observing the burning process of a match stick in 4d, using high speed synchrotron phase contrast x-ray tomography recordings. The resulting movies reveal the structural changes of the wood cells during the combustion.

Critical examination of the uniformity requirements for single-photon emission computed tomography.

PubMed

O'Connor, M K; Vermeersch, C

1991-01-01

It is generally recognized that single-photon emission computed tomography (SPECT) imposes very stringent requirements on gamma camera uniformity to prevent the occurrence of ring artifacts. The purpose of this study was to examine the relationship between nonuniformities in the planar data and the magnitude of the consequential ring artifacts in the transaxial data, and how the perception of these artifacts is influenced by factors such as reconstruction matrix size, reconstruction filter, and image noise. The study indicates that the relationship between ring artifact magnitude and image noise is essentially independent of the acquisition or reconstruction matrix sizes, but is strongly dependent upon the type of smoothing filter applied during the reconstruction process. Furthermore, the degree to which a ring artifact can be perceived above image noise is dependent on the size and location of the nonuniformity in the planar data, with small nonuniformities (1-2 pixels wide) close to the center of rotation being less perceptible than those further out (8-20 pixels). Small defects or nonuniformities close to the center of rotation are thought to cause the greatest potential corruption to tomographic data. The study indicates that such may not be the case. Hence the uniformity requirements for SPECT may be less demanding than was previously thought.

Reducing computational costs in large scale 3D EIT by using a sparse Jacobian matrix with block-wise CGLS reconstruction.

PubMed

Yang, C L; Wei, H Y; Adler, A; Soleimani, M

2013-06-01

Electrical impedance tomography (EIT) is a fast and cost-effective technique to provide a tomographic conductivity image of a subject from boundary current-voltage data. This paper proposes a time and memory efficient method for solving a large scale 3D EIT inverse problem using a parallel conjugate gradient (CG) algorithm. The 3D EIT system with a large number of measurement data can produce a large size of Jacobian matrix; this could cause difficulties in computer storage and the inversion process. One of challenges in 3D EIT is to decrease the reconstruction time and memory usage, at the same time retaining the image quality. Firstly, a sparse matrix reduction technique is proposed using thresholding to set very small values of the Jacobian matrix to zero. By adjusting the Jacobian matrix into a sparse format, the element with zeros would be eliminated, which results in a saving of memory requirement. Secondly, a block-wise CG method for parallel reconstruction has been developed. The proposed method has been tested using simulated data as well as experimental test samples. Sparse Jacobian with a block-wise CG enables the large scale EIT problem to be solved efficiently. Image quality measures are presented to quantify the effect of sparse matrix reduction in reconstruction results.

Field-portable lensfree tomographic microscope†

PubMed Central

Isikman, Serhan O.; Bishara, Waheb; Sikora, Uzair; Yaglidere, Oguzhan; Yeah, John; Ozcan, Aydogan

2011-01-01

We present a field-portable lensfree tomographic microscope, which can achieve sectional imaging of a large volume (~20 mm3) on a chip with an axial resolution of <7 μm. In this compact tomographic imaging platform (weighing only ~110 grams), 24 light-emitting diodes (LEDs) that are each butt-coupled to a fibre-optic waveguide are controlled through a cost-effective micro-processor to sequentially illuminate the sample from different angles to record lensfree holograms of the sample that is placed on the top of a digital sensor array. In order to generate pixel super-resolved (SR) lensfree holograms and hence digitally improve the achievable lateral resolution, multiple sub-pixel shifted holograms are recorded at each illumination angle by electromagnetically actuating the fibre-optic waveguides using compact coils and magnets. These SR projection holograms obtained over an angular range of ~50° are rapidly reconstructed to yield projection images of the sample, which can then be back-projected to compute tomograms of the objects on the sensor-chip. The performance of this compact and light-weight lensfree tomographic microscope is validated by imaging micro-beads of different dimensions as well as a Hymenolepis nana egg, which is an infectious parasitic flatworm. Achieving a decent three-dimensional spatial resolution, this field-portable on-chip optical tomographic microscope might provide a useful toolset for telemedicine and high-throughput imaging applications in resource-poor settings. PMID:21573311

Scalar localization of the electrode array after cochlear implantation: clinical experience using 64-slice multidetector computed tomography.

PubMed

Lane, John I; Witte, Robert J; Driscoll, Colin L W; Shallop, Jon K; Beatty, Charles W; Primak, Andrew N

2007-08-01

To use the improved resolution available with 64-slice multidetector computed tomography (MDCT) in vivo to localize the cochlear implant electrode array within the basal turn. Sixty-four-slice MDCT examinations of the temporal bones were retrospectively reviewed in 17 patients. Twenty-three implants were evaluated. Tertiary referral facility. All patients with previous cochlear implantation evaluated at our center between January 2004 and March 2006 were offered a computed tomographic examination as part of the study. In addition, preoperative computed tomographic examinations in patients being evaluated for a second bilateral device were included. Sixty-four-slice MDCT examination of the temporal bones. Localization of the electrode array within the basal turn from multiplanar reconstructions of the cochlea. Twenty-three implants were imaged in 17 patients. We were able to localize the electrode array within the scala tympani within the basal turn in 10 implants. In 3 implants, the electrode array was localized to the scala vestibuli. Migration of the electrode array from scala tympani to scala vestibuli was observed in three implants. Of the 7 implants in which localization of the electrode array was indeterminate, all had disease entities that obscured the definition of the normal cochlear anatomy. Sixty-four-slice MDCT with multiplanar reconstructions of the postoperative cochlea after cochlear implantation allows for accurate localization of the electrode array within the basal turn where normal cochlear anatomy is not obscured by the underlying disease process. Correlating the position of the electrode in the basal turn with surgical technique and implant design could be helpful in improving outcomes.

Overview of positron emission tomography chemistry: clinical and technical considerations and combination with computed tomography.

PubMed

Koukourakis, G; Maravelis, G; Koukouraki, S; Padelakos, P; Kouloulias, V

2009-01-01

The concept of emission and transmission tomography was introduced by David Kuhl and Roy Edwards in the late 1950s. Their work later led to the design and construction of several tomographic instruments at the University of Pennsylvania. Tomographic imaging techniques were further developed by Michel Ter-Pogossian, Michael E. Phelps and others at the Washington University School of Medicine. Positron emission tomography (PET) is a nuclear medicine imaging technique which produces a 3-dimensional image or map of functional processes in the body. The system detects pairs of gamma rays emitted indirectly by a positron-emitting radionuclide (tracer), which is introduced into the body on a biologically active molecule. Images of tracer concentration in 3-dimensional space within the body are then reconstructed by computer analysis. In modern scanners, this reconstruction is often accomplished with the aid of a CT X-ray scan performed on the patient during the same session, in the same machine. If the biologically active molecule chosen for PET is 18F-fluorodeoxyglucose (FDG), an analogue of glucose, the concentrations of tracer imaged give tissue metabolic activity in terms of regional glucose uptake. Although use of this tracer results in the most common type of PET scan, other tracer molecules are used in PET to image the tissue concentration of many other types of molecules of interest. The main role of this article was to analyse the available types of radiopharmaceuticals used in PET-CT along with the principles of its clinical and technical considerations.

Simulating multi-spacecraft Heliospheric Imager observations for tomographic reconstruction of interplanetary CMEs

NASA Astrophysics Data System (ADS)

Barnes, D.

2017-12-01

The multiple, spatially separated vantage points afforded by the STEREO and SOHO missions provide physicists with a means to infer the three-dimensional structure of the solar corona via tomographic imaging. The reconstruction process combines these multiple projections of the optically thin plasma to constrain its three-dimensional density structure and has been successfully applied to the low corona using the STEREO and SOHO coronagraphs. However, the technique is also possible at larger, inter-planetary distances using wide-angle imagers, such as the STEREO Heliospheric Imagers (HIs), to observe faint solar wind plasma and Coronal Mass Ejections (CMEs). Limited small-scale structure may be inferred from only three, or fewer, viewpoints and the work presented here is done so with the aim of establishing techniques for observing CMEs with upcoming and future HI-like technology. We use simulated solar wind densities to compute realistic white-light HI observations, with which we explore the requirements of such instruments for determining solar wind plasma density structure via tomography. We exploit this information to investigate the optimal orbital characteristics, such as spacecraft number, separation, inclination and eccentricity, necessary to perform the technique with HIs. Further to this we argue that tomography may be greatly enhanced by means of improved instrumentation; specifically, the use of wide-angle imagers capable of measuring polarised light. This work has obvious space weather applications, serving as a demonstration for potential future missions (such as at L1 and L5) and will prove timely in fully exploiting the science return from the upcoming Solar Orbiter and Parker Solar Probe missions.

Solar multi-conjugate adaptive optics performance improvement

NASA Astrophysics Data System (ADS)

Zhang, Zhicheng; Zhang, Xiaofang; Song, Jie

2015-08-01

In order to overcome the effect of the atmospheric anisoplanatism, Multi-Conjugate Adaptive Optics (MCAO), which was developed based on turbulence correction by means of several deformable mirrors (DMs) conjugated to different altitude and by which the limit of a small corrected FOV that is achievable with AO is overcome and a wider FOV is able to be corrected, has been widely used to widen the field-of-view (FOV) of a solar telescope. With the assistance of the multi-threaded Adaptive Optics Simulator (MAOS), we can make a 3D reconstruction of the distorted wavefront. The correction is applied by one or more DMs. This technique benefits from information about atmospheric turbulence at different layers, which can be used to reconstruct the wavefront extremely well. In MAOS, the sensors are either simulated as idealized wavefront gradient sensors, tip-tilt sensors based on the best Zernike fit, or a WFS using physical optics and incorporating user specified pixel characteristics and a matched filter pixel processing algorithm. Only considering the atmospheric anisoplanatism, we focus on how the performance of a solar MCAO system is related to the numbers of DMs and their conjugate heights. We theoretically quantify the performance of the tomographic solar MCAO system. The results indicate that the tomographic AO system can improve the average Strehl ratio of a solar telescope by only employing one or two DMs conjugated to the optimum altitude. And the S.R. has a significant increase when more deformable mirrors are used. Furthermore, we discuss the effects of DM conjugate altitude on the correction achievable by the MCAO system, and present the optimum DM conjugate altitudes.

Computational diffraction tomographic microscopy with transport of intensity equation using a light-emitting diode array

NASA Astrophysics Data System (ADS)

Li, Jiaji; Chen, Qian; Zhang, Jialin; Zuo, Chao

2017-10-01

Optical diffraction tomography (ODT) is an effective label-free technique for quantitatively refractive index imaging, which enables long-term monitoring of the internal three-dimensional (3D) structures and molecular composition of biological cells with minimal perturbation. However, existing optical tomographic methods generally rely on interferometric configuration for phase measurement and sophisticated mechanical systems for sample rotation or beam scanning. Thereby, the measurement is suspect to phase error coming from the coherent speckle, environmental vibrations, and mechanical error during data acquisition process. To overcome these limitations, we present a new ODT technique based on non-interferometric phase retrieval and programmable illumination emitting from a light-emitting diode (LED) array. The experimental system is built based on a traditional bright field microscope, with the light source replaced by a programmable LED array, which provides angle-variable quasi-monochromatic illumination with an angular coverage of +/-37 degrees in both x and y directions (corresponding to an illumination numerical aperture of ˜ 0.6). Transport of intensity equation (TIE) is utilized to recover the phase at different illumination angles, and the refractive index distribution is reconstructed based on the ODT framework under first Rytov approximation. The missing-cone problem in ODT is addressed by using the iterative non-negative constraint algorithm, and the misalignment of the LED array is further numerically corrected to improve the accuracy of refractive index quantification. Experiments on polystyrene beads and thick biological specimens show that the proposed approach allows accurate refractive index reconstruction while greatly reduced the system complexity and environmental sensitivity compared to conventional interferometric ODT approaches.

Osteomyocutaneous fibular flap harvesting: Computer-assisted planning of perforator vessels using Computed Tomographic Angiography scan and cutting guide.

PubMed

Battaglia, Salvatore; Maiolo, Vincenzo; Savastio, Gabriella; Zompatori, Maurizio; Contedini, Federico; Antoniazzi, Elisa; Cipriani, Riccardo; Marchetti, Claudio; Tarsitano, Achille

2017-10-01

Mandibular reconstruction performed after virtual planning has become more common during recent years. The gold standard for extensive mandibular reconstruction is of course a fibular free flap. In designing an osteomyocutaneous fibula flap, poor planning, aberrant anatomy and/or inadequate perforator vessels are the most frequent causes of complications and may force the surgeon to modify the flap design, explore the contralateral leg or harvest an additional microvascular flap. The goal of our study was to pre-operatively evaluate the vascular anatomy of the fibula and localize the cutaneous perforator vessels, so to create the fibular cutting guide based on the position of the cutaneous perforator and safely harvest the reconstructive flap. Twenty consecutive patients who were candidates for mandibular reconstruction using a fibular microvascular free flap were enrolled in this study between January 2016 and August 2016. The patients were preoperatively assessed with a Computed Tomographic scan of head and neck and with a Computed Tomographic Angiography (CTA) scan of the lower limbs to evaluate the vascular anatomy of the fibula. Virtual planning was carried out for all patients. The fibular cutting guide was based on the position of the perforator cutaneous vessels, which were used to harvest the cutaneous part of the flap. Preoperative CT measurements were performed in order to identify the cutaneous perforators on the patients' skin. Intraoperative checking was performed to evaluate the accuracy of the perforators' position and the reproducibility of the virtual planning. In 5 patients out of 20 (25%), anatomical anomalies were discovered, without clinical evidence. The perforator vessels were localized in all patients. The average difference between the CTA and the intraoperative perforator localization was 1 mm (range 0-2 mm). Fibular cutting guide was positioned and fitted the anatomy of the patients in all treated patients. This allowed us to perform the planned segmentation of the fibula, obtaining the correct number of segments. In all cases, flap insetting was carried out and skin paddle was positioned as preoperatively planned. Neither donor site complications nor flap complications occurred. Preoperative evaluation of the legs using CTA, in patients who undergo an osteomyocutaneous fibular free flap for mandibular reconstruction, is a valuable approach to reduce altered-anatomy related complications and to improve the accuracy and outcomes of the reconstruction, especially in reconstructions of complex defects. In these cases, a soft tissue-based cutting guide can be planned based on the perforator vessels of the skin paddle, minimizing the harvesting risks of vascular lesions. Further studies and longer follow-ups are needed to evaluate the long-term outcomes and advantages of this procedure. Copyright © 2017 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights reserved.

Imaging and characterizing cells using tomography

PubMed Central

Do, Myan; Isaacson, Samuel A.; McDermott, Gerry; Le Gros, Mark A.; Larabell, Carolyn A.

2015-01-01

We can learn much about cell function by imaging and quantifying sub-cellular structures, especially if this is done non-destructively without altering said structures. Soft x-ray tomography (SXT) is a high-resolution imaging technique for visualizing cells and their interior structure in 3D. A tomogram of the cell, reconstructed from a series of 2D projection images, can be easily segmented and analyzed. SXT has a very high specimen throughput compared to other high-resolution structure imaging modalities; for example, tomographic data for reconstructing an entire eukaryotic cell is acquired in a matter of minutes. SXT visualizes cells without the need for chemical fixation, dehydration, or staining of the specimen. As a result, the SXT reconstructions are close representations of cells in their native state. SXT is applicable to most cell types. The deep penetration of soft x-rays allows cells, even mammalian cells, to be imaged without being sectioned. Image contrast in SXT is generated by the differential attenuation soft x-ray illumination as it passes through the specimen. Accordingly, each voxel in the tomographic reconstruction has a measured linear absorption coefficient (LAC) value. LAC values are quantitative and give rise to each sub-cellular component having a characteristic LAC profile, allowing organelles to be identified and segmented from the milieu of other cell contents. In this chapter, we describe the fundamentals of SXT imaging and how this technique can answer real world questions in the study of the nucleus. We also describe the development of correlative methods for the localization of specific molecules in a SXT reconstruction. The combination of fluorescence and SXT data acquired from the same specimen produces composite 3D images, rich with detailed information on the inner workings of cells. PMID:25602704

Tomographic sensing and localization of fluorescently labeled circulating cells in mice in vivo

NASA Astrophysics Data System (ADS)

Zettergren, Eric; Swamy, Tushar; Runnels, Judith; Lin, Charles P.; Niedre, Mark

2012-07-01

Sensing and enumeration of specific types of circulating cells in small animals is an important problem in many areas of biomedical research. Microscopy-based fluorescence in vivo flow cytometry methods have been developed previously, but these are typically limited to sampling of very small blood volumes, so that very rare circulating cells may escape detection. Recently, we described the development of a ‘diffuse fluorescence flow cytometer’ (DFFC) that allows sampling of much larger blood vessels and therefore circulating blood volumes in the hindlimb, forelimb or tail of a mouse. In this work, we extend this concept by developing and validating a method to tomographically localize circulating fluorescently labeled cells in the cross section of a tissue simulating optical flow phantom and mouse limb. This was achieved using two modulated light sources and an array of six fiber-coupled detectors that allowed rapid, high-sensitivity acquisition of full tomographic data sets at 10 Hz. These were reconstructed into two-dimensional cross-sectional images using Monte Carlo models of light propagation and the randomized algebraic reconstruction technique. We were able to obtain continuous images of moving cells in the sample cross section with 0.5 mm accuracy or better. We first demonstrated this concept in limb-mimicking optical flow photons with up to four flow channels, and then in the tails of mice with fluorescently labeled multiple myeloma cells. This approach increases the overall diagnostic utility of our DFFC instrument.

Multifunctional, three-dimensional tomography for analysis of eletrectrohydrodynamic jetting

NASA Astrophysics Data System (ADS)

Nguyen, Xuan Hung; Gim, Yeonghyeon; Ko, Han Seo

2015-05-01

A three-dimensional optical tomography technique was developed to reconstruct three-dimensional objects using a set of two-dimensional shadowgraphic images and normal gray images. From three high-speed cameras, which were positioned at an offset angle of 45° between each other, number, size, and location of electrohydrodynamic jets with respect to the nozzle position were analyzed using shadowgraphic tomography employing multiplicative algebraic reconstruction technique (MART). Additionally, a flow field inside a cone-shaped liquid (Taylor cone) induced under an electric field was observed using a simultaneous multiplicative algebraic reconstruction technique (SMART), a tomographic method for reconstructing light intensities of particles, combined with three-dimensional cross-correlation. Various velocity fields of circulating flows inside the cone-shaped liquid caused by various physico-chemical properties of liquid were also investigated.

Real-time quasi-3D tomographic reconstruction

NASA Astrophysics Data System (ADS)

Buurlage, Jan-Willem; Kohr, Holger; Palenstijn, Willem Jan; Joost Batenburg, K.

2018-06-01

Developments in acquisition technology and a growing need for time-resolved experiments pose great computational challenges in tomography. In addition, access to reconstructions in real time is a highly demanded feature but has so far been out of reach. We show that by exploiting the mathematical properties of filtered backprojection-type methods, having access to real-time reconstructions of arbitrarily oriented slices becomes feasible. Furthermore, we present , software for visualization and on-demand reconstruction of slices. A user of can interactively shift and rotate slices in a GUI, while the software updates the slice in real time. For certain use cases, the possibility to study arbitrarily oriented slices in real time directly from the measured data provides sufficient visual and quantitative insight. Two such applications are discussed in this article.

Mid-infrared laser absorption tomography for quantitative 2D thermochemistry measurements in premixed jet flames

NASA Astrophysics Data System (ADS)

Wei, Chuyu; Pineda, Daniel I.; Paxton, Laurel; Egolfopoulos, Fokion N.; Spearrin, R. Mitchell

2018-06-01

A tomographic laser absorption spectroscopy technique, utilizing mid-infrared light sources, is presented as a quantitative method to spatially resolve species and temperature profiles in small-diameter reacting flows relevant to combustion systems. Here, tunable quantum and interband cascade lasers are used to spectrally resolve select rovibrational transitions near 4.98 and 4.19 μm to measure CO and {CO2}, respectively, as well as their vibrational temperatures, in piloted premixed jet flames. Signal processing methods are detailed for the reconstruction of axial and radial profiles of thermochemical structure in a canonical ethylene-air jet flame. The method is further demonstrated to quantitatively distinguish between different turbulent flow conditions.

Three-dimensional propagation in near-field tomographic X-ray phase retrieval

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

Ruhlandt, Aike, E-mail: aruhlan@gwdg.de; Salditt, Tim

An extension of phase retrieval algorithms for near-field X-ray (propagation) imaging to three dimensions is presented, enhancing the quality of the reconstruction by exploiting previously unused three-dimensional consistency constraints. This paper presents an extension of phase retrieval algorithms for near-field X-ray (propagation) imaging to three dimensions, enhancing the quality of the reconstruction by exploiting previously unused three-dimensional consistency constraints. The approach is based on a novel three-dimensional propagator and is derived for the case of optically weak objects. It can be easily implemented in current phase retrieval architectures, is computationally efficient and reduces the need for restrictive prior assumptions, resultingmore » in superior reconstruction quality.« less

Real-time turbulence profiling with a pair of laser guide star Shack-Hartmann wavefront sensors for wide-field adaptive optics systems on large to extremely large telescopes.

PubMed

Gilles, L; Ellerbroek, B L

2010-11-01

Real-time turbulence profiling is necessary to tune tomographic wavefront reconstruction algorithms for wide-field adaptive optics (AO) systems on large to extremely large telescopes, and to perform a variety of image post-processing tasks involving point-spread function reconstruction. This paper describes a computationally efficient and accurate numerical technique inspired by the slope detection and ranging (SLODAR) method to perform this task in real time from properly selected Shack-Hartmann wavefront sensor measurements accumulated over a few hundred frames from a pair of laser guide stars, thus eliminating the need for an additional instrument. The algorithm is introduced, followed by a theoretical influence function analysis illustrating its impulse response to high-resolution turbulence profiles. Finally, its performance is assessed in the context of the Thirty Meter Telescope multi-conjugate adaptive optics system via end-to-end wave optics Monte Carlo simulations.

Diffuse Optical Tomography for Brain Imaging: Continuous Wave Instrumentation and Linear Analysis Methods

NASA Astrophysics Data System (ADS)

Giacometti, Paolo; Diamond, Solomon G.

Diffuse optical tomography (DOT) is a functional brain imaging technique that measures cerebral blood oxygenation and blood volume changes. This technique is particularly useful in human neuroimaging measurements because of the coupling between neural and hemodynamic activity in the brain. DOT is a multichannel imaging extension of near-infrared spectroscopy (NIRS). NIRS uses laser sources and light detectors on the scalp to obtain noninvasive hemodynamic measurements from spectroscopic analysis of the remitted light. This review explains how NIRS data analysis is performed using a combination of the modified Beer-Lambert law (MBLL) and the diffusion approximation to the radiative transport equation (RTE). Laser diodes, photodiode detectors, and optical terminals that contact the scalp are the main components in most NIRS systems. Placing multiple sources and detectors over the surface of the scalp allows for tomographic reconstructions that extend the individual measurements of NIRS into DOT. Mathematically arranging the DOT measurements into a linear system of equations that can be inverted provides a way to obtain tomographic reconstructions of hemodynamics in the brain.

In vivo tomographic imaging of lung colonization of tumour in mouse with simultaneous fluorescence and X-ray CT.

PubMed

Zhang, Bin; Gao, Fuping; Wang, Mengjiao; Cao, Xu; Liu, Fei; Wang, Xin; Luo, Jianwen; Wang, Guangzhi; Bai, Jing

2014-01-01

Non-invasive in vivo imaging of diffuse and wide-spread colonization within the lungs, rather than distinct solid primary tumors, is still a challenging work. In this work, a lung colonization mouse model bearing A549 human lung tumor was simultaneously scanned by a dual-modality fluorescence molecular tomography (FMT) and X-ray computed tomography (CT) system in vivo. A two steps method which incorporates CT structural information into the FMT reconstruction procedure is employed to provide concurrent anatomical and functional information. By using the target-specific fluorescence agent, the fluorescence tomographic results show elevated fluorescence intensity deep within the lungs which is colonized with diffuse and wide-spread tumors. The results were confirmed with ex vivo fluorescence reflectance imaging and histological examination of the lung tissues. With FMT reconstruction combined with the CT information, the dual-modality FMT/micro-CT system is expected to offer sensitive and noninvasive imaging of diffuse tumor colonization within the lungs in vivo. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Methods to mitigate data truncation artifacts in multi-contrast tomosynthesis image reconstructions

NASA Astrophysics Data System (ADS)

Garrett, John; Ge, Yongshuai; Li, Ke; Chen, Guang-Hong

2015-03-01

Differential phase contrast imaging is a promising new image modality that utilizes the refraction rather than the absorption of x-rays to image an object. A Talbot-Lau interferometer may be used to permit differential phase contrast imaging with a conventional medical x-ray source and detector. However, the current size of the gratings fabricated for these interferometers are often relatively small. As a result, data truncation image artifacts are often observed in a tomographic acquisition and reconstruction. When data are truncated in x-ray absorption imaging, the methods have been introduced to mitigate the truncation artifacts. However, the same strategy to mitigate absorption truncation artifacts may not be appropriate for differential phase contrast or dark field tomographic imaging. In this work, several new methods to mitigate data truncation artifacts in a multi-contrast imaging system have been proposed and evaluated for tomosynthesis data acquisitions. The proposed methods were validated using experimental data acquired for a bovine udder as well as several cadaver breast specimens using a benchtop system at our facility.

Exemplar-based inpainting as a solution to the missing wedge problem in electron tomography.

PubMed

Trampert, Patrick; Wang, Wu; Chen, Delei; Ravelli, Raimond B G; Dahmen, Tim; Peters, Peter J; Kübel, Christian; Slusallek, Philipp

2018-04-21

A new method for dealing with incomplete projection sets in electron tomography is proposed. The approach is inspired by exemplar-based inpainting techniques in image processing and heuristically generates data for missing projection directions. The method has been extended to work on three dimensional data. In general, electron tomography reconstructions suffer from elongation artifacts along the beam direction. These artifacts can be seen in the corresponding Fourier domain as a missing wedge. The new method synthetically generates projections for these missing directions with the help of a dictionary based approach that is able to convey both structure and texture at the same time. It constitutes a preprocessing step that can be combined with any tomographic reconstruction algorithm. The new algorithm was applied to phantom data, to a real electron tomography data set taken from a catalyst, as well as to a real dataset containing solely colloidal gold particles. Visually, the synthetic projections, reconstructions, and corresponding Fourier power spectra showed a decrease of the typical missing wedge artifacts. Quantitatively, the inpainting method is capable to reduce missing wedge artifacts and improves tomogram quality with respect to full width half maximum measurements. Copyright © 2018. Published by Elsevier B.V.

Advanced Ionospheric Sensing using GROUP-C and LITES aboard the ISS

NASA Astrophysics Data System (ADS)

Budzien, S. A.; Stephan, A. W.; Chakrabarti, S.; Finn, S. C.; Cook, T.; Powell, S. P.; O'Hanlon, B.; Bishop, R. L.

2015-12-01

The GPS Radio Occultation and Ultraviolet Photometer Co-located (GROUP-C) and Limb-imaging Ionospheric and Thermospheric Extreme-ultraviolet Spectrograph (LITES) experiments are manifested for flight aboard the International Space Station (ISS) in 2016 as part of the Space Test Program Houston #5 payload. The two experiments provide technical development and risk-reduction for future DoD space weather sensors suitable for ionospheric specification, space situational awareness, and data products for global ionosphere assimilative models. In addition, the combined instrument complement of these two experiments offers a unique opportunity to study structures of the nighttime ionosphere. GROUP-C includes an advanced GPS receiver providing ionospheric electron density profiles and scintillation measurements and a high-sensitivity far-ultraviolet photometer measuring horizontal ionospheric gradients. LITES is an imaging spectrograph that spans 60-140 nm and will obtain high-cadence limb profiles of the ionosphere and thermosphere from 150-350 km altitude. In the nighttime ionosphere, recombination of O+ and electrons produces optically thin emissions at 91.1 and 135.6 nm that can be used to tomographically reconstruct the two-dimensional plasma distribution in the orbital plane below ISS altitudes. Ionospheric irregularities, such as plasma bubbles and blobs, are transient features of the low and middle latitude ionosphere with important implications for operational systems. Irregularity structures have been studied primarily using ground-based systems, though some spaced-based remote and in-situ sensing has been performed. An ionospheric observatory aboard the ISS would provide new capability to study low- and mid-latitude ionospheric structures on a global scale. By combining for the first time high-sensitivity in-track photometry, vertical ionospheric airglow spectrographic imagery, and recent advancements in UV tomography, high-fidelity tomographic reconstruction of nighttime structures can be performed from the ISS. We discuss the tomographic approach, simulated reconstructions, and value added by including complementary ground-based observations. Acknowledgements: This work is supported by NRL Work Unit 76-1C09-05.

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.

Minimal tomography with entanglement witnesses

NASA Astrophysics Data System (ADS)

Zhu, Huangjun; Teo, Yong Siah; Englert, Berthold-Georg

2010-05-01

We introduce informationally complete measurements whose outcomes are entanglement witnesses and so answer the question of how many witnesses need to be measured to decide whether an arbitrary state is entangled or not: as many as the dimension of the state space. The witnesses can be measured successively; if all of them give an inconclusive result, one exploits their tomographic completeness for a reconstruction of the quantum state and can then determine its entanglement properties by data processing. There are witnesses that are optimal for this purpose. The optimized witness-based measurement can provide exponential improvement with respect to witness efficiency in high-dimensional Hilbert spaces, at the price of a reduction in the tomographic efficiency. We describe a systematic construction and illustrate the matter with the example of two qubits. For the case of two polarization qubits of photons, we show how existing technology can be used to implement the optimized witnesses in a very efficient way. Owing to the details of the implementation, which actually measures the eigenstate basis of the witness rather than solely determining the expectation value of the witness, one does not need to measure more than six witnesses in this example of a 16-dimensional state space.

A flexible, small positron emission tomography prototype for resource-limited laboratories

NASA Astrophysics Data System (ADS)

Miranda-Menchaca, A.; Martínez-Dávalos, A.; Murrieta-Rodríguez, T.; Alva-Sánchez, H.; Rodríguez-Villafuerte, M.

2015-05-01

Modern small-animal PET scanners typically consist of a large number of detectors along with complex electronics to provide tomographic images for research in the preclinical sciences that use animal models. These systems can be expensive, especially for resource-limited educational and academic institutions in developing countries. In this work we show that a small-animal PET scanner can be built with a relatively reduced budget while, at the same time, achieving relatively high performance. The prototype consists of four detector modules each composed of LYSO pixelated crystal arrays (individual crystal elements of dimensions 1 × 1 × 10 mm3) coupled to position-sensitive photomultiplier tubes. Tomographic images are obtained by rotating the subject to complete enough projections for image reconstruction. Image quality was evaluated for different reconstruction algorithms including filtered back-projection and iterative reconstruction with maximum likelihood-expectation maximization and maximum a posteriori methods. The system matrix was computed both with geometric considerations and by Monte Carlo simulations. Prior to image reconstruction, Fourier data rebinning was used to increase the number of lines of response used. The system was evaluated for energy resolution at 511 keV (best 18.2%), system sensitivity (0.24%), spatial resolution (best 0.87 mm), scatter fraction (4.8%) and noise equivalent count-rate. The system can be scaled-up to include up to 8 detector modules, increasing detection efficiency, and its price may be reduced as newer solid state detectors become available replacing the traditional photomultiplier tubes. Prototypes like this may prove to be very valuable for educational, training, preclinical and other biological research purposes.

MO-DE-BRA-06: 3D Image Acquisition and Reconstruction Explained with Online Animations

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

Kesner, A

Purpose: Understanding the principles of 3D imaging and image reconstruction is fundamental to the field of medical imaging. Clinicians, technologists, physicists, patients, students, and inquisitive minds all stand to benefit from greater comprehension of the supporting technologies. To help explain the basic principles of 3D imaging, we developed multi-frame animations that convey the concepts of tomographic imaging. The series of free (gif) animations are accessible online, and provide a multimedia introduction to the main concepts of image reconstruction. Methods: Text and animations were created to convey the principles of analytic tomography in CT, PET, and SPECT. Specific topics covered included:more » principles of sinograms/image data storage, forward projection, principles of PET acquisitions, and filtered backprojection. A total of 8 animations were created and presented for CT, PET, and digital phantom formats. In addition, a free executable is also provided to allow users to create their own tomographic animations – providing an opportunity for interaction and personalization to help foster user interest. Results: Tutorial text and animations have been posted online, freely available to view or download. The animations are in first position in a google search of “image reconstruction animations”. The website currently receives approximately 200 hits/month, from all over the world, and the usage is growing. Positive feedback has been collected from users. Conclusion: We identified a need for improved teaching tools to help visualize the (temporally variant) concepts of image reconstruction, and have shown that animations can be a useful tool for this aspect of education. Furthermore, posting animations freely on the web has shown to be a good way to maximize their impact in the community. In future endeavors, we hope to expand this animated content, to cover principles of iterative reconstruction, as well as other phenomena relating to imaging.« less

Nonlinear inversion of borehole-radar tomography data to reconstruct velocity and attenuation distribution in earth materials

USGS Publications Warehouse

Zhou, C.; Liu, L.; Lane, J.W.

2001-01-01

A nonlinear tomographic inversion method that uses first-arrival travel-time and amplitude-spectra information from cross-hole radar measurements was developed to simultaneously reconstruct electromagnetic velocity and attenuation distribution in earth materials. Inversion methods were developed to analyze single cross-hole tomography surveys and differential tomography surveys. Assuming the earth behaves as a linear system, the inversion methods do not require estimation of source radiation pattern, receiver coupling, or geometrical spreading. The data analysis and tomographic inversion algorithm were applied to synthetic test data and to cross-hole radar field data provided by the US Geological Survey (USGS). The cross-hole radar field data were acquired at the USGS fractured-rock field research site at Mirror Lake near Thornton, New Hampshire, before and after injection of a saline tracer, to monitor the transport of electrically conductive fluids in the image plane. Results from the synthetic data test demonstrate the algorithm computational efficiency and indicate that the method robustly can reconstruct electromagnetic (EM) wave velocity and attenuation distribution in earth materials. The field test results outline zones of velocity and attenuation anomalies consistent with the finding of previous investigators; however, the tomograms appear to be quite smooth. Further work is needed to effectively find the optimal smoothness criterion in applying the Tikhonov regularization in the nonlinear inversion algorithms for cross-hole radar tomography. ?? 2001 Elsevier Science B.V. All rights reserved.

A Kullback-Leibler approach for 3D reconstruction of spectral CT data corrupted by Poisson noise

NASA Astrophysics Data System (ADS)

Hohweiller, Tom; Ducros, Nicolas; Peyrin, Françoise; Sixou, Bruno

2017-09-01

While standard computed tomography (CT) data do not depend on energy, spectral computed tomography (SPCT) acquire energy-resolved data, which allows material decomposition of the object of interest. Decompo- sitions in the projection domain allow creating projection mass density (PMD) per materials. From decomposed projections, a tomographic reconstruction creates 3D material density volume. The decomposition is made pos- sible by minimizing a cost function. The variational approach is preferred since this is an ill-posed non-linear inverse problem. Moreover, noise plays a critical role when decomposing data. That is why in this paper, a new data fidelity term is used to take into account of the photonic noise. In this work two data fidelity terms were investigated: a weighted least squares (WLS) term, adapted to Gaussian noise, and the Kullback-Leibler distance (KL), adapted to Poisson noise. A regularized Gauss-Newton algorithm minimizes the cost function iteratively. Both methods decompose materials from a numerical phantom of a mouse. Soft tissues and bones are decomposed in the projection domain; then a tomographic reconstruction creates a 3D material density volume for each material. Comparing relative errors, KL is shown to outperform WLS for low photon counts, in 2D and 3D. This new method could be of particular interest when low-dose acquisitions are performed.

Open-path TDL-Spectrometry for a Tomographic Reconstruction of 2D H2O-Concentration Fields in the Soil-Air-Boundary-Layer of Permafrost

NASA Astrophysics Data System (ADS)

Seidel, Anne; Wagner, Steven; Dreizler, Andreas; Ebert, Volker

2013-04-01

The melting of permafrost soils in arctic regions is one of the effects of climate change. It is recognized that climatically relevant gases are emitted during the thawing process, and that they may lead to a positive atmospheric feedback [1]. For a better understanding of these developments, a quantification of the gases emitted from the soil would be required. Extractive sensors with local point-wise gas sampling are currently used for this task, but are hampered due to the complex spatial structure of the soil surface, which complicates the situation due to the essential need for finding a representative gas sampling point. For this situation it would be much preferred if a sensor for detecting 2D-concentration fields of e.g. water vapor, (and in the mid-term also for methane or carbon dioxide) directly in the soil-atmosphere-boundary layer of permafrost soils would be available. However, it also has to be kept in mind that field measurements over long time periods in such a harsh environment require very sturdy instrumentation preferably without the need for sensor calibration. Therefore we are currently developing a new, robust TDLAS (tuneable diode laser absorption spectroscopy)-spectrometer based on cheap reflective foils [2]. The spectrometer is easily transportable, requires hardly any alignment and consists of industrially available, very stable components (e.g. diode lasers and glass fibers). Our measurement technique, open path TDLAS, allows for calibration-free measurements of absolute H2O concentrations. The static instrument for sampling open-path H2O concentrations consists of a joint sending and receiving optics at one side of the measurement path and a reflective element at the other side. The latter is very easy to align, since it is a foil usually applied for traffic purposes that retro-reflects the light to its origin even for large angles of misalignment (up to 60°). With this instrument, we achieved normalized detection limits of up to 0.9 ppmv?m??Hz. For absorption path lengths of up to 2 m and time resolution of 0.2 sec, we attained detection limits of 1 ppmv. Furthermore we realized a wide dynamic range covering concentrations between 200 ppmv and 12300 ppmv. The static spectrometer will now be extended to a spatially scanning TDL sensor using rapidly rotating polygon mirrors. In combination with tomographic reconstruction methods, spatially resolved 2D-fields will be measured and retrieved. The aim is to capture concentration fields with at least 1 m2 spatial coverage with concentration detection faster than 1 Hz rate. We simulated various measurements from typical concentration distributions ("phantoms") and used Algebraic Reconstruction Techniques (ART) to compute the according 2D-fields. The reconstructions look very promising and demonstrate the potential of the measurement method. In the presentation we will describe and discuss the optical setup of the stationary instrument and explain the concept of extending this instrument to a spatially scanning tomographic TDL instrument for soil studies. Further we present first results evaluating the capabilities of the selected ART reconstruction on tomographic phantoms. [1] E. Schuur, J. G. Vogel, K. G. Crummer, H. Lee, J. O. Sickman, and T. E. Osterkamp, "The effect of permafrost thaw on old carbon release and net carbon exchange from tundra.," Nature, vol. 459, no. 7246, pp. 556-9, May 2009. [2] A. Seidel, S. Wagner, and V. Ebert, "TDLAS-based open-path laser hygrometer using simple reflective foils as scattering targets," Applied Physics B, vol. 109, no. 3, pp. 497-504, Oct. 2012.

Experimental Investigation of Material Flows Within FSWs Using 3D Tomography

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

Charles R. Tolle; Timothy A. White; Karen S. Miller

2008-06-01

There exists significant prior work using tracers or pre-placed hardened markers within friction stir welding (FSWing) to experimentally explore material flow within the FSW process. Our experiments replaced markers with a thin sheet of copper foil placed between the 6061 aluminum lap and butt joints that were then welded. The absorption characteristics of x-rays for copper and aluminum are significantly different allowing for non-destructive evaluation (NDE) methods such as x-ray computed tomography (CT) to be used to demonstrate the material movement within the weldment on a much larger scale than previously shown. 3D CT reconstruction of the copper components ofmore » the weldment allows for a unique view into the final turbulent state of the welding process as process parameters are varied. The x-ray CT data of a section of the weld region was collected using a cone-beam x-ray imaging system developed at the INL. Six-hundred projections were collected over 360-degrees using a 160-kVp Bremsstrahlung x-ray generator (25-micrometer focal spot) and amorphoussilicon x-ray detector. The region of the object that was imaged was about 3cm tall and 1.5cm x 1cm in cross section, and was imaged at a magnification of about 3.6x. The data were reconstructed on a 0.5x0.5x0.5 mm3 voxel grid. After reconstruction, the aluminum and copper could be easily discriminated using a gray level threshold allowing visualization of the copper components. Fractal analysis of the tomographic reconstructed material topology is investigated as a means to quantify macro level material flow based on process parameters. The results of multi-pass FSWs show increased refinement of the copper trace material. Implications of these techniques for quantifying process flow are discussed.« less

Building a symbolic computer algebra toolbox to compute 2D Fourier transforms in polar coordinates.

PubMed

Dovlo, Edem; Baddour, Natalie

2015-01-01

The development of a symbolic computer algebra toolbox for the computation of two dimensional (2D) Fourier transforms in polar coordinates is presented. Multidimensional Fourier transforms are widely used in image processing, tomographic reconstructions and in fact any application that requires a multidimensional convolution. By examining a function in the frequency domain, additional information and insights may be obtained. The advantages of our method include: •The implementation of the 2D Fourier transform in polar coordinates within the toolbox via the combination of two significantly simpler transforms.•The modular approach along with the idea of lookup tables implemented help avoid the issue of indeterminate results which may occur when attempting to directly evaluate the transform.•The concept also helps prevent unnecessary computation of already known transforms thereby saving memory and processing time.

Hierarchical multimodal tomographic x-ray imaging at a superbend

NASA Astrophysics Data System (ADS)

Stampanoni, M.; Marone, F.; Mikuljan, G.; Jefimovs, K.; Trtik, P.; Vila-Comamala, J.; David, C.; Abela, R.

2008-08-01

Over the last decade, synchrotron-based X-ray tomographic microscopy has established itself as a fundamental tool for non-invasive, quantitative investigations of a broad variety of samples, with application ranging from space research and materials science to biology and medicine. Thanks to the brilliance of modern third generation sources, voxel sizes in the micrometer range are routinely achieved by the major X-ray microtomography devices around the world, while the isotropic 100 nm barrier is reached and trespassed only by few instruments. The beamline for TOmographic Microscopy and Coherent rAdiology experiments (TOMCAT) of the Swiss Light Source at the Paul Scherrer Institut, operates a multimodal endstation which offers tomographic capabilities in the micrometer range in absorption contrast - of course - as well as phase contrast imaging. Recently, the beamline has been equipped with a full field, hard X-rays microscope with a theoretical pixel size down to 30 nm and a field of view of 50 microns. The nanoscope performs well at X-ray energies between 8 and 12 keV, selected from the white beam of a 2.9 T superbend by a [Ru/C]100 fixed exit multilayer monochromator. In this work we illustrate the experimental setup dedicated to the nanoscope, in particular the ad-hoc designed X-ray optics needed to produce a homogeneous, square illumination of the sample imaging plane as well as the magnifying zone plate. Tomographic reconstructions at 60 nm voxel size will be shown and discussed.

Field-portable lensfree tomographic microscope.

PubMed

Isikman, Serhan O; Bishara, Waheb; Sikora, Uzair; Yaglidere, Oguzhan; Yeah, John; Ozcan, Aydogan

2011-07-07

We present a field-portable lensfree tomographic microscope, which can achieve sectional imaging of a large volume (∼20 mm(3)) on a chip with an axial resolution of <7 μm. In this compact tomographic imaging platform (weighing only ∼110 grams), 24 light-emitting diodes (LEDs) that are each butt-coupled to a fibre-optic waveguide are controlled through a cost-effective micro-processor to sequentially illuminate the sample from different angles to record lensfree holograms of the sample that is placed on the top of a digital sensor array. In order to generate pixel super-resolved (SR) lensfree holograms and hence digitally improve the achievable lateral resolution, multiple sub-pixel shifted holograms are recorded at each illumination angle by electromagnetically actuating the fibre-optic waveguides using compact coils and magnets. These SR projection holograms obtained over an angular range of ±50° are rapidly reconstructed to yield projection images of the sample, which can then be back-projected to compute tomograms of the objects on the sensor-chip. The performance of this compact and light-weight lensfree tomographic microscope is validated by imaging micro-beads of different dimensions as well as a Hymenolepis nana egg, which is an infectious parasitic flatworm. Achieving a decent three-dimensional spatial resolution, this field-portable on-chip optical tomographic microscope might provide a useful toolset for telemedicine and high-throughput imaging applications in resource-poor settings. This journal is © The Royal Society of Chemistry 2011

Improved scatter correction with factor analysis for planar and SPECT imaging

NASA Astrophysics Data System (ADS)

Knoll, Peter; Rahmim, Arman; Gültekin, Selma; Šámal, Martin; Ljungberg, Michael; Mirzaei, Siroos; Segars, Paul; Szczupak, Boguslaw

2017-09-01

Quantitative nuclear medicine imaging is an increasingly important frontier. In order to achieve quantitative imaging, various interactions of photons with matter have to be modeled and compensated. Although correction for photon attenuation has been addressed by including x-ray CT scans (accurate), correction for Compton scatter remains an open issue. The inclusion of scattered photons within the energy window used for planar or SPECT data acquisition decreases the contrast of the image. While a number of methods for scatter correction have been proposed in the past, in this work, we propose and assess a novel, user-independent framework applying factor analysis (FA). Extensive Monte Carlo simulations for planar and tomographic imaging were performed using the SIMIND software. Furthermore, planar acquisition of two Petri dishes filled with 99mTc solutions and a Jaszczak phantom study (Data Spectrum Corporation, Durham, NC, USA) using a dual head gamma camera were performed. In order to use FA for scatter correction, we subdivided the applied energy window into a number of sub-windows, serving as input data. FA results in two factor images (photo-peak, scatter) and two corresponding factor curves (energy spectra). Planar and tomographic Jaszczak phantom gamma camera measurements were recorded. The tomographic data (simulations and measurements) were processed for each angular position resulting in a photo-peak and a scatter data set. The reconstructed transaxial slices of the Jaszczak phantom were quantified using an ImageJ plugin. The data obtained by FA showed good agreement with the energy spectra, photo-peak, and scatter images obtained in all Monte Carlo simulated data sets. For comparison, the standard dual-energy window (DEW) approach was additionally applied for scatter correction. FA in comparison with the DEW method results in significant improvements in image accuracy for both planar and tomographic data sets. FA can be used as a user-independent approach for scatter correction in nuclear medicine.

A Hybrid Approach to Data Assimilation for Reconstructing the Evolution of Mantle Dynamics

NASA Astrophysics Data System (ADS)

Zhou, Quan; Liu, Lijun

2017-11-01

Quantifying past mantle dynamic processes represents a major challenge in understanding the temporal evolution of the solid earth. Mantle convection modeling with data assimilation is one of the most powerful tools to investigate the dynamics of plate subduction and mantle convection. Although various data assimilation methods, both forward and inverse, have been created, these methods all have limitations in their capabilities to represent the real earth. Pure forward models tend to miss important mantle structures due to the incorrect initial condition and thus may lead to incorrect mantle evolution. In contrast, pure tomography-based models cannot effectively resolve the fine slab structure and would fail to predict important subduction-zone dynamic processes. Here we propose a hybrid data assimilation approach that combines the unique power of the sequential and adjoint algorithms, which can properly capture the detailed evolution of the downgoing slab and the tomographically constrained mantle structures, respectively. We apply this new method to reconstructing mantle dynamics below the western U.S. while considering large lateral viscosity variations. By comparing this result with those from several existing data assimilation methods, we demonstrate that the hybrid modeling approach recovers the realistic 4-D mantle dynamics the best.

To image analysis in computed tomography

NASA Astrophysics Data System (ADS)

Chukalina, Marina; Nikolaev, Dmitry; Ingacheva, Anastasia; Buzmakov, Alexey; Yakimchuk, Ivan; Asadchikov, Victor

2017-03-01

The presence of errors in tomographic image may lead to misdiagnosis when computed tomography (CT) is used in medicine, or the wrong decision about parameters of technological processes when CT is used in the industrial applications. Two main reasons produce these errors. First, the errors occur on the step corresponding to the measurement, e.g. incorrect calibration and estimation of geometric parameters of the set-up. The second reason is the nature of the tomography reconstruction step. At the stage a mathematical model to calculate the projection data is created. Applied optimization and regularization methods along with their numerical implementations of the method chosen have their own specific errors. Nowadays, a lot of research teams try to analyze these errors and construct the relations between error sources. In this paper, we do not analyze the nature of the final error, but present a new approach for the calculation of its distribution in the reconstructed volume. We hope that the visualization of the error distribution will allow experts to clarify the medical report impression or expert summary given by them after analyzing of CT results. To illustrate the efficiency of the proposed approach we present both the simulation and real data processing results.

A Hybrid Forward-Adjoint Data Assimilation Method for Reconstructing the Temporal Evolution of Mantle Dynamics

NASA Astrophysics Data System (ADS)

Zhou, Q.; Liu, L.

2017-12-01

Quantifying past mantle dynamic processes represents a major challenge in understanding the temporal evolution of the solid earth. Mantle convection modeling with data assimilation is one of the most powerful tools to investigate the dynamics of plate subduction and mantle convection. Although various data assimilation methods, both forward and inverse, have been created, these methods all have limitations in their capabilities to represent the real earth. Pure forward models tend to miss important mantle structures due to the incorrect initial condition and thus may lead to incorrect mantle evolution. In contrast, pure tomography-based models cannot effectively resolve the fine slab structure and would fail to predict important subduction-zone dynamic processes. Here we propose a hybrid data assimilation method that combines the unique power of the sequential and adjoint algorithms, which can properly capture the detailed evolution of the downgoing slab and the tomographically constrained mantle structures, respectively. We apply this new method to reconstructing mantle dynamics below the western U.S. while considering large lateral viscosity variations. By comparing this result with those from several existing data assimilation methods, we demonstrate that the hybrid modeling approach recovers the realistic 4-D mantle dynamics to the best.

Statistical iterative material image reconstruction for spectral CT using a semi-empirical forward model

NASA Astrophysics Data System (ADS)

Mechlem, Korbinian; Ehn, Sebastian; Sellerer, Thorsten; Pfeiffer, Franz; Noël, Peter B.

2017-03-01

In spectral computed tomography (spectral CT), the additional information about the energy dependence of attenuation coefficients can be exploited to generate material selective images. These images have found applications in various areas such as artifact reduction, quantitative imaging or clinical diagnosis. However, significant noise amplification on material decomposed images remains a fundamental problem of spectral CT. Most spectral CT algorithms separate the process of material decomposition and image reconstruction. Separating these steps is suboptimal because the full statistical information contained in the spectral tomographic measurements cannot be exploited. Statistical iterative reconstruction (SIR) techniques provide an alternative, mathematically elegant approach to obtaining material selective images with improved tradeoffs between noise and resolution. Furthermore, image reconstruction and material decomposition can be performed jointly. This is accomplished by a forward model which directly connects the (expected) spectral projection measurements and the material selective images. To obtain this forward model, detailed knowledge of the different photon energy spectra and the detector response was assumed in previous work. However, accurately determining the spectrum is often difficult in practice. In this work, a new algorithm for statistical iterative material decomposition is presented. It uses a semi-empirical forward model which relies on simple calibration measurements. Furthermore, an efficient optimization algorithm based on separable surrogate functions is employed. This partially negates one of the major shortcomings of SIR, namely high computational cost and long reconstruction times. Numerical simulations and real experiments show strongly improved image quality and reduced statistical bias compared to projection-based material decomposition.

Emerging Techniques for Dose Optimization in Abdominal CT

PubMed Central

Platt, Joel F.; Goodsitt, Mitchell M.; Al-Hawary, Mahmoud M.; Maturen, Katherine E.; Wasnik, Ashish P.; Pandya, Amit

2014-01-01

Recent advances in computed tomographic (CT) scanning technique such as automated tube current modulation (ATCM), optimized x-ray tube voltage, and better use of iterative image reconstruction have allowed maintenance of good CT image quality with reduced radiation dose. ATCM varies the tube current during scanning to account for differences in patient attenuation, ensuring a more homogeneous image quality, although selection of the appropriate image quality parameter is essential for achieving optimal dose reduction. Reducing the x-ray tube voltage is best suited for evaluating iodinated structures, since the effective energy of the x-ray beam will be closer to the k-edge of iodine, resulting in a higher attenuation for the iodine. The optimal kilovoltage for a CT study should be chosen on the basis of imaging task and patient habitus. The aim of iterative image reconstruction is to identify factors that contribute to noise on CT images with use of statistical models of noise (statistical iterative reconstruction) and selective removal of noise to improve image quality. The degree of noise suppression achieved with statistical iterative reconstruction can be customized to minimize the effect of altered image quality on CT images. Unlike with statistical iterative reconstruction, model-based iterative reconstruction algorithms model both the statistical noise and the physical acquisition process, allowing CT to be performed with further reduction in radiation dose without an increase in image noise or loss of spatial resolution. Understanding these recently developed scanning techniques is essential for optimization of imaging protocols designed to achieve the desired image quality with a reduced dose. © RSNA, 2014 PMID:24428277

Tomographic reconstruction of ionospheric electron density during the storm of 5-6 August 2011 using multi-source data

PubMed Central

Tang, Jun; Yao, Yibin; Zhang, Liang; Kong, Jian

2015-01-01

The insufficiency of data is the essential reason for ill-posed problem existed in computerized ionospheric tomography (CIT) technique. Therefore, the method of integrating multi-source data is proposed. Currently, the multiple satellite navigation systems and various ionospheric observing instruments provide abundant data which can be employed to reconstruct ionospheric electron density (IED). In order to improve the vertical resolution of IED, we do research on IED reconstruction by integration of ground-based GPS data, occultation data from the LEO satellite, satellite altimetry data from Jason-1 and Jason-2 and ionosonde data. We used the CIT results to compare with incoherent scatter radar (ISR) observations, and found that the multi-source data fusion was effective and reliable to reconstruct electron density, showing its superiority than CIT with GPS data alone. PMID:26266764

Tomographic reconstruction of ionospheric electron density during the storm of 5-6 August 2011 using multi-source data.

PubMed

Tang, Jun; Yao, Yibin; Zhang, Liang; Kong, Jian

2015-08-12

The insufficiency of data is the essential reason for ill-posed problem existed in computerized ionospheric tomography (CIT) technique. Therefore, the method of integrating multi-source data is proposed. Currently, the multiple satellite navigation systems and various ionospheric observing instruments provide abundant data which can be employed to reconstruct ionospheric electron density (IED). In order to improve the vertical resolution of IED, we do research on IED reconstruction by integration of ground-based GPS data, occultation data from the LEO satellite, satellite altimetry data from Jason-1 and Jason-2 and ionosonde data. We used the CIT results to compare with incoherent scatter radar (ISR) observations, and found that the multi-source data fusion was effective and reliable to reconstruct electron density, showing its superiority than CIT with GPS data alone.

Locating knots by industrial tomography- A feasibility study

Treesearch

Fred W. Taylor; Francis G. Wagner; Charles W. McMillin; Ira L. Morgan; Forrest F. Hopkins

1984-01-01

Industrial photon tomography was used to scan four southern pine logs and one red oak log. The logs were scanned at 16 cross-sectional slice planes located 1 centimeter apart along their longitudinal axes. Tomographic reconstructions were made from the scan data collected at these slice planes, and a cursory image analysis technique was developed to locate the log...

Hybrid Photoacoustic/Ultrasound Tomograph for Real-Time Finger Imaging.

PubMed

Oeri, Milan; Bost, Wolfgang; Sénégond, Nicolas; Tretbar, Steffen; Fournelle, Marc

2017-10-01

We report a target-enclosing, hybrid tomograph with a total of 768 elements based on capacitive micromachined ultrasound transducer technology and providing fast, high-resolution 2-D/3-D photoacoustic and ultrasound tomography tailored to finger imaging. A freely programmable ultrasound beamforming platform sampling data at 80 MHz was developed to realize plane wave transmission under multiple angles. A multiplexing unit enables the connection and control of a large number of elements. Fast image reconstruction is provided by GPU processing. The tomograph is composed of four independent and fully automated movable arc-shaped transducers, allowing imaging of all three finger joints. The system benefits from photoacoustics, yielding high optical contrast and enabling visualization of finger vascularization, and ultrasound provides morphologic information on joints and surrounding tissue. A diode-pumped, Q-switched Nd:YAG laser and an optical parametric oscillator are used to broaden the spectrum of emitted wavelengths to provide multispectral imaging. Custom-made optical fiber bundles enable illumination of the region of interest in the plane of acoustic detection. Precision in positioning of the probe in motion is ensured by use of a motor-driven guide slide. The current position of the probe is encoded by the stage and used to relate ultrasound and photoacoustic signals to the corresponding region of interest of the suspicious finger joint. The system is characterized in phantoms and a healthy human finger in vivo. The results obtained promise to provide new opportunities in finger diagnostics and establish photoacoustic/ultrasound-tomography in medical routine. Copyright © 2017 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.

Phase contrast imaging of cochlear soft tissue.

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

Smith, S.; Hwang, M.; Rau, C.

A noninvasive technique to image soft tissue could expedite diagnosis and disease management in the auditory system. We propose inline phase contrast imaging with hard X-rays as a novel method that overcomes the limitations of conventional absorption radiography for imaging soft tissue. In this study, phase contrast imaging of mouse cochleae was performed at the Argonne National Laboratory Advanced Photon Source. The phase contrast tomographic reconstructions show soft tissue structures of the cochlea, including the inner pillar cells, the inner spiral sulcus, the tectorial membrane, the basilar membrane, and the Reissner's membrane. The results suggest that phase contrast X-ray imagingmore » and tomographic techniques hold promise to noninvasively image cochlear structures at an unprecedented cellular level.« less

A tomographic technique for the simultaneous imaging of temperature, chemical species, and pressure in reactive flows using absorption spectroscopy with frequency-agile lasers

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

Cai, Weiwei; Kaminski, Clemens F., E-mail: cfk23@cam.ac.uk

2014-01-20

This paper proposes a technique that can simultaneously retrieve distributions of temperature, concentration of chemical species, and pressure based on broad bandwidth, frequency-agile tomographic absorption spectroscopy. The technique holds particular promise for the study of dynamic combusting flows. A proof-of-concept numerical demonstration is presented, using representative phantoms to model conditions typically prevailing in near-atmospheric or high pressure flames. The simulations reveal both the feasibility of the proposed technique and its robustness. Our calculations indicate precisions of ∼70 K at flame temperatures and ∼0.05 bars at high pressure from reconstructions featuring as much as 5% Gaussian noise in the projections.

Digital x-ray tomosynthesis with interpolated projection data for thin slab objects

NASA Astrophysics Data System (ADS)

Ha, S.; Yun, J.; Kim, H. K.

2017-11-01

In relation with a thin slab-object inspection, we propose a digital tomosynthesis reconstruction with fewer numbers of measured projections in combinations with additional virtual projections, which are produced by interpolating the measured projections. Hence we can reconstruct tomographic images with less few-view artifacts. The projection interpolation assumes that variations in cone-beam ray path-lengths through an object are negligible and the object is rigid. The interpolation is performed in the projection-space domain. Pixel values in the interpolated projection are the weighted sum of pixel values of the measured projections considering their projection angles. The experimental simulation shows that the proposed method can enhance the contrast-to-noise performance in reconstructed images while sacrificing the spatial resolving power.

Optical tomography for flow visualization of the density field around a revolving helicopter rotor blade

NASA Technical Reports Server (NTRS)

Snyder, R.; Hesselink, L.

1984-01-01

In this paper, a tomographic procedure for reconstructing the density field around a helicopter rotor blade tip from remote optical line-of-sight measurements is discussed. Numerical model studies have been carried out to investigate the influence of the number of available views, limited width viewing, and ray bending on the reconstruction. Performance is measured in terms of the mean-square error. It is found that very good reconstructions can be obtained using only a small number of views even when the width of view is smaller than the spatial extent of the object. An iterative procedure is used to correct for ray bending due to refraction associated with the sharp density gradients (shocks).

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.

A semi-automatic method for positioning a femoral bone reconstruction for strict view generation.

PubMed

Milano, Federico; Ritacco, Lucas; Gomez, Adrian; Gonzalez Bernaldo de Quiros, Fernan; Risk, Marcelo

2010-01-01

In this paper we present a semi-automatic method for femoral bone positioning after 3D image reconstruction from Computed Tomography images. This serves as grounding for the definition of strict axial, longitudinal and anterior-posterior views, overcoming the problem of patient positioning biases in 2D femoral bone measuring methods. After the bone reconstruction is aligned to a standard reference frame, new tomographic slices can be generated, on which unbiased measures may be taken. This could allow not only accurate inter-patient comparisons but also intra-patient comparisons, i.e., comparisons of images of the same patient taken at different times. This method could enable medical doctors to diagnose and follow up several bone deformities more easily.

Optical diffraction tomography: accuracy of an off-axis reconstruction

NASA Astrophysics Data System (ADS)

Kostencka, Julianna; Kozacki, Tomasz

2014-05-01

Optical diffraction tomography is an increasingly popular method that allows for reconstruction of three-dimensional refractive index distribution of semi-transparent samples using multiple measurements of an optical field transmitted through the sample for various illumination directions. The process of assembly of the angular measurements is usually performed with one of two methods: filtered backprojection (FBPJ) or filtered backpropagation (FBPP) tomographic reconstruction algorithm. The former approach, although conceptually very simple, provides an accurate reconstruction for the object regions located close to the plane of focus. However, since FBPJ ignores diffraction, its use for spatially extended structures is arguable. According to the theory of scattering, more precise restoration of a 3D structure shall be achieved with the FBPP algorithm, which unlike the former approach incorporates diffraction. It is believed that with this method one is allowed to obtain a high accuracy reconstruction in a large measurement volume exceeding depth of focus of an imaging system. However, some studies have suggested that a considerable improvement of the FBPP results can be achieved with prior propagation of the transmitted fields back to the centre of the object. This, supposedly, enables reduction of errors due to approximated diffraction formulas used in FBPP. In our view this finding casts doubt on quality of the FBPP reconstruction in the regions far from the rotation axis. The objective of this paper is to investigate limitation of the FBPP algorithm in terms of an off-axis reconstruction and compare its performance with the FBPJ approach. Moreover, in this work we propose some modifications to the FBPP algorithm that allow for more precise restoration of a sample structure in off-axis locations. The research is based on extensive numerical simulations supported with wave-propagation method.

Tomographic reconstruction of atmospheric gravity wave parameters from airglow observations

NASA Astrophysics Data System (ADS)

Song, Rui; Kaufmann, Martin; Ungermann, Jörn; Ern, Manfred; Liu, Guang; Riese, Martin

2017-11-01

Gravity waves (GWs) play an important role in the dynamics of the mesosphere and lower thermosphere (MLT). Therefore, global observations of GWs in the MLT region are of particular interest. The small scales of GWs, however, pose a major problem for the observation of GWs from space. We propose a new observation strategy for GWs in the mesopause region by combining limb and sub-limb satellite-borne remote sensing measurements for improving the spatial resolution of temperatures that are retrieved from atmospheric soundings. In our study, we simulate satellite observations of the rotational structure of the O2 A-band nightglow. A key element of the new method is the ability of the instrument or the satellite to operate in so-called target mode, i.e. to point at a particular point in the atmosphere and collect radiances at different viewing angles. These multi-angle measurements of a selected region allow for tomographic 2-D reconstruction of the atmospheric state, in particular of GW structures. The feasibility of this tomographic retrieval approach is assessed using simulated measurements. It shows that one major advantage of this observation strategy is that GWs can be observed on a much smaller scale than conventional observations. We derive a GW sensitivity function, and it is shown that target mode observations are able to capture GWs with horizontal wavelengths as short as ˜ 50 km for a large range of vertical wavelengths. This is far better than the horizontal wavelength limit of 100-200 km obtained from conventional limb sounding.

Meaning of Interior Tomography

PubMed Central

Wang, Ge; Yu, Hengyong

2013-01-01

The classic imaging geometry for computed tomography is for collection of un-truncated projections and reconstruction of a global image, with the Fourier transform as the theoretical foundation that is intrinsically non-local. Recently, interior tomography research has led to theoretically exact relationships between localities in the projection and image spaces and practically promising reconstruction algorithms. Initially, interior tomography was developed for x-ray computed tomography. Then, it has been elevated as a general imaging principle. Finally, a novel framework known as “omni-tomography” is being developed for grand fusion of multiple imaging modalities, allowing tomographic synchrony of diversified features. PMID:23912256

Tunable diode laser absorption spectroscopy-based tomography system for on-line monitoring of two-dimensional distributions of temperature and H{sub 2}O mole fraction

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

Xu, Lijun, E-mail: lijunxu@buaa.edu.cn; Liu, Chang; Jing, Wenyang

2016-01-15

To monitor two-dimensional (2D) distributions of temperature and H{sub 2}O mole fraction, an on-line tomography system based on tunable diode laser absorption spectroscopy (TDLAS) was developed. To the best of the authors’ knowledge, this is the first report on a multi-view TDLAS-based system for simultaneous tomographic visualization of temperature and H{sub 2}O mole fraction in real time. The system consists of two distributed feedback (DFB) laser diodes, a tomographic sensor, electronic circuits, and a computer. The central frequencies of the two DFB laser diodes are at 7444.36 cm{sup −1} (1343.3 nm) and 7185.6 cm{sup −1} (1391.67 nm), respectively. The tomographicmore » sensor is used to generate fan-beam illumination from five views and to produce 60 ray measurements. The electronic circuits not only provide stable temperature and precise current controlling signals for the laser diodes but also can accurately sample the transmitted laser intensities and extract integrated absorbances in real time. Finally, the integrated absorbances are transferred to the computer, in which the 2D distributions of temperature and H{sub 2}O mole fraction are reconstructed by using a modified Landweber algorithm. In the experiments, the TDLAS-based tomography system was validated by using asymmetric premixed flames with fixed and time-varying equivalent ratios, respectively. The results demonstrate that the system is able to reconstruct the profiles of the 2D distributions of temperature and H{sub 2}O mole fraction of the flame and effectively capture the dynamics of the combustion process, which exhibits good potential for flame monitoring and on-line combustion diagnosis.« less

Cone-beam computed tomographic evaluation of the temporomandibular joint and dental characteristics of patients with Class II subdivision malocclusion and asymmetry

PubMed Central

Huang, Mingna; Hu, Yun; Yu, Jinfeng; Sun, Jicheng; Ming, Ye

2017-01-01

Objective Treating Class II subdivision malocclusion with asymmetry has been a challenge for orthodontists because of the complicated characteristics of asymmetry. This study aimed to explore the characteristics of dental and skeletal asymmetry in Class II subdivision malocclusion, and to assess the relationship between the condyle-glenoid fossa and first molar. Methods Cone-beam computed tomographic images of 32 patients with Class II subdivision malocclusion were three-dimensionally reconstructed using the Mimics software. Forty-five anatomic landmarks on the reconstructed structures were selected and 27 linear and angular measurements were performed. Paired-samples t-tests were used to compare the average differences between the Class I and Class II sides; Pearson correlation coefficient (r) was used for analyzing the linear association. Results The faciolingual crown angulation of the mandibular first molar (p < 0.05), sagittal position of the maxillary and mandibular first molars (p < 0.01), condylar head height (p < 0.01), condylar process height (p < 0.05), and angle of the posterior wall of the articular tubercle and coronal position of the glenoid fossa (p < 0.01) were significantly different between the two sides. The morphology and position of the condyle-glenoid fossa significantly correlated with the three-dimensional changes in the first molar. Conclusions Asymmetry in the sagittal position of the maxillary and mandibular first molars between the two sides and significant lingual inclination of the mandibular first molar on the Class II side were the dental characteristics of Class II subdivision malocclusion. Condylar morphology and glenoid fossa position asymmetries were the major components of skeletal asymmetry and were well correlated with the three-dimensional position of the first molar. PMID:28861389

Mapping chemicals in air using an environmental CAT scanning system: evaluation of algorithms

NASA Astrophysics Data System (ADS)

Samanta, A.; Todd, L. A.

A new technique is being developed which creates near real-time maps of chemical concentrations in air for environmental and occupational environmental applications. This technique, we call Environmental CAT Scanning, combines the real-time measuring technique of open-path Fourier transform infrared spectroscopy with the mapping capabilitites of computed tomography to produce two-dimensional concentration maps. With this system, a network of open-path measurements is obtained over an area; measurements are then processed using a tomographic algorithm to reconstruct the concentrations. This research focussed on the process of evaluating and selecting appropriate reconstruction algorithms, for use in the field, by using test concentration data from both computer simultation and laboratory chamber studies. Four algorithms were tested using three types of data: (1) experimental open-path data from studies that used a prototype opne-path Fourier transform/computed tomography system in an exposure chamber; (2) synthetic open-path data generated from maps created by kriging point samples taken in the chamber studies (in 1), and; (3) synthetic open-path data generated using a chemical dispersion model to create time seires maps. The iterative algorithms used to reconstruct the concentration data were: Algebraic Reconstruction Technique without Weights (ART1), Algebraic Reconstruction Technique with Weights (ARTW), Maximum Likelihood with Expectation Maximization (MLEM) and Multiplicative Algebraic Reconstruction Technique (MART). Maps were evaluated quantitatively and qualitatively. In general, MART and MLEM performed best, followed by ARTW and ART1. However, algorithm performance varied under different contaminant scenarios. This study showed the importance of using a variety of maps, particulary those generated using dispersion models. The time series maps provided a more rigorous test of the algorithms and allowed distinctions to be made among the algorithms. A comprehensive evaluation of algorithms, for the environmental application of tomography, requires the use of a battery of test concentration data before field implementation, which models reality and tests the limits of the algorithms.

Modified interferometric imaging condition for reverse-time migration

NASA Astrophysics Data System (ADS)

Guo, Xue-Bao; Liu, Hong; Shi, Ying

2018-01-01

For reverse-time migration, high-resolution imaging mainly depends on the accuracy of the velocity model and the imaging condition. In practice, however, the small-scale components of the velocity model cannot be estimated by tomographical methods; therefore, the wavefields are not accurately reconstructed from the background velocity, and the imaging process will generate artefacts. Some of the noise is due to cross-correlation of unrelated seismic events. Interferometric imaging condition suppresses imaging noise very effectively, especially the unknown random disturbance of the small-scale part. The conventional interferometric imaging condition is extended in this study to obtain a new imaging condition based on the pseudo-Wigner distribution function (WDF). Numerical examples show that the modified interferometric imaging condition improves imaging precision.

Microanatomy of the cochlear hook

NASA Astrophysics Data System (ADS)

Kwan, Changyow Claire; Tan, Xiaodong; Stock, Stuart R.; Soriano, Carmen; Xiao, Xianghui; Richter, Claus-Peter

2017-09-01

Communication among humans occurs through coding and decoding of acoustic information. The inner ear or cochlea acts as a frequency analyzer and divides the acoustic signal into small frequency bands, which are processed at different sites along the cochlea. The mechano-electrical conversion is accomplished by the soft tissue structures in the cochlea. While the anatomy for most of the cochlea has been well described, a detailed description of the very high frequency and vulnerable cochlear hook region is missing. To study the cochlear hook, mice cochleae were imaged with synchrotron radiation and high-resolution reconstructions have been made from the tomographic scans. This is the first detailed description of the bony and soft tissues of the hook region of the mammalian cochlea.

Tomographic reconstruction of atmospheric turbulence with the use of time-dependent stochastic inversion.

PubMed

Vecherin, Sergey N; Ostashev, Vladimir E; Ziemann, A; Wilson, D Keith; Arnold, K; Barth, M

2007-09-01

Acoustic travel-time tomography allows one to reconstruct temperature and wind velocity fields in the atmosphere. In a recently published paper [S. Vecherin et al., J. Acoust. Soc. Am. 119, 2579 (2006)], a time-dependent stochastic inversion (TDSI) was developed for the reconstruction of these fields from travel times of sound propagation between sources and receivers in a tomography array. TDSI accounts for the correlation of temperature and wind velocity fluctuations both in space and time and therefore yields more accurate reconstruction of these fields in comparison with algebraic techniques and regular stochastic inversion. To use TDSI, one needs to estimate spatial-temporal covariance functions of temperature and wind velocity fluctuations. In this paper, these spatial-temporal covariance functions are derived for locally frozen turbulence which is a more general concept than a widely used hypothesis of frozen turbulence. The developed theory is applied to reconstruction of temperature and wind velocity fields in the acoustic tomography experiment carried out by University of Leipzig, Germany. The reconstructed temperature and velocity fields are presented and errors in reconstruction of these fields are studied.

Outcomes of the JNT 1955 Phase I Viability Study of Gamma Emission Tomography for Spent Fuel Verification

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

Jacobsson-Svard, Staffan; Smith, Leon E.; White, Timothy

The potential for gamma emission tomography (GET) to detect partial defects within a spent nuclear fuel assembly has been assessed within the IAEA Support Program project JNT 1955, phase I, which was completed and reported to the IAEA in October 2016. Two safeguards verification objectives were identified in the project; (1) independent determination of the number of active pins that are present in a measured assembly, in the absence of a priori information about the assembly; and (2) quantitative assessment of pin-by-pin properties, for example the activity of key isotopes or pin attributes such as cooling time and relative burnup,more » under the assumption that basic fuel parameters (e.g., assembly type and nominal fuel composition) are known. The efficacy of GET to meet these two verification objectives was evaluated across a range of fuel types, burnups and cooling times, while targeting a total interrogation time of less than 60 minutes. The evaluations were founded on a modelling and analysis framework applied to existing and emerging GET instrument designs. Monte Carlo models of different fuel types were used to produce simulated tomographer responses to large populations of “virtual” fuel assemblies. The simulated instrument response data were then processed using a variety of tomographic-reconstruction and image-processing methods, and scoring metrics were defined and used to evaluate the performance of the methods.This paper describes the analysis framework and metrics used to predict tomographer performance. It also presents the design of a “universal” GET (UGET) instrument intended to support the full range of verification scenarios envisioned by the IAEA. Finally, it gives examples of the expected partial-defect detection capabilities for some fuels and diversion scenarios, and it provides a comparison of predicted performance for the notional UGET design and an optimized variant of an existing IAEA instrument.« less

Parallel-scanning tomosynthesis using a slot scanning technique: Fixed-focus reconstruction and the resulting image quality

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

Shibata, Koichi, E-mail: shibatak@suzuka-u.ac.jp; Notohara, Daisuke; Sakai, Takihito

2014-11-01

Purpose: Parallel-scanning tomosynthesis (PS-TS) is a novel technique that fuses the slot scanning technique and the conventional tomosynthesis (TS) technique. This approach allows one to obtain long-view tomosynthesis images in addition to normally sized tomosynthesis images, even when using a system that has no linear tomographic scanning function. The reconstruction technique and an evaluation of the resulting image quality for PS-TS are described in this paper. Methods: The PS-TS image-reconstruction technique consists of several steps (1) the projection images are divided into strips, (2) the strips are stitched together to construct images corresponding to the reconstruction plane, (3) the stitchedmore » images are filtered, and (4) the filtered stitched images are back-projected. In the case of PS-TS using the fixed-focus reconstruction method (PS-TS-F), one set of stitched images is used for the reconstruction planes at all heights, thus avoiding the necessity of repeating steps (1)–(3). A physical evaluation of the image quality of PS-TS-F compared with that of the conventional linear TS was performed using a R/F table (Sonialvision safire, Shimadzu Corp., Kyoto, Japan). The tomographic plane with the best theoretical spatial resolution (the in-focus plane, IFP) was set at a height of 100 mm from the table top by adjusting the reconstruction program. First, the spatial frequency response was evaluated at heights of −100, −50, 0, 50, 100, and 150 mm from the IFP using the edge of a 0.3-mm-thick copper plate. Second, the spatial resolution at each height was visually evaluated using an x-ray test pattern (Model No. 38, PTW Freiburg, Germany). Third, the slice sensitivity at each height was evaluated via the wire method using a 0.1-mm-diameter tungsten wire. Phantom studies using a knee phantom and a whole-body phantom were also performed. Results: The spatial frequency response of PS-TS-F yielded the best results at the IFP and degraded slightly as the distance from the IFP increased. A visual evaluation of the spatial resolution using the x-ray test pattern indicated that the resolution was 1.8 lp/mm at the IFP and 1.2 lp/mm at heights of −100 and 100 mm from the IFP. The authors demonstrated that a spatial resolution of 1.2–1.8 lp/mm could be obtained within heights of 200 mm of the IFP. The slice sensitivity varied between 11.1 and 13.8 mm for heights between −50 and 100 mm, and there was no critical change in the slice sensitivity within a height range of 150 mm around the IFP. The phantom results demonstrated that tomosynthesis and long-view images could be reconstructed. Conclusions: PS-TS-F provides tomosynthesis images while using low-cost systems that have no tomographic scanning function, such as tableside-controlled universal R/F systems or universal radiographic systems.« less

Unbiased nonorthogonal bases for tomographic reconstruction

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

Sainz, Isabel; Klimov, Andrei B.; Roa, Luis

2010-05-15

We have developed a general method for constructing a set of nonorthogonal bases with equal separations between all different basis states in prime dimensions. The results are that the corresponding biorthogonal counterparts are pairwise unbiased with the components of the original bases. Using these bases, we derive an explicit expression for the optimal tomography in nonorthogonal bases. A special two-dimensional case is analyzed separately.

3D acoustic atmospheric tomography

NASA Astrophysics Data System (ADS)

Rogers, Kevin; Finn, Anthony

2014-10-01

This paper presents a method for tomographically reconstructing spatially varying 3D atmospheric temperature profiles and wind velocity fields based. Measurements of the acoustic signature measured onboard a small Unmanned Aerial Vehicle (UAV) are compared to ground-based observations of the same signals. The frequency-shifted signal variations are then used to estimate the acoustic propagation delay between the UAV and the ground microphones, which are also affected by atmospheric temperature and wind speed vectors along each sound ray path. The wind and temperature profiles are modelled as the weighted sum of Radial Basis Functions (RBFs), which also allow local meteorological measurements made at the UAV and ground receivers to supplement any acoustic observations. Tomography is used to provide a full 3D reconstruction/visualisation of the observed atmosphere. The technique offers observational mobility under direct user control and the capacity to monitor hazardous atmospheric environments, otherwise not justifiable on the basis of cost or risk. This paper summarises the tomographic technique and reports on the results of simulations and initial field trials. The technique has practical applications for atmospheric research, sound propagation studies, boundary layer meteorology, air pollution measurements, analysis of wind shear, and wind farm surveys.

Evaluation Experiment of Ultrasound Computed Tomography for the Abdominal Sound Speed Imaging

NASA Astrophysics Data System (ADS)

Nogami, Keisuke; Yamada, Akira

2007-07-01

Abdominal sound speed tomographic imaging using through-transmission travel time data on the body surface was investigated. To this end, a hundred kHz range low-frequency wave was used to reduce the wave attenuation within an inner body medium. A method was investigated for the reconstruction of the image with the smallest possible number of path data around the abdominal surface. Specifically, the data from a strong scattering spinal cord should be avoided. To fulfill the requirement, the smoothed path algebraic reconstruction technique was introduced. The validity of this method was examined both on the numerically synthesized data and the experimentally measured data for the phantom specimen and actual human subject. It was shown that an abdominal tomographic sound speed image could be successfully obtained by preparing only 32 transducer locations at the circumference around the abdominal surface and their combination of less than 100 number of observation path data as well as by avoiding the data intersecting the spinal cord. In addition, fat regions were extracted having a sound speed lower than the threshold value to demonstrate the possibility of this method for metabolic syndrome diagnosis.

Assessment of Normal Eyeball Protrusion Using Computed Tomographic Imaging and Three-Dimensional Reconstruction in Korean Adults.

PubMed

Shin, Kang-Jae; Gil, Young-Chun; Lee, Shin-Hyo; Kim, Jeong-Nam; Yoo, Ja-Young; Kim, Soon-Heum; Choi, Hyun-Gon; Shin, Hyun Jin; Koh, Ki-Seok; Song, Wu-Chul

2017-01-01

The aim of the present study was to assess normal eyeball protrusion from the orbital rim using two- and three-dimensional images and demonstrate the better suitability of CT images for assessment of exophthalmos. The facial computed tomographic (CT) images of Korean adults were acquired in sagittal and transverse views. The CT images were used in reconstructing three-dimensional volume of faces using computer software. The protrusion distances from orbital rims and the diameters of eyeballs were measured in the two views of the CT image and three-dimensional volume of the face. Relative exophthalmometry was calculated by the difference in protrusion distance between the right and left sides. The eyeball protrusion was 4.9 and 12.5 mm in sagittal and transverse views, respectively. The protrusion distances were 2.9 mm in the three-dimensional volume of face. There were no significant differences between right and left sides in the degree of protrusion, and the difference was within 2 mm in more than 90% of the subjects. The results of the present study will provide reliable criteria for precise diagnosis and postoperative monitoring using CT imaging of diseases such as thyroid-associated ophthalmopathy and orbital tumors.

Navigation-supported diagnosis of the substantia nigra by matching midbrain sonography and MRI

NASA Astrophysics Data System (ADS)

Salah, Zein; Weise, David; Preim, Bernhard; Classen, Joseph; Rose, Georg

2012-03-01

Transcranial sonography (TCS) is a well-established neuroimaging technique that allows for visualizing several brainstem structures, including the substantia nigra, and helps for the diagnosis and differential diagnosis of various movement disorders, especially in Parkinsonian syndromes. However, proximate brainstem anatomy can hardly be recognized due to the limited image quality of B-scans. In this paper, a visualization system for the diagnosis of the substantia nigra is presented, which utilizes neuronavigated TCS to reconstruct tomographical slices from registered MRI datasets and visualizes them simultaneously with corresponding TCS planes in realtime. To generate MRI tomographical slices, the tracking data of the calibrated ultrasound probe are passed to an optimized slicing algorithm, which computes cross sections at arbitrary positions and orientations from the registered MRI dataset. The extracted MRI cross sections are finally fused with the region of interest from the ultrasound image. The system allows for the computation and visualization of slices at a near real-time rate. Primary tests of the system show an added value to the pure sonographic imaging. The system also allows for reconstructing volumetric (3D) ultrasonic data of the region of interest, and thus contributes to enhancing the diagnostic yield of midbrain sonography.

Laser microbeam CT scanning of dosimetry gels

NASA Astrophysics Data System (ADS)

Maryanski, Marek J.; Ranade, Manisha K.

2001-06-01

A novel design of an optical tomographic scanner is described that can be used for 3D mapping of optical attenuation coefficient within translucent cylindrical objects with spatial resolution on the order of 100 microns. Our scanner design utilizes the cylindrical geometry of the imaged object to obtain the desired paths of the scanning light rays. A rotating mirror and a photodetector are placed at two opposite foci of the translucent cylinder that acts as a cylindrical lens. A He-Ne laser beam passes first through a focusing lens and then is reflected by the rotating mirror, so as to scan the interior of the cylinder with focused and parallel paraxial rays that are subsequently collected by the photodetector to produce the projection data, as the cylinder rotates in small angle increments between projections. Filtered backprojection is then used to reconstruct planar distributions of optical attenuation coefficient in the cylinder. Multiplanar scans are used to obtain a complete 3D tomographic reconstruction. Among other applications, the scanner can be used in radiation therapy dosimetry and quality assurance for mapping 3D radiation dose distributions in various types of tissue-equivalent gel phantoms that change their optical attenuation coefficients in proportion to the absorbed radiation dose.

Singular value decomposition: a diagnostic tool for ill-posed inverse problems in optical computed tomography

NASA Astrophysics Data System (ADS)

Lanen, Theo A.; Watt, David W.

1995-10-01

Singular value decomposition has served as a diagnostic tool in optical computed tomography by using its capability to provide insight into the condition of ill-posed inverse problems. Various tomographic geometries are compared to one another through the singular value spectrum of their weight matrices. The number of significant singular values in the singular value spectrum of a weight matrix is a quantitative measure of the condition of the system of linear equations defined by a tomographic geometery. The analysis involves variation of the following five parameters, characterizing a tomographic geometry: 1) the spatial resolution of the reconstruction domain, 2) the number of views, 3) the number of projection rays per view, 4) the total observation angle spanned by the views, and 5) the selected basis function. Five local basis functions are considered: the square pulse, the triangle, the cubic B-spline, the Hanning window, and the Gaussian distribution. Also items like the presence of noise in the views, the coding accuracy of the weight matrix, as well as the accuracy of the accuracy of the singular value decomposition procedure itself are assessed.

Multispectral x-ray CT: multivariate statistical analysis for efficient reconstruction

NASA Astrophysics Data System (ADS)

Kheirabadi, Mina; Mustafa, Wail; Lyksborg, Mark; Lund Olsen, Ulrik; Bjorholm Dahl, Anders

2017-10-01

Recent developments in multispectral X-ray detectors allow for an efficient identification of materials based on their chemical composition. This has a range of applications including security inspection, which is our motivation. In this paper, we analyze data from a tomographic setup employing the MultiX detector, that records projection data in 128 energy bins covering the range from 20 to 160 keV. Obtaining all information from this data requires reconstructing 128 tomograms, which is computationally expensive. Instead, we propose to reduce the dimensionality of projection data prior to reconstruction and reconstruct from the reduced data. We analyze three linear methods for dimensionality reduction using a dataset with 37 equally-spaced projection angles. Four bottles with different materials are recorded for which we are able to obtain similar discrimination of their content using a very reduced subset of tomograms compared to the 128 tomograms that would otherwise be needed without dimensionality reduction.

Comparative analysis of fluorescent angiography, computed tomographic angiography and magnetic resonance angiography for planning autologous breast reconstruction

PubMed Central

Chae, Michael P.; Hunter-Smith, David J.

2015-01-01

Background The high incidence of breast cancer and growing number of breast cancer patients undergoing mastectomy has led to breast reconstruction becoming an important part of holistic treatment for these patients. In planning autologous reconstructions, preoperative assessment of donor site microvascular anatomy with advanced imaging modalities has assisted in the appropriate selection of flap donor site, individual perforators, and lead to an overall improvement in flap outcomes. In this review, we compare the accuracy of fluorescent angiography, computed tomographic angiography (CTA), and magnetic resonance angiography (MRA) and their impact on clinical outcomes. Methods A review of the published English literature dating from 1950 to 2015 using databases, such as PubMed, Medline, Web of Science, and EMBASE was undertaken. Results Fluorescent angiography is technically limited by its inability to evaluate deep-lying perforators and hence, it has a minimal role in the preoperative setting. However, it may be useful intraoperatively in evaluating microvascular anastomotic patency and the mastectomy skin perfusion. CTA is currently widely considered the standard, due to its high accuracy and reliability. Multiple studies have demonstrated its ability to improve clinical outcomes, such as operative length and flap complications. However, concerns surrounding exposure to radiation and nephrotoxic contrast agents exist. MRA has been explored, however despite recent advances, the image quality of MRA is considered inferior to CTA. Conclusions Preoperative imaging is an essential component in planning autologous breast reconstruction. Fluorescent angiography presents minimal role as a preoperative imaging modality, but may be a useful intraoperative adjunct to assess the anastomosis and the mastectomy skin perfusion. Currently, CTA is the gold standard preoperatively. MRA has a role, particularly for women of younger age, iodine allergy, and renal impairment. PMID:26005648

Tomographic phase analysis to detect the site of accessory conduction pathway in Wolff-Parkinson-White syndrome

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

Nakajima, K.; Bunko, H.; Tada, A.

1984-01-01

Phase analysis has been applied to Wolff-Parkinson-White syndrome (WPW) to detect the site of accessory conduction pathway (ACP); however, there was a limitation to estimate the precise location of ACP by planar phase analysis. In this study, the authors applied phase analysis to gated blood pool tomography. Twelve patients with WPW who underwent epicardial mapping and surgical division of ACP were studied by both of gated emission computed tomography (GECT) and routine gated blood pool study (GBPS). The GBPS was performed with Tc-99m red blood cells in multiple projections; modified left anterior oblique, right anterior oblique and/or left lateral views.more » In GECT, short axial, horizontal and vertical long axial blood pool images were reconstructed. Phase analysis was performed using fundamental frequency of the Fourier transform in both GECT and GBPS images, and abnormal initial contractions on both the planar and tomographic phase analysis were compared with the location of surgically confirmed ACPs. In planar phase analysis, abnormal initial phase was identified in 7 out of 12 (58%) patients, while in tomographic phase analysis, the localization of ACP was predicted in 11 out of 12 (92%) patients. Tomographic phase analysis is superior to planar phase images in 8 out of 12 patients to estimate the location of ACP. Phase analysis by GECT can avoid overlap of blood pool in cardiac chambers and has advantage to identify the propagation of phase three-dimensionally. Tomographic phase analysis is a good adjunctive method for patients with WPW to estimate the site of ACP.« less

Building a symbolic computer algebra toolbox to compute 2D Fourier transforms in polar coordinates

PubMed Central

Dovlo, Edem; Baddour, Natalie

2015-01-01

The development of a symbolic computer algebra toolbox for the computation of two dimensional (2D) Fourier transforms in polar coordinates is presented. Multidimensional Fourier transforms are widely used in image processing, tomographic reconstructions and in fact any application that requires a multidimensional convolution. By examining a function in the frequency domain, additional information and insights may be obtained. The advantages of our method include: • The implementation of the 2D Fourier transform in polar coordinates within the toolbox via the combination of two significantly simpler transforms. • The modular approach along with the idea of lookup tables implemented help avoid the issue of indeterminate results which may occur when attempting to directly evaluate the transform. • The concept also helps prevent unnecessary computation of already known transforms thereby saving memory and processing time. PMID:26150988

Development of the algorithm of measurement data and tomographic section reconstruction results processing for evaluating the respiratory activity of the lungs using the multi-angle electric impedance tomography

NASA Astrophysics Data System (ADS)

Aleksanyan, Grayr; Shcherbakov, Ivan; Kucher, Artem; Sulyz, Andrew

2018-04-01

Continuous monitoring of the patient's breathing by the method of multi-angle electric impedance tomography allows to obtain images of conduction change in the chest cavity during the monitoring. Direct analysis of images is difficult due to the large amount of information and low resolution images obtained by multi-angle electrical impedance tomography. This work presents a method for obtaining a graph of respiratory activity of the lungs based on the results of continuous lung monitoring using the multi-angle electrical impedance tomography method. The method makes it possible to obtain a graph of the respiratory activity of the left and right lungs separately, as well as a summary graph, to which it is possible to apply methods of processing the results of spirography.

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

Di, Zichao; Leyffer, Sven; Wild, Stefan M.

Fluorescence tomographic reconstruction, based on the detection of photons coming from fluorescent emission, can be used for revealing the internal elemental composition of a sample. On the other hand, conventional X-ray transmission tomography can be used for reconstructing the spatial distribution of the absorption coefficient inside a sample. In this work, we integrate both X-ray fluorescence and X-ray transmission data modalities and formulate a nonlinear optimization-based approach for reconstruction of the elemental composition of a given object. This model provides a simultaneous reconstruction of both the quantitative spatial distribution of all elements and the absorption effect in the sample. Mathematicallymore » speaking, we show that compared with the single-modality inversion (i.e., the X-ray transmission or fluorescence alone), the joint inversion provides a better-posed problem, which implies a better recovery. Therefore, the challenges in X-ray fluorescence tomography arising mainly from the effects of self-absorption in the sample are partially mitigated. The use of this technique is demonstrated on the reconstruction of several synthetic samples.« less

Image-guided filtering for improving photoacoustic tomographic image reconstruction.

PubMed

Awasthi, Navchetan; Kalva, Sandeep Kumar; Pramanik, Manojit; Yalavarthy, Phaneendra K

2018-06-01

Several algorithms exist to solve the photoacoustic image reconstruction problem depending on the expected reconstructed image features. These reconstruction algorithms promote typically one feature, such as being smooth or sharp, in the output image. Combining these features using a guided filtering approach was attempted in this work, which requires an input and guiding image. This approach act as a postprocessing step to improve commonly used Tikhonov or total variational regularization method. The result obtained from linear backprojection was used as a guiding image to improve these results. Using both numerical and experimental phantom cases, it was shown that the proposed guided filtering approach was able to improve (as high as 11.23 dB) the signal-to-noise ratio of the reconstructed images with the added advantage being computationally efficient. This approach was compared with state-of-the-art basis pursuit deconvolution as well as standard denoising methods and shown to outperform them. (2018) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE).

syris: a flexible and efficient framework for X-ray imaging experiments simulation.

PubMed

Faragó, Tomáš; Mikulík, Petr; Ershov, Alexey; Vogelgesang, Matthias; Hänschke, Daniel; Baumbach, Tilo

2017-11-01

An open-source framework for conducting a broad range of virtual X-ray imaging experiments, syris, is presented. The simulated wavefield created by a source propagates through an arbitrary number of objects until it reaches a detector. The objects in the light path and the source are time-dependent, which enables simulations of dynamic experiments, e.g. four-dimensional time-resolved tomography and laminography. The high-level interface of syris is written in Python and its modularity makes the framework very flexible. The computationally demanding parts behind this interface are implemented in OpenCL, which enables fast calculations on modern graphics processing units. The combination of flexibility and speed opens new possibilities for studying novel imaging methods and systematic search of optimal combinations of measurement conditions and data processing parameters. This can help to increase the success rates and efficiency of valuable synchrotron beam time. To demonstrate the capabilities of the framework, various experiments have been simulated and compared with real data. To show the use case of measurement and data processing parameter optimization based on simulation, a virtual counterpart of a high-speed radiography experiment was created and the simulated data were used to select a suitable motion estimation algorithm; one of its parameters was optimized in order to achieve the best motion estimation accuracy when applied on the real data. syris was also used to simulate tomographic data sets under various imaging conditions which impact the tomographic reconstruction accuracy, and it is shown how the accuracy may guide the selection of imaging conditions for particular use cases.

Development of time-resolved reflectance diffuse optical tomography for breast cancer monitoring

NASA Astrophysics Data System (ADS)

Yoshimoto, Kenji; Ohmae, Etsuko; Yamashita, Daisuke; Suzuki, Hiroaki; Homma, Shu; Mimura, Tetsuya; Wada, Hiroko; Suzuki, Toshihiko; Yoshizawa, Nobuko; Nasu, Hatsuko; Ogura, Hiroyuki; Sakahara, Harumi; Yamashita, Yutaka; Ueda, Yukio

2017-02-01

We developed a time-resolved reflectance diffuse optical tomography (RDOT) system to measure tumor responses to chemotherapy in breast cancer patients at the bedside. This system irradiates the breast with a three-wavelength pulsed laser (760, 800, and 830 nm) through a source fiber specified by an optical switch. The light collected by detector fibers is guided to a detector unit consisting of variable attenuators and photomultiplier tubes. Thirteen irradiation and 12 detection points were set to a measurement area of 50 × 50 mm for a hand-held probe. The data acquisition time required to obtain the temporal profiles within the measurement area is about 2 minutes. The RDOT system generates topographic and tomographic images of tissue properties such as hemoglobin concentration and tissue oxygen saturation using two imaging methods. Topographic images are obtained from the optical properties determined for each source-detector pair using a curve-fitting method based on the photon diffusion theory, while tomographic images are reconstructed using an iterative image reconstruction method. In an experiment using a tissue-like solid phantom, a tumor-like cylindrical target (15 mm diameter, 15 mm high) embedded in a breast tissue-like background medium was successfully reconstructed. Preliminary clinical measurements indicated that the tumor in a breast cancer patient was detected as a region of high hemoglobin concentration. In addition, the total hemoglobin concentration decreased during chemotherapy. These results demonstrate the potential of RDOT for evaluating the effectiveness of chemotherapy in patients with breast cancer.

Conical Fourier shell correlation applied to electron tomograms.

PubMed

Diebolder, C A; Faas, F G A; Koster, A J; Koning, R I

2015-05-01

The resolution of electron tomograms is anisotropic due to geometrical constraints during data collection, such as the limited tilt range and single axis tilt series acquisition. Acquisition of dual axis tilt series can decrease these effects. However, in cryo-electron tomography, to limit the electron radiation damage that occurs during imaging, the total dose should not increase and must be fractionated over the two tilt series. Here we set out to determine whether it is beneficial fractionate electron dose for recording dual axis cryo electron tilt series or whether it is better to perform single axis acquisition. To assess the quality of tomographic reconstructions in different directions here we introduce conical Fourier shell correlation (cFSCe/o). Employing cFSCe/o, we compared the resolution isotropy of single-axis and dual-axis (cryo-)electron tomograms using even/odd split data sets. We show that the resolution of dual-axis simulated and cryo-electron tomograms in the plane orthogonal to the electron beam becomes more isotropic compared to single-axis tomograms and high resolution peaks along the tilt axis disappear. cFSCe/o also allowed us to compare different methods for the alignment of dual-axis tomograms. We show that different tomographic reconstruction programs produce different anisotropic resolution in dual axis tomograms. We anticipate that cFSCe/o can also be useful for comparisons of acquisition and reconstruction parameters, and different hardware implementations. Copyright © 2015 Elsevier Inc. All rights reserved.

Why do commercial CT scanners still employ traditional, filtered back-projection for image reconstruction?

PubMed Central

Pan, Xiaochuan; Sidky, Emil Y; Vannier, Michael

2010-01-01

Despite major advances in x-ray sources, detector arrays, gantry mechanical design and especially computer performance, one component of computed tomography (CT) scanners has remained virtually constant for the past 25 years—the reconstruction algorithm. Fundamental advances have been made in the solution of inverse problems, especially tomographic reconstruction, but these works have not been translated into clinical and related practice. The reasons are not obvious and seldom discussed. This review seeks to examine the reasons for this discrepancy and provides recommendations on how it can be resolved. We take the example of field of compressive sensing (CS), summarizing this new area of research from the eyes of practical medical physicists and explaining the disconnection between theoretical and application-oriented research. Using a few issues specific to CT, which engineers have addressed in very specific ways, we try to distill the mathematical problem underlying each of these issues with the hope of demonstrating that there are interesting mathematical problems of general importance that can result from in depth analysis of specific issues. We then sketch some unconventional CT-imaging designs that have the potential to impact on CT applications, if the link between applied mathematicians and engineers/physicists were stronger. Finally, we close with some observations on how the link could be strengthened. There is, we believe, an important opportunity to rapidly improve the performance of CT and related tomographic imaging techniques by addressing these issues. PMID:20376330

TOPICAL REVIEW: Why do commercial CT scanners still employ traditional, filtered back-projection for image reconstruction?

NASA Astrophysics Data System (ADS)

Pan, Xiaochuan; Sidky, Emil Y.; Vannier, Michael

2009-12-01

Despite major advances in x-ray sources, detector arrays, gantry mechanical design and especially computer performance, one component of computed tomography (CT) scanners has remained virtually constant for the past 25 years—the reconstruction algorithm. Fundamental advances have been made in the solution of inverse problems, especially tomographic reconstruction, but these works have not been translated into clinical and related practice. The reasons are not obvious and seldom discussed. This review seeks to examine the reasons for this discrepancy and provides recommendations on how it can be resolved. We take the example of field of compressive sensing (CS), summarizing this new area of research from the eyes of practical medical physicists and explaining the disconnection between theoretical and application-oriented research. Using a few issues specific to CT, which engineers have addressed in very specific ways, we try to distill the mathematical problem underlying each of these issues with the hope of demonstrating that there are interesting mathematical problems of general importance that can result from in depth analysis of specific issues. We then sketch some unconventional CT-imaging designs that have the potential to impact on CT applications, if the link between applied mathematicians and engineers/physicists were stronger. Finally, we close with some observations on how the link could be strengthened. There is, we believe, an important opportunity to rapidly improve the performance of CT and related tomographic imaging techniques by addressing these issues.

ISC-EHB: Reconstruction of a robust earthquake dataset

NASA Astrophysics Data System (ADS)

Weston, J.; Engdahl, E. R.; Harris, J.; Di Giacomo, D.; Storchak, D. A.

2018-04-01

The EHB Bulletin of hypocentres and associated travel-time residuals was originally developed with procedures described by Engdahl, Van der Hilst and Buland (1998) and currently ends in 2008. It is a widely used seismological dataset, which is now expanded and reconstructed, partly by exploiting updated procedures at the International Seismological Centre (ISC), to produce the ISC-EHB. The reconstruction begins in the modern period (2000-2013) to which new and more rigorous procedures for event selection, data preparation, processing, and relocation are applied. The selection criteria minimise the location bias produced by unmodelled 3D Earth structure, resulting in events that are relatively well located in any given region. Depths of the selected events are significantly improved by a more comprehensive review of near station and secondary phase travel-time residuals based on ISC data, especially for the depth phases pP, pwP and sP, as well as by a rigorous review of the event depths in subduction zone cross sections. The resulting cross sections and associated maps are shown to provide details of seismicity in subduction zones in much greater detail than previously achievable. The new ISC-EHB dataset will be especially useful for global seismicity studies and high-frequency regional and global tomographic inversions.

Patient specific pointer tool for corrective osteotomy: Quality of symmetry based planning and case study of ulnar reconstruction surgery.

PubMed

Mueller, Samuel; Kahrs, Lueder A; Gaa, Johannes; Ortmaier, Tobias; Clausen, Jan-Dierk; Krettek, Christian

2017-07-01

Malunion after forearm fractures are described to appear in 2% to 10% of cases. Reconstructive surgeries ensure adequate anatomical repositioning. Their importance derives from the fact that malunion can often lead to severe pain as well as deformities causing loss of function and aesthetic issues not only in the forearm, but also the wrist and elbow joint. In this paper a clinical case will be presented using a Patient Specific Instrument (PSI) as navigational aid for reconstructive surgery after malunion of a proximal ulnar fracture combined with allograft surgery of the radial head and radial condyle due to chronic traumatic radial head luxation (Monteggia fracture). A planning method based on symmetry is described and evaluated on twelve Computed Tomographic (CT) data sets of intact forearms. The absolute point to point deviation at distal end of the ulnar styloid process was used as a characteristic value for accuracy evaluation. It is 7.9±4.9mm when using only the proximal end of the ulna for registration. The simulated change of ulnar variance is -1.4±1.9mm. Design and concept of the PSI are proven in a clinical trial. Copyright © 2017 Elsevier Ltd. All rights reserved.

A new probe using hybrid virus-dye nanoparticles for near-infrared fluorescence tomography

NASA Astrophysics Data System (ADS)

Wu, Changfeng; Barnhill, Hannah; Liang, Xiaoping; Wang, Qian; Jiang, Huabei

2005-11-01

A fluorescent probe based on bionanoparticle cowpea mosaic virus has been developed for near-infrared fluorescence tomography. A unique advantage of this probe is that over 30 dye molecules can be loaded onto each viral nanoparticle with an average diameter of 30 nm, making high local dye concentration (∼1.8 mM) possible without significant fluorescence quenching. This ability of high loading of local dye concentration would increase the signal-to-noise ratio considerably, thus sensitivity for detection. We demonstrate successful tomographic fluorescence imaging of a target containing the virus-dye nanoparticles embedded in a tissue-like phantom. Tomographic fluorescence data were obtained through a multi-channel frequency-domain system and the spatial maps of fluorescence quantum yield were recovered with a finite-element-based reconstruction algorithm.

A new apparatus for electron tomography in the scanning electron microscope

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

Morandi, V., E-mail: morandi@bo.imm.cnr.it; Maccagnani, P.; Masini, L.

2015-06-23

The three-dimensional reconstruction of a microscopic specimen has been obtained by applying the tomographic algorithm to a set of images acquired in a Scanning Electron Microscope. This result was achieved starting from a series of projections obtained by stepwise rotating the sample under the beam raster. The Scanning Electron Microscope was operated in the scanning-transmission imaging mode, where the intensity of the transmitted electron beam is a monotonic function of the local mass-density and thickness of the specimen. The detection strategy has been implemented and tailored in order to maintain the projection requirement over the large tilt range, as requiredmore » by the tomographic workflow. A Si-based electron detector and an eucentric-rotation specimen holder have been specifically developed for the purpose.« less

Singular value decomposition for the truncated Hilbert transform

NASA Astrophysics Data System (ADS)

Katsevich, A.

2010-11-01

Starting from a breakthrough result by Gelfand and Graev, inversion of the Hilbert transform became a very important tool for image reconstruction in tomography. In particular, their result is useful when the tomographic data are truncated and one deals with an interior problem. As was established recently, the interior problem admits a stable and unique solution when some a priori information about the object being scanned is available. The most common approach to solving the interior problem is based on converting it to the Hilbert transform and performing analytic continuation. Depending on what type of tomographic data are available, one gets different Hilbert inversion problems. In this paper, we consider two such problems and establish singular value decomposition for the operators involved. We also propose algorithms for performing analytic continuation.

Fisher's method of scoring in statistical image reconstruction: comparison of Jacobi and Gauss-Seidel iterative schemes.

PubMed

Hudson, H M; Ma, J; Green, P

1994-01-01

Many algorithms for medical image reconstruction adopt versions of the expectation-maximization (EM) algorithm. In this approach, parameter estimates are obtained which maximize a complete data likelihood or penalized likelihood, in each iteration. Implicitly (and sometimes explicitly) penalized algorithms require smoothing of the current reconstruction in the image domain as part of their iteration scheme. In this paper, we discuss alternatives to EM which adapt Fisher's method of scoring (FS) and other methods for direct maximization of the incomplete data likelihood. Jacobi and Gauss-Seidel methods for non-linear optimization provide efficient algorithms applying FS in tomography. One approach uses smoothed projection data in its iterations. We investigate the convergence of Jacobi and Gauss-Seidel algorithms with clinical tomographic projection data.

GPU-accelerated iterative reconstruction from Compton scattered data using a matched pair of conic projector and backprojector.

PubMed

Nguyen, Van-Giang; Lee, Soo-Jin

2016-07-01

Iterative reconstruction from Compton scattered data is known to be computationally more challenging than that from conventional line-projection based emission data in that the gamma rays that undergo Compton scattering are modeled as conic projections rather than line projections. In conventional tomographic reconstruction, to parallelize the projection and backprojection operations using the graphics processing unit (GPU), approximated methods that use an unmatched pair of ray-tracing forward projector and voxel-driven backprojector have been widely used. In this work, we propose a new GPU-accelerated method for Compton camera reconstruction which is more accurate by using exactly matched pair of projector and backprojector. To calculate conic forward projection, we first sample the cone surface into conic rays and accumulate the intersecting chord lengths of the conic rays passing through voxels using a fast ray-tracing method (RTM). For conic backprojection, to obtain the true adjoint of the conic forward projection, while retaining the computational efficiency of the GPU, we use a voxel-driven RTM which is essentially the same as the standard RTM used for the conic forward projector. Our simulation results show that, while the new method is about 3 times slower than the approximated method, it is still about 16 times faster than the CPU-based method without any loss of accuracy. The net conclusion is that our proposed method is guaranteed to retain the reconstruction accuracy regardless of the number of iterations by providing a perfectly matched projector-backprojector pair, which makes iterative reconstruction methods for Compton imaging faster and more accurate. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Variational 3D-PIV with sparse descriptors

NASA Astrophysics Data System (ADS)

Lasinger, Katrin; Vogel, Christoph; Pock, Thomas; Schindler, Konrad

2018-06-01

3D particle imaging velocimetry (3D-PIV) aims to recover the flow field in a volume of fluid, which has been seeded with tracer particles and observed from multiple camera viewpoints. The first step of 3D-PIV is to reconstruct the 3D locations of the tracer particles from synchronous views of the volume. We propose a new method for iterative particle reconstruction, in which the locations and intensities of all particles are inferred in one joint energy minimization. The energy function is designed to penalize deviations between the reconstructed 3D particles and the image evidence, while at the same time aiming for a sparse set of particles. We find that the new method, without any post-processing, achieves significantly cleaner particle volumes than a conventional, tomographic MART reconstruction, and can handle a wide range of particle densities. The second step of 3D-PIV is to then recover the dense motion field from two consecutive particle reconstructions. We propose a variational model, which makes it possible to directly include physical properties, such as incompressibility and viscosity, in the estimation of the motion field. To further exploit the sparse nature of the input data, we propose a novel, compact descriptor of the local particle layout. Hence, we avoid the memory-intensive storage of high-resolution intensity volumes. Our framework is generic and allows for a variety of different data costs (correlation measures) and regularizers. We quantitatively evaluate it with both the sum of squared differences and the normalized cross-correlation, respectively with both a hard and a soft version of the incompressibility constraint.

Pseudodynamic systems approach based on a quadratic approximation of update equations for diffuse optical tomography.

PubMed

Biswas, Samir Kumar; Kanhirodan, Rajan; Vasu, Ram Mohan; Roy, Debasish

2011-08-01

We explore a pseudodynamic form of the quadratic parameter update equation for diffuse optical tomographic reconstruction from noisy data. A few explicit and implicit strategies for obtaining the parameter updates via a semianalytical integration of the pseudodynamic equations are proposed. Despite the ill-posedness of the inverse problem associated with diffuse optical tomography, adoption of the quadratic update scheme combined with the pseudotime integration appears not only to yield higher convergence, but also a muted sensitivity to the regularization parameters, which include the pseudotime step size for integration. These observations are validated through reconstructions with both numerically generated and experimentally acquired data.

Tomographic reconstruction of layered tissue structures

NASA Astrophysics Data System (ADS)

Hielscher, Andreas H.; Azeez-Jan, Mohideen; Bartel, Sebastian

2001-11-01

In recent years the interest in the determination of optical properties of layered tissue structure has resurfaced. Applications include, for example, studies on layered skin tissue and underlying muscles, imaging of the brain underneath layers of skin, skull, and meninges, and imaging of the fetal head in utero beneath the layered structures of the maternal abdomen. In this work we approach the problem of layered structures in the framework of model-based iterative image reconstruction schemes. These schemes are currently developed to determine the optical properties inside tissue from measurement on the surface. If applied to layered structure these techniques yield substantial improvements over currently available semi-analytical approaches.

Analysis of the multigroup model for muon tomography based threat detection

NASA Astrophysics Data System (ADS)

Perry, J. O.; Bacon, J. D.; Borozdin, K. N.; Fabritius, J. M.; Morris, C. L.

2014-02-01

We compare different algorithms for detecting a 5 cm tungsten cube using cosmic ray muon technology. In each case, a simple tomographic technique was used for position reconstruction, but the scattering angles were used differently to obtain a density signal. Receiver operating characteristic curves were used to compare images made using average angle squared, median angle squared, average of the squared angle, and a multi-energy group fit of the angular distributions for scenes with and without a 5 cm tungsten cube. The receiver operating characteristic curves show that the multi-energy group treatment of the scattering angle distributions is the superior method for image reconstruction.

Studies of discrete symmetries in a purely leptonic system using the Jagiellonian Positron Emission Tomograph

NASA Astrophysics Data System (ADS)

Moskal, P.; Alfs, D.; Bednarski, T.; Białas, P.; Curceanu, C.; Czerwiński, E.; Dulski, K.; Gajos, A.; Głowacz, B.; Gupta-Sharma, N.; Gorgol, M.; Hiesmayr, B. C.; Jasińska, B.; Kamińska, D.; Khreptak, O.; Korcyl, G.; Kowalski, P.; Krzemień, W.; Krawczyk, N.; Kubicz, E.; Mohammed, M.; Niedźwiecki, Sz.; Pawlik-Niedńwiecka, M.; Raczyński, L.; Rudy, Z.; Silarski, M.; Smyrski, J.; Wieczorek, A.; Wiślicki, W.; Zgardzińska, B.; Zieliński, M.

2016-11-01

Discrete symmetries such as parity (P), charge-conjugation (C) and time reversal (T) are of fundamental importance in physics and cosmology. Breaking of charge conjugation symmetry (C) and its combination with parity (CP) constitute necessary conditions for the existence of the asymmetry between matter and antimatter in the observed Universe. The presently known sources of discrete symmetries violations can account for only a tiny fraction of the excess of matter over antimatter. So far CP and T symmetries violations were observed only for systems involving quarks and they were never reported for the purely leptonic objects. In this article we describe briefly an experimental proposal for the test of discrete symmetries in the decays of positronium atom which is made exclusively of leptons. The experiments are conducted by means of the Jagiellonian Positron Emission Tomograph (J-PET) which is constructed from strips of plastic scintillators enabling registration of photons from the positronium annihilation. J-PET tomograph together with the positronium target system enable to measure expectation values for the discrete symmetries odd operators constructed from (i) spin vector of the ortho-positronium atom, (ii) momentum vectors of photons originating from the decay of positronium, and (iii) linear polarization direction of annihilation photons. Linearly polarized positronium will be produced in the highly porous aerogel or polymer targets, exploiting longitudinally polarized positrons emitted by the sodium 22Na isotope. Information about the polarization vector of orthopositronium will be available on the event by event basis and will be reconstructed from the known position of the positron source and the reconstructed position of the orthopositronium annihilation. In 2016 the first tests and calibration runs are planned, and the data collection with high statistics will commence in the year 2017.

SXR measurement and W transport survey using GEM tomographic system on WEST

NASA Astrophysics Data System (ADS)

Mazon, D.; Jardin, A.; Malard, P.; Chernyshova, M.; Coston, C.; Malard, P.; O'Mullane, M.; Czarski, T.; Malinowski, K.; Faisse, F.; Ferlay, F.; Verger, J. M.; Bec, A.; Larroque, S.; Kasprowicz, G.; Wojenski, A.; Pozniak, K.

2017-11-01

Measuring Soft X-Ray (SXR) radiation (0.1-20 keV) of fusion plasmas is a standard way of accessing valuable information on particle transport. Since heavy impurities like tungsten (W) could degrade plasma core performances and cause radiative collapses, it is necessary to develop new diagnostics to be able to monitor the impurity distribution in harsh fusion environments like ITER. A gaseous detector with energy discrimination would be a very good candidate for this purpose. The design and implementation of a new SXR diagnostic developed for the WEST project, based on a triple Gas Electron Multiplier (GEM) detector is presented. This detector works in photon counting mode and presents energy discrimination capabilities. The SXR system is composed of two 1D cameras (vertical and horizontal views respectively), located in the same poloidal cross-section to allow for tomographic reconstruction. An array (20 cm × 2 cm) consists of up to 128 detectors in front of a beryllium pinhole (equipped with a 1 mm diameter diaphragm) inserted at about 50 cm depth inside a cooled thimble in order to retrieve a wide plasma view. Acquisition of low energy spectrum is insured by a helium buffer installed between the pinhole and the detector. Complementary cooling systems (water) are used to maintain a constant temperature (25oC) inside the thimble. Finally a real-time automatic extraction system has been developed to protect the diagnostic during baking phases or any overheating unwanted events. Preliminary simulations of plasma emissivity and W distribution have been performed for WEST using a recently developed synthetic diagnostic coupled to a tomographic algorithm based on the minimum Fisher information (MFI) inversion method. First GEM acquisitions are presented as well as estimation of transport effect in presence of ICRH on W density reconstruction capabilities of the GEM.

Stress wave velocity patterns in the longitudinal-radial plane of trees for defect diagnosis

Treesearch

Guanghui Li; Xiang Weng; Xiaocheng Du; Xiping Wang; Hailin Feng

2016-01-01

Acoustic tomography for urban tree inspection typically uses stress wave data to reconstruct tomographic images for the trunk cross section using interpolation algorithm. This traditional technique does not take into account the stress wave velocity patterns along tree height. In this study, we proposed an analytical model for the wave velocity in the longitudinal–...

Measurement scheme for purity based on two two-body gates

NASA Astrophysics Data System (ADS)

Nakazato, H.; Tanaka, T.; Yuasa, K.; Florio, G.; Pascazio, S.

2012-04-01

A scheme for measuring the purity of a quantum system with a finite number of levels is presented. The method makes use of two swap gates and hinges only on measurements performed on a reference system, prepared in a certain pure state and coupled with the target system. Neither tomographic methods, with the complete reconstruction of the state, nor interferometric setups are needed.

Upgraded X-ray topography and microtomography beamline at the Kurchatov synchrotron radiation source

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

Senin, R. A., E-mail: senin_ra@rrcki.ru; Khlebnikov, A. S.; Vyazovetskova, A. E.

2013-05-15

An upgraded X-ray Topography and Microtomography (XRT-MT) station is described, the parameters of the optical schemes and detectors are given, and the experimental possibilities of the station are analyzed. Examples of tomographic reconstructions are reported which demonstrate spatial resolutions of 2.5 and 10 {mu}m at fields of view of 2.5 and 10 mm, respectively.

Comment on "Assessing Discrepancies Between Previous Plate Kinematic Models of Mesozoic Iberia and Their Constraints" by Barnett-Moore Et Al.

NASA Astrophysics Data System (ADS)

van Hinsbergen, Douwe J. J.; Spakman, Wim; Vissers, Reinoud L. M.; van der Meer, Douwe G.

2017-12-01

In their recent paper, Barnett-Moore et al. (2016) reflect on current models of Iberian plate motion in the Jurassic and Cretaceous as well as ongoing debates on the reliability of the various types of kinematic data that form independent constraints on Iberia's motion relative to Eurasia. They question the validity of various marine geophysical, seismic, tomographic, geological, and paleomagnetic data sets from the Bay of Biscay, Central Atlantic Ocean, and Iberia for kinematic reconstruction of Iberia and conclude that neither models invoking Aptian-Albian transtension, nor compression, are consistent with currently available data. An important element in their analysis is that they discard the large paleomagnetic data set from the Jurassic and Cretaceous from Iberia based on perceived limitations of that data set. In addition, they argue that seismic tomographic images exclude a scenario of subduction in the Aptian-Albian in the Pyrenees, and based on this "question the validity of current plate reconstructions, their constraints, and geodynamic scenarios, which are in support of this scenario [e.g., Vissers et al., 2016]." We welcome the discussion raised by Barnett-Moore et al. (2016) on the reliability and usefulness of paleomagnetic data as independent constraint for Iberia's plate motion in the Mesozoic. Taking these paleomagnetic data at face value, Vissers et al. (2016) recently showed that these are consistent with an 40° counterclockwise rotation of Iberia in the Aptian, requiring up to 500 km of Aptian convergence across the Pyrenees, that is, through subduction. In this comment, we aim to critically assess whether and how the concerns on the quality of paleomagnetic data raised by Barnett-Moore et al. (2016) may allow for an alternative explanation, particularly one with a Mesozoic rotation of Iberia that is small enough so as to not requiring subduction. We also reassess whether seismic tomographic images indeed refute subduction scenarios, using 8 S wave and P wave tomographic models including those used in Barnett-Moore et al. (2016).

Deformable 3D-2D registration for CT and its application to low dose tomographic fluoroscopy

NASA Astrophysics Data System (ADS)

Flach, Barbara; Brehm, Marcus; Sawall, Stefan; Kachelrieß, Marc

2014-12-01

Many applications in medical imaging include image registration for matching of images from the same or different modalities. In the case of full data sampling, the respective reconstructed images are usually of such a good image quality that standard deformable volume-to-volume (3D-3D) registration approaches can be applied. But research in temporal-correlated image reconstruction and dose reductions increases the number of cases where rawdata are available from only few projection angles. Here, deteriorated image quality leads to non-acceptable deformable volume-to-volume registration results. Therefore a registration approach is required that is robust against a decreasing number of projections defining the target position. We propose a deformable volume-to-rawdata (3D-2D) registration method that aims at finding a displacement vector field maximizing the alignment of a CT volume and the acquired rawdata based on the sum of squared differences in rawdata domain. The registration is constrained by a regularization term in accordance with a fluid-based diffusion. Both cost function components, the rawdata fidelity and the regularization term, are optimized in an alternating manner. The matching criterion is optimized by a conjugate gradient descent for nonlinear functions, while the regularization is realized by convolution of the vector fields with Gaussian kernels. We validate the proposed method and compare it to the demons algorithm, a well-known 3D-3D registration method. The comparison is done for a range of 4-60 target projections using datasets from low dose tomographic fluoroscopy as an application example. The results show a high correlation to the ground truth target position without introducing artifacts even in the case of very few projections. In particular the matching in the rawdata domain is improved compared to the 3D-3D registration for the investigated range. The proposed volume-to-rawdata registration increases the robustness regarding sparse rawdata and provides more stable results than volume-to-volume approaches. By applying the proposed registration approach to low dose tomographic fluoroscopy it is possible to improve the temporal resolution and thus to increase the robustness of low dose tomographic fluoroscopy.

PSF reconstruction validated using on-sky CANARY data in MOAO mode

NASA Astrophysics Data System (ADS)

Martin, O. A.; Correia, C. M.; Gendron, E.; Rousset, G.; Gratadour, D.; Vidal, F.; Morris, T. J.; Basden, A. G.; Myers, R. M.; Neichel, B.; Fusco, T.

2016-07-01

CANARY is an open-loop tomographic adaptive optics (AO) demonstrator that was designed for use at the 4.2m William Herschel Telescope (WHT) in La Palma. Gearing up to extensive statistical studies of high redshifted galaxies surveyed with Multi-Object Spectrographs (MOS), the demonstrator CANARY has been designed to tackle technical challenges related to open-loop Adaptive-Optics (AO) control with mixed Natural Guide Star (NGS) and Laser Guide Star (LGS) tomography. We have developed a Point Spread Function (PSF)-Reconstruction algorithm dedicated to MOAO systems using system telemetry to estimate the PSF potentially anywhere in the observed field, a prerequisite to deconvolve AO-corrected science observations in Integral Field Spectroscopy (IFS). Additionally the ability to accurately reconstruct the PSF is the materialization of the broad and fine-detailed understanding of the residual error contributors, both atmospheric and opto-mechanical. In this paper we compare the classical PSF-r approach from Véran (1) that we take as reference on-axis using the truth-sensor telemetry to one tailored to atmospheric tomography by handling the off-axis data only. We've post-processed over 450 on-sky CANARY data sets with which we observe 92% and 88% of correlation on respectively the reconstructed Strehl Ratio (SR)/Full Width at Half Maximum (FWHM) compared to the sky values. The reference method achieves 95% and 92.5% exploiting directly the measurements of the residual phase from the Canary Truth Sensor (TS).

Maximum-Likelihood Methods for Processing Signals From Gamma-Ray Detectors

PubMed Central

Barrett, Harrison H.; Hunter, William C. J.; Miller, Brian William; Moore, Stephen K.; Chen, Yichun; Furenlid, Lars R.

2009-01-01

In any gamma-ray detector, each event produces electrical signals on one or more circuit elements. From these signals, we may wish to determine the presence of an interaction; whether multiple interactions occurred; the spatial coordinates in two or three dimensions of at least the primary interaction; or the total energy deposited in that interaction. We may also want to compute listmode probabilities for tomographic reconstruction. Maximum-likelihood methods provide a rigorous and in some senses optimal approach to extracting this information, and the associated Fisher information matrix provides a way of quantifying and optimizing the information conveyed by the detector. This paper will review the principles of likelihood methods as applied to gamma-ray detectors and illustrate their power with recent results from the Center for Gamma-ray Imaging. PMID:20107527

Review of possible applications of cosmic muon tomography

NASA Astrophysics Data System (ADS)

Checchia, P.

2016-12-01

Muon radiographic methods can be used to explore inaccessible volumes profiting of the property of muons to penetrate thick materials. An extension of the muon radiographic methods, the muon scattering tomography, was proposed for the first time in 2003 and it is based on the measurement of the multiple Coulomb scattering of muons crossing the volume under investigation. In this talk, the principles of tomographic image reconstruction are first outlined and then the experimental setup and the most adequate detectors are described. A review of the possible applications of this technique is reported, with specific reference to security in transports and monitoring of industrial processes. The technique can also be used to provide precise measurements of the properties of various materials. The experimental challenge related to this activity is discussed.

General rigid motion correction for computed tomography imaging based on locally linear embedding

NASA Astrophysics Data System (ADS)

Chen, Mianyi; He, Peng; Feng, Peng; Liu, Baodong; Yang, Qingsong; Wei, Biao; Wang, Ge

2018-02-01

The patient motion can damage the quality of computed tomography images, which are typically acquired in cone-beam geometry. The rigid patient motion is characterized by six geometric parameters and are more challenging to correct than in fan-beam geometry. We extend our previous rigid patient motion correction method based on the principle of locally linear embedding (LLE) from fan-beam to cone-beam geometry and accelerate the computational procedure with the graphics processing unit (GPU)-based all scale tomographic reconstruction Antwerp toolbox. The major merit of our method is that we need neither fiducial markers nor motion-tracking devices. The numerical and experimental studies show that the LLE-based patient motion correction is capable of calibrating the six parameters of the patient motion simultaneously, reducing patient motion artifacts significantly.

Practical implementation of tetrahedral mesh reconstruction in emission tomography

PubMed Central

Boutchko, R.; Sitek, A.; Gullberg, G. T.

2014-01-01

This paper presents a practical implementation of image reconstruction on tetrahedral meshes optimized for emission computed tomography with parallel beam geometry. Tetrahedral mesh built on a point cloud is a convenient image representation method, intrinsically three-dimensional and with a multi-level resolution property. Image intensities are defined at the mesh nodes and linearly interpolated inside each tetrahedron. For the given mesh geometry, the intensities can be computed directly from tomographic projections using iterative reconstruction algorithms with a system matrix calculated using an exact analytical formula. The mesh geometry is optimized for a specific patient using a two stage process. First, a noisy image is reconstructed on a finely-spaced uniform cloud. Then, the geometry of the representation is adaptively transformed through boundary-preserving node motion and elimination. Nodes are removed in constant intensity regions, merged along the boundaries, and moved in the direction of the mean local intensity gradient in order to provide higher node density in the boundary regions. Attenuation correction and detector geometric response are included in the system matrix. Once the mesh geometry is optimized, it is used to generate the final system matrix for ML-EM reconstruction of node intensities and for visualization of the reconstructed images. In dynamic PET or SPECT imaging, the system matrix generation procedure is performed using a quasi-static sinogram, generated by summing projection data from multiple time frames. This system matrix is then used to reconstruct the individual time frame projections. Performance of the new method is evaluated by reconstructing simulated projections of the NCAT phantom and the method is then applied to dynamic SPECT phantom and patient studies and to a dynamic microPET rat study. Tetrahedral mesh-based images are compared to the standard voxel-based reconstruction for both high and low signal-to-noise ratio projection datasets. The results demonstrate that the reconstructed images represented as tetrahedral meshes based on point clouds offer image quality comparable to that achievable using a standard voxel grid while allowing substantial reduction in the number of unknown intensities to be reconstructed and reducing the noise. PMID:23588373

Practical implementation of tetrahedral mesh reconstruction in emission tomography

NASA Astrophysics Data System (ADS)

Boutchko, R.; Sitek, A.; Gullberg, G. T.

2013-05-01

This paper presents a practical implementation of image reconstruction on tetrahedral meshes optimized for emission computed tomography with parallel beam geometry. Tetrahedral mesh built on a point cloud is a convenient image representation method, intrinsically three-dimensional and with a multi-level resolution property. Image intensities are defined at the mesh nodes and linearly interpolated inside each tetrahedron. For the given mesh geometry, the intensities can be computed directly from tomographic projections using iterative reconstruction algorithms with a system matrix calculated using an exact analytical formula. The mesh geometry is optimized for a specific patient using a two stage process. First, a noisy image is reconstructed on a finely-spaced uniform cloud. Then, the geometry of the representation is adaptively transformed through boundary-preserving node motion and elimination. Nodes are removed in constant intensity regions, merged along the boundaries, and moved in the direction of the mean local intensity gradient in order to provide higher node density in the boundary regions. Attenuation correction and detector geometric response are included in the system matrix. Once the mesh geometry is optimized, it is used to generate the final system matrix for ML-EM reconstruction of node intensities and for visualization of the reconstructed images. In dynamic PET or SPECT imaging, the system matrix generation procedure is performed using a quasi-static sinogram, generated by summing projection data from multiple time frames. This system matrix is then used to reconstruct the individual time frame projections. Performance of the new method is evaluated by reconstructing simulated projections of the NCAT phantom and the method is then applied to dynamic SPECT phantom and patient studies and to a dynamic microPET rat study. Tetrahedral mesh-based images are compared to the standard voxel-based reconstruction for both high and low signal-to-noise ratio projection datasets. The results demonstrate that the reconstructed images represented as tetrahedral meshes based on point clouds offer image quality comparable to that achievable using a standard voxel grid while allowing substantial reduction in the number of unknown intensities to be reconstructed and reducing the noise.

The Reconstruction Toolkit (RTK), an open-source cone-beam CT reconstruction toolkit based on the Insight Toolkit (ITK)

NASA Astrophysics Data System (ADS)

Rit, S.; Vila Oliva, M.; Brousmiche, S.; Labarbe, R.; Sarrut, D.; Sharp, G. C.

2014-03-01

We propose the Reconstruction Toolkit (RTK, http://www.openrtk.org), an open-source toolkit for fast cone-beam CT reconstruction, based on the Insight Toolkit (ITK) and using GPU code extracted from Plastimatch. RTK is developed by an open consortium (see affiliations) under the non-contaminating Apache 2.0 license. The quality of the platform is daily checked with regression tests in partnership with Kitware, the company supporting ITK. Several features are already available: Elekta, Varian and IBA inputs, multi-threaded Feldkamp-David-Kress reconstruction on CPU and GPU, Parker short scan weighting, multi-threaded CPU and GPU forward projectors, etc. Each feature is either accessible through command line tools or C++ classes that can be included in independent software. A MIDAS community has been opened to share CatPhan datasets of several vendors (Elekta, Varian and IBA). RTK will be used in the upcoming cone-beam CT scanner developed by IBA for proton therapy rooms. Many features are under development: new input format support, iterative reconstruction, hybrid Monte Carlo / deterministic CBCT simulation, etc. RTK has been built to freely share tomographic reconstruction developments between researchers and is open for new contributions.

Tomographic inversion techniques incorporating physical constraints for line integrated spectroscopy in stellarators and tokamaks

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

Pablant, N. A.; Bell, R. E.; Bitter, M.

2014-11-15

Accurate tomographic inversion is important for diagnostic systems on stellarators and tokamaks which rely on measurements of line integrated emission spectra. A tomographic inversion technique based on spline optimization with enforcement of constraints is described that can produce unique and physically relevant inversions even in situations with noisy or incomplete input data. This inversion technique is routinely used in the analysis of data from the x-ray imaging crystal spectrometer (XICS) installed at the Large Helical Device. The XICS diagnostic records a 1D image of line integrated emission spectra from impurities in the plasma. Through the use of Doppler spectroscopy andmore » tomographic inversion, XICS can provide profile measurements of the local emissivity, temperature, and plasma flow. Tomographic inversion requires the assumption that these measured quantities are flux surface functions, and that a known plasma equilibrium reconstruction is available. In the case of low signal levels or partial spatial coverage of the plasma cross-section, standard inversion techniques utilizing matrix inversion and linear-regularization often cannot produce unique and physically relevant solutions. The addition of physical constraints, such as parameter ranges, derivative directions, and boundary conditions, allow for unique solutions to be reliably found. The constrained inversion technique described here utilizes a modified Levenberg-Marquardt optimization scheme, which introduces a condition avoidance mechanism by selective reduction of search directions. The constrained inversion technique also allows for the addition of more complicated parameter dependencies, for example, geometrical dependence of the emissivity due to asymmetries in the plasma density arising from fast rotation. The accuracy of this constrained inversion technique is discussed, with an emphasis on its applicability to systems with limited plasma coverage.« less

Tomographic inversion techniques incorporating physical constraints for line integrated spectroscopy in stellarators and tokamaksa)

DOE PAGES

Pablant, N. A.; Bell, R. E.; Bitter, M.; ...

2014-08-08

Accurate tomographic inversion is important for diagnostic systems on stellarators and tokamaks which rely on measurements of line integrated emission spectra. A tomographic inversion technique based on spline optimization with enforcement of constraints is described that can produce unique and physically relevant inversions even in situations with noisy or incomplete input data. This inversion technique is routinely used in the analysis of data from the x-ray imaging crystal spectrometer (XICS) installed at LHD. The XICS diagnostic records a 1D image of line integrated emission spectra from impurities in the plasma. Through the use of Doppler spectroscopy and tomographic inversion, XICSmore » can provide pro file measurements of the local emissivity, temperature and plasma flow. Tomographic inversion requires the assumption that these measured quantities are flux surface functions, and that a known plasma equilibrium reconstruction is available. In the case of low signal levels or partial spatial coverage of the plasma cross-section, standard inversion techniques utilizing matrix inversion and linear-regularization often cannot produce unique and physically relevant solutions. The addition of physical constraints, such as parameter ranges, derivative directions, and boundary conditions, allow for unique solutions to be reliably found. The constrained inversion technique described here utilizes a modifi ed Levenberg-Marquardt optimization scheme, which introduces a condition avoidance mechanism by selective reduction of search directions. The constrained inversion technique also allows for the addition of more complicated parameter dependencies, for example geometrical dependence of the emissivity due to asymmetries in the plasma density arising from fast rotation. The accuracy of this constrained inversion technique is discussed, with an emphasis on its applicability to systems with limited plasma coverage.« less

Sustainable data policy for a data production facility: a work in (continual) progress

NASA Astrophysics Data System (ADS)

Ketcham, R. A.

2017-12-01

The University of Texas High-Resolution X-Ray Computed Tomography Facility (UTCT) has been producing volumetric data and data products of geological and other scientific specimens and engineering materials for over 20 years. Data volumes, both in terms of the size of individual data sets and overall facility production, have progressively grown and fluctuated near the upper boundary of what can be managed by contemporary workstations and lab-scale servers and network infrastructure, making data policy a preoccupation for our entire history. Although all projects have been archived since our first day of operation, policies on which data to keep (raw, reconstructed after corrections, processed) have varied, and been periodically revisited in consideration of the cost of curation and the likelihood of revisiting and reprocessing data when better techniques become available, such as improved artifact corrections or iterative tomographic reconstruction. Advances in instrumentation regularly make old data obsolete and more advantageous to reacquire, but the simple act of getting a sample to a scanning facility is a practical barrier that cannot be overlooked. In our experience, the main times that raw data have been revisited using improved processing to improve image quality were predictable, high-impact charismatic projects (e.g., Archaeopteryx, A. Afarensis "Lucy"). These cases actually provided the impetus for development of the new techniques (ring and beam hardening artifact reduction), which were subsequently incorporated into our data processing pipeline going forward but were rarely if ever retroactively applied to earlier data sets. The only other times raw data have been reprocessed were when reconstruction parameters were inappropriate, due to unnoticed sample features or human error, which are usually recognized fairly quickly. The optimal data retention policy thus remains an open question, although erring on the side of caution remains the default position.

Imaging a photodynamic therapy photosensitizer in vivo with a time-gated fluorescence tomography system

NASA Astrophysics Data System (ADS)

Mo, Weirong; Rohrbach, Daniel; Sunar, Ulas

2012-07-01

We report the tomographic imaging of a photodynamic therapy (PDT) photosensitizer, 2-(1-hexyloxyethyl)-2-devinyl pyropheophorbide-a (HPPH) in vivo with time-domain fluorescence diffuse optical tomography (TD-FDOT). Simultaneous reconstruction of fluorescence yield and lifetime of HPPH was performed before and after PDT. The methodology was validated in phantom experiments, and depth-resolved in vivo imaging was achieved through simultaneous three-dimensional (3-D) mappings of fluorescence yield and lifetime contrasts. The tomographic images of a human head-and-neck xenograft in a mouse confirmed the preferential uptake and retention of HPPH by the tumor 24-h post-injection. HPPH-mediated PDT induced significant changes in fluorescence yield and lifetime. This pilot study demonstrates that TD-FDOT may be a good imaging modality for assessing photosensitizer distributions in deep tissue during PDT monitoring.

A Comparison of 3D3C Velocity Measurement Techniques

NASA Astrophysics Data System (ADS)

La Foy, Roderick; Vlachos, Pavlos

2013-11-01

The velocity measurement fidelity of several 3D3C PIV measurement techniques including tomographic PIV, synthetic aperture PIV, plenoptic PIV, defocusing PIV, and 3D PTV are compared in simulations. A physically realistic ray-tracing algorithm is used to generate synthetic images of a standard calibration grid and of illuminated particle fields advected by homogeneous isotropic turbulence. The simulated images for the tomographic, synthetic aperture, and plenoptic PIV cases are then used to create three-dimensional reconstructions upon which cross-correlations are performed to yield the measured velocity field. Particle tracking algorithms are applied to the images for the defocusing PIV and 3D PTV to directly yield the three-dimensional velocity field. In all cases the measured velocity fields are compared to one-another and to the true velocity field using several metrics.

Method and apparatus for ultrasonic doppler velocimetry using speed of sound and reflection mode pulsed wideband doppler

DOEpatents

Shekarriz, Alireza; Sheen, David M.

2000-01-01

According to the present invention, a method and apparatus rely upon tomographic measurement of the speed of sound and fluid velocity in a pipe. The invention provides a more accurate profile of velocity within flow fields where the speed of sound varies within the cross-section of the pipe. This profile is obtained by reconstruction of the velocity profile from the local speed of sound measurement simultaneously with the flow velocity. The method of the present invention is real-time tomographic ultrasonic Doppler velocimetry utilizing a to plurality of ultrasonic transmission and reflection measurements along two orthogonal sets of parallel acoustic lines-of-sight. The fluid velocity profile and the acoustic velocity profile are determined by iteration between determining a fluid velocity profile and measuring local acoustic velocity until convergence is reached.

Magnetic particle imaging: from proof of principle to preclinical applications

NASA Astrophysics Data System (ADS)

Knopp, T.; Gdaniec, N.; Möddel, M.

2017-07-01

Tomographic imaging has become a mandatory tool for the diagnosis of a majority of diseases in clinical routine. Since each method has its pros and cons, a variety of them is regularly used in clinics to satisfy all application needs. Magnetic particle imaging (MPI) is a relatively new tomographic imaging technique that images magnetic nanoparticles with a high spatiotemporal resolution in a quantitative way, and in turn is highly suited for vascular and targeted imaging. MPI was introduced in 2005 and now enters the preclinical research phase, where medical researchers get access to this new technology and exploit its potential under physiological conditions. Within this paper, we review the development of MPI since its introduction in 2005. Besides an in-depth description of the basic principles, we provide detailed discussions on imaging sequences, reconstruction algorithms, scanner instrumentation and potential medical applications.

Magnified hard x-ray microtomography: toward tomography with submicron resolution

NASA Astrophysics Data System (ADS)

Schroer, Christian G.; Benner, Boris; Guenzler, Til F.; Kuhlmann, Marion; Lengeler, Bruno; Rau, Christoph; Weitkamp, Timm; Snigirev, Anatoly A.; Snigireva, Irina

2002-01-01

Parabolic compound refractive lenses (PCRLs) are high quality imaging optics for hard x-rays that can be used as an objective lens in a new type of hard x-ray full field microscope. Using an aluminium PCRL, this new type of microscope has been shown to have a resolution of 350 nm. Further improvement of the resolution down to 50 nm can be expected using beryllium as a lens material. The large depth of field (several mm) of the microscope results in sharp projection images for samples that fit into the field of view of about 300 micrometers. This allows to combine magnified imaging with tomographic techniques. First results of magnified microtomography are shown. Contrast formation in the microscope and the consequences for tomographic reconstruction are discussed. An outlook on further developments is given.

X-ray fluorescence tomographic system design and image reconstruction.

PubMed

Cong, Wenxiang; Shen, Haiou; Cao, Guohua; Liu, Hong; Wang, Ge

2013-01-01

In this paper, we presented a new design of x-ray fluorescence CT imaging system. For detecting fuorescence signals of gold nanoparticles in-vivo, multiple spectroscopic detectors are arranged and rotated orthogonal to an excited region of interest so that a localized scan can be acquired with a maximized efficiency. Excitation filtration was employed to minimize the effects of low-energy x-rays and background scattering for lowering radiation dose to the object. Numerical simulations showed that the radiation dose is less than 300 mGy/second for a complete 30 views tomographic scan; and the sensitivity of 3D fluorescence signal detection is up to 0.2% contrast concentrations of nanoparticles. The x-ray fluorescence computed tomography is an important molecular imaging tool. It can be used directly in samall animal research. It has great translational potential for future clinical applications.

Ultrasound Imaging Using Diffraction Tomography in a Cylindrical Geometry

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

Chambers, D H; Littrup, P

2002-01-24

Tomographic images of tissue phantoms and a sample of breast tissue have been produced from an acoustic synthetic array system for frequencies near 500 kHz. The images for sound speed and attenuation show millimeter resolution and demonstrate the feasibility of obtaining high-resolution tomographic images with frequencies that can deeply penetrate tissue. The image reconstruction method is based on the Born approximation to acoustic scattering and is a simplified version of a method previously used by Andre (Andre, et. al., Int. J. Imaging Systems and Technology, Vol 8, No. 1, 1997) for a circular acoustic array system. The images have comparablemore » resolution to conventional ultrasound images at much higher frequencies (3-5 MHz) but with lower speckle noise. This shows the potential of low frequency, deeply penetrating, ultrasound for high-resolution quantitative imaging.« less

System for tomographic determination of the power distribution in electron beams

DOEpatents

Elmer, John W.; Teruya, Alan T.; O'Brien, Dennis W.

1995-01-01

A tomographic technique for measuring the current density distribution in electron beams using electron beam profile data acquired from a modified Faraday cup to create an image of the current density in high and low power beams. The modified Faraday cup includes a narrow slit and is rotated by a stepper motor and can be moved in the x, y and z directions. The beam is swept across the slit perpendicular thereto and controlled by deflection coils, and the slit rotated such that waveforms are taken every few degrees form 0.degree. to 360.degree. and the waveforms are recorded by a digitizing storage oscilloscope. Two-dimensional and three-dimensional images of the current density distribution in the beam can be reconstructed by computer tomography from this information, providing quantitative information about the beam focus and alignment.

System for tomographic determination of the power distribution in electron beams

DOEpatents

Elmer, J.W.; Teruya, A.T.; O`Brien, D.W.

1995-11-21

A tomographic technique for measuring the current density distribution in electron beams using electron beam profile data acquired from a modified Faraday cup to create an image of the current density in high and low power beams. The modified Faraday cup includes a narrow slit and is rotated by a stepper motor and can be moved in the x, y and z directions. The beam is swept across the slit perpendicular thereto and controlled by deflection coils, and the slit rotated such that waveforms are taken every few degrees form 0{degree} to 360{degree} and the waveforms are recorded by a digitizing storage oscilloscope. Two-dimensional and three-dimensional images of the current density distribution in the beam can be reconstructed by computer tomography from this information, providing quantitative information about the beam focus and alignment. 12 figs.

The spatial resolution of a rotating gamma camera tomographic facility.

PubMed

Webb, S; Flower, M A; Ott, R J; Leach, M O; Inamdar, R

1983-12-01

An important feature determining the spatial resolution in transverse sections reconstructed by convolution and back-projection is the frequency filter corresponding to the convolution kernel. Equations have been derived giving the theoretical spatial resolution, for a perfect detector and noise-free data, using four filter functions. Experiments have shown that physical constraints will always limit the resolution that can be achieved with a given system. The experiments indicate that the region of the frequency spectrum between KN/2 and KN where KN is the Nyquist frequency does not contribute significantly to resolution. In order to investigate the physical effect of these filter functions, the spatial resolution of reconstructed images obtained with a GE 400T rotating gamma camera has been measured. The results obtained serve as an aid to choosing appropriate reconstruction filters for use with a rotating gamma camera system.

Electrocardiographically gated 16-section CT of the thorax: cardiac motion suppression.

PubMed

Hofmann, Lars K; Zou, Kelly H; Costello, Philip; Schoepf, U Joseph

2004-12-01

Thirty patients underwent 16-section multi-detector row computed tomographic (CT) angiography of the thorax with retrospective electrocardiographic gating. Institutional review board approval was obtained for retrospective analysis of CT scan data and records; patient informed consent was not required. Images reconstructed at six different time points (0%, 20%, 40%, 50%, 60%, 80%) within the R-R interval on the electrocardiogram were analyzed by two radiologists for diagnostic quality, to identify suitable reconstruction intervals for optimal suppression of cardiac motion. Five regions of interest (left coronary artery, aortic root, ascending and descending aorta, pulmonary arteries) were evaluated. Best image quality was achieved by referencing image reconstruction to middiastole (50%-60%) for the left coronary artery, aortic root, and ascending aorta. The pulmonary arteries are best displayed during mid- to late diastole (80%). (c) RSNA, 2004

Cryo-tomography Tilt-series Alignment with Consideration of the Beam-induced Sample Motion

PubMed Central

Fernandez, Jose-Jesus; Li, Sam; Bharat, Tanmay A. M.; Agard, David A.

2018-01-01

Recent evidence suggests that the beam-induced motion of the sample during tilt-series acquisition is a major resolution-limiting factor in electron cryo-tomography (cryoET). It causes suboptimal tilt-series alignment and thus deterioration of the reconstruction quality. Here we present a novel approach to tilt-series alignment and tomographic reconstruction that considers the beam-induced sample motion through the tilt-series. It extends the standard fiducial-based alignment approach in cryoET by introducing quadratic polynomials to model the sample motion. The model can be used during reconstruction to yield a motion-compensated tomogram. We evaluated our method on various datasets with different sample sizes. The results demonstrate that our method could be a useful tool to improve the quality of tomograms and the resolution in cryoET. PMID:29410148

Plenoptic projection fluorescence tomography.

PubMed

Iglesias, Ignacio; Ripoll, Jorge

2014-09-22

A new method to obtain the three-dimensional localization of fluorochrome distributions in micrometric samples is presented. It uses a microlens array coupled to the image port of a standard microscope to obtain tomographic data by a filtered back-projection algorithm. Scanning of the microlens array is proposed to obtain a dense data set for reconstruction. Simulation and experimental results are shown and the implications of this approach in fast 3D imaging are discussed.

Holographic interferometry of transparent media using light scattered by embedded test objects

NASA Technical Reports Server (NTRS)

Prikryl, I.; Vest, C. M.

1982-01-01

Fringe formation and localization in holographic interferometry of transparent media are discussed for configurations in which light enters the medium and is scattered back through it by an embedded diffuse object. Fringe order numbers are doubled, and the fringe localization region is translated and compressed by a factor of two. The results are applicable to tomographic reconstruction of aerodynamic density fields around opaque test objects.

Travel-time-based thermal tracer tomography

NASA Astrophysics Data System (ADS)

Somogyvári, Márk; Bayer, Peter; Brauchler, Ralf

2016-05-01

Active thermal tracer testing is a technique to get information about the flow and transport properties of an aquifer. In this paper we propose an innovative methodology using active thermal tracers in a tomographic setup to reconstruct cross-well hydraulic conductivity profiles. This is facilitated by assuming that the propagation of the injected thermal tracer is mainly controlled by advection. To reduce the effects of density and viscosity changes and thermal diffusion, early-time diagnostics are used and specific travel times of the tracer breakthrough curves are extracted. These travel times are inverted with an eikonal solver using the staggered grid method to reduce constraints from the pre-defined grid geometry and to improve the resolution. Finally, non-reliable pixels are removed from the derived hydraulic conductivity tomograms. The method is applied to successfully reconstruct cross-well profiles as well as a 3-D block of a high-resolution fluvio-aeolian aquifer analog data set. Sensitivity analysis reveals a negligible role of the injection temperature, but more attention has to be drawn to other technical parameters such as the injection rate. This is investigated in more detail through model-based testing using diverse hydraulic and thermal conditions in order to delineate the feasible range of applications for the new tomographic approach.

Maximum likelihood bolometric tomography for the determination of the uncertainties in the radiation emission on JET TOKAMAK

NASA Astrophysics Data System (ADS)

Craciunescu, Teddy; Peluso, Emmanuele; Murari, Andrea; Gelfusa, Michela; JET Contributors

2018-05-01

The total emission of radiation is a crucial quantity to calculate the power balances and to understand the physics of any Tokamak. Bolometric systems are the main tool to measure this important physical quantity through quite sophisticated tomographic inversion methods. On the Joint European Torus, the coverage of the bolometric diagnostic, due to the availability of basically only two projection angles, is quite limited, rendering the inversion a very ill-posed mathematical problem. A new approach, based on the maximum likelihood, has therefore been developed and implemented to alleviate one of the major weaknesses of traditional tomographic techniques: the difficulty to determine routinely the confidence intervals in the results. The method has been validated by numerical simulations with phantoms to assess the quality of the results and to optimise the configuration of the parameters for the main types of emissivity encountered experimentally. The typical levels of statistical errors, which may significantly influence the quality of the reconstructions, have been identified. The systematic tests with phantoms indicate that the errors in the reconstructions are quite limited and their effect on the total radiated power remains well below 10%. A comparison with other approaches to the inversion and to the regularization has also been performed.

Hyperspectral and multispectral bioluminescence optical tomography for small animal imaging.

PubMed

Chaudhari, Abhijit J; Darvas, Felix; Bading, James R; Moats, Rex A; Conti, Peter S; Smith, Desmond J; Cherry, Simon R; Leahy, Richard M

2005-12-07

For bioluminescence imaging studies in small animals, it is important to be able to accurately localize the three-dimensional (3D) distribution of the underlying bioluminescent source. The spectrum of light produced by the source that escapes the subject varies with the depth of the emission source because of the wavelength-dependence of the optical properties of tissue. Consequently, multispectral or hyperspectral data acquisition should help in the 3D localization of deep sources. In this paper, we describe a framework for fully 3D bioluminescence tomographic image acquisition and reconstruction that exploits spectral information. We describe regularized tomographic reconstruction techniques that use semi-infinite slab or FEM-based diffusion approximations of photon transport through turbid media. Singular value decomposition analysis was used for data dimensionality reduction and to illustrate the advantage of using hyperspectral rather than achromatic data. Simulation studies in an atlas-mouse geometry indicated that sub-millimeter resolution may be attainable given accurate knowledge of the optical properties of the animal. A fixed arrangement of mirrors and a single CCD camera were used for simultaneous acquisition of multispectral imaging data over most of the surface of the animal. Phantom studies conducted using this system demonstrated our ability to accurately localize deep point-like sources and show that a resolution of 1.5 to 2.2 mm for depths up to 6 mm can be achieved. We also include an in vivo study of a mouse with a brain tumour expressing firefly luciferase. Co-registration of the reconstructed 3D bioluminescent image with magnetic resonance images indicated good anatomical localization of the tumour.

Muscle tension line concept in nasolabial muscle complex--based on 3-dimensional reconstruction of nasolabial muscle fibers.

PubMed

Yin, Ningbei; Wu, Jiajun; Chen, Bo; Song, Tao; Ma, Hengyuan; Zhao, Zhenmin; Wang, Yongqian; Li, Haidong; Wu, Di

2015-03-01

Plastic surgeons have attempted various ways to rebuild the aesthetic subunits of the upper lip in patients with cleft lip with less than perfect results in most cases. We propose that repairing the 3 muscle tension line groups in the nasolabial complex will have improved aesthetic results. Micro-computed tomographic scans were performed on the nasolabial tissues of 5 normal aborted fetuses and used to construct a 3-dimensional model to study the nasolabial muscle complex structure. The micro-computed tomographic (CT) scans showed the close relationship and interaction between the muscle fibers of nasalis, pars peripheralis, levator labii superioris, and pars marginalis. Based on the 2-dimensional images obtained from the micro-computed tomographic scans, we suggest the concept of nasolabial muscle complex and muscle tension line group theory: there is a close relationship among the alar part of the nasalis, depressor septi muscle, orbicularis oris muscle, and levator labii superioris alaeque nasi. The tension line groups are 3 tension line structures in the nasolabial muscle complex that interlock with each other at the intersections and maintain the specific shape and aesthetics of the lip and nose.

Osteochondroma of the mandibular condyle: a classification system based on computed tomographic appearances.

PubMed

Chen, Min-jie; Yang, Chi; Qiu, Ya-ting; Zhou, Qin; Huang, Dong; Shi, Hui-min

2014-09-01

The objectives of this study were to introduce the classification of osteochondroma of the mandibular condyle based on computed tomographic images and to present our treatment experiences. From January 2002 and December 2012, a total of 61 patients with condylar osteochondroma were treated in our division. Both clinical and radiologic aspects were reviewed. The average follow-up period was 24.3 months with a range of 6 to 120 months. Two types of condylar osteochondroma were presented: type 1 (protruding expansion) in 50 patients (82.0%) and type 2 (globular expansion) in 11 patients (18.0%). Type 1 condylar osteochondroma presented 5 forms: anterior/anteromedial (58%), posterior/posteromedial (6%), medial (16%), lateral (6%), and gigantic (14%). Local resection was performed on patients with type 1 condylar osteochondroma. Subtotal condylectomy/total condylectomy using costochondral graft reconstruction with/without orthognathic surgeries was performed on patients with type 2 condylar osteochondroma. During the follow-up period, tumor reformation, condyle absorption, and new deformity were not detected. The patients almost reattained facial symmetry. Preoperative classification based on computed tomographic images will help surgeons to choose the suitable surgical procedure to treat the condylar osteochondroma.

Direct reconstruction of pharmacokinetic parameters in dynamic fluorescence molecular tomography by the augmented Lagrangian method

NASA Astrophysics Data System (ADS)

Zhu, Dianwen; Zhang, Wei; Zhao, Yue; Li, Changqing

2016-03-01

Dynamic fluorescence molecular tomography (FMT) has the potential to quantify physiological or biochemical information, known as pharmacokinetic parameters, which are important for cancer detection, drug development and delivery etc. To image those parameters, there are indirect methods, which are easier to implement but tend to provide images with low signal-to-noise ratio, and direct methods, which model all the measurement noises together and are statistically more efficient. The direct reconstruction methods in dynamic FMT have attracted a lot of attention recently. However, the coupling of tomographic image reconstruction and nonlinearity of kinetic parameter estimation due to the compartment modeling has imposed a huge computational burden to the direct reconstruction of the kinetic parameters. In this paper, we propose to take advantage of both the direct and indirect reconstruction ideas through a variable splitting strategy under the augmented Lagrangian framework. Each iteration of the direct reconstruction is split into two steps: the dynamic FMT image reconstruction and the node-wise nonlinear least squares fitting of the pharmacokinetic parameter images. Through numerical simulation studies, we have found that the proposed algorithm can achieve good reconstruction results within a small amount of time. This will be the first step for a combined dynamic PET and FMT imaging in the future.

An interior-point method for total variation regularized positron emission tomography image reconstruction

NASA Astrophysics Data System (ADS)

Bai, Bing

2012-03-01

There has been a lot of work on total variation (TV) regularized tomographic image reconstruction recently. Many of them use gradient-based optimization algorithms with a differentiable approximation of the TV functional. In this paper we apply TV regularization in Positron Emission Tomography (PET) image reconstruction. We reconstruct the PET image in a Bayesian framework, using Poisson noise model and TV prior functional. The original optimization problem is transformed to an equivalent problem with inequality constraints by adding auxiliary variables. Then we use an interior point method with logarithmic barrier functions to solve the constrained optimization problem. In this method, a series of points approaching the solution from inside the feasible region are found by solving a sequence of subproblems characterized by an increasing positive parameter. We use preconditioned conjugate gradient (PCG) algorithm to solve the subproblems directly. The nonnegativity constraint is enforced by bend line search. The exact expression of the TV functional is used in our calculations. Simulation results show that the algorithm converges fast and the convergence is insensitive to the values of the regularization and reconstruction parameters.

Cryo-Electron Microscopy of Viruses Infecting Bacterium

NASA Astrophysics Data System (ADS)

Chiu, Wah

2010-03-01

Single particle cryo-EM can yield structures of infectious bacterial viruses with and without imposed icosahedral symmetry at subnanometer resolution. Reconstructions of infectious and empty phage particles show substantial differences in the portal vertex protein complex at one of the 12 pentameric vertices in the icosahedral virus particle through which the viral genomes are packaged or released. In addition, electron cryo-tomography of viruses during infecting its bacterial host cell displayed multiple conformations of the tail fiber of the virus. Our structural observations by single particle and tomographic reconstructions suggest a mechanism whereby the viral tail fibers, upon binding to the host cell, induce a cascade of structural alterations of the portal vertex protein complex that triggers DNA release.

Solitary kidney with renal artery aneurysm repaired by ex vivo reconstruction.

PubMed

Palcau, Laura; Gouicem, Djelloul; Joguet, Etienne; Cameliere, Lucie; Berger, Ludovic

2014-01-01

A 22-year-old pregnant female with pyelonephritis was found to have a 26-mm left renal artery aneurysm with unknown right kidney agenesis diagnosed by magnetic resonance imaging. Computed tomographic angiography with 3-dimensional reconstructions confirmed a saccular aneurysm localized at the bifurcation of the left posterior segmental artery. The patient ultimately underwent successful ex vivo left renal artery aneurysm repair with autotransplantation. Pathologic evaluation of the resected aneurysm confirmed the diagnosis of fibromuscular dysplasia. Fibromuscular dysplasia is the most common cause of renal artery stenosis and renovascular hypertension and can, in rare cases, be associated with the development of renal artery aneurysms. © The Author(s) 2014.

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.

Influence of Iterative Reconstruction Algorithms on PET Image Resolution

NASA Astrophysics Data System (ADS)

Karpetas, G. E.; Michail, C. M.; Fountos, G. P.; Valais, I. G.; Nikolopoulos, D.; Kandarakis, I. S.; Panayiotakis, G. S.

2015-09-01

The aim of the present study was to assess image quality of PET scanners through a thin layer chromatography (TLC) plane source. The source was simulated using a previously validated Monte Carlo model. The model was developed by using the GATE MC package and reconstructed images obtained with the STIR software for tomographic image reconstruction. The simulated PET scanner was the GE DiscoveryST. A plane source consisted of a TLC plate, was simulated by a layer of silica gel on aluminum (Al) foil substrates, immersed in 18F-FDG bath solution (1MBq). Image quality was assessed in terms of the modulation transfer function (MTF). MTF curves were estimated from transverse reconstructed images of the plane source. Images were reconstructed by the maximum likelihood estimation (MLE)-OSMAPOSL, the ordered subsets separable paraboloidal surrogate (OSSPS), the median root prior (MRP) and OSMAPOSL with quadratic prior, algorithms. OSMAPOSL reconstruction was assessed by using fixed subsets and various iterations, as well as by using various beta (hyper) parameter values. MTF values were found to increase with increasing iterations. MTF also improves by using lower beta values. The simulated PET evaluation method, based on the TLC plane source, can be useful in the resolution assessment of PET scanners.

Progressive Stochastic Reconstruction Technique (PSRT) for cryo electron tomography.

PubMed

Turoňová, Beata; Marsalek, Lukas; Davidovič, Tomáš; Slusallek, Philipp

2015-03-01

Cryo Electron Tomography (cryoET) plays an essential role in Structural Biology, as it is the only technique that allows to study the structure of large macromolecular complexes in their close to native environment in situ. The reconstruction methods currently in use, such as Weighted Back Projection (WBP) or Simultaneous Iterative Reconstruction Technique (SIRT), deliver noisy and low-contrast reconstructions, which complicates the application of high-resolution protocols, such as Subtomogram Averaging (SA). We propose a Progressive Stochastic Reconstruction Technique (PSRT) - a novel iterative approach to tomographic reconstruction in cryoET based on Monte Carlo random walks guided by Metropolis-Hastings sampling strategy. We design a progressive reconstruction scheme to suit the conditions present in cryoET and apply it successfully to reconstructions of macromolecular complexes from both synthetic and experimental datasets. We show how to integrate PSRT into SA, where it provides an elegant solution to the region-of-interest problem and delivers high-contrast reconstructions that significantly improve template-based localization without any loss of high-resolution structural information. Furthermore, the locality of SA is exploited to design an importance sampling scheme which significantly speeds up the otherwise slow Monte Carlo approach. Finally, we design a new memory efficient solution for the specimen-level interior problem of cryoET, removing all associated artifacts. Copyright © 2015 Elsevier Inc. All rights reserved.

Update on orbital reconstruction.

PubMed

Chen, Chien-Tzung; Chen, Yu-Ray

2010-08-01

Orbital trauma is common and frequently complicated by ocular injuries. The recent literature on orbital fracture is analyzed with emphasis on epidemiological data assessment, surgical timing, method of approach and reconstruction materials. Computed tomographic (CT) scan has become a routine evaluation tool for orbital trauma, and mobile CT can be applied intraoperatively if necessary. Concomitant serious ocular injury should be carefully evaluated preoperatively. Patients presenting with nonresolving oculocardiac reflex, 'white-eyed' blowout fracture, or diplopia with a positive forced duction test and CT evidence of orbital tissue entrapment require early surgical repair. Otherwise, enophthalmos can be corrected by late surgery with a similar outcome to early surgery. The use of an endoscope-assisted approach for orbital reconstruction continues to grow, offering an alternative method. Advances in alloplastic materials have improved surgical outcome and shortened operating time. In this review of modern orbital reconstruction, several controversial issues such as surgical indication, surgical timing, method of approach and choice of reconstruction material are discussed. Preoperative fine-cut CT image and thorough ophthalmologic examination are key elements to determine surgical indications. The choice of surgical approach and reconstruction materials much depends on the surgeon's experience and the reconstruction area. Prefabricated alloplastic implants together with image software and stereolithographic models are significant advances that help to more accurately reconstruct the traumatized orbit. The recent evolution of orbit reconstruction improves functional and aesthetic results and minimizes surgical complications.

Synchronized multiartifact reduction with tomographic reconstruction (SMART-RECON): A statistical model based iterative image reconstruction method to eliminate limited-view artifacts and to mitigate the temporal-average artifacts in time-resolved CT.

PubMed

Chen, Guang-Hong; Li, Yinsheng

2015-08-01

In x-ray computed tomography (CT), a violation of the Tuy data sufficiency condition leads to limited-view artifacts. In some applications, it is desirable to use data corresponding to a narrow temporal window to reconstruct images with reduced temporal-average artifacts. However, the need to reduce temporal-average artifacts in practice may result in a violation of the Tuy condition and thus undesirable limited-view artifacts. In this paper, the authors present a new iterative reconstruction method, synchronized multiartifact reduction with tomographic reconstruction (SMART-RECON), to eliminate limited-view artifacts using data acquired within an ultranarrow temporal window that severely violates the Tuy condition. In time-resolved contrast enhanced CT acquisitions, image contrast dynamically changes during data acquisition. Each image reconstructed from data acquired in a given temporal window represents one time frame and can be denoted as an image vector. Conventionally, each individual time frame is reconstructed independently. In this paper, all image frames are grouped into a spatial-temporal image matrix and are reconstructed together. Rather than the spatial and/or temporal smoothing regularizers commonly used in iterative image reconstruction, the nuclear norm of the spatial-temporal image matrix is used in SMART-RECON to regularize the reconstruction of all image time frames. This regularizer exploits the low-dimensional structure of the spatial-temporal image matrix to mitigate limited-view artifacts when an ultranarrow temporal window is desired in some applications to reduce temporal-average artifacts. Both numerical simulations in two dimensional image slices with known ground truth and in vivo human subject data acquired in a contrast enhanced cone beam CT exam have been used to validate the proposed SMART-RECON algorithm and to demonstrate the initial performance of the algorithm. Reconstruction errors and temporal fidelity of the reconstructed images were quantified using the relative root mean square error (rRMSE) and the universal quality index (UQI) in numerical simulations. The performance of the SMART-RECON algorithm was compared with that of the prior image constrained compressed sensing (PICCS) reconstruction quantitatively in simulations and qualitatively in human subject exam. In numerical simulations, the 240(∘) short scan angular span was divided into four consecutive 60(∘) angular subsectors. SMART-RECON enables four high temporal fidelity images without limited-view artifacts. The average rRMSE is 16% and UQIs are 0.96 and 0.95 for the two local regions of interest, respectively. In contrast, the corresponding average rRMSE and UQIs are 25%, 0.78, and 0.81, respectively, for the PICCS reconstruction. Note that only one filtered backprojection image can be reconstructed from the same data set with an average rRMSE and UQIs are 45%, 0.71, and 0.79, respectively, to benchmark reconstruction accuracies. For in vivo contrast enhanced cone beam CT data acquired from a short scan angular span of 200(∘), three 66(∘) angular subsectors were used in SMART-RECON. The results demonstrated clear contrast difference in three SMART-RECON reconstructed image volumes without limited-view artifacts. In contrast, for the same angular sectors, PICCS cannot reconstruct images without limited-view artifacts and with clear contrast difference in three reconstructed image volumes. In time-resolved CT, the proposed SMART-RECON method provides a new method to eliminate limited-view artifacts using data acquired in an ultranarrow temporal window, which corresponds to approximately 60(∘) angular subsectors.

Classification of cryo electron microscopy images, noisy tomographic images recorded with unknown projection directions, by simultaneously estimating reconstructions and application to an assembly mutant of Cowpea Chlorotic Mottle Virus and portals of the bacteriophage P22

NASA Astrophysics Data System (ADS)

Lee, Junghoon; Zheng, Yili; Yin, Zhye; Doerschuk, Peter C.; Johnson, John E.

2010-08-01

Cryo electron microscopy is frequently used on biological specimens that show a mixture of different types of object. Because the electron beam rapidly destroys the specimen, the beam current is minimized which leads to noisy images (SNR substantially less than 1) and only one projection image per object (with an unknown projection direction) is collected. For situations where the objects can reasonably be described as coming from a finite set of classes, an approach based on joint maximum likelihood estimation of the reconstruction of each class and then use of the reconstructions to label the class of each image is described and demonstrated on two challenging problems: an assembly mutant of Cowpea Chlorotic Mottle Virus and portals of the bacteriophage P22.

Correction of scatter in megavoltage cone-beam CT

NASA Astrophysics Data System (ADS)

Spies, L.; Ebert, M.; Groh, B. A.; Hesse, B. M.; Bortfeld, T.

2001-03-01

The role of scatter in a cone-beam computed tomography system using the therapeutic beam of a medical linear accelerator and a commercial electronic portal imaging device (EPID) is investigated. A scatter correction method is presented which is based on a superposition of Monte Carlo generated scatter kernels. The kernels are adapted to both the spectral response of the EPID and the dimensions of the phantom being scanned. The method is part of a calibration procedure which converts the measured transmission data acquired for each projection angle into water-equivalent thicknesses. Tomographic reconstruction of the projections then yields an estimate of the electron density distribution of the phantom. It is found that scatter produces cupping artefacts in the reconstructed tomograms. Furthermore, reconstructed electron densities deviate greatly (by about 30%) from their expected values. The scatter correction method removes the cupping artefacts and decreases the deviations from 30% down to about 8%.

Characterising encapsulated nuclear waste using cosmic-ray muon tomography

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.; Yang, G.; Zimmerman, C.

2015-03-01

Tomographic imaging techniques using the Coulomb scattering of cosmic-ray muons have been shown previously to successfully identify and characterise low- and high-Z materials within an air matrix using a prototype scintillating-fibre tracker system. Those studies were performed as the first in a series to assess the feasibility of this technology and image reconstruction techniques in characterising the potential high-Z contents of legacy nuclear waste containers for the U.K. Nuclear Industry. The present work continues the feasibility study and presents the first images reconstructed from experimental data collected using this small-scale prototype system of low- and high-Z materials encapsulated within a concrete-filled stainless-steel container. Clear discrimination is observed between the thick steel casing, the concrete matrix and the sample materials assayed. These reconstructed objects are presented and discussed in detail alongside the implications for future industrial scenarios.

Tomo3D 2.0--exploitation of advanced vector extensions (AVX) for 3D reconstruction.

PubMed

Agulleiro, Jose-Ignacio; Fernandez, Jose-Jesus

2015-02-01

Tomo3D is a program for fast tomographic reconstruction on multicore computers. Its high speed stems from code optimization, vectorization with Streaming SIMD Extensions (SSE), multithreading and optimization of disk access. Recently, Advanced Vector eXtensions (AVX) have been introduced in the x86 processor architecture. Compared to SSE, AVX double the number of simultaneous operations, thus pointing to a potential twofold gain in speed. However, in practice, achieving this potential is extremely difficult. Here, we provide a technical description and an assessment of the optimizations included in Tomo3D to take advantage of AVX instructions. Tomo3D 2.0 allows huge reconstructions to be calculated in standard computers in a matter of minutes. Thus, it will be a valuable tool for electron tomography studies with increasing resolution needs. Copyright © 2014 Elsevier Inc. All rights reserved.

Vertical structure of medium-scale traveling ionospheric disturbances

NASA Astrophysics Data System (ADS)

Ssessanga, Nicholas; Kim, Yong Ha; Kim, Eunsol

2015-11-01

We develop an algorithm of computerized ionospheric tomography (CIT) to infer information on the vertical and horizontal structuring of electron density during nighttime medium-scale traveling ionospheric disturbances (MSTIDs). To facilitate digital CIT we have adopted total electron contents (TEC) from a dense Global Positioning System (GPS) receiver network, GEONET, which contains more than 1000 receivers. A multiplicative algebraic reconstruction technique was utilized with a calibrated IRI-2012 model as an initial solution. The reconstructed F2 peak layer varied in altitude with average peak-to-peak amplitude of ~52 km. In addition, the F2 peak layer anticorrelated with TEC variations. This feature supports a theory in which nighttime MSTID is composed of oscillating electric fields due to conductivity variations. Moreover, reconstructed TEC variations over two stations were reasonably close to variations directly derived from the measured TEC data set. Our tomographic analysis may thus help understand three-dimensional structure of MSTIDs in a quantitative way.

An ANN-Based Smart Tomographic Reconstructor in a Dynamic Environment

PubMed Central

de Cos Juez, Francisco J.; Lasheras, Fernando Sánchez; Roqueñí, Nieves; Osborn, James

2012-01-01

In astronomy, the light emitted by an object travels through the vacuum of space and then the turbulent atmosphere before arriving at a ground based telescope. By passing through the atmosphere a series of turbulent layers modify the light's wave-front in such a way that Adaptive Optics reconstruction techniques are needed to improve the image quality. A novel reconstruction technique based in Artificial Neural Networks (ANN) is proposed. The network is designed to use the local tilts of the wave-front measured by a Shack Hartmann Wave-front Sensor (SHWFS) as inputs and estimate the turbulence in terms of Zernike coefficients. The ANN used is a Multi-Layer Perceptron (MLP) trained with simulated data with one turbulent layer changing in altitude. The reconstructor was tested using three different atmospheric profiles and compared with two existing reconstruction techniques: Least Squares type Matrix Vector Multiplication (LS) and Learn and Apply (L + A). PMID:23012524

Comparison of SIRT and SQS for Regularized Weighted Least Squares Image Reconstruction

PubMed Central

Gregor, Jens; Fessler, Jeffrey A.

2015-01-01

Tomographic image reconstruction is often formulated as a regularized weighted least squares (RWLS) problem optimized by iterative algorithms that are either inherently algebraic or derived from a statistical point of view. This paper compares a modified version of SIRT (Simultaneous Iterative Reconstruction Technique), which is of the former type, with a version of SQS (Separable Quadratic Surrogates), which is of the latter type. We show that the two algorithms minimize the same criterion function using similar forms of preconditioned gradient descent. We present near-optimal relaxation for both based on eigenvalue bounds and include a heuristic extension for use with ordered subsets. We provide empirical evidence that SIRT and SQS converge at the same rate for all intents and purposes. For context, we compare their performance with an implementation of preconditioned conjugate gradient. The illustrative application is X-ray CT of luggage for aviation security. PMID:26478906

Theory and preliminary experimental verification of quantitative edge illumination x-ray phase contrast tomography.

PubMed

Hagen, C K; Diemoz, P C; Endrizzi, M; Rigon, L; Dreossi, D; Arfelli, F; Lopez, F C M; Longo, R; Olivo, A

2014-04-07

X-ray phase contrast imaging (XPCi) methods are sensitive to phase in addition to attenuation effects and, therefore, can achieve improved image contrast for weakly attenuating materials, such as often encountered in biomedical applications. Several XPCi methods exist, most of which have already been implemented in computed tomographic (CT) modality, thus allowing volumetric imaging. The Edge Illumination (EI) XPCi method had, until now, not been implemented as a CT modality. This article provides indications that quantitative 3D maps of an object's phase and attenuation can be reconstructed from EI XPCi measurements. Moreover, a theory for the reconstruction of combined phase and attenuation maps is presented. Both reconstruction strategies find applications in tissue characterisation and the identification of faint, weakly attenuating details. Experimental results for wires of known materials and for a biological object validate the theory and confirm the superiority of the phase over conventional, attenuation-based image contrast.

Benefit from NASA

NASA Image and Video Library

2001-09-01

The high-tech art of digital signal processing (DSP) was pioneered at NASA's Jet Propulsion Laboratory (JPL) in the mid-1960s for use in the Apollo Lunar Landing Program. Designed to computer enhance pictures of the Moon, this technology became the basis for the Landsat Earth resources satellites and subsequently has been incorporated into a broad range of Earthbound medical and diagnostic tools. DSP is employed in advanced body imaging techniques including Computer-Aided Tomography, also known as CT and CATScan, and Magnetic Resonance Imaging (MRI). CT images are collected by irradiating a thin slice of the body with a fan-shaped x-ray beam from a number of directions around the body's perimeter. A tomographic (slice-like) picture is reconstructed from these multiple views by a computer. MRI employs a magnetic field and radio waves, rather than x-rays, to create images.

EPR oximetry in three spatial dimensions using sparse spin distribution

NASA Astrophysics Data System (ADS)

Som, Subhojit; Potter, Lee C.; Ahmad, Rizwan; Vikram, Deepti S.; Kuppusamy, Periannan

2008-08-01

A method is presented to use continuous wave electron paramagnetic resonance imaging for rapid measurement of oxygen partial pressure in three spatial dimensions. A particulate paramagnetic probe is employed to create a sparse distribution of spins in a volume of interest. Information encoding location and spectral linewidth is collected by varying the spatial orientation and strength of an applied magnetic gradient field. Data processing exploits the spatial sparseness of spins to detect voxels with nonzero spin and to estimate the spectral linewidth for those voxels. The parsimonious representation of spin locations and linewidths permits an order of magnitude reduction in data acquisition time, compared to four-dimensional tomographic reconstruction using traditional spectral-spatial imaging. The proposed oximetry method is experimentally demonstrated for a lithium octa- n-butoxy naphthalocyanine (LiNc-BuO) probe using an L-band EPR spectrometer.

Neutron tomographic analysis: Material characterization of silver and electrum coins from the 6th and 5th centuries BCE

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

Salvemini, F., E-mail: filomena.salvemini@ansto.go

Neutron tomography was applied to study a set of Greek silver coins and a single Lydian electrum coin minted in the 6 and 5th centuries BCE. The investigation was conducted at the new neutron imaging station DINGO at ANSTO in order to demonstrate capabilities and to explore limits of this non-invasive method in characterizing numismatic materials. From the reconstructed volume of each sample, the morphology, porosity, inclusions, and presence of composite structures can be revealed and evaluated. This information can be used to elucidate ancient minting technology and to prove authenticity. Moreover, the state of conservation, corrosion processes and attemptsmore » to repair the coins can be determined. - Highlights: •Pre-Roman coins •Non-destructive analysis •Neutron tomography: limit and capability.« less

Unconditional room-temperature quantum memory

NASA Astrophysics Data System (ADS)

Hosseini, M.; Campbell, G.; Sparkes, B. M.; Lam, P. K.; Buchler, B. C.

2011-10-01

Just as classical information systems require buffers and memory, the same is true for quantum information systems. The potential that optical quantum information processing holds for revolutionizing computation and communication is therefore driving significant research into developing optical quantum memory. A practical optical quantum memory must be able to store and recall quantum states on demand with high efficiency and low noise. Ideally, the platform for the memory would also be simple and inexpensive. Here, we present a complete tomographic reconstruction of quantum states that have been stored in the ground states of rubidium in a vapour cell operating at around 80°C. Without conditional measurements, we show recall fidelity up to 98% for coherent pulses containing around one photon. To unambiguously verify that our memory beats the quantum no-cloning limit we employ state-independent verification using conditional variance and signal-transfer coefficients.

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.

Tomographic imaging of non-local media based on space-fractional diffusion models

NASA Astrophysics Data System (ADS)

Buonocore, Salvatore; Semperlotti, Fabio

2018-06-01

We investigate a generalized tomographic imaging framework applicable to a class of inhomogeneous media characterized by non-local diffusive energy transport. Under these conditions, the transport mechanism is well described by fractional-order continuum models capable of capturing anomalous diffusion that would otherwise remain undetected when using traditional integer-order models. Although the underlying idea of the proposed framework is applicable to any transport mechanism, the case of fractional heat conduction is presented as a specific example to illustrate the methodology. By using numerical simulations, we show how complex inhomogeneous media involving non-local transport can be successfully imaged if fractional order models are used. In particular, results will show that by properly recognizing and accounting for the fractional character of the host medium not only allows achieving increased resolution but, in case of strong and spatially distributed non-locality, it represents the only viable approach to achieve a successful reconstruction.

Introducing minimum Fisher regularisation tomography to AXUV and soft x-ray diagnostic systems of the COMPASS tokamak

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

Mlynar, J.; Weinzettl, V.; Imrisek, M.

2012-10-15

The contribution focuses on plasma tomography via the minimum Fisher regularisation (MFR) algorithm applied on data from the recently commissioned tomographic diagnostics on the COMPASS tokamak. The MFR expertise is based on previous applications at Joint European Torus (JET), as exemplified in a new case study of the plasma position analyses based on JET soft x-ray (SXR) tomographic reconstruction. Subsequent application of the MFR algorithm on COMPASS data from cameras with absolute extreme ultraviolet (AXUV) photodiodes disclosed a peaked radiating region near the limiter. Moreover, its time evolution indicates transient plasma edge cooling following a radial plasma shift. In themore » SXR data, MFR demonstrated that a high resolution plasma positioning independent of the magnetic diagnostics would be possible provided that a proper calibration of the cameras on an x-ray source is undertaken.« less

A tomographic technique for aerodynamics at transonic speeds

NASA Technical Reports Server (NTRS)

Lee, G.

1985-01-01

Computer aided tomography (CAT) provides a means of noninvasively measuring the air density distribution around an aerodynamic model. This technique is global in that a large portion of the flow field can be measured. A test of the applicability of CAT to transonic velocities was studied. A hemispherical-nose cylinder afterbody model was tested at a Mach number of 0.8 with a new laser holographic interferometer at the 2- by 2-Foot Transonic Wind Tunnel. Holograms of the flow field were taken and were reconstructed into interferograms. The fringe distribution (a measure of the local densities) was digitized for subsequent data reduction. A computer program based on the Fourier-transform technique was developed to convert the fringe distribution into three-dimensional densities around the model. Theoretical aerodynamic densities were calculated for evaluating and assessing the accuracy of the data obtained from the tomographic method.

System for tomographic determination of the power distribution in electron beams

DOEpatents

Elmer, J.W.; Teruya, A.T.; O'Brien, D.W.

1995-01-17

A tomographic technique is disclosed for measuring the current density distribution in electron beams using electron beam profile data acquired from a modified Faraday cup to create an image of the current density in high and low power beams. The modified Faraday cup includes a narrow slit and is rotated by a stepper motor and can be moved in the x, y and z directions. The beam is swept across the slit perpendicular thereto and controlled by deflection coils, and the slit rotated such that waveforms are taken every few degrees form 0[degree] to 360[degree] and the waveforms are recorded by a digitizing storage oscilloscope. Two-dimensional and three-dimensional images of the current density distribution in the beam can be reconstructed by computer tomography from this information, providing quantitative information about the beam focus and alignment. 12 figures.

Photoelectron circular dichroism of bicyclic ketones from multiphoton ionization with femtosecond laser pulses.

PubMed

Lux, Christian; Wollenhaupt, Matthias; Sarpe, Cristian; Baumert, Thomas

2015-01-12

Photoelectron circular dichroism (PECD) is a CD effect up to the ten-percent regime and shows contributions from higher-order Legendre polynomials when multiphoton ionization is compared to single-photon ionization. We give a full account of our experimental methodology for measuring the multiphoton PECD and derive quantitative measures that we apply on camphor, fenchone and norcamphor. Different modulations and amplitudes of the contributing Legendre polynomials are observed despite the similarity in chemical structure. In addition, we study PECD for elliptically polarized light employing tomographic reconstruction methods. Intensity studies reveal dissociative ionization as the origin of the observed PECD effect, whereas ionization of the intermediate resonance is dominating the signal. As a perspective, we suggest to make use of our tomographic data as an experimental basis for a complete photoionization experiment and give a prospect of PECD as an analytic tool. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Laser-wakefield accelerators as hard x-ray sources for 3D medical imaging of human bone

PubMed Central

Cole, J. M.; Wood, J. C.; Lopes, N. C.; Poder, K.; Abel, R. L.; Alatabi, S.; Bryant, J. S. J.; Jin, A.; Kneip, S.; Mecseki, K.; Symes, D. R.; Mangles, S. P. D.; Najmudin, Z.

2015-01-01

A bright μm-sized source of hard synchrotron x-rays (critical energy Ecrit > 30 keV) based on the betatron oscillations of laser wakefield accelerated electrons has been developed. The potential of this source for medical imaging was demonstrated by performing micro-computed tomography of a human femoral trabecular bone sample, allowing full 3D reconstruction to a resolution below 50 μm. The use of a 1 cm long wakefield accelerator means that the length of the beamline (excluding the laser) is dominated by the x-ray imaging distances rather than the electron acceleration distances. The source possesses high peak brightness, which allows each image to be recorded with a single exposure and reduces the time required for a full tomographic scan. These properties make this an interesting laboratory source for many tomographic imaging applications. PMID:26283308

Assessment of Severity of Ovine Smoke Inhalation Injury by Analysis of Computed Tomographic Scans

DTIC Science & Technology

2003-09-01

Computerized analysis of three- dimensional reconstructed scans was also performed, based on Hounsfield unit ranges: hyperinflated, 1,000 to 900; normal...the interactive segmentation function of the software. The pulmonary parenchyma was separated into four regions based on the Hounsfield unit (HU...SII) severity. Methods: Twenty anesthetized sheep underwent graded SII: group I, no smoke; group II, 5 smoke units ; group III, 10 units ; and group IV

Portable Ultrasound Imaging of the Brain for Use in Forward Battlefield Areas

DTIC Science & Technology

2011-03-01

ultrasound measurement of skull thickness and sound speed, phase correction of beam distortion, the tomographic reconstruction algorithm, and the final...produce a coherent imaging source. We propose a corrective technique that will use ultrasound-based phased -array beam correction [3], optimized...not expected to be a significant factor in the ability to phase -correct the imaging beam . In addition to planning (2.2.1), the data is also be used

Nanoscale Fresnel coherent diffraction imaging tomography using ptychography.

PubMed

Peterson, I; Abbey, B; Putkunz, C T; Vine, D J; van Riessen, G A; Cadenazzi, G A; Balaur, E; Ryan, R; Quiney, H M; McNulty, I; Peele, A G; Nugent, K A

2012-10-22

We demonstrate Fresnel Coherent Diffractive Imaging (FCDI) tomography in the X-ray regime. The method uses an incident X-ray illumination with known curvature in combination with ptychography to overcome existing problems in diffraction imaging. The resulting tomographic reconstruction represents a 3D map of the specimen's complex refractive index at nano-scale resolution. We use this technique to image a lithographically fabricated glass capillary, in which features down to 70nm are clearly resolved.

An observational study on the Strength and Movement of EIA in the Indian zone - Results from the Indian Tomography Experiment (CRABEX)

NASA Astrophysics Data System (ADS)

Thampi, S. V.; Devasia, C. V.; Ravindran, S.; Pant, T. K.; Sridharan, R.

To investigate the equatorial ionospheric processes like the Equatorial Ionization Anomaly (EIA) and Equatorial Spread F and their inter relationships, a network of five stations receiving the 150 and 400 MHz transmissions from the Low Earth Orbiting Satellites (LEOs) covering the region from Trivandrum (8.5°N, Dip ˜0.3N°) to New Delhi (28°N, Dip ˜20°N) is set up along the 77-78°E longitude. The receivers measure the relative phase of 150 MHz with respect to 400 MHz, which is proportional to the slant relative Total Electron Content (TEC) along the line of sight. These simultaneous TEC measurements are inverted to obtain the tomographic image of the latitudinal distribution of electron densities in the meridional plane. The inversion is done using the Algebraic Reconstruction Technique (ART). In this paper, the tomographic images of the equatorial ionosphere along the 77-78° E meridians are presented. The images indicate the movement of the anomaly crest, as well as the strength of EIA at various local times, which in turn control the over all electrodynamics of the evening time ionosphere, favoring the occurrence of Equatorial Spread F (ESF) irregularities. These features are discussed in detail under varying geophysical conditions. The results of the sensitivity analysis of the inversion algorithm using model ionospheres are also presented.

The Relationship of Obesity to Increasing Health-Care Burden in the Setting of Orthopaedic Polytrauma.

PubMed

Licht, Heather; Murray, Mark; Vassaur, John; Jupiter, Daniel C; Regner, Justin L; Chaput, Christopher D

2015-11-18

With the rise of obesity in the American population, there has been a proportionate increase of obesity in the trauma population. The purpose of this study was to use a computed tomography-based measurement of adiposity to determine if obesity is associated with an increased burden to the health-care system in patients with orthopaedic polytrauma. A prospective comprehensive trauma database at a level-I trauma center was utilized to identify 301 patients with polytrauma who had orthopaedic injuries and intensive care unit admission from 2006 to 2011. Routine thoracoabdominal computed tomographic scans allowed for measurement of the truncal adiposity volume. The truncal three-dimensional reconstruction body mass index was calculated from the computed tomography-based volumes based on a previously validated algorithm. A truncal three-dimensional reconstruction body mass index of <30 kg/m(2) denoted non-obese patients and ≥ 30 kg/m(2) denoted obese patients. The need for orthopaedic surgical procedure, in-hospital mortality, length of stay, hospital charges, and discharge disposition were compared between the two groups. Of the 301 patients, 21.6% were classified as obese (truncal three-dimensional reconstruction body mass index of ≥ 30 kg/m(2)). Higher truncal three-dimensional reconstruction body mass index was associated with longer hospital length of stay (p = 0.02), more days spent in the intensive care unit (p = 0.03), more frequent discharge to a long-term care facility (p < 0.0002), higher rate of orthopaedic surgical intervention (p < 0.01), and increased total hospital charges (p < 0.001). Computed tomographic scans, routinely obtained at the time of admission, can be utilized to calculate truncal adiposity and to investigate the impact of obesity on patients with polytrauma. Obese patients were found to have higher total hospital charges, longer hospital stays, discharge to a continuing-care facility, and a higher rate of orthopaedic surgical intervention. Copyright © 2015 by The Journal of Bone and Joint Surgery, Incorporated.

Time-Resolved C-Arm Computed Tomographic Angiography Derived From Computed Tomographic Perfusion Acquisition: New Capability for One-Stop-Shop Acute Ischemic Stroke Treatment in the Angiosuite.

PubMed

Yang, Pengfei; Niu, Kai; Wu, Yijing; Struffert, Tobias; Dorfler, Arnd; Schafer, Sebastian; Royalty, Kevin; Strother, Charles; Chen, Guang-Hong

2015-12-01

Multimodal imaging using cone beam C-arm computed tomography (CT) may shorten the delay from ictus to revascularization for acute ischemic stroke patients with a large vessel occlusion. Largely because of limited temporal resolution, reconstruction of time-resolved CT angiography (CTA) from these systems has not yielded satisfactory results. We evaluated the image quality and diagnostic value of time-resolved C-arm CTA reconstructed using novel image processing algorithms. Studies were done under an Institutional Review Board approved protocol. Postprocessing of data from 21 C-arm CT dynamic perfusion acquisitions from 17 patients with acute ischemic stroke were done to derive time-resolved C-arm CTA images. Two observers independently evaluated image quality and diagnostic content for each case. ICC and receiver-operating characteristic analysis were performed to evaluate interobserver agreement and diagnostic value of this novel imaging modality. Time-resolved C-arm CTA images were successfully generated from 20 data sets (95.2%, 20/21). Two observers agreed well that the image quality for large cerebral arteries was good but was more limited for small cerebral arteries (distal to M1, A1, and P1). receiver-operating characteristic curves demonstrated excellent diagnostic value for detecting large vessel occlusions (area under the curve=0.987-1). Time-resolved CTAs derived from C-arm CT perfusion acquisitions provide high quality images that allowed accurate diagnosis of large vessel occlusions. Although image quality of smaller arteries in this study was not optimal ongoing modifications of the postprocessing algorithm will likely remove this limitation. Adding time-resolved C-arm CTAs to the capabilities of the angiography suite further enhances its suitability as a one-stop shop for care for patients with acute ischemic stroke. © 2015 American Heart Association, Inc.

In-situ Micro-structural Studies of Gas Hydrate Formation in Sedimentary Matrices

NASA Astrophysics Data System (ADS)

Kuhs, Werner F.; Chaouachi, Marwen; Falenty, Andrzej; Sell, Kathleen; Schwarz, Jens-Oliver; Wolf, Martin; Enzmann, Frieder; Kersten, Michael; Haberthür, David

2015-04-01

The formation process of gas hydrates in sedimentary matrices is of crucial importance for the physical and transport properties of the resulting aggregates. This process has never been observed in-situ with sub-micron resolution. Here, we report on synchrotron-based micro-tomographic studies by which the nucleation and growth processes of gas hydrate were observed in different sedimentary matrices (natural quartz, glass beds with different surface properties, with and without admixtures of kaolinite and montmorillonite) at varying water saturation. The nucleation sites can be easily identified and the growth pattern is clearly established. In under-saturated sediments the nucleation starts at the water-gas interface and proceeds from there to form predominantly isometric single crystals of 10-20μm size. Using a newly developed synchrotron-based method we have determined the crystallite size distributions (CSD) of the gas hydrate in the sedimentary matrix confirming in a quantitative and statistically relevant manner the impressions from the tomographic reconstructions. It is noteworthy that the CSDs from synthetic hydrates are distinctly smaller than those of natural gas hydrates [1], which suggest that coarsening processes take place in the sedimentary matrix after the initial hydrate formation. Understanding the processes of formation and coarsening may eventually permit the determination of the age of gas hydrates in sedimentary matrices [2], which are largely unknown at present. Furthermore, the full micro-structural picture and its evolution will enable quantitative digital rock physics modeling to reveal poroelastic properties and in this way to support the exploration and exploitation of gas hydrate resources in the future. [1] Klapp S.A., Hemes S., Klein H., Bohrmann G., McDonald I., Kuhs W.F. Grain size measurements of natural gas hydrates. Marine Geology 2010; 274(1-4):85-94. [2] Klapp S.A., Klein H, Kuhs W.F. First determination of gas hydrate crystallite size distribution using high-energy synchrotron radiation. Geophys.Res.Letters, 2007 ; 34 : L13608, DOI:10.1029/2006GL029134

Combined algorithmic and GPU acceleration for ultra-fast circular conebeam backprojection

NASA Astrophysics Data System (ADS)

Brokish, Jeffrey; Sack, Paul; Bresler, Yoram

2010-04-01

In this paper, we describe the first implementation and performance of a fast O(N3logN) hierarchical backprojection algorithm for cone beam CT with a circular trajectory1,developed on a modern Graphics Processing Unit (GPU). The resulting tomographic backprojection system for 3D cone beam geometry combines speedup through algorithmic improvements provided by the hierarchical backprojection algorithm with speedup from a massively parallel hardware accelerator. For data parameters typical in diagnostic CT and using a mid-range GPU card, we report reconstruction speeds of up to 360 frames per second, and relative speedup of almost 6x compared to conventional backprojection on the same hardware. The significance of these results is twofold. First, they demonstrate that the reduction in operation counts demonstrated previously for the FHBP algorithm can be translated to a comparable run-time improvement in a massively parallel hardware implementation, while preserving stringent diagnostic image quality. Second, the dramatic speedup and throughput numbers achieved indicate the feasibility of systems based on this technology, which achieve real-time 3D reconstruction for state-of-the art diagnostic CT scanners with small footprint, high-reliability, and affordable cost.

Inverse scattering and refraction corrected reflection for breast cancer imaging

NASA Astrophysics Data System (ADS)

Wiskin, J.; Borup, D.; Johnson, S.; Berggren, M.; Robinson, D.; Smith, J.; Chen, J.; Parisky, Y.; Klock, John

2010-03-01

Reflection ultrasound (US) has been utilized as an adjunct imaging modality for over 30 years. TechniScan, Inc. has developed unique, transmission and concomitant reflection algorithms which are used to reconstruct images from data gathered during a tomographic breast scanning process called Warm Bath Ultrasound (WBU™). The transmission algorithm yields high resolution, 3D, attenuation and speed of sound (SOS) images. The reflection algorithm is based on canonical ray tracing utilizing refraction correction via the SOS and attenuation reconstructions. The refraction correction reflection algorithm allows 360 degree compounding resulting in the reflection image. The requisite data are collected when scanning the entire breast in a 33° C water bath, on average in 8 minutes. This presentation explains how the data are collected and processed by the 3D transmission and reflection imaging mode algorithms. The processing is carried out using two NVIDIA® Tesla™ GPU processors, accessing data on a 4-TeraByte RAID. The WBU™ images are displayed in a DICOM viewer that allows registration of all three modalities. Several representative cases are presented to demonstrate potential diagnostic capability including: a cyst, fibroadenoma, and a carcinoma. WBU™ images (SOS, attenuation, and reflection modalities) are shown along with their respective mammograms and standard ultrasound images. In addition, anatomical studies are shown comparing WBU™ images and MRI images of a cadaver breast. This innovative technology is designed to provide additional tools in the armamentarium for diagnosis of breast disease.

A small animal time-resolved optical tomography platform using wide-field excitation

NASA Astrophysics Data System (ADS)

Venugopal, Vivek

Small animal imaging plays a critical role in present day biomedical research by filling an important gap in the translation of research from the bench to the bedside. Optical techniques constitute an emerging imaging modality which have tremendous potential in preclinical applications. Optical imaging methods are capable of non-invasive assessment of the functional and molecular characteristics of biological tissue. The three-dimensional optical imaging technique, referred to as diffuse optical tomography, provides an approach for the whole-body imaging of small animal models and can provide volumetric maps of tissue functional parameters (e.g. blood volume, oxygen saturation etc.) and/or provide 3D localization and quantification of fluorescence-based molecular markers in vivo. However, the complex mathematical reconstruction problem associated with optical tomography and the cumbersome instrumental designs limits its adoption as a high-throughput quantitative whole-body imaging modality in current biomedical research. The development of new optical imaging paradigms is thus necessary for a wide-acceptance of this new technology. In this thesis, the design, development, characterization and optimization of a small animal optical tomography system is discussed. Specifically, the platform combines a highly sensitive time-resolved imaging paradigm with multi-spectral excitation capability and CCD-based detection to provide a system capable of generating spatially, spectrally and temporally dense measurement datasets. The acquisition of such data sets however can take long and translate to often unrealistic acquisition times when using the classical point source based excitation scheme. The novel approach in the design of this platform is the adoption of a wide-field excitation scheme which employs extended excitation sources and in the process allows an estimated ten-fold reduction in the acquisition time. The work described herein details the design of the imaging platform employing DLP-based excitation and time-gated intensified CCD detection and the optimal system operation parameters are determined. The feasibility this imaging approach and accuracy of the system in reconstructing functional parameters and fluorescence markers based on lifetime contrast is established through phantom studies. As a part of the system characterization, the effect of noise in time-resolved optical tomography is investigated and propagation of system noise in optical reconstructions is established. Furthermore, data processing and measurement calibration techniques aimed at reducing the effect of noise in reconstructions are defined. The optimization of excitation pattern selection is established through a novel measurement-guided iterative pattern correction scheme. This technique referred to as Adaptive Full-Field Optical Tomography was shown to improve reconstruction performances in murine models by reducing the dynamic range in photon flux measurements on the surface. Lastly, the application of the unique attributes of this platform to a biologically relevant imaging application, referred to as Forster Resonance Energy Transfer is described. The tomographic imaging of FRET interaction in vivo on a whole-body scale is achieved using the wide-field imaging approach based on lifetime contrast. This technique represents the first demonstration of tomographic FRET imaging in small animals and has significant potential in the development of optical imaging techniques in varied applications ranging from drug discovery to in vivo study of protein-protein interaction.

Electron Microscopy Imaging of Zinc Soaps Nucleation in Oil Paint.

PubMed

Hermans, Joen; Osmond, Gillian; van Loon, Annelies; Iedema, Piet; Chapman, Robyn; Drennan, John; Jack, Kevin; Rasch, Ronald; Morgan, Garry; Zhang, Zhi; Monteiro, Michael; Keune, Katrien

2018-06-04

Using the recently developed techniques of electron tomography, we have explored the first stages of disfiguring formation of zinc soaps in modern oil paintings. The formation of complexes of zinc ions with fatty acids in paint layers is a major threat to the stability and appearance of many late 19th and early 20th century oil paintings. Moreover, the occurrence of zinc soaps in oil paintings leading to defects is disturbingly common, but the chemical reactions and migration mechanisms leading to large zinc soap aggregates or zones remain poorly understood. State-of-the-art scanning (SEM) and transmission (TEM) electron microscopy techniques, primarily developed for biological specimens, have enabled us to visualize the earliest stages of crystalline zinc soap growth in a reconstructed zinc white (ZnO) oil paint sample. In situ sectioning techniques and sequential imaging within the SEM allowed three-dimensional tomographic reconstruction of sample morphology. Improvements in the detection and discrimination of backscattered electrons enabled us to identify local precipitation processes with small atomic number contrast. The SEM images were correlated to low-dose and high-sensitivity TEM images, with high-resolution tomography providing unprecedented insight into the structure of nucleating zinc soaps at the molecular level. The correlative approach applied here to study phase separation, and crystallization processes specific to a problem in art conservation creates possibilities for visualization of phase formation in a wide range of soft materials.

A digital-signal-processor-based optical tomographic system for dynamic imaging of joint diseases

NASA Astrophysics Data System (ADS)

Lasker, Joseph M.

Over the last decade, optical tomography (OT) has emerged as viable biomedical imaging modality. Various imaging systems have been developed that are employed in preclinical as well as clinical studies, mostly targeting breast imaging, brain imaging, and cancer related studies. Of particular interest are so-called dynamic imaging studies where one attempts to image changes in optical properties and/or physiological parameters as they occur during a system perturbation. To successfully perform dynamic imaging studies, great effort is put towards system development that offers increasingly enhanced signal-to-noise performance at ever shorter data acquisition times, thus capturing high fidelity tomographic data within narrower time periods. Towards this goal, I have developed in this thesis a dynamic optical tomography system that is, unlike currently available analog instrumentation, based on digital data acquisition and filtering techniques. At the core of this instrument is a digital signal processor (DSP) that collects, collates, and processes the digitized data set. Complementary protocols between the DSP and a complex programmable logic device synchronizes the sampling process and organizes data flow. Instrument control is implemented through a comprehensive graphical user interface which integrates automated calibration, data acquisition, and signal post-processing. Real-time data is generated at frame rates as high as 140 Hz. An extensive dynamic range (˜190 dB) accommodates a wide scope of measurement geometries and tissue types. Performance analysis demonstrates very low system noise (˜1 pW rms noise equivalent power), excellent signal precision (˜0.04%--0.2%) and long term system stability (˜1% over 40 min). Experiments on tissue phantoms validate spatial and temporal accuracy of the system. As a potential new application of dynamic optical imaging I present the first application of this method to use vascular hemodynamics as a means of characterizing joint diseases, especially effects of rheumatoid arthritis (RA) in the proximal interphalangeal finger joints. Using a dual-wavelength tomographic imaging system and previously implemented reconstruction scheme, I have performed initial dynamic imaging case studies on healthy volunteers and patients diagnosed with RA. These studies support our hypothesis that differences in the vascular and metabolic reactivity exist between affected and unaffected joints and can be used for diagnostic purposes.

Frequency-domain optical tomographic image reconstruction algorithm with the simplified spherical harmonics (SP3) light propagation model.

PubMed

Kim, Hyun Keol; Montejo, Ludguier D; Jia, Jingfei; Hielscher, Andreas H

2017-06-01

We introduce here the finite volume formulation of the frequency-domain simplified spherical harmonics model with n -th order absorption coefficients (FD-SP N ) that approximates the frequency-domain equation of radiative transfer (FD-ERT). We then present the FD-SP N based reconstruction algorithm that recovers absorption and scattering coefficients in biological tissue. The FD-SP N model with 3 rd order absorption coefficient (i.e., FD-SP 3 ) is used as a forward model to solve the inverse problem. The FD-SP 3 is discretized with a node-centered finite volume scheme and solved with a restarted generalized minimum residual (GMRES) algorithm. The absorption and scattering coefficients are retrieved using a limited-memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS) algorithm. Finally, the forward and inverse algorithms are evaluated using numerical phantoms with optical properties and size that mimic small-volume tissue such as finger joints and small animals. The forward results show that the FD-SP 3 model approximates the FD-ERT (S 12 ) solution within relatively high accuracy; the average error in the phase (<3.7%) and the amplitude (<7.1%) of the partial current at the boundary are reported. From the inverse results we find that the absorption and scattering coefficient maps are more accurately reconstructed with the SP 3 model than those with the SP 1 model. Therefore, this work shows that the FD-SP 3 is an efficient model for optical tomographic imaging of small-volume media with non-diffuse properties both in terms of computational time and accuracy as it requires significantly lower CPU time than the FD-ERT (S 12 ) and also it is more accurate than the FD-SP 1 .

Accurate Measurements of the Skin Surface Area of the Healthy Auricle and Skin Deficiency in Microtia Patients

PubMed Central

van Doremalen, Rob F. M.; Melchels, Ferry P. W.; Kolodzynski, Michail N.; Pouran, Behdad; Malda, Jos; Kon, Moshe; Breugem, Corstiaan C.

2016-01-01

Background: The limited cranial skin covering auricular implants is an important yet underrated factor in auricular reconstruction for both reconstruction surgery and tissue engineering strategies. We report exact measurements on skin deficiency in microtia patients and propose an accessible preoperative method for these measurements. Methods: Plaster ear models (n = 11; male:female = 2:1) of lobular-type microtia patients admitted to the University Medical Center Utrecht in The Netherlands were scanned using a micro-computed tomographic scanner or a cone-beam computed tomographic scanner. The resulting images were converted into mesh models from which the surface area could be calculated. Results: The mean total skin area of an adult-size healthy ear was 47.3 cm2, with 49.0 cm2 in men and 44.3 cm2 in women. Microtia ears averaged 14.5 cm2, with 15.6 cm2 in men and 12.6 cm2 in women. The amount of skin deficiency was 25.4 cm2, with 26.7 cm2 in men and 23.1 cm2 in women. Conclusions: This study proposes a novel method to provide quantitative data on the skin surface area of the healthy adult auricle and the amount of skin deficiency in microtia patients. We demonstrate that the microtia ear has less than 50% of skin available compared with healthy ears. Limited skin availability in microtia patients can lead to healing problems after auricular reconstruction and poses a significant challenge in the development of tissue-engineered cartilage implants. The results of this study could be used to evaluate outcomes and investigate new techniques with regard to tissue-engineered auricular constructs. PMID:28293505

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

Shin, H; Yoon, D; Jung, J

Purpose: The purpose of this study is to suggest a tumor monitoring technique using prompt gamma rays emitted during the reaction between an antiproton and a boron particle, and to verify the increase of the therapeutic effectiveness of the antiproton boron fusion therapy using Monte Carlo simulation code. Methods: We acquired the percentage depth dose of the antiproton beam from a water phantom with and without three boron uptake regions (region A, B, and C) using F6 tally of MCNPX. The tomographic image was reconstructed using prompt gamma ray events from the reaction between the antiproton and boron during themore » treatment from 32 projections (reconstruction algorithm: MLEM). For the image reconstruction, we were performed using a 80 × 80 pixel matrix with a pixel size of 5 mm. The energy window was set as a 10 % energy window. Results: The prompt gamma ray peak for imaging was observed at 719 keV in the energy spectrum using the F8 tally fuction (energy deposition tally) of the MCNPX code. The tomographic image shows that the boron uptake regions were successfully identified from the simulation results. In terms of the receiver operating characteristic curve analysis, the area under the curve values were 0.647 (region A), 0.679 (region B), and 0.632 (region C). The SNR values increased as the tumor diameter increased. The CNR indicated the relative signal intensity within different regions. The CNR values also increased as the different of BURs diamter increased. Conclusion: We confirmed the feasibility of tumor monitoring during the antiproton therapy as well as the superior therapeutic effect of the antiproton boron fusion therapy. This result can be beneficial for the development of a more accurate particle therapy.« less

Minehunting sonar system research and development

NASA Astrophysics Data System (ADS)

Ferguson, Brian

2002-05-01

Sea mines have the potential to threaten the freedom of the seas by disrupting maritime trade and restricting the freedom of maneuver of navies. The acoustic detection, localization, and classification of sea mines involves a sequence of operations starting with the transmission of a sonar pulse and ending with an operator interpreting the information on a sonar display. A recent improvement to the process stems from the application of neural networks to the computed aided detection of sea mines. The advent of ultrawideband sonar transducers together with pulse compression techniques offers a thousandfold increase in the bandwidth-time product of conventional minehunting sonar transmissions enabling stealth mines to be detected at longer ranges. These wideband signals also enable mines to be imaged at safe standoff distances by applying tomographic image reconstruction techniques. The coupling of wideband transducer technology with synthetic aperture processing enhances the resolution of side scan sonars in both the cross-track and along-track directions. The principles on which conventional and advanced minehunting sonars are based are reviewed and the results of applying novel sonar signal processing algorithms to high-frequency sonar data collected in Australian waters are presented.

Iterative methods for dose reduction and image enhancement in tomography

DOEpatents

Miao, Jianwei; Fahimian, Benjamin Pooya

2012-09-18

A system and method for creating a three dimensional cross sectional image of an object by the reconstruction of its projections that have been iteratively refined through modification in object space and Fourier space is disclosed. The invention provides systems and methods for use with any tomographic imaging system that reconstructs an object from its projections. In one embodiment, the invention presents a method to eliminate interpolations present in conventional tomography. The method has been experimentally shown to provide higher resolution and improved image quality parameters over existing approaches. A primary benefit of the method is radiation dose reduction since the invention can produce an image of a desired quality with a fewer number projections than seen with conventional methods.

Enhanced x-ray imaging for a thin film cochlear implant with metal artefacts using phase retrieval tomography

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

Arhatari, B. D.; ARC Centre of Excellence for Coherent X-ray Science, Melbourne; Harris, A. R.

Phase retrieval tomography has been successfully used to enhance imaging in systems that exhibit poor absorption contrast. However, when highly absorbing regions are present in a sample, so-called metal artefacts can appear in the tomographic reconstruction. We demonstrate that straightforward approaches for metal artefact reconstruction, developed in absorption contrast tomography, can be applied when using phase retrieval. Using a prototype thin film cochlear implant that has high and low absorption components made from iridium (or platinum) and plastic, respectively, we show that segmentation of the various components is possible and hence measurement of the electrode geometry and relative location tomore » other regions of interest can be achieved.« less

Image reconstructions from super-sampled data sets with resolution modeling in PET imaging.

PubMed

Li, Yusheng; Matej, Samuel; Metzler, Scott D

2014-12-01

Spatial resolution in positron emission tomography (PET) is still a limiting factor in many imaging applications. To improve the spatial resolution for an existing scanner with fixed crystal sizes, mechanical movements such as scanner wobbling and object shifting have been considered for PET systems. Multiple acquisitions from different positions can provide complementary information and increased spatial sampling. The objective of this paper is to explore an efficient and useful reconstruction framework to reconstruct super-resolution images from super-sampled low-resolution data sets. The authors introduce a super-sampling data acquisition model based on the physical processes with tomographic, downsampling, and shifting matrices as its building blocks. Based on the model, we extend the MLEM and Landweber algorithms to reconstruct images from super-sampled data sets. The authors also derive a backprojection-filtration-like (BPF-like) method for the super-sampling reconstruction. Furthermore, they explore variant methods for super-sampling reconstructions: the separate super-sampling resolution-modeling reconstruction and the reconstruction without downsampling to further improve image quality at the cost of more computation. The authors use simulated reconstruction of a resolution phantom to evaluate the three types of algorithms with different super-samplings at different count levels. Contrast recovery coefficient (CRC) versus background variability, as an image-quality metric, is calculated at each iteration for all reconstructions. The authors observe that all three algorithms can significantly and consistently achieve increased CRCs at fixed background variability and reduce background artifacts with super-sampled data sets at the same count levels. For the same super-sampled data sets, the MLEM method achieves better image quality than the Landweber method, which in turn achieves better image quality than the BPF-like method. The authors also demonstrate that the reconstructions from super-sampled data sets using a fine system matrix yield improved image quality compared to the reconstructions using a coarse system matrix. Super-sampling reconstructions with different count levels showed that the more spatial-resolution improvement can be obtained with higher count at a larger iteration number. The authors developed a super-sampling reconstruction framework that can reconstruct super-resolution images using the super-sampling data sets simultaneously with known acquisition motion. The super-sampling PET acquisition using the proposed algorithms provides an effective and economic way to improve image quality for PET imaging, which has an important implication in preclinical and clinical region-of-interest PET imaging applications.

Penalized maximum likelihood reconstruction for x-ray differential phase-contrast tomography

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

Brendel, Bernhard, E-mail: bernhard.brendel@philips.com; Teuffenbach, Maximilian von; Noël, Peter B.

2016-01-15

Purpose: The purpose of this work is to propose a cost function with regularization to iteratively reconstruct attenuation, phase, and scatter images simultaneously from differential phase contrast (DPC) acquisitions, without the need of phase retrieval, and examine its properties. Furthermore this reconstruction method is applied to an acquisition pattern that is suitable for a DPC tomographic system with continuously rotating gantry (sliding window acquisition), overcoming the severe smearing in noniterative reconstruction. Methods: We derive a penalized maximum likelihood reconstruction algorithm to directly reconstruct attenuation, phase, and scatter image from the measured detector values of a DPC acquisition. The proposed penaltymore » comprises, for each of the three images, an independent smoothing prior. Image quality of the proposed reconstruction is compared to images generated with FBP and iterative reconstruction after phase retrieval. Furthermore, the influence between the priors is analyzed. Finally, the proposed reconstruction algorithm is applied to experimental sliding window data acquired at a synchrotron and results are compared to reconstructions based on phase retrieval. Results: The results show that the proposed algorithm significantly increases image quality in comparison to reconstructions based on phase retrieval. No significant mutual influence between the proposed independent priors could be observed. Further it could be illustrated that the iterative reconstruction of a sliding window acquisition results in images with substantially reduced smearing artifacts. Conclusions: Although the proposed cost function is inherently nonconvex, it can be used to reconstruct images with less aliasing artifacts and less streak artifacts than reconstruction methods based on phase retrieval. Furthermore, the proposed method can be used to reconstruct images of sliding window acquisitions with negligible smearing artifacts.« less

Laser Absorption spectrometer instrument for tomographic 2D-measurement of climate gas emission from soils

NASA Astrophysics Data System (ADS)

Seidel, Anne; Wagner, Steven; Dreizler, Andreas; Ebert, Volker

2014-05-01

One of the most intricate effects in climate modelling is the role of permafrost thawing during the global warming process. Soil that has formerly never totally lost its ice cover now emits climate gases due to melting processes[1]. For a better prediction of climate development and possible feedback mechanisms, insights into physical procedures (like e.g. gas emission from underground reservoirs) are required[2]. Therefore, a long-term quantification of greenhouse gas concentrations (and further on fluxes) is necessary and the related structures that are responsible for emission need to be identified. In particular the spatial heterogeneity of soils caused by soil internal structures (e.g. soil composition changes or surface cracks) or by surface modifications (e.g. by plant growth) generate considerable complexities and difficulties for local measurements, for example with soil chambers. For such situations, which often cannot be avoided, a spatially resolved 2D-measurement to identify and quantify the gas emission from the structured soil would be needed, to better understand the influence of the soil sub-structures on the emission behavior. Thus we designed a spatially scanning laser absorption spectrometer setup to determine a 2D-gas concentration map in the soil-air boundary layer. The setup is designed to cover the surfaces in the range of square meters in a horizontal plane above the soil to be investigated. Existing field instruments for gas concentration or flux measurements are based on point-wise measurements, so structure identification is very tedious or even impossible. For this reason, we have developed a tomographic in-situ instrument based on TDLAS ('tunable diode laser absorption spectroscopy') that delivers absolute gas concentration distributions of areas with 0.8m × 0.8m size, without any need for reference measurements with a calibration gas. It is a simple and robust device based on a combination of scanning mirrors and reflecting foils, so that only very little optical alignment is necessary in the field. The measurement rate for a complete 2D field is presently up to 2.5 Hz. The measurement field size is currently limited only by laboratory conditions and could be extended easily to the range of several meters, as previous tests have confirmed[3]. A fast laser tuning rate of more than 5 kHz leads to high measurement path density, and overall more than 70% of a square shaped field area is covered. With this instrument, measurements of H2O- and CH4 - concentration distributions have taken place so far. We are going to discuss the instrument setup and the spectroscopic performance and present numerical studies concerning the tomographic reconstruction quality as well as first 2D reconstructions in the laboratory. The applicability to 2D CO2 detection and the improvement of frame rate and reconstruction quality using faster laser tuning will be discussed. [1] K. M. Walter Anthony, P. Anthony, G. Grosse, and J. Chanton, 'Geologic methane seeps along boundaries of Arctic permafrost thaw and melting glaciers,' Nat. Geosci., vol. 5, no. 6, pp. 419-426, May 2012. [2] B. Elberling, A. Michelsen, C. Schädel, E. A. G. Schuur, H. H. Christiansen, L. Tamstorf, M. P. Berg, and C. Sigsgaard, 'Long-term CO2 production following permafrost thaw,' Nat. Clim. Chang., vol. 3, no. 10, pp. 890-894, 2013. [3] A. Seidel, S. Wagner, and V. Ebert, 'TDLAS-based open-path laser hygrometer using simple reflective foils as scattering targets,' Appl. Phys. B, vol. 109, no. 3, pp. 497-504, Oct. 2012.

Experimentally enhanced model-based deconvolution of propagation-based phase-contrast data

NASA Astrophysics Data System (ADS)

Pichotka, M.; Palma, K.; Hasn, S.; Jakubek, J.; Vavrik, D.

2016-12-01

In recent years phase-contrast has become a much investigated modality in radiographic imaging. The radiographic setups employed in phase-contrast imaging are typically rather costly and complex, e.g. high performance Talbot-Laue interferometers operated at synchrotron light sources. In-line phase-contrast imaging states the most pedestrian approach towards phase-contrast enhancement. Utilizing small angle deflection within the imaged sample and the entailed interference of the deflected and un-deflected beam during spatial propagation, in-line phase-contrast imaging only requires a well collimated X-ray source with a high contrast & high resolution detector. Employing high magnification the above conditions are intrinsically fulfilled in cone-beam micro-tomography. As opposed of 2D imaging, where contrast enhancement is generally considered beneficial, in tomographic modalities the in-line phase-contrast effect can be quite a nuisance since it renders the inverse problem posed by tomographic reconstruction inconsistent, thus causing reconstruction artifacts. We present an experimentally enhanced model-based approach to disentangle absorption and in-line phase-contrast. The approach employs comparison of transmission data to a system model computed iteratively on-line. By comparison of the forward model to absorption data acquired in continuous rotation strong local deviations of the data residual are successively identified as likely candidates for in-line phase-contrast. By inducing minimal vibrations (few mrad) to the sample around the peaks of such deviations the transmission signal can be decomposed into a constant absorptive fraction and an oscillating signal caused by phase-contrast which again allows to generate separate maps for absorption and phase-contrast. The contributions of phase-contrast and the corresponding artifacts are subsequently removed from the tomographic dataset. In principle, if a 3D handling of the sample is available, this method also allows to track discontinuities throughout the volume and therefore states a powerful tool in 3D defectoscopy.

Application of the GNSS-R in tomographic sounding of the Earth atmosphere

NASA Astrophysics Data System (ADS)

Jaberi Shafei, Milad; Mashhadi-Hossainali, Masoud

2018-07-01

Reflected GNSS signals offer a great opportunity for detecting and monitoring of water level variation, land surface roughness and the atmosphere around the Earth. The application type intensely depends on satellites' geometry and the topography of study area. GNSS-R can be used in sounding the water vapor as one of the most important parameters in troposphere. In view of temporal and spatial changes, retrieval of this parameter is complicated. GNSS tomography is a common approach for this purpose. Considering the dependency of this inverse approach to the number of stations and satellites' coverage at study area, tomographic reconstruction of water vapor is an ill-posed problem. Additional constraints are usually used to find a solution. In this research reflected signals known as GNSS-R are offered for the first time to resolve the rank deficiency of this problem. This has been implemented to a tomographic model which has been already developed for modeling the water vapor in the North West of Iran. In view of low number of GPS stations in this area, the design matrix of the model is rank deficient. Simulated results demonstrate that the rank deficiency of this matrix can be reduced by implementing appropriate number of GNSS-R stations when the spatial resolution of model is optimized. Resolution matrix is used as a measure for analyzing the efficiency of the proposed method. Results from DOY 300 and 301 in year 2011 show that the applied method can even remedy the rank deficiency of the design matrix. The satellites' constellation and the time response of the model are the effective parameters in this respect. On average the rank deficiency of the design matrix is improved more than 90% when the reflected signals are used. This is easily seen in terms of the resolution matrix of the model. Here, the mean bias and RMSE of reconstructed image are 0.2593 and 1.847 ppm, respectively.

On the Feasibility of Multi-kHz Acquisition Rate Tomographic-PIV in Turbulent Flames

DTIC Science & Technology

2013-10-01

developed measurement technique used to acquire volumetric velocity field data in liquid and gaseous flows. The technique relies on line-of-sight...changes resulting from local heat-release may inhibit reconstruction and thereby render the technique infeasible. The objective of this study was to test...four CMOS cameras and a dual-cavity Nd:YAG laser was implemented to test the technique in a lifted turbulent jet flame. While the cameras were capable

Controlled wavelet domain sparsity for x-ray tomography

NASA Astrophysics Data System (ADS)

Purisha, Zenith; Rimpeläinen, Juho; Bubba, Tatiana; Siltanen, Samuli

2018-01-01

Tomographic reconstruction is an ill-posed inverse problem that calls for regularization. One possibility is to require sparsity of the unknown in an orthonormal wavelet basis. This, in turn, can be achieved by variational regularization, where the penalty term is the sum of the absolute values of the wavelet coefficients. The primal-dual fixed point algorithm showed that the minimizer of the variational regularization functional can be computed iteratively using a soft-thresholding operation. Choosing the soft-thresholding parameter \

Direct integration of the inverse Radon equation for X-ray computed tomography.

PubMed

Libin, E E; Chakhlov, S V; Trinca, D

2016-11-22

A new mathematical appoach using the inverse Radon equation for restoration of images in problems of linear two-dimensional x-ray tomography is formulated. In this approach, Fourier transformation is not used, and it gives the chance to create the practical computing algorithms having more reliable mathematical substantiation. Results of software implementation show that for especially for low number of projections, the described approach performs better than standard X-ray tomographic reconstruction algorithms.

Three-dimensional x-ray diffraction nanoscopy

NASA Astrophysics Data System (ADS)

Nikulin, Andrei Y.; Dilanian, Ruben A.; Zatsepin, Nadia A.; Muddle, Barry C.

2008-08-01

A novel approach to x-ray diffraction data analysis for non-destructive determination of the shape of nanoscale particles and clusters in three-dimensions is illustrated with representative examples of composite nanostructures. The technique is insensitive to the x-rays coherence, which allows 3D reconstruction of a modal image without tomographic synthesis and in-situ analysis of large (over a several cubic millimeters) volume of material with a spatial resolution of few nanometers, rendering the approach suitable for laboratory facilities.

Measurement of radioactivity concentration in blood by using newly developed ToT LuAG-APD based small animal PET tomograph.

PubMed

Malik, Azhar H; Shimazoe, Kenji; Takahashi, Hiroyuki

2013-01-01

In order to obtain plasma time activity curve (PTAC), input function for almost all quantitative PET studies, patient blood is sampled manually from the artery or vein which has various drawbacks. Recently a novel compact Time over Threshold (ToT) based Pr:LuAG-APD animal PET tomograph is developed in our laboratory which has 10% energy resolution, 4.2 ns time resolution and 1.76 mm spatial resolution. The measured value of spatial resolution shows much promise for imaging the blood vascular, i.e; artery of diameter 2.3-2.4mm, and hence, to measure PTAC for quantitative PET studies. To find the measurement time required to obtain reasonable counts for image reconstruction, the most important parameter is the sensitivity of the system. Usually small animal PET systems are characterized by using a point source in air. We used Electron Gamma Shower 5 (EGS5) code to simulate a point source at different positions inside the sensitive volume of tomograph and the axial and radial variations in the sensitivity are studied in air and phantom equivalent water cylinder. An average sensitivity difference of 34% in axial direction and 24.6% in radial direction is observed when point source is displaced inside water cylinder instead of air.

Derivation of site-specific relationships between hydraulic parameters and p-wave velocities based on hydraulic and seismic tomography

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

Brauchler, R.; Doetsch, J.; Dietrich, P.

2012-01-10

In this study, hydraulic and seismic tomographic measurements were used to derive a site-specific relationship between the geophysical parameter p-wave velocity and the hydraulic parameters, diffusivity and specific storage. Our field study includes diffusivity tomograms derived from hydraulic travel time tomography, specific storage tomograms, derived from hydraulic attenuation tomography, and p-wave velocity tomograms, derived from seismic tomography. The tomographic inversion was performed in all three cases with the SIRT (Simultaneous Iterative Reconstruction Technique) algorithm, using a ray tracing technique with curved trajectories. The experimental set-up was designed such that the p-wave velocity tomogram overlaps the hydraulic tomograms by half. Themore » experiments were performed at a wellcharacterized sand and gravel aquifer, located in the Leine River valley near Göttingen, Germany. Access to the shallow subsurface was provided by direct-push technology. The high spatial resolution of hydraulic and seismic tomography was exploited to derive representative site-specific relationships between the hydraulic and geophysical parameters, based on the area where geophysical and hydraulic tests were performed. The transformation of the p-wave velocities into hydraulic properties was undertaken using a k-means cluster analysis. Results demonstrate that the combination of hydraulic and geophysical tomographic data is a promising approach to improve hydrogeophysical site characterization.« less

Tomographic Imaging of a Forested Area By Airborne Multi-Baseline P-Band SAR.

PubMed

Frey, Othmar; Morsdorf, Felix; Meier, Erich

2008-09-24

In recent years, various attempts have been undertaken to obtain information about the structure of forested areas from multi-baseline synthetic aperture radar data. Tomographic processing of such data has been demonstrated for airborne L-band data but the quality of the focused tomographic images is limited by several factors. In particular, the common Fourierbased focusing methods are susceptible to irregular and sparse sampling, two problems, that are unavoidable in case of multi-pass, multi-baseline SAR data acquired by an airborne system. In this paper, a tomographic focusing method based on the time-domain back-projection algorithm is proposed, which maintains the geometric relationship between the original sensor positions and the imaged target and is therefore able to cope with irregular sampling without introducing any approximations with respect to the geometry. The tomographic focusing quality is assessed by analysing the impulse response of simulated point targets and an in-scene corner reflector. And, in particular, several tomographic slices of a volume representing a forested area are given. The respective P-band tomographic data set consisting of eleven flight tracks has been acquired by the airborne E-SAR sensor of the German Aerospace Center (DLR).

Online geometrical calibration of a mobile C-arm using external sensors

NASA Astrophysics Data System (ADS)

Mitschke, Matthias M.; Navab, Nassir; Schuetz, Oliver

2000-04-01

3D tomographic reconstruction of high contrast objects such as contrast agent enhanced blood vessels or bones from x-ray images acquired by isocentric C-arm systems recently gained interest. For tomographic reconstruction, a sequence of images is captured during the C-arm rotation around the patient and the precise projection geometry has to be determined for each image. This is a difficult task, as C- arms usually do not provide accurate information about their projection geometry. Standard methods propose the use of an x-ray calibration phantom and an offline calibration, when the motion of the C-arm is supposed to be reproducible between calibration and patient run. However, mobile C-arms usually do not have this desirable property. Therefore, an online recovery of projection geometry is necessary. Here, we study the use of external tracking systems such as Polaris or Optotrak from Northern Digital, Inc., for online calibration. In order to use the external tracking system for recovery of x-ray projection geometry two unknown transformations have to be estimated. We describe our attempt to solve this calibration problem. These are the relations between x-ray imaging system and marker plate of the tracking system as well as worked and sensor coordinate system. Experimental result son anatomical data are presented and visually compared with the results of estimating the projection geometry with an x-ray calibration phantom.