Science.gov

Sample records for 3d computer tomography

  1. Glasses for 3D ultrasound computer tomography: phase compensation

    NASA Astrophysics Data System (ADS)

    Zapf, M.; Hopp, T.; Ruiter, N. V.

    2016-03-01

    Ultrasound Computer Tomography (USCT), developed at KIT, is a promising new imaging system for breast cancer diagnosis, and was successfully tested in a pilot study. The 3D USCT II prototype consists of several hundreds of ultrasound (US) transducers on a semi-ellipsoidal aperture. Spherical waves are sequentially emitted by individual transducers and received in parallel by many transducers. Reflectivity volumes are reconstructed by synthetic aperture focusing (SAFT). However, straight forward SAFT imaging leads to blurred images due to system imperfections. We present an extension of a previously proposed approach to enhance the images. This approach includes additional a priori information and system characteristics. Now spatial phase compensation was included. The approach was evaluated with a simulation and clinical data sets. An increase in the image quality was observed and quantitatively measured by SNR and other metrics.

  2. 3D ultrasound computer tomography: update from a clinical study

    NASA Astrophysics Data System (ADS)

    Hopp, T.; Zapf, M.; Kretzek, E.; Henrich, J.; Tukalo, A.; Gemmeke, H.; Kaiser, C.; Knaudt, J.; Ruiter, N. V.

    2016-04-01

    Ultrasound Computer Tomography (USCT) is a promising new imaging method for breast cancer diagnosis. We developed a 3D USCT system and tested it in a pilot study with encouraging results: 3D USCT was able to depict two carcinomas, which were present in contrast enhanced MRI volumes serving as ground truth. To overcome severe differences in the breast shape, an image registration was applied. We analyzed the correlation between average sound speed in the breast and the breast density estimated from segmented MRIs and found a positive correlation with R=0.70. Based on the results of the pilot study we now carry out a successive clinical study with 200 patients. For this we integrated our reconstruction methods and image post-processing into a comprehensive workflow. It includes a dedicated DICOM viewer for interactive assessment of fused USCT images. A new preview mode now allows intuitive and faster patient positioning. We updated the USCT system to decrease the data acquisition time by approximately factor two and to increase the penetration depth of the breast into the USCT aperture by 1 cm. Furthermore the compute-intensive reflectivity reconstruction was considerably accelerated, now allowing a sub-millimeter volume reconstruction in approximately 16 minutes. The updates made it possible to successfully image first patients in our ongoing clinical study.

  3. Building a 3D Computed Tomography Scanner From Surplus Parts.

    PubMed

    Haidekker, Mark A

    2014-01-01

    Computed tomography (CT) scanners are expensive imaging devices, often out of reach for small research groups. Designing and building a CT scanner from modular components is possible, and this article demonstrates that realization of a CT scanner from components is surprisingly easy. However, the high costs of a modular X-ray source and detector limit the overall cost savings. In this article, the possibility of building a CT scanner with available surplus X-ray parts is discussed, and a practical device is described that incurred costs of less than $16,000. The image quality of this device is comparable with commercial devices. The disadvantage is that design constraints imposed by the available components lead to slow scan speeds and a resolution of 0.5 mm. Despite these limitations, a device such as this is attractive for imaging studies in the biological and biomedical sciences, as well as for advancing CT technology itself.

  4. 3D Multislice and Cone-beam Computed Tomography Systems for Dental Identification.

    PubMed

    Eliášová, Hana; Dostálová, Taťjana

    2017-01-01

    3D Multislice and Cone-beam computed tomography (CBCT) in forensic odontology has been shown to be useful not only in terms of one or a few of dead bodies but also in multiple fatality incidents. 3D Multislice and Cone-beam computed tomography and digital radiography were demonstrated in a forensic examination form. 3D images of the skull and teeth were analysed and validated for long ante mortem/post mortem intervals. The image acquisition was instantaneous; the images were able to be optically enlarged, measured, superimposed and compared prima vista or using special software and exported as a file. Digital radiology and computer tomography has been shown to be important both in common criminalistics practices and in multiple fatality incidents. Our study demonstrated that CBCT imaging offers less image artifacts, low image reconstruction times, mobility of the unit and considerably lower equipment cost.

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

    PubMed

    Uchida, Masafumi

    2014-04-01

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

  6. Analyzing 3D xylem networks in Vitis vinifera using High Resolution Computed Tomography (HRCT)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Recent developments in High Resolution Computed Tomography (HRCT) have made it possible to visualize three dimensional (3D) xylem networks without time consuming, labor intensive physical sectioning. Here we describe a new method to visualize complex vessel networks in plants and produce a quantitat...

  7. Computed Tomography and its Application for the 3D Characterization of Coarse Grained Meteorites

    NASA Technical Reports Server (NTRS)

    Gillies, Donald C.; Engel, H. P.; Carpenter, P. K.

    2004-01-01

    With judicious selection of parameters, computed tomography can provide high precision density data. Such data can lead to a non-destructive determination of the phases and phase distribution within large solid objects. Of particular interest is the structure of the Mundrabilla meteorite, which has 25 volumes, percent of a sulfide within a metallic meteorite. 3D digital imaging has enabled a quantitative evaluation of the distribution and contiguity of the phases to be determined.

  8. 3D image reconstruction on x-ray micro-computed tomography

    NASA Astrophysics Data System (ADS)

    Louk, Andreas C.

    2015-03-01

    A model for 3D image reconstruction of x-ray micro-computed tomography scanner (micro-CTScan) has been developed. A small object has been put under inspection on an x-ray micro-CTScan. The object cross-section was assumed on the x-y plane, while its height was along the z-axis. Using a radiography plane detector, a set of digital radiographs represents multiple angle of views from 0º to 360º with an interval of 1º was obtained. Then, a set of crosssectional tomography, slice by slice was reconstructed. At the end, all image slices were stacked together sequentially to obtain a 3D image model of the object being inspected. From this development, lessons on the way to have better understanding on the internal structure of the object can be approached based on the cross-sectional image slice by slice and surface skin.

  9. Computing elastic moduli on 3-D X-ray computed tomography image stacks

    NASA Astrophysics Data System (ADS)

    Garboczi, E. J.; Kushch, V. I.

    2015-03-01

    A numerical task of current interest is to compute the effective elastic properties of a random composite material by operating on a 3D digital image of its microstructure obtained via X-ray computed tomography (CT). The 3-D image is usually sub-sampled since an X-ray CT image is typically of order 10003 voxels or larger, which is considered to be a very large finite element problem. Two main questions for the validity of any such study are then: can the sub-sample size be made sufficiently large to capture enough of the important details of the random microstructure so that the computed moduli can be thought of as accurate, and what boundary conditions should be chosen for these sub-samples? This paper contributes to the answer of both questions by studying a simulated X-ray CT cylindrical microstructure with three phases, cut from a random model system with known elastic properties. A new hybrid numerical method is introduced, which makes use of finite element solutions coupled with exact solutions for elastic moduli of square arrays of parallel cylindrical fibers. The new method allows, in principle, all of the microstructural data to be used when the X-ray CT image is in the form of a cylinder, which is often the case. Appendix A describes a similar algorithm for spherical sub-samples, which may be of use when examining the mechanical properties of particles. Cubic sub-samples are also taken from this simulated X-ray CT structure to investigate the effect of two different kinds of boundary conditions: forced periodic and fixed displacements. It is found that using forced periodic displacements on the non-geometrically periodic cubic sub-samples always gave more accurate results than using fixed displacements, although with about the same precision. The larger the cubic sub-sample, the more accurate and precise was the elastic computation, and using the complete cylindrical sample with the new method gave still more accurate and precise results. Fortran 90

  10. Computed tomography measurement of 3D combustion chemiluminescence using single camera

    NASA Astrophysics Data System (ADS)

    Wang, Kuanliang; Li, Fei; Zeng, Hui; Zhang, Shaohua; Yu, Xilong

    2016-10-01

    Instantaneous measurement of flame spatial structure has been long desired for complicated combustion condition (gas turbine, ramjet et.). Three dimensional computed tomography of chemiluminescence (3D-CTC) is a potential testing technology for its simplicity, low cost, high temporal and spatial resolution. In most former studies, multi-lens and multi-CCD are used to capture projects from different view angles. In order to improve adaptability, only one CCD was utilized to build 3D-CTC system combined with customized fiber-based endoscopes (FBEs). It makes this technique more economic and simple. Validate experiments were made using 10 small CH4 diffusion flame arranging in a ring structure. Based on one instantaneous image, computed tomography can be conducted using Algebraic Reconstruction Technique (ART) algorithm. The reconstructed results, including the flame number, ring shape of the flames, the inner and outer diameter of ring, all well match the physical structure. It indicates that 3D combustion chemiluminescence could be well reconstructed using single camera.

  11. High-performance computational and geostatistical experiments for testing the capabilities of 3-d electrical tomography

    SciTech Connect

    Carle, S. F.; Daily, W. D.; Newmark, R. L.; Ramirez, A.; Tompson, A.

    1999-01-19

    This project explores the feasibility of combining geologic insight, geostatistics, and high-performance computing to analyze the capabilities of 3-D electrical resistance tomography (ERT). Geostatistical methods are used to characterize the spatial variability of geologic facies that control sub-surface variability of permeability and electrical resistivity Synthetic ERT data sets are generated from geostatistical realizations of alluvial facies architecture. The synthetic data sets enable comparison of the "truth" to inversion results, quantification of the ability to detect particular facies at particular locations, and sensitivity studies on inversion parameters

  12. A review of automated image understanding within 3D baggage computed tomography security screening.

    PubMed

    Mouton, Andre; Breckon, Toby P

    2015-01-01

    Baggage inspection is the principal safeguard against the transportation of prohibited and potentially dangerous materials at airport security checkpoints. Although traditionally performed by 2D X-ray based scanning, increasingly stringent security regulations have led to a growing demand for more advanced imaging technologies. The role of X-ray Computed Tomography is thus rapidly expanding beyond the traditional materials-based detection of explosives. The development of computer vision and image processing techniques for the automated understanding of 3D baggage-CT imagery is however, complicated by poor image resolutions, image clutter and high levels of noise and artefacts. We discuss the recent and most pertinent advancements and identify topics for future research within the challenging domain of automated image understanding for baggage security screening CT.

  13. Optimization of the aperture and the transducer characteristics of a 3D ultrasound computer tomography system

    NASA Astrophysics Data System (ADS)

    Ruiter, Nicole V.; Zapf, Michael; Hopp, Torsten; Dapp, Robin; Gemmeke, Hartmut

    2014-03-01

    A promising candidate for improved imaging of breast cancer is ultrasound computer tomography (USCT). The aim of this work was to design a new aperture for our full 3D USCT which extends the properties of the current aperture to a larger ROI fitting the buoyant breast in water and decreasing artifacts in transmission tomography. The optimization resulted in a larger opening angle of the transducers, a larger diameter of the aperture and an approximately homogeneous distribution of the transducers, with locally random distances. The developed optimization methods allow us to automatically generate an optimized aperture for given diameters of apertures and transducer arrays, as well as quantitative comparison to other arbitrary apertures. Thus, during the design phase of the next generation KIT 3D USCT, the image quality can be balanced against the specification parameters and given hardware and cost limitations. The methods can be applied for general aperture optimization, only limited by the assumptions of a hemispherical aperture and circular transducer arrays.

  14. 3D cephalometric analysis obtained from computed tomography. Review of the literature

    PubMed Central

    Rossini, Giulia; Cavallini, Costanza; Cassetta, Michele; Barbato, Ersilia

    2012-01-01

    Summary Introduction The aim of this systematic review is to estimate accuracy and reproducibility of craniometric measurements and reliability of landmarks identified with computed tomography (CT) techniques in 3D cephalometric analysis. Methods Computerized and manual searches were conducted up to 2011 for studies that addressed these objectives. The selection criteria were: (1) the use of human specimen; (2) the comparison between 2D and 3D cephalometric analysis; (3) the assessment of accuracy, reproducibility of measurements and reliability of landmark identification with CT images compared with two-dimensional conventional radiographs. The Cochrane Handbook for Systematic Reviews of Interventions was used as the guideline for this article. Results Twenty-seven articles met the inclusion criteria. Most of them demonstrated high measurements accuracy and reproducibility, and landmarks reliability, but their cephalometric analysis methodology varied widely. Conclusion These differencies among the studies in making measurements don’t permit a direct comparison between them. The future developments in the knowledge of these techniques should provide a standardized method to conduct the 3D CT cephalometric analysis. PMID:22545187

  15. Registration of 3D ultrasound computer tomography and MRI for evaluation of tissue correspondences

    NASA Astrophysics Data System (ADS)

    Hopp, T.; Dapp, R.; Zapf, M.; Kretzek, E.; Gemmeke, H.; Ruiter, N. V.

    2015-03-01

    3D Ultrasound Computer Tomography (USCT) is a new imaging method for breast cancer diagnosis. In the current state of development it is essential to correlate USCT with a known imaging modality like MRI to evaluate how different tissue types are depicted. Due to different imaging conditions, e.g. with the breast subject to buoyancy in USCT, a direct correlation is demanding. We present a 3D image registration method to reduce positioning differences and allow direct side-by-side comparison of USCT and MRI volumes. It is based on a two-step approach including a buoyancy simulation with a biomechanical model and free form deformations using cubic B-Splines for a surface refinement. Simulation parameters are optimized patient-specifically in a simulated annealing scheme. The method was evaluated with in-vivo datasets resulting in an average registration error below 5mm. Correlating tissue structures can thereby be located in the same or nearby slices in both modalities and three-dimensional non-linear deformations due to the buoyancy are reduced. Image fusion of MRI volumes and USCT sound speed volumes was performed for intuitive display. By applying the registration to data of our first in-vivo study with the KIT 3D USCT, we could correlate several tissue structures in MRI and USCT images and learn how connective tissue, carcinomas and breast implants observed in the MRI are depicted in the USCT imaging modes.

  16. Pore detection in Computed Tomography (CT) soil 3D images using singularity map analysis

    NASA Astrophysics Data System (ADS)

    Sotoca, Juan J. Martin; Tarquis, Ana M.; Saa Requejo, Antonio; Grau, Juan B.

    2016-04-01

    X-ray Computed Tomography (CT) images have significantly helped the study of the internal soil structure. This technique has two main advantages: 1) it is a non-invasive technique, i.e., it doesńt modify the internal soil structure, and 2) it provides a good resolution. The major disadvantage is that these images are sometimes low-contrast in the solid/pore interface. One of the main problems in analyzing soil structure through CT images is to segment them in solid/pore space. To do so, we have different segmentation techniques at our disposal that are mainly based on thresholding methods in which global or local thresholds are calculated to separate pore space from solid space. The aim of this presentation is to develop the fractal approach to soil structure using "singularity maps" and the "Concentration-Area (CA) method". We will establish an analogy between mineralization processes in ore deposits and morphogenesis processes in soils. Resulting from this analogy a new 3D segmentation method is proposed, the "3D Singularity-CA" method. A comparison with traditional 3D segmentation methods will be performed to show the main differences among them.

  17. A Computational Method for 3D Anisotropic Travel-time Tomography of Rocks in the Laboratory

    NASA Astrophysics Data System (ADS)

    Ghofranitabari, Mehdi; Young, R. Paul

    2013-04-01

    True triaxial loading in the laboratory applies three principal stresses on a cubic rock specimen. Elliptical anisotropy and distributed heterogeneities are introduced in the rock due to closure and opening of the pre-existing cracks and creation and growth of the new aligned cracks. The rock sample is tested in a Geophysical Imaging Cell that is armed with an Acoustic Emission monitoring system which can perform transducer to transducer velocity surveys to image velocity structure of the sample during the experiment. Ultrasonic travel-time tomography as a non-destructive method outfits a map of wave propagation velocity in the sample in order to detect the uniformly distributed or localised heterogeneities and provide the spatial variation and temporal evolution of induced damages in rocks at various stages of loading. The rock sample is partitioned into cubic grid cells as model space. Ray-based tomography method measuring body wave travel time along ray paths between pairs of emitting and receiving transducers is used to calculate isotropic ray-path segment matrix elements (Gij) which contain segment lengths of the ith ray in the jth cell in three dimensions. Synthetic P wave travel times are computed between pairs of transducers in a hypothetical isotropic heterogeneous cubic sample as data space along with an error due to precision of measurement. 3D strain of the squeezed rock and the consequent geometrical deformation is also included in computations for further accuracy. Singular Value Decomposition method is used for the inversion from data space to model space. In the next step, the anisotropic ray-path segment matrix and the corresponded data space are computed for hypothetical anisotropic heterogeneous samples based on the elliptical anisotropic model of velocity which is obtained from the real laboratory experimental data. The method is examined for several different synthetic heterogeneous models. An "Inaccuracy factor" is utilized to inquire the

  18. Analysis of bite marks in foodstuffs by computer tomography (cone beam CT)--3D reconstruction.

    PubMed

    Marques, Jeidson; Musse, Jamilly; Caetano, Catarina; Corte-Real, Francisco; Corte-Real, Ana Teresa

    2013-12-01

    The use of three-dimensional (3D) analysis of forensic evidence is highlighted in comparison with traditional methods. This three-dimensional analysis is based on the registration of the surface from a bitten object. The authors propose to use Cone Beam Computed Tomography (CBCT), which is used in dental practice, in order to study the surface and interior of bitten objects and dental casts of suspects. In this study, CBCT is applied to the analysis of bite marks in foodstuffs, which may be found in a forensic case scenario. 6 different types of foodstuffs were used: chocolate, cheese, apple, chewing gum, pizza and tart (flaky pastry and custard). The food was bitten into and dental casts of the possible suspects were made. The dental casts and bitten objects were registered using an x-ray source and the CBCT equipment iCAT® (Pennsylvania, EUA). The software InVivo5® (Anatomage Inc, EUA) was used to visualize and analyze the tomographic slices and 3D reconstructions of the objects. For each material an estimate of its density was assessed by two methods: HU values and specific gravity. All the used materials were successfully reconstructed as good quality 3D images. The relative densities of the materials in study were compared. Amongst the foodstuffs, the chocolate had the highest density (median value 100.5 HU and 1,36 g/cm(3)), while the pizza showed to have the lowest (median value -775 HU and 0,39 g/cm(3)), on both scales. Through tomographic slices and three-dimensional reconstructions it was possible to perform the metric analysis of the bite marks in all the foodstuffs, except for the pizza. These measurements could also be obtained from the dental casts. The depth of the bite mark was also successfully determined in all the foodstuffs except for the pizza. Cone Beam Computed Tomography has the potential to become an important tool for forensic sciences, namely for the registration and analysis of bite marks in foodstuffs that may be found in a crime

  19. Projection-based metal-artifact reduction for industrial 3D X-ray computed tomography.

    PubMed

    Amirkhanov, Artem; Heinzl, Christoph; Reiter, Michael; Kastner, Johann; Gröller, M Eduard

    2011-12-01

    Multi-material components, which contain metal parts surrounded by plastic materials, are highly interesting for inspection using industrial 3D X-ray computed tomography (3DXCT). Examples of this application scenario are connectors or housings with metal inlays in the electronic or automotive industry. A major problem of this type of components is the presence of metal, which causes streaking artifacts and distorts the surrounding media in the reconstructed volume. Streaking artifacts and dark-band artifacts around metal components significantly influence the material characterization (especially for the plastic components). In specific cases these artifacts even prevent a further analysis. Due to the nature and the different characteristics of artifacts, the development of an efficient artifact-reduction technique in reconstruction-space is rather complicated. In this paper we present a projection-space pipeline for metal-artifacts reduction. The proposed technique first segments the metal in the spatial domain of the reconstructed volume in order to separate it from the other materials. Then metal parts are forward-projected on the set of projections in a way that metal-projection regions are treated as voids. Subsequently the voids, which are left by the removed metal, are interpolated in the 2D projections. Finally, the metal is inserted back into the reconstructed 3D volume during the fusion stage. We present a visual analysis tool, allowing for interactive parameter estimation of the metal segmentation. The results of the proposed artifact-reduction technique are demonstrated on a test part as well as on real world components. For these specimens we achieve a significant reduction of metal artifacts, allowing an enhanced material characterization.

  20. Craniosynostosis: prenatal diagnosis by 2D/3D ultrasound, magnetic resonance imaging and computed tomography.

    PubMed

    Helfer, Talita Micheletti; Peixoto, Alberto Borges; Tonni, Gabriele; Araujo Júnior, Edward

    2016-09-01

    Craniosynostosis is defined as the process of premature fusion of one or more of the cranial sutures. It is a common condition that occurs in about 1 to 2,000 live births. Craniosynostosis may be classified in primary or secondary. It is also classified as nonsyndromic or syndromic. According to suture commitment, craniosynostosis may affect a single suture or multiple sutures. There is a wide range of syndromes involving craniosynostosis and the most common are Apert, Pffeifer, Crouzon, Shaethre-Chotzen and Muenke syndromes. The underlying etiology of nonsyndromic craniosynostosis is unknown. Mutations in the fibroblast growth factor (FGF) signalling pathway play a crucial role in the etiology of craniosynostosis syndromes. Prenatal ultrasound`s detection rate of craniosynostosis is low. Nowadays, different methods can be applied for prenatal diagnosis of craniosynostosis, such as two-dimensional (2D) and three-dimensional (3D) ultrasound, magnetic resonance imaging (MRI), computed tomography (CT) scan and, finally, molecular diagnosis. The presence of craniosynostosis may affect the birthing process. Fetuses with craniosynostosis also have higher rates of perinatal complications. In order to avoid the risks of untreated craniosynostosis, children are usually treated surgically soon after postnatal diagnosis.

  1. Computed Tomography 3-D Imaging of the Metal Deformation Flow Path in Friction Stir Welding

    NASA Technical Reports Server (NTRS)

    Schneider, Judy; Beshears, Ronald; Nunes, Arthur C., Jr.

    2005-01-01

    In friction stir welding (FSW), a rotating threaded pin tool is inserted into a weld seam and literally stirs the edges of the seam together. To determine optimal processing parameters for producing a defect free weld, a better understanding of the resulting metal deformation flow path is required. Marker studies are the principal method of studying the metal deformation flow path around the FSW pin tool. In our study, we have used computed tomography (CT) scans to reveal the flow pattern of a lead wire embedded in a FSW weld seam. At the welding temperature of aluminum, the lead becomes molten and is carried with the macro-flow of the weld metal. By using CT images, a 3-dimensional (3D) image of the lead flow pattern can be reconstructed. CT imaging was found to be a convenient and comprehensive way of collecting and displaying tracer data. It marks an advance over previous more tedious and ambiguous radiographic/metallographic data collection methods.

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  3. Detection of bone erosions in early rheumatoid arthritis: 3D ultrasonography versus computed tomography.

    PubMed

    Peluso, G; Bosello, S L; Gremese, E; Mirone, L; Di Gregorio, F; Di Molfetta, V; Pirronti, T; Ferraccioli, G

    2015-07-01

    Three-dimensional (3D) volumetric ultrasonography (US) is an interesting tool that could improve the traditional approach to musculoskeletal US in rheumatology, due to its virtual operator independence and reduced examination time. The aim of this study was to investigate the performance of 3DUS in the detection of bone erosions in hand and wrist joints of early rheumatoid arthritis (ERA) patients, with computed tomography (CT) as the reference method. Twenty ERA patients without erosions on standard radiography of hands and wrists underwent 3DUS and CT evaluation of eleven joints: radiocarpal, intercarpal, ulnocarpal, second to fifth metacarpo-phalangeal (MCP), and second to fifth proximal interphalangeal (PIP) joints of dominant hand. Eleven (55.0%) patients were erosive with CT and ten of them were erosive also at 3DUS evaluation. In five patients, 3DUS identified cortical breaks that were not erosions at CT evaluation. Considering CT as the gold standard to identify erosive patients, the 3DUS sensitivity, specificity, PPV, and NPV were 0.9, 0.55, 0.71, and 0.83, respectively. A total of 32 erosions were detected with CT, 15 of them were also observed at the same sites with 3DUS, whereas 17 were not seen on 3DUS evaluation. The majority of these 3DUS false-negative erosions were in the wrist joints. Furthermore, 18 erosions recorded by 3DUS were false positive. The majority of these 3DUS false-positive erosions were located at PIP joints. This study underlines the limits of 3DUS in detecting individual bone erosion, mostly at the wrist, despite the good sensitivity in identifying erosive patients.

  4. 3D chemical imaging in the laboratory by hyperspectral X-ray computed tomography

    PubMed Central

    Egan, C. K.; Jacques, S. D. M.; Wilson, M. D.; Veale, M. C.; Seller, P.; Beale, A. M.; Pattrick, R. A. D.; Withers, P. J.; Cernik, R. J.

    2015-01-01

    We report the development of laboratory based hyperspectral X-ray computed tomography which allows the internal elemental chemistry of an object to be reconstructed and visualised in three dimensions. The method employs a spectroscopic X-ray imaging detector with sufficient energy resolution to distinguish individual elemental absorption edges. Elemental distributions can then be made by K-edge subtraction, or alternatively by voxel-wise spectral fitting to give relative atomic concentrations. We demonstrate its application to two material systems: studying the distribution of catalyst material on porous substrates for industrial scale chemical processing; and mapping of minerals and inclusion phases inside a mineralised ore sample. The method makes use of a standard laboratory X-ray source with measurement times similar to that required for conventional computed tomography. PMID:26514938

  5. 3D chemical imaging in the laboratory by hyperspectral X-ray computed tomography

    NASA Astrophysics Data System (ADS)

    Egan, C. K.; Jacques, S. D. M.; Wilson, M. D.; Veale, M. C.; Seller, P.; Beale, A. M.; Pattrick, R. A. D.; Withers, P. J.; Cernik, R. J.

    2015-10-01

    We report the development of laboratory based hyperspectral X-ray computed tomography which allows the internal elemental chemistry of an object to be reconstructed and visualised in three dimensions. The method employs a spectroscopic X-ray imaging detector with sufficient energy resolution to distinguish individual elemental absorption edges. Elemental distributions can then be made by K-edge subtraction, or alternatively by voxel-wise spectral fitting to give relative atomic concentrations. We demonstrate its application to two material systems: studying the distribution of catalyst material on porous substrates for industrial scale chemical processing; and mapping of minerals and inclusion phases inside a mineralised ore sample. The method makes use of a standard laboratory X-ray source with measurement times similar to that required for conventional computed tomography.

  6. Breast density measurement: 3D cone beam computed tomography (CBCT) images versus 2D digital mammograms

    NASA Astrophysics Data System (ADS)

    Han, Tao; Lai, Chao-Jen; Chen, Lingyun; Liu, Xinming; Shen, Youtao; Zhong, Yuncheng; Ge, Shuaiping; Yi, Ying; Wang, Tianpeng; Yang, Wei T.; Shaw, Chris C.

    2009-02-01

    Breast density has been recognized as one of the major risk factors for breast cancer. However, breast density is currently estimated using mammograms which are intrinsically 2D in nature and cannot accurately represent the real breast anatomy. In this study, a novel technique for measuring breast density based on the segmentation of 3D cone beam CT (CBCT) images was developed and the results were compared to those obtained from 2D digital mammograms. 16 mastectomy breast specimens were imaged with a bench top flat-panel based CBCT system. The reconstructed 3D CT images were corrected for the cupping artifacts and then filtered to reduce the noise level, followed by using threshold-based segmentation to separate the dense tissue from the adipose tissue. For each breast specimen, volumes of the dense tissue structures and the entire breast were computed and used to calculate the volumetric breast density. BI-RADS categories were derived from the measured breast densities and compared with those estimated from conventional digital mammograms. The results show that in 10 of 16 cases the BI-RADS categories derived from the CBCT images were lower than those derived from the mammograms by one category. Thus, breasts considered as dense in mammographic examinations may not be considered as dense with the CBCT images. This result indicates that the relation between breast cancer risk and true (volumetric) breast density needs to be further investigated.

  7. Use of micro computed-tomography and 3D printing for reverse engineering of mouse embryo nasal capsule

    NASA Astrophysics Data System (ADS)

    Tesařová, M.; Zikmund, T.; Kaucká, M.; Adameyko, I.; Jaroš, J.; Paloušek, D.; Škaroupka, D.; Kaiser, J.

    2016-03-01

    Imaging of increasingly complex cartilage in vertebrate embryos is one of the key tasks of developmental biology. This is especially important to study shape-organizing processes during initial skeletal formation and growth. Advanced imaging techniques that are reflecting biological needs give a powerful impulse to push the boundaries of biological visualization. Recently, techniques for contrasting tissues and organs have improved considerably, extending traditional 2D imaging approaches to 3D . X-ray micro computed tomography (μCT), which allows 3D imaging of biological objects including their internal structures with a resolution in the micrometer range, in combination with contrasting techniques seems to be the most suitable approach for non-destructive imaging of embryonic developing cartilage. Despite there are many software-based ways for visualization of 3D data sets, having a real solid model of the studied object might give novel opportunities to fully understand the shape-organizing processes in the developing body. In this feasibility study we demonstrated the full procedure of creating a real 3D object of mouse embryo nasal capsule, i.e. the staining, the μCT scanning combined by the advanced data processing and the 3D printing.

  8. Laser cone beam computed tomography scanner geometry for large volume 3D dosimetry

    NASA Astrophysics Data System (ADS)

    Jordan, K. J.; Turnbull, D.; Batista, J. J.

    2013-06-01

    A new scanner geometry for fast optical cone-beam computed tomography is reported. The system consists of a low power laser beam, raster scanned, under computer control, through a transparent object in a refractive index matching aquarium. The transmitted beam is scattered from a diffuser screen and detected by a photomultiplier tube. Modest stray light is present in the projection images since only a single ray is present in the object during measurement and there is no imaging optics to introduce further stray light in the form of glare. A scan time of 30 minutes was required for 512 projections with a field of view of 12 × 18 cm. Initial performance from scanning a 15 cm diameter jar with black solutions is presented. Averaged reconstruction coefficients are within 2% along the height of the jar and within the central 85% of diameter, due to the index mismatch of the jar. Agreement with spectrometer measurements was better than 0.5% for a minimum transmission of 4% and within 4% for a dark, 0.1% transmission sample. This geometry's advantages include high dynamic range and low cost of scaling to larger (>15 cm) fields of view.

  9. Scanning laser optical computed tomography system for large volume 3D dosimetry

    NASA Astrophysics Data System (ADS)

    Dekker, Kurtis H.; Battista, Jerry J.; Jordan, Kevin J.

    2017-04-01

    Stray light causes artifacts in optical computed tomography (CT) that negatively affect the accuracy of radiation dosimetry in gels or solids. Scatter effects are exacerbated by a large dosimeter volume, which is desirable for direct verification of modern radiotherapy treatment plans such as multiple-isocenter radiosurgery. The goal in this study was to design and characterize an optical CT system that achieves high accuracy primary transmission measurements through effective stray light rejection, while maintaining sufficient scan speed for practical application. We present an optical imaging platform that uses a galvanometer mirror for horizontal scanning, and a translation stage for vertical movement of a laser beam and small area detector for minimal stray light production and acceptance. This is coupled with a custom lens-shaped optical CT aquarium for parallel ray sampling of projections. The scanner images 15 cm diameter, 12 cm height cylindrical volumes at 0.33 mm resolution in approximately 30 min. Attenuation coefficients reconstructed from CT scans agreed with independent cuvette measurements within 2% for both absorbing and scattering solutions as well as small 1.25 cm diameter absorbing phantoms placed within a large, scattering medium that mimics gel. Excellent linearity between the optical CT scanner and the independent measurement was observed for solutions with between 90% and 2% transmission. These results indicate that the scanner should achieve highly accurate dosimetry of large volume dosimeters in a reasonable timeframe for clinical application to radiotherapy dose verification procedures.

  10. Scanning laser optical computed tomography system for large volume 3D dosimetry.

    PubMed

    Dekker, Kurtis H; Battista, Jerry J; Jordan, Kevin J

    2017-04-07

    Stray light causes artifacts in optical computed tomography (CT) that negatively affect the accuracy of radiation dosimetry in gels or solids. Scatter effects are exacerbated by a large dosimeter volume, which is desirable for direct verification of modern radiotherapy treatment plans such as multiple-isocenter radiosurgery. The goal in this study was to design and characterize an optical CT system that achieves high accuracy primary transmission measurements through effective stray light rejection, while maintaining sufficient scan speed for practical application. We present an optical imaging platform that uses a galvanometer mirror for horizontal scanning, and a translation stage for vertical movement of a laser beam and small area detector for minimal stray light production and acceptance. This is coupled with a custom lens-shaped optical CT aquarium for parallel ray sampling of projections. The scanner images 15 cm diameter, 12 cm height cylindrical volumes at 0.33 mm resolution in approximately 30 min. Attenuation coefficients reconstructed from CT scans agreed with independent cuvette measurements within 2% for both absorbing and scattering solutions as well as small 1.25 cm diameter absorbing phantoms placed within a large, scattering medium that mimics gel. Excellent linearity between the optical CT scanner and the independent measurement was observed for solutions with between 90% and 2% transmission. These results indicate that the scanner should achieve highly accurate dosimetry of large volume dosimeters in a reasonable timeframe for clinical application to radiotherapy dose verification procedures.

  11. Post-mortem computed tomography and 3D imaging: anthropological applications for juvenile remains.

    PubMed

    Brough, Alison L; Rutty, Guy N; Black, Sue; Morgan, Bruno

    2012-09-01

    Anthropological examination of defleshed bones is routinely used in medico-legal investigations to establish an individual's biological profile. However, when dealing with the recently deceased, the removal of soft tissue from bone can be an extremely time consuming procedure that requires the presence of a trained anthropologist. In addition, due to its invasive nature, in some disaster victim identification scenarios the maceration of bones is discouraged by religious practices and beliefs, or even prohibited by national laws and regulations. Currently, three different radiological techniques may be used in the investigative process; plain X-ray, dental X-ray and fluoroscopy. However, recent advances in multi-detector computed tomography (MDCT) mean that it is now possible to acquire morphological skeletal information from high resolution images, reducing the necessity for invasive procedures. This review paper considers the possible applications of a virtual anthropological examination by reviewing the main juvenile age determination methods used by anthropologists at present and their possible adaption to MDCT.

  12. Measurement error of 3D cranial landmarks of an ontogenetic sample using Computed Tomography

    PubMed Central

    Barbeito-Andrés, Jimena; Anzelmo, Marisol; Ventrice, Fernando; Sardi, Marina L.

    2012-01-01

    Background/Aim Computed Tomography (CT) is a powerful tool in craniofacial research that focuses on morphological variation. In this field, an ontogenetic approach has been taken to study the developmental sources of variation and to understand the basis of morphological evolution. This work aimed to determine measurement error (ME) in cranial CT in diverse developmental stages and to characterize how this error relates to different types of landmarks. Material and methods We used a sample of fifteen skulls ranging from 0 to 31 years. Two observers placed landmarks in each image three times. Measurement error was assessed before and after Generalized Procrustes Analysis. Results The results indicated that ME is larger in neurocranial structures, which are described mainly by type III landmarks and semilandmarks. In addition, adult and infant specimens showed the same level of ME. These results are specially relevant in the context of craniofacial growth research. Conclusion CT images have become a frequent evidence to study cranial variation. Evaluation of ME gives insight into the potential source of error in interpreting results. Neural structures present higher ME which is mainly associated to landmark localization. However, this error is irrespective of age. If landmarks are correctly selected, they can be analyzed with the same level of reliability in adults and subadults. PMID:25737840

  13. Computer Tomography 3-D Imaging of the Metal Deformation Flow Path in Friction Stir Welding

    NASA Technical Reports Server (NTRS)

    Schneider, Judy; Beshears, Ronald; Nunes, Arthur C., Jr.

    2004-01-01

    In friction stir welding, a rotating threaded pin tool is inserted into a weld seam and literally stirs the edges of the seam together. This solid-state technique has been successfully used in the joining of materials that are difficult to fusion weld such as aluminum alloys. To determine optimal processing parameters for producing a defect free weld, a better understanding of the resulting metal deformation flow path is required. Marker studies are the principal method of studying the metal deformation flow path around the FSW pin tool. In our study, we have used computed tomography (CT) scans to reveal the flow pattern of a lead wire embedded in a FSW weld seam. At the welding temperature of aluminum, the lead becomes molten and thus tracks the aluminum deformation flow paths in a unique 3-dimensional manner. CT scanning is a convenient and comprehensive way of collecting and displaying tracer data. It marks an advance over previous more tedious and ambiguous radiographic/metallographic data collection methods.

  14. Quantification of arthritic bone degradation by analysis of 3D micro-computed tomography data

    PubMed Central

    Svensson, Carl-Magnus; Hoffmann, Bianca; Irmler, Ingo M.; Straßburger, Maria; Figge, Marc Thilo; Saluz, Hans Peter

    2017-01-01

    The use of animal models of arthritis is a key component in the evaluation of therapeutic strategies against the human disease rheumatoid arthritis (RA). Here we present quantitative measurements of bone degradation characterised by the cortical bone profile using glucose-6-phosphate isomerase (G6PI) induced arthritis. We applied micro-computed tomography (μCT) during three arthritis experiments and one control experiment to image the metatarsals of the hind paws and to investigate the effect of experimental arthritis on their cortical bone profile. For measurements of the cortical profile we automatically identified slices that are orthogonal to individual metatarsals, thereby making the measurements independent of animal placement in the scanner. We measured the average cortical thickness index (CTI) of the metatarsals, as well as the thickness changes along the metatarsal. In this study we introduced the cortical thickness gradient (CTG) as a new measure and we investigated how arthritis affects this measure. We found that in general both CTI and CTG are able to quantify arthritic progression, whilst CTG was found to be the more sensitive measure. PMID:28290525

  15. A preliminary 3D computed tomography study of the human maxillary sinus and nasal cavity.

    PubMed

    Butaric, Lauren N; McCarthy, Robert C; Broadfield, Douglas C

    2010-11-01

    Despite centuries of investigation, the function of the maxillary sinus (MS) and underlying patterns governing its form remain elusive. In this study, we articulate a methodology for collecting volumetric data for the MS and nasal cavity (NC) from computed tomography (CT) scans and report details for a small sample of 39 dried human crania of known ecogeographic provenience useful for assessing variation in MS size and shape. We use scaling analyses to preliminarily test the hypothesis that volumes of the nasal cavity (NCV) and maxillary sinus (MSV) are inversely correlated such that the NC covaries with size of the face, whereas the MS "fills in" the leftover space [proposed by Shea: Am J Phys Anthropol 47 (1977):289-300]. Against expectation, MSV is not significantly correlated with NCV or any cranial size variable. NCV, on the other hand, scales isometrically with facial size. The results of this pilot study suggest that NCV covaries with facial size, but that the MS does not simply fill in the leftover space in the face. The role, if any, of the MSs in midfacial function and architecture remains unclear. Larger sample sizes, additional environmental variables, and assessment of MS and NC shape are necessary to resolve this issue.

  16. Complex anatomy surrounding the left atrial posterior wall: analysis with 3D computed tomography.

    PubMed

    Maeda, Shingo; Iesaka, Yoshito; Uno, Kikuya; Otomo, Kiyoshi; Nagata, Yasutoshi; Suzuki, Kenji; Hachiya, Hitoshi; Goya, Masahiko; Takahashi, Atsushi; Fujiwara, Hideomi; Hiraoka, Masayasu; Isobe, Mitsuaki

    2012-01-01

    Few studies have explored the topographic anatomy of the esophagus, posterior wall of the left atrium (LA), or fat pads using multidetector computed tomography (MDCT) to prevent the risk of esophageal injury during atrial fibrillation (AF) ablation. MDCT was performed in 110 consecutive patients with paroxysmal or persistent AF before the ablation procedure to understand the anatomic relationship of the esophagus. Two major types of esophagus routes were demonstrated. Leftward (type A) and rightward (type B) routes were found in 90 and 10% of the patients, respectively. A type A route had a larger mean size of the LA than type B. The fat pad was identifiable at the level of the inferior pulmonary vein in 91% of the patients without any predominance of either type. The thickness of the fat pad was thinner in the patients with a dilated LA (>42 mm) than in those with a normal LA size (≤42 mm) (p = 0.01). The results demonstrated that the majority of cases had a leftward route of the esophagus. There was a close association between the LA dilatation and fat pad thinning. With a dilated LA, the esophagus may become easily susceptible to direct thermal injury during AF ablation. Visualization of the anatomic relationship may contribute to the prevention of the potential risk of an esophageal injury.

  17. Small-Field Measurements of 3D Polymer Gel Dosimeters through Optical Computed Tomography

    PubMed Central

    Shih, Cheng-Ting; Lee, Yao-Ting; Wu, Shin-Hua; Yao, Chun-Hsu; Hsieh, Bor-Tsung

    2016-01-01

    With advances in therapeutic instruments and techniques, three-dimensional dose delivery has been widely used in radiotherapy. The verification of dose distribution in a small field becomes critical because of the obvious dose gradient within the field. The study investigates the dose distributions of various field sizes by using NIPAM polymer gel dosimeter. The dosimeter consists of 5% gelatin, 5% monomers, 3% cross linkers, and 5 mM THPC. After irradiation, a 24 to 96 hour delay was applied, and the gel dosimeters were read by a cone beam optical computed tomography (optical CT) scanner. The dose distributions measured by the NIPAM gel dosimeter were compared to the outputs of the treatment planning system using gamma evaluation. For the criteria of 3%/3 mm, the pass rates for 5 × 5, 3 × 3, 2 × 2, 1 × 1, and 0.5 × 0.5 cm2 were as high as 91.7%, 90.7%, 88.2%, 74.8%, and 37.3%, respectively. For the criteria of 5%/5 mm, the gamma pass rates of the 5 × 5, 3 × 3, and 2 × 2 cm2 fields were over 99%. The NIPAM gel dosimeter provides high chemical stability. With cone-beam optical CT readouts, the NIPAM polymer gel dosimeter has potential for clinical dose verification of small-field irradiation. PMID:26974434

  18. Micro-computed tomography image-based evaluation of 3D anisotropy degree of polymer scaffolds.

    PubMed

    Pérez-Ramírez, Ursula; López-Orive, Jesús Javier; Arana, Estanislao; Salmerón-Sánchez, Manuel; Moratal, David

    2015-01-01

    Anisotropy is one of the most meaningful determinants of biomechanical behaviour. This study employs micro-computed tomography (μCT) and image techniques for analysing the anisotropy of regenerative medicine polymer scaffolds. For this purpose, three three-dimensional anisotropy evaluation image methods were used: ellipsoid of inertia (EI), mean intercept length (MIL) and tensor scale (t-scale). These were applied to three patterns (a sphere, a cube and a right prism) and to two polymer scaffold topologies (cylindrical orthogonal pore mesh and spherical pores). For the patterns, the three methods provided good results. Regarding the scaffolds, EI mistook both topologies (0.0158, [-0.5683; 0.6001]; mean difference and 95% confidence interval), and MIL showed no significant differences (0.3509, [0.0656; 0.6362]). T-scale is the preferable method because it gave the best capability (0.3441, [0.1779; 0.5102]) to differentiate both topologies. This methodology results in the development of non-destructive tools to engineer biomimetic scaffolds, incorporating anisotropy as a fundamental property to be mimicked from the original tissue and permitting its assessment by means of μCT image analysis.

  19. A novel structured dictionary for fast processing of 3D medical images, with application to computed tomography restoration and denoising

    NASA Astrophysics Data System (ADS)

    Karimi, Davood; Ward, Rabab K.

    2016-03-01

    Sparse representation of signals in learned overcomplete dictionaries has proven to be a powerful tool with applications in denoising, restoration, compression, reconstruction, and more. Recent research has shown that learned overcomplete dictionaries can lead to better results than analytical dictionaries such as wavelets in almost all image processing applications. However, a major disadvantage of these dictionaries is that their learning and usage is very computationally intensive. In particular, finding the sparse representation of a signal in these dictionaries requires solving an optimization problem that leads to very long computational times, especially in 3D image processing. Moreover, the sparse representation found by greedy algorithms is usually sub-optimal. In this paper, we propose a novel two-level dictionary structure that improves the performance and the speed of standard greedy sparse coding methods. The first (i.e., the top) level in our dictionary is a fixed orthonormal basis, whereas the second level includes the atoms that are learned from the training data. We explain how such a dictionary can be learned from the training data and how the sparse representation of a new signal in this dictionary can be computed. As an application, we use the proposed dictionary structure for removing the noise and artifacts in 3D computed tomography (CT) images. Our experiments with real CT images show that the proposed method achieves results that are comparable with standard dictionary-based methods while substantially reducing the computational time.

  20. Classification and quantification of pore shapes in sandstone reservoir rocks with 3-D X-ray micro-computed tomography

    NASA Astrophysics Data System (ADS)

    Schmitt, Mayka; Halisch, Matthias; Müller, Cornelia; Peres Fernandes, Celso

    2016-02-01

    Recent years have seen a growing interest in the characterization of the pore morphologies of reservoir rocks and how the spatial organization of pore traits affects the macro behavior of rock-fluid systems. With the availability of 3-D high-resolution imaging, such as x-ray micro-computed tomography (µ-CT), the detailed quantification of particle shapes has been facilitated by progress in computer science. Here, we show how the shapes of irregular rock particles (pores) can be classified and quantified based on binary 3-D images. The methodology requires the measurement of basic 3-D particle descriptors (length, width, and thickness) and a shape classification that involves the similarity of artificial objects, which is based on main pore network detachments and 3-D sample sizes. Two main pore components were identified from the analyzed volumes: pore networks and residual pore ganglia. A watershed algorithm was applied to preserve the pore morphology after separating the main pore networks, which is essential for the pore shape characterization. The results were validated for three sandstones (S1, S2, and S3) from distinct reservoirs, and most of the pore shapes were found to be plate- and cube-like, ranging from 39.49 to 50.94 % and from 58.80 to 45.18 % when the Feret caliper descriptor was investigated in a 10003 voxel volume. Furthermore, this study generalizes a practical way to correlate specific particle shapes, such as rods, blades, cuboids, plates, and cubes to characterize asymmetric particles of any material type with 3-D image analysis.

  1. A fully 3D approach for metal artifact reduction in computed tomography

    SciTech Connect

    Kratz, Baerbel; Weyers, Imke; Buzug, Thorsten M.

    2012-11-15

    Purpose: In computed tomography imaging metal objects in the region of interest introduce inconsistencies during data acquisition. Reconstructing these data leads to an image in spatial domain including star-shaped or stripe-like artifacts. In order to enhance the quality of the resulting image the influence of the metal objects can be reduced. Here, a metal artifact reduction (MAR) approach is proposed that is based on a recomputation of the inconsistent projection data using a fully three-dimensional Fourier-based interpolation. The success of the projection space restoration depends sensitively on a sensible continuation of neighboring structures into the recomputed area. Fortunately, structural information of the entire data is inherently included in the Fourier space of the data. This can be used for a reasonable recomputation of the inconsistent projection data. Methods: The key step of the proposed MAR strategy is the recomputation of the inconsistent projection data based on an interpolation using nonequispaced fast Fourier transforms (NFFT). The NFFT interpolation can be applied in arbitrary dimension. The approach overcomes the problem of adequate neighborhood definitions on irregular grids, since this is inherently given through the usage of higher dimensional Fourier transforms. Here, applications up to the third interpolation dimension are presented and validated. Furthermore, prior knowledge may be included by an appropriate damping of the transform during the interpolation step. This MAR method is applicable on each angular view of a detector row, on two-dimensional projection data as well as on three-dimensional projection data, e.g., a set of sequential acquisitions at different spatial positions, projection data of a spiral acquisition, or cone-beam projection data. Results: Results of the novel MAR scheme based on one-, two-, and three-dimensional NFFT interpolations are presented. All results are compared in projection data space and spatial

  2. 3D artificial bones for bone repair prepared by computed tomography-guided fused deposition modeling for bone repair.

    PubMed

    Xu, Ning; Ye, Xiaojian; Wei, Daixu; Zhong, Jian; Chen, Yuyun; Xu, Guohua; He, Dannong

    2014-09-10

    The medical community has expressed significant interest in the development of new types of artificial bones that mimic natural bones. In this study, computed tomography (CT)-guided fused deposition modeling (FDM) was employed to fabricate polycaprolactone (PCL)/hydroxyapatite (HA) and PCL 3D artificial bones to mimic natural goat femurs. The in vitro mechanical properties, in vitro cell biocompatibility, and in vivo performance of the artificial bones in a long load-bearing goat femur bone segmental defect model were studied. All of the results indicate that CT-guided FDM is a simple, convenient, relatively low-cost method that is suitable for fabricating natural bonelike artificial bones. Moreover, PCL/HA 3D artificial bones prepared by CT-guided FDM have more close mechanics to natural bone, good in vitro cell biocompatibility, biodegradation ability, and appropriate in vivo new bone formation ability. Therefore, PCL/HA 3D artificial bones could be potentially be of use in the treatment of patients with clinical bone defects.

  3. A C-Shaped Canal in a Maxillary Second Molar: Prexion 3D Cone-Beam Computed Tomography Analysis

    PubMed Central

    Lopes, Daniela Siqueira; Câmara, Andréa Cruz; do Nascimento, Monikelly do Carmo Chagas; Farias de Araújo, Luciane

    2016-01-01

    Objective: The aim of this study was to present an atypical case of a C-shaped root canal that was present in the vestibular root of a permanent maxillary second molar using PreXion 3-D cone-beam computed tomography (CBCT) as a diagnostic device. Materials and Methods: A 50-year-old female patient was referred for routine examination to a private diagnostic imaging clinic in Recife-Pernambuco. During the physical examination, the presence of an unusual C-shaped anatomy in the vestibular canal with a mesiodistal interconnection that extended from the apical to the cervical third was detected in axial slices acquired with a PreXion 3-D scanner. Results: Although C-shaped root canals are most frequently observed in the mandibular second molar, this case presented a rare finding in the permanent maxillary second molar. Conclusions: PreXion 3-D CBCT has emerged as a new high-resolution imaging test technology, thus assisting with the diagnosis of anatomical variations such as C-shaped root canals. However, such imaging technology is not recommended for routine use. PMID:28275283

  4. Characterization of Pore Defects and Fatigue Cracks in Die Cast AM60 Using 3D X-ray Computed Tomography

    NASA Astrophysics Data System (ADS)

    Yang, Zhuofei; Kang, Jidong; Wilkinson, David S.

    2015-08-01

    AM60 high pressure die castings have been used in automobile applications to reduce the weight of vehicles. However, the pore defects that are inherent in die casting may negatively affect mechanical properties, especially the fatigue properties. Here we have studied damage ( e.g., pore defects, fatigue cracks) during strained-controlled fatigue using 3-dimensional X-ray computed tomography (XCT). The fatigue test was interrupted every 2000 cycles and the specimen was removed to be scanned using a desktop micro-CT system. XCT reveals pore defects, cracks, and fracture surfaces. The results show that pores can be accurately measured and modeled in 3D. Defect bands are found to be made of pores under 50 µm (based on volume-equivalent sphere diameter). Larger pores are randomly distributed in the region between the defect bands. Observation of fatigue cracks by XCT is performed in three ways such that the 3D model gives the best illustration of crack-porosity interaction while the other two methods, with the cracks being viewed on transverse or longitudinal cross sections, have better detectability on crack initiation and crack tip observation. XCT is also of value in failure analysis on fracture surfaces. By assessing XCT data during fatigue testing and observing fracture surfaces on a 3D model, a better understanding on the crack initiation, crack-porosity interaction, and the morphology of fracture surface is achieved.

  5. Hemifacial microsomia with spinal and rib anomalies: prenatal diagnosis and postmortem confirmation using 3-D computed tomography reconstruction.

    PubMed

    Haratz, Karina; Vinkler, Chana; Lev, Dorit; Schreiber, Letizia; Malinger, Gustavo

    2011-01-01

    Hemifacial microsomia (OMIM164210) is a condition featuring unilateral ear anomalies and ocular epibulbar dermoids associated with unilateral underdevelopment of the craniofacial bony structures. Other associated anomalies have also been described, especially spinal malformations, and the term oculoauriculovertebral dysplasia spectrum (OVAS) was suggested to include the three predominant systems involved. Both genetic and environmental causes are implied in the pathogenesis of the syndrome, with a 3% recurrence rate according to reports of both vertical transmission and affected siblings. No specific gene was identified, albeit mutations in chromosome 10 and deficiencies of genes in the endothelin pathway in mice exhibited the same clinical features. We hereby describe the first case of prenatal diagnosis of spinal and rib malformations associated to hemifacial microsomia by means of 2-D and 3-D ultrasound in a 23-week fetus. The sonographic study depicted fetal scoliosis due to the presence of hemivertebrae, Sprengel's deformity of the left shoulder, ribs fusion, asymmetric ears with unilateral microtia, mandible unilateral hypoplasia as well as single umbilical artery and a 'golf ball' sign in the left ventricle of the heart. The diagnosis of OVAS was suggested and the family received proper genetic consultation. After termination of the pregnancy, the syndrome was confirmed by postmortem 3-D computed tomography study. In view of the grim outcome, prenatal death rate and high mortality and morbidity when three or more systems are involved, prenatal diagnosis and appropriate counseling are warranted.

  6. Thoracic Temporal Subtraction Three Dimensional Computed Tomography (3D-CT): Screening for Vertebral Metastases of Primary Lung Cancers

    PubMed Central

    Iwano, Shingo; Ito, Rintaro; Umakoshi, Hiroyasu; Karino, Takatoshi; Inoue, Tsutomu; Li, Yuanzhong; Naganawa, Shinji

    2017-01-01

    Purpose We developed an original, computer-aided diagnosis (CAD) software that subtracts the initial thoracic vertebral three-dimensional computed tomography (3D-CT) image from the follow-up 3D-CT image. The aim of this study was to investigate the efficacy of this CAD software during screening for vertebral metastases on follow-up CT images of primary lung cancer patients. Materials and Methods The interpretation experiment included 30 sets of follow-up CT scans in primary lung cancer patients and was performed by two readers (readers A and B), who each had 2.5 years’ experience reading CT images. In 395 vertebrae from C6 to L3, 46 vertebral metastases were identified as follows: osteolytic metastases (n = 17), osteoblastic metastases (n = 14), combined osteolytic and osteoblastic metastases (n = 6), and pathological fractures (n = 9). Thirty-six lesions were in the anterior component (vertebral body), and 10 lesions were in the posterior component (vertebral arch, transverse process, and spinous process). The area under the curve (AUC) by receiver operating characteristic (ROC) curve analysis and the sensitivity and specificity for detecting vertebral metastases were compared with and without CAD for each observer. Results Reader A detected 47 abnormalities on CT images without CAD, and 33 of them were true-positive metastatic lesions. Using CAD, reader A detected 57 abnormalities, and 38 were true positives. The sensitivity increased from 0.717 to 0.826, and on ROC curve analysis, AUC with CAD was significantly higher than that without CAD (0.849 vs. 0.902, p = 0.021). Reader B detected 40 abnormalities on CT images without CAD, and 36 of them were true-positive metastatic lesions. Using CAD, reader B detected 44 abnormalities, and 39 were true positives. The sensitivity increased from 0.783 to 0.848, and AUC with CAD was nonsignificantly higher than that without CAD (0.889 vs. 0.910, p = 0.341). Both readers detected more osteolytic and osteoblastic

  7. Advanced 3D textile composites reinforcements meso F.E analyses based on X-ray computed tomography

    NASA Astrophysics Data System (ADS)

    Naouar, Naim; Vidal-Salle, Emmanuelle; Boisse, Philippe

    2016-10-01

    Meso-FE modelling of 3D textile composites is a powerful tool, which can help determine mechanical properties and permeability of the reinforcements or composites. The quality of the meso FE analyses depends on the quality of the initial model. A direct method based on X-ray tomography imaging is introduced to determine finite element models based on the real geometry of 3D composite reinforcements. The method is particularly suitable regarding 3D textile reinforcements for which internal geometries are numerous and complex. The approach used for the separation of the yarns in different directions is specialized because the fibres flow in three-dimensional space. An analysis of the image's texture is performed. A hyperelastic model developed for fibre bundles is used for the simulation of the deformation of the 3D reinforcement.

  8. Computed Tomography Image Origin Identification based on Original Sensor Pattern Noise and 3D Image Reconstruction Algorithm Footprints.

    PubMed

    Duan, Yuping; Bouslimi, Dalel; Yang, Guanyu; Shu, Huazhong; Coatrieux, Gouenou

    2016-06-08

    In this paper, we focus on the "blind" identification of the Computed Tomography (CT) scanner that has produced a CT image. To do so, we propose a set of noise features derived from the image chain acquisition and which can be used as CT-Scanner footprint. Basically, we propose two approaches. The first one aims at identifying a CT-Scanner based on an Original Sensor Pattern Noise (OSPN) that is intrinsic to the X-ray detectors. The second one identifies an acquisition system based on the way this noise is modified by its 3D image reconstruction algorithm. As these reconstruction algorithms are manufacturer dependent and kept secret, our features are used as input to train an SVM based classifier so as to discriminate acquisition systems. Experiments conducted on images issued from 15 different CT-Scanner models of 4 distinct manufacturers demonstrate that our system identifies the origin of one CT image with a detection rate of at least 94% and that it achieves better performance than Sensor Pattern Noise (SPN) based strategy proposed for general public camera devices.

  9. Bayesian 3D X-ray computed tomography image reconstruction with a scaled Gaussian mixture prior model

    NASA Astrophysics Data System (ADS)

    Wang, Li; Gac, Nicolas; Mohammad-Djafari, Ali

    2015-01-01

    In order to improve quality of 3D X-ray tomography reconstruction for Non Destructive Testing (NDT), we investigate in this paper hierarchical Bayesian methods. In NDT, useful prior information on the volume like the limited number of materials or the presence of homogeneous area can be included in the iterative reconstruction algorithms. In hierarchical Bayesian methods, not only the volume is estimated thanks to the prior model of the volume but also the hyper parameters of this prior. This additional complexity in the reconstruction methods when applied to large volumes (from 5123 to 81923 voxels) results in an increasing computational cost. To reduce it, the hierarchical Bayesian methods investigated in this paper lead to an algorithm acceleration by Variational Bayesian Approximation (VBA) [1] and hardware acceleration thanks to projection and back-projection operators paralleled on many core processors like GPU [2]. In this paper, we will consider a Student-t prior on the gradient of the image implemented in a hierarchical way [3, 4, 1]. Operators H (forward or projection) and Ht (adjoint or back-projection) implanted in multi-GPU [2] have been used in this study. Different methods will be evalued on synthetic volume "Shepp and Logan" in terms of quality and time of reconstruction. We used several simple regularizations of order 1 and order 2. Other prior models also exists [5]. Sometimes for a discrete image, we can do the segmentation and reconstruction at the same time, then the reconstruction can be done with less projections.

  10. 3D-Microarchitectural patterns of Hyperostosis frontalis interna: a micro-computed tomography study in aged women.

    PubMed

    Bracanovic, Djurdja; Djonic, Danijela; Nikolic, Slobodan; Milovanovic, Petar; Rakocevic, Zoran; Zivkovic, Vladimir; Djuric, Marija

    2016-11-01

    Although seen frequently during dissections and autopsies, Hyperostosis frontalis interna (HFI) - a morphological pattern of the frontal bone thickening - is often ignored and its nature and development are not yet understood sufficiently. Current macroscopic classification defines four grades/stages of HFI based on the morphological appearance and size of the affected area; however, it is unclear if these stages also depict the successive phases in the HFI development. Here we assessed 3D-microarchitecture of the frontal bone in women with various degrees of HFI expression and in an age- and sex-matched control group, hypothesizing that the bone microarchitecture bears imprints of the pathogenesis of HFI and may clarify the phases of its development. Frontal bone samples were collected during routine autopsies from 20 women with HFI (age: 69.9 ± 11.1 years) and 14 women without HFI (age: 74.1 ± 9.7 years). We classified the HFI samples into four groups, each group demonstrating different macroscopic type or stage of HFI. All samples were scanned by micro-computed tomography to evaluate 3D bone microarchitecture in the following regions of interest: total sample, outer table, diploe and inner table. Our results revealed that, compared to the control group, the women with HFI showed a significantly increased bone volume fraction in the region of diploe, along with significantly thicker and more plate-like shaped trabeculae and reduced trabecular separation and connectivity density. Moreover, the inner table of the frontal bone in women with HFI displayed significantly increased total porosity and mean pore diameter compared to controls. Microstructural reorganization of the frontal bone in women with HFI was also reflected in significantly higher porosity and lower bone volume fraction in the inner vs. outer table due to an increased number of pores larger than 100 μm. The individual comparisons between the control group and different macroscopic stages of

  11. APPLICATION OF 3D COMPUTER-AIDED TOMOGRAPHY TO THE QUANTIFICATION OF MARINE SEDIMENT COMMUNITIES IN POLLUTION GRADIENTS

    EPA Science Inventory

    Computer-Aided Tomography (CT) has been demonstrated to be a cost efficient tool for the qualitative and quantitative study of estuarine benthic communities along pollution gradients.
    Now we have advanced this technology to successfully visualize and discriminate three dimen...

  12. Classification and quantification of pore shapes in sandstone reservoir rocks with 3-D X-ray micro-computed tomography

    NASA Astrophysics Data System (ADS)

    Schmitt, M.; Halisch, M.; Müller, C.; Fernandes, C. P.

    2015-12-01

    Recent years have seen a growing interest in the characterization of the pore morphologies of reservoir rocks and how the spatial organization of pore traits affects the macro behaviour of rock-fluid systems. With the availability of 3-D high-resolution imaging (e.g. μ-CT), the detailed quantification of particle shapes has been facilitated by progress in computer science. Here, we show how the shapes of irregular rock particles (pores) can be classified and quantified based on binary 3-D images. The methodology requires the measurement of basic 3-D particle descriptors and a shape classification that involves the similarity of artificial objects, which is based on main pore network detachments and 3-D sample sizes. The results were validated for three sandstones (S1, S2 and S3) from distinct reservoirs, and most of the pore shapes were found to be plate- and cube-like. Furthermore, this study generalizes a practical way to correlate specific particle shapes, such as rods, blades, cuboids, plates and cubes, to characterize asymmetric particles of any material type with 3-D image analysis.

  13. Cardiac C-arm computed tomography using a 3D + time ROI reconstruction method with spatial and temporal regularization

    SciTech Connect

    Mory, Cyril; Auvray, Vincent; Zhang, Bo; Grass, Michael; Schäfer, Dirk; Chen, S. James; Carroll, John D.; Rit, Simon; Peyrin, Françoise; Douek, Philippe; Boussel, Loïc

    2014-02-15

    Purpose: Reconstruction of the beating heart in 3D + time in the catheter laboratory using only the available C-arm system would improve diagnosis, guidance, device sizing, and outcome control for intracardiac interventions, e.g., electrophysiology, valvular disease treatment, structural or congenital heart disease. To obtain such a reconstruction, the patient's electrocardiogram (ECG) must be recorded during the acquisition and used in the reconstruction. In this paper, the authors present a 4D reconstruction method aiming to reconstruct the heart from a single sweep 10 s acquisition. Methods: The authors introduce the 4D RecOnstructiOn using Spatial and TEmporal Regularization (short 4D ROOSTER) method, which reconstructs all cardiac phases at once, as a 3D + time volume. The algorithm alternates between a reconstruction step based on conjugate gradient and four regularization steps: enforcing positivity, averaging along time outside a motion mask that contains the heart and vessels, 3D spatial total variation minimization, and 1D temporal total variation minimization. Results: 4D ROOSTER recovers the different temporal representations of a moving Shepp and Logan phantom, and outperforms both ECG-gated simultaneous algebraic reconstruction technique and prior image constrained compressed sensing on a clinical case. It generates 3D + time reconstructions with sharp edges which can be used, for example, to estimate the patient's left ventricular ejection fraction. Conclusions: 4D ROOSTER can be applied for human cardiac C-arm CT, and potentially in other dynamic tomography areas. It can easily be adapted to other problems as regularization is decoupled from projection and back projection.

  14. 3D Imaging with Holographic Tomography

    NASA Astrophysics Data System (ADS)

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

    2010-04-01

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

  15. Optical microcavity scanning 3D tomography.

    PubMed

    Di Donato, Andrea; Criante, Luigino; LoTurco, Sara; Farina, Marco

    2014-10-01

    A scanning optical microcavity is exploited to achieve lens-free 3D tomography of microfluidic channels. The microcavity, powered by a low-coherence source, is realized by approaching a cleaved fiber to few tens of micrometers over the sample. The interference of scattered waves inside the cavity shapes the transverse field distribution by focusing the beam and overcoming the diffraction limit due to the optical-fiber numerical aperture. The focusing effect is also preserved in the inner layers of the sample, allowing optical 3D tomography. Analysis of microfluidic channels was demonstrated through this noninvasive technique. Although the experimental setup recalls the well-known fiber-optic Fourier-domain common-path optical coherence tomography, the proposed method has intrinsic characteristics that distinguish it from the former one.

  16. 3D reconstruction of emergency cranial computed tomography scans as a tool in clinical forensic radiology after survived blunt head trauma--report of two cases.

    PubMed

    Grassberger, M; Gehl, A; Püschel, K; Turk, E E

    2011-04-15

    When requested to evaluate surviving victims of blunt head trauma the forensic expert has to draw mainly on medical documentation from the time of hospital admission. In many cases these consist of written clinical records, radiographs and in some cases photographic documentation of the injuries. We report two cases of survived severe blunt head trauma where CT images, which had primarily been obtained for clinical diagnostic purposes, were used for forensic assessment. 3D reconstructions of the clinical CT-images yielded valuable information regarding the sequence, number and direction of the impacts to the head, their gross morphology and the inflicting weapon. We conclude that computed tomography and related imaging methods, along with their 3D reconstruction capabilities, provide a useful tool to approach questions in clinical forensic casework.

  17. Virtual forensic entomology: improving estimates of minimum post-mortem interval with 3D micro-computed tomography.

    PubMed

    Richards, Cameron S; Simonsen, Thomas J; Abel, Richard L; Hall, Martin J R; Schwyn, Daniel A; Wicklein, Martina

    2012-07-10

    We demonstrate how micro-computed tomography (micro-CT) can be a powerful tool for describing internal and external morphological changes in Calliphora vicina (Diptera: Calliphoridae) during metamorphosis. Pupae were sampled during the 1st, 2nd, 3rd and 4th quarter of development after the onset of pupariation at 23 °C, and placed directly into 80% ethanol for preservation. In order to find the optimal contrast, four batches of pupae were treated differently: batch one was stained in 0.5M aqueous iodine for 1 day; two for 7 days; three was tagged with a radiopaque dye; four was left unstained (control). Pupae stained for 7d in iodine resulted in the best contrast micro-CT scans. The scans were of sufficiently high spatial resolution (17.2 μm) to visualise the internal morphology of developing pharate adults at all four ages. A combination of external and internal morphological characters was shown to have the potential to estimate the age of blowfly pupae with a higher degree of accuracy and precision than using external morphological characters alone. Age specific developmental characters are described. The technique could be used as a measure to estimate a minimum post-mortem interval in cases of suspicious death where pupae are the oldest stages of insect evidence collected.

  18. 3D algebraic iterative reconstruction for cone-beam x-ray differential phase-contrast computed tomography.

    PubMed

    Fu, Jian; Hu, Xinhua; Velroyen, Astrid; Bech, Martin; Jiang, Ming; Pfeiffer, Franz

    2015-01-01

    Due to the potential of compact imaging systems with magnified spatial resolution and contrast, cone-beam x-ray differential phase-contrast computed tomography (DPC-CT) has attracted significant interest. The current proposed FDK reconstruction algorithm with the Hilbert imaginary filter will induce severe cone-beam artifacts when the cone-beam angle becomes large. In this paper, we propose an algebraic iterative reconstruction (AIR) method for cone-beam DPC-CT and report its experiment results. This approach considers the reconstruction process as the optimization of a discrete representation of the object function to satisfy a system of equations that describes the cone-beam DPC-CT imaging modality. Unlike the conventional iterative algorithms for absorption-based CT, it involves the derivative operation to the forward projections of the reconstructed intermediate image to take into account the differential nature of the DPC projections. This method is based on the algebraic reconstruction technique, reconstructs the image ray by ray, and is expected to provide better derivative estimates in iterations. This work comprises a numerical study of the algorithm and its experimental verification using a dataset measured with a three-grating interferometer and a mini-focus x-ray tube source. It is shown that the proposed method can reduce the cone-beam artifacts and performs better than FDK under large cone-beam angles. This algorithm is of interest for future cone-beam DPC-CT applications.

  19. Computed tomography quantification of pulmonary vessels in chronic obstructive pulmonary disease as identified by 3D automated approach

    PubMed Central

    Yu, Nan; Wei, Xia; Li, Yan; Deng, Lei; Jin, Chen-wang; Guo, Youmin

    2016-01-01

    Abstract The aim of this study was to investigate the vascular alteration of the whole lung and individual lobes in patients with COPD, and assess the association between pulmonary vessels and the extent and distribution of emphysema as well as pulmonary function by a 3-dimensional automated approach. A total of 83 computed tomography images from COPD patients were analyzed. Automated computerized approach was used to measure the total number of vessels at the fifth generation. The extent of emphysema (%LAA-950) in the whole lung and individual lobes were also calculated automatically. The association between the vascular number and the extent and distribution of emphysema, as well as the pulmonary function were assessed. Both the vascular number of fifth generation in the upper lobe and in the lower lobe were significantly negatively correlated with %LAA-950 (P < 0.05). Furthermore, there were significant, yet weak correlations between the vascular number and FEV1% predicted (R = 0.556, P = 0.039) and FEV1/FVC (R = 0.538, P = 0.047). In contrast, the vascular numbers were strongly correlated with DLco (R = 0.770, P = 0.003). Finally, the vascular number correlated closer with %LAA-950 of upper lobes than with %LAA-950 of lower lobes. Pulmonary vessel alteration can be measured; it is related to the extent of emphysema rather than the distribution of emphysema. PMID:27749587

  20. Efficient 3D nonlinear warping of computed tomography: two high-performance implementations using OpenGL

    NASA Astrophysics Data System (ADS)

    Levin, David; Dey, Damini; Slomka, Piotr

    2005-04-01

    We have implemented two hardware accelerated Thin Plate Spline (TPS) warping algorithms. The first algorithm is a hardware-software approach (HW-TPS) that uses OpenGL Vertex Shaders to perform a grid warp. The second is a Graphics Processor based approach (GPU-TPS) that uses the OpenGL Shading Language to perform all warping calculations on the GPU. Comparison with a software TPS algorithm was used to gauge the speed and quality of both hardware algorithms. Quality was analyzed visually and using the Sum of Absolute Difference (SAD) similarity metric. Warping was performed using 92 user-defined displacement vectors for 512x512x173 serial lung CT studies, matching normal-breathing and deep-inspiration scans. On a Xeon 2.2 Ghz machine with an ATI Radeon 9800XT GPU the GPU-TPS required 26.1 seconds to perform a per-voxel warp compared to 148.2 seconds for the software algorithm. The HW-TPS needed 1.63 seconds to warp the same study while the GPU-TPS required 1.94 seconds and the software grid transform required 22.8 seconds. The SAD values calculated between the outputs of each algorithm and the target CT volume were 15.2%, 15.4% and 15.5% for the HW-TPS, GPU-TPS and both software algorithms respectively. The computing power of ubiquitous 3D graphics cards can be exploited in medical image processing to provide order of magnitude acceleration of nonlinear warping algorithms without sacrificing output quality.

  1. 3D analysis of bone formation around titanium implants using micro-computed tomography (μCT)

    NASA Astrophysics Data System (ADS)

    Bernhardt, Ricardo; Scharnweber, Dieter; Müller, Bert; Beckmann, Felix; Goebbels, Jürgen; Jansen, John; Schliephake, Henning; Worch, Hartmut

    2006-08-01

    The quantitative analysis of bone formation around biofunctionalised metallic implants is an important tool for the further development of implants with higher success rates. This is, nowadays, especially important in cases of additional diseases like diabetes or osteoporosis. Micro computed tomography (μCT), as non-destructive technique, offers the possibility for quantitative three-dimensional recording of bone close to the implant's surface with micrometer resolution, which is the range of the relevant bony structures. Within different animal models using cylindrical and screw-shaped Ti6Al4V implants we have compared visualization and quantitative analysis of newly formed bone by the use of synchrotron-radiation-based CT-systems in comparison with histological findings. The SRμCT experiments were performed at the beamline BW 5 (HASYLAB at DESY, Hamburg, Germany; at the BAMline (BESSY, Berlin, Germany). For the experiments, PMMA-embedded samples were prepared with diameters of about 8 mm, which contain in the center the implant surrounded by the bony tissue. To (locally) quantify the bone formation, models were developed and optimized. The comparison of the results obtained by SRμCT and histology demonstrates the advantages and disadvantages of both approaches, although the bone formation values for the different biofunctionalized implants are identical within the error bars. SRμCT allows the clear identification of fully mineralized bone around the different titanium implants. As hundreds of virtual slices were easily generated for the individual samples, the quantification and interactive bone detection led to conclusions of high precision and statistical relevance. In this way, SRμCT in combination with interactive data analysis is proven to be more significant with respect to classical histology.

  2. 2D–3D radiograph to cone-beam computed tomography (CBCT) registration for C-arm image-guided robotic surgery

    PubMed Central

    Liu, Wen Pei; Otake, Yoshito; Azizian, Mahdi; Wagner, Oliver J.; Sorger, Jonathan M.; Armand, Mehran; Taylor, Russell H.

    2015-01-01

    Purpose C-arm radiographs are commonly used for intraoperative image guidance in surgical interventions. Fluoroscopy is a cost-effective real-time modality, although image quality can vary greatly depending on the target anatomy. Cone-beam computed tomography (CBCT) scans are sometimes available, so 2D–3D registration is needed for intra-procedural guidance. C-arm radiographs were registered to CBCT scans and used for 3D localization of peritumor fiducials during a minimally invasive thoracic intervention with a da Vinci Si robot. Methods Intensity-based 2D–3D registration of intraoperative radiographs to CBCT was performed. The feasible range of X-ray projections achievable by a C-arm positioned around a da Vinci Si surgical robot, configured for robotic wedge resection, was determined using phantom models. Experiments were conducted on synthetic phantoms and animals imaged with an OEC 9600 and a Siemens Artis zeego, representing the spectrum of different C-arm systems currently available for clinical use. Results The image guidance workflow was feasible using either an optically tracked OEC 9600 or a Siemens Artis zeego C-arm, resulting in an angular difference of Δθ : ~ 30°. The two C-arm systems provided TREmean ≤ 2.5 mm and TREmean ≤ 2.0 mm, respectively (i.e., comparable to standard clinical intraoperative navigation systems). Conclusions C-arm 3D localization from dual 2D–3D registered radiographs was feasible and applicable for intraoperative image guidance during da Vinci robotic thoracic interventions using the proposed workflow. Tissue deformation and in vivo experiments are required before clinical evaluation of this system. PMID:25503592

  3. Novel experimental technique for 3D investigation of high-speed cavitating diesel fuel flows by X-ray micro computed tomography

    NASA Astrophysics Data System (ADS)

    Lorenzi, M.; Mitroglou, N.; Santini, M.; Gavaises, M.

    2017-03-01

    An experimental technique for the estimation of the temporal-averaged vapour volume fraction within high-speed cavitating flow orifices is presented. The scientific instrument is designed to employ X-ray micro computed tomography (microCT) as a quantitative 3D measuring technique applied to custom designed, large-scale, orifice-type flow channels made from Polyether-ether-ketone (PEEK). The attenuation of the ionising electromagnetic radiation by the fluid under examination depends on its local density; the transmitted radiation through the cavitation volume is compared to the incident radiation, and combination of radiographies from sufficient number of angles leads to the reconstruction of attenuation coefficients versus the spatial position. This results to a 3D volume fraction distribution measurement of the developing multiphase flow. The experimental results obtained are compared against the high speed shadowgraph visualisation images obtained in an optically transparent nozzle with identical injection geometry; comparison between the temporal mean image and the microCT reconstruction shows excellent agreement. At the same time, the real 3D internal channel geometry (possibly eroded) has been measured and compared to the nominal manufacturing CAD drawing of the test nozzle.

  4. Development of a lab-scale, high-resolution, tube-generated X-ray computed-tomography system for three-dimensional (3D) materials characterization

    SciTech Connect

    Mertens, J.C.E. Williams, J.J. Chawla, Nikhilesh

    2014-06-01

    The design and construction of a modular high resolution X-ray computed tomography (XCT) system is highlighted in this paper. The design approach is detailed for meeting a specified set of instrument performance goals tailored towards experimental versatility and high resolution imaging. The XCT tool is unique in the detector and X-ray source design configuration, enabling control in the balance between detection efficiency and spatial resolution. The system package is also unique: The sample manipulation approach implemented enables a wide gamut of in situ experimentation to analyze structure evolution under applied stimulus, by optimizing scan conditions through a high degree of controllability. The component selection and design process is detailed: Incorporated components are specified, custom designs are shared, and the approach for their integration into a fully functional XCT scanner is provided. Custom designs discussed include the dual-target X-ray source cradle which maintains position and trajectory of the beam between the two X-ray target configurations with respect to a scintillator mounting and positioning assembly and the imaging sensor, as well as a novel large-format X-ray detector with enhanced adaptability. The instrument is discussed from an operational point of view, including the details of data acquisition and processing implemented for 3D imaging via micro-CT. The performance of the instrument is demonstrated on a silica-glass particle/hydroxyl-terminated-polybutadiene (HTPB) matrix binder PBX simulant. Post-scan data processing, specifically segmentation of the sample's relevant microstructure from the 3D reconstruction, is provided to demonstrate the utility of the instrument. - Highlights: • Custom built X-ray tomography system for microstructural characterization • Detector design for maximizing polychromatic X-ray detection efficiency • X-ray design offered for maximizing X-ray flux with respect to imaging resolution • Novel lab

  5. A patent ductus arteriosus complicating cardiopulmonary bypass for combined coronary artery bypass grafting and aortic valve replacement only discovered by computed tomography 3D reconstruction.

    PubMed

    van Middendorp, Lars B; Maessen, Jos G; Sardari Nia, Peyman

    2014-12-01

    We describe the case of a 59-year old male patient undergoing combined coronary artery bypass grafting and aortic valve replacement. Manipulation of the heart during cardiopulmonary bypass significantly decreased venous return. Several measures were necessary to improve venous return to a level at which continuation of the procedure was safe. Based on the initial troubles with venous return, we decided to selectively cross-clamp the aorta. This resulted in a large amount of backflow of oxygenated blood from the left ventricle, necessitating additional vents in the pulmonary artery and directly in the left ventricle. The procedure was continued uneventfully, and postoperative recovery was without significant complications. Postoperative 2D computed tomography did not show any signs of a shunt, but 3D reconstruction showed a small patent ductus arteriosus.

  6. Imaging the Aqueous Humor Outflow Pathway in Human Eyes by Three-dimensional Micro-computed Tomography (3D micro-CT)

    SciTech Connect

    C Hann; M Bentley; A Vercnocke; E Ritman; M Fautsch

    2011-12-31

    The site of outflow resistance leading to elevated intraocular pressure in primary open-angle glaucoma is believed to be located in the region of Schlemm's canal inner wall endothelium, its basement membrane and the adjacent juxtacanalicular tissue. Evidence also suggests collector channels and intrascleral vessels may have a role in intraocular pressure in both normal and glaucoma eyes. Traditional imaging modalities limit the ability to view both proximal and distal portions of the trabecular outflow pathway as a single unit. In this study, we examined the effectiveness of three-dimensional micro-computed tomography (3D micro-CT) as a potential method to view the trabecular outflow pathway. Two normal human eyes were used: one immersion fixed in 4% paraformaldehyde and one with anterior chamber perfusion at 10 mmHg followed by perfusion fixation in 4% paraformaldehyde/2% glutaraldehyde. Both eyes were postfixed in 1% osmium tetroxide and scanned with 3D micro-CT at 2 {mu}m or 5 {mu}m voxel resolution. In the immersion fixed eye, 24 collector channels were identified with an average orifice size of 27.5 {+-} 5 {mu}m. In comparison, the perfusion fixed eye had 29 collector channels with a mean orifice size of 40.5 {+-} 13 {mu}m. Collector channels were not evenly dispersed around the circumference of the eye. There was no significant difference in the length of Schlemm's canal in the immersed versus the perfused eye (33.2 versus 35.1 mm). Structures, locations and size measurements identified by 3D micro-CT were confirmed by correlative light microscopy. These findings confirm 3D micro-CT can be used effectively for the non-invasive examination of the trabecular meshwork, Schlemm's canal, collector channels and intrascleral vasculature that comprise the distal outflow pathway. This imaging modality will be useful for non-invasive study of the role of the trabecular outflow pathway as a whole unit.

  7. A new 3D method for measuring cranio-facial relationships with cone beam computed tomography (CBCT)

    PubMed Central

    Cibrián, Rosa; Gandia, Jose L.; Paredes, Vanessa

    2013-01-01

    Objectives: CBCT systems, with their high precision 3D reconstructions, 1:1 images and accuracy in locating cephalometric landmarks, allows us to evaluate measurements from craniofacial structures, so enabling us to replace the anthropometric methods or bidimensional methods used until now. The aims are to analyse cranio-facial relationships in a sample of patients who had previously undergone a CBCT and create a new 3D cephalometric method for assessing and measuring patients. Study Design: 90 patients who had a CBCT (i-Cat®) as a diagnostic register were selected. 12 cephalometric landmarks on the three spatial planes (X,Y,Z) were defined and 21 linear measurements were established. Using these measurements, 7 triangles were described and analysed. With the sides of the triangles: (CdR-Me-CdL); (FzR-Me-FzL); (GoR-N-GoL); and the Gl-Me distance, the ratios between them were analysed. In addition, 4 triangles in the mandible were measured (body: GoR-DB-Me and GoL-DB-Me and ramus: KrR-CdR-GoR and KrL-CdL-GoL). Results: When analyzing the sides of the CdR-Me-CdL triangle, it was found that the 69.33% of the patients could be considered symmetric. Regarding the ratios between the sides of the following triangles: CdR-Me-CdL, FzR-Me-FzL, GoR-N-GoL and the Gl-Me distance, it was found that almost all ratios were close to 1:1 except between the CdR-CdL side with respect the rest of the sides. With regard to the ratios of the 4 triangles of the mandible, it was found that the most symmetrical relationships were those corresponding to the sides of the body of the mandible and the most asymmetrical ones were those corresponding to the base of such triangles. Conclusions: A new method for assessing cranio-facial relationshps using CBCT has been established. It could be used for diverse purposes including diagnosis and treatment planning. Key words:Craniofacial relationship, CBCT, 3D cephalometry. PMID:23524427

  8. Translation of First North American 50 and 70 cc Total Artificial Heart Virtual and Clinical Implantations: Utility of 3D Computed Tomography to Test Fit Devices.

    PubMed

    Ferng, Alice S; Oliva, Isabel; Jokerst, Clinton; Avery, Ryan; Connell, Alana M; Tran, Phat L; Smith, Richard G; Khalpey, Zain

    2016-11-10

    Since the creation of SynCardia's 50 cc Total Artificial Hearts (TAHs), patients with irreversible biventricular failure now have two sizing options. Herein, a case series of three patients who have undergone successful 50 and 70 cc TAH implantation with complete closure of the chest cavity utilizing preoperative "virtual implantation" of different sized devices for surgical planning are presented. Computed tomography (CT) images were used for preoperative planning prior to TAH implantation. Three-dimensional (3D) reconstructions of preoperative chest CT images were generated and both 50 and 70 cc TAHs were virtually implanted into patients' thoracic cavities. During the simulation, the TAHs were projected over the native hearts in a similar position to the actual implantation, and the relationship between the devices and the atria, ventricles, chest wall, and diaphragm were assessed. The 3D reconstructed images and virtual modeling were used to simulate and determine for each patient if the 50 or 70 cc TAH would have a higher likelihood of successful implantation without complications. Subsequently, all three patients received clinical implants of the properly sized TAH based on virtual modeling, and their chest cavities were fully closed. This virtual implantation increases our confidence that the selected TAH will better fit within the thoracic cavity allowing for improved surgical outcome. Clinical implantation of the TAHs showed that our virtual modeling was an effective method for determining the correct fit and sizing of 50 and 70 cc TAHs.

  9. A comparison of 3-D computed tomography versus 2-D radiography measurements of ulnar variance and ulnolunate distance during forearm rotation.

    PubMed

    Kawanishi, Y; Moritomo, H; Omori, S; Kataoka, T; Murase, T; Sugamoto, K

    2014-06-01

    Positive ulnar variance is associated with ulnar impaction syndrome and ulnar variance is reported to increase with pronation. However, radiographic measurement can be affected markedly by the incident angle of the X-ray beam. We performed three-dimensional (3-D) computed tomography measurements of ulnar variance and ulnolunate distance during forearm rotation and compared these with plain radiographic measurements in 15 healthy wrists. From supination to pronation, ulnar variance increased in all cases on the radiographs; mean ulnar variance increased significantly and mean ulnolunate distance decreased significantly. However on 3-D imaging, ulna variance decreased in 12 cases on moving into pronation and increased in three cases; neither the mean ulnar variance nor mean ulnolunate distance changed significantly. Our results suggest that the forearm position in which ulnar variance increased varies among individuals. This may explain why some patients with ulnar impaction syndrome complain of wrist pain exacerbated by forearm supination. It also suggests that standard radiographic assessments of ulnar variance are unreliable.

  10. A technique for evaluating bone ingrowth into 3D printed, porous Ti6Al4V implants accurately using X-ray micro-computed tomography and histomorphometry.

    PubMed

    Palmquist, Anders; Shah, Furqan A; Emanuelsson, Lena; Omar, Omar; Suska, Felicia

    2017-03-01

    This paper investigates the application of X-ray micro-computed tomography (micro-CT) to accurately evaluate bone formation within 3D printed, porous Ti6Al4V implants manufactured using Electron Beam Melting (EBM), retrieved after six months of healing in sheep femur and tibia. All samples were scanned twice (i.e., before and after resin embedding), using fast, low-resolution scans (Skyscan 1172; Bruker micro-CT, Kontich, Belgium), and were analysed by 2D and 3D morphometry. The main questions posed were: (i) Can low resolution, fast scans provide morphometric data of bone formed inside (and around) metal implants with a complex, open-pore architecture?, (ii) Can micro-CT be used to accurately quantify both the bone area (BA) and bone-implant contact (BIC)?, (iii) What degree of error is introduced in the quantitative data by varying the threshold values?, and (iv) Does resin embedding influence the accuracy of the analysis? To validate the accuracy of micro-CT measurements, each data set was correlated with a corresponding centrally cut histological section. The results show that quantitative histomorphometry corresponds strongly with 3D measurements made by micro-CT, where a high correlation exists between the two techniques for bone area/volume measurements around and inside the porous network. On the contrary, the direct bone-implant contact is challenging to estimate accurately or reproducibly. Large errors may be introduced in micro-CT measurements when segmentation is performed without calibrating the data set against a corresponding histological section. Generally, the bone area measurement is strongly influenced by the lower threshold limit, while the upper threshold limit has little or no effect. Resin embedding does not compromise the accuracy of micro-CT measurements, although there is a change in the contrast distributions and optimisation of the threshold ranges is required.

  11. Diffusible iodine-based contrast-enhanced computed tomography (diceCT): an emerging tool for rapid, high-resolution, 3-D imaging of metazoan soft tissues.

    PubMed

    Gignac, Paul M; Kley, Nathan J; Clarke, Julia A; Colbert, Matthew W; Morhardt, Ashley C; Cerio, Donald; Cost, Ian N; Cox, Philip G; Daza, Juan D; Early, Catherine M; Echols, M Scott; Henkelman, R Mark; Herdina, A Nele; Holliday, Casey M; Li, Zhiheng; Mahlow, Kristin; Merchant, Samer; Müller, Johannes; Orsbon, Courtney P; Paluh, Daniel J; Thies, Monte L; Tsai, Henry P; Witmer, Lawrence M

    2016-06-01

    Morphologists have historically had to rely on destructive procedures to visualize the three-dimensional (3-D) anatomy of animals. More recently, however, non-destructive techniques have come to the forefront. These include X-ray computed tomography (CT), which has been used most commonly to examine the mineralized, hard-tissue anatomy of living and fossil metazoans. One relatively new and potentially transformative aspect of current CT-based research is the use of chemical agents to render visible, and differentiate between, soft-tissue structures in X-ray images. Specifically, iodine has emerged as one of the most widely used of these contrast agents among animal morphologists due to its ease of handling, cost effectiveness, and differential affinities for major types of soft tissues. The rapid adoption of iodine-based contrast agents has resulted in a proliferation of distinct specimen preparations and scanning parameter choices, as well as an increasing variety of imaging hardware and software preferences. Here we provide a critical review of the recent contributions to iodine-based, contrast-enhanced CT research to enable researchers just beginning to employ contrast enhancement to make sense of this complex new landscape of methodologies. We provide a detailed summary of recent case studies, assess factors that govern success at each step of the specimen storage, preparation, and imaging processes, and make recommendations for standardizing both techniques and reporting practices. Finally, we discuss potential cutting-edge applications of diffusible iodine-based contrast-enhanced computed tomography (diceCT) and the issues that must still be overcome to facilitate the broader adoption of diceCT going forward.

  12. An adaptive 3D region growing algorithm to automatically segment and identify thoracic aorta and its centerline using computed tomography angiography scans

    NASA Astrophysics Data System (ADS)

    Ferreira, F.; Dehmeshki, J.; Amin, H.; Dehkordi, M. E.; Belli, A.; Jouannic, A.; Qanadli, S.

    2010-03-01

    Thoracic Aortic Aneurysm (TAA) is a localized swelling of the thoracic aorta. The progressive growth of an aneurysm may eventually cause a rupture if not diagnosed or treated. This necessitates the need for an accurate measurement which in turn calls for the accurate segmentation of the aneurysm regions. Computer Aided Detection (CAD) is a tool to automatically detect and segment the TAA in the Computer tomography angiography (CTA) images. The fundamental major step of developing such a system is to develop a robust method for the detection of main vessel and measuring its diameters. In this paper we propose a novel adaptive method to simultaneously segment the thoracic aorta and to indentify its center line. For this purpose, an adaptive parametric 3D region growing is proposed in which its seed will be automatically selected through the detection of the celiac artery and the parameters of the method will be re-estimated while the region is growing thorough the aorta. At each phase of region growing the initial center line of aorta will also be identified and modified through the process. Thus the proposed method simultaneously detect aorta and identify its centerline. The method has been applied on CT images from 20 patients with good agreement with the visual assessment by two radiologists.

  13. 3D Computations and Experiments

    SciTech Connect

    Couch, R; Faux, D; Goto, D; Nikkel, D

    2004-04-05

    This project consists of two activities. Task A, Simulations and Measurements, combines all the material model development and associated numerical work with the materials-oriented experimental activities. The goal of this effort is to provide an improved understanding of dynamic material properties and to provide accurate numerical representations of those properties for use in analysis codes. Task B, ALE3D Development, involves general development activities in the ALE3D code with the focus of improving simulation capabilities for problems of mutual interest to DoD and DOE. Emphasis is on problems involving multi-phase flow, blast loading of structures and system safety/vulnerability studies.

  14. 3D False Color Computed Tomography for Diagnosis and Follow-Up of Permanent Denervated Human Muscles Submitted to Home-Based Functional Electrical Stimulation.

    PubMed

    Carraro, Ugo; Edmunds, Kyle J; Gargiulo, Paolo

    2015-03-11

    This report outlines the use of a customized false-color 3D computed tomography (CT) protocol for the imaging of the rectus femoris of spinal cord injury (SCI) patients suffering from complete and permanent denervation, as characterized by complete Conus and Cauda Equina syndrome. This muscle imaging method elicits the progression of the syndrome from initial atrophy to eventual degeneration, as well as the extent to which patients' quadriceps could be recovered during four years of home-based functional electrical stimulation (h-b FES). Patients were pre-selected from several European hospitals and functionally tested by, and enrolled in the EU Commission Shared Cost Project RISE (Contract n. QLG5-CT-2001-02191) at the Department of Physical Medicine, Wilhelminenspital, Vienna, Austria. Denervated muscles were electrically stimulated using a custom-designed stimulator, large surface electrodes, and customized progressive stimulation settings. Spiral CT images and specialized computational tools were used to isolate the rectus femoris muscle and produce 3D and 2D reconstructions of the denervated muscles. The cross sections of the muscles were determined by 2D Color CT, while muscle volumes were reconstructed by 3D Color CT. Shape, volume, and density changes were measured over the entirety of each rectus femoris muscle. Changes in tissue composition within the muscle were visualized by associating different colors to specified Hounsfield unit (HU) values for fat, (yellow: [-200; -10]), loose connective tissue or atrophic muscle, (cyan: [-9; 40]), and normal muscle, fascia and tendons included, (red: [41; 200]). The results from this analysis are presented as the average HU values within the rectus femoris muscle reconstruction, as well as the percentage of these tissues with respect to the total muscle volume. Results from this study demonstrate that h-b FES induces a compliance-dependent recovery of muscle volume and size of muscle fibers, as evidenced by the

  15. 3D False Color Computed Tomography for Diagnosis and Follow-Up of Permanent Denervated Human Muscles Submitted to Home-Based Functional Electrical Stimulation

    PubMed Central

    Carraro, Ugo; Edmunds, Kyle J.

    2015-01-01

    This report outlines the use of a customized false-color 3D computed tomography (CT) protocol for the imaging of the rectus femoris of spinal cord injury (SCI) patients suffering from complete and permanent denervation, as characterized by complete Conus and Cauda Equina syndrome. This muscle imaging method elicits the progression of the syndrome from initial atrophy to eventual degeneration, as well as the extent to which patients' quadriceps could be recovered during four years of home-based functional electrical stimulation (h-b FES). Patients were pre-selected from several European hospitals and functionally tested by, and enrolled in the EU Commission Shared Cost Project RISE (Contract n. QLG5-CT-2001-02191) at the Department of Physical Medicine, Wilhelminenspital, Vienna, Austria. Denervated muscles were electrically stimulated using a custom-designed stimulator, large surface electrodes, and customized progressive stimulation settings. Spiral CT images and specialized computational tools were used to isolate the rectus femoris muscle and produce 3D and 2D reconstructions of the denervated muscles. The cross sections of the muscles were determined by 2D Color CT, while muscle volumes were reconstructed by 3D Color CT. Shape, volume, and density changes were measured over the entirety of each rectus femoris muscle. Changes in tissue composition within the muscle were visualized by associating different colors to specified Hounsfield unit (HU) values for fat, (yellow: [-200; -10]), loose connective tissue or atrophic muscle, (cyan: [-9; 40]), and normal muscle, fascia and tendons included, (red: [41; 200]). The results from this analysis are presented as the average HU values within the rectus femoris muscle reconstruction, as well as the percentage of these tissues with respect to the total muscle volume. Results from this study demonstrate that h-b FES induces a compliance-dependent recovery of muscle volume and size of muscle fibers, as evidenced by the

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

    SciTech Connect

    Glaeser, R.M.

    1997-02-01

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

  17. Integrated 3D view of postmating responses by the Drosophila melanogaster female reproductive tract, obtained by micro-computed tomography scanning.

    PubMed

    Mattei, Alexandra L; Riccio, Mark L; Avila, Frank W; Wolfner, Mariana F

    2015-07-07

    Physiological changes in females during and after mating are triggered by seminal fluid components in conjunction with female-derived molecules. In insects, these changes include increased egg production, storage of sperm, and changes in muscle contraction within the reproductive tract (RT). Such postmating changes have been studied in dissected RT tissues, but understanding their coordination in vivo requires a holistic view of the tissues and their interrelationships. Here, we used high-resolution, multiscale micro-computed tomography (CT) scans to visualize and measure postmating changes in situ in the Drosophila female RT before, during, and after mating. These studies reveal previously unidentified dynamic changes in the conformation of the female RT that occur after mating. Our results also reveal how the reproductive organs temporally shift in concert within the confines of the abdomen. For example, we observed chiral loops in the uterus and in the upper common oviduct that relax and constrict throughout sperm storage and egg movement. We found that specific seminal fluid proteins or female secretions mediate some of the postmating changes in morphology. The morphological movements, in turn, can cause further changes due to the connections among organs. In addition, we observed apparent copulatory damage to the female intima, suggesting a mechanism for entry of seminal proteins, or other exogenous components, into the female's circulatory system. The 3D reconstructions provided by high-resolution micro-CT scans reveal how male and female molecules and anatomy interface to carry out and coordinate mating-dependent changes in the female's reproductive physiology.

  18. Advances toward field application of 3D hydraulic tomography

    NASA Astrophysics Data System (ADS)

    Cardiff, M. A.; Barrash, W.; Kitanidis, P. K.

    2011-12-01

    Hydraulic tomography (HT) is a technique that shows great potential for aquifer characterization and one that holds the promise of producing 3D hydraulic property distributions, given suitable equipment. First suggested over 15 years ago, HT assimilates distributed aquifer pressure (head) response data collected during a series of multiple pumping tests to produce estimates of aquifer property variability. Unlike traditional curve-matching analyses, which assume homogeneity or "effective" parameters within the radius of influence of a hydrologic test, HT analysis relies on numerical models with detailed heterogeneity in order to invert for the highly resolved 3D parameter distribution that jointly fits all data. Several numerical and laboratory investigations of characterization using HT have shown that property distributions can be accurately estimated between observation locations when experiments are correctly designed - a property not always shared by other, simpler 1D characterization approaches such as partially-penetrating slug tests. HT may represent one of the best methods available for obtaining detailed 3D aquifer property descriptions, especially in deep or "hard" aquifer materials, where direct-push methods may not be feasible. However, to date HT has not yet been widely adopted at contaminated field sites. We believe that current perceived impediments to HT adoption center around four key issues: 1) A paucity in the scientific literature of proven, cross-validated 3D field applications 2) A lack of guidelines and best practices for performing field 3D HT experiments; 3) Practical difficulty and time commitment associated with the installation of a large number of high-accuracy sampling locations, and the running of a large number of pumping tests; and 4) Computational difficulty associated with solving large-scale inverse problems for parameter identification. In this talk, we present current results in 3D HT research that addresses these four issues

  19. 3D liver surgery simulation: computer-assisted surgical planning with 3D simulation software and 3D printing.

    PubMed

    Oshiro, Yukio; Ohkohchi, Nobuhiro

    2017-03-27

    To perform accurate hepatectomy without injury, it is necessary to understand the anatomical relationship among the branches of Glisson's sheath, hepatic veins, and tumor. In Japan, three-dimensional (3D) preoperative simulation for liver surgery is becoming increasingly common, and liver 3D modeling and 3D hepatectomy simulation by 3D analysis software for liver surgery have been covered by universal healthcare insurance since 2012. Herein, we review the history of virtual hepatectomy using computer-aided surgery (CAS) and our research to date, and we discuss the future prospects of CAS. We have used the SYNAPSE VINCENT medical imaging system (Fujifilm Medical, Tokyo, Japan) for 3D visualization and virtual resection of the liver since 2010. We developed a novel fusion imaging technique combining 3D computed tomography (CT) with magnetic resonance imaging (MRI). The fusion image enables us to easily visualize anatomic relationships among the hepatic arteries, portal veins, bile duct, and tumor in the hepatic hilum. In 2013, we developed an original software, called Liversim, that enables real-time deformation of the liver using physical simulation, and a randomized control trial has recently been conducted to evaluate the use of Liversim and SYNAPSE VINCENT for preoperative simulation and planning. Furthermore, we developed a novel hollow 3D-printed liver model whose surface is covered with frames. This model is useful for safe liver resection, has better visibility, and the production cost is reduced to one-third of a previous model. Preoperative simulation and navigation with CAS in liver resection are expected to help planning and conducting a surgery and surgical education. Thus, a novel CAS system will contribute to not only the performance of reliable hepatectomy but also to surgical education.

  20. A single element 3D ultrasound tomography system.

    PubMed

    Xiang Zhang; Fincke, Jonathan; Kuzmin, Andrey; Lempitsky, Victor; Anthony, Brian

    2015-08-01

    Over the past decade, substantial effort has been directed toward developing ultrasonic systems for medical imaging. With advances in computational power, previously theorized scanning methods such as ultrasound tomography can now be realized. In this paper, we present the design, error analysis, and initial backprojection images from a single element 3D ultrasound tomography system. The system enables volumetric pulse-echo or transmission imaging of distal limbs. The motivating clinical applications include: improving prosthetic fittings, monitoring bone density, and characterizing muscle health. The system is designed as a flexible mechanical platform for iterative development of algorithms targeting imaging of soft tissue and bone. The mechanical system independently controls movement of two single element ultrasound transducers in a cylindrical water tank. Each transducer can independently circle about the center of the tank as well as move vertically in depth. High resolution positioning feedback (~1μm) and control enables flexible positioning of the transmitter and the receiver around the cylindrical tank; exchangeable transducers enable algorithm testing with varying transducer frequencies and beam geometries. High speed data acquisition (DAQ) through a dedicated National Instrument PXI setup streams digitized data directly to the host PC. System positioning error has been quantified and is within limits for the imaging requirements of the motivating applications.

  1. Precise 3D image alignment in micro-axial tomography.

    PubMed

    Matula, P; Kozubek, M; Staier, F; Hausmann, M

    2003-02-01

    Micro (micro-) axial tomography is a challenging technique in microscopy which improves quantitative imaging especially in cytogenetic applications by means of defined sample rotation under the microscope objective. The advantage of micro-axial tomography is an effective improvement of the precision of distance measurements between point-like objects. Under certain circumstances, the effective (3D) resolution can be improved by optimized acquisition depending on subsequent, multi-perspective image recording of the same objects followed by reconstruction methods. This requires, however, a very precise alignment of the tilted views. We present a novel feature-based image alignment method with a precision better than the full width at half maximum of the point spread function. The features are the positions (centres of gravity) of all fluorescent objects observed in the images (e.g. cell nuclei, fluorescent signals inside cell nuclei, fluorescent beads, etc.). Thus, real alignment precision depends on the localization precision of these objects. The method automatically determines the corresponding objects in subsequently tilted perspectives using a weighted bipartite graph. The optimum transformation function is computed in a least squares manner based on the coordinates of the centres of gravity of the matched objects. The theoretically feasible precision of the method was calculated using computer-generated data and confirmed by tests on real image series obtained from data sets of 200 nm fluorescent nano-particles. The advantages of the proposed algorithm are its speed and accuracy, which means that if enough objects are included, the real alignment precision is better than the axial localization precision of a single object. The alignment precision can be assessed directly from the algorithm's output. Thus, the method can be applied not only for image alignment and object matching in tilted view series in order to reconstruct (3D) images, but also to validate the

  2. Multimodal evaluation of 2-D and 3-D ultrasound, computed tomography and magnetic resonance imaging in measurements of the thyroid volume using universally applicable cross-sectional imaging software: a phantom study.

    PubMed

    Freesmeyer, Martin; Wiegand, Steffen; Schierz, Jan-Henning; Winkens, Thomas; Licht, Katharina

    2014-07-01

    A precise estimate of thyroid volume is necessary for making adequate therapeutic decisions and planning, as well as for monitoring therapy response. The goal of this study was to compare the precision of different volumetry methods. Thyroid-shaped phantoms were subjected to volumetry via 2-D and 3-D ultrasonography (US), computed tomography (CT) and magnetic resonance imaging (MRI). The 3-D US scans were performed using sensor navigation and mechanical sweeping methods. Volumetry calculation ensued with the conventional ellipsoid model and the manual tracing method. The study confirmed the superiority of manual tracing with CT and MRI volumetry of the thyroid, but extended this knowledge also to the superiority of the 3-D US method, regardless of whether sensor navigation or mechanical sweeping is used. A novel aspect was successful use of the same universally applicable cross-imaging software for all modalities.

  3. Accuracy and benefits of 3D bone surface modelling: a comparison of two methods of surface data acquisition reconstructed by laser scanning and computed tomography outputs.

    PubMed

    Brzobohatá, Hana; Prokop, Josef; Horák, Martin; Jancárek, Alexandr; Velemínská, Jana

    2012-09-01

    The aim of this study is to compare two different methods of frontal bone surface model acquisition. Three dimensional models acquired by laser scanning were compared with models of the same bones acquired by virtual replicas reconstructed from a sequence of computed tomography (CT) images. The influence of volumetric CT data processing (namely thresholding), which immediately preceded the generation of the three-dimensional surface model, was also considered and explored in detail in one sample. Despite identifying certain areas where both models showed deviations across all samples, their conformity can be generally classified as satisfactory, and the differences can be regarded as minimal. The average deviation of registered surface models was 0.27 mm for 90% of the data, and its value was therefore very close to the resolution of the laser scanner used.

  4. Fast and Accurate Data Extraction for Near Real-Time Registration of 3-D Ultrasound and Computed Tomography in Orthopedic Surgery.

    PubMed

    Brounstein, Anna; Hacihaliloglu, Ilker; Guy, Pierre; Hodgson, Antony; Abugharbieh, Rafeef

    2015-12-01

    Automatic, accurate and real-time registration is an important step in providing effective guidance and successful anatomic restoration in ultrasound (US)-based computer assisted orthopedic surgery. We propose a method in which local phase-based bone surfaces, extracted from intra-operative US data, are registered to pre-operatively segmented computed tomography data. Extracted bone surfaces are downsampled and reinforced with high curvature features. A novel hierarchical simplification algorithm is used to further optimize the point clouds. The final point clouds are represented as Gaussian mixture models and iteratively matched by minimizing the dissimilarity between them using an L2 metric. For 44 clinical data sets from 25 pelvic fracture patients and 49 phantom data sets, we report mean surface registration accuracies of 0.31 and 0.77 mm, respectively, with an average registration time of 1.41 s. Our results suggest the viability and potential of the chosen method for real-time intra-operative registration in orthopedic surgery.

  5. Applications of Doppler Tomography in 2D and 3D

    NASA Astrophysics Data System (ADS)

    Richards, M.; Budaj, J.; Agafonov, M.; Sharova, O.

    2010-12-01

    Over the past few years, the applications of Doppler tomography have been extended beyond the usual calculation of 2D velocity images of circumstellar gas flows. This technique has now been used with the new Shellspec spectrum synthesis code to demonstrate the effective modeling of the accretion disk and gas stream in the TT Hya Algol binary. The 2D tomography procedure projects all sources of emission onto a single central (Vx, Vy) velocity plane even though the gas is expected to flow beyond that plane. So, new 3D velocity images were derived with the Radioastronomical Approach method by assuming a grid of Vz values transverse to the central 2D plane. The 3D approach has been applied to the U CrB and RS Vul Algol-type binaries to reveal substantial flow structures beyond the central velocity plane.

  6. Structure from Motion Photogrammetry and Micro X-Ray Computed Tomography 3-D Reconstruction Data Fusion for Non-Destructive Conservation Documentation of Lunar Samples

    NASA Technical Reports Server (NTRS)

    Beaulieu, K. R.; Blumenfeld, E. H.; Liddle, D. A.; Oshel, E. R.; Evans, C. A.; Zeigler, R. A.; Righter, K.; Hanna, R. D.; Ketcham, R. A.

    2017-01-01

    Our team is developing a modern, cross-disciplinary approach to documentation and preservation of astromaterials, specifically lunar and meteorite samples stored at the Johnson Space Center (JSC) Lunar Sample Laboratory Facility. Apollo Lunar Sample 60639, collected as part of rake sample 60610 during the 3rd Extra-Vehicular Activity of the Apollo 16 mission in 1972, served as the first NASA-preserved lunar sample to be examined by our team in the development of a novel approach to internal and external sample visualization. Apollo Sample 60639 is classified as a breccia with a glass-coated side and pristine mare basalt and anorthosite clasts. The aim was to accurately register a 3-dimensional Micro X-Ray Computed Tomography (XCT)-derived internal composition data set and a Structure-From-Motion (SFM) Photogrammetry-derived high-fidelity, textured external polygonal model of Apollo Sample 60639. The developed process provided the means for accurate, comprehensive, non-destructive visualization of NASA's heritage lunar samples. The data products, to be ultimately served via an end-user web interface, will allow researchers and the public to interact with the unique heritage samples, providing a platform to "slice through" a photo-realistic rendering of a sample to analyze both its external visual and internal composition simultaneously.

  7. Performance evaluation of an improved optical computed tomography polymer gel dosimeter system for 3D dose verification of static and dynamic phantom deliveries

    SciTech Connect

    Lopatiuk-Tirpak, O.; Langen, K. M.; Meeks, S. L.; Kupelian, P. A.; Zeidan, O. A.; Maryanski, M. J.

    2008-09-15

    The performance of a next-generation optical computed tomography scanner (OCTOPUS-5X) is characterized in the context of three-dimensional gel dosimetry. Large-volume (2.2 L), muscle-equivalent, radiation-sensitive polymer gel dosimeters (BANG-3) were used. Improvements in scanner design leading to shorter acquisition times are discussed. The spatial resolution, detectable absorbance range, and reproducibility are assessed. An efficient method for calibrating gel dosimeters using the depth-dose relationship is applied, with photon- and electron-based deliveries yielding equivalent results. A procedure involving a preirradiation scan was used to reduce the edge artifacts in reconstructed images, thereby increasing the useful cross-sectional area of the dosimeter by nearly a factor of 2. Dose distributions derived from optical density measurements using the calibration coefficient show good agreement with the treatment planning system simulations and radiographic film measurements. The feasibility of use for motion (four-dimensional) dosimetry is demonstrated on an example comparing dose distributions from static and dynamic delivery of a single-field photon plan. The capability to visualize three-dimensional dose distributions is also illustrated.

  8. Performance evaluation of an improved optical computed tomography polymer gel dosimeter system for 3D dose verification of static and dynamic phantom deliveries.

    PubMed

    Lopatiuk-Tirpak, O; Langen, K M; Meeks, S L; Kupelian, P A; Zeidan, O A; Maryanski, M J

    2008-09-01

    The performance of a next-generation optical computed tomography scanner (OCTOPUS-5X) is characterized in the context of three-dimensional gel dosimetry. Large-volume (2.2 L), muscle-equivalent, radiation-sensitive polymer gel dosimeters (BANG-3) were used. Improvements in scanner design leading to shorter acquisition times are discussed. The spatial resolution, detectable absorbance range, and reproducibility are assessed. An efficient method for calibrating gel dosimeters using the depth-dose relationship is applied, with photon- and electron-based deliveries yielding equivalent results. A procedure involving a preirradiation scan was used to reduce the edge artifacts in reconstructed images, thereby increasing the useful cross-sectional area of the dosimeter by nearly a factor of 2. Dose distributions derived from optical density measurements using the calibration coefficient show good agreement with the treatment planning system simulations and radiographic film measurements. The feasibility of use for motion (four-dimensional) dosimetry is demonstrated on an example comparing dose distributions from static and dynamic delivery of a single-field photon plan. The capability to visualize three-dimensional dose distributions is also illustrated.

  9. 3D Segmentation of Maxilla in Cone-beam Computed Tomography Imaging Using Base Invariant Wavelet Active Shape Model on Customized Two-manifold Topology

    PubMed Central

    Chang, Yu-Bing; Xia, James J.; Yuan, Peng; Kuo, Tai-Hong; Xiong, Zixiang; Gateno, Jaime; Zhou, Xiaobo

    2013-01-01

    Recent advances in cone-beam computed tomography (CBCT) have rapidly enabled widepsread applications of dentomaxillofacial imaging and orthodontic practices in the past decades due to its low radiation dose, high spatial resolution, and accessibility. However, low contrast resolution in CBCT image has become its major limitation in building skull models. Intensive hand-segmentation is usually required to reconstruct the skull models. One of the regions affected by this limitation the most is the thin bone images. This paper presents a novel segmentation approach based on wavelet density model (WDM) for a particular interest in the outer surface of anterior wall of maxilla. Nineteen CBCT datasets are used to conduct two experiments. This mode-based segmentation approach is validated and compared with three different segmentation approaches. The results show that the performance of this model-based segmentation approach is better than those of the other approaches. It can achieve 0.25 ± 0.2mm of surface error from ground truth of bone surface. PMID:23694914

  10. High-resolution 3D analyses of the shape and internal constituents of small volcanic ash particles: The contribution of SEM micro-computed tomography (SEM micro-CT)

    NASA Astrophysics Data System (ADS)

    Vonlanthen, Pierre; Rausch, Juanita; Ketcham, Richard A.; Putlitz, Benita; Baumgartner, Lukas P.; Grobéty, Bernard

    2015-02-01

    The morphology of small volcanic ash particles is fundamental to our understanding of magma fragmentation, and in transport modeling of volcanic plumes and clouds. Until recently, the analysis of 3D features in small objects (< 250 μm) was either restricted to extrapolations from 2D approaches, partial stereo-imaging, or CT methods having limited spatial resolution and/or accessibility. In this study, an X-ray computed-tomography technique known as SEM micro-CT, also called 3D X-ray ultramicroscopy (3D XuM), was used to investigate the 3D morphology of small volcanic ash particles (125-250 μm sieve fraction), as well as their vesicle and microcrystal distribution. The samples were selected from four stratigraphically well-established tephra layers of the Meerfelder Maar (West Eifel Volcanic Field, Germany). Resolution tests performed on a Beametr v1 pattern sample along with Monte Carlo simulations of X-ray emission volumes indicated that a spatial resolution of 0.65 μm was obtained for X-ray shadow projections using a standard thermionic SEM and a bulk brass target as X-ray source. Analysis of a smaller volcanic ash particle (64-125 μm sieve fraction) showed that features with volumes > 20 μm3 (~ 3.5 μm in diameter) can be successfully reconstructed and quantified. In addition, new functionalities of the Blob3D software were developed to allow the particle shape factors frequently used as input parameters in ash transport and dispersion models to be calculated. This study indicates that SEM micro-CT is very well suited to quantify the various aspects of shape in fine volcanic ash, and potentially also to investigate the 3D morphology and internal structure of any object < 0.1 mm3.

  11. Registration of a needle-positioning robot to high-resolution 3D ultrasound and computed tomography for image-guided interventions in small animals

    NASA Astrophysics Data System (ADS)

    Waspe, Adam C.; Lacefield, James C.; Holdsworth, David W.; Fenster, Aaron

    2008-03-01

    Preclinical research often requires the delivery of biological substances to specific locations in small animals. Guiding a needle to targets in small animals with an error < 200 μm requires accurate registration. We are developing techniques to register a needle-positioning robot to high-resolution three-dimensional ultrasound and computed tomography small animal imaging systems. Both techniques involve moving the needle to predetermined robot coordinates and determining corresponding needle locations in image coordinates. Registration accuracy will therefore be affected by the robot positioning error and is assessed by measuring the target registration error (TRE). A point-based registration between robot and micro-ultrasound coordinates was accomplished by attaching a fiducial phantom onto the needle. A TRE of 145 μm was achieved when moving the needle to a set of robot coordinates and registering the coordinates to needle tip locations determined from ultrasound fiducial measurements. Registration between robot and micro-CT coordinates was accomplished by injecting barium sulfate into tracks created when the robot withdraws the needle from a phantom. Points along cross-sectional slices of the segmented needle tracks were determined using an intensity-weighted centroiding algorithm. A minimum distance TRE of 194 +/- 18 μm was achieved by registering centroid points to robot trajectories using the iterative closest point (ICP) algorithm. Simulations, incorporating both robot and ultrasound fiducial localization errors, verify that robot error is a significant component of the experimental registration. Simulations of micro-CT to robot ICP registration similarly agree with the experimental results. Both registration techniques produce a TRE < 200 μm, meeting design specification.

  12. 3D and 4D magnetic susceptibility tomography based on complex MR images

    DOEpatents

    Chen, Zikuan; Calhoun, Vince D

    2014-11-11

    Magnetic susceptibility is the physical property for T2*-weighted magnetic resonance imaging (T2*MRI). The invention relates to methods for reconstructing an internal distribution (3D map) of magnetic susceptibility values, .chi. (x,y,z), of an object, from 3D T2*MRI phase images, by using Computed Inverse Magnetic Resonance Imaging (CIMRI) tomography. The CIMRI technique solves the inverse problem of the 3D convolution by executing a 3D Total Variation (TV) regularized iterative convolution scheme, using a split Bregman iteration algorithm. The reconstruction of .chi. (x,y,z) can be designed for low-pass, band-pass, and high-pass features by using a convolution kernel that is modified from the standard dipole kernel. Multiple reconstructions can be implemented in parallel, and averaging the reconstructions can suppress noise. 4D dynamic magnetic susceptibility tomography can be implemented by reconstructing a 3D susceptibility volume from a 3D phase volume by performing 3D CIMRI magnetic susceptibility tomography at each snapshot time.

  13. Complete Tem-Tomography: 3D Structure of Gems Cluster

    NASA Technical Reports Server (NTRS)

    Matsuno, J.; Miyake, A.; Tsuchiyama, A.; Messenger, S.; Nakamura-Messenger, K.

    2015-01-01

    GEMS (glass with embedded metal and sulfide) grains in interplanetary dust particles (IDPs) are considered to be one of the ubiquitous and fundamental building blocks of solids in the Solar System. They have been considered to be interstellar silicate dust that survived various metamorphism or alteration processes in the protoplanetary disk but the elemental and isotopic composition measurements suggest that most of them have been formed in the protoplanetary disk as condensates from high temperature gas. This formation model is also supported by the formation of GEMS-like grains with respect to the size, mineral assemblage, texture and infrared spectrum by condensation experiments from mean GEMS composition materials. Previous GEMS studies were performed only with 2D observation by transmission electron microscopy (TEM) or scanning TEM (STEM). However, the 3D shape and structure of GEMS grains and the spatial distribution of Fe/FeS's has critical information about their formation and origin. Recently, the 3D structure of GEMS grains in ultrathin sections of cluster IDPs was revealed by electron tomography using a TEM/STEM (JEM-2100F, JEOL). However, CT images of thin sections mounted on Cu grids acquired by conventional TEM-tomography are limited to low tilt angles (e. g., less than absolute value of 75 deg. In fact, previous 3D TEM observations of GEMS were affected by some artifacts related to the limited tilt range in the TEM used. Complete tomographic images should be acquired by rotating the sample tilt angle over a range of more than absolute value of 80 deg otherwise the CT images lose their correct structures. In order to constrain the origin and formation process of GEMS grains more clearly, we performed complete electron tomography for GEMS grains. Here we report the sample preparation method we have developed for this study, and the preliminary results.

  14. 3D Human cartilage surface characterization by optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Brill, Nicolai; Riedel, Jörn; Schmitt, Robert; Tingart, Markus; Truhn, Daniel; Pufe, Thomas; Jahr, Holger; Nebelung, Sven

    2015-10-01

    Early diagnosis and treatment of cartilage degeneration is of high clinical interest. Loss of surface integrity is considered one of the earliest and most reliable signs of degeneration, but cannot currently be evaluated objectively. Optical Coherence Tomography (OCT) is an arthroscopically available light-based non-destructive real-time imaging technology that allows imaging at micrometre resolutions to millimetre depths. As OCT-based surface evaluation standards remain to be defined, the present study investigated the diagnostic potential of 3D surface profile parameters in the comprehensive evaluation of cartilage degeneration. To this end, 45 cartilage samples of different degenerative grades were obtained from total knee replacements (2 males, 10 females; mean age 63.8 years), cut to standard size and imaged using a spectral-domain OCT device (Thorlabs, Germany). 3D OCT datasets of 8  ×  8, 4  ×  4 and 1  ×  1 mm (width  ×  length) were obtained and pre-processed (image adjustments, morphological filtering). Subsequent automated surface identification algorithms were used to obtain the 3D primary profiles, which were then filtered and processed using established algorithms employing ISO standards. The 3D surface profile thus obtained was used to calculate a set of 21 3D surface profile parameters, i.e. height (e.g. Sa), functional (e.g. Sk), hybrid (e.g. Sdq) and segmentation-related parameters (e.g. Spd). Samples underwent reference histological assessment according to the Degenerative Joint Disease classification. Statistical analyses included calculation of Spearman’s rho and assessment of inter-group differences using the Kruskal Wallis test. Overall, the majority of 3D surface profile parameters revealed significant degeneration-dependent differences and correlations with the exception of severe end-stage degeneration and were of distinct diagnostic value in the assessment of surface integrity. None of the 3D

  15. Weapon identification using antemortem computed tomography with virtual 3D and rapid prototype modeling--a report in a case of blunt force head injury.

    PubMed

    Woźniak, Krzysztof; Rzepecka-Woźniak, Ewa; Moskała, Artur; Pohl, Jerzy; Latacz, Katarzyna; Dybała, Bogdan

    2012-10-10

    A frequent request of a prosecutor referring to forensic autopsy is to determine the mechanism of an injury and to identify the weapons used to cause those injuries. This task could be problematic in many ways, including changes in the primary injury caused by medical intervention and the process of healing. To accomplish this task, the forensic pathologist has to gather all possible information during the post-mortem examination. The more data is collected, the easier it is to obtain an accurate answer to the prosecutor's question. The authors present a case of head injuries that the victim sustained under unknown circumstances. The patient underwent neurosurgical treatment which resulted in alteration of the bone fracture pattern. The only way to evaluate this injury was to analyze antemortem clinical data, especially CT scans, with virtual 3D reconstruction of the fractured skull. A physical model of a part of the broken skull was created with the use of 3D printing. These advanced techniques, applied for the first time in Poland for forensic purposes, allowed investigators to extract enough data to develop a hypothesis about the mechanism of injury and the weapon most likely used.

  16. Comparison of 2D Radiographic Images and 3D Cone Beam Computed Tomography for Positioning Head-and-Neck Radiotherapy Patients

    SciTech Connect

    Li Heng; Zhu, X. Ronald Zhang Lifei; Dong Lei; Tung, Sam; Ahamad, Anesa M.D.; Chao, K. S. Clifford; Morrison, William H.; Rosenthal, David I.; Schwartz, David L.; Mohan, Radhe; Garden, Adam S.

    2008-07-01

    Purpose: To assess the positioning accuracy using two-dimensional kilovoltage (2DkV) imaging and three-dimensional cone beam CT (CBCT) in patients with head and neck (H and N) cancer receiving radiation therapy. To assess the benefit of patient-specific headrest. Materials and Methods: All 21 patients studied were immobilized using thermoplastic masks with either a patient-specific vacuum bag (11 of 21, IMA) or standard clear plastic (10 of 21, IMB) headrests. Each patient was imaged with a pair of orthogonal 2DkV images in treatment position using onboard imaging before the CBCT procedure. The 2DkV and CBCT images were acquired weekly during the same session. The 2DkV images were reviewed by oncologists and also analyzed by a software tool based on mutual information (MI). Results: Ninety-eight pairs of assessable 2DkV-CBCT alignment sets were obtained. Systematic and random errors were <1.6 mm for both 2DkV and CBCT alignments. When we compared shifts determined by CBCT and 2DkV for the same patient setup, statistically significant correlations were observed in all three major directions. Among all CBCT couch shifts, 4.1% {>=} 0.5 cm and 18.7% {>=} 0.3 cm, whereas among all 2DkV (MI) shifts, 1.7% {>=} 0.5 cm and 11.2% {>=} 0.3 cm. Statistically significant difference was found on anteroposterior direction between IMA and IMB with the CBCT alignment only. Conclusions: The differences between 2D and 3D alignments were mainly caused by the relative flexibility of certain H and N structures and possibly by rotation. Better immobilization of the flexible neck is required to further reduce the setup errors for H and N patients receiving radiotherapy.

  17. Freehand photoacoustic tomography for 3D angiography using local gradient information

    NASA Astrophysics Data System (ADS)

    Kirchner, Thomas; Wild, Esther; Maier-Hein, Klaus H.; Maier-Hein, Lena

    2016-03-01

    Photo-acoustic tomography (PAT) is capable of imaging optical absorption in depths beyond the diffusion limit. As blood is one of the main absorbers in tissue, one important application is the visualization of vasculature, which can provide important clues for diagnosing diseases like cancer. While the state-of-the-art work in photo-acoustic 3D angiography has focused on computed tomography systems involving complex setups, we propose an approach based on optically tracking a freehand linear ultrasound probe that can be smoothly integrated into the clinical workflow. To this end, we present a method for calibration of a PAT system using an N-wire phantom specifically designed for PAT and show how to use local gradient information in the 3D reconstructed volume to significantly enhance the signal. According to experiments performed with a tissue mimicking intra-lipid phantom, the signal-to-noise ratio, contrast and contrast-to-noise ratio measured in the full field of view of the linear probe can be improved by factors of 1.7+/-0.7, 14.6+/-5.8 and 2.8+/-1.2 respectively, when comparing the post envelope detection reconstructed 3D volume with the processed one. Qualitative validation performed in tissue mimicking gelatin phantoms further showed good agreement of the reconstructed vasculature with corresponding structures extracted from X-ray computed tomographies. As our method provides high contrast 3D images of the vasculature despite a low hardware complexity its potential for clinical application is high.

  18. High resolution 3D fluorescence tomography using ballistic photons

    NASA Astrophysics Data System (ADS)

    Zheng, Jie; Nouizi, Farouk; Cho, Jaedu; Kwong, Jessica; Gulsen, Gultekin

    2015-03-01

    We are developing a ballistic-photon based approach for improving the spatial resolution of fluorescence tomography using time-domain measurements. This approach uses early photon information contained in measured time-of-fight distributions originating from fluorescence emission. The time point spread functions (TPSF) from both excitation light and emission light are acquired with gated single photon Avalanche detector (SPAD) and time-correlated single photon counting after a short laser pulse. To determine the ballistic photons for reconstruction, the lifetime of the fluorophore and the time gate from the excitation profiles will be used for calibration, and then the time gate of the fluorescence profile can be defined by a simple time convolution. By mimicking first generation CT data acquisition, the sourcedetector pair will translate across and also rotate around the subject. The measurement from each source-detector position will be reshaped into a histogram that can be used by a simple back-projection algorithm in order to reconstruct high resolution fluorescence images. Finally, from these 2D sectioning slides, a 3D inclusion can be reconstructed accurately. To validate the approach, simulation of light transport is performed for biological tissue-like media with embedded fluorescent inclusion by solving the diffusion equation with Finite Element Method using COMSOL Multiphysics simulation. The reconstruction results from simulation studies have confirmed that this approach drastically improves the spatial resolution of fluorescence tomography. Moreover, all the results have shown the feasibility of this technique for high resolution small animal imaging up to several centimeters.

  19. Computed 3D visualisation of an extinct cephalopod using computer tomographs

    PubMed Central

    Lukeneder, Alexander

    2012-01-01

    The first 3D visualisation of a heteromorph cephalopod species from the Southern Alps (Dolomites, northern Italy) is presented. Computed tomography, palaeontological data and 3D reconstructions were included in the production of a movie, which shows a life reconstruction of the extinct organism. This detailed reconstruction is according to the current knowledge of the shape and mode of life as well as habitat of this animal. The results are based on the most complete shell known thus far of the genus Dissimilites. Object-based combined analyses from computed tomography and various computed 3D facility programmes help to understand morphological details as well as their ontogentical changes in fossil material. In this study, an additional goal was to show changes in locomotion during different ontogenetic phases of such fossil, marine shell-bearing animals (ammonoids). Hence, the presented models and tools can serve as starting points for discussions on morphology and locomotion of extinct cephalopods in general, and of the genus Dissimilites in particular. The heteromorph ammonoid genus Dissimilites is interpreted here as an active swimmer of the Tethyan Ocean. This study portrays non-destructive methods of 3D visualisation applied on palaeontological material, starting with computed tomography resulting in animated, high-quality video clips. The here presented 3D geometrical models and animation, which are based on palaeontological material, demonstrate the wide range of applications, analytical techniques and also outline possible limitations of 3D models in earth sciences and palaeontology. The realistic 3D models and motion pictures can easily be shared amongst palaeontologists. Data, images and short clips can be discussed online and, if necessary, adapted in morphological details and motion-style to better represent the cephalopod animal. PMID:24850976

  20. Computed 3D visualisation of an extinct cephalopod using computer tomographs

    NASA Astrophysics Data System (ADS)

    Lukeneder, Alexander

    2012-08-01

    The first 3D visualisation of a heteromorph cephalopod species from the Southern Alps (Dolomites, northern Italy) is presented. Computed tomography, palaeontological data and 3D reconstructions were included in the production of a movie, which shows a life reconstruction of the extinct organism. This detailed reconstruction is according to the current knowledge of the shape and mode of life as well as habitat of this animal. The results are based on the most complete shell known thus far of the genus Dissimilites. Object-based combined analyses from computed tomography and various computed 3D facility programmes help to understand morphological details as well as their ontogentical changes in fossil material. In this study, an additional goal was to show changes in locomotion during different ontogenetic phases of such fossil, marine shell-bearing animals (ammonoids). Hence, the presented models and tools can serve as starting points for discussions on morphology and locomotion of extinct cephalopods in general, and of the genus Dissimilites in particular. The heteromorph ammonoid genus Dissimilites is interpreted here as an active swimmer of the Tethyan Ocean. This study portrays non-destructive methods of 3D visualisation applied on palaeontological material, starting with computed tomography resulting in animated, high-quality video clips. The here presented 3D geometrical models and animation, which are based on palaeontological material, demonstrate the wide range of applications, analytical techniques and also outline possible limitations of 3D models in earth sciences and palaeontology. The realistic 3D models and motion pictures can easily be shared amongst palaeontologists. Data, images and short clips can be discussed online and, if necessary, adapted in morphological details and motion-style to better represent the cephalopod animal.

  1. Infiltration front monitoring using 3D Electrical Resistivity Tomography

    NASA Astrophysics Data System (ADS)

    Oxarango, Laurent; Audebert, Marine; Guyard, Helene; Clement, Remi

    2016-04-01

    The electrical resistivity tomography (ERT) geophysical method is commonly used to identify the spatial distribution of electrical resisitivity in the soil at the field scale. Recent progress in commercial acquisition systems allows repeating fast acquisitions (10 min) in order to monitor a 3D dynamic phenomenon. Since the ERT method is sensitive to moisture content variations, it can thus be used to delineate the infiltration shape during water infiltration. In heterogeneous conditions, the 3D infiltration shape is a crucial information because it could differ significantly from the homogeneous behavior. In a first step, the ERT method is validated at small scale (<1m) studying a suction infiltrometer test. The experiment is carried out in a pit filled with a homogenous silty-sandy soil. It is instrumented by 17 resistivity probes and 3 commercial capacitive moisture content probes to provide local measurements of the moisture content variation. The Multiple Inversion and Clustering Strategy (MICS) (Audebert et al 2014) is used to delineate the infiltration patern. A satisfying agreement between infiltration delineation and sensor measurements is obtained with a few centimeter accuracy on the moisture front location. In a second step, the same methodology is applied at a larger scale (> 10m). Two examples of leachate injection monitoring in municipal solid waste landfills are used to put forward benefits and limitations of the ERT-MICS method. Effective infiltration porosities in a range between 3% and 8% support the assumption of a flow in heterogeneous media. Audebert, M., R. Clément, N. Touze-Foltz, T. Günther, S. Moreau, and C. Duquennoi (2014), Time-lapse ERT interpretation methodology for leachate injection monitoring based on multiple inversions and a clustering strategy (MICS), Journal of Applied Geophysics, 111, 320-333. Keywords: ERT, infiltration front, field survey

  2. Advanced prior modeling for 3D bright field electron tomography

    NASA Astrophysics Data System (ADS)

    Sreehari, Suhas; Venkatakrishnan, S. V.; Drummy, Lawrence F.; Simmons, Jeffrey P.; Bouman, Charles A.

    2015-03-01

    Many important imaging problems in material science involve reconstruction of images containing repetitive non-local structures. Model-based iterative reconstruction (MBIR) could in principle exploit such redundancies through the selection of a log prior probability term. However, in practice, determining such a log prior term that accounts for the similarity between distant structures in the image is quite challenging. Much progress has been made in the development of denoising algorithms like non-local means and BM3D, and these are known to successfully capture non-local redundancies in images. But the fact that these denoising operations are not explicitly formulated as cost functions makes it unclear as to how to incorporate them in the MBIR framework. In this paper, we formulate a solution to bright field electron tomography by augmenting the existing bright field MBIR method to incorporate any non-local denoising operator as a prior model. We accomplish this using a framework we call plug-and-play priors that decouples the log likelihood and the log prior probability terms in the MBIR cost function. We specifically use 3D non-local means (NLM) as the prior model in the plug-and-play framework, and showcase high quality tomographic reconstructions of a simulated aluminum spheres dataset, and two real datasets of aluminum spheres and ferritin structures. We observe that streak and smear artifacts are visibly suppressed, and that edges are preserved. Also, we report lower RMSE values compared to the conventional MBIR reconstruction using qGGMRF as the prior model.

  3. Contribution of 3D inversion of Electrical Resistivity Tomography data applied to volcanic structures

    NASA Astrophysics Data System (ADS)

    Portal, Angélie; Fargier, Yannick; Lénat, Jean-François; Labazuy, Philippe

    2016-04-01

    The electrical resistivity tomography (ERT) method, initially developed for environmental and engineering exploration, is now commonly used for geological structures imaging. Such structures can present complex characteristics that conventional 2D inversion processes cannot perfectly integrate. Here we present a new 3D inversion algorithm named EResI, firstly developed for levee investigation, and presently applied to the study of a complex lava dome (the Puy de Dôme volcano, France). EResI algorithm is based on a conventional regularized Gauss-Newton inversion scheme and a 3D non-structured discretization of the model (double grid method based on tetrahedrons). This discretization allows to accurately model the topography of investigated structure (without a mesh deformation procedure) and also permits a precise location of the electrodes. Moreover, we demonstrate that a complete 3D unstructured discretization limits the number of inversion cells and is better adapted to the resolution capacity of tomography than a structured discretization. This study shows that a 3D inversion with a non-structured parametrization has some advantages compared to classical 2D inversions. The first advantage comes from the fact that a 2D inversion leads to artefacts due to 3D effects (3D topography, 3D internal resistivity). The second advantage comes from the fact that the capacity to experimentally align electrodes along an axis (for 2D surveys) depends on the constrains on the field (topography...). In this case, a 2D assumption induced by 2.5D inversion software prevents its capacity to model electrodes outside this axis leading to artefacts in the inversion result. The last limitation comes from the use of mesh deformation techniques used to accurately model the topography in 2D softwares. This technique used for structured discretization (Res2dinv) is prohibed for strong topography (>60 %) and leads to a small computational errors. A wide geophysical survey was carried out

  4. 3D Observation of GEMS by Electron Tomography

    NASA Technical Reports Server (NTRS)

    Matsuno, Junya; Miyake, Akira; Tsuchiyama, Akira; Nakamura-Messenger, Keiko; Messenger, Scott

    2014-01-01

    Amorphous silicates in chondritic porous interplanetary dust particles (CP-IDPs) coming from comets are dominated by glass with embedded metal and sulfides (GEMS). GEMS grains are submicron-sized rounded objects (typically 100-500) nm in diameter) with anaometer-sized (10-50 nm) Fe-Ni metal and sulfide grains embedded in an amorphous silicate matrix. Several formation processes for GEMS grains have been proposed so far, but these models are still being debated [2-5]. Bradley et al. proposed that GEMS grains are interstellar silicate dust that survived various metamorphism or alteration processes in the protoplanetary disk and that they are amorphiation products of crystalline silicates in the interstellar medium by sputter-deposition of cosmic ray irradiation, similar to space weathering [2,4]. This consideration is based on the observation of nano-sized crystals (approximately 10 nm) called relict grains in GEMS grains and their shapes are pseudomorphs to the host GEMS grains. On the other hand, Keller and Messenger proposed that most GEMS formed in the protoplanetary disk as condensates from high temperature gas [3,5]. This model is based on the fact that most GEMS grains have solar isotopic compositions and have extremely heterogeneous and non-solar elemental compositions. Keller and Messenger (2011) also reported that amorphous silicates in GEMS grains are surrounded by sulfide grains, which formed as sulfidization of metallic iron grains located on the GEMS surface. The previous studies were performed with 2D observation by using transmission electron microscopy (TEM) or scanning TEM (STEM). In order to understand the structure of GEMS grains described above more clearly, we observed 3D structure of GEMS grains by electron tomography using a TEM/STEM (JEM-2100F, JEOL) at Kyoto University. Electron tomography gives not only 3D structures but also gives higher spatial resolution (approximately a few nm) than that in conventional 2D image, which is restricted by

  5. Computed Tomography (CT) -- Sinuses

    MedlinePlus

    ... More Info Images/Videos About Us News Physician Resources Professions Site Index A-Z Computed Tomography (CT) - Sinuses Computed tomography (CT) of the sinuses uses special x-ray equipment to evaluate the paranasal sinus cavities – hollow, air-filled spaces within the bones of the face surrounding the ...

  6. Nasal computed tomography.

    PubMed

    Kuehn, Ned F

    2006-05-01

    Chronic nasal disease is often a challenge to diagnose. Computed tomography greatly enhances the ability to diagnose chronic nasal disease in dogs and cats. Nasal computed tomography provides detailed information regarding the extent of disease, accurate discrimination of neoplastic versus nonneoplastic diseases, and identification of areas of the nose to examine rhinoscopically and suspicious regions to target for biopsy.

  7. Contribution of 3-D electrical resistivity tomography for landmines detection

    NASA Astrophysics Data System (ADS)

    Metwaly, M.; El-Qady, G.; Matsushima, J.; Szalai, S.; Al-Arifi, N. S. N.; Taha, A.

    2008-12-01

    Landmines are a type of inexpensive weapons widely used in the pre-conflicted areas in many countries worldwide. The two main types are the metallic and non-metallic (mostly plastic) landmines. They are most commonly investigated by magnetic, ground penetrating radar (GPR), and metal detector (MD) techniques. These geophysical techniques however have significant limitations in resolving the non-metallic landmines and wherever the host materials are conductive. In this work, the 3-D electric resistivity tomography (ERT) technique is evaluated as an alternative and/or confirmation detection system for both landmine types, which are buried in different soil conditions and at different depths. This can be achieved using the capacitive resistivity imaging system, which does not need direct contact with the ground surface. Synthetic models for each case have been introduced using metallic and non-metallic bodies buried in wet and dry environments. The inversion results using the L1 norm least-squares optimization method tend to produce robust blocky models of the landmine body. The dipole axial and the dipole equatorial arrays tend to have the most favorable geometry by applying dynamic capacitive electrode and they show significant signal strength for data sets with up to 5% noise. Increasing the burial depth relative to the electrode spacing as well as the noise percentage in the resistivity data is crucial in resolving the landmines at different environments. The landmine with dimension and burial depth of one electrode separation unit is over estimated while the spatial resolutions decrease as the burial depth and noise percentage increase.

  8. Classification and 3D averaging with missing wedge correction in biological electron tomography

    PubMed Central

    Bartesaghi, A.; Sprechmann, P.; Liu, J.; Randall, G.; Sapiro, G.; Subramaniam, S.

    2008-01-01

    Strategies for the determination of 3D structures of biological macromolecules using electron crystallography and single-particle electron microscopy utilize powerful tools for the averaging of information obtained from 2D projection images of structurally homogeneous specimens. In contrast, electron tomographic approaches have often been used to study the 3D structures of heterogeneous, one-of-a-kind objects such as whole cells where image-averaging strategies are not applicable. Complex entities such as cells and viruses, nevertheless, contain multiple copies of numerous macromolecules that can individually be subjected to 3D averaging. Here we present a complete framework for alignment, classification, and averaging of volumes derived by electron tomography that is computationally efficient and effectively accounts for the missing wedge that is inherent to limited-angle electron tomography. Modeling the missing data as a multiplying mask in reciprocal space we show that the effect of the missing wedge can be accounted for seamlessly in all alignment and classification operations. We solve the alignment problem using the convolution theorem in harmonic analysis, thus eliminating the need for approaches that require exhaustive angular search, and adopt an iterative approach to alignment and classification that does not require the use of external references. We demonstrate that our method can be successfully applied for 3D classification and averaging of phantom volumes as well as experimentally obtained tomograms of GroEL where the outcomes of the analysis can be quantitatively compared against the expected results. PMID:18440828

  9. CASTLE3D - A Computer Aided System for Labelling Archaeological Excavations in 3D

    NASA Astrophysics Data System (ADS)

    Houshiar, H.; Borrmann, D.; Elseberg, J.; Nüchter, A.; Näth, F.; Winkler, S.

    2015-08-01

    Documentation of archaeological excavation sites with conventional methods and tools such as hand drawings, measuring tape and archaeological notes is time consuming. This process is prone to human errors and the quality of the documentation depends on the qualification of the archaeologist on site. Use of modern technology and methods in 3D surveying and 3D robotics facilitate and improve this process. Computer-aided systems and databases improve the documentation quality and increase the speed of data acquisition. 3D laser scanning is the state of the art in modelling archaeological excavation sites, historical sites and even entire cities or landscapes. Modern laser scanners are capable of data acquisition of up to 1 million points per second. This provides a very detailed 3D point cloud of the environment. 3D point clouds and 3D models of an excavation site provide a better representation of the environment for the archaeologist and for documentation. The point cloud can be used both for further studies on the excavation and for the presentation of results. This paper introduces a Computer aided system for labelling archaeological excavations in 3D (CASTLE3D). Consisting of a set of tools for recording and georeferencing the 3D data from an excavation site, CASTLE3D is a novel documentation approach in industrial archaeology. It provides a 2D and 3D visualisation of the data and an easy-to-use interface that enables the archaeologist to select regions of interest and to interact with the data in both representations. The 2D visualisation and a 3D orthogonal view of the data provide cuts of the environment that resemble the traditional hand drawings. The 3D perspective view gives a realistic view of the environment. CASTLE3D is designed as an easy-to-use on-site semantic mapping tool for archaeologists. Each project contains a predefined set of semantic information that can be used to label findings in the data. Multiple regions of interest can be joined under

  10. Computational modeling of RNA 3D structures and interactions.

    PubMed

    Dawson, Wayne K; Bujnicki, Janusz M

    2016-04-01

    RNA molecules have key functions in cellular processes beyond being carriers of protein-coding information. These functions are often dependent on the ability to form complex three-dimensional (3D) structures. However, experimental determination of RNA 3D structures is difficult, which has prompted the development of computational methods for structure prediction from sequence. Recent progress in 3D structure modeling of RNA and emerging approaches for predicting RNA interactions with ions, ligands and proteins have been stimulated by successes in protein 3D structure modeling.

  11. Modeling the Coast Mountains Batholith, British Columbia, Canada with 3D Seismic Tomography

    NASA Astrophysics Data System (ADS)

    Quinonez, S. M.; Olaya, J. C.; Miller, K. C.; Romero, R.; Velasco, A. A.; Harder, S. H.; Cerda, I.

    2011-12-01

    The Coast Mountains Batholith on the west coast of British Columbia, Canada comprises a series of granitic to tonalitic plutons; where felsic continental crust is generated from the subduction of mafic oceanic crust by partial melting and fractionation, leaving ultra-mafic roots. In July of 2009, a large controlled-source experiment was conducted along a 400km east - west transect from Bella Bella into central British Columbia. Student volunteers from multiple universities deployed 1,800 one-component and 200 three-component geophones plus 2400 Texan data recorders with 200-m spacing intervals and shot spacing at 30-km. The 18-point sources ranged from 160 to 1,000 kg of high explosive. The geoscience component of the NSF-funded Cyber-ShARE project at UTEP focuses on fusing models developed from different data sets to develop 3-D Earth models. Created in 2007, the Cyber-ShARE Center brings together experts in computer science, computational mathematics, education, earth science, and environmental science. We leverage the Cyber-ShARE work to implement an enhanced 3-D finite difference tomography approach for P-wave delays times (Hole, 1992) with a graphical user interface and visualization framework. In particular, to account for model sensitivity to picked P-wave arrival times, we use a model fusion approach (Ochoa et al., 2010) to generate a model with the lowest RMS residual that a combination of a set of Monte Carlo sample models. In order to make the seismic tomography process more interactive at many points, visualizations of model perturbation at each iteration will help to troubleshoot when a model is not converging to highlight where the RMS residual values are the highest to pinpoint where changes need to be made to achieve model convergence. Finally, a model of the upper mantle using 3-D P-wave tomography will be made to determine the location of these ultra-mafic roots.

  12. Lensfree diffractive tomography for the imaging of 3D cell cultures

    PubMed Central

    Momey, F.; Berdeu, A.; Bordy, T.; Dinten, J.-M.; Marcel, F. Kermarrec; Picollet-D’hahan, N.; Gidrol, X.; Allier, C.

    2016-01-01

    New microscopes are needed to help realize the full potential of 3D organoid culture studies. In order to image large volumes of 3D organoid cultures while preserving the ability to catch every single cell, we propose a new imaging platform based on lensfree microscopy. We have built a lensfree diffractive tomography setup performing multi-angle acquisitions of 3D organoid culture embedded in Matrigel and developed a dedicated 3D holographic reconstruction algorithm based on the Fourier diffraction theorem. With this new imaging platform, we have been able to reconstruct a 3D volume as large as 21.5 mm3 of a 3D organoid culture of prostatic RWPE1 cells showing the ability of these cells to assemble in 3D intricate cellular network at the mesoscopic scale. Importantly, comparisons with 2D images show that it is possible to resolve single cells isolated from the main cellular structure with our lensfree diffractive tomography setup. PMID:27231600

  13. In vivo bioluminescence tomography based on multi-view projection and 3D surface reconstruction

    NASA Astrophysics Data System (ADS)

    Zhang, Shuang; Wang, Kun; Leng, Chengcai; Deng, Kexin; Hu, Yifang; Tian, Jie

    2015-03-01

    Bioluminescence tomography (BLT) is a powerful optical molecular imaging modality, which enables non-invasive realtime in vivo imaging as well as 3D quantitative analysis in preclinical studies. In order to solve the inverse problem and reconstruct inner light sources accurately, the prior structural information is commonly necessary and obtained from computed tomography or magnetic resonance imaging. This strategy requires expensive hybrid imaging system, complicated operation protocol and possible involvement of ionizing radiation. The overall robustness highly depends on the fusion accuracy between the optical and structural information. In this study we present a pure optical bioluminescence tomographic system (POBTS) and a novel BLT method based on multi-view projection acquisition and 3D surface reconstruction. The POBTS acquired a sparse set of white light surface images and bioluminescent images of a mouse. Then the white light images were applied to an approximate surface model to generate a high quality textured 3D surface reconstruction of the mouse. After that we integrated multi-view luminescent images based on the previous reconstruction, and applied an algorithm to calibrate and quantify the surface luminescent flux in 3D.Finally, the internal bioluminescence source reconstruction was achieved with this prior information. A BALB/C mouse with breast tumor of 4T1-fLuc cells mouse model were used to evaluate the performance of the new system and technique. Compared with the conventional hybrid optical-CT approach using the same inverse reconstruction method, the reconstruction accuracy of this technique was improved. The distance error between the actual and reconstructed internal source was decreased by 0.184 mm.

  14. Computational and methodological developments towards 3D full waveform inversion

    NASA Astrophysics Data System (ADS)

    Etienne, V.; Virieux, J.; Hu, G.; Jia, Y.; Operto, S.

    2010-12-01

    Full waveform inversion (FWI) is one of the most promising techniques for seismic imaging. It relies on a formalism taking into account every piece of information contained in the seismic data as opposed to more classical techniques such as travel time tomography. As a result, FWI is a high resolution imaging process able to reach a spatial accuracy equal to half a wavelength. FWI is based on a local optimization scheme and therefore the main limitation concerns the starting model which has to be closed enough to the real one in order to converge to the global minimum. Another counterpart of FWI is the required computational resources when considering models and frequencies of interest. The task becomes even more tremendous when one tends to perform the inversion using the elastic equation instead of using the acoustic approximation. This is the reason why until recently most studies were limited to 2D cases. In the last few years, due to the increase of the available computational power, FWI has focused a lot of interests and continuous efforts towards inversion of 3D models, leading to remarkable applications up to the continental scale. We investigate the computational burden induced by FWI in 3D elastic media and propose some strategic features leading to the reduction of the numerical cost while providing a great flexibility in the inversion parametrization. First, in order to release the memory requirements, we developed our FWI algorithm in the frequency domain and take benefit of the wave-number redundancy in the seismic data to process a quite reduced number of frequencies. To do so, we extract frequency solutions from time marching techniques which are efficient for 3D structures. Moreover, this frequency approach permits a multi-resolution strategy by proceeding from low to high frequencies: the final model at one frequency is used as the starting model for the next frequency. This procedure overcomes partially the non-linear behavior of the inversion

  15. Computational challenges of emerging novel true 3D holographic displays

    NASA Astrophysics Data System (ADS)

    Cameron, Colin D.; Pain, Douglas A.; Stanley, Maurice; Slinger, Christopher W.

    2000-11-01

    A hologram can produce all the 3D depth cues that the human visual system uses to interpret and perceive real 3D objects. As such it is arguably the ultimate display technology. Computer generated holography, in which a computer calculates a hologram that is then displayed using a highly complex modulator, combines the ultimate qualities of a traditional hologram with the dynamic capabilities of a computer display producing a true 3D real image floating in space. This technology is set to emerge over the next decade, potentially revolutionizing application areas such as virtual prototyping (CAD-CAM, CAID etc.), tactical information displays, data visualization and simulation. In this paper we focus on the computational challenges of this technology. We consider different classes of computational algorithms from true computer-generated holograms (CGH) to holographic stereograms. Each has different characteristics in terms of image qualities, computational resources required, total CGH information content, and system performance. Possible trade- offs will be discussed including reducing the parallax. The software and hardware architectures used to implement the CGH algorithms have many possible forms. Different schemes, from high performance computing architectures to graphics based cluster architectures will be discussed and compared. Assessment will be made of current and future trends looking forward to a practical dynamic CGH based 3D display.

  16. 3D optical coherence tomography image registration for guiding cochlear implant insertion

    NASA Astrophysics Data System (ADS)

    Cheon, Gyeong-Woo; Jeong, Hyun-Woo; Chalasani, Preetham; Chien, Wade W.; Iordachita, Iulian; Taylor, Russell; Niparko, John; Kang, Jin U.

    2014-03-01

    In cochlear implant surgery, an electrode array is inserted into the cochlear canal to restore hearing to a person who is profoundly deaf or significantly hearing impaired. One critical part of the procedure is the insertion of the electrode array, which looks like a thin wire, into the cochlear canal. Although X-ray or computed tomography (CT) could be used as a reference to evaluate the pathway of the whole electrode array, there is no way to depict the intra-cochlear canal and basal turn intra-operatively to help guide insertion of the electrode array. Optical coherent tomography (OCT) is a highly effective way of visualizing internal structures of cochlea. Swept source OCT (SSOCT) having center wavelength of 1.3 micron and 2D Galvonometer mirrors was used to achieve 7-mm depth 3-D imaging. Graphics processing unit (GPU), OpenGL, C++ and C# were integrated for real-time volumetric rendering simultaneously. The 3D volume images taken by the OCT system were assembled and registered which could be used to guide a cochlear implant. We performed a feasibility study using both dry and wet temporal bones and the result is presented.

  17. Test target for characterizing 3D resolution of optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Hu, Zhixiong; Hao, Bingtao; Liu, Wenli; Hong, Baoyu; Li, Jiao

    2014-12-01

    Optical coherence tomography (OCT) is a non-invasive 3D imaging technology which has been applied or investigated in many diagnostic fields including ophthalmology, dermatology, dentistry, cardiovasology, endoscopy, brain imaging and so on. Optical resolution is an important characteristic that can describe the quality and utility of an image acquiring system. We employ 3D printing technology to design and fabricate a test target for characterizing 3D resolution of optical coherence tomography. The test target which mimics USAF 1951 test chart was produced with photopolymer. By measuring the 3D test target, axial resolution as well as lateral resolution of a spectral domain OCT system was evaluated. For comparison, conventional microscope and surface profiler were employed to characterize the 3D test targets. The results demonstrate that the 3D resolution test targets have the potential of qualitatively and quantitatively validating the performance of OCT systems.

  18. XEDS STEM Tomography For 3D Chemical Characterization Of Nanoscale Particles

    SciTech Connect

    Genc, Arda; Kovarik, Libor; Gu, Meng; Cheng, Huikai; Plachinda, Pavel; Pullan, Lee; Freitag, Bert; Wang, Chong M.

    2013-08-01

    We present a tomography technique which couples scanning transmission electron microscopy (STEM) and X-ray energy dispersive spectrometry (XEDS) to resolve 3D distribution of elements in nanoscale materials. STEM imaging when combined with a symmetrically arranged XEDS detector design around the specimen overcomes many of the obstacles in 3D spectroscopic tomography of nanoscale materials and successfully elucidate the 3D chemical information in a large field of view of the TEM sample. We employed this technique to investigate 3D distribution of Nickel (Ni), Manganese (Mn) and Oxygen (O) in Li(NiMn)O2 battery cathode material. For this purpose, 2D elemental maps were acquired for a range of tilt angles and reconstructed to obtain 3D elemental distribution in an isolated Li(NiMnO2) nanoparticle. The results highlight the strength of this technique in 3D chemical analysis of nanoscale materials by successfully resolving Ni, Mn and O elemental distributions in 3D and discovering the new phenomenon of Ni surface segregation in this material. Furthermore, the comparison of simultaneously acquired HAADF STEM and XEDS STEM tomography results show that XEDS STEM tomography provides additional 3D chemical information of the material especially when there is low atomic number (Z) contrast in the material of interest.

  19. Parallel beam optical tomography apparatus for 3D radiation dosimetry

    NASA Astrophysics Data System (ADS)

    Krstajic, Nikola; Doran, Simon J.

    2005-06-01

    Since the discovery of X rays radiotherapy has had the same aim - to deliver a precisely measured dose of radiation to a defined tumour volume with minimal damage to surrounding healthy tissue. Recent developments in radiotherapy such as intensity modulated radiotherapy (IMRT) can generate complex shapes of dose distributions. Until recently it has not been possible to verify that the delivered dose matches the planned dose. However, one often wants to know the real three-dimensional dose distribution. Three-dimensional radiation dosimeters have been developed since the early 1980s. Most chemical formulations involve a radiosensitive species immobilised in space by gelling agent. Magnetic Resonance Imaging (MRI) and optical techniques have been the most successful gel scanning techniques so far. Optical techniques rely on gels changing colour once irradiated. Parallel beam optical tomography has been developed at the University of Surrey since the late 1990s. The apparatus involves light emitting diode light source collimated to a wide (12cm) parallel beam. The beam is attenuated or scattered (depending on the chemical formulation) as it passes through the gel. Focusing optics projects the beam onto a CCD chip. The dosimeter sits on a rotation stage. The tomography scan involves continuously rotating the dosimeter and taking CCD images. Once the dosimeter has been rotated over 180 degrees the images are processed by filtered back projection. The work presented discusses the optics of the apparatus in more detail.

  20. Laboratory-based x-ray phase-contrast tomography enables 3D virtual histology

    NASA Astrophysics Data System (ADS)

    Töpperwien, Mareike; Krenkel, Martin; Quade, Felix; Salditt, Tim

    2016-09-01

    Due to the large penetration depth and small wavelength hard x-rays offer a unique potential for 3D biomedical and biological imaging, combining capabilities of high resolution and large sample volume. However, in classical absorption-based computed tomography, soft tissue only shows a weak contrast, limiting the actual resolution. With the advent of phase-contrast methods, the much stronger phase shift induced by the sample can now be exploited. For high resolution, free space propagation behind the sample is particularly well suited to make the phase shift visible. Contrast formation is based on the self-interference of the transmitted beam, resulting in object-induced intensity modulations in the detector plane. As this method requires a sufficiently high degree of spatial coherence, it was since long perceived as a synchrotron-based imaging technique. In this contribution we show that by combination of high brightness liquid-metal jet microfocus sources and suitable sample preparation techniques, as well as optimized geometry, detection and phase retrieval, excellent three-dimensional image quality can be obtained, revealing the anatomy of a cobweb spider in high detail. This opens up new opportunities for 3D virtual histology of small organisms. Importantly, the image quality is finally augmented to a level accessible to automatic 3D segmentation.

  1. Multitasking the code ARC3D. [for computational fluid dynamics

    NASA Technical Reports Server (NTRS)

    Barton, John T.; Hsiung, Christopher C.

    1986-01-01

    The CRAY multitasking system was developed in order to utilize all four processors and sharply reduce the wall clock run time. This paper describes the techniques used to modify the computational fluid dynamics code ARC3D for this run and analyzes the achieved speedup. The ARC3D code solves either the Euler or thin-layer N-S equations using an implicit approximate factorization scheme. Results indicate that multitask processing can be used to achieve wall clock speedup factors of over three times, depending on the nature of the program code being used. Multitasking appears to be particularly advantageous for large-memory problems running on multiple CPU computers.

  2. Image quality enhancement and computation acceleration of 3D holographic display using a symmetrical 3D GS algorithm.

    PubMed

    Zhou, Pengcheng; Bi, Yong; Sun, Minyuan; Wang, Hao; Li, Fang; Qi, Yan

    2014-09-20

    The 3D Gerchberg-Saxton (GS) algorithm can be used to compute a computer-generated hologram (CGH) to produce a 3D holographic display. But, using the 3D GS method, there exists a serious distortion in reconstructions of binary input images. We have eliminated the distortion and improved the image quality of the reconstructions by a maximum of 486%, using a symmetrical 3D GS algorithm that is developed based on a traditional 3D GS algorithm. In addition, the hologram computation speed has been accelerated by 9.28 times, which is significant for real-time holographic displays.

  3. 3D measurement system based on computer-generated gratings

    NASA Astrophysics Data System (ADS)

    Zhu, Yongjian; Pan, Weiqing; Luo, Yanliang

    2010-08-01

    A new kind of 3D measurement system has been developed to achieve the 3D profile of complex object. The principle of measurement system is based on the triangular measurement of digital fringe projection, and the fringes are fully generated from computer. Thus the computer-generated four fringes form the data source of phase-shifting 3D profilometry. The hardware of system includes the computer, video camera, projector, image grabber, and VGA board with two ports (one port links to the screen, another to the projector). The software of system consists of grating projection module, image grabbing module, phase reconstructing module and 3D display module. A software-based synchronizing method between grating projection and image capture is proposed. As for the nonlinear error of captured fringes, a compensating method is introduced based on the pixel-to-pixel gray correction. At the same time, a least square phase unwrapping is used to solve the problem of phase reconstruction by using the combination of Log Modulation Amplitude and Phase Derivative Variance (LMAPDV) as weight. The system adopts an algorithm from Matlab Tool Box for camera calibration. The 3D measurement system has an accuracy of 0.05mm. The execution time of system is 3~5s for one-time measurement.

  4. Focusing optics of a parallel beam CCD optical tomography apparatus for 3D radiation gel dosimetry.

    PubMed

    Krstajić, Nikola; Doran, Simon J

    2006-04-21

    Optical tomography of gel dosimeters is a promising and cost-effective avenue for quality control of radiotherapy treatments such as intensity-modulated radiotherapy (IMRT). Systems based on a laser coupled to a photodiode have so far shown the best results within the context of optical scanning of radiosensitive gels, but are very slow ( approximately 9 min per slice) and poorly suited to measurements that require many slices. Here, we describe a fast, three-dimensional (3D) optical computed tomography (optical-CT) apparatus, based on a broad, collimated beam, obtained from a high power LED and detected by a charged coupled detector (CCD). The main advantages of such a system are (i) an acquisition speed approximately two orders of magnitude higher than a laser-based system when 3D data are required, and (ii) a greater simplicity of design. This paper advances our previous work by introducing a new design of focusing optics, which take information from a suitably positioned focal plane and project an image onto the CCD. An analysis of the ray optics is presented, which explains the roles of telecentricity, focusing, acceptance angle and depth-of-field (DOF) in the formation of projections. A discussion of the approximation involved in measuring the line integrals required for filtered backprojection reconstruction is given. Experimental results demonstrate (i) the effect on projections of changing the position of the focal plane of the apparatus, (ii) how to measure the acceptance angle of the optics, and (iii) the ability of the new scanner to image both absorbing and scattering gel phantoms. The quality of reconstructed images is very promising and suggests that the new apparatus may be useful in a clinical setting for fast and accurate 3D dosimetry.

  5. [Computed tomography and cranial paleoanthropology].

    PubMed

    Cabanis, Emmanuel Alain; Badawi-Fayad, Jackie; Iba-Zizen, Marie-Thérèse; Istoc, Adrian; de Lumley, Henry; de Lumley, Marie-Antoinette; Coppens, Yves

    2007-06-01

    Since its invention in 1972, computed tomography (C.T.) has significantly evolved. With the advent of multi-slice detectors (500 times more sensitive than conventional radiography) and high-powered computer programs, medical applications have also improved. CT is now contributing to paleoanthropological research. Its non-destructive nature is the biggest advantage for studying fossil skulls. The second advantage is the possibility of image analysis, storage, and transmission. Potential disadvantages include the possible loss of files and the need to keep up with rapid technological advances. Our experience since the late 1970s, and a recent PhD thesis, led us to describe routine applications of this method. The main contributions of CT to cranial paleoanthropology are five-fold: --Numerical anatomy with rapid acquisition and high spatial resolution (helicoidal and multidetector CT) offering digital storage and stereolithography (3D printing). --Numerical biometry (2D and 3D) can be used to create "normograms" such as the 3D craniofacial reference model used in maxillofacial surgery. --Numerical analysis offers thorough characterization of the specimen and its state of conservation and/or restoration. --From "surrealism" to virtual imaging, anatomical structures can be reconstructed, providing access to hidden or dangerous zones. --The time dimension (4D imaging) confers movement and the possibility for endoscopic simulation and internal navigation (see Iconography). New technical developments will focus on data processing and networking. It remains our duty to deal respectfully with human fossils.

  6. 3-D Adaptive Sparsity Based Image Compression with Applications to Optical Coherence Tomography

    PubMed Central

    Fang, Leyuan; Li, Shutao; Kang, Xudong; Izatt, Joseph A.; Farsiu, Sina

    2015-01-01

    We present a novel general-purpose compression method for tomographic images, termed 3D adaptive sparse representation based compression (3D-ASRC). In this paper, we focus on applications of 3D-ASRC for the compression of ophthalmic 3D optical coherence tomography (OCT) images. The 3D-ASRC algorithm exploits correlations among adjacent OCT images to improve compression performance, yet is sensitive to preserving their differences. Due to the inherent denoising mechanism of the sparsity based 3D-ASRC, the quality of the compressed images are often better than the raw images they are based on. Experiments on clinical-grade retinal OCT images demonstrate the superiority of the proposed 3D-ASRC over other well-known compression methods. PMID:25561591

  7. The 3-D inelastic analyses for computational structural mechanics

    NASA Technical Reports Server (NTRS)

    Hopkins, D. A.; Chamis, C. C.

    1989-01-01

    The 3-D inelastic analysis method is a focused program with the objective to develop computationally effective analysis methods and attendant computer codes for three-dimensional, nonlinear time and temperature dependent problems present in the hot section of turbojet engine structures. Development of these methods was a major part of the Hot Section Technology (HOST) program over the past five years at Lewis Research Center.

  8. Education System Using Interactive 3D Computer Graphics (3D-CG) Animation and Scenario Language for Teaching Materials

    ERIC Educational Resources Information Center

    Matsuda, Hiroshi; Shindo, Yoshiaki

    2006-01-01

    The 3D computer graphics (3D-CG) animation using a virtual actor's speaking is very effective as an educational medium. But it takes a long time to produce a 3D-CG animation. To reduce the cost of producing 3D-CG educational contents and improve the capability of the education system, we have developed a new education system using Virtual Actor.…

  9. Note: design and construction of a multi-scale, high-resolution, tube-generated x-ray computed-tomography system for three-dimensional (3D) imaging.

    PubMed

    Mertens, J C E; Williams, J J; Chawla, Nikhilesh

    2014-01-01

    The design and construction of a high resolution modular x-ray computed tomography (XCT) system is described. The approach for meeting a specified set of performance goals tailored toward experimental versatility is highlighted. The instrument is unique in its detector and x-ray source configuration, both of which enable elevated optimization of spatial and temporal resolution. The process for component selection is provided. The selected components are specified, the custom component design discussed, and the integration of both into a fully functional XCT instrument is outlined. The novelty of this design is a new lab-scale detector and imaging optimization through x-ray source and detector modularity.

  10. FUN3D and CFL3D Computations for the First High Lift Prediction Workshop

    NASA Technical Reports Server (NTRS)

    Park, Michael A.; Lee-Rausch, Elizabeth M.; Rumsey, Christopher L.

    2011-01-01

    Two Reynolds-averaged Navier-Stokes codes were used to compute flow over the NASA Trapezoidal Wing at high lift conditions for the 1st AIAA CFD High Lift Prediction Workshop, held in Chicago in June 2010. The unstructured-grid code FUN3D and the structured-grid code CFL3D were applied to several different grid systems. The effects of code, grid system, turbulence model, viscous term treatment, and brackets were studied. The SST model on this configuration predicted lower lift than the Spalart-Allmaras model at high angles of attack; the Spalart-Allmaras model agreed better with experiment. Neglecting viscous cross-derivative terms caused poorer prediction in the wing tip vortex region. Output-based grid adaptation was applied to the unstructured-grid solutions. The adapted grids better resolved wake structures and reduced flap flow separation, which was also observed in uniform grid refinement studies. Limitations of the adaptation method as well as areas for future improvement were identified.

  11. Computed tomography status

    SciTech Connect

    Hansche, B.D.

    1983-01-01

    Computed tomography (CT) is a relatively new radiographic technique which has become widely used in the medical field, where it is better known as computerized axial tomographic (CAT) scanning. This technique is also being adopted by the industrial radiographic community, although the greater range of densities, variation in samples sizes, plus possible requirement for finer resolution make it difficult to duplicate the excellent results that the medical scanners have achieved.

  12. Computed Tomography Status

    DOE R&D Accomplishments Database

    Hansche, B. D.

    1983-01-01

    Computed tomography (CT) is a relatively new radiographic technique which has become widely used in the medical field, where it is better known as computerized axial tomographic (CAT) scanning. This technique is also being adopted by the industrial radiographic community, although the greater range of densities, variation in samples sizes, plus possible requirement for finer resolution make it difficult to duplicate the excellent results that the medical scanners have achieved.

  13. Proton computed tomography

    NASA Astrophysics Data System (ADS)

    Bucciantonio, Martina; Sauli, Fabio

    2015-05-01

    Proton computed tomography (pCT) is a diagnostic method capable of in situ imaging the three-dimensional density distribution in a patient before irradiation with charged particle beams. Proposed long time ago, this technology has been developed by several groups, and may become an essential tool for advanced quality assessment in hadrontherapy. We describe the basic principles of the method, its performance and limitations as well as provide a summary of experimental systems and of results achieved.

  14. High Resolution Computed Tomography

    DTIC Science & Technology

    1992-07-31

    samples. 14. SUBJECTTERMS 15. NUMBER OF PAGES 38 High Resolution, Microfocus , Characterization, X - Ray , Micrography, Computed Tomography (CT), Failure...high resolutions (50 g.tm feature sensitivity) when a small field of view (50 mm) is used [11]. Specially designed detectors and a microfocus X - ray ...Wright Laboratories. Feldkamp [14] at Ford used a microfocus X - ray source and an X - ray image intensifier to develop a system capable of 20 g.m

  15. Direct ambient noise tomography for 3-D near surface shear velocity structure: methodology and applications

    NASA Astrophysics Data System (ADS)

    Yao, H.; Fang, H.; Li, C.; Liu, Y.; Zhang, H.; van der Hilst, R. D.; Huang, Y. C.

    2014-12-01

    Ambient noise tomography has provided essential constraints on crustal and uppermost mantle shear velocity structure in global seismology. Recent studies demonstrate that high frequency (e.g., ~ 1 Hz) surface waves between receivers at short distances can be successfully retrieved from ambient noise cross-correlation and then be used for imaging near surface or shallow crustal shear velocity structures. This approach provides important information for strong ground motion prediction in seismically active area and overburden structure characterization in oil and gas fields. Here we propose a new tomographic method to invert all surface wave dispersion data for 3-D variations of shear wavespeed without the intermediate step of phase or group velocity maps.The method uses frequency-dependent propagation paths and a wavelet-based sparsity-constrained tomographic inversion. A fast marching method is used to compute, at each period, surface wave traveltimes and ray paths between sources and receivers. This avoids the assumption of great-circle propagation that is used in most surface wave tomographic studies, but which is not appropriate in complex media. The wavelet coefficients of the velocity model are estimated with an iteratively reweighted least squares (IRLS) algorithm, and upon iterations the surface wave ray paths and the data sensitivity matrix are updated from the newly obtained velocity model. We apply this new method to determine the 3-D near surface wavespeed variations in the Taipei basin of Taiwan, Hefei urban area and a shale and gas production field in China using the high-frequency interstation Rayleigh wave dispersion data extracted from ambient noisecross-correlation. The results reveal strong effects of off-great-circle propagation of high-frequency surface waves in these regions with above 30% shear wavespeed variations. The proposed approach is more efficient and robust than the traditional two-step surface wave tomography for imaging complex

  16. NASA's 3D Flight Computer for Space Applications

    NASA Technical Reports Server (NTRS)

    Alkalai, Leon

    2000-01-01

    The New Millennium Program (NMP) Integrated Product Development Team (IPDT) for Microelectronics Systems was planning to validate a newly developed 3D Flight Computer system on its first deep-space flight, DS1, launched in October 1998. This computer, developed in the 1995-97 time frame, contains many new computer technologies previously never used in deep-space systems. They include: advanced 3D packaging architecture for future low-mass and low-volume avionics systems; high-density 3D packaged chip-stacks for both volatile and non-volatile mass memory: 400 Mbytes of local DRAM memory, and 128 Mbytes of Flash memory; high-bandwidth Peripheral Component Interface (Per) local-bus with a bridge to VME; high-bandwidth (20 Mbps) fiber-optic serial bus; and other attributes, such as standard support for Design for Testability (DFT). Even though this computer system did not complete on time for delivery to the DS1 project, it was an important development along a technology roadmap towards highly integrated and highly miniaturized avionics systems for deep-space applications. This continued technology development is now being performed by NASA's Deep Space System Development Program (also known as X2000) and within JPL's Center for Integrated Space Microsystems (CISM).

  17. Regional application of multi-layer artificial neural networks in 3-D ionosphere tomography

    NASA Astrophysics Data System (ADS)

    Ghaffari Razin, Mir Reza; Voosoghi, Behzad

    2016-08-01

    Tomography is a very cost-effective method to study physical properties of the ionosphere. In this paper, residual minimization training neural network (RMTNN) is used in voxel-based tomography to reconstruct of 3-D ionosphere electron density with high spatial resolution. For numerical experiments, observations collected at 37 GPS stations from Iranian permanent GPS network (IPGN) are used. A smoothed TEC approach was used for absolute STEC recovery. To improve the vertical resolution, empirical orthogonal functions (EOFs) obtained from international reference ionosphere 2012 (IRI-2012) used as object function in training neural network. Ionosonde observations is used for validate reliability of the proposed method. Minimum relative error for RMTNN is 1.64% and maximum relative error is 15.61%. Also root mean square error (RMSE) of 0.17 × 1011 (electrons/m3) is computed for RMTNN which is less than RMSE of IRI2012. The results show that RMTNN has higher accuracy and compiles speed than other ionosphere reconstruction methods.

  18. Computational issues connected with 3D N-body simulations

    NASA Astrophysics Data System (ADS)

    Pfenniger, D.; Friedli, D.

    1993-03-01

    Computational problems related to modeling gravitational systems, and running and analyzing 3D N-body models are discussed. N-body simulations using Particle-Mesh techniques with polar grids are especially well-suited, and physically justified, when studying quiet evolutionary processes in disk galaxies. This technique allows large N, high central resolution, and is still the fastest one. Regardless of the method chosen to compute gravitation, softening is a compromise between HF amplification and resolution. Softened spherical and ellipsoidal kernels with variable resolution are set up. Detailed characteristics of the 3D polar grid, tests, code performances, and vectorization rates are also given. For integrating motion in rotating coordinates, a stable symplectic extension of the leap-frog algorithm is described. The technique used to search for periodic orbits in arbitrary N-body potentials and to determine their stability is explained.

  19. Advanced computational tools for 3-D seismic analysis

    SciTech Connect

    Barhen, J.; Glover, C.W.; Protopopescu, V.A.

    1996-06-01

    The global objective of this effort is to develop advanced computational tools for 3-D seismic analysis, and test the products using a model dataset developed under the joint aegis of the United States` Society of Exploration Geophysicists (SEG) and the European Association of Exploration Geophysicists (EAEG). The goal is to enhance the value to the oil industry of the SEG/EAEG modeling project, carried out with US Department of Energy (DOE) funding in FY` 93-95. The primary objective of the ORNL Center for Engineering Systems Advanced Research (CESAR) is to spearhead the computational innovations techniques that would enable a revolutionary advance in 3-D seismic analysis. The CESAR effort is carried out in collaboration with world-class domain experts from leading universities, and in close coordination with other national laboratories and oil industry partners.

  20. Development of a computer controlled 3-d braiding machine

    SciTech Connect

    Yan Jianhua; Li Jialu

    1994-12-31

    This paper deals with development of a large size, multiuse, controlled 3-D cartesian grid braiding machine, its function and application. The 180 column and 120 tracks, the flexible and low power consuming driving system, the error detector systems and the computer controlling system are the major parts of the machine. The machine can produce wide variety of size. shape and pattern of fabrics and can also produce several fabrics at a time.

  1. Noninvasive computational imaging of cardiac electrophysiology for 3-D infarct.

    PubMed

    Wang, Linwei; Wong, Ken C L; Zhang, Heye; Liu, Huafeng; Shi, Pengcheng

    2011-04-01

    Myocardial infarction (MI) creates electrophysiologically altered substrates that are responsible for ventricular arrhythmias, such as tachycardia and fibrillation. The presence, size, location, and composition of infarct scar bear significant prognostic and therapeutic implications for individual subjects. We have developed a statistical physiological model-constrained framework that uses noninvasive body-surface-potential data and tomographic images to estimate subject-specific transmembrane-potential (TMP) dynamics inside the 3-D myocardium. In this paper, we adapt this framework for the purpose of noninvasive imaging, detection, and quantification of 3-D scar mass for postMI patients: the framework requires no prior knowledge of MI and converges to final subject-specific TMP estimates after several passes of estimation with intermediate feedback; based on the primary features of the estimated spatiotemporal TMP dynamics, we provide 3-D imaging of scar tissue and quantitative evaluation of scar location and extent. Phantom experiments were performed on a computational model of realistic heart-torso geometry, considering 87 transmural infarct scars of different sizes and locations inside the myocardium, and 12 compact infarct scars (extent between 10% and 30%) at different transmural depths. Real-data experiments were carried out on BSP and magnetic resonance imaging (MRI) data from four postMI patients, validated by gold standards and existing results. This framework shows unique advantage of noninvasive, quantitative, computational imaging of subject-specific TMP dynamics and infarct mass of the 3-D myocardium, with the potential to reflect details in the spatial structure and tissue composition/heterogeneity of 3-D infarct scar.

  2. Analysis of the 3D distribution of stacked self-assembled quantum dots by electron tomography

    PubMed Central

    2012-01-01

    The 3D distribution of self-assembled stacked quantum dots (QDs) is a key parameter to obtain the highest performance in a variety of optoelectronic devices. In this work, we have measured this distribution in 3D using a combined procedure of needle-shaped specimen preparation and electron tomography. We show that conventional 2D measurements of the distribution of QDs are not reliable, and only 3D analysis allows an accurate correlation between the growth design and the structural characteristics. PMID:23249477

  3. The applicability of 3D Doppler tomography to studies of polars

    NASA Astrophysics Data System (ADS)

    Kononov, D. A.; Agafonov, M. I.; Sharova, O. I.; Bisikalo, D. V.; Zhilkin, A. G.; Sidorov, M. Yu.

    2014-12-01

    The applicability of 3D Doppler tomography to mapping gas flows in polars is considered. Synthetic profiles of emission lines are calculated using solutions (for the densities, temperatures, and velocity components) obtained from 3D MHD modeling, which are then used to construct 3D Doppler tomograms in the velocity space ( V x , V y , V z ). Subsequent analysis of these tomograms applying observational constraints (the signal-to-noise ratio, number of input profiles, etc.) enables evaluation of limits to the method's applicability.

  4. Efficient curve-skeleton computation for the analysis of biomedical 3d images - biomed 2010.

    PubMed

    Brun, Francesco; Dreossi, Diego

    2010-01-01

    Advances in three dimensional (3D) biomedical imaging techniques, such as magnetic resonance (MR) and computed tomography (CT), make it easy to reconstruct high quality 3D models of portions of human body and other biological specimens. A major challenge lies in the quantitative analysis of the resulting models thus allowing a more comprehensive characterization of the object under investigation. An interesting approach is based on curve-skeleton (or medial axis) extraction, which gives basic information concerning the topology and the geometry. Curve-skeletons have been applied in the analysis of vascular networks and the diagnosis of tracheal stenoses as well as a 3D flight path in virtual endoscopy. However curve-skeleton computation is a crucial task. An effective skeletonization algorithm was introduced by N. Cornea in [1] but it lacks in computational performances. Thanks to the advances in imaging techniques the resolution of 3D images is increasing more and more, therefore there is the need for efficient algorithms in order to analyze significant Volumes of Interest (VOIs). In the present paper an improved skeletonization algorithm based on the idea proposed in [1] is presented. A computational comparison between the original and the proposed method is also reported. The obtained results show that the proposed method allows a significant computational improvement making more appealing the adoption of the skeleton representation in biomedical image analysis applications.

  5. Abdominal perfusion computed tomography.

    PubMed

    Ogul, Hayri; Bayraktutan, Ummugulsum; Kizrak, Yesim; Pirimoglu, Berhan; Yuceler, Zeynep; Sagsoz, M Erdem; Yilmaz, Omer; Aydinli, Bulent; Ozturk, Gurkan; Kantarci, Mecit

    2013-02-01

    The purpose of this article is to provide an up to date review on the spectrum of applications of perfusion computed tomography (CT) in the abdomen. New imaging techniques have been developed with the objective of obtaining a structural and functional analysis of different organs. Recently, perfusion CT has aroused the interest of many researchers who are studying the applicability of imaging modalities in the evaluation of abdominal organs and diseases. Per-fusion CT enables fast, non-invasive imaging of the tumor vascular physiology. Moreover, it can act as an in vivo biomarker of tumor-related angiogenesis.

  6. Abdominal Perfusion Computed Tomography

    PubMed Central

    Ogul, Hayri; Bayraktutan, Ummugulsum; Kizrak, Yesim; Pirimoglu, Berhan; Yuceler, Zeynep; Sagsoz, M. Erdem; Yilmaz, Omer; Aydinli, Bulent; Ozturk, Gurkan; Kantarci, Mecit

    2013-01-01

    The purpose of this article is to provide an up to date review on the spectrum of applications of perfusion computed tomography (CT) in the abdomen. New imaging techniques have been developed with the objective of obtaining a structural and functional analysis of different organs. Recently, perfusion CT has aroused the interest of many researchers who are studying the applicability of imaging modalities in the evaluation of abdominal organs and diseases. Per-fusion CT enables fast, non-invasive imaging of the tumor vascular physiology. Moreover, it can act as an in vivo biomarker of tumor-related angiogenesis. PMID:25610249

  7. 3D seismic imaging on massively parallel computers

    SciTech Connect

    Womble, D.E.; Ober, C.C.; Oldfield, R.

    1997-02-01

    The ability to image complex geologies such as salt domes in the Gulf of Mexico and thrusts in mountainous regions is a key to reducing the risk and cost associated with oil and gas exploration. Imaging these structures, however, is computationally expensive. Datasets can be terabytes in size, and the processing time required for the multiple iterations needed to produce a velocity model can take months, even with the massively parallel computers available today. Some algorithms, such as 3D, finite-difference, prestack, depth migration remain beyond the capacity of production seismic processing. Massively parallel processors (MPPs) and algorithms research are the tools that will enable this project to provide new seismic processing capabilities to the oil and gas industry. The goals of this work are to (1) develop finite-difference algorithms for 3D, prestack, depth migration; (2) develop efficient computational approaches for seismic imaging and for processing terabyte datasets on massively parallel computers; and (3) develop a modular, portable, seismic imaging code.

  8. 3-D crustal and uppermost mantle structure beneath NE China revealed by ambient noise adjoint tomography

    NASA Astrophysics Data System (ADS)

    Liu, Yaning; Niu, Fenglin; Chen, Min; Yang, Wencai

    2017-03-01

    We construct a new 3-D shear wave speed model of the crust and the uppermost mantle beneath Northeast China using the ambient noise adjoint tomography method. Without intermediate steps of measuring phase dispersion, the adjoint tomography inverts for shear wave speeds of the crust and uppermost mantle directly from 6-40 s waveforms of Empirical Green's functions (EGFs) of Rayleigh waves, which are derived from interferometry of two years of ambient noise data recorded by the 127 Northeast China Extended Seismic Array stations. With an initial 3-D model derived from traditional asymptotic surface wave tomography method, adjoint tomography refines the 3-D model by iteratively minimizing the frequency-dependent traveltime misfits between EGFs and synthetic Green's functions measured in four period bands: 6-15 s, 10-20 s, 15-30 s, and 20-40 s. Our new model shows shear wave speed anomalies that are spatially correlated with known tectonic units such as the Great Xing'an range and the Changbaishan mountain range. The new model also reveals low wave speed conduits in the mid-lower crust and the uppermost mantle with a wave speed reduction indicative of partial melting beneath the Halaha, Xilinhot-Abaga, and Jingpohu volcanic complexes, suggesting that the Cenozoic volcanism in the area has a deep origin. Overall, the adjoint tomographic images show more vertically continuous velocity anomalies with larger amplitudes due to the consideration of the finite frequency and 3-D effects.

  9. Capacitance Measurement with a Sigma Delta Converter for 3D Electrical Capacitance Tomography

    NASA Technical Reports Server (NTRS)

    Nurge, Mark

    2005-01-01

    This paper will explore suitability of a newly available capacitance to digital converter for use in a 3D Electrical Capacitance Tomography system. A switch design is presented along with circuitry needed to extend the range of the capacitance to digital converter. Results are then discussed for a 15+ hour drift and noise test.

  10. 3D structure of eukaryotic flagella/cilia by cryo-electron tomography.

    PubMed

    Ishikawa, Takashi

    2013-01-01

    Flagella/cilia are motile organelles with more than 400 proteins. To understand the mechanism of such complex systems, we need methods to describe molecular arrange-ments and conformations three-dimensionally in vivo. Cryo-electron tomography enabled us such a 3D structural analysis. Our group has been working on 3D structure of flagella/cilia using this method and revealed highly ordered and beautifully organized molecular arrangement. 3D structure gave us insights into the mechanism to gener-ate bending motion with well defined waveforms. In this review, I summarize our recent structural studies on fla-gella/cilia by cryo-electron tomography, mainly focusing on dynein microtubule-based ATPase motor proteins and the radial spoke, a regulatory protein complex.

  11. Computing Radiative Transfer in a 3D Medium

    NASA Technical Reports Server (NTRS)

    Von Allmen, Paul; Lee, Seungwon

    2012-01-01

    A package of software computes the time-dependent propagation of a narrow laser beam in an arbitrary three- dimensional (3D) medium with absorption and scattering, using the transient-discrete-ordinates method and a direct integration method. Unlike prior software that utilizes a Monte Carlo method, this software enables simulation at very small signal-to-noise ratios. The ability to simulate propagation of a narrow laser beam in a 3D medium is an improvement over other discrete-ordinate software. Unlike other direct-integration software, this software is not limited to simulation of propagation of thermal radiation with broad angular spread in three dimensions or of a laser pulse with narrow angular spread in two dimensions. Uses for this software include (1) computing scattering of a pulsed laser beam on a material having given elastic scattering and absorption profiles, and (2) evaluating concepts for laser-based instruments for sensing oceanic turbulence and related measurements of oceanic mixed-layer depths. With suitable augmentation, this software could be used to compute radiative transfer in ultrasound imaging in biological tissues, radiative transfer in the upper Earth crust for oil exploration, and propagation of laser pulses in telecommunication applications.

  12. 3D investigation of inclusions in diamonds using X-ray micro-tomography

    NASA Astrophysics Data System (ADS)

    Parisatto, M.; Nestola, F.; Artioli, G.; Nimis, P.; Harris, J. W.; Kopylova, M.; Pearson, G. D.

    2012-04-01

    The study of mineral inclusions in diamonds is providing invaluable insights into the geochemistry, geodynamics and geophysics of the Earth's mantle. Over the last two decades, the identification of different inclusion assemblages allowed to recognize diamonds deriving from the deep upper mantle, the transition zone and even the lower mantle. In such research field the in-situ investigation of inclusions using non-destructive techniques is often essential but still remains a challenging task. In particular, conventional 2D imaging techniques (e.g. SEM) are limited to the investigation of surfaces and the lack of access to the third dimension represents a major limitation when trying to extract quantitative information. Another critical aspect is related to sample preparation (cutting, polishing) which is typically very invasive. Nowadays, X-ray computed micro-tomography (X-μCT) allows to overcome such limitations, enabling the internal microstructure of totally undisturbed samples to be visualized in a three-dimensional (3D) manner at the sub-micrometric scale. The final output of a micro-tomography experiment is a greyvalue 3D map of the variations of the X-ray attenuation coefficient (µ) within the studied object. The high X-ray absorption contrast between diamond (almost transparent to X-rays) and the typical inclusion-forming minerals (olivines, garnets, pyroxenes, oxides and sulphides) makes X-μCT a straightforward method for the 3D visualization of inclusions and for the study of their spatial relationships with the diamond host. In this work we applied microfocus X-μCT to investigate silicate inclusions still trapped in diamonds, in order to obtain in-situ information on their exact position, crystal size, shape and X-ray absorption coefficient (which is related to their composition). We selected diamond samples from different deposits containing mainly olivine and garnet inclusions. The investigated samples derived from the Udachnaya pipe (Siberia

  13. The `L' Array, a method to model 3D Electrical Resistivity Tomography (ERT) data

    NASA Astrophysics Data System (ADS)

    Chavez Segura, R. E.; Chavez-Hernandez, G.; Delgado, C.; Tejero-Andrade, A.

    2010-12-01

    The electrical resistivity tomography (ERT) is a method designed to calculate the distribution of apparent electrical resistivities in the subsoil by means of a great number of observations with the aim of determining an electrical image displaying the distribution of true resistivities in the subsoil. Such process can be carried out to define 2D or 3D models of the subsurface. For a 3D ERT, usually, the electrodes are placed in a squared grid keeping the distance between adjacent electrodes constant in the x and y directions. Another design employed, consists of a series of parallel lines whose space inter-lines must be smaller or equal to four times the electrode separation. The most common electrode arrays frequently employed for this type of studies are the pole-pole, pole-dipole and dipole-dipole. Unfortunately, ERT surface sampling schemes are limited by physical conditions or obstacles, like buildings, highly populated urban zones, and geologic/topographic features, where the lines of electrodes cannot be set. However, it is always necessary to characterize the subsoil beneath such anthropogenic or natural features. The ‘L’ shaped array has the main purpose to overcome such difficulties by surrounding the study area with a square of electrode lines. The measurements are obtained by switching automatically current and potential electrodes from one line to the other. Each observation adds a level of information, from one profile to the other. Once the total levels of data are completed, the opposite ‘L’ array can be measured following the same process. The complete square is computed after the parallel profiles are observed as well. At the end, the computed resistivities are combined to form a 3D matrix of observations. Such set of data can be inverted to obtain the true resistivity distribution at depth in the form of a working cube, which can be interpreted. The method was tested with theoretical models, which included a set of two resistive cubes

  14. Sampling of finite elements for sparse recovery in large scale 3D electrical impedance tomography.

    PubMed

    Javaherian, Ashkan; Soleimani, Manuchehr; Moeller, Knut

    2015-01-01

    This study proposes a method to improve performance of sparse recovery inverse solvers in 3D electrical impedance tomography (3D EIT), especially when the volume under study contains small-sized inclusions, e.g. 3D imaging of breast tumours. Initially, a quadratic regularized inverse solver is applied in a fast manner with a stopping threshold much greater than the optimum. Based on assuming a fixed level of sparsity for the conductivity field, finite elements are then sampled via applying a compressive sensing (CS) algorithm to the rough blurred estimation previously made by the quadratic solver. Finally, a sparse inverse solver is applied solely to the sampled finite elements, with the solution to the CS as its initial guess. The results show the great potential of the proposed CS-based sparse recovery in improving accuracy of sparse solution to the large-size 3D EIT.

  15. Feasibility of half-data image reconstruction in 3-D reflectivity tomography with a spherical aperture.

    PubMed

    Anastasio, Mark A; Zhang, Jin; Sidky, Emil Y; Zou, Yu; Xia, Dan; Pan, Xiaochuan

    2005-09-01

    Reflectivity tomography is an imaging technique that seeks to reconstruct certain acoustic properties of a weakly scattering object. Besides being applicable to pure ultrasound imaging techniques, the reconstruction theory of reflectivity tomography is also pertinent to hybrid imaging techniques such as thermoacoustic tomography. In this work, assuming spherical scanning apertures, redundancies in the three-dimensional (3-D) reflectivity tomography data function are identified and formulated mathematically. These data redundancies are used to demonstrate that knowledge of the measured data function over half of its domain uniquely specifies the 3-D object function. This indicates that, in principle, exact image reconstruction can be performed using a "half-scan" data function, which corresponds to temporally untruncated measurements acquired on a hemi-spherical aperture, or using a "half-time" data function, which corresponds to temporally truncated measurements acquired on the entire spherical aperture. Both of these minimal scanning configurations have important biological imaging applications. An iterative reconstruction method is utilized for reconstruction of a simulated 3-D object from noiseless and noisy half-scan and half-time data functions.

  16. A hybrid method for the computation of quasi-3D seismograms.

    NASA Astrophysics Data System (ADS)

    Masson, Yder; Romanowicz, Barbara

    2013-04-01

    The development of powerful computer clusters and efficient numerical computation methods, such as the Spectral Element Method (SEM) made possible the computation of seismic wave propagation in a heterogeneous 3D earth. However, the cost of theses computations is still problematic for global scale tomography that requires hundreds of such simulations. Part of the ongoing research effort is dedicated to the development of faster modeling methods based on the spectral element method. Capdeville et al. (2002) proposed to couple SEM simulations with normal modes calculation (C-SEM). Nissen-Meyer et al. (2007) used 2D SEM simulations to compute 3D seismograms in a 1D earth model. Thanks to these developments, and for the first time, Lekic et al. (2011) developed a 3D global model of the upper mantle using SEM simulations. At the local and continental scale, adjoint tomography that is using a lot of SEM simulation can be implemented on current computers (Tape, Liu et al. 2009). Due to their smaller size, these models offer higher resolution. They provide us with images of the crust and the upper part of the mantle. In an attempt to teleport such local adjoint tomographic inversions into the deep earth, we are developing a hybrid method where SEM computation are limited to a region of interest within the earth. That region can have an arbitrary shape and size. Outside this region, the seismic wavefield is extrapolated to obtain synthetic data at the Earth's surface. A key feature of the method is the use of a time reversal mirror to inject the wavefield induced by distant seismic source into the region of interest (Robertsson and Chapman 2000). We compute synthetic seismograms as follow: Inside the region of interest, we are using regional spectral element software RegSEM to compute wave propagation in 3D. Outside this region, the wavefield is extrapolated to the surface by convolution with the Green's functions from the mirror to the seismic stations. For now, these

  17. Cone beam computed tomography use in orthodontics.

    PubMed

    Nervina, J M

    2012-03-01

    Cone beam computed tomography (CBCT) is widely used by orthodontists to obtain three-dimensional (3-D) images of their patients. This is of value as malocclusion results from discrepancies in three planes of space. This review tracks the use of CBCT in orthodontics, from its validation as an accurate and reliable tool, to its use in diagnosing and treatment planning, and in assessing treatment outcomes in orthodontics.

  18. In situ visualization of magma deformation at high temperature using time-lapse 3D tomography

    NASA Astrophysics Data System (ADS)

    Godinho, jose; Lee, Peter; Lavallee, Yan; Kendrick, Jackie; Von-Aulock, Felix

    2016-04-01

    We use synchrotron based x-ray computed micro-tomography (sCT) to visualize, in situ, the microstructural evolution of magma samples 3 mm diameter with a resolution of 3 μm during heating and uniaxial compression at temperatures up to 1040 °C. The interaction between crystals, melt and gas bubbles is analysed in 4D (3D + time) during sample deformation. The ability to observe the changes of the microstructure as a function of time allow us to: a) study the effect of temperature in the ability of magma to fracture or deform; b) quantify bubble nucleation and growth rates during heating; c) study the relation between crystal displacement and volatile exsolution. We will show unique beautiful videos of how bubbles grow and coalescence, how samples and crystals within the sample fracture, heal and deform. Our study establishes in situ sCT as a powerful tool to quantify and visualize with micro-scale resolution fast processes taking place in magma that are essential to understand ascent in a volcanic conduit and validate existing models for determining the explosivity of volcanic eruptions. Tracking simultaneously the time and spatial changes of magma microstructures is shown to be primordial to study disequilibrium processes between crystals, melt and gas phases.

  19. Controlled Cardiac Computed Tomography

    PubMed Central

    Wang, Chenglin; Liu, Ying; Wang, Ge

    2006-01-01

    Cardiac computed tomography (CT) has been a hot topic for years because of the clinical importance of cardiac diseases and the rapid evolution of CT systems. In this paper, we propose a novel strategy for controlled cardiac CT that may effectively reduce image artifacts due to cardiac and respiratory motions. Our approach is radically different from existing ones and is based on controlling the X-ray source rotation velocity and powering status in reference to the cardiac motion. We theoretically show that by such a control-based intervention the data acquisition process can be optimized for cardiac CT in the cases of periodic and quasiperiodic cardiac motions. Specifically, we formulate the corresponding coordination/control schemes for either exact or approximate matches between the ideal and actual source positions, and report representative simulation results that support our analytic findings. PMID:23165017

  20. Computational analysis of flow in 3D propulsive transition ducts

    NASA Technical Reports Server (NTRS)

    Sepri, Paavo

    1990-01-01

    A numerical analysis of fully three dimensional, statistically steady flows in propulsive transition ducts being considered for use in future aircraft of higher maneuverability is investigated. The purpose of the transition duct is to convert axisymmetric flow from conventional propulsion systems to that of a rectangular geometry of high aspect ratio. In an optimal design, the transition duct would be of minimal length in order to reduce the weight penalty, while the geometrical change would be gradual enough to avoid detrimental flow perturbations. Recent experiments conducted at the Propulsion Aerodynamics Branch have indicated that thrust losses in ducts of superelliptic cross-section can be surprisingly low, even if flow separation occurs near the divergent walls. In order to address the objective of developing a rational design procedure for optimal transition ducts, it is necessary to have available a reliable computational tool for the analysis of flows achieved in a sequence of configurations. Current CFD efforts involving complicated geometries usually must contend with two separate but interactive aspects: namely, grid generation and flow solution. The first two avenues of the present investigation were comprised of suitable grid generation for a class of transition ducts of superelliptic cross-section, and the subsequent application of the flow solver PAB3D to this geometry. The code, PAB3D, was developed as a comprehensive tool for the solution of both internal and external high speed flows. The third avenue of investigation has involved analytical formulations to aid in the understanding of the nature of duct flows, and also to provide a basis of comparison for subsequent numerical solutions. Numerical results to date include the generation of two preliminary grid systems for duct flows, and the initial application of PAB3D to the corresponding geometries, which are of the class tested experimentally.

  1. Evaluation of Jumping and Creeping Regularization Approaches Applied to 3D Seismic Tomography

    NASA Astrophysics Data System (ADS)

    Liu, M.; Ramachandran, K.

    2011-12-01

    are evaluated on a synthetic 3-D true model obtained from a large scale experiment. The evaluation is performed for jumping and creeping approaches for various levels of smoothing constraints, and initial models. The final models are compared against the true models to compute residual distance between the models. Horizontal and vertical roughness in the final models are computed and compared with the true model roughness. Correlation between the true and final models is computed to evaluate the similarities of spatial patterns in the models. The study is also used to show that average 1-D models derived from the final models are very close, indicating that this will be an optimal approach to construct 1-D starting models.

  2. Computed tomography of cryogenic cells

    SciTech Connect

    Schneider, Gerd; Anderson, E.; Vogt, S.; Knochel, C.; Weiss, D.; LeGros, M.; Larabell, C.

    2001-08-30

    Due to the short wavelengths of X-rays and low numerical aperture of the Fresnel zone plates used as X-ray objectives, the depth of field is several microns. Within the focal depth, imaging a thick specimen is to a good approximation equivalent to projecting the specimen absorption. Therefore, computed tomography based on a tilt series of X-ray microscopic images can be used to reconstruct the local linear absorption coefficient and image the three-dimensional specimen structure. To preserve the structural integrity of biological objects during image acquisition, microscopy is performed at cryogenic temperatures. Tomography based on X-ray microscopic images was applied to study the distribution of male specific lethal 1 (MSL-1), a nuclear protein involved in dosage compensation in Drosophila melanogaster, which ensures that males with single X chromosome have the same amount of most X-linked gene products as females with two X chromosomes. Tomographic reconstructions of X-ray microscopic images were used to compute the local three-dimensional linear absorption coefficient revealing the arrangement of internal structures of Drosophila melanogaster cells. Combined with labelling techniques, nanotomography is a new technique to study the 3D distribution of selected proteins inside whole cells. We want to improve this technique with respect to resolution and specimen preparation. The resolution in the reconstruction can be significantly improved by reducing the angular step size to collect more viewing angles, which requires an automated data acquisition. In addition, fast-freezing with liquid ethane instead of cryogenic He gas will be applied to improve the vitrification of the hydrated samples. We also plan to apply cryo X-ray nanotomography in order to study different types of cells and their nuclear protein distributions.

  3. Computational model of mesenchymal migration in 3D under chemotaxis

    PubMed Central

    Ribeiro, F. O.; Gómez-Benito, M. J.; Folgado, J.; Fernandes, P. R.; García-Aznar, J. M.

    2017-01-01

    Abstract Cell chemotaxis is an important characteristic of cellular migration, which takes part in crucial aspects of life and development. In this work, we propose a novel in silico model of mesenchymal 3D migration with competing protrusions under a chemotactic gradient. Based on recent experimental observations, we identify three main stages that can regulate mesenchymal chemotaxis: chemosensing, dendritic protrusion dynamics and cell–matrix interactions. Therefore, each of these features is considered as a different module of the main regulatory computational algorithm. The numerical model was particularized for the case of fibroblast chemotaxis under a PDGF-bb gradient. Fibroblasts migration was simulated embedded in two different 3D matrices – collagen and fibrin – and under several PDGF-bb concentrations. Validation of the model results was provided through qualitative and quantitative comparison with in vitro studies. Our numerical predictions of cell trajectories and speeds were within the measured in vitro ranges in both collagen and fibrin matrices. Although in fibrin, the migration speed of fibroblasts is very low, because fibrin is a stiffer and more entangling matrix. Testing PDGF-bb concentrations, we noticed that an increment of this factor produces a speed increment. At 1 ng mL−1 a speed peak is reached after which the migration speed diminishes again. Moreover, we observed that fibrin exerts a dampening behavior on migration, significantly affecting the migration efficiency. PMID:27336322

  4. Computational model of mesenchymal migration in 3D under chemotaxis.

    PubMed

    Ribeiro, F O; Gómez-Benito, M J; Folgado, J; Fernandes, P R; García-Aznar, J M

    2017-01-01

    Cell chemotaxis is an important characteristic of cellular migration, which takes part in crucial aspects of life and development. In this work, we propose a novel in silico model of mesenchymal 3D migration with competing protrusions under a chemotactic gradient. Based on recent experimental observations, we identify three main stages that can regulate mesenchymal chemotaxis: chemosensing, dendritic protrusion dynamics and cell-matrix interactions. Therefore, each of these features is considered as a different module of the main regulatory computational algorithm. The numerical model was particularized for the case of fibroblast chemotaxis under a PDGF-bb gradient. Fibroblasts migration was simulated embedded in two different 3D matrices - collagen and fibrin - and under several PDGF-bb concentrations. Validation of the model results was provided through qualitative and quantitative comparison with in vitro studies. Our numerical predictions of cell trajectories and speeds were within the measured in vitro ranges in both collagen and fibrin matrices. Although in fibrin, the migration speed of fibroblasts is very low, because fibrin is a stiffer and more entangling matrix. Testing PDGF-bb concentrations, we noticed that an increment of this factor produces a speed increment. At 1 ng mL(-1) a speed peak is reached after which the migration speed diminishes again. Moreover, we observed that fibrin exerts a dampening behavior on migration, significantly affecting the migration efficiency.

  5. TOPICAL REVIEW: Computational approaches to 3D modeling of RNA

    NASA Astrophysics Data System (ADS)

    Laing, Christian; Schlick, Tamar

    2010-07-01

    Many exciting discoveries have recently revealed the versatility of RNA and its importance in a variety of functions within the cell. Since the structural features of RNA are of major importance to their biological function, there is much interest in predicting RNA structure, either in free form or in interaction with various ligands, including proteins, metabolites and other molecules. In recent years, an increasing number of researchers have developed novel RNA algorithms for predicting RNA secondary and tertiary structures. In this review, we describe current experimental and computational advances and discuss recent ideas that are transforming the traditional view of RNA folding. To evaluate the performance of the most recent RNA 3D folding algorithms, we provide a comparative study in order to test the performance of available 3D structure prediction algorithms for an RNA data set of 43 structures of various lengths and motifs. We find that the algorithms vary widely in terms of prediction quality across different RNA lengths and topologies; most predictions have very large root mean square deviations from the experimental structure. We conclude by outlining some suggestions for future RNA folding research.

  6. 3-D X-ray tomography of diamondiferous mantle eclogite xenoliths, Siberia: A review

    NASA Astrophysics Data System (ADS)

    Howarth, Geoffrey H.; Sobolev, Nikolay V.; Pernet-Fisher, John F.; Ketcham, Richard A.; Maisano, Jessica A.; Pokhilenko, Lyudmila N.; Taylor, Dawn; Taylor, Lawrence A.

    2015-04-01

    -systems'. Diamonds observed completely enclosed in garnets suggest an early diamond-forming event prior to major re-crystallization and eclogite formation during subduction. The occurrence of diamond in association with embayed garnets suggests that diamond grew at the expense of the hosting silicate protolith. In addition, the spatial relationships of diamonds with metasomatic pathways, which are generally interpreted to result from late-stage proto-kimberlitic fluid percolation, indicate a period of diamond growth occurring close to, but prior to, the time of kimberlite emplacement. Furthermore, the paragenesis of sulfides within eclogite xenoliths are described using 3-D models for entire xenoliths volumes, providing important constraints of the timing of sulfide mobilization within the mantle. Three-D animations created using X-ray tomography data for ten of the xenoliths can be viewed at the following link: http://eps.utk.edu/faculty/taylor/tomography.php

  7. 3D dynamic rupture simulation and local tomography studies following the 2010 Haiti earthquake

    NASA Astrophysics Data System (ADS)

    Douilly, Roby

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

  8. IDA3D: An Ionospheric Data Assimilative Three Dimensional Tomography Processor

    DTIC Science & Technology

    2001-09-30

    region electron densities, it can contribute important spatial and temporal information to the Joule heating at high latitudes. Figure 2: 2D...using the Greenland tomography data with IDA3D to investigate E-region electron densities and the related Joule heating effects. • Alaska...for long term monitoring of the Alaska ionosphere in support of HAARP activities and to do scientific studies of neutral wind coupling to the

  9. 3D finite-difference seismic migration with parallel computers

    SciTech Connect

    Ober, C.C.; Gjertsen, R.; Minkoff, S.; Womble, D.E.

    1998-11-01

    The ability to image complex geologies such as salt domes in the Gulf of Mexico and thrusts in mountainous regions is essential for reducing the risk associated with oil exploration. Imaging these structures, however, is computationally expensive as datasets can be terabytes in size. Traditional ray-tracing migration methods cannot handle complex velocity variations commonly found near such salt structures. Instead the authors use the full 3D acoustic wave equation, discretized via a finite difference algorithm. They reduce the cost of solving the apraxial wave equation by a number of numerical techniques including the method of fractional steps and pipelining the tridiagonal solves. The imaging code, Salvo, uses both frequency parallelism (generally 90% efficient) and spatial parallelism (65% efficient). Salvo has been tested on synthetic and real data and produces clear images of the subsurface even beneath complicated salt structures.

  10. Wearable 3-D Photoacoustic Tomography for Functional Brain Imaging in Behaving Rats

    PubMed Central

    Tang, Jianbo; Coleman, Jason E.; Dai, Xianjin; Jiang, Huabei

    2016-01-01

    Understanding the relationship between brain function and behavior remains a major challenge in neuroscience. Photoacoustic tomography (PAT) is an emerging technique that allows for noninvasive in vivo brain imaging at micrometer-millisecond spatiotemporal resolution. In this article, a novel, miniaturized 3D wearable PAT (3D-wPAT) technique is described for brain imaging in behaving rats. 3D-wPAT has three layers of fully functional acoustic transducer arrays. Phantom imaging experiments revealed that the in-plane X-Y spatial resolutions were ~200 μm for each acoustic detection layer. The functional imaging capacity of 3D-wPAT was demonstrated by mapping the cerebral oxygen saturation via multi-wavelength irradiation in behaving hyperoxic rats. In addition, we demonstrated that 3D-wPAT could be used for monitoring sensory stimulus-evoked responses in behaving rats by measuring hemodynamic responses in the primary visual cortex during visual stimulation. Together, these results show the potential of 3D-wPAT for brain study in behaving rodents. PMID:27146026

  11. Alignment of 3-D optical coherence tomography scans to correct eye movement using a particle filtering.

    PubMed

    Xu, Juan; Ishikawa, Hiroshi; Wollstein, Gadi; Kagemann, Larry; Schuman, Joel S

    2012-07-01

    Eye movement artifacts occurring during 3-D optical coherence tomography (OCT) scanning is a well-recognized problem that may adversely affect image analysis and interpretation. A particle filtering algorithm is presented in this paper to correct motion in a 3-D dataset by considering eye movement as a target tracking problem in a dynamic system. The proposed particle filtering algorithm is an independent 3-D alignment approach, which does not rely on any reference image. 3-D OCT data is considered as a dynamic system, while the location of each A-scan is represented by the state space. A particle set is used to approximate the probability density of the state in the dynamic system. The state of the system is updated frame by frame to detect A-scan movement. The proposed method was applied on both simulated data for objective evaluation and experimental data for subjective evaluation. The sensitivity and specificity of the x-movement detection were 98.85% and 99.43%, respectively, in the simulated data. For the experimental data (74 3-D OCT images), all the images were improved after z-alignment, while 81.1% images were improved after x-alignment. The proposed algorithm is an efficient way to align 3-D OCT volume data and correct the eye movement without using references.

  12. Wearable 3-D Photoacoustic Tomography for Functional Brain Imaging in Behaving Rats.

    PubMed

    Tang, Jianbo; Coleman, Jason E; Dai, Xianjin; Jiang, Huabei

    2016-05-05

    Understanding the relationship between brain function and behavior remains a major challenge in neuroscience. Photoacoustic tomography (PAT) is an emerging technique that allows for noninvasive in vivo brain imaging at micrometer-millisecond spatiotemporal resolution. In this article, a novel, miniaturized 3D wearable PAT (3D-wPAT) technique is described for brain imaging in behaving rats. 3D-wPAT has three layers of fully functional acoustic transducer arrays. Phantom imaging experiments revealed that the in-plane X-Y spatial resolutions were ~200 μm for each acoustic detection layer. The functional imaging capacity of 3D-wPAT was demonstrated by mapping the cerebral oxygen saturation via multi-wavelength irradiation in behaving hyperoxic rats. In addition, we demonstrated that 3D-wPAT could be used for monitoring sensory stimulus-evoked responses in behaving rats by measuring hemodynamic responses in the primary visual cortex during visual stimulation. Together, these results show the potential of 3D-wPAT for brain study in behaving rodents.

  13. Mesoscopic in vivo 3-D tracking of sparse cell populations using angular multiplexed optical projection tomography.

    PubMed

    Chen, Lingling; Alexandrov, Yuriy; Kumar, Sunil; Andrews, Natalie; Dallman, Margaret J; French, Paul M W; McGinty, James

    2015-04-01

    We describe an angular multiplexed imaging technique for 3-D in vivo cell tracking of sparse cell distributions and optical projection tomography (OPT) with superior time-lapse resolution and a significantly reduced light dose compared to volumetric time-lapse techniques. We demonstrate that using dual axis OPT, where two images are acquired simultaneously at different projection angles, can enable localization and tracking of features in 3-D with a time resolution equal to the camera frame rate. This is achieved with a 200x reduction in light dose compared to an equivalent volumetric time-lapse single camera OPT acquisition with 200 projection angles. We demonstrate the application of this technique to mapping the 3-D neutrophil migration pattern observed over ~25.5 minutes in a live 2 day post-fertilisation transgenic LysC:GFP zebrafish embryo following a tail wound.

  14. Investigations and improvements of digital holographic tomography applied for 3D studies of transmissive photonics microelements

    NASA Astrophysics Data System (ADS)

    Kujawinska, Malgorzata; Jozwicka, Agata; Kozacki, Tomasz

    2008-08-01

    In order to control performance of photonics microelements it is necessary to receive 3D information about their amplitude and phase distributions. To perform this task we propose to apply tomography based on projections gather by digital holography (DH). Specifically the DH capability to register several angular views of the object during a single hologram capture is employed, which may in future shorten significantly the measurement time or even allow for tomographic analysis of dynamic media. However such a new approach brings a lot of new issues to be considered. Therefore, in this paper the method limitations, with special emphasis on holographic reconstruction process, are investigated through extensive numerical experiments with special focus on 3D refractive index distribution determination.. The main errors and means of their elimination are presented. The possibility of 3D refractive index distribution determination by means of DHT is proved numerically and experimentally.

  15. 3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography

    DOE PAGES

    Zhang, Xing; Zhang, Lei; Tong, Huimin; ...

    2015-05-05

    Commonly used methods for determining protein structure, including X-ray crystallography and single-particle reconstruction, often provide a single and unique three-dimensional (3D) structure. However, in these methods, the protein dynamics and flexibility/fluctuation remain mostly unknown. Here, we utilized advances in electron tomography (ET) to study the antibody flexibility and fluctuation through structural determination of individual antibody particles rather than averaging multiple antibody particles together. Through individual-particle electron tomography (IPET) 3D reconstruction from negatively-stained ET images, we obtained 120 ab-initio 3D density maps at an intermediate resolution (~1–3 nm) from 120 individual IgG1 antibody particles. Using these maps as a constraint, wemore » derived 120 conformations of the antibody via structural flexible docking of the crystal structure to these maps by targeted molecular dynamics simulations. Statistical analysis of the various conformations disclosed the antibody 3D conformational flexibility through the distribution of its domain distances and orientations. This blueprint approach, if extended to other flexible proteins, may serve as a useful methodology towards understanding protein dynamics and functions.« less

  16. 3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography

    SciTech Connect

    Zhang, Xing; Zhang, Lei; Tong, Huimin; Peng, Bo; Rames, Matthew J.; Zhang, Shengli; Ren, Gang

    2015-05-05

    Commonly used methods for determining protein structure, including X-ray crystallography and single-particle reconstruction, often provide a single and unique three-dimensional (3D) structure. However, in these methods, the protein dynamics and flexibility/fluctuation remain mostly unknown. Here, we utilized advances in electron tomography (ET) to study the antibody flexibility and fluctuation through structural determination of individual antibody particles rather than averaging multiple antibody particles together. Through individual-particle electron tomography (IPET) 3D reconstruction from negatively-stained ET images, we obtained 120 ab-initio 3D density maps at an intermediate resolution (~1–3 nm) from 120 individual IgG1 antibody particles. Using these maps as a constraint, we derived 120 conformations of the antibody via structural flexible docking of the crystal structure to these maps by targeted molecular dynamics simulations. Statistical analysis of the various conformations disclosed the antibody 3D conformational flexibility through the distribution of its domain distances and orientations. This blueprint approach, if extended to other flexible proteins, may serve as a useful methodology towards understanding protein dynamics and functions.

  17. WE-G-207-03: Mask Guided Image Reconstruction (MGIR): A Novel Method for Ultra-Low-Dose 3D and Enhanced 4D Cone-Beam Computer-Tomography

    SciTech Connect

    Park, C; Zhang, H; Chen, Y; Fan, Q; Kahler, D; Li, J; Liu, C; Lu, B

    2015-06-15

    Purpose: Recently, compressed sensing (CS) based iterative reconstruction (IR) method is receiving attentions to reconstruct high quality cone beam computed tomography (CBCT) images using sparsely sampled or noisy projections. The aim of this study is to develop a novel baseline algorithm called Mask Guided Image Reconstruction (MGIR), which can provide superior image quality for both low-dose 3DCBCT and 4DCBCT under single mathematical framework. Methods: In MGIR, the unknown CBCT volume was mathematically modeled as a combination of two regions where anatomical structures are 1) within the priori-defined mask and 2) outside the mask. Then we update each part of images alternatively thorough solving minimization problems based on CS type IR. For low-dose 3DCBCT, the former region is defined as the anatomically complex region where it is focused to preserve edge information while latter region is defined as contrast uniform, and hence aggressively updated to remove noise/artifact. In 4DCBCT, the regions are separated as the common static part and moving part. Then, static volume and moving volumes were updated with global and phase sorted projection respectively, to optimize the image quality of both moving and static part simultaneously. Results: Examination of MGIR algorithm showed that high quality of both low-dose 3DCBCT and 4DCBCT images can be reconstructed without compromising the image resolution and imaging dose or scanning time respectively. For low-dose 3DCBCT, a clinical viable and high resolution head-and-neck image can be obtained while cutting the dose by 83%. In 4DCBCT, excellent quality 4DCBCT images could be reconstructed while requiring no more projection data and imaging dose than a typical clinical 3DCBCT scan. Conclusion: The results shown that the image quality of MGIR was superior compared to other published CS based IR algorithms for both 4DCBCT and low-dose 3DCBCT. This makes our MGIR algorithm potentially useful in various on

  18. Local 3-D Toroidal Plasma Tomography Using the Phillips-Tikhonov Regularization Method

    NASA Astrophysics Data System (ADS)

    Lee, Seung Hun; Kim, Junghee; Choe, Wonho

    2008-11-01

    Tomography is one of a powerful diagnostic method for obtaining the local information from the line-integrated plasma emission in fusion devices. The 3-D tomography is a complicated task compared to the 2-D tomography. Because of the limitation of the spatial distribution of the array detectors around a torus, the regularization algorithm such as the Phillips-Tikhonov method is advantageous to achieve more reliable reconstruction. In this work, we performed a feasibility study of 3-D tomography for toroidal plasmas. Four tangentially-viewing array detectors of each array consisting of 16x16 detector elements were assumed to be implemented. The reconstruction area is configured as 70 cm x 50 cm of poloidal cross-section and 40 toroidal layers, which has spatial resolution of 5 cm. We chose the phantoms which are KSTAR plasma-like profiles combined with the equilibrium flux surfaces with n = 0, 1, 2, 3 modes. The change of the emission peak in each layer in the reconstruction result agrees reasonably well with that of the phantom, with relative error of 5 - 10 %.

  19. Protein 3D structure computed from evolutionary sequence variation.

    PubMed

    Marks, Debora S; Colwell, Lucy J; Sheridan, Robert; Hopf, Thomas A; Pagnani, Andrea; Zecchina, Riccardo; Sander, Chris

    2011-01-01

    The evolutionary trajectory of a protein through sequence space is constrained by its function. Collections of sequence homologs record the outcomes of millions of evolutionary experiments in which the protein evolves according to these constraints. Deciphering the evolutionary record held in these sequences and exploiting it for predictive and engineering purposes presents a formidable challenge. The potential benefit of solving this challenge is amplified by the advent of inexpensive high-throughput genomic sequencing.In this paper we ask whether we can infer evolutionary constraints from a set of sequence homologs of a protein. The challenge is to distinguish true co-evolution couplings from the noisy set of observed correlations. We address this challenge using a maximum entropy model of the protein sequence, constrained by the statistics of the multiple sequence alignment, to infer residue pair couplings. Surprisingly, we find that the strength of these inferred couplings is an excellent predictor of residue-residue proximity in folded structures. Indeed, the top-scoring residue couplings are sufficiently accurate and well-distributed to define the 3D protein fold with remarkable accuracy.We quantify this observation by computing, from sequence alone, all-atom 3D structures of fifteen test proteins from different fold classes, ranging in size from 50 to 260 residues, including a G-protein coupled receptor. These blinded inferences are de novo, i.e., they do not use homology modeling or sequence-similar fragments from known structures. The co-evolution signals provide sufficient information to determine accurate 3D protein structure to 2.7-4.8 Å C(α)-RMSD error relative to the observed structure, over at least two-thirds of the protein (method called EVfold, details at http://EVfold.org). This discovery provides insight into essential interactions constraining protein evolution and will facilitate a comprehensive survey of the universe of protein structures

  20. Electrical resistivity tomography applied to a complex lava dome: 2D and 3D models comparison

    NASA Astrophysics Data System (ADS)

    Portal, Angélie; Fargier, Yannick; Lénat, Jean-François; Labazuy, Philippe

    2015-04-01

    interpretation. Geometry and location of ERT profiles on the Puy de Dôme volcano allow to compute 3D inversion models of the electrical resistivity distribution with a new inversion code. This code uses tetrahedrons to discretize the 3D model and uses also a conventional Gauss-Newton inversion scheme combined to an Occam regularisation to process the data. It allows to take into account all the data information and prevents the construction of 3D artefacts present in conventional 2D inversion results. Inversion results show a strong electrical resistivity heterogeneity of the entire dome. Underlying volcanic edifices are clearly identified below the lava dome. Generally speaking, the flanks of the volcano show high resistivity values, and the summit part is more conductive but also very heterogeneous.

  1. Children's (Pediatric) CT (Computed Tomography)

    MedlinePlus

    ... which are then displayed on a monitor. Special software can also generate three-dimensional (3-D) images ... When the image slices are reassembled by computer software, the result is a very detailed multidimensional view ...

  2. TOMO3D: 3-D joint refraction and reflection traveltime tomography parallel code for active-source seismic data—synthetic test

    NASA Astrophysics Data System (ADS)

    Meléndez, A.; Korenaga, J.; Sallarès, V.; Miniussi, A.; Ranero, C. R.

    2015-10-01

    We present a new 3-D traveltime tomography code (TOMO3D) for the modelling of active-source seismic data that uses the arrival times of both refracted and reflected seismic phases to derive the velocity distribution and the geometry of reflecting boundaries in the subsurface. This code is based on its popular 2-D version TOMO2D from which it inherited the methods to solve the forward and inverse problems. The traveltime calculations are done using a hybrid ray-tracing technique combining the graph and bending methods. The LSQR algorithm is used to perform the iterative regularized inversion to improve the initial velocity and depth models. In order to cope with an increased computational demand due to the incorporation of the third dimension, the forward problem solver, which takes most of the run time (˜90 per cent in the test presented here), has been parallelized with a combination of multi-processing and message passing interface standards. This parallelization distributes the ray-tracing and traveltime calculations among available computational resources. The code's performance is illustrated with a realistic synthetic example, including a checkerboard anomaly and two reflectors, which simulates the geometry of a subduction zone. The code is designed to invert for a single reflector at a time. A data-driven layer-stripping strategy is proposed for cases involving multiple reflectors, and it is tested for the successive inversion of the two reflectors. Layers are bound by consecutive reflectors, and an initial velocity model for each inversion step incorporates the results from previous steps. This strategy poses simpler inversion problems at each step, allowing the recovery of strong velocity discontinuities that would otherwise be smoothened.

  3. A physical model eye with 3D resolution test targets for optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Hu, Zhixiong; Liu, Wenli; Hong, Baoyu; Hao, Bingtao; Wang, Lele; Li, Jiao

    2014-09-01

    Optical coherence tomography (OCT) has been widely employed as non-invasive 3D imaging diagnostic instrument, particularly in the field of ophthalmology. Although OCT has been approved for use in clinic in USA, Europe and Asia, international standardization of this technology is still in progress. Validation of OCT imaging capabilities is considered extremely important to ensure its effective use in clinical diagnoses. Phantom with appropriate test targets can assist evaluate and calibrate imaging performance of OCT at both installation and throughout lifetime of the instrument. In this paper, we design and fabricate a physical model eye with 3D resolution test targets to characterize OCT imaging performance. The model eye was fabricated with transparent resin to simulate realistic ophthalmic testing environment, and most key optical elements including cornea, lens and vitreous body were realized. The test targets which mimic USAF 1951 test chart were fabricated on the fundus of the model eye by 3D printing technology. Differing from traditional two dimensional USAF 1951 test chart, a group of patterns which have different thickness in depth were fabricated. By measuring the 3D test targets, axial resolution as well as lateral resolution of an OCT system can be evaluated at the same time with this model eye. To investigate this specialized model eye, it was measured by a scientific spectral domain OCT instrument and a clinical OCT system respectively. The results demonstrate that the model eye with 3D resolution test targets have the potential of qualitatively and quantitatively validating the performance of OCT systems.

  4. 3D Magnetic Induction Maps of Nanoscale Materials Revealed by Electron Holographic Tomography

    PubMed Central

    2015-01-01

    The investigation of three-dimensional (3D) ferromagnetic nanoscale materials constitutes one of the key research areas of the current magnetism roadmap and carries great potential to impact areas such as data storage, sensing, and biomagnetism. The properties of such nanostructures are closely connected with their 3D magnetic nanostructure, making their determination highly valuable. Up to now, quantitative 3D maps providing both the internal magnetic and electric configuration of the same specimen with high spatial resolution are missing. Here, we demonstrate the quantitative 3D reconstruction of the dominant axial component of the magnetic induction and electrostatic potential within a cobalt nanowire (NW) of 100 nm in diameter with spatial resolution below 10 nm by applying electron holographic tomography. The tomogram was obtained using a dedicated TEM sample holder for acquisition, in combination with advanced alignment and tomographic reconstruction routines. The powerful approach presented here is widely applicable to a broad range of 3D magnetic nanostructures and may trigger the progress of novel spintronic nonplanar nanodevices. PMID:27182110

  5. VirtoScan - a mobile, low-cost photogrammetry setup for fast post-mortem 3D full-body documentations in x-ray computed tomography and autopsy suites.

    PubMed

    Kottner, Sören; Ebert, Lars C; Ampanozi, Garyfalia; Braun, Marcel; Thali, Michael J; Gascho, Dominic

    2017-03-01

    Injuries such as bite marks or boot prints can leave distinct patterns on the body's surface and can be used for 3D reconstructions. Although various systems for 3D surface imaging have been introduced in the forensic field, most techniques are both cost-intensive and time-consuming. In this article, we present the VirtoScan, a mobile, multi-camera rig based on close-range photogrammetry. The system can be integrated into automated PMCT scanning procedures or used manually together with lifting carts, autopsy tables and examination couch. The VirtoScan is based on a moveable frame that carries 7 digital single-lens reflex cameras. A remote control is attached to each camera and allows the simultaneous triggering of the shutter release of all cameras. Data acquisition in combination with the PMCT scanning procedures took 3:34 min for the 3D surface documentation of one side of the body compared to 20:20 min of acquisition time when using our in-house standard. A surface model comparison between the high resolution output from our in-house standard and a high resolution model from the multi-camera rig showed a mean surface deviation of 0.36 mm for the whole body scan and 0.13 mm for a second comparison of a detailed section of the scan. The use of the multi-camera rig reduces the acquisition time for whole-body surface documentations in medico-legal examinations and provides a low-cost 3D surface scanning alternative for forensic investigations.

  6. Computer assisted 3D pre-operative planning tool for femur fracture orthopedic surgery

    NASA Astrophysics Data System (ADS)

    Gamage, Pavan; Xie, Sheng Quan; Delmas, Patrice; Xu, Wei Liang

    2010-02-01

    Femur shaft fractures are caused by high impact injuries and can affect gait functionality if not treated correctly. Until recently, the pre-operative planning for femur fractures has relied on two-dimensional (2D) radiographs, light boxes, tracing paper, and transparent bone templates. The recent availability of digital radiographic equipment has to some extent improved the workflow for preoperative planning. Nevertheless, imaging is still in 2D X-rays and planning/simulation tools to support fragment manipulation and implant selection are still not available. Direct three-dimensional (3D) imaging modalities such as Computed Tomography (CT) are also still restricted to a minority of complex orthopedic procedures. This paper proposes a software tool which allows orthopedic surgeons to visualize, diagnose, plan and simulate femur shaft fracture reduction procedures in 3D. The tool utilizes frontal and lateral 2D radiographs to model the fracture surface, separate a generic bone into the two fractured fragments, identify the pose of each fragment, and automatically customize the shape of the bone. The use of 3D imaging allows full spatial inspection of the fracture providing different views through the manipulation of the interactively reconstructed 3D model, and ultimately better pre-operative planning.

  7. Reducing Disk Storage of Full-3D Seismic Waveform Tomography (F3DT) Through Lossy Online Compression

    SciTech Connect

    Lindstrom, Peter; Chen, Po; Lee, En-Jui

    2016-05-05

    Full-3D seismic waveform tomography (F3DT) is the latest seismic tomography technique that can assimilate broadband, multi-component seismic waveform observations into high-resolution 3D subsurface seismic structure models. The main drawback in the current F3DT implementation, in particular the scattering-integral implementation (F3DT-SI), is the high disk storage cost and the associated I/O overhead of archiving the 4D space-time wavefields of the receiver- or source-side strain tensors. The strain tensor fields are needed for computing the data sensitivity kernels, which are used for constructing the Jacobian matrix in the Gauss-Newton optimization algorithm. In this study, we have successfully integrated a lossy compression algorithm into our F3DT SI workflow to significantly reduce the disk space for storing the strain tensor fields. The compressor supports a user-specified tolerance for bounding the error, and can be integrated into our finite-difference wave-propagation simulation code used for computing the strain fields. The decompressor can be integrated into the kernel calculation code that reads the strain fields from the disk and compute the data sensitivity kernels. During the wave-propagation simulations, we compress the strain fields before writing them to the disk. To compute the data sensitivity kernels, we read the compressed strain fields from the disk and decompress them before using them in kernel calculations. Experiments using a realistic dataset in our California statewide F3DT project have shown that we can reduce the strain-field disk storage by at least an order of magnitude with acceptable loss, and also improve the overall I/O performance of the entire F3DT-SI workflow significantly. The integration of the lossy online compressor may potentially open up the possibilities of the wide adoption of F3DT-SI in routine seismic tomography practices in the near future.

  8. Reducing disk storage of full-3D seismic waveform tomography (F3DT) through lossy online compression

    NASA Astrophysics Data System (ADS)

    Lindstrom, Peter; Chen, Po; Lee, En-Jui

    2016-08-01

    Full-3D seismic waveform tomography (F3DT) is the latest seismic tomography technique that can assimilate broadband, multi-component seismic waveform observations into high-resolution 3D subsurface seismic structure models. The main drawback in the current F3DT implementation, in particular the scattering-integral implementation (F3DT-SI), is the high disk storage cost and the associated I/O overhead of archiving the 4D space-time wavefields of the receiver- or source-side strain tensors. The strain tensor fields are needed for computing the data sensitivity kernels, which are used for constructing the Jacobian matrix in the Gauss-Newton optimization algorithm. In this study, we have successfully integrated a lossy compression algorithm into our F3DT-SI workflow to significantly reduce the disk space for storing the strain tensor fields. The compressor supports a user-specified tolerance for bounding the error, and can be integrated into our finite-difference wave-propagation simulation code used for computing the strain fields. The decompressor can be integrated into the kernel calculation code that reads the strain fields from the disk and compute the data sensitivity kernels. During the wave-propagation simulations, we compress the strain fields before writing them to the disk. To compute the data sensitivity kernels, we read the compressed strain fields from the disk and decompress them before using them in kernel calculations. Experiments using a realistic dataset in our California statewide F3DT project have shown that we can reduce the strain-field disk storage by at least an order of magnitude with acceptable loss, and also improve the overall I/O performance of the entire F3DT-SI workflow significantly. The integration of the lossy online compressor may potentially open up the possibilities of the wide adoption of F3DT-SI in routine seismic tomography practices in the near future.

  9. 3D Vectorial Time Domain Computational Integrated Photonics

    SciTech Connect

    Kallman, J S; Bond, T C; Koning, J M; Stowell, M L

    2007-02-16

    The design of integrated photonic structures poses considerable challenges. 3D-Time-Domain design tools are fundamental in enabling technologies such as all-optical logic, photonic bandgap sensors, THz imaging, and fast radiation diagnostics. Such technologies are essential to LLNL and WFO sponsors for a broad range of applications: encryption for communications and surveillance sensors (NSA, NAI and IDIV/PAT); high density optical interconnects for high-performance computing (ASCI); high-bandwidth instrumentation for NIF diagnostics; micro-sensor development for weapon miniaturization within the Stockpile Stewardship and DNT programs; and applications within HSO for CBNP detection devices. While there exist a number of photonics simulation tools on the market, they primarily model devices of interest to the communications industry. We saw the need to extend our previous software to match the Laboratory's unique emerging needs. These include modeling novel material effects (such as those of radiation induced carrier concentrations on refractive index) and device configurations (RadTracker bulk optics with radiation induced details, Optical Logic edge emitting lasers with lateral optical inputs). In addition we foresaw significant advantages to expanding our own internal simulation codes: parallel supercomputing could be incorporated from the start, and the simulation source code would be accessible for modification and extension. This work addressed Engineering's Simulation Technology Focus Area, specifically photonics. Problems addressed from the Engineering roadmap of the time included modeling the Auston switch (an important THz source/receiver), modeling Vertical Cavity Surface Emitting Lasers (VCSELs, which had been envisioned as part of fast radiation sensors), and multi-scale modeling of optical systems (for a variety of applications). We proposed to develop novel techniques to numerically solve the 3D multi-scale propagation problem for both the microchip

  10. 3D Anisotropic structure of the south-central Mongolia from Rayleigh and Love wave tomography

    NASA Astrophysics Data System (ADS)

    Yu, D.; Wu, Q.; Montagner, J. P.

    2014-12-01

    A better understanding of the geodynamics of the crust and mantle below Baikal-Mongolia is required to identify the role of mantle processes versus that of far-field tectonic effects from India-Asia collision. Anisotropy tomography can provide new perspective to the continental growth mechanism. In order to study the 3D anisotropic structure of the upper mantle in the south-central Mongolia, we collected the vertical and transverse components of seismograms recorded at 69 broadband seismic stations. We have measured inter-station phase velocities of 7181 Rayleigh waves and 901 Love waves using the frequency-time analysis of wavelet transformation method for the fundamental mode at period range 10~80s. The lateral phase velocity variations are computed by using a regionalization method. These phase velocities have been inverted to obtain the first anisotropic model including Sv velocities, azimuthal and radial anisotropy. The Middle Gobi is associated with low velocity. Based on the distribution of the Cenozoic basalts in the Middle Gobi, it refers that the low velocity anomaly is related to the Cenozoic volcanism. In the northern domain, near to Baikal zone, the azimuthal anisotropy is normal to the Baikal rift and consistent with the fast direction of previous SKS splitting measurements. In the South Gobi, north to Main Mongolian Lineament, the azimuthal anisotropy is NEE-SWW in the crust and NW-SE in the mantle. It indicates that the crust and mantle are decoupled. We propose that the crustal deformation is related to the far-field effects of India-Asia collision and that the mantle flow is correlated with the Baikal rift activity. Further study in process will provide more evidence and insight to better understand the geodynamics in this region.

  11. Experimental Investigation of Material Flows Within FSWs Using 3D Tomography

    SciTech Connect

    Charles R. Tolle; Timothy A. White; Karen S. Miller; Denis E. Clark; Herschel B. Smartt

    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 of 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.

  12. An optimal transport approach for seismic tomography: application to 3D full waveform inversion

    NASA Astrophysics Data System (ADS)

    Métivier, L.; Brossier, R.; Mérigot, Q.; Oudet, E.; Virieux, J.

    2016-11-01

    The use of optimal transport distance has recently yielded significant progress in image processing for pattern recognition, shape identification, and histograms matching. In this study, the use of this distance is investigated for a seismic tomography problem exploiting the complete waveform; the full waveform inversion. In its conventional formulation, this high resolution seismic imaging method is based on the minimization of the L 2 distance between predicted and observed data. Application of this method is generally hampered by the local minima of the associated L 2 misfit function, which correspond to velocity models matching the data up to one or several phase shifts. Conversely, the optimal transport distance appears as a more suitable tool to compare the misfit between oscillatory signals, for its ability to detect shifted patterns. However, its application to the full waveform inversion is not straightforward, as the mass conservation between the compared data cannot be guaranteed, a crucial assumption for optimal transport. In this study, the use of a distance based on the Kantorovich-Rubinstein norm is introduced to overcome this difficulty. Its mathematical link with the optimal transport distance is made clear. An efficient numerical strategy for its computation, based on a proximal splitting technique, is introduced. We demonstrate that each iteration of the corresponding algorithm requires solving the Poisson equation, for which fast solvers can be used, relying either on the fast Fourier transform or on multigrid techniques. The development of this numerical method make possible applications to industrial scale data, involving tenths of millions of discrete unknowns. The results we obtain on such large scale synthetic data illustrate the potentialities of the optimal transport for seismic imaging. Starting from crude initial velocity models, optimal transport based inversion yields significantly better velocity reconstructions than those based on

  13. 3D imaging of the Corinth rift from a new passive seismic tomography and receiver function analysis

    NASA Astrophysics Data System (ADS)

    Godano, Maxime; Gesret, Alexandrine; Noble, Mark; Lyon-Caen, Hélène; Gautier, Stéphanie; Deschamps, Anne

    2016-04-01

    The Corinth Rift is the most seismically active zone in Europe. The area is characterized by very localized NS extension at a rate of ~ 1.5cm/year, the occurrence of frequent and intensive microseismic crises and occasional moderate to large earthquakes like in 1995 (Mw=6.1). Since the year 2000, the Corinth Rift Laboratory (CRL, http://crlab.eu) consisting in a multidisciplinary natural observatory, aims at understanding the mechanics of faulting and earthquake nucleation in the Rift. Recent studies have improved our view about fault geometry and mechanics within CRL, but there is still a critical need for a better knowledge of the structure at depth both for the accuracy of earthquake locations and for mechanical interpretation of the seismicity. In this project, we aim to analyze the complete seismological database (13 years of recordings) of CRL by using recently developed methodologies of structural imaging, in order to determine at the same time and with high resolution, the local 3D structure and the earthquake locations. We perform an iterative joint determination of 3D velocity model and earthquake coordinates. In a first step, P and S velocity models are determined using first arrival time tomography method proposed by Taillandier et al. (2009). It consists in the minimization of the cost function between observed and theoretical arrival times which is achieved by the steepest descent method (e.g. Tarantola 1987). This latter requires computing the gradient of the cost function by using the adjoint state method (Chavent 1974). In a second step, earthquakes are located in the new velocity model with a non-linear inversion method based on a Bayesian formulation (Gesret et al. 2015). Step 1 and 2 are repeated until the cost function no longer decreases. We present preliminary results consisting in: (1) the adjustement of a 1D velocity model that is used as initial model of the 3D tomography and (2) a first attempt of the joint determination of 3D velocity

  14. Data-driven layer-stripping strategy in 3-D joint refraction and reflection travel-time tomography with TOMO3D

    NASA Astrophysics Data System (ADS)

    Meléndez, Adrià; Korenaga, Jun; Sallarès, Valentí; Miniussi, Alain; Ranero, César

    2015-04-01

    We present a new 3-D travel-time tomography code (TOMO3D) for the modelling of active-source seismic data that uses the arrival times of both refracted and reflected seismic phases to derive the propagation velocity distribution and the geometry of reflecting boundaries in the subsurface. The combination of refracted and reflected data provides a denser coverage of the study area. Moreover, because refractions only depend on the velocity parameters, they contribute to the mitigation of the negative effect of the ambiguity between layer thickness and propagation velocity that is intrinsic to the reflections that define these boundaries. This code is based on its renowned 2-D version TOMO2D from which it inherited the methods to solve the forward and inverse problems. The forward travel-time calculations are conducted using a hybrid ray-tracing technique combining the graph or shortest path method and the bending method. The LSQR algorithm is used to perform the iterative inversion of travel-time residuals to update the initial velocity and depth models. In order to cope with the increased computational demand due to the incorporation of the third dimension, the forward problem solver, which takes by far most of the run time (~90%), has been parallelised with a combination of MP and MPI standards. This parallelisation distributes the ray-tracing and travel-time calculations among the available computational resources, allowing the user to set the number of nodes, processors and cores to be used. The code's performance was evaluated with a complex synthetic case simulating a subduction zone. The objective is to retrieve the velocity distribution of both upper and lower plates and the geometry of the interplate and Moho boundaries. Our tomography method is designed to deal with a single reflector per inversion, and we show that a data-driven layer-stripping strategy allows to successfully recover several reflectors in successive inversions. This strategy consists in

  15. Automatic procedure for realistic 3D finite element modelling of human brain for bioelectromagnetic computations

    NASA Astrophysics Data System (ADS)

    Aristovich, K. Y.; Khan, S. H.

    2010-07-01

    Realistic computer modelling of biological objects requires building of very accurate and realistic computer models based on geometric and material data, type, and accuracy of numerical analyses. This paper presents some of the automatic tools and algorithms that were used to build accurate and realistic 3D finite element (FE) model of whole-brain. These models were used to solve the forward problem in magnetic field tomography (MFT) based on Magnetoencephalography (MEG). The forward problem involves modelling and computation of magnetic fields produced by human brain during cognitive processing. The geometric parameters of the model were obtained from accurate Magnetic Resonance Imaging (MRI) data and the material properties - from those obtained from Diffusion Tensor MRI (DTMRI). The 3D FE models of the brain built using this approach has been shown to be very accurate in terms of both geometric and material properties. The model is stored on the computer in Computer-Aided Parametrical Design (CAD) format. This allows the model to be used in a wide a range of methods of analysis, such as finite element method (FEM), Boundary Element Method (BEM), Monte-Carlo Simulations, etc. The generic model building approach presented here could be used for accurate and realistic modelling of human brain and many other biological objects.

  16. Computer acquisition of 3D images utilizing dynamic speckles

    NASA Astrophysics Data System (ADS)

    Kamshilin, Alexei A.; Semenov, Dmitry V.; Nippolainen, Ervin; Raita, Erik

    2006-05-01

    We present novel technique for fast non-contact and continuous profile measurements of rough surfaces by use of dynamic speckles. The dynamic speckle pattern is generated when the laser beam scans the surface under study. The most impressive feature of the proposed technique is its ability to work at extremely high scanning speed of hundreds meters per second. The technique is based on the continuous frequency measurements of the light-power modulation after spatial filtering of the scattered light. The complete optical-electronic system was designed and fabricated for fast measurement of the speckles velocity, its recalculation into the distance, and further data acquisition into computer. The measured surface profile is displayed in a PC monitor in real time. The response time of the measuring system is below 1 μs. Important parameters of the system such as accuracy, range of measurements, and spatial resolution are analyzed. Limits of the spatial filtering technique used for continuous tracking of the speckle-pattern velocity are shown. Possible ways of further improvement of the measurements accuracy are demonstrated. Owing to its extremely fast operation, the proposed technique could be applied for online control of the 3D-shape of complex objects (e.g., electronic circuits) during their assembling.

  17. Characterization of landslide geometry using 3D seismic refraction traveltime tomography

    NASA Astrophysics Data System (ADS)

    Samyn, K.; Travelletti, J.; Bitri, A.; Grandjean, G.; Malet, J. P.

    2012-04-01

    The geometry of the bedrock, internal layers and shear surfaces/bands controls the deformation pattern and the mechanisms of landslides. A challenge to progress in the forecast of landslide acceleration in terms of early-warning is therefore to characterize the 3D geometry of the unstable mass at a high level of spatial resolution, both in the horizontal and vertical directions, by integrating information from different surveying techniques. For such characterization, seismic investigations are potentially of a great interest. In the case of complex structures, the measure and the processing of seismic data need to be performed in 3D. The objective of this work is to present the implementation of a 3D seismic refraction traveltime tomography technique based on an existing 2D Simultaneous Iterative Reconstruction Technique (SIRT). First the processing algorithm is detailed and its performance is discussed, and second an application to the La Valette complex landslide is presented. Inversion of first-arrival traveltimes produces a 3D tomogram that underlines the presence of many areas characterized by low P-wave velocity of 500-1800 m.s-1. These low P-wave velocity structures result from the presence of reworked blocks, surficial cracks and in-depth fracture zones. These structures seem to extend to around 25 m in depth over a 80 x 130 m area. Based on borehole geotechnical data and previous geophysical investigations, an interface corresponding to an internal slip surface can be suspected near the isovalue of 1200 m.s-1 at a depth of -10 to -15 m. The stable substratum is characterized by higher values of P-wave velocity of 1800-3000 m.s-1. The features identified in the 3D tomogram allow to better (1) delineate the boundary between the landslide and the surrounding stable slopes, and (2) understand the morphological structures within the landslide at a hectometric scale. The integration of the 3D seismic tomography interpretation to previous geophysical

  18. Full 3D Microwave Tomography enhanced GPR surveys: a case study

    NASA Astrophysics Data System (ADS)

    Catapano, Ilaria; Soldovieri, Francesco; Affinito, Antonio; Hugenschmidt, Johannes

    2014-05-01

    Ground Penetrating Radar (GPR) systems are well assessed non-invasive diagnostic tools capable of providing high resolution images of the inner structure of the probed spatial region. Owing to this capability, GPR systems are nowadays more and more considered in the frame of civil engineering surveys since they may give information on constructive details as well as on the aging and risk factors affecting the healthiness of an infrastructure. In this frame, accurate, reliable and easily interpretable images of the probed scenarios are mandatory in order to support the management of maintenance works and assure the safety of structures. Such a requirement motivates the use of different and sophisticated data processing approaches in order to compare more than one image of the same scene, thus improving the reliability and objectiveness of the GPR survey results. Among GPR data processing procedures, Microwave Tomography approaches based on the Born approximation face the imaging as the solution of a linear inverse problem, which is solved by using the Truncated Singular Value Decomposition as a regularized inversion scheme [1]. So far, an approach exploiting a 2D scalar model of the scattering phenomenon have been adopted to process GPR data gathered along a single scan. In this case, 3D images are obtained by interpolating 2D reconstructions (this is referred commonly as pseudo 3D imaging). Such an imaging approach have provided valuable results in several real cases dealing with not only surveys for civil engineering but also archeological prospection, subservice monitoring, security surveys and so on [1-4]. These encouraging results have motivated the development of a full 3D Microwave Tomography approach capable of accounting for the vectorial nature of the wave propagation. The reconstruction capabilities of this novel approach have been assessed mainly against experimental data collected in laboratory controlled conditions. The obtained results corroborate

  19. Parametric estimation of 3D tubular structures for diffuse optical tomography

    PubMed Central

    Larusson, Fridrik; Anderson, Pamela G.; Rosenberg, Elizabeth; Kilmer, Misha E.; Sassaroli, Angelo; Fantini, Sergio; Miller, Eric L.

    2013-01-01

    We explore the use of diffuse optical tomography (DOT) for the recovery of 3D tubular shapes representing vascular structures in breast tissue. Using a parametric level set method (PaLS) our method incorporates the connectedness of vascular structures in breast tissue to reconstruct shape and absorption values from severely limited data sets. The approach is based on a decomposition of the unknown structure into a series of two dimensional slices. Using a simplified physical model that ignores 3D effects of the complete structure, we develop a novel inter-slice regularization strategy to obtain global regularity. We report on simulated and experimental reconstructions using realistic optical contrasts where our method provides a more accurate estimate compared to an unregularized approach and a pixel based reconstruction. PMID:23411913

  20. Parametric estimation of 3D tubular structures for diffuse optical tomography.

    PubMed

    Larusson, Fridrik; Anderson, Pamela G; Rosenberg, Elizabeth; Kilmer, Misha E; Sassaroli, Angelo; Fantini, Sergio; Miller, Eric L

    2013-02-01

    We explore the use of diffuse optical tomography (DOT) for the recovery of 3D tubular shapes representing vascular structures in breast tissue. Using a parametric level set method (PaLS) our method incorporates the connectedness of vascular structures in breast tissue to reconstruct shape and absorption values from severely limited data sets. The approach is based on a decomposition of the unknown structure into a series of two dimensional slices. Using a simplified physical model that ignores 3D effects of the complete structure, we develop a novel inter-slice regularization strategy to obtain global regularity. We report on simulated and experimental reconstructions using realistic optical contrasts where our method provides a more accurate estimate compared to an unregularized approach and a pixel based reconstruction.

  1. Macro optical projection tomography for large scale 3D imaging of plant structures and gene activity.

    PubMed

    Lee, Karen J I; Calder, Grant M; Hindle, Christopher R; Newman, Jacob L; Robinson, Simon N; Avondo, Jerome J H Y; Coen, Enrico S

    2016-12-26

    Optical projection tomography (OPT) is a well-established method for visualising gene activity in plants and animals. However, a limitation of conventional OPT is that the specimen upper size limit precludes its application to larger structures. To address this problem we constructed a macro version called Macro OPT (M-OPT). We apply M-OPT to 3D live imaging of gene activity in growing whole plants and to visualise structural morphology in large optically cleared plant and insect specimens up to 60 mm tall and 45 mm deep. We also show how M-OPT can be used to image gene expression domains in 3D within fixed tissue and to visualise gene activity in 3D in clones of growing young whole Arabidopsis plants. A further application of M-OPT is to visualise plant-insect interactions. Thus M-OPT provides an effective 3D imaging platform that allows the study of gene activity, internal plant structures and plant-insect interactions at a macroscopic scale.

  2. A fast rebinning algorithm for 3D positron emission tomography using John's equation

    NASA Astrophysics Data System (ADS)

    Defrise, Michel; Liu, Xuan

    1999-08-01

    Volume imaging in positron emission tomography (PET) requires the inversion of the three-dimensional (3D) x-ray transform. The usual solution to this problem is based on 3D filtered-backprojection (FBP), but is slow. Alternative methods have been proposed which factor the 3D data into independent 2D data sets corresponding to the 2D Radon transforms of a stack of parallel slices. Each slice is then reconstructed using 2D FBP. These so-called rebinning methods are numerically efficient but are approximate. In this paper a new exact rebinning method is derived by exploiting the fact that the 3D x-ray transform of a function is the solution to the second-order partial differential equation first studied by John. The method is proposed for two sampling schemes, one corresponding to a pair of infinite plane detectors and another one corresponding to a cylindrical multi-ring PET scanner. The new FORE-J algorithm has been implemented for this latter geometry and was compared with the approximate Fourier rebinning algorithm FORE and with another exact rebinning algorithm, FOREX. Results with simulated data demonstrate a significant improvement in accuracy compared to FORE, while the reconstruction time is doubled. Compared to FOREX, the FORE-J algorithm is slightly less accurate but more than three times faster.

  3. Structural and functional imaging of 3D microfluidic mixers using optical coherence tomography.

    PubMed

    Xi, Chuanwu; Marks, Daniel L; Parikh, Devang S; Raskin, Lutgarde; Boppart, Stephen A

    2004-05-18

    To achieve high mixing efficiency in microfluidic devices, complex designs are often required. Microfluidic devices have been evaluated with light and confocal microscopy, but fluid-flow characteristics at different depths are difficult to separate from the en face images produced. By using optical coherence tomography (OCT), an imaging modality capable of imaging 3D microstructures at micrometer-scale resolutions over millimeter-size scales, we obtained 3D dynamic functional and structural data for three representative microfluidic mixers: a Y channel mixer, a 3D serpentine mixer, and a vortex mixer. In the serpentine mixer, OCT image analysis revealed that the mixing efficiency was linearly dependent on the Reynolds number, whereas it appeared to have exponential dependence when imaged with light microscopy. The visual overlap of fluid flows in light-microscopy images leads to an overestimation of the mixing efficiency, an effect that was eliminated with OCT imaging. Doppler OCT measurements determined velocity profiles at various points in the serpentine mixer. Mixing patterns in the vortex mixer were compared with light-microscopy and OCT image analysis. These results demonstrate that OCT can significantly improve the characterization of 3D microfluidic device structure and function.

  4. Quantifying axis orientation in 3D using polarization-sensitive optical coherence tomography (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Liu, Chao; Black, Adam J.; Wang, Hui; Akkin, Taner

    2016-03-01

    The optic axis of birefringent tissues indicates the direction of structural anisotropy. Polarization-sensitive Optical Coherence Tomography (PS-OCT) can provide reflectivity contrast as well as retardance and optic axis orientation contrasts that originate from tissue birefringence. We introduce imaging 3D tissue anisotropy by using a single-camera and polarization-maintaining fiber (PMF) based PS-OCT, which utilizes normal and angled illuminations. Because environmental factors such as the movement of PMF and temperature fluctuations induce arbitrary phase changes, the optic axis orientation measurement has a time-varying offset. In order to measure the absolute axis orientation, we add a calibration path which dynamically provides the arbitrary offset to be subtracted from the relative axis orientation values. The axis orientation on the normal plane is the 2D projection of the fiber direction in 3D space. We propose to characterize the axis orientation in different planes (xy, xy' and x'y planes) by using normal and angled illuminations. This allows calculation of the polar angle that completes the orientation information in 3D. Polarization-based optical systems relying on one illumination angle measure the "apparent birefringence" that light encounters rather than the "true birefringence". Birefringence as a measure of anisotropy is quantified with the orientation information in 3D. The method and validation with a biological tissue are presented. The study can facilitate imaging and mapping the structural connections in anisotropic tissues including the brain.

  5. 3D Imaging.

    ERIC Educational Resources Information Center

    Hastings, S. K.

    2002-01-01

    Discusses 3 D imaging as it relates to digital representations in virtual library collections. Highlights include X-ray computed tomography (X-ray CT); the National Science Foundation (NSF) Digital Library Initiatives; output peripherals; image retrieval systems, including metadata; and applications of 3 D imaging for libraries and museums. (LRW)

  6. 3D structure of eukaryotic flagella in a quiescent state revealed by cryo-electron tomography

    PubMed Central

    Nicastro, Daniela; McIntosh, J. Richard; Baumeister, Wolfgang

    2005-01-01

    We have used cryo-electron tomography to investigate the 3D structure and macromolecular organization of intact, frozen-hydrated sea urchin sperm flagella in a quiescent state. The tomographic reconstructions provide information at a resolution better than 6 nm about the in situ arrangements of macromolecules that are key for flagellar motility. We have visualized the heptameric rings of the motor domains in the outer dynein arm complex and determined that they lie parallel to the plane that contains the axes of neighboring flagellar microtubules. Both the material associated with the central pair of microtubules and the radial spokes display a plane of symmetry that helps to explain the planar beat pattern of these flagella. Cryo-electron tomography has proven to be a powerful technique for helping us understand the relationships between flagellar structure and function and the design of macromolecular machines in situ. PMID:16246999

  7. Overview of 3D-TRACE, a NASA Initiative in Three-Dimensional Tomography of the Aerosol-Cloud Environment

    NASA Astrophysics Data System (ADS)

    Davis, Anthony; Diner, David; Yanovsky, Igor; Garay, Michael; Xu, Feng; Bal, Guillaume; Schechner, Yoav; Aides, Amit; Qu, Zheng; Emde, Claudia

    2013-04-01

    microphysical properties, can be reconstructed from multi-angle/multi-spectral imaging radiometry and, more and more, polarimetry. Specific technologies of interest are computed tomography (reconstruction from projections), optical tomography (using cross-pixel radiation transport in the diffusion limit), stereoscopy (depth/height retrievals), blind source and scale separation (signal unmixing), and disocclusion (information recovery in the presence of obstructions). Later on, these potentially powerful inverse problem solutions will be fully integrated in a versatile satellite data analysis toolbox. At present, we can report substantial progress at the component level. Specifically, we will focus on the most elementary problems in atmospheric tomography with an emphasis on the vastly under-exploited class of multi-pixel techniques. One basic problem is to infer the outer shape and mean opacity of 3D clouds, along with a bulk measure of cloud particle size. Another is to separate high and low cloud layers based on their characteristically different spatial textures. Yet another is to reconstruct the 3D spatial distribution of aerosol density based on passive imaging. This suite of independent feasibility studies amounts to a compelling proofof- concept for the ambitious 3D-Tomographic Reconstruction of the Aerosol-Cloud Environment (3D-TRACE) project as a whole.

  8. 3D site specific sample preparation and analysis of 3D devices (FinFETs) by atom probe tomography.

    PubMed

    Kambham, Ajay Kumar; Kumar, Arul; Gilbert, Matthieu; Vandervorst, Wilfried

    2013-09-01

    With the transition from planar to three-dimensional device architectures such as Fin field-effect-transistors (FinFETs), new metrology approaches are required to meet the needs of semiconductor technology. It is important to characterize the 3D-dopant distributions precisely as their extent, positioning relative to gate edges and absolute concentration determine the device performance in great detail. At present the atom probe has shown its ability to analyze dopant distributions in semiconductor and thin insulating materials with sub-nm 3D-resolution and good dopant sensitivity. However, so far most reports have dealt with planar devices or restricted the measurements to 2D test structures which represent only limited challenges in terms of localization and site specific sample preparation. In this paper we will discuss the methodology to extract the dopant distribution from real 3D-devices such as a 3D-FinFET device, requiring the sample preparation to be carried out at a site specific location with a positioning accuracy ∼50 nm.

  9. Testing & Validating: 3D Seismic Travel Time Tomography (Detailed Shallow Subsurface Imaging)

    NASA Astrophysics Data System (ADS)

    Marti, David; Marzan, Ignacio; Alvarez-Marron, Joaquina; Carbonell, Ramon

    2016-04-01

    A detailed full 3 dimensional P wave seismic velocity model was constrained by a high-resolution seismic tomography experiment. A regular and dense grid of shots and receivers was use to image a 500x500x200 m volume of the shallow subsurface. 10 GEODE's resulting in a 240 channels recording system and a 250 kg weight drop were used for the acquisition. The recording geometry consisted in 10x20m geophone grid spacing, and a 20x20 m stagered source spacing. A total of 1200 receivers and 676 source points. The study area is located within the Iberian Meseta, in Villar de Cañas (Cuenca, Spain). The lithological/geological target consisted in a Neogen sedimentary sequence formed from bottom to top by a transition from gyspum to silstones. The main objectives consisted in resolving the underground structure: contacts/discontinuities; constrain the 3D geometry of the lithology (possible cavities, faults/fractures). These targets were achieved by mapping the 3D distribution of the physical properties (P-wave velocity). The regularly space dense acquisition grid forced to acquire the survey in different stages and with a variety of weather conditions. Therefore, a careful quality control was required. More than a half million first arrivals were inverted to provide a 3D Vp velocity model that reached depths of 120 m in the areas with the highest ray coverage. An extended borehole campaign, that included borehole geophysical measurements in some wells provided unique tight constraints on the lithology an a validation scheme for the tomographic results. The final image reveals a laterally variable structure consisting of four different lithological units. In this methodological validation test travel-time tomography features a high capacity of imaging in detail the lithological contrasts for complex structures located at very shallow depths.

  10. Time-lapse 3D electrical resistivity tomography to monitor soil-plant interactions

    NASA Astrophysics Data System (ADS)

    Boaga, Jacopo; Rossi, Matteo; Cassiani, Giorgio; Putti, Mario

    2013-04-01

    In this work we present the application of time-lapse non-invasive 3D micro- electrical tomography (ERT) to monitor soil-plant interactions in the root zone in the framework of the FP7 Project CLIMB (Climate Induced Changes on the Hydrology of Mediterranean Basins). The goal of the study is to gain a better understanding of the soil-vegetation interactions by the use of non-invasive techniques. We designed, built and installed a 3D electrical tomography apparatus for the monitoring of the root zone of a single apple tree in an orchard located in the Trentino region, Northern Italy. The micro-ERT apparatus consists of 48 buried electrodes on 4 instrumented micro boreholes plus 24 mini-electrodes on the surface spaced 0.1 m on a square grid. We collected repeated ERT and TDR soil moisture measurements for one year and performed two different controlled irrigation tests: one during a very dry Summer and one during a very wet and highly dynamic plant growing Spring period. We also ran laboratory analyses on soil specimens, in order to evaluate the electrical response at different saturation steps. The results demonstrate that 3D micro-ERT is capable of characterizing subsoil conditions and monitoring root zone activities, especially in terms of root zone suction regions. In particular, we note that in very dry conditions, 3D micro ERT can image water plumes in the shallow subsoil produced by a drip irrigation system. In the very dynamic growing season, under abundant irrigation, micro 3D ERT can detect the main suction zones caused by the tree root activity. Even though the quantitative use of this technique for moisture content balance suffers from well-known inversion difficulties, even the pure imaging of the active root zone is a valuable contribution. However the integration of the measurements in a fully coupled hydrogeophysical inversion is the way forward for a better understanding of subsoil interactions between biomass, hydrosphere and atmosphere.

  11. Iterative alternating sequential (IAS) method for radio tomography of asteroids in 3D

    NASA Astrophysics Data System (ADS)

    Pursiainen, S.; Kaasalainen, M.

    2013-07-01

    We present a feasibility study of the radio tomography of asteroids. We consider the simplest and most robust type of a radio experiment and physical model, related to the CONSERT (Comet Nucleus Sounding Experiment by Radiowave Transmission) setup, where an orbiter measures the propagation time and amplitude of a radio frequency signal between the orbiter and a transponder placed on an asteroid's surface. Contrary to CONSERT, we consider the simultaneous use of multiple transponders. We study two main questions: (i) what is the basic information content (reconstruction potential) of the data and the minimum number of transponders for recovering most of it and (ii) how to formulate Bayesian methods for an efficient 3D reconstruction. Our approach was to reconstruct the perturbations of a non-constant refractive index inside the asteroid based on simulated signal travel time measurements. We formulate this ill-posed inverse problem by an approximative linear forward (data prediction) model through optical path length and Snell's law, resulting in a formula closely related to the cone-beam and Radon transforms. The linear forward model was applied to three-dimensional asteroid geometries involving an isotropic and piecewise constant refractive index distribution composed of the unknown perturbation and a background given a priori. The inverse approach was based on a hierarchical Bayesian model. The reconstructions were produced via the iterative alternating sequential (IAS) maximum a posteriori (MAP) estimation algorithm. We explored the various aspects of the problem by considering the recovery of empty cavities inside an asteroid. Two different transponder setups, a spherical and a realistic computation geometry, as well as various cavity distributions were tested. The results suggest that (i) the information content of the travel time data is robust and allows a unique reconstruction with suitable methods; (ii) finding a reasonable reconstruction requires the use

  12. Finite element 3D reconstruction of the pulmonary acinus imaged by synchrotron X-ray tomography

    PubMed Central

    Tsuda, A.; Filipovic, N.; Haberthür, D.; Dickie, R.; Matsui, Y.; Stampanoni, M.; Schittny, J. C.

    2008-01-01

    The alveolated structure of the pulmonary acinus plays a vital role in gas exchange function. Three-dimensional (3D) analysis of the parenchymal region is fundamental to understanding this structure-function relationship, but only a limited number of attempts have been conducted in the past because of technical limitations. In this study, we developed a new image processing methodology based on finite element (FE) analysis for accurate 3D structural reconstruction of the gas exchange regions of the lung. Stereologically well characterized rat lung samples (Pediatr Res 53: 72–80, 2003) were imaged using high-resolution synchrotron radiation-based X-ray tomographic microscopy. A stack of 1,024 images (each slice: 1024 × 1024 pixels) with resolution of 1.4 μm3 per voxel were generated. For the development of FE algorithm, regions of interest (ROI), containing ∼7.5 million voxels, were further extracted as a working subunit. 3D FEs were created overlaying the voxel map using a grid-based hexahedral algorithm. A proper threshold value for appropriate segmentation was iteratively determined to match the calculated volume density of tissue to the stereologically determined value (Pediatr Res 53: 72–80, 2003). The resulting 3D FEs are ready to be used for 3D structural analysis as well as for subsequent FE computational analyses like fluid dynamics and skeletonization. PMID:18583378

  13. Use of 3-D magnetic resonance electrical impedance tomography in detecting human cerebral stroke: a simulation study*

    PubMed Central

    Gao, Nuo; Zhu, Shan-an; He, Bin

    2005-01-01

    We have developed a new three dimensional (3-D) conductivity imaging approach and have used it to detect human brain conductivity changes corresponding to acute cerebral stroke. The proposed Magnetic Resonance Electrical Impedance Tomography (MREIT) approach is based on the J-Substitution algorithm and is expanded to imaging 3-D subject conductivity distribution changes. Computer simulation studies have been conducted to evaluate the present MREIT imaging approach. Simulations of both types of cerebral stroke, hemorrhagic stroke and ischemic stroke, were performed on a four-sphere head model. Simulation results showed that the correlation coefficient (CC) and relative error (RE) between target and estimated conductivity distributions were 0.9245±0.0068 and 8.9997%±0.0084%, for hemorrhagic stroke, and 0.6748±0.0197 and 8.8986%±0.0089%, for ischemic stroke, when the SNR (signal-to-noise radio) of added GWN (Gaussian White Noise) was 40. The convergence characteristic was also evaluated according to the changes of CC and RE with different iteration numbers. The CC increases and RE decreases monotonously with the increasing number of iterations. The present simulation results show the feasibility of the proposed 3-D MREIT approach in hemorrhagic and ischemic stroke detection and suggest that the method may become a useful alternative in clinical diagnosis of acute cerebral stroke in humans. PMID:15822161

  14. High Resolution 3-D Waveform Tomography of the Lithospheric Structure of the Hellenic Subduction Zone

    NASA Astrophysics Data System (ADS)

    Lamara, Samir; Friederich, Wolfgang; Schumacher, Florian; Meier, Thomas; Egelados Working Group

    2015-04-01

    We present a high-resolution lithospheric shear-wave velocity model of the Hellenic subduction zone obtained by full waveform tomography of the EGELADOS project data. This high quality data was collected with the broadband amphibian seismic network EGELADOS that was deployed all over the southern Aegean from October 2005 to April 2007 providing a sampling of the south Aegean lithosphere with a resolution never reached before. Because of the strong deformations in the Hellenic subduction zone and the linear approximation in solving the full waveform inverse problem, a special care was taken to guarantee the best possible accuracy of earthquakes parameters and initial reference models. The accurate locations of the selected earthquakes were hence re-estimated and the best moment tensors were selected by computing the misfits between the observed seismograms for one event and a set of synthetics calculated for every value of the fault angles (strike, dip and rake) and hypocenter depths. On the other hand, instead of using an average 1D reference model for the complete region, a 1D path-specific approach permitted to obtain the 1D initial model for each source-receiver pair by waveform fitting using a grid search varying the Moho depth and the average S-wave velocity in the crust. These models were then refined by a 1D inversion and used to calculate the sensitivity kernels for each source-receiver pair. For the inversion, we adopted a special formulation including a correction term which permits to use the path-specific sensitivity kernels in an inversion for 3D velocity perturbations relative to a single 1D reference model constructed from all these 1D initial models. The inversion was done in frequency domain with a frequency window ranging from 0.03 Hz to 0.1 Hz. For the selected 2695 paths the total number of data values reached 140140. The model was discretized in volume cells with a varying vertical width and a fixed lateral one of approximately 15 km, resulting

  15. Modeling Computer Communication Networks in a Realistic 3D Environment

    DTIC Science & Technology

    2010-03-01

    visualization in OPNET . . . . . . . . . . . . 13 6. Sample NetViz visualization . . . . . . . . . . . . . . . . . . . 15 7. Realistic 3D terrains...scenario in OPNET . . . 19 10. OPNET 3DNV only displays connectivity . . . . . . . . . . . . 29 11. The digitally connected battlefield...confirmation tool 12 OPNET Optimized Network Evaluation Tool . . . . . . . . . . . . 13 NetViz Network Visualization

  16. Computed Tomography (CT) -- Head

    MedlinePlus

    ... ray beam follows a spiral path. A special computer program processes this large volume of data to create ... When the image slices are reassembled by computer software, the result is a very detailed multidimensional view ...

  17. Computed Tomography (CT) - Spine

    MedlinePlus

    ... ray beam follows a spiral path. A special computer program processes this large volume of data to create ... When the image slices are reassembled by computer software, the result is a very detailed multidimensional view ...

  18. Optoacoustic 3D whole-body tomography: experiments in nude mice

    NASA Astrophysics Data System (ADS)

    Brecht, Hans-Peter; Su, Richard; Fronheiser, Matt; Ermilov, Sergey A.; Conjusteau, André; Liopo, Anton; Motamedi, Massoud; Oraevsky, Alexander A.

    2009-02-01

    We developed a 3D whole-body optoacoustic tomography system for applications in preclinical research on mice. The system is capable of generating images with resolution better than 0.6 mm. Two pulsed lasers, an Alexandrite laser operating at 755 nm and a Nd:YAG laser operating at 532 nm and 1064nm were used for light delivery. The tomographic images were obtained while the objects of study (phantoms or mice) were rotated within a sphere outlined by a concave arc-shaped array of 64 piezo-composite transducers. During the scan, the mouse was illuminated orthogonally to the array with two wide beams of light from a bifurcated fiber bundle. Illumination at 532 nm showed superficial vasculature, but limited penetration depth at this wavelength prevented the detection of deeper structures. Illumination at 755 and 1064 nm showed organs and blood vessels, respectively. Filtering of the optoacoustic signals using high frequency enhancing wavelets further emphasized the smaller blood vessels.

  19. 3D mapping of nanoscale electric potentials in semiconductor structures using electron-holographic tomography

    NASA Astrophysics Data System (ADS)

    Wolf, Daniel; Lubk, Axel; Prete, Paola; Lovergine, Nico; Lichte, Hannes

    2016-09-01

    Off-axis electron holography (EH) is a powerful method for mapping projected electric potentials, such as built-in potentials in semiconductor devices, in two dimensions (2D) at nanometer resolution. However, not well-defined thickness profiles, surface effects, and composition changes of the sample under investigation complicate the interpretation of the projected potentials. Here, we demonstrate how these problems can be overcome by combining EH with tomographic techniques, that is, electron holographic tomography (EHT), reconstructing electric potentials in 3D. We present EHT reconstructions of an n-type MOSFET including its dopant-related built-in potentials inside the device, as well as of a GaAs/AlGaAs core-multishell nanowire containing a 5 nm thick quantum well tube.

  20. Reducing Disk Storage of Full-3D Seismic Waveform Tomography (F3DT) Through Lossy Online Compression

    DOE PAGES

    Lindstrom, Peter; Chen, Po; Lee, En-Jui

    2016-05-05

    Full-3D seismic waveform tomography (F3DT) is the latest seismic tomography technique that can assimilate broadband, multi-component seismic waveform observations into high-resolution 3D subsurface seismic structure models. The main drawback in the current F3DT implementation, in particular the scattering-integral implementation (F3DT-SI), is the high disk storage cost and the associated I/O overhead of archiving the 4D space-time wavefields of the receiver- or source-side strain tensors. The strain tensor fields are needed for computing the data sensitivity kernels, which are used for constructing the Jacobian matrix in the Gauss-Newton optimization algorithm. In this study, we have successfully integrated a lossy compression algorithmmore » into our F3DT SI workflow to significantly reduce the disk space for storing the strain tensor fields. The compressor supports a user-specified tolerance for bounding the error, and can be integrated into our finite-difference wave-propagation simulation code used for computing the strain fields. The decompressor can be integrated into the kernel calculation code that reads the strain fields from the disk and compute the data sensitivity kernels. During the wave-propagation simulations, we compress the strain fields before writing them to the disk. To compute the data sensitivity kernels, we read the compressed strain fields from the disk and decompress them before using them in kernel calculations. Experiments using a realistic dataset in our California statewide F3DT project have shown that we can reduce the strain-field disk storage by at least an order of magnitude with acceptable loss, and also improve the overall I/O performance of the entire F3DT-SI workflow significantly. The integration of the lossy online compressor may potentially open up the possibilities of the wide adoption of F3DT-SI in routine seismic tomography practices in the near future.« less

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

    PubMed

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

    2016-01-01

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

  2. Digital holographic tomography method for 3D observation of domain patterns in ferroelectric single crystals

    NASA Astrophysics Data System (ADS)

    Mokrý, Pavel; Psota, Pavel; Steiger, Kateřina; Václavík, Jan; Vápenka, David; Doleček, Roman; Vojtíšek, Petr; Sládek, Juraj; Lédl, Vít.

    2016-11-01

    We report on the development and implementation of the digital holographic tomography for the three-dimensio- nal (3D) observations of the domain patterns in the ferroelectric single crystals. Ferroelectric materials represent a group of materials, whose macroscopic dielectric, electromechanical, and elastic properties are greatly in uenced by the presence of domain patterns. Understanding the role of domain patterns on the aforementioned properties require the experimental techniques, which allow the precise 3D measurements of the spatial distribution of ferroelectric domains in the single crystal. Unfortunately, such techniques are rather limited at this time. The most frequently used piezoelectric atomic force microscopy allows 2D observations on the ferroelectric sample surface. Optical methods based on the birefringence measurements provide parameters of the domain patterns averaged over the sample volume. In this paper, we analyze the possibility that the spatial distribution of the ferroelectric domains can be obtained by means of the measurement of the wavefront deformation of the transmitted optical wave. We demonstrate that the spatial distribution of the ferroelectric domains can be determined by means of the measurement of the spatial distribution of the refractive index. Finally, it is demonstrated that the measurements of wavefront deformations generated in ferroelectric polydomain systems with small variations of the refractive index provide data, which can be further processed by means of the conventional tomographic methods.

  3. Implementation Of True 3D Cursors In Computer Graphics

    NASA Astrophysics Data System (ADS)

    Butts, David R.; McAllister, David F.

    1988-06-01

    The advances in stereoscopic image display techniques have shown an increased need for real-time interaction with the three-dimensional image. We have developed a prototype real-time stereoscopic cursor to investigate this interaction. The results have pointed out areas where hardware speeds are a limiting factor, as well as areas where various methodologies cause perceptual difficulties. This paper addresses the psychological and perceptual anomalies involved in stereo image techniques, cursor generation and motion, and the use of the device as a 3D drawing and depth measuring tool.

  4. Computed tomography of intracranial ependymomas

    SciTech Connect

    Swartz, J.D.; Zimmerman, R.A.; Bilaniuk, L.T.

    1982-04-01

    Twenty-six patients with ependymoma were evaluated by computed tomography (CT) over a period of 5 1/2 years. The usual CT appearance was an isodense, partially calcified mass, capable of contrast enhancement, occurring in the posterior fossa (73%) in an infant or child (77%). Outcome remains poor despite modern diagnostic and therapeutic methods.

  5. Computed tomography:the details.

    SciTech Connect

    Doerry, Armin Walter

    2007-07-01

    Computed Tomography (CT) is a well established technique, particularly in medical imaging, but also applied in Synthetic Aperture Radar (SAR) imaging. Basic CT imaging via back-projection is treated in many texts, but often with insufficient detail to appreciate subtleties such as the role of non-uniform sampling densities. Herein are given some details often neglected in many texts.

  6. Computed tomography of the thorax

    SciTech Connect

    Naidich, D.P.; Zerhouni, E.A.; Siegelman, S.S.

    1984-01-01

    This book contains chapters on: Principles and Techniques of Chest Computed Tomography; Aortic Arch and Great Vessels; Normal Anatomy and Variants; Mediastinum/Airways/Lobar Collapse/Pulmonary Hila/Pulmonary Nodule/Pulmonary Parenchyma/Pleura and Chest Wall/Pericardium/Diaphragm.

  7. Computed tomography in hepatic echinococcosis

    SciTech Connect

    Choliz, J.D.; Olaverri, F.J.L.; Casas, T.F.; Zubieta, S.O.

    1982-10-01

    Computed tomography (CT) was used to evaluate 50 cases of hydatid disease of the liver. It was definite in 49 cases and negative in one case. Pre- and postcontrast scans were performed. CT may reveal the exact location and extension of cysts and possible complications. However, a false-negative case was found in a hydatid cyst located in a fatty liver.

  8. Laminar optical tomography: high-resolution 3D functional imaging of superficial tissues

    NASA Astrophysics Data System (ADS)

    Hillman, Elizabeth M. C.; Devor, Anna; Dunn, Andrew K.; Boas, David A.

    2006-03-01

    Laminar Optical Tomography (LOT) is a new medical imaging modality for high-resolution, depth-resolved, functional imaging of superficial tissue such as rodent cortex, skin and the retina. LOT uses visible laser light to image to depths of >2mm (far deeper than microscopy) and is highly sensitive to absorption and fluorescence contrast, enabling spectroscopic functional information such as hemoglobin oxygenation to be imaged with 100-200 micron resolution. LOT has been used to image the hemodynamic response to stimulus in the somatosensory cortex of rats. The resulting three-dimensional (3D) images through the depth of the cortex can be used to delineate the arterial, capillary and venous responses, revealing new information about the intricacies of the oxygenation and blood flow dynamics related to neuronal activation. Additional applications of LOT are being explored, including the integration of 3D Voltage Sensitive Dye fluorescence imaging. LOT imaging uses a system similar to a confocal microscope, quickly scanning a focused beam of light over the surface of the tissue (~8Hz frame rate). Light is detected from both the focus of the scanning beam, and also at increasing distances from the beam's focus. This scattered light has penetrated more deeply into the tissue, and allows features at different depths to be distinguished. An algorithm that includes photon migration modeling of light scattering converts the raw data into 3D images. The motivation for functional optical imaging will be outlined, the basic principles of LOT imaging will be described, and the latest in-vivo results will be presented.

  9. 3D imaging of dental hard tissues with Fourier domain optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Chen, Yueli L.; Yang, Yi; Ma, Jing; Yan, Jun; Shou, Yuanxin; Wang, Tianheng; Ramesh, Aruna; Zhao, Jing; Zhu, Quing

    2011-03-01

    A fiber optical coherence tomography (OCT) probe is used for three dimensional dental imaging. The probe has a lightweight miniaturized design with a size of a pen to facilitate clinic in vivo diagnostics. The probe is interfaced with a swept-source / Fourier domain optical coherence tomography at 20K axial scanning rate. The tooth samples were scanned from occlusal, buccal, lingual, mesial, and distal orientations. Three dimensional imaging covers tooth surface area up to 10 mm x 10 mm with a depth about 5 mm, where a majority of caries affection occurs. OCT image provides better resolution and contrast compared to gold standard dental radiography (X-ray). In particular, the technology is well suited for occlusal caries detection. This is complementary to X-ray as occlusal caries affection is difficult to be detected due to the X-ray projectile scan geometry. The 3D topology of occlusal surface as well as the dentin-enamel junction (DEJ) surface inside the tooth can be visualized. The lesion area appears with much stronger back scattering signal intensity.

  10. Immuno- and correlative light microscopy-electron tomography methods for 3D protein localization in yeast.

    PubMed

    Mari, Muriel; Geerts, Willie J C; Reggiori, Fulvio

    2014-10-01

    Compartmentalization of eukaryotic cells is created and maintained through membrane rearrangements that include membrane transport and organelle biogenesis. Three-dimensional reconstructions with nanoscale resolution in combination with protein localization are essential for an accurate molecular dissection of these processes. The yeast Saccharomyces cerevisiae is a key model system for identifying genes and characterizing pathways essential for the organization of cellular ultrastructures. Electron microscopy studies of yeast, however, have been hampered by the presence of a cell wall that obstructs penetration of resins and cryoprotectants, and by the protein dense cytoplasm, which obscures the membrane details. Here we present an immuno-electron tomography (IET) method, which allows the determination of protein distribution patterns on reconstructed organelles from yeast. In addition, we extend this IET approach into a correlative light microscopy-electron tomography procedure where structures positive for a specific protein localized through a fluorescent signal are resolved in 3D. These new investigative tools for yeast will help to advance our understanding of the endomembrane system organization in eukaryotic cells.

  11. Soft computing approach to 3D lung nodule segmentation in CT.

    PubMed

    Badura, P; Pietka, E

    2014-10-01

    This paper presents a novel, multilevel approach to the segmentation of various types of pulmonary nodules in computed tomography studies. It is based on two branches of computational intelligence: the fuzzy connectedness (FC) and the evolutionary computation. First, the image and auxiliary data are prepared for the 3D FC analysis during the first stage of an algorithm - the masks generation. Its main goal is to process some specific types of nodules connected to the pleura or vessels. It consists of some basic image processing operations as well as dedicated routines for the specific cases of nodules. The evolutionary computation is performed on the image and seed points in order to shorten the FC analysis and improve its accuracy. After the FC application, the remaining vessels are removed during the postprocessing stage. The method has been validated using the first dataset of studies acquired and described by the Lung Image Database Consortium (LIDC) and by its latest release - the LIDC-IDRI (Image Database Resource Initiative) database.

  12. Computed tomography of the gastrointestinal tract

    SciTech Connect

    Meyers, M.A.

    1986-01-01

    This volume presents computed tomography of the major disease states involving the gastrointestinal tract, mesentery, and peritoneal cavity. Computed Tomography of the Gastrointestinal Tract combined experience of l5 authorities includes illustrations (most of these radiographs).

  13. 3-D structures of crack-tip dislocations and their shielding effect revealed by electron tomography.

    PubMed

    Tanaka, Masaki; Honda, Masaki; Sadamatsu, Sunao; Higashida, Kenji

    2010-08-01

    Three-dimensional structures of crack-tip dislocations in silicon crystals have been examined by combining scanning transmission electron microscopy and computed tomography. Cracks were introduced by a Vickers hardness tester at room temperature, and the sample was heated at 823 K for 1 h in order to introduce dislocations around the crack tips. Dislocation segments cut out from loops were observed around the crack tip, the three-dimensional structure of which was characterized by using by electron tomography. Their Burgers vectors including the sings were also determined by oscillating contrasts along dislocations. In order to investigate the effect of the dislocations on fracture behaviours, local stress intensity factor due to one dislocation was calculated, which indicates the dislocations observed were shielding type to increase fracture toughness.

  14. NASA's computed tomography system

    NASA Astrophysics Data System (ADS)

    Engel, H. Peter

    1989-03-01

    The computerized industrial tomographic analyzer (CITA) is designed to examine the internal structure and material integrity of a wide variety of aerospace-related objects, particularly in the NASA space program. The nondestructive examination is performed by producing a two-dimensional picture of a selected slice through an object. The penetrating sources that yield data for reconstructing the slice picture are radioactive cobalt or a high-power X-ray tube. A series of pictures and computed tomograms are presented which illustrate a few of the applications the CITA has been used for since its August 1986 initial service at the Kennedy Space Center.

  15. Computation of tooth axes of existent and missing teeth from 3D CT images.

    PubMed

    Wang, Yang; Wu, Lin; Guo, Huayan; Qiu, Tiantian; Huang, Yuanliang; Lin, Bin; Wang, Lisheng

    2015-12-01

    Orientations of tooth axes are important quantitative information used in dental diagnosis and surgery planning. However, their computation is a complex problem, and the existing methods have respective limitations. This paper proposes new methods to compute 3D tooth axes from 3D CT images for existent teeth with single root or multiple roots and to estimate 3D tooth axes from 3D CT images for missing teeth. The tooth axis of a single-root tooth will be determined by segmenting the pulp cavity of the tooth and computing the principal direction of the pulp cavity, and the estimation of tooth axes of the missing teeth is modeled as an interpolation problem of some quaternions along a 3D curve. The proposed methods can either avoid the difficult teeth segmentation problem or improve the limitations of existing methods. Their effectiveness and practicality are demonstrated by experimental results of different 3D CT images from the clinic.

  16. Intra-retinal layer segmentation of 3D optical coherence tomography using coarse grained diffusion map.

    PubMed

    Kafieh, Raheleh; Rabbani, Hossein; Abramoff, Michael D; Sonka, Milan

    2013-12-01

    Optical coherence tomography (OCT) is a powerful and noninvasive method for retinal imaging. In this paper, we introduce a fast segmentation method based on a new variant of spectral graph theory named diffusion maps. The research is performed on spectral domain (SD) OCT images depicting macular and optic nerve head appearance. The presented approach does not require edge-based image information in localizing most of boundaries and relies on regional image texture. Consequently, the proposed method demonstrates robustness in situations of low image contrast or poor layer-to-layer image gradients. Diffusion mapping applied to 2D and 3D OCT datasets is composed of two steps, one for partitioning the data into important and less important sections, and another one for localization of internal layers. In the first step, the pixels/voxels are grouped in rectangular/cubic sets to form a graph node. The weights of the graph are calculated based on geometric distances between pixels/voxels and differences of their mean intensity. The first diffusion map clusters the data into three parts, the second of which is the area of interest. The other two sections are eliminated from the remaining calculations. In the second step, the remaining area is subjected to another diffusion map assessment and the internal layers are localized based on their textural similarities. The proposed method was tested on 23 datasets from two patient groups (glaucoma and normals). The mean unsigned border positioning errors (mean ± SD) was 8.52 ± 3.13 and 7.56 ± 2.95 μm for the 2D and 3D methods, respectively.

  17. Real-time 3D Fourier-domain optical coherence tomography guided microvascular anastomosis

    NASA Astrophysics Data System (ADS)

    Huang, Yong; Ibrahim, Zuhaib; Lee, W. P. A.; Brandacher, Gerald; Kang, Jin U.

    2013-03-01

    Vascular and microvascular anastomosis is considered to be the foundation of plastic and reconstructive surgery, hand surgery, transplant surgery, vascular surgery and cardiac surgery. In the last two decades innovative techniques, such as vascular coupling devices, thermo-reversible poloxamers and suture-less cuff have been introduced. Intra-operative surgical guidance using a surgical imaging modality that provides in-depth view and 3D imaging can improve outcome following both conventional and innovative anastomosis techniques. Optical coherence tomography (OCT) is a noninvasive high-resolution (micron level), high-speed, 3D imaging modality that has been adopted widely in biomedical and clinical applications. In this work we performed a proof-of-concept evaluation study of OCT as an assisted intraoperative and post-operative imaging modality for microvascular anastomosis of rodent femoral vessels. The OCT imaging modality provided lateral resolution of 12 μm and 3.0 μm axial resolution in air and 0.27 volume/s imaging speed, which could provide the surgeon with clearly visualized vessel lumen wall and suture needle position relative to the vessel during intraoperative imaging. Graphics processing unit (GPU) accelerated phase-resolved Doppler OCT (PRDOCT) imaging of the surgical site was performed as a post-operative evaluation of the anastomosed vessels and to visualize the blood flow and thrombus formation. This information could help surgeons improve surgical precision in this highly challenging anastomosis of rodent vessels with diameter less than 0.5 mm. Our imaging modality could not only detect accidental suture through the back wall of lumen but also promptly diagnose and predict thrombosis immediately after reperfusion. Hence, real-time OCT can assist in decision-making process intra-operatively and avoid post-operative complications.

  18. Towards the Next Generation Upper-Mantle 3D Anelastic Tomography

    NASA Astrophysics Data System (ADS)

    Karaoglu, H.; Romanowicz, B. A.

    2015-12-01

    In order to distinguish the thermal and compositional heterogeneities in the mantle, it is crucial to resolve the lateral variations not only in seismic velocities but also in intrinsic attenuation. Indeed, the high sensitivity of intrinsic attenuation to temperature and water content, governed by a form of Arrhenius equation, contrasts with the quasi-linear dependence of velocities on both temperature and major element composition. The major challenge in imaging attenuation lies in separating its effects on seismic waves from the elastic ones. The latter originate from the wave propagation in media with strong lateral elastic gradients causing (de)focusing and scattering. We have previously developed a 3D upper-mantle shear attenuation model based on time domain waveform inversion of long period (T > 60s) fundamental and overtone surface wave data (Gung & Romanowicz, 2004). However, at that time, resolution was limited to very long wavelength structure, because elastic models were still rather smooth, and the effects of focusing could only be estimated approximately, using asymptotic normal mode perturbation theory.With recent progress in constraining global mantle shear velocity from waveform tomography based on the Spectral Element Method (e.g. SEMUCB_WM1, French & Romanowicz, 2014), we are now in a position to develop an improved global 3D model of shear attenuation in the upper mantle. In doing so, we use a similar time domain waveform inversion approach, but (1) start with a higher resolution elastic model with better constraints on lateral elastic gradients and (2) jointly invert, in an iterative fashion, for shear attenuation and elastic parameters. Here, we present the results of synthetic tests that confirm our inversion strategy, as well as preliminary results towards the construction of the next generation upper-mantle anelastic model.

  19. Cellular uptake mechanisms of functionalised multi-walled carbon nanotubes by 3D electron tomography imaging

    NASA Astrophysics Data System (ADS)

    Al-Jamal, Khuloud T.; Nerl, Hannah; Müller, Karin H.; Ali-Boucetta, Hanene; Li, Shouping; Haynes, Peter D.; Jinschek, Joerg R.; Prato, Maurizio; Bianco, Alberto; Kostarelos, Kostas; Porter, Alexandra E.

    2011-06-01

    Carbon nanotubes (CNTs) are being investigated for a variety of biomedical applications. Despite numerous studies, the pathways by which carbon nanotubes enter cells and their subsequent intracellular trafficking and distribution remain poorly determined. Here, we use 3-D electron tomography techniques that offer optimum enhancement of contrast between carbon nanotubes and the plasma membrane to investigate the mechanisms involved in the cellular uptake of shortened, functionalised multi-walled carbon nanotubes (MWNT-NH3+). Both human lung epithelial (A549) cells, that are almost incapable of phagocytosis and primary macrophages, capable of extremely efficient phagocytosis, were used. We observed that MWNT-NH3+ were internalised in both phagocytic and non-phagocytic cells by any one of three mechanisms: (a) individually via membrane wrapping; (b) individually by direct membrane translocation; and (c) in clusters within vesicular compartments. At early time points following intracellular translocation, we noticed accumulation of nanotube material within various intracellular compartments, while a long-term (14-day) study using primary human macrophages revealed that MWNT-NH3+ were able to escape vesicular (phagosome) entrapment by translocating directly into the cytoplasm.Carbon nanotubes (CNTs) are being investigated for a variety of biomedical applications. Despite numerous studies, the pathways by which carbon nanotubes enter cells and their subsequent intracellular trafficking and distribution remain poorly determined. Here, we use 3-D electron tomography techniques that offer optimum enhancement of contrast between carbon nanotubes and the plasma membrane to investigate the mechanisms involved in the cellular uptake of shortened, functionalised multi-walled carbon nanotubes (MWNT-NH3+). Both human lung epithelial (A549) cells, that are almost incapable of phagocytosis and primary macrophages, capable of extremely efficient phagocytosis, were used. We observed

  20. Pediatric cranial computed tomography

    SciTech Connect

    Yamada, H.

    1984-01-01

    The introduction of CT in the investigation of intercranial pathology has revolutionized the approach to clinical neurological and neurosurgical practice. This book applies the advances of cranial CT to the pediatric patient. The test is divided into two sections. The first portion describes the practical methodology, anatomy and normal and abnormal CT scan appearance, including high or low density lesions, cystic lesions and ventricular or subarachnoid space dilation. The characteristic scans for various neurological diseases are presented and discussed. The author has given special attention to the CT diagnosis of congenital malformations and cerebral neoplasms. Partial Contents: Normal Computed Tomographic Anatomy/ High Density Lesions/Low Density Lesions/Cystic Lesions; Supratentorial/Cystic Lesions; Infratentorial/Increased Head Circumference/Increased Ventricular Size/Small Ventricular Size/Cranial Lesions/Spinal Lesions/CT Cisternography/Part II CT in Neonates/Congenital Craniocerebral Malformations/Hydrocephalus/Craniosynostosis/Head Trauma/Cerebrovascular Lesions/Intracranial Lesions/Seizure Disorders/Intracranial and Other Chronic Neurological Disorders.

  1. Computational ocean acoustics: Advances in 3D ocean acoustic modeling

    NASA Astrophysics Data System (ADS)

    Schmidt, Henrik; Jensen, Finn B.

    2012-11-01

    The numerical model of ocean acoustic propagation developed in the 1980's are still in widespread use today, and the field of computational ocean acoustics is often considered a mature field. However, the explosive increase in computational power available to the community has created opportunities for modeling phenomena that earlier were beyond reach. Most notably, three-dimensional propagation and scattering problems have been prohibitive computationally, but are now addressed routinely using brute force numerical approaches such as the Finite Element Method, in particular for target scattering problems, where they are being combined with the traditional wave theory propagation models in hybrid modeling frameworks. Also, recent years has seen the development of hybrid approaches coupling oceanographic circulation models with acoustic propagation models, enabling the forecasting of sonar performance uncertainty in dynamic ocean environments. These and other advances made over the last couple of decades support the notion that the field of computational ocean acoustics is far from being mature. [Work supported by the Office of Naval Research, Code 321OA].

  2. Computational 3-D Model of the Human Respiratory System

    EPA Science Inventory

    We are developing a comprehensive, morphologically-realistic computational model of the human respiratory system that can be used to study the inhalation, deposition, and clearance of contaminants, while being adaptable for age, race, gender, and health/disease status. The model ...

  3. Tools for 3D scientific visualization in computational aerodynamics

    NASA Technical Reports Server (NTRS)

    Bancroft, Gordon; Plessel, Todd; Merritt, Fergus; Watson, Val

    1989-01-01

    The purpose is to describe the tools and techniques in use at the NASA Ames Research Center for performing visualization of computational aerodynamics, for example visualization of flow fields from computer simulations of fluid dynamics about vehicles such as the Space Shuttle. The hardware used for visualization is a high-performance graphics workstation connected to a super computer with a high speed channel. At present, the workstation is a Silicon Graphics IRIS 3130, the supercomputer is a CRAY2, and the high speed channel is a hyperchannel. The three techniques used for visualization are post-processing, tracking, and steering. Post-processing analysis is done after the simulation. Tracking analysis is done during a simulation but is not interactive, whereas steering analysis involves modifying the simulation interactively during the simulation. Using post-processing methods, a flow simulation is executed on a supercomputer and, after the simulation is complete, the results of the simulation are processed for viewing. The software in use and under development at NASA Ames Research Center for performing these types of tasks in computational aerodynamics is described. Workstation performance issues, benchmarking, and high-performance networks for this purpose are also discussed as well as descriptions of other hardware for digital video and film recording.

  4. X-ray computed tomography

    NASA Astrophysics Data System (ADS)

    1993-05-01

    The primary advantage of the X-ray computed tomography (XRCT) NDE method is that features are not superposed in the image, thereby rendering them easier to interpret than radiographic projection images. Industrial XRCT systems, unlike medical diagnostic systems, have no size and dosage constraints; they are accordingly used for systems from the scale of gas turbine blades, with hundreds-of-kV energies, to those of the scale of ICBMs, requiring MV-level X-ray energies.

  5. Computed tomography of neutropenic colitis

    SciTech Connect

    Frick, M.P.; Maile, C.W.; Crass, J.R.; Goldberg, M.E.; Delaney, J.P.

    1984-10-01

    Four patients developed neutropenic colitis as a complication of acute leukemia (three) or aplastic anemia (one). On computed tomography (CT), neutropenic colitis was characterized by cecal wall thickening (four) and pneumatosis (one). Intramural areas of lower density presumably reflected edema or hemorrhage. Clinical improvement and return of adequate numbers of functioning neutrophils coincided with decrease in cecal wall thickening on CT. Prompt radiologic recognition of this serious condition is crucial, since surgical intervention is probably best avoided.

  6. Computed tomography of gynecologic diseases

    SciTech Connect

    Gross, B.H.; Moss, A.A.; Mihara, K.; Goldberg, H.I.; Glazer, G.M.

    1983-10-01

    Although computed tomography (CT) provides superb images of all areas of the body, sonography, because of its lack of ionizing radiation and its real-time and multiplanar capacities, has become the preferred initial method of evaluating the female pelvis. This has resulted in a relative paucity of information in the literature concerning CT features of benign pelvic disorders in particular and prompted the authors to review our experience with third-generation CT scanning of the uterus and ovaries.

  7. Automatic 2D and 3D segmentation of liver from Computerised Tomography

    NASA Astrophysics Data System (ADS)

    Evans, Alun

    As part of the diagnosis of liver disease, a Computerised Tomography (CT) scan is taken of the patient, which the clinician then uses for assistance in determining the presence and extent of the disease. This thesis presents the background, methodology, results and future work of a project that employs automated methods to segment liver tissue. The clinical motivation behind this work is the desire to facilitate the diagnosis of liver disease such as cirrhosis or cancer, assist in volume determination for liver transplantation, and possibly assist in measuring the effect of any treatment given to the liver. Previous attempts at automatic segmentation of liver tissue have relied on 2D, low-level segmentation techniques, such as thresholding and mathematical morphology, to obtain the basic liver structure. The derived boundary can then be smoothed or refined using more advanced methods. The 2D results presented in this thesis improve greatly on this previous work by using a topology adaptive active contour model to accurately segment liver tissue from CT images. The use of conventional snakes for liver segmentation is difficult due to the presence of other organs closely surrounding the liver this new technique avoids this problem by adding an inflationary force to the basic snake equation, and initialising the snake inside the liver. The concepts underlying the 2D technique are extended to 3D, and results of full 3D segmentation of the liver are presented. The 3D technique makes use of an inflationary active surface model which is adaptively reparameterised, according to its size and local curvature, in order that it may more accurately segment the organ. Statistical analysis of the accuracy of the segmentation is presented for 18 healthy liver datasets, and results of the segmentation of unhealthy livers are also shown. The novel work developed during the course of this project has possibilities for use in other areas of medical imaging research, for example the

  8. Tensor3D: A computer graphics program to simulate 3D real-time deformation and visualization of geometric bodies

    NASA Astrophysics Data System (ADS)

    Pallozzi Lavorante, Luca; Dirk Ebert, Hans

    2008-07-01

    Tensor3D is a geometric modeling program with the capacity to simulate and visualize in real-time the deformation, specified through a tensor matrix and applied to triangulated models representing geological bodies. 3D visualization allows the study of deformational processes that are traditionally conducted in 2D, such as simple and pure shears. Besides geometric objects that are immediately available in the program window, the program can read other models from disk, thus being able to import objects created with different open-source or proprietary programs. A strain ellipsoid and a bounding box are simultaneously shown and instantly deformed with the main object. The principal axes of strain are visualized as well to provide graphical information about the orientation of the tensor's normal components. The deformed models can also be saved, retrieved later and deformed again, in order to study different steps of progressive strain, or to make this data available to other programs. The shape of stress ellipsoids and the corresponding Mohr circles defined by any stress tensor can also be represented. The application was written using the Visualization ToolKit, a powerful scientific visualization library in the public domain. This development choice, allied to the use of the Tcl/Tk programming language, which is independent on the host computational platform, makes the program a useful tool for the study of geometric deformations directly in three dimensions in teaching as well as research activities.

  9. Combining 3D Hydraulic Tomography with Tracer Tests for Improved Transport Characterization.

    PubMed

    Sanchez-León, E; Leven, C; Haslauer, C P; Cirpka, O A

    2016-07-01

    Hydraulic tomography (HT) is a method for resolving the spatial distribution of hydraulic parameters to some extent, but many details important for solute transport usually remain unresolved. We present a methodology to improve solute transport predictions by combining data from HT with the breakthrough curve (BTC) of a single forced-gradient tracer test. We estimated the three dimensional (3D) hydraulic-conductivity field in an alluvial aquifer by inverting tomographic pumping tests performed at the Hydrogeological Research Site Lauswiesen close to Tübingen, Germany, using a regularized pilot-point method. We compared the estimated parameter field to available profiles of hydraulic-conductivity variations from direct-push injection logging (DPIL), and validated the hydraulic-conductivity field with hydraulic-head measurements of tests not used in the inversion. After validation, spatially uniform parameters for dual-domain transport were estimated by fitting tracer data collected during a forced-gradient tracer test. The dual-domain assumption was used to parameterize effects of the unresolved heterogeneity of the aquifer and deemed necessary to fit the shape of the BTC using reasonable parameter values. The estimated hydraulic-conductivity field and transport parameters were subsequently used to successfully predict a second independent tracer test. Our work provides an efficient and practical approach to predict solute transport in heterogeneous aquifers without performing elaborate field tracer tests with a tomographic layout.

  10. Large area 3-D optical coherence tomography imaging of lumpectomy specimens for radiation treatment planning

    NASA Astrophysics Data System (ADS)

    Wang, Cuihuan; Kim, Leonard; Barnard, Nicola; Khan, Atif; Pierce, Mark C.

    2016-02-01

    Our long term goal is to develop a high-resolution imaging method for comprehensive assessment of tissue removed during lumpectomy procedures. By identifying regions of high-grade disease within the excised specimen, we aim to develop patient-specific post-operative radiation treatment regimens. We have assembled a benchtop spectral-domain optical coherence tomography (SD-OCT) system with 1320 nm center wavelength. Automated beam scanning enables "sub-volumes" spanning 5 mm x 5 mm x 2 mm (500 A-lines x 500 B-scans x 2 mm in depth) to be collected in under 15 seconds. A motorized sample positioning stage enables multiple sub-volumes to be acquired across an entire tissue specimen. Sub-volumes are rendered from individual B-scans in 3D Slicer software and en face (XY) images are extracted at specific depths. These images are then tiled together using MosaicJ software to produce a large area en face view (up to 40 mm x 25 mm). After OCT imaging, specimens were sectioned and stained with HE, allowing comparison between OCT image features and disease markers on histopathology. This manuscript describes the technical aspects of image acquisition and reconstruction, and reports initial qualitative comparison between large area en face OCT images and HE stained tissue sections. Future goals include developing image reconstruction algorithms for mapping an entire sample, and registering OCT image volumes with clinical CT and MRI images for post-operative treatment planning.

  11. Automated multilayer segmentation and characterization in 3D spectral-domain optical coherence tomography images

    NASA Astrophysics Data System (ADS)

    Hu, Zhihong; Wu, Xiaodong; Hariri, Amirhossein; Sadda, SriniVas R.

    2013-03-01

    Spectral-domain optical coherence tomography (SD-OCT) is a 3-D imaging technique, allowing direct visualization of retinal morphology and architecture. The various layers of the retina may be affected differentially by various diseases. In this study, an automated graph-based multilayer approach was developed to sequentially segment eleven retinal surfaces including the inner retinal bands to the outer retinal bands in normal SD-OCT volume scans at three different stages. For stage 1, the four most detectable and/or distinct surfaces were identified in the four-times-downsampled images and were used as a priori positional information to limit the graph search for other surfaces at stage 2. Eleven surfaces were then detected in the two-times-downsampled images at stage 2, and refined in the original image space at stage 3 using the graph search integrating the estimated morphological shape models. Twenty macular SD-OCT (Heidelberg Spectralis) volume scans from 20 normal subjects (one eye per subject) were used in this study. The overall mean and absolute mean differences in border positions between the automated and manual segmentation for all 11 segmented surfaces were -0.20 +/- 0.53 voxels (-0.76 +/- 2.06 μm) and 0.82 +/- 0.64 voxels (3.19 +/- 2.46 μm). Intensity and thickness properties in the resultant retinal layers were investigated. This investigation in normal subjects may provide a comparative reference for subsequent investigations in eyes with disease.

  12. 3D imaging of tomato seeds using frequency domain optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Fan, Chuanmao; Yao, Gang

    2012-05-01

    A fast imaging system that can reveal internal sample structures is important for research and quality controls of seeds. Optical coherence tomography (OCT) is a non-invasive optical imaging technique that can acquire high speed, high resolution depth-resolved images in scattering samples. It has found numerous applications in studying various biological tissues and other materials in vivo. A few studies have reported the use of OCT in studying seed morphology. However, 3D imaging of internal seed structure has not been reported before. In this study, we used a frequency domain OCT system to image tomato seeds. The system has a central wavelength of 844nm with a 46.8 nm FWHM bandwidth. The requirement for depth scan was eliminated by using a Fourier domain implementation. The B-scan imaging speed was limited by the spectroscopic imaging CCD at 52 kHz. The calibrated system has a 6.7μm depth resolution and a 15.4μm lateral resolution. Our results show that major seed structures can be clearly visualized in OCT images.

  13. Passive 3D imaging of nuclear waste containers with Muon Scattering Tomography

    NASA Astrophysics Data System (ADS)

    Thomay, C.; Velthuis, J.; Poffley, T.; Baesso, P.; Cussans, D.; Frazão, L.

    2016-03-01

    The non-invasive imaging of dense objects is of particular interest in the context of nuclear waste management, where it is important to know the contents of waste containers without opening them. Using Muon Scattering Tomography (MST), it is possible to obtain a detailed 3D image of the contents of a waste container on reasonable timescales, showing both the high and low density materials inside. We show the performance of such a method on a Monte Carlo simulation of a dummy waste drum object containing objects of different shapes and materials. The simulation has been tuned with our MST prototype detector performance. In particular, we show that both a tungsten penny of 2 cm radius and 1 cm thickness, and a uranium sheet of 0.5 cm thickness can be clearly identified. We also show the performance of a novel edge finding technique, by which the edges of embedded objects can be identified more precisely than by solely using the imaging method.

  14. Computed Tomography software and standards

    SciTech Connect

    Azevedo, S.G.; Martz, H.E.; Skeate, M.F.; Schneberk, D.J.; Roberson, G.P.

    1990-02-20

    This document establishes the software design, nomenclature, and conventions for industrial Computed Tomography (CT) used in the Nondestructive Evaluation Section at Lawrence Livermore National Laboratory. It is mainly a users guide to the technical use of the CT computer codes, but also presents a proposed standard for describing CT experiments and reconstructions. Each part of this document specifies different aspects of the CT software organization. A set of tables at the end describes the CT parameters of interest in our project. 4 refs., 6 figs., 1 tab.

  15. GEO3D - Three-Dimensional Computer Model of a Ground Source Heat Pump System

    SciTech Connect

    James Menart

    2013-06-07

    This file is the setup file for the computer program GEO3D. GEO3D is a computer program written by Jim Menart to simulate vertical wells in conjunction with a heat pump for ground source heat pump (GSHP) systems. This is a very detailed three-dimensional computer model. This program produces detailed heat transfer and temperature field information for a vertical GSHP system.

  16. Quality assessment of clinical computed tomography

    NASA Astrophysics Data System (ADS)

    Berndt, Dorothea; Luckow, Marlen; Lambrecht, J. Thomas; Beckmann, Felix; Müller, Bert

    2008-08-01

    Three-dimensional images are vital for the diagnosis in dentistry and cranio-maxillofacial surgery. Artifacts caused by highly absorbing components such as metallic implants, however, limit the value of the tomograms. The dominant artifacts observed are blowout and streaks. Investigating the artifacts generated by metallic implants in a pig jaw, the data acquisition for the patients in dentistry should be optimized in a quantitative manner. A freshly explanted pig jaw including related soft-tissues served as a model system. Images were recorded varying the accelerating voltage and the beam current. The comparison with multi-slice and micro computed tomography (CT) helps to validate the approach with the dental CT system (3D-Accuitomo, Morita, Japan). The data are rigidly registered to comparatively quantify their quality. The micro CT data provide a reasonable standard for quantitative data assessment of clinical CT.

  17. A 3D reconstruction algorithm for magneto-acoustic tomography with magnetic induction based on ultrasound transducer characteristics

    NASA Astrophysics Data System (ADS)

    Ma, Ren; Zhou, Xiaoqing; Zhang, Shunqi; Yin, Tao; Liu, Zhipeng

    2016-12-01

    In this study we present a three-dimensional (3D) reconstruction algorithm for magneto-acoustic tomography with magnetic induction (MAT-MI) based on the characteristics of the ultrasound transducer. The algorithm is investigated to solve the blur problem of the MAT-MI acoustic source image, which is caused by the ultrasound transducer and the scanning geometry. First, we established a transducer model matrix using measured data from the real transducer. With reference to the S-L model used in the computed tomography algorithm, a 3D phantom model of electrical conductivity is set up. Both sphere scanning and cylinder scanning geometries are adopted in the computer simulation. Then, using finite element analysis, the distribution of the eddy current and the acoustic source as well as the acoustic pressure can be obtained with the transducer model matrix. Next, using singular value decomposition, the inverse transducer model matrix together with the reconstruction algorithm are worked out. The acoustic source and the conductivity images are reconstructed using the proposed algorithm. Comparisons between an ideal point transducer and the realistic transducer are made to evaluate the algorithms. Finally, an experiment is performed using a graphite phantom. We found that images of the acoustic source reconstructed using the proposed algorithm are a better match than those using the previous one, the correlation coefficient of sphere scanning geometry is 98.49% and that of cylinder scanning geometry is 94.96%. Comparison between the ideal point transducer and the realistic transducer shows that the correlation coefficients are 90.2% in sphere scanning geometry and 86.35% in cylinder scanning geometry. The reconstruction of the graphite phantom experiment also shows a higher resolution using the proposed algorithm. We conclude that the proposed reconstruction algorithm, which considers the characteristics of the transducer, can obviously improve the resolution of the

  18. 3D parallel-detection microwave tomography for clinical breast imaging

    NASA Astrophysics Data System (ADS)

    Epstein, N. R.; Meaney, P. M.; Paulsen, K. D.

    2014-12-01

    A biomedical microwave tomography system with 3D-imaging capabilities has been constructed and translated to the clinic. Updates to the hardware and reconfiguration of the electronic-network layouts in a more compartmentalized construct have streamlined system packaging. Upgrades to the data acquisition and microwave components have increased data-acquisition speeds and improved system performance. By incorporating analog-to-digital boards that accommodate the linear amplification and dynamic-range coverage our system requires, a complete set of data (for a fixed array position at a single frequency) is now acquired in 5.8 s. Replacement of key components (e.g., switches and power dividers) by devices with improved operational bandwidths has enhanced system response over a wider frequency range. High-integrity, low-power signals are routinely measured down to -130 dBm for frequencies ranging from 500 to 2300 MHz. Adequate inter-channel isolation has been maintained, and a dynamic range >110 dB has been achieved for the full operating frequency range (500-2900 MHz). For our primary band of interest, the associated measurement deviations are less than 0.33% and 0.5° for signal amplitude and phase values, respectively. A modified monopole antenna array (composed of two interwoven eight-element sub-arrays), in conjunction with an updated motion-control system capable of independently moving the sub-arrays to various in-plane and cross-plane positions within the illumination chamber, has been configured in the new design for full volumetric data acquisition. Signal-to-noise ratios (SNRs) are more than adequate for all transmit/receive antenna pairs over the full frequency range and for the variety of in-plane and cross-plane configurations. For proximal receivers, in-plane SNRs greater than 80 dB are observed up to 2900 MHz, while cross-plane SNRs greater than 80 dB are seen for 6 cm sub-array spacing (for frequencies up to 1500 MHz). We demonstrate accurate recovery

  19. 3D parallel-detection microwave tomography for clinical breast imaging.

    PubMed

    Epstein, N R; Meaney, P M; Paulsen, K D

    2014-12-01

    A biomedical microwave tomography system with 3D-imaging capabilities has been constructed and translated to the clinic. Updates to the hardware and reconfiguration of the electronic-network layouts in a more compartmentalized construct have streamlined system packaging. Upgrades to the data acquisition and microwave components have increased data-acquisition speeds and improved system performance. By incorporating analog-to-digital boards that accommodate the linear amplification and dynamic-range coverage our system requires, a complete set of data (for a fixed array position at a single frequency) is now acquired in 5.8 s. Replacement of key components (e.g., switches and power dividers) by devices with improved operational bandwidths has enhanced system response over a wider frequency range. High-integrity, low-power signals are routinely measured down to -130 dBm for frequencies ranging from 500 to 2300 MHz. Adequate inter-channel isolation has been maintained, and a dynamic range >110 dB has been achieved for the full operating frequency range (500-2900 MHz). For our primary band of interest, the associated measurement deviations are less than 0.33% and 0.5° for signal amplitude and phase values, respectively. A modified monopole antenna array (composed of two interwoven eight-element sub-arrays), in conjunction with an updated motion-control system capable of independently moving the sub-arrays to various in-plane and cross-plane positions within the illumination chamber, has been configured in the new design for full volumetric data acquisition. Signal-to-noise ratios (SNRs) are more than adequate for all transmit/receive antenna pairs over the full frequency range and for the variety of in-plane and cross-plane configurations. For proximal receivers, in-plane SNRs greater than 80 dB are observed up to 2900 MHz, while cross-plane SNRs greater than 80 dB are seen for 6 cm sub-array spacing (for frequencies up to 1500 MHz). We demonstrate accurate recovery

  20. 3D parallel-detection microwave tomography for clinical breast imaging

    SciTech Connect

    Epstein, N. R.; Meaney, P. M.; Paulsen, K. D.

    2014-12-15

    A biomedical microwave tomography system with 3D-imaging capabilities has been constructed and translated to the clinic. Updates to the hardware and reconfiguration of the electronic-network layouts in a more compartmentalized construct have streamlined system packaging. Upgrades to the data acquisition and microwave components have increased data-acquisition speeds and improved system performance. By incorporating analog-to-digital boards that accommodate the linear amplification and dynamic-range coverage our system requires, a complete set of data (for a fixed array position at a single frequency) is now acquired in 5.8 s. Replacement of key components (e.g., switches and power dividers) by devices with improved operational bandwidths has enhanced system response over a wider frequency range. High-integrity, low-power signals are routinely measured down to −130 dBm for frequencies ranging from 500 to 2300 MHz. Adequate inter-channel isolation has been maintained, and a dynamic range >110 dB has been achieved for the full operating frequency range (500–2900 MHz). For our primary band of interest, the associated measurement deviations are less than 0.33% and 0.5° for signal amplitude and phase values, respectively. A modified monopole antenna array (composed of two interwoven eight-element sub-arrays), in conjunction with an updated motion-control system capable of independently moving the sub-arrays to various in-plane and cross-plane positions within the illumination chamber, has been configured in the new design for full volumetric data acquisition. Signal-to-noise ratios (SNRs) are more than adequate for all transmit/receive antenna pairs over the full frequency range and for the variety of in-plane and cross-plane configurations. For proximal receivers, in-plane SNRs greater than 80 dB are observed up to 2900 MHz, while cross-plane SNRs greater than 80 dB are seen for 6 cm sub-array spacing (for frequencies up to 1500 MHz). We demonstrate accurate

  1. 3D parallel-detection microwave tomography for clinical breast imaging

    PubMed Central

    Meaney, P. M.; Paulsen, K. D.

    2014-01-01

    A biomedical microwave tomography system with 3D-imaging capabilities has been constructed and translated to the clinic. Updates to the hardware and reconfiguration of the electronic-network layouts in a more compartmentalized construct have streamlined system packaging. Upgrades to the data acquisition and microwave components have increased data-acquisition speeds and improved system performance. By incorporating analog-to-digital boards that accommodate the linear amplification and dynamic-range coverage our system requires, a complete set of data (for a fixed array position at a single frequency) is now acquired in 5.8 s. Replacement of key components (e.g., switches and power dividers) by devices with improved operational bandwidths has enhanced system response over a wider frequency range. High-integrity, low-power signals are routinely measured down to −130 dBm for frequencies ranging from 500 to 2300 MHz. Adequate inter-channel isolation has been maintained, and a dynamic range >110 dB has been achieved for the full operating frequency range (500–2900 MHz). For our primary band of interest, the associated measurement deviations are less than 0.33% and 0.5° for signal amplitude and phase values, respectively. A modified monopole antenna array (composed of two interwoven eight-element sub-arrays), in conjunction with an updated motion-control system capable of independently moving the sub-arrays to various in-plane and cross-plane positions within the illumination chamber, has been configured in the new design for full volumetric data acquisition. Signal-to-noise ratios (SNRs) are more than adequate for all transmit/receive antenna pairs over the full frequency range and for the variety of in-plane and cross-plane configurations. For proximal receivers, in-plane SNRs greater than 80 dB are observed up to 2900 MHz, while cross-plane SNRs greater than 80 dB are seen for 6 cm sub-array spacing (for frequencies up to 1500 MHz). We demonstrate accurate

  2. 3D Electrical resistivity tomography monitoring of an artificial tracer injected within the hyporheic zone

    NASA Astrophysics Data System (ADS)

    Houzé, Clémence; Pessel, Marc; Durand, Veronique

    2016-04-01

    Due to the high complexity level of hyporheic flow paths, hydrological and biogeochemical processes which occur in this mixing place are not fully understood yet. Some previous studies made in flumes show that hyporheic flow is strongly connected to the streambed morphology and sediment heterogeneity . There is still a lack of practical field experiment considering a natural environment and representation of natural streambed heterogeneities will be always limited in laboratories. The purpose of this project is to propose an innovative method using 3D Electrical Resistivity Tomography (ERT) monitoring of an artificial tracer injection directly within the streambed sediments in order to visualize the water pathways within the hyporheic zone. Field experiment on a small stream was conducted using a plastic tube as an injection piezometer and home-made electrodes strips arranged in a rectangular form made of 180 electrodes (15 strips of 12 electrodes each). The injection of tracer (NaCl) lasted approximatively 90 minutes, and 24h monitoring with increasing step times was performed. The physical properties of the water are controlled by CTD probes installed upstream and downstream within the river. Inverse time-lapse tomographs show development and persistence of a conductive water plume around the injection point. Due to the low hydraulic conductivity of streambed sediments (clay and overlying loess), the tracer movement is barely visible, as it dilutes gradually in the pore water. Impact of boundary conditions on inversion results can lead to significant differences on images, especially in the shallow part of the profiles. Preferential paths of transport are not highlighted here, but this experiment allows to follow spatially and temporarily the evolution of the tracer in a complex natural environment .

  3. Comparative velocity structure of active Hawaiian volcanoes from 3-D onshore-offshore seismic tomography

    USGS Publications Warehouse

    Park, J.; Morgan, J.K.; Zelt, C.A.; Okubo, P.G.; Peters, L.; Benesh, N.

    2007-01-01

    We present a 3-D P-wave velocity model of the combined subaerial and submarine portions of the southeastern part of the Island of Hawaii, based on first-arrival seismic tomography of marine airgun shots recorded by the onland seismic network. Our model shows that high-velocity materials (6.5-7.0??km/s) lie beneath Kilauea's summit, Koae fault zone, and the upper Southwest Rift Zone (SWRZ) and upper and middle East Rift Zone (ERZ), indicative of magma cumulates within the volcanic edifice. A separate high-velocity body of 6.5-6.9??km/s within Kilauea's lower ERZ and upper Puna Ridge suggests a distinct body of magma cumulates, possibly connected to the summit magma cumulates at depth. The two cumulate bodies within Kilauea's ERZ may have undergone separate ductile flow seaward, influencing the submarine morphology of Kilauea's south flank. Low velocities (5.0-6.3??km/s) seaward of Kilauea's Hilina fault zone, and along Mauna Loa's seaward facing Kao'iki fault zone, are attributed to thick piles of volcaniclastic sediments deposited on the submarine flanks. Loihi seamount shows high-velocity anomalies beneath the summit and along the rift zones, similar to the interpreted magma cumulates below Mauna Loa and Kilauea volcanoes, and a low-velocity anomaly beneath the oceanic crust, probably indicative of melt within the upper mantle. Around Kilauea's submarine flank, a high-velocity anomaly beneath the outer bench suggests the presence of an ancient seamount that may obstruct outward spreading of the flank. Mauna Loa's southeast flank is also marked by a large, anomalously high-velocity feature (7.0-7.4??km/s), interpreted to define an inactive, buried volcanic rift zone, which might provide a new explanation for the westward migration of Mauna Loa's current SWRZ and the growth of Kilauea's SWRZ. ?? 2007 Elsevier B.V. All rights reserved.

  4. Micro 3D ERT tomography for data assimilation modelling of active root zone

    NASA Astrophysics Data System (ADS)

    Vanella, Daniela; Busato, Laura; Boaga, Jacopo; Cassiani, Giorgio; Binley, Andrew; Putti, Mario; Consoli, Simona

    2016-04-01

    Within the soil-plant-atmosphere system, root activity plays a fundamental role, as it connects different domains and allows a large part of the water and nutrient exchanges necessary for plant sustenance. The understanding of these processes is not only useful from an environmental point of view, making a fundamental contribution to the understanding of the critical zone dynamics, but also plays a pivotal role in precision agriculture, where the optimisation of water resources exploitation is mandatory and often carried out through deficit irrigation techniques. In this work, we present the results of non-invasive monitoring of the active root zone of two orange trees (Citrus sinensis, cv Tarocco Ippolito) located in an orange orchard in eastern Sicily (Italy) and drip irrigated with two different techniques: partial root drying and 100% crop evapotranspiration. The main goal of the monitoring activity is to assess possible differences between the developed root systems and the root water uptake between the two irrigation strategies. The monitoring is conducted using 3D micro-electrical resistivity tomography (ERT) based on an apparatus composed of a number of micro-boreholes (about 1.2 m deep) housing 12 electrodes each, plus a number of surface electrodes. Time-lapse measurements conducted both with long-term periodicity and short-term repetition before and after irrigation clearly highlight the presence and distribution of root water uptake zone both at shallow and larger depth, likely to correspond to zones utilized during the irrigation period (shallow) and during the time when the crop is not irrigated (deep). Subsidiary information is available in terms of precipitation, sap flow measurements and micrometeorological evapotranspiration estimates. This data ensemble lends itself to the assimilation into a variably saturated flow model, where both soil hydraulic parameters and root distribution shall be identified. Preliminary results in this directions show

  5. Micro 3D ERT tomography for data assimilation modelling of active root zone

    NASA Astrophysics Data System (ADS)

    Cassiani, G.; Boaga, J.; Busato, L.; Vanella, D.; Consoli, S.; Binley, A. M.

    2015-12-01

    Within the soil-plant-atmosphere system, root activity plays a fundamental role, as it connects different domains and allows a large part of the water and nutrient exchanges necessary for plant sustenance. The understanding of these processes is not only useful from an environmental point of view, making a fundamental contribution to the understanding of the critical zone dynamics, but also plays a pivotal role in precision agriculture, where the optimisation of water resources exploitation is mandatory and often carried out through deficit irrigation techniques. In this work, we present the results of non-invasive monitoring of the active root zone of two orange trees (Citrus sinensis, cv Tarocco Ippolito) located in an orange orchard in eastern Sicily (Italy) and drip irrigated with two different techniques: partial root drying and 100% crop evapotranspiration. The main goal of the monitoring activity is to assess possible differences between the developed root systems and the root water uptake between the two irrigation strategies. The monitoring is conducted using 3D micro-electrical resistivity tomography (ERT) based on an apparatus composed of a number of micro-boreholes (about 1.2 m deep) housing 12 electrodes each, plus a number of surface electrodes. Time-lapse measurements conducted both with long-term periodicity and short-term repetition before and after irrigation clearly highlight the presence and distribution of root water uptake zone both at shallow and larger depth, likely to correspond to zones utilized during the irrigation period (shallow) and during the time when the crop is not irrigated (deep). Subsidiary information is available in terms of precipitation, sap flow measurements and micrometeorological evapotranspiration estimates. This data ensemble lends itself to the assimilation into a variably saturated flow model, where both soil hydraulic parameters and root distribution shall be identified. Preliminary results in this directions show

  6. Lithospheric Structure of the Western North Anatolian Fault Zone from 3-D Teleseismic Tomography

    NASA Astrophysics Data System (ADS)

    Papaleo, E.

    2015-12-01

    The North Anatolian Fault Zone (NAFZ) is a 1500 km long active strike-slip fault that spans northern Turkey. During the past century a series of migrating earthquakes have sequentially activated different segments of the fault. The last major events of this sequence are the 1999 Izmit and Düzce earthquakes, which are consistent with a gradual westward migration in seismicity. The next active segment of the fault may be close to the city of Istanbul, posing a major risk for its population. Historically, the NAFZ exhibits a recurrent migrating sequence of high magnitude earthquakes along the fault zone, suggesting that it accommodates most of the plate motion between Anatolian and Eurasian plates in a narrow shear zone. From GPS studies following the Izmit and Düzce events, this motion does not appear to be constrained to the upper crust, and may extend at least to the lower crust. However, the geometry of the fault in the lower crust and upper mantle is at present poorly understood and previous tomographic studies do not provide a consistent picture of the velocity structure in this region. To better constrain the geometry of the shear zone at depth, in particular beneath the most recently active segment of the fault, an array of 70 temporary seismic stations with a 7 km spacing was deployed for 18 months as part of the FaultLab project. Amongst all the events recorded, those of magnitude ≥ 5 and situated between 27 and 98 degrees from the centre of the array were selected to perform 3D teleseismic tomography. Synthetic resolution tests indicate that structures as small as the average station spacing can be recovered to a depth of approximately 80 km. The work aims to provide a higher resolution image of the velocity structure beneath the western segment of the NAFZ, leading to a better understanding of the shear zone in the lower crust and upper mantle.

  7. The integration of 3-D cell printing and mesoscopic fluorescence molecular tomography of vascular constructs within thick hydrogel scaffolds.

    PubMed

    Zhao, Lingling; Lee, Vivian K; Yoo, Seung-Schik; Dai, Guohao; Intes, Xavier

    2012-07-01

    Developing methods that provide adequate vascular perfusion is an important step toward engineering large functional tissues. Meanwhile, an imaging modality to assess the three-dimensional (3-D) structures and functions of the vascular channels is lacking for thick matrices (>2 ≈ 3 mm). Herein, we report on an original approach to construct and image 3-D dynamically perfused vascular structures in thick hydrogel scaffolds. In this work, we integrated a robotic 3-D cell printing technology with a mesoscopic fluorescence molecular tomography imaging system, and demonstrated the capability of the platform to construct perfused collagen scaffolds with endothelial lining and to image both the fluid flow and fluorescent-labeled living endothelial cells at high-frame rates, with high sensitivity and accuracy. These results establish the potential of integrating both 3-D cell printing and fluorescence mesoscopic imaging for functional and molecular studies in complex tissue-engineered tissues.

  8. 3-D-Observation of Matrix of MIL 090657 Meteorite by Absorption-Phase Tomography

    NASA Technical Reports Server (NTRS)

    Miyama, Sugimoto; Tsuchiyama, Akira; Matsuno, Junya; Miyake, Akira; Nakano, Tsukasa; Uesugi, Kentaro; Takeuchi, Akihisa; Takigawa, Aki; Takayama, Akiko; Nakamura-Messenger, Keiko; Burton, Aaron S.; Messenger, Scott

    2017-01-01

    MIL 090657 meteorite (CR2.7) is one of the least altered primitive carbonaceous c hondrites [1]. This meteorite has amorphous silicates like GEMS (glass with embedded metal and sulfide), which are characteristically contained in cometary dust, in matrix [2,3] as with the Paris meteorite [4]. Three lithologies have been recognized; lithology-1 (L 1) dominated by submicron anhydrous silicates, lithology-2 (L2) by GEMS-like amorphous silicates and lithology-3 (L3) by phyllosilicates [2]. Organic materials are abundant in L 1 and L2 [2,3]. L 1 and L2 were further divided into sub-lithology respectively based on their textures and compositions [5]. These studies were performed by 2D SEM and TEM observations of sample surfaces and thin sections that are unable to reveal what constitute each lithology and how these lithologies are distributed and related to each other. This information will provide important insights into alteration and aggregation processes on asteroids and in the early solar nebula. In this study, MIL 090657 matrix was examined in 3D using two types of X-ray tomography; DET (dual-energy tomography) [6] and SIXM (scanning-imaging X-ray microscopy) [7]. Mineral phases can be discriminated based on absorption contrasts at two different X-ray energies in DET. In SIXM, materials composed of light elements such as water or organic materials can be identified based on phase and absorption contrasts. By combining these methods, we can discriminate not only organic materials from voids but also hydrous alteration products, such as hydrated silicates and carbonates, from anhydrous minerals [8]. In this study, we first observed cross sections of MIL 090657 matrix fragments C1 00 mm) in detail using FE-SEM/ EDS. Based on the results, three house-shaped samples (3 0 -50 mm) were extracted from L 1, L2 and their boundary (H1, H3 and H5, respectively) using FIB. 3D imaging of these samples were conducted at BL47XU of SPring-8, a synchrotron radiation facility, with

  9. Computed Tomography Imaging in Oncology.

    PubMed

    Forrest, Lisa J

    2016-05-01

    Computed tomography (CT) imaging has become the mainstay of oncology, providing accurate tumor staging and follow-up imaging to monitor treatment response. Presurgical evaluation of tumors is becoming commonplace and guides surgeons as to the extent and whether complete tumor resection is possible. CT imaging plays a crucial role in radiotherapy treatment planning. CT imaging in oncology has become ubiquitous in veterinary medicine because of increased availability of this imaging modality. This article focuses on CT cancer staging in veterinary oncology, CT imaging for surgical planning, and advances in CT simulation for radiation therapy planning.

  10. Computed tomography of stress fracture

    SciTech Connect

    Murcia, M.; Brennan, R.E.; Edeiken, J.

    1982-06-01

    An athletic young female developed gradual onset of pain in the right leg. Plain radiographs demonstrated solid periosteal reaction in the tibia compatible with stress fracture. She stopped sport activites but her pain continued. Follow-up radiographs of the tibia revealed changes suspicious for osteoid osteoma. Computed tomography (CT) scan demonstrated periosteal reaction, but in addition, lucent fracture lines in the tibial cortex were evident. CT obviated the need for more invasive diagnostic procedures in this patient. In selected cases CT may be useful to confirm the diagnosis of stress fracture when plain radiographic or routine tomographic studies are not diagnostic.

  11. Computed tomography of intrathoracic goiters

    SciTech Connect

    Bashist, B.; Ellis, K.; Gold, R.P.

    1983-03-01

    Ten patients with intrathoracic goiters were evaluated by computed tomography (CT). In comparison with chest radiographs, CT showed additional features helpful in suggesting the correct diagnosis. These observations included: (1) clear continuity with the cervical thyroid gland (8/10 cases); (2) well defined borders (9/10); (3) punctate, coarse, or ringlike calcifications (8/10); (4) nonhomogeneity (9/10) often with discrete, nonenhancing, low-density areas (6/10); (5) precontrast attenuation values at least 15 H greater than adjacent muscles (4/10) with more than 25 H after contrast enhancement (8/8); and (6) characteristic patterns of goiter extension into mediastinum.

  12. LLNL-Earth3D

    SciTech Connect

    2013-10-01

    Earth3D is a computer code designed to allow fast calculation of seismic rays and travel times through a 3D model of the Earth. LLNL is using this for earthquake location and global tomography efforts and such codes are of great interest to the Earth Science community.

  13. Linking snow microstructure to its macroscopic elastic stiffness tensor: A numerical homogenization method and its application to 3-D images from X-ray tomography

    NASA Astrophysics Data System (ADS)

    Wautier, A.; Geindreau, C.; Flin, F.

    2015-10-01

    The full 3-D macroscopic mechanical behavior of snow is investigated by solving kinematically uniform boundary condition problems derived from homogenization theories over 3-D images obtained by X-ray tomography. Snow is modeled as a porous cohesive material, and its mechanical stiffness tensor is computed within the framework of the elastic behavior of ice. The size of the optimal representative elementary volume, expressed in terms of correlation lengths, is determined through a convergence analysis of the computed effective properties. A wide range of snow densities is explored, and power laws with high regression coefficients are proposed to link the Young's and shear moduli of snow to its density. The degree of anisotropy of these properties is quantified, and Poisson's ratios are also provided. Finally, the influence of the main types of metamorphism (isothermal, temperature gradient, and wet snow metamorphism) on the elastic properties of snow and on their anisotropy is reported.

  14. Anthropological facial approximation in three dimensions (AFA3D): computer-assisted estimation of the facial morphology using geometric morphometrics.

    PubMed

    Guyomarc'h, Pierre; Dutailly, Bruno; Charton, Jérôme; Santos, Frédéric; Desbarats, Pascal; Coqueugniot, Hélène

    2014-11-01

    This study presents Anthropological Facial Approximation in Three Dimensions (AFA3D), a new computerized method for estimating face shape based on computed tomography (CT) scans of 500 French individuals. Facial soft tissue depths are estimated based on age, sex, corpulence, and craniometrics, and projected using reference planes to obtain the global facial appearance. Position and shape of the eyes, nose, mouth, and ears are inferred from cranial landmarks through geometric morphometrics. The 100 estimated cutaneous landmarks are then used to warp a generic face to the target facial approximation. A validation by re-sampling on a subsample demonstrated an average accuracy of c. 4 mm for the overall face. The resulting approximation is an objective probable facial shape, but is also synthetic (i.e., without texture), and therefore needs to be enhanced artistically prior to its use in forensic cases. AFA3D, integrated in the TIVMI software, is available freely for further testing.

  15. Association of achondroplasia with Down syndrome: difficulty in prenatal diagnosis by sonographic and 3-D helical computed tomographic analyses.

    PubMed

    Kaga, Akimune; Murotsuki, Jun; Kamimura, Miki; Kimura, Masato; Saito-Hakoda, Akiko; Kanno, Junko; Hoshi, Kazuhiko; Kure, Shigeo; Fujiwara, Ikuma

    2015-05-01

    Achondroplasia and Down syndrome are relatively common conditions individually. But co-occurrence of both conditions in the same patient is rare and there have been no reports of fetal analysis of this condition by prenatal sonographic and three-dimensional (3-D) helical computed tomography (CT). Prenatal sonographic findings seen in persons with Down syndrome, such as a thickened nuchal fold, cardiac defects, and echogenic bowel were not found in the patient. A prenatal 3-D helical CT revealed a large head with frontal bossing, metaphyseal flaring of the long bones, and small iliac wings, which suggested achondroplasia. In a case with combination of achondroplasia and Down syndrome, it may be difficult to diagnose the co-occurrence prenatally without typical markers of Down syndrome.

  16. Theoretical analysis of volume moiré tomography based on double orthogonal gratings for real 3D flow fields diagnosis

    NASA Astrophysics Data System (ADS)

    Sun, Nan; Song, Yang; Wang, Jia; Li, Zhen-hua; He, An-zhi

    2012-11-01

    Moiré tomography is an important technique to diagnose the flow field. However, the traditional moiré deflectometry cannot meet the requirements of Volume Moiré Tomography (VMT). In this Letter, an improved moiré deflected system based on double orthogonal gratings is introduced for real 3-D reconstruction. The proposed method could obtain the first-order partial derivatives in two vertical directions of the projection in one time. Comparing with the traditional moiré deflectometry, the proposed system is more effective and easier to realize the multi-direction data acquisition.

  17. Optical cone beam tomography of Cherenkov-mediated signals for fast 3D dosimetry of x-ray photon beams in water

    SciTech Connect

    Glaser, Adam K. E-mail: Brian.W.Pogue@dartmouth.edu; Andreozzi, Jacqueline M.; Zhang, Rongxiao; Pogue, Brian W. E-mail: Brian.W.Pogue@dartmouth.edu; Gladstone, David J.

    2015-07-15

    Purpose: To test the use of a three-dimensional (3D) optical cone beam computed tomography reconstruction algorithm, for estimation of the imparted 3D dose distribution from megavoltage photon beams in a water tank for quality assurance, by imaging the induced Cherenkov-excited fluorescence (CEF). Methods: An intensified charge-coupled device coupled to a standard nontelecentric camera lens was used to tomographically acquire two-dimensional (2D) projection images of CEF from a complex multileaf collimator (MLC) shaped 6 MV linear accelerator x-ray photon beam operating at a dose rate of 600 MU/min. The resulting projections were used to reconstruct the 3D CEF light distribution, a potential surrogate of imparted dose, using a Feldkamp–Davis–Kress cone beam back reconstruction algorithm. Finally, the reconstructed light distributions were compared to the expected dose values from one-dimensional diode scans, 2D film measurements, and the 3D distribution generated from the clinical Varian ECLIPSE treatment planning system using a gamma index analysis. A Monte Carlo derived correction was applied to the Cherenkov reconstructions to account for beam hardening artifacts. Results: 3D light volumes were successfully reconstructed over a 400 × 400 × 350 mm{sup 3} volume at a resolution of 1 mm. The Cherenkov reconstructions showed agreement with all comparative methods and were also able to recover both inter- and intra-MLC leaf leakage. Based upon a 3%/3 mm criterion, the experimental Cherenkov light measurements showed an 83%–99% pass fraction depending on the chosen threshold dose. Conclusions: The results from this study demonstrate the use of optical cone beam computed tomography using CEF for the profiling of the imparted dose distribution from large area megavoltage photon beams in water.

  18. Optical cone beam tomography of Cherenkov-mediated signals for fast 3D dosimetry of x-ray photon beams in water

    PubMed Central

    Glaser, Adam K.; Andreozzi, Jacqueline M.; Zhang, Rongxiao; Pogue, Brian W.; Gladstone, David J.

    2015-01-01

    Purpose: To test the use of a three-dimensional (3D) optical cone beam computed tomography reconstruction algorithm, for estimation of the imparted 3D dose distribution from megavoltage photon beams in a water tank for quality assurance, by imaging the induced Cherenkov-excited fluorescence (CEF). Methods: An intensified charge-coupled device coupled to a standard nontelecentric camera lens was used to tomographically acquire two-dimensional (2D) projection images of CEF from a complex multileaf collimator (MLC) shaped 6 MV linear accelerator x-ray photon beam operating at a dose rate of 600 MU/min. The resulting projections were used to reconstruct the 3D CEF light distribution, a potential surrogate of imparted dose, using a Feldkamp–Davis–Kress cone beam back reconstruction algorithm. Finally, the reconstructed light distributions were compared to the expected dose values from one-dimensional diode scans, 2D film measurements, and the 3D distribution generated from the clinical Varian ECLIPSE treatment planning system using a gamma index analysis. A Monte Carlo derived correction was applied to the Cherenkov reconstructions to account for beam hardening artifacts. Results: 3D light volumes were successfully reconstructed over a 400 × 400 × 350 mm3 volume at a resolution of 1 mm. The Cherenkov reconstructions showed agreement with all comparative methods and were also able to recover both inter- and intra-MLC leaf leakage. Based upon a 3%/3 mm criterion, the experimental Cherenkov light measurements showed an 83%–99% pass fraction depending on the chosen threshold dose. Conclusions: The results from this study demonstrate the use of optical cone beam computed tomography using CEF for the profiling of the imparted dose distribution from large area megavoltage photon beams in water. PMID:26133613

  19. Electro-holography display using computer generated hologram of 3D objects based on projection spectra

    NASA Astrophysics Data System (ADS)

    Huang, Sujuan; Wang, Duocheng; He, Chao

    2012-11-01

    A new method of synthesizing computer-generated hologram of three-dimensional (3D) objects is proposed from their projection images. A series of projection images of 3D objects are recorded with one-dimensional azimuth scanning. According to the principles of paraboloid of revolution in 3D Fourier space and 3D central slice theorem, spectra information of 3D objects can be gathered from their projection images. Considering quantization error of horizontal and vertical directions, the spectrum information from each projection image is efficiently extracted in double circle and four circles shape, to enhance the utilization of projection spectra. Then spectra information of 3D objects from all projection images is encoded into computer-generated hologram based on Fourier transform using conjugate-symmetric extension. The hologram includes 3D information of objects. Experimental results for numerical reconstruction of the CGH at different distance validate the proposed methods and show its good performance. Electro-holographic reconstruction can be realized by using an electronic addressing reflective liquid-crystal display (LCD) spatial light modulator. The CGH from the computer is loaded onto the LCD. By illuminating a reference light from a laser source to the LCD, the amplitude and phase information included in the CGH will be reconstructed due to the diffraction of the light modulated by the LCD.

  20. Additive Manufacturing of Anatomical Models from Computed Tomography Scan Data.

    PubMed

    Gür, Y

    2014-12-01

    The purpose of the study presented here was to investigate the manufacturability of human anatomical models from Computed Tomography (CT) scan data via a 3D desktop printer which uses fused deposition modelling (FDM) technology. First, Digital Imaging and Communications in Medicine (DICOM) CT scan data were converted to 3D Standard Triangle Language (STL) format by using In Vaselius digital imaging program. Once this STL file is obtained, a 3D physical version of the anatomical model can be fabricated by a desktop 3D FDM printer. As a case study, a patient's skull CT scan data was considered, and a tangible version of the skull was manufactured by a 3D FDM desktop printer. During the 3D printing process, the skull was built using acrylonitrile-butadiene-styrene (ABS) co-polymer plastic. The printed model showed that the 3D FDM printing technology is able to fabricate anatomical models with high accuracy. As a result, the skull model can be used for preoperative surgical planning, medical training activities, implant design and simulation to show the potential of the FDM technology in medical field. It will also improve communication between medical stuff and patients. Current result indicates that a 3D desktop printer which uses FDM technology can be used to obtain accurate anatomical models.

  1. 3D Lifetime Tomography Reveals How CdCl2 Improves Recombination Throughout CdTe Solar Cells.

    PubMed

    Barnard, Edward S; Ursprung, Benedikt; Colegrove, Eric; Moutinho, Helio R; Borys, Nicholas J; Hardin, Brian E; Peters, Craig H; Metzger, Wyatt K; Schuck, P James

    2017-01-01

    Using two-photon tomography, carrier lifetimes are mapped in polycrystalline CdTe photovoltaic devices. These 3D maps probe subsurface carrier dynamics that are inaccessible with traditional optical techniques. They reveal that CdCl2 treatment of CdTe solar cells suppresses nonradiative recombination and enhances carrier lifetimes throughout the film with substantial improvements particularly near subsurface grain boundaries and the critical buried p-n junction.

  2. 3D Lifetime Tomography Reveals How CdCl 2 Improves Recombination Throughout CdTe Solar Cells

    SciTech Connect

    Barnard, Edward S.; Ursprung, Benedikt; Colegrove, Eric; Moutinho, Helio R.; Borys, Nicholas J.; Hardin, Brian E.; Peters, Craig H.; Metzger, Wyatt K.; Schuck, P. James

    2016-11-15

    Using two-photon tomography, carrier lifetimes are mapped in polycrystalline CdTe photovoltaic devices. These 3D maps probe subsurface carrier dynamics that are inaccessible with traditional optical techniques. They reveal that CdCl2 treatment of CdTe solar cells suppresses nonradiative recombination and enhances carrier lifetimes throughout the film with substantial improvements particularly near subsurface grain boundaries and the critical buried p-n junction.

  3. Dimensionality Reduction Based Optimization Algorithm for Sparse 3-D Image Reconstruction in Diffuse Optical Tomography.

    PubMed

    Bhowmik, Tanmoy; Liu, Hanli; Ye, Zhou; Oraintara, Soontorn

    2016-03-04

    Diffuse optical tomography (DOT) is a relatively low cost and portable imaging modality for reconstruction of optical properties in a highly scattering medium, such as human tissue. The inverse problem in DOT is highly ill-posed, making reconstruction of high-quality image a critical challenge. Because of the nature of sparsity in DOT, sparsity regularization has been utilized to achieve high-quality DOT reconstruction. However, conventional approaches using sparse optimization are computationally expensive and have no selection criteria to optimize the regularization parameter. In this paper, a novel algorithm, Dimensionality Reduction based Optimization for DOT (DRO-DOT), is proposed. It reduces the dimensionality of the inverse DOT problem by reducing the number of unknowns in two steps and thereby makes the overall process fast. First, it constructs a low resolution voxel basis based on the sensing-matrix properties to find an image support. Second, it reconstructs the sparse image inside this support. To compensate for the reduced sensitivity with increasing depth, depth compensation is incorporated in DRO-DOT. An efficient method to optimally select the regularization parameter is proposed for obtaining a high-quality DOT image. DRO-DOT is also able to reconstruct high-resolution images even with a limited number of optodes in a spatially limited imaging set-up.

  4. Dimensionality Reduction Based Optimization Algorithm for Sparse 3-D Image Reconstruction in Diffuse Optical Tomography

    PubMed Central

    Bhowmik, Tanmoy; Liu, Hanli; Ye, Zhou; Oraintara, Soontorn

    2016-01-01

    Diffuse optical tomography (DOT) is a relatively low cost and portable imaging modality for reconstruction of optical properties in a highly scattering medium, such as human tissue. The inverse problem in DOT is highly ill-posed, making reconstruction of high-quality image a critical challenge. Because of the nature of sparsity in DOT, sparsity regularization has been utilized to achieve high-quality DOT reconstruction. However, conventional approaches using sparse optimization are computationally expensive and have no selection criteria to optimize the regularization parameter. In this paper, a novel algorithm, Dimensionality Reduction based Optimization for DOT (DRO-DOT), is proposed. It reduces the dimensionality of the inverse DOT problem by reducing the number of unknowns in two steps and thereby makes the overall process fast. First, it constructs a low resolution voxel basis based on the sensing-matrix properties to find an image support. Second, it reconstructs the sparse image inside this support. To compensate for the reduced sensitivity with increasing depth, depth compensation is incorporated in DRO-DOT. An efficient method to optimally select the regularization parameter is proposed for obtaining a high-quality DOT image. DRO-DOT is also able to reconstruct high-resolution images even with a limited number of optodes in a spatially limited imaging set-up. PMID:26940661

  5. Phase-retrieved optical projection tomography for 3D imaging through scattering layers

    NASA Astrophysics Data System (ADS)

    Ancora, Daniele; Di Battista, Diego; Giasafaki, Georgia; Psycharakis, Stylianos; Liapis, Evangelos; Zacharopoulos, Athanasios; Zacharakis, Giannis

    2016-03-01

    Recently great progress has been made in biological and biomedical imaging by combining non-invasive optical methods, novel adaptive light manipulation and computational techniques for intensity-based phase recovery and three dimensional image reconstruction. In particular and in relation to the work presented here, Optical Projection Tomography (OPT) is a well-established technique for imaging mostly transparent absorbing biological models such as C. Elegans and Danio Rerio. On the contrary, scattering layers like the cocoon surrounding the Drosophila during the pupae stage constitutes a challenge for three dimensional imaging through such a complex structure. However, recent studies enabled image reconstruction through scattering curtains up to few transport mean free paths via phase retrieval iterative algorithms allowing to uncover objects hidden behind complex layers. By combining these two techniques we explore the possibility to perform a three dimensional image reconstruction of fluorescent objects embedded between scattering layers without compromising its structural integrity. Dynamical cross correlation registration was implemented for the registration process due to translational and flipping ambiguity of the phase retrieval problem, in order to provide the correct aligned set of data to perform the back-projection reconstruction. We have thus managed to reconstruct a hidden complex object between static scattering curtains and compared with the effective reconstruction to fully understand the process before the in-vivo biological implementation.

  6. Computer tomography of large dust clouds in complex plasmas.

    PubMed

    Killer, Carsten; Himpel, Michael; Melzer, André

    2014-10-01

    The dust density is a central parameter of a dusty plasma. Here, a tomography setup for the determination of the three-dimensionally resolved density distribution of spatially extended dust clouds is presented. The dust clouds consist of micron-sized particles confined in a radio frequency argon plasma, where they fill almost the entire discharge volume. First, a line-of-sight integrated dust density is obtained from extinction measurements, where the incident light from an LED panel is scattered and absorbed by the dust. Performing these extinction measurements from many different angles allows the reconstruction of the 3D dust density distribution, analogous to a computer tomography in medical applications.

  7. Computer tomography of large dust clouds in complex plasmas

    SciTech Connect

    Killer, Carsten; Himpel, Michael; Melzer, André

    2014-10-15

    The dust density is a central parameter of a dusty plasma. Here, a tomography setup for the determination of the three-dimensionally resolved density distribution of spatially extended dust clouds is presented. The dust clouds consist of micron-sized particles confined in a radio frequency argon plasma, where they fill almost the entire discharge volume. First, a line-of-sight integrated dust density is obtained from extinction measurements, where the incident light from an LED panel is scattered and absorbed by the dust. Performing these extinction measurements from many different angles allows the reconstruction of the 3D dust density distribution, analogous to a computer tomography in medical applications.

  8. Time- and computation-efficient calibration of MEMS 3D accelerometers and gyroscopes.

    PubMed

    Stančin, Sara; Tomažič, Sašo

    2014-08-13

    We propose calibration methods for microelectromechanical system (MEMS) 3D accelerometers and gyroscopes that are efficient in terms of time and computational complexity. The calibration process for both sensors is simple, does not require additional expensive equipment, and can be performed in the field before or between motion measurements. The methods rely on a small number of defined calibration measurements that are used to obtain the values of 12 calibration parameters. This process enables the static compensation of sensor inaccuracies. The values detected by the 3D sensor are interpreted using a generalized 3D sensor model. The model assumes that the values detected by the sensor are equal to the projections of the measured value on the sensor sensitivity axes. Although this finding is trivial for 3D accelerometers, its validity for 3D gyroscopes is not immediately apparent; thus, this paper elaborates on this latter topic. For an example sensor device, calibration parameters were established using calibration measurements of approximately 1.5 min in duration for the 3D accelerometer and 2.5 min in duration for the 3D gyroscope. Correction of each detected 3D value using the established calibration parameters in further measurements requires only nine addition and nine multiplication operations.

  9. Extended gray level co-occurrence matrix computation for 3D image volume

    NASA Astrophysics Data System (ADS)

    Salih, Nurulazirah M.; Dewi, Dyah Ekashanti Octorina

    2017-02-01

    Gray Level Co-occurrence Matrix (GLCM) is one of the main techniques for texture analysis that has been widely used in many applications. Conventional GLCMs usually focus on two-dimensional (2D) image texture analysis only. However, a three-dimensional (3D) image volume requires specific texture analysis computation. In this paper, an extended 2D to 3D GLCM approach based on the concept of multiple 2D plane positions and pixel orientation directions in the 3D environment is proposed. The algorithm was implemented by breaking down the 3D image volume into 2D slices based on five different plane positions (coordinate axes and oblique axes) resulting in 13 independent directions, then calculating the GLCMs. The resulted GLCMs were averaged to obtain normalized values, then the 3D texture features were calculated. A preliminary examination was performed on a 3D image volume (64 x 64 x 64 voxels). Our analysis confirmed that the proposed technique is capable of extracting the 3D texture features from the extended GLCMs approach. It is a simple and comprehensive technique that can contribute to the 3D image analysis.

  10. Multi-GPU Jacobian Accelerated Computing for Soft Field Tomography

    PubMed Central

    Borsic, A.; Attardo, E. A.; Halter, R. J.

    2012-01-01

    Image reconstruction in soft-field tomography is based on an inverse problem formulation, where a forward model is fitted to the data. In medical applications, where the anatomy presents complex shapes, it is common to use Finite Element Models to represent the volume of interest and to solve a partial differential equation that models the physics of the system. Over the last decade, there has been a shifting interest from 2D modeling to 3D modeling, as the underlying physics of most problems are three-dimensional. Though the increased computational power of modern computers allows working with much larger FEM models, the computational time required to reconstruct 3D images on a fine 3D FEM model can be significant, on the order of hours. For example, in Electrical Impedance Tomography applications using a dense 3D FEM mesh with half a million elements, a single reconstruction iteration takes approximately 15 to 20 minutes with optimized routines running on a modern multi-core PC. It is desirable to accelerate image reconstruction to enable researchers to more easily and rapidly explore data and reconstruction parameters. Further, providing high-speed reconstructions are essential for some promising clinical application of EIT. For 3D problems 70% of the computing time is spent building the Jacobian matrix, and 25% of the time in forward solving. In the present work, we focus on accelerating the Jacobian computation by using single and multiple GPUs. First, we discuss an optimized implementation on a modern multi-core PC architecture and show how computing time is bounded by the CPU-to-memory bandwidth; this factor limits the rate at which data can be fetched by the CPU. Gains associated with use of multiple CPU cores are minimal, since data operands cannot be fetched fast enough to saturate the processing power of even a single CPU core. GPUs have a much faster memory bandwidths compared to CPUs and better parallelism. We are able to obtain acceleration factors of

  11. Computing 3-D structure of rigid objects using stereo and motion

    NASA Technical Reports Server (NTRS)

    Nguyen, Thinh V.

    1987-01-01

    Work performed as a step toward an intelligent automatic machine vision system for 3-D imaging is discussed. The problem considered is the quantitative 3-D reconstruction of rigid objects. Motion and stereo are the two clues considered in this system. The system basically consists of three processes: the low level process to extract image features, the middle level process to establish the correspondence in the stereo (spatial) and motion (temporal) modalities, and the high level process to compute the 3-D coordinates of the corner points by integrating the spatial and temporal correspondences.

  12. Computed tomography of Krukenberg tumors

    SciTech Connect

    Cho, K.C.; Gold, B.M.

    1985-08-01

    Computed tomography (CT) of three patients with Kurkenberg tumor was reviewed retrospectively. CT showed large, lobulated, multicystic masses with soft-tissue components, indistinguishable from primary ovarian carcinoma. Much has been written about metastatic ovarian tumor, but this is the first report in the radiologic literature about their CT features. The authors emphasize the importance of recognizing the ovary as a frequent site of metastases and the proper approach to this problem. In patients with a history of colon or gastric carcinoma, the mixed cystic and solid ovarian mass on CT should be regarded as metastatic tumor until proven otherwise. A careful search for gastrointestinal tract signs or symptoms should be done in any patient with a pelvic tumor. When CT is done for evaluation of ovarian tumor, the stomach and colon should be carefully evaluated, and the ovaries routinely examined in the preoperative CT staging of gastric or colon carcinoma.

  13. Single photon emission computed tomography

    SciTech Connect

    Piez, C.W. Jr.; Holman, B.L.

    1985-07-01

    Single photon emission computed tomography (SPECT) is becoming an increasingly important part of routine clinical nuclear medicine. By providing tomographic reconstructions in multiple planes through the patient, SPECT expands the clinical applications in nuclear medicine as well as providing better contrast, edge definition and separation of target from background activities. Imaging techniques have been developed for the evaluation of regional cerebral blood flow using radiolabeled amines. Thus, cerebral functional imaging can be used in the diagnosis of acute cerebral infarction, cerebral vascular disease, dementia and epilepsy. SPECT plays a complementary role in the evaluation of coronary artery disease, particularly when it is coupled with thallium-201 and exercise testing. SPECT extends our diagnostic capabilities in additional areas, such as liver and bone scintigraphy as well as tumor imaging with gallium-67.

  14. 3-D field computation: The near-triumph of commerical codes

    SciTech Connect

    Turner, L.R.

    1995-07-01

    In recent years, more and more of those who design and analyze magnets and other devices are using commercial codes rather than developing their own. This paper considers the commercial codes and the features available with them. Other recent trends with 3-D field computation include parallel computation and visualization methods such as virtual reality systems.

  15. Multiscale microstructural characterization of Sn-rich alloys by three dimensional (3D) X-ray synchrotron tomography and focused ion beam (FIB) tomography

    SciTech Connect

    Yazzie, K.E.; Williams, J.J.; Phillips, N.C.; De Carlo, F.; Chawla, N.

    2012-08-15

    Sn-rich (Pb-free) alloys serve as electrical and mechanical interconnects in electronic packaging. It is critical to quantify the microstructures of Sn-rich alloys to obtain a fundamental understanding of their properties. In this work, the intermetallic precipitates in Sn-3.5Ag and Sn-0.7Cu, and globular lamellae in Sn-37Pb solder joints were visualized and quantified using 3D X-ray synchrotron tomography and focused ion beam (FIB) tomography. 3D reconstructions were analyzed to extract statistics on particle size and spatial distribution. In the Sn-Pb alloy the interconnectivity of Sn-rich and Pb-rich constituents was quantified. It will be shown that multiscale characterization using 3D X-ray and FIB tomography enabled the characterization of the complex morphology, distribution, and statistics of precipitates and contiguous phases over a range of length scales. - Highlights: Black-Right-Pointing-Pointer Multiscale characterization by X-ray synchrotron and focused ion beam tomography. Black-Right-Pointing-Pointer Characterized microstructural features in several Sn-based alloys. Black-Right-Pointing-Pointer Quantified size, fraction, and clustering of microstructural features.

  16. A new 3D computational model for shaped charge jet breakup

    SciTech Connect

    Zernow, L.; Chapyak, E.J.; Mosso, S.J.

    1996-09-01

    This paper reviews prior 1D and 2D axisymmetric, analytical and computational studies, as well as empirical studies of the shaped charge jet particulation problem and discusses their associated insights and problems. It proposes a new 3D computational model of the particulation process, based upon a simplified version of the observed counter-rotating, double helical surface perturbations, found on softly recovered shaped charge jet particles, from both copper and tantalum jets. This 3D approach contrasts with the random, axisymmetric surface perturbations which have previously been used, to try to infer the observed length distribution of jet particles, on the basis of the most unstable wavelength concept, which leads to the expectation of a continuous distribution of particle lengths. The 3D model, by its very nature, leads to a non-random, periodic distribution of potential initial necking loci, on alternate sides of the stretching jet. This in turn infers a potentially periodic, overlapping, multi-modal distribution of associated jet particle lengths. Since it is unlikely that all potential initial necking sites will be activated simultaneously, the 3D model also suggests that longer jet particles containing partial, but unseparated necks, should be observed fairly often. The computational analysis is in its very early stages and the problems involved in inserting the two helical grooves and in defining the initial conditions and boundary conditions for the computation will be discussed. Available initial results from the 3D computation will be discussed and interpreted.

  17. Understanding Plasticity and Fracture in Aluminum Alloys and their Composites by 3D X-ray Synchrotron Tomography and Microdiffraction

    NASA Astrophysics Data System (ADS)

    Hruby, Peter

    Aluminum alloys and their composites are attractive materials for applications requiring high strength-to-weight ratios and reasonable cost. Many of these applications, such as those in the aerospace industry, undergo fatigue loading. An understanding of the microstructural damage that occurs in these materials is critical in assessing their fatigue resistance. Two distinct experimental studies were performed to further the understanding of fatigue damage mechanisms in aluminum alloys and their composites, specifically fracture and plasticity. Fatigue resistance of metal matrix composites (MMCs) depends on many aspects of composite microstructure. Fatigue crack growth behavior is particularly dependent on the reinforcement characteristics and matrix microstructure. The goal of this work was to obtain a fundamental understanding of fatigue crack growth behavior in SiC particle-reinforced 2080 Al alloy composites. In situ X-ray synchrotron tomography was performed on two samples at low (R=0.1) and at high (R=0.6) R-ratios. The resulting reconstructed images were used to obtain three-dimensional (3D) rendering of the particles and fatigue crack. Behaviors of the particles and crack, as well as their interaction, were analyzed and quantified. Four-dimensional (4D) visual representations were constructed to aid in the overall understanding of damage evolution. During fatigue crack growth in ductile materials, a plastic zone is created in the region surrounding the crack tip. Knowledge of the plastic zone is important for the understanding of fatigue crack formation as well as subsequent growth behavior. The goal of this work was to quantify the 3D size and shape of the plastic zone in 7075 Al alloys. X-ray synchrotron tomography and Laue microdiffraction were used to non-destructively characterize the volume surrounding a fatigue crack tip. The precise 3D crack profile was segmented from the reconstructed tomography data. Depth-resolved Laue patterns were obtained using

  18. 3D Slicer as an Image Computing Platform for the Quantitative Imaging Network

    PubMed Central

    Fedorov, Andriy; Beichel, Reinhard; Kalpathy-Cramer, Jayashree; Finet, Julien; Fillion-Robin, Jean-Christophe; Pujol, Sonia; Bauer, Christian; Jennings, Dominique; Fennessy, Fiona; Sonka, Milan; Buatti, John; Aylward, Stephen; Miller, James V.; Pieper, Steve; Kikinis, Ron

    2012-01-01

    Quantitative analysis has tremendous but mostly unrealized potential in healthcare to support objective and accurate interpretation of the clinical imaging. In 2008, the National Cancer Institute began building the Quantitative Imaging Network (QIN) initiative with the goal of advancing quantitative imaging in the context of personalized therapy and evaluation of treatment response. Computerized analysis is an important component contributing to reproducibility and efficiency of the quantitative imaging techniques. The success of quantitative imaging is contingent on robust analysis methods and software tools to bring these methods from bench to bedside. 3D Slicer is a free open source software application for medical image computing. As a clinical research tool, 3D Slicer is similar to a radiology workstation that supports versatile visualizations but also provides advanced functionality such as automated segmentation and registration for a variety of application domains. Unlike a typical radiology workstation, 3D Slicer is free and is not tied to specific hardware. As a programming platform, 3D Slicer facilitates translation and evaluation of the new quantitative methods by allowing the biomedical researcher to focus on the implementation of the algorithm, and providing abstractions for the common tasks of data communication, visualization and user interface development. Compared to other tools that provide aspects of this functionality, 3D Slicer is fully open source and can be readily extended and redistributed. In addition, 3D Slicer is designed to facilitate the development of new functionality in the form of 3D Slicer extensions. In this paper, we present an overview of 3D Slicer as a platform for prototyping, development and evaluation of image analysis tools for clinical research applications. To illustrate the utility of the platform in the scope of QIN, we discuss several use cases of 3D Slicer by the existing QIN teams, and we elaborate on the future

  19. Complementary X-ray tomography techniques for histology-validated 3D imaging of soft and hard tissues using plaque-containing blood vessels as examples.

    PubMed

    Holme, Margaret N; Schulz, Georg; Deyhle, Hans; Weitkamp, Timm; Beckmann, Felix; Lobrinus, Johannes A; Rikhtegar, Farhad; Kurtcuoglu, Vartan; Zanette, Irene; Saxer, Till; Müller, Bert

    2014-01-01

    A key problem in X-ray computed tomography is choosing photon energies for postmortem specimens containing both soft and hard tissues. Increasing X-ray energy reduces image artifacts from highly absorbing hard tissues including plaque, but it simultaneously decreases contrast in soft tissues including the endothelium. Therefore, identifying the lumen within plaque-containing vessels is challenging. Destructive histology, the gold standard for tissue evaluation, reaches submicron resolution in two dimensions, whereas slice thickness limits spatial resolution in the third. We present a protocol to systematically analyze heterogeneous tissues containing weakly and highly absorbing components in the original wet state, postmortem. Taking the example of atherosclerotic human coronary arteries, the successively acquired 3D data of benchtop and synchrotron radiation-based tomography are validated by histology. The entire protocol requires ∼20 working days, enables differentiation between plaque, muscle and fat tissues without using contrast agents and permits blood flow simulations in vessels with plaque-induced constrictions.

  20. Prospectively gated cardiac computed tomography.

    PubMed

    Moore, S C; Judy, P F; Garnic, J D; Kambic, G X; Bonk, F; Cochran, G; Margosian, P; McCroskey, W; Foote, F

    1983-01-01

    A fourth-generation scanner has been modified to perform prospectively gated cardiac computed tomography (CT). A computer program monitors the electrocardiogram (ECG) and predicts when to initiate the next scan in a gated series in order to acquire all projection data for a desired phase of the heart cycle. The system has been tested with dogs and has produced cross-sectional images of all phases of the cardiac cycle. Eight to ten scans per series were sufficient to obtain reproducible images of each transverse section in the end-diastolic and end-systolic phases. The radiation dose to the skin was approximately 1.4 cGy per scan. The prospectively gated system is more than twice as efficient as a retrospectively gated system in obtaining complete angular projection data for a 10% heart cycle window. A temporal smoothing technique to suppress reconstruction artifacts due to sorting inconsistent projection data was developed and evaluated. Image noise was reduced by averaging together any overlapping projection data. Prospectively gated cardiac CT has also been used to demonstrate that the error in attenuation measured with a single nongated CT scan through the heart can be as large as 50-60 CT numbers outside the heart in the lung field.

  1. Meta!Blast computer game: a pipeline from science to 3D art to education

    NASA Astrophysics Data System (ADS)

    Schneller, William; Campbell, P. J.; Bassham, Diane; Wurtele, Eve Syrkin

    2012-03-01

    Meta!Blast (http://www.metablast.org) is designed to address the challenges students often encounter in understanding cell and metabolic biology. Developed by faculty and students in biology, biochemistry, computer science, game design, pedagogy, art and story, Meta!Blast is being created using Maya (http://usa.autodesk.com/maya/) and the Unity 3D (http://unity3d.com/) game engine, for Macs and PCs in classrooms; it has also been exhibited in an immersive environment. Here, we describe the pipeline from protein structural data and holographic information to art to the threedimensional (3D) environment to the game engine, by which we provide a publicly-available interactive 3D cellular world that mimics a photosynthetic plant cell.

  2. Transient Hydraulic Tomography in the Field: 3-D K Estimation and Validation in a Highly Heterogeneous Unconfined Aquifer

    NASA Astrophysics Data System (ADS)

    Hochstetler, D. L.; Barrash, W.; Kitanidis, P. K.

    2014-12-01

    Characterizing subsurface hydraulic properties is essential for predicting flow and transport, and thus, for making informed decisions, such as selection and execution of a groundwater remediation strategy; however, obtaining accurate estimates at the necessary resolution with quantified uncertainty is an ongoing challenge. For over a decade, the development of hydraulic tomography (HT) - i.e., conducting a series of discrete interval hydraulic tests, observing distributed pressure signals, and analyzing the data through inversion of all tests together - has shown promise as a subsurface imaging method. Numerical and laboratory 3-D HT studies have enhanced and validated such methodologies, but there have been far fewer 3-D field characterization studies. We use 3-D transient hydraulic tomography (3-D THT) to characterize a highly heterogeneous unconfined alluvial aquifer at an active industrial site near Assemini, Italy. With 26 pumping tests conducted from 13 isolated vertical locations, and pressure responses measured at 63 spatial locations through five clusters of continuous multichannel tubing, we recorded over 800 drawdown curves during the field testing. Selected measurements from each curve were inverted in order to obtain an estimate of the distributed hydraulic conductivity field K(x) as well as uniform ("effective") values of specific storage Ss and specific yield Sy. The estimated K values varied across seven orders of magnitude, suggesting that this is one of the most heterogeneous sites at which HT has ever been conducted. Furthermore, these results are validated using drawdown observations from seven independent tests with pumping performed at multiple locations other than the main pumping well. The validation results are encouraging, especially given the uncertain nature of the problem. Overall, this research demonstrates the ability of 3-D THT to provide high-resolution of structure and local K at a non-research site at the scale of a contaminant

  3. Plant Tissues in 3D via X-Ray Tomography: Simple Contrasting Methods Allow High Resolution Imaging

    PubMed Central

    Staedler, Yannick M.; Masson, David; Schönenberger, Jürg

    2013-01-01

    Computed tomography remains strongly underused in plant sciences despite its high potential in delivering detailed 3D phenotypical information because of the low X-ray absorption of most plant tissues. Existing protocols to study soft tissues display poor performance, especially when compared to those used on animals. More efficient protocols to study plant material are therefore needed. Flowers of Arabidopsis thaliana and Marcgravia caudata were immersed in a selection of contrasting agents used to treat samples for transmission electron microscopy. Grayscale values for floral tissues and background were measured as a function of time. Contrast was quantified via a contrast index. The thick buds of Marcgravia were scanned to determine which contrasting agents best penetrate thick tissues. The highest contrast increase with cytoplasm-rich tissues was obtained with phosphotungstate, whereas osmium tetroxide and bismuth tatrate displayed the highest contrast increase with vacuolated tissues. Phosphotungstate also displayed the best sample penetration. Furthermore, infiltration with phosphotungstate allowed imaging of all plants parts at a high resolution of 3 µm, which approaches the maximum resolution of our equipment: 1.5 µm. The high affinity of phosphotungstate for vasculature, cytoplasm-rich tissue, and pollen causes these tissues to absorb more X-rays than the surrounding tissues, which, in turn, makes these tissues appear brighter on the scan data. Tissues with different brightness can then be virtually dissected from each other by selecting the bracket of grayscale to be visualized. Promising directions for the future include in silico phenotyping and developmental studies of plant inner parts (e.g., ovules, vasculature, pollen, and cell nuclei) via virtual dissection as well as correlations of quantitative phenotypes with omics datasets. Therefore, this work represents a crucial improvement of previous methods, allowing new directions of research to be

  4. Plant tissues in 3D via X-ray tomography: simple contrasting methods allow high resolution imaging.

    PubMed

    Staedler, Yannick M; Masson, David; Schönenberger, Jürg

    2013-01-01

    Computed tomography remains strongly underused in plant sciences despite its high potential in delivering detailed 3D phenotypical information because of the low X-ray absorption of most plant tissues. Existing protocols to study soft tissues display poor performance, especially when compared to those used on animals. More efficient protocols to study plant material are therefore needed. Flowers of Arabidopsis thaliana and Marcgravia caudata were immersed in a selection of contrasting agents used to treat samples for transmission electron microscopy. Grayscale values for floral tissues and background were measured as a function of time. Contrast was quantified via a contrast index. The thick buds of Marcgravia were scanned to determine which contrasting agents best penetrate thick tissues. The highest contrast increase with cytoplasm-rich tissues was obtained with phosphotungstate, whereas osmium tetroxide and bismuth tatrate displayed the highest contrast increase with vacuolated tissues. Phosphotungstate also displayed the best sample penetration. Furthermore, infiltration with phosphotungstate allowed imaging of all plants parts at a high resolution of 3 µm, which approaches the maximum resolution of our equipment: 1.5 µm. The high affinity of phosphotungstate for vasculature, cytoplasm-rich tissue, and pollen causes these tissues to absorb more X-rays than the surrounding tissues, which, in turn, makes these tissues appear brighter on the scan data. Tissues with different brightness can then be virtually dissected from each other by selecting the bracket of grayscale to be visualized. Promising directions for the future include in silico phenotyping and developmental studies of plant inner parts (e.g., ovules, vasculature, pollen, and cell nuclei) via virtual dissection as well as correlations of quantitative phenotypes with omics datasets. Therefore, this work represents a crucial improvement of previous methods, allowing new directions of research to be

  5. Imaging quadrupolar geophysical anomaly sources by 3D probability tomography: application to near-surface geoelectrical surveys

    NASA Astrophysics Data System (ADS)

    Alaia, Raffaele; Patella, Domenico; Mauriello, Paolo

    2008-12-01

    We present the theory of the source quadrupole occurrence probability tomography method within a general approach including the source pole and source dipole occurrence probability tomographies, developed and amply discussed and tested in previous papers. In this new formulation, poles and dipoles still have the original meaning to represent centres and boundaries, respectively, of elementary bodies with constant constitutive parameters, while quadrupoles are assumed to simulate sharp corner elements. The purpose of quadrupole analysis is to improve the resolution power of geophysical methods, using once more probability as a suitable paradigm allowing all possible equivalent solutions to be included into a unique 3D tomography image. The new approach is described by first assuming that any geophysical field dataset can be hypothesized to be caused by a discrete number of source poles, dipoles and quadrupoles. Then, the previously published theory of the source pole and dipole occurrence probability tomography is symbolically extended to include source quadrupoles. Finally, the new formalism is explicitly written for the geoelectrical method, for which a few simple synthetic examples are discussed in order to demonstrate how the combined pole, dipole and quadrupole tomographies can provide a complete resolution of the most probable buried sources of the anomalies detected within a datum domain. A field example related to a geoelectrical survey carried out in the archaeological park of Pompei is presented, aiming at detecting remains of ancient Roman urbanization.

  6. Computational methods for constructing protein structure models from 3D electron microscopy maps.

    PubMed

    Esquivel-Rodríguez, Juan; Kihara, Daisuke

    2013-10-01

    Protein structure determination by cryo-electron microscopy (EM) has made significant progress in the past decades. Resolutions of EM maps have been improving as evidenced by recently reported structures that are solved at high resolutions close to 3Å. Computational methods play a key role in interpreting EM data. Among many computational procedures applied to an EM map to obtain protein structure information, in this article we focus on reviewing computational methods that model protein three-dimensional (3D) structures from a 3D EM density map that is constructed from two-dimensional (2D) maps. The computational methods we discuss range from de novo methods, which identify structural elements in an EM map, to structure fitting methods, where known high resolution structures are fit into a low-resolution EM map. A list of available computational tools is also provided.

  7. Introduction of the ASP3D Computer Program for Unsteady Aerodynamic and Aeroelastic Analyses

    NASA Technical Reports Server (NTRS)

    Batina, John T.

    2005-01-01

    A new computer program has been developed called ASP3D (Advanced Small Perturbation 3D), which solves the small perturbation potential flow equation in an advanced form including mass-consistent surface and trailing wake boundary conditions, and entropy, vorticity, and viscous effects. The purpose of the program is for unsteady aerodynamic and aeroelastic analyses, especially in the nonlinear transonic flight regime. The program exploits the simplicity of stationary Cartesian meshes with the movement or deformation of the configuration under consideration incorporated into the solution algorithm through a planar surface boundary condition. The new ASP3D code is the result of a decade of developmental work on improvements to the small perturbation formulation, performed while the author was employed as a Senior Research Scientist in the Configuration Aerodynamics Branch at the NASA Langley Research Center. The ASP3D code is a significant improvement to the state-of-the-art for transonic aeroelastic analyses over the CAP-TSD code (Computational Aeroelasticity Program Transonic Small Disturbance), which was developed principally by the author in the mid-1980s. The author is in a unique position as the developer of both computer programs to compare, contrast, and ultimately make conclusions regarding the underlying formulations and utility of each code. The paper describes the salient features of the ASP3D code including the rationale for improvements in comparison with CAP-TSD. Numerous results are presented to demonstrate the ASP3D capability. The general conclusion is that the new ASP3D capability is superior to the older CAP-TSD code because of the myriad improvements developed and incorporated.

  8. [Computer tomography of the brain in neurology].

    PubMed

    Shmidt, E V; Vereshchagin, N V; Bragina, L K; Vavilov, S B

    1978-01-01

    The results of the studies, obtained in a computer head tomography confirms its effectiveness in the diagnosis of ischemic and hemorrhagic strokes, tumor and degenerative brain diseases, as well as in investigations of the brain ventricular systems and subarachnoidal spaces. A computer head tomography--is a perspective method in the study of brain lesions with the aid of X-ray equipment and computers.

  9. Computer-Assisted Hepatocellular Carcinoma Ablation Planning Based on 3-D Ultrasound Imaging.

    PubMed

    Li, Kai; Su, Zhongzhen; Xu, Erjiao; Guan, Peishan; Li, Liu-Jun; Zheng, Rongqin

    2016-08-01

    To evaluate computer-assisted hepatocellular carcinoma (HCC) ablation planning based on 3-D ultrasound, 3-D ultrasound images of 60 HCC lesions from 58 patients were obtained and transferred to a research toolkit. Compared with virtual manual ablation planning (MAP), virtual computer-assisted ablation planning (CAP) consumed less time and needle insertion numbers and exhibited a higher rate of complete tumor coverage and lower rate of critical structure injury. In MAP, junior operators used less time, but had more critical structure injury than senior operators. For large lesions, CAP performed better than MAP. For lesions near critical structures, CAP resulted in better outcomes than MAP. Compared with MAP, CAP based on 3-D ultrasound imaging was more effective and achieved a higher rate of complete tumor coverage and a lower rate of critical structure injury; it is especially useful for junior operators and with large lesions, and lesions near critical structures.

  10. Characterization of a landslide geometry using 3D seismic refraction traveltime tomography: The La Valette landslide case history

    NASA Astrophysics Data System (ADS)

    Samyn, K.; Travelletti, J.; Bitri, A.; Grandjean, G.; Malet, J.-P.

    2012-11-01

    The geometry of the bedrock, internal layers and shear surfaces/bands controls the deformation pattern and the mechanisms of landslides. A challenge to progress in the forecast of landslide acceleration in terms of early-warning is therefore to characterize the 3D geometry of the unstable mass at a high level of spatial resolution, both in the horizontal and vertical directions, by integrating information from different surveying techniques. For such characterization, seismic investigations are potentially of a great interest. In the case of complex structures, the measure and the processing of seismic data need to be performed in 3D. The objective of this work is to present the development of a 3D extension of a seismic refraction traveltime tomography technique based on a Simultaneous Iterative Reconstruction Technique (SIRT). First the processing algorithm is detailed and its performance is discussed, and second an application to the La Valette complex landslide is presented. Inversion of first-arrival traveltimes produces a 3D tomogram that underlines the presence of many areas characterized by low P-wave velocity of 500-1800 m.s- 1. These low P-wave velocity structures result from the presence of reworked blocks, surficial cracks and in-depth fracture zones. These structures seem to extend to around 25 m in depth over a 80 × 130 m area. Based on borehole geotechnical data and previous geophysical investigations, an interface corresponding to an internal slip surface can be suspected near the isovalue of 1200 m.s- 1 at a depth of - 10 to - 15 m. The stable substratum is characterized by higher values of P-wave velocity of 1800-3000 m.s- 1. The features identified in the 3D tomogram allow to better (1) delineate the boundary between the landslide and the surrounding stable slopes, and (2) understand the morphological structures within the landslide at a hectometric scale. The integration of the 3D seismic tomography interpretation to previous geophysical

  11. Computer-assisted 3D planned corrective osteotomies in eight malunited radius fractures.

    PubMed

    Walenkamp, M M J; de Muinck Keizer, R J O; Dobbe, J G G; Streekstra, G J; Goslings, J C; Kloen, P; Strackee, S D; Schep, N W L

    2015-08-01

    In corrective osteotomy of the radius, detailed preoperative planning is essential to optimising functional outcome. However, complex malunions are not completely addressed with conventional preoperative planning. Computer-assisted preoperative planning may optimise the results of corrective osteotomy of the radius. We analysed the pre- and postoperative radiological result of computer-assisted 3D planned corrective osteotomy in a series of patients with a malunited radius and assessed postoperative function. We included eight patients aged 13-64 who underwent a computer-assisted 3D planned corrective osteotomy of the radius for the treatment of a symptomatic radius malunion. We evaluated pre- and postoperative residual malpositioning on 3D reconstructions as expressed in six positioning parameters (three displacements along and three rotations about the axes of a 3D anatomical coordinate system) and assessed postoperative wrist range of motion. In this small case series, dorsopalmar tilt was significantly improved (p = 0.05). Ulnoradial shift, however, increased by the correction osteotomy (6 of 8 cases, 75 %). Postoperative 3D evaluation revealed improved positioning parameters for patients in axial rotational alignment (62.5 %), radial inclination (75 %), proximodistal shift (83 %) and volodorsal shift (88 %), although the cohort was not large enough to confirm this by statistical significance. All but one patient experienced improved range of motion (88 %). Computer-assisted 3D planning ameliorates alignment of radial malunions and improves functional results in patients with a symptomatic malunion of the radius. Further development is required to improve transfer of the planned position to the intra-operative bone. Level of evidence IV.

  12. Patient-specific reconstruction utilizing computer assisted 3D modelling for partial bone flap defect in hybrid cranioplasty

    NASA Astrophysics Data System (ADS)

    Hueh, Low Peh; Abdullah, Johari Yap; Abdullah, Abdul Manaf; Yahya, Suzana; Idris, Zamzuri; Mohamad, Dasmawati

    2016-12-01

    Autologous cranioplasty using a patient's original bone flap remain the commonest practice nowadays. However, partial bone flap defect is commonly encountered. Replacing the bone flap with pre-moulded synthetic bone flap is costly and not affordable to many patients. Hence most of the small to medium size defect was topped up with alloplastic material on a free hand basis intra-operatively which often resulted in inaccurate implant approximation with unsatisfactory cosmetic result. This study aims to evaluate implant accuracy and cosmetic outcome of cranioplasty candidates who underwent partial bone flap reconstruction utilising computer assisted 3D modelling. 3D images of the skull were obtained from post-craniectomy axial 1-mm spiral computed tomography (CT) scans and a virtual 3D model was generated using the Materialise Mimics software. The Materialise 3-Matic was then utilised to design a patient-specific implant. Prefabrication of the implant was performed by the 3D Objet printer, and a negative gypsum mold was created with the prefabricated cranial implant. Intraoperatively, a hybrid polymethyl methacrylate (PMMA)-autologous cranial implant was produced using the gypsum mold, and fit into the cranial defect. This study is still ongoing at the moment. To date, two men has underwent partial bone flap reconstruction utilising this technique and both revealed satisfactory implant alignment with favourable cosmesis. Mean implant size was 12cm2, and the mean duration of intraoperative reconstruction for the partial bone flap defect was 40 minutes. No significant complication was reported. As a conclusion, this new technique and approach resulted in satisfactory implant alignment and favourable cosmetic outcome. However, more study samples are needed to increase the validity of the study results.

  13. A Microscopic Optically Tracking Navigation System That Uses High-resolution 3D Computer Graphics.

    PubMed

    Yoshino, Masanori; Saito, Toki; Kin, Taichi; Nakagawa, Daichi; Nakatomi, Hirofumi; Oyama, Hiroshi; Saito, Nobuhito

    2015-01-01

    Three-dimensional (3D) computer graphics (CG) are useful for preoperative planning of neurosurgical operations. However, application of 3D CG to intraoperative navigation is not widespread because existing commercial operative navigation systems do not show 3D CG in sufficient detail. We have developed a microscopic optically tracking navigation system that uses high-resolution 3D CG. This article presents the technical details of our microscopic optically tracking navigation system. Our navigation system consists of three components: the operative microscope, registration, and the image display system. An optical tracker was attached to the microscope to monitor the position and attitude of the microscope in real time; point-pair registration was used to register the operation room coordinate system, and the image coordinate system; and the image display system showed the 3D CG image in the field-of-view of the microscope. Ten neurosurgeons (seven males, two females; mean age 32.9 years) participated in an experiment to assess the accuracy of this system using a phantom model. Accuracy of our system was compared with the commercial system. The 3D CG provided by the navigation system coincided well with the operative scene under the microscope. Target registration error for our system was 2.9 ± 1.9 mm. Our navigation system provides a clear image of the operation position and the surrounding structures. Systems like this may reduce intraoperative complications.

  14. Novel fully integrated computer system for custom footwear: from 3D digitization to manufacturing

    NASA Astrophysics Data System (ADS)

    Houle, Pascal-Simon; Beaulieu, Eric; Liu, Zhaoheng

    1998-03-01

    This paper presents a recently developed custom footwear system, which integrates 3D digitization technology, range image fusion techniques, a 3D graphical environment for corrective actions, parametric curved surface representation and computer numerical control (CNC) machining. In this system, a support designed with the help of biomechanics experts can stabilize the foot in a correct and neutral position. The foot surface is then captured by a 3D camera using active ranging techniques. A software using a library of documented foot pathologies suggests corrective actions on the orthosis. Three kinds of deformations can be achieved. The first method uses previously scanned pad surfaces by our 3D scanner, which can be easily mapped onto the foot surface to locally modify the surface shape. The second kind of deformation is construction of B-Spline surfaces by manipulating control points and modifying knot vectors in a 3D graphical environment to build desired deformation. The last one is a manual electronic 3D pen, which may be of different shapes and sizes, and has an adjustable 'pressure' information. All applied deformations should respect a G1 surface continuity, which ensure that the surface can accustom a foot. Once the surface modification process is completed, the resulting data is sent to manufacturing software for CNC machining.

  15. The Effects of 3D Computer Simulation on Biology Students' Achievement and Memory Retention

    ERIC Educational Resources Information Center

    Elangovan, Tavasuria; Ismail, Zurida

    2014-01-01

    A quasi experimental study was conducted for six weeks to determine the effectiveness of two different 3D computer simulation based teaching methods, that is, realistic simulation and non-realistic simulation on Form Four Biology students' achievement and memory retention in Perak, Malaysia. A sample of 136 Form Four Biology students in Perak,…

  16. Analysis of thoracic aorta hemodynamics using 3D particle tracking velocimetry and computational fluid dynamics.

    PubMed

    Gallo, Diego; Gülan, Utku; Di Stefano, Antonietta; Ponzini, Raffaele; Lüthi, Beat; Holzner, Markus; Morbiducci, Umberto

    2014-09-22

    Parallel to the massive use of image-based computational hemodynamics to study the complex flow establishing in the human aorta, the need for suitable experimental techniques and ad hoc cases for the validation and benchmarking of numerical codes has grown more and more. Here we present a study where the 3D pulsatile flow in an anatomically realistic phantom of human ascending aorta is investigated both experimentally and computationally. The experimental study uses 3D particle tracking velocimetry (PTV) to characterize the flow field in vitro, while finite volume method is applied to numerically solve the governing equations of motion in the same domain, under the same conditions. Our findings show that there is an excellent agreement between computational and measured flow fields during the forward flow phase, while the agreement is poorer during the reverse flow phase. In conclusion, here we demonstrate that 3D PTV is very suitable for a detailed study of complex unsteady flows as in aorta and for validating computational models of aortic hemodynamics. In a future step, it will be possible to take advantage from the ability of 3D PTV to evaluate velocity fluctuations and, for this reason, to gain further knowledge on the process of transition to turbulence occurring in the thoracic aorta.

  17. Using 3D Computer Graphics Multimedia to Motivate Preservice Teachers' Learning of Geometry and Pedagogy

    ERIC Educational Resources Information Center

    Goodson-Espy, Tracy; Lynch-Davis, Kathleen; Schram, Pamela; Quickenton, Art

    2010-01-01

    This paper describes the genesis and purpose of our geometry methods course, focusing on a geometry-teaching technology we created using NVIDIA[R] Chameleon demonstration. This article presents examples from a sequence of lessons centered about a 3D computer graphics demonstration of the chameleon and its geometry. In addition, we present data…

  18. Adaptive 3D single-block grids for the computation of viscous flows around wings

    SciTech Connect

    Hagmeijer, R.; Kok, J.C.

    1996-12-31

    A robust algorithm for the adaption of a 3D single-block structured grid suitable for the computation of viscous flows around a wing is presented and demonstrated by application to the ONERA M6 wing. The effects of grid adaption on the flow solution and accuracy improvements is analyzed. Reynolds number variations are studied.

  19. First steps toward 3D high resolution imaging using adaptive optics and full-field optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Blanco, Leonardo; Blavier, Marie; Glanc, Marie; Pouplard, Florence; Tick, Sarah; Maksimovic, Ivan; Chenegros, Guillaume; Mugnier, Laurent; Lacombe, Francois; Rousset, Gérard; Paques, Michel; Le Gargasson, Jean-François; Sahel, Jose-Alain

    2008-09-01

    We describe here two parts of our future 3D fundus camera coupling Adaptive Optics and full-field Optical Coherence Tomography. The first part is an Adaptive Optics flood imager installed at the Quinze-Vingts Hospital, regularly used on healthy and pathological eyes. A posteriori image reconstruction is performed, increasing the final image quality and field of view. The instrument lateral resolution is better than 2 microns. The second part is a full-field Optical Coherence Tomograph, which has demonstrated capability of performing a simple kind of "4 phases" image reconstruction of non biological samples and ex situ retinas. Final aim is to couple both parts in order to achieve 3D high resolution mapping of in vivo retinas.

  20. A joint estimation detection of Glaucoma progression in 3D spectral domain optical coherence tomography optic nerve head images

    PubMed Central

    Belghith, Akram; Bowd, Christopher; Weinreb, Robert N.; Zangwill, Linda M.

    2014-01-01

    Glaucoma is an ocular disease characterized by distinctive changes in the optic nerve head (ONH) and visual field. Glaucoma can strike without symptoms and causes blindness if it remains without treatment. Therefore, early disease detection is important so that treatment can be initiated and blindness prevented. In this context, important advances in technology for non-invasive imaging of the eye have been made providing quantitative tools to measure structural changes in ONH topography, an essential element for glaucoma detection and monitoring. 3D spectral domain optical coherence tomography (SD-OCT), an optical imaging technique, has been commonly used to discriminate glaucomatous from healthy subjects. In this paper, we present a new framework for detection of glaucoma progression using 3D SD-OCT images. In contrast to previous works that the retinal nerve fiber layer (RNFL) thickness measurement provided by commercially available spectral-domain optical coherence tomograph, we consider the whole 3D volume for change detection. To integrate a priori knowledge and in particular the spatial voxel dependency in the change detection map, we propose the use of the Markov Random Field to handle a such dependency. To accommodate the presence of false positive detection, the estimated change detection map is then used to classify a 3D SDOCT image into the “non-progressing” and “progressing” glaucoma classes, based on a fuzzy logic classifier. We compared the diagnostic performance of the proposed framework to existing methods of progression detection. PMID:25606299

  1. Label-free subcellular 3D live imaging of preimplantation mouse embryos with full-field optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Zheng, Jing-gao; Lu, Danyu; Chen, Tianyuan; Wang, Chengming; Tian, Ning; Zhao, Fengying; Huo, Tiancheng; Zhang, Ning; Chen, Dieyan; Ma, Wanyun; Sun, Jia-lin; Xue, Ping

    2012-07-01

    Early patterning and polarity is of fundamental interest in preimplantation embryonic development. Label-free subcellular 3D live imaging is very helpful to its related studies. We have developed a novel system of full-field optical coherence tomography (FF-OCT) for noninvasive 3D subcellular live imaging of preimplantation mouse embryos with no need of dye labeling. 3D digitized embryos can be obtained by image processing. Label-free 3D live imaging is demonstrated for the mouse embryos at various typical preimplantation stages with a spatial resolution of 0.7 μm and imaging rate of 24 fps. Factors that relate to early patterning and polarity, such as pronuclei in zygote, shapes of zona pellucida, location of second polar body, cleavage planes, and the blastocyst axis, can be quantitatively measured. The angle between the two second cleavage planes is accurately measured to be 87 deg. It is shown that FF-OCT provides a potential breakthrough for early patterning, polarity formation, and many other preimplantation-related studies in mammalian developmental biology.

  2. A joint estimation detection of Glaucoma progression in 3D spectral domain optical coherence tomography optic nerve head images

    NASA Astrophysics Data System (ADS)

    Belghith, Akram; Bowd, Christopher; Weinreb, Robert N.; Zangwill, Linda M.

    2014-03-01

    Glaucoma is an ocular disease characterized by distinctive changes in the optic nerve head (ONH) and visual field. Glaucoma can strike without symptoms and causes blindness if it remains without treatment. Therefore, early disease detection is important so that treatment can be initiated and blindness prevented. In this context, important advances in technology for non-invasive imaging of the eye have been made providing quantitative tools to measure structural changes in ONH topography, an essential element for glaucoma detection and monitoring. 3D spectral domain optical coherence tomography (SD-OCT), an optical imaging technique, has been commonly used to discriminate glaucomatous from healthy subjects. In this paper, we present a new framework for detection of glaucoma progression using 3D SD-OCT images. In contrast to previous works that the retinal nerve fiber layer (RNFL) thickness measurement provided by commercially available spectral-domain optical coherence tomograph, we consider the whole 3D volume for change detection. To integrate a priori knowledge and in particular the spatial voxel dependency in the change detection map, we propose the use of the Markov Random Field to handle a such dependency. To accommodate the presence of false positive detection, the estimated change detection map is then used to classify a 3D SDOCT image into the "non-progressing" and "progressing" glaucoma classes, based on a fuzzy logic classifier. We compared the diagnostic performance of the proposed framework to existing methods of progression detection.

  3. P and S automatic picks for 3D earthquake tomography in NE Italy

    NASA Astrophysics Data System (ADS)

    Lovisa, L.; Bragato, P.; Gentili, S.

    2006-12-01

    Earthquake tomography is useful to study structural and geological features of the crust. In particular, it uses P and S arrival times for reconstructing weaves velocity fields and locating earthquakes hypocenters. However, tomography needs a large effort to provide a high number of manual picks. On the other side, many automatic picking methods have been proposed, but they are usually applied to preliminary elaboration of the data (fast alert and automatic bulletin generation); they are generally considered not reliable for tomography. In this work, we present and discuss the results of Vp, Vs and Vp/Vs tomographies obtained using automatic picks generated by the system TAPNEI (Gentili and Bragato 2006), applied in the NE Italy. Preliminarily, in order to estimate the error in comparison with the unknown true arrival times, an analysis on the picking quality is done. The tests have been performed using two dataset: the first is made up by 240 earthquakes automatically picked by TAPNEI; the second counts in the same earthquakes but manually picked (OGS database). The grid and the software used to perform tomography (Sim28, Michelini and Mc Evilly, 1991) are the same in the two cases. Vp, Vs and Vp/Vs fields of the two tomographies and their differences are shown on vertical sections. In addiction, the differences in earthquakes locations are studied; in particular, the quality of the accuracy of the localizations has been analyzed by estimating the distance of the hypocenter distributions with respect to the manual locations. The analysis include also a qualitative comparison with an independent tomography (Gentile et al., 2000) performed using Simulps (Evans et al, 1994) on a set of 224 earthquakes accurately selected and manually relocated. The quality of the pickings and the comparison with the tomography obtained by manual data suggest that earthquake tomography with automatic data can provide reliable results. We suggest the use of such data when a large

  4. Computed tomography characterisation of additive manufacturing materials.

    PubMed

    Bibb, Richard; Thompson, Darren; Winder, John

    2011-06-01

    Additive manufacturing, covering processes frequently referred to as rapid prototyping and rapid manufacturing, provides new opportunities in the manufacture of highly complex and custom-fitting medical devices and products. Whilst many medical applications of AM have been explored and physical properties of the resulting parts have been studied, the characterisation of AM materials in computed tomography has not been explored. The aim of this study was to determine the CT number of commonly used AM materials. There are many potential applications of the information resulting from this study in the design and manufacture of wearable medical devices, implants, prostheses and medical imaging test phantoms. A selection of 19 AM material samples were CT scanned and the resultant images analysed to ascertain the materials' CT number and appearance in the images. It was found that some AM materials have CT numbers very similar to human tissues, FDM, SLA and SLS produce samples that appear uniform on CT images and that 3D printed materials show a variation in internal structure.

  5. Application of geoelectrical 3D probability tomography in a test-site of the archaeological park of Pompei (Naples, Italy)

    NASA Astrophysics Data System (ADS)

    Alaia, Raffaele; Patella, Domenico; Mauriello, Paolo

    2008-03-01

    The 3D geoelectric probability tomography method has been previously developed as a powerful approach to localize in the subsoil the sources of the apparent resistivity anomalies detected on the ground surface. We show that this method can be successfully applied in the archaeological park of Pompei to recognize buried remains of the ancient Roman urbanization including roads, squares and buildings which were heavily damaged and totally buried under a thick cover of volcanic fall products resulting from the well-known disastrous 79 AD Vesuvius eruption. A further development is made in this work concerning the identification of source poles and dipoles underground, ascribable to the physical centre of the bodies with anomalous resistivity and to their boundaries, respectively. Different imaging systems are used to enhance the quality of information derived from the tomography analysis.

  6. 3D Computational Modeling of Proteins Using Sparse Paramagnetic NMR Data.

    PubMed

    Pilla, Kala Bharath; Otting, Gottfried; Huber, Thomas

    2017-01-01

    Computational modeling of proteins using evolutionary or de novo approaches offers rapid structural characterization, but often suffers from low success rates in generating high quality models comparable to the accuracy of structures observed in X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. A computational/experimental hybrid approach incorporating sparse experimental restraints in computational modeling algorithms drastically improves reliability and accuracy of 3D models. This chapter discusses the use of structural information obtained from various paramagnetic NMR measurements and demonstrates computational algorithms implementing pseudocontact shifts as restraints to determine the structure of proteins at atomic resolution.

  7. Initial results obtained from a 3D computational model of the shaped charge jet particulation process

    SciTech Connect

    Zernow, L.; Chapyak, E.J.

    1998-02-01

    In a previous paper, the authors discussed a 3D computational model for the particulation of a stretching shaped charge jet, based on the experimentally observed double-helix surface perturbations on softly recovered jet particles. The 3D problem was derived from the unperturbed 2D problem, which was first used to generate a stretching jet. A portion of this 2D jet was selected for study in the cylindrical 3D mode, and the double-helix perturbations were placed on the cylinder surface. This initial computation was greatly simplified, to make it feasible to run on a CM 200 massively parallel processor. The initial output of this computation, which is being published here for the first time, leads to a significant simplification of the analysis of the particulation process, by avoiding the search for the elusive ``most favored wavelength`` which is characteristic of 2D axi-symmetric analyses. Previously unnoticed characteristics of flash radiographs from Viper jets, appear to support the computational results obtained, despite a counter-intuitive prediction of the location of necking loci, relative to the perturbing helices. The approximations used in this initial computation are discussed critically. Planned improvements are defined. A vision of future fundamental computations, which become possible with more powerful ASCI machines, is projected.

  8. Tri-Dimensional Electric Resistivity Tomography (ERT-3D) Technique, an Efficient Tool to Unveil the Subsoil of Archaeological Structures

    NASA Astrophysics Data System (ADS)

    Chavez, R. E.; Vargas, D.; Cifuentes-Nava, G.; HernaNdez-Quintero, J. E.; Tejero, A.

    2014-12-01

    Three-Dimensional Electrical Resistivity Tomography techniques (ERT-3D) have demonstrated to be an efficient tool to study the subsurface of areas of archaeological interest by special arrays designed to 'illuminate' the subsoil beneath the structure under study. 'L'- and 'Corner'-arrays are applied to design alternative electrode geometries, which attempt to cover the subsurface with enough resistivity observations underneath the studied target. Two examples are presented where novel geometries can be applied to investigate the subsoil of two important pyramids in Mexico. First, the archaeological site of Cuicuilco is studied. The area is found towards the southern portion of the Mexican Basin. This pyramid presents a circular structure of 110 m in diameter and a total height of 25 m. The region is partially covered by the lava flows that came from an eruptive event form the Xitle Volcano 1500 years ago. The geophysical study was carried out at the base of the pyramid. 48 electrodes were deployed along a circular transect, with an electrode separation of 5.4 m. A total of 1716 apparent resistivity observations were measured. The inverted model computed is obtained with an investigation depth of 30 m, approximately (Figure 1, in color). A resistive anomaly can be observed towards the central portion of the model. This anomaly can be associated to a burial chamber, excavated by the archaeologists. The second example corresponds to the pyiramid El Castillo, located in the archaeological site of Chichen Itza, in the southern lowlands of Mexico, within the Yucatan Peninsula. Previous GPR studies carried out within the pyramid's Plaza provided evidences of a buried tunnel excavated within the limestone rocks. Such feature seemed to run beneath the eastern flank of the pyramide. The geophysical study was carried out by employing 96 flat-surface electrodes, which surrounded the edifice forming a square geometry. A total of 5,350 apparent resistivity observations were

  9. Application of 3D electrical capacitance tomography in probing anomalous blocks in water

    NASA Astrophysics Data System (ADS)

    Liao, Aimin; Zhou, Qiyou; Zhang, Yun

    2015-06-01

    Water usually acts as a high-permittivity dielectric in many fields such as geophysics, hydrology, hydrogeology, aquaculture, etc. Thus, it may be of significance to adapt ECT to the fields with a high permittivity in which the conventional ECT is scarcely involved. To achieve this objective, a simplified 3D-ECT system was constructed with a high-precision inductance capacitance resistance meter and programmable logic controllers. In the aspect of sensing unit of the system, two geometries (i.e. cylinder and cube) of 3D sensors were constructed to probe anomalous blocks in water. Numerical simulations and physical experiments for both the sensors were performed to test the effectiveness of the constructed system to probe anomalous blocks in water. Furthermore, to justify the availability of this system in some possible fields, two experiments associated with applications of the 3D-ECT system were performed to measure the distribution of a plant root system in water, and to monitor the infiltration of water in soil in field. The experimental results demonstrate that the ECT system is capable of probing the location and rough size of anomalous blocks in water with both the sensors, determining the distribution of a plant root system in water, and monitoring the infiltration process of water in soil.

  10. 3D image reconstruction for PET by multi-slice rebinning and axial filtering. [Positron Emission Tomography (PET)

    SciTech Connect

    Lewitt, R.M. Pennsylvania Univ., Philadelphia, PA . Dept. of Radiology); Muehllehner, G. ); Karp, J.S. . Dept. of Radiology)

    1991-01-01

    Two different approaches are used at present to reconstruct from 3D coincidence data in PET. We refer to these approaches as the single-slice rebinning approach and the fully-3D approach. The single-slice rebinning approach involves geometrical approximations, but it requires the least possible amount of computation. Fully-3D reconstruction algorithms, both iterative and non-iterative, do not make such approximations, but require much more computation. Multi-slice rebinning with axial filtering is a new approach which attempts to achieve the geometrical accuracy of the fully-3D approach with the simplicity and modest amount of computation of the single-slice rebinning approach. The first step (multi-slice rebinning) involves rebinning of coincidence lines into a stack of 2D sinograms, where multiple sinograms are incremented for each oblique coincidence line. This operation is followed by an axial filtering operation, either before or after slice-by-slice reconstruction, to reduce the blurring in the axial direction. Tests with simulated and experimental data indicate that the new method has better geometrical accuracy than single-slice rebinning, at the cost of only a modest increase in computation. 11 refs.

  11. 3D dynamic computer model of the head-neck complex.

    PubMed

    Sierra, Daniel A; Enderle, John D

    2006-01-01

    A 3D dynamic computer model for the movement of the head is presented that incorporates anatomically correct information about the diverse elements forming the system. The skeleton is considered as a set of interconnected rigid 3D bodies following the Newton-Euler laws of movement. The muscles are modeled using Enderle's linear model. Finally, the soft tissues, namely the ligaments, intervertebral disks, and zigapophysial joints, are modeled using the finite elements approach. The model is intended to study the neural network that controls movement and maintains the balance of the head-neck complex during eye movements.

  12. The measurement of 3-D asymmetric temperature field by using real time laser interferometric tomography

    NASA Astrophysics Data System (ADS)

    Wang, Dezhong; Zhuang, Tiange

    2001-09-01

    A real time nondestructive temperature measurement technique based on laser holographic interference tomography technique is presented. An He-Ne laser is used as light source, and a CCD video camera is used to grab the interferogram. This laser holographic tomography technique is applied to the measurement of the temperature fields generated by two heated rods. Since data error is inevitable in engineering measurement, it is necessary to study the reconstruction techniques for reconstructing the temperature field. Three techniques including convolution back projection (CBP), algebra reconstruction technique (ART) and simultaneous iterative reconstruction technique (SIRT) are studied. Based on the reconstruction techniques and experimental situation, ART is used to reconstruct the asymmetric temperature fields. The thermocouples are used to measure the temperatures of the two heated rods. Comparing the reconstructed result with the measured temperature value, a satisfactory result is obtained.

  13. The Dark Side of EDX Tomography: Modeling Detector Shadowing to Aid 3D Elemental Signal Analysis.

    PubMed

    Yeoh, Catriona S M; Rossouw, David; Saghi, Zineb; Burdet, Pierre; Leary, Rowan K; Midgley, Paul A

    2015-06-01

    A simple model is proposed to account for the loss of collected X-ray signal by the shadowing of X-ray detectors in the scanning transmission electron microscope. The model is intended to aid the analysis of three-dimensional elemental data sets acquired using energy-dispersive X-ray tomography methods where shadow-free specimen holders are unsuitable or unavailable. The model also provides a useful measure of the detection system geometry.

  14. A field proof-of-concept of aquifer imaging using 3-D transient hydraulic tomography with modular, temporarily-emplaced equipment

    NASA Astrophysics Data System (ADS)

    Cardiff, M.; Barrash, W.; Kitanidis, P. K.

    2012-05-01

    Hydraulic tomography is a field scale aquifer characterization method capable of estimating 3-D heterogeneous parameter distributions, and is directly sensitive to hydraulic conductivity (K), thus providing a useful data source for improving flow and transport models. We present results from a proof-of-concept field and modeling study in which we apply 3-D transient hydraulic tomography (3DTHT) to the relatively high-K and moderately heterogeneous unconfined aquifer at the Boise Hydrogeophysical Research Site. Short-duration (20 min) partially penetrating pumping tests, for which observed responses do not reach steady state, are used as the aquifer stimulation. To collect field data, we utilize a system of temporarily emplaced packer equipment to isolate multiple discrete intervals in boreholes. To analyze the data, we utilize MODFLOW combined with geostatistical inversion code based on the quasilinear approach of Kitanidis (1995). This combination of practical software allows inversion of large datasets (>250 drawdown curves, and almost 1000 individual data points) and estimation of K at >100,000 locations; reasonable runtimes are obtained using a single multicore computer with 12 GB of RAM. The K heterogeneity results from 3DTHT are cross-validated against K characterization from a large set of partially penetrating slug tests, and found to be quite consistent. The use of portable, modular equipment for field implementation means that 3DTHT data collection can be performed (including mobilization/demobilization) within a matter of days. Likewise, use of a practical, efficient and scalable numerical modeling and inversion strategy means that computational effort is drastically reduced, such that 3-D aquifer property distributions can be estimated quickly.

  15. A Field Proof-of-Concept of Aquifer Imaging Using 3-D Transient Hydraulic Tomography with Modular, Temporarily-Emplaced Equipment

    SciTech Connect

    Cardiff, Michael A.; Barrash, Warren; Kitanidis, P. K.

    2012-05-19

    Hydraulic tomography is a field scale aquifer characterization method capable of estimating 3-D heterogeneous parameter distributions, and is directly sensitive to hydraulic conductivity (K), thus providing a useful data source for improving flow and transport models. We present results from a proof-of-concept field and modeling study in which we apply 3-D transient hydraulic tomography (3DTHT) to the relatively high-K and moderately heterogeneous unconfined aquifer at the Boise Hydrogeophysical Research Site. Short-duration (20 min) partially penetrating pumping tests, for which observed responses do not reach steady state, are used as the aquifer stimulation. To collect field data, we utilize a system of temporarily emplaced packer equipment to isolate multiple discrete intervals in boreholes. To analyze the data, we utilize MODFLOW combined with geostatistical inversion code based on the quasilinear approach of Kitanidis (1995). This combination of practical software allows inversion of large datasets (>250 drawdown curves, and almost 1000 individual data points) and estimation of K at >100,000 locations; reasonable runtimes are obtained using a single multicore computer with 12 GB of RAM. The K heterogeneity results from 3DTHT are cross-validated against K characterization from a large set of partially penetrating slug tests, and found to be quite consistent. The use of portable, modular equipment for field implementation means that 3DTHT data collection can be performed (including mobilization/demobilization) within a matter of days. Likewise, use of a practical, efficient and scalable numerical modeling and inversion strategy means that computational effort is drastically reduced, such that 3-D aquifer property distributions can be estimated quickly.

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

    PubMed

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

    2008-06-01

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

  17. [Clinical application of computed tomography in cattle].

    PubMed

    Nuss, K; Schnetzler, C; Hagen, R; Schwarz, A; Kircher, P

    2011-01-01

    Computed tomography involves the use of x-rays to produce cross-sectional images of body regions. It provides non-overlapping, two-dimensional images of all desired planes as well as three-dimensional reconstruction of regions of interest. There are few reports on the clinical use of computed tomography in farm animals. Its use in cattle is limited by high cost, the application of off-label drugs and the need for general anaesthesia. In cattle computed tomography is indicated primarily for diseases of the head, e.g. dental diseases and otitis media, and neurological disorders. Less often it is used for diseases of the vertebrae and limbs. In valuable cattle, the results of computed tomography can be an important part of preoperative planning or be used to avoid unnecessary surgery when the prognosis is poor.

  18. Computed tomography of orbital-facial neurofibromatosis

    SciTech Connect

    Zimmerman, R.A.; Bilaniuk, L.T.; Metzger, R.A.; Grossman, R.I.; Schut, L.; Bruce, D.A.

    1983-01-01

    Twenty-four patients with orbital-facial manifestations of neurofibromations were examined by computed tomography. Delineation of the extent of the disease, and differentiation of the disease processes (orbital tumor, osseous orbital dysplasia, plexiform neurofibromatosis, and buphthalmos) was possible.

  19. Intraperitoneal contrast agents for computed tomography

    SciTech Connect

    Stork, J.

    1985-08-01

    Intraperitoneal contrast agents have been used to diagnose mass lesions, adhesions, and hernias using conventional radiographic techniques. The use of intraperitoneal contrast agents in conjunction with computed tomography (CT) has been limited and is the subject of this report.

  20. Interlaced X-ray diffraction computed tomography

    PubMed Central

    Vamvakeros, Antonios; Jacques, Simon D. M.; Di Michiel, Marco; Senecal, Pierre; Middelkoop, Vesna; Cernik, Robert J.; Beale, Andrew M.

    2016-01-01

    An X-ray diffraction computed tomography data-collection strategy that allows, post experiment, a choice between temporal and spatial resolution is reported. This strategy enables time-resolved studies on comparatively short timescales, or alternatively allows for improved spatial resolution if the system under study, or components within it, appear to be unchanging. The application of the method for studying an Mn–Na–W/SiO2 fixed-bed reactor in situ is demonstrated. Additionally, the opportunities to improve the data-collection strategy further, enabling post-collection tuning between statistical, temporal and spatial resolutions, are discussed. In principle, the interlaced scanning approach can also be applied to other pencil-beam tomographic techniques, like X-ray fluorescence computed tomography, X-ray absorption fine structure computed tomography, pair distribution function computed tomography and tomographic scanning transmission X-ray microscopy. PMID:27047305

  1. Interlaced X-ray diffraction computed tomography.

    PubMed

    Vamvakeros, Antonios; Jacques, Simon D M; Di Michiel, Marco; Senecal, Pierre; Middelkoop, Vesna; Cernik, Robert J; Beale, Andrew M

    2016-04-01

    An X-ray diffraction computed tomography data-collection strategy that allows, post experiment, a choice between temporal and spatial resolution is reported. This strategy enables time-resolved studies on comparatively short timescales, or alternatively allows for improved spatial resolution if the system under study, or components within it, appear to be unchanging. The application of the method for studying an Mn-Na-W/SiO2 fixed-bed reactor in situ is demonstrated. Additionally, the opportunities to improve the data-collection strategy further, enabling post-collection tuning between statistical, temporal and spatial resolutions, are discussed. In principle, the interlaced scanning approach can also be applied to other pencil-beam tomographic techniques, like X-ray fluorescence computed tomography, X-ray absorption fine structure computed tomography, pair distribution function computed tomography and tomographic scanning transmission X-ray microscopy.

  2. Computed Tomography of the Musculoskeletal System.

    PubMed

    Ballegeer, Elizabeth A

    2016-05-01

    Computed tomography (CT) has specific uses in veterinary species' appendicular musculoskeletal system. Parameters for acquisition of images, interpretation limitations, as well as published information regarding its use in small animals is reviewed.

  3. Using the CAVE virtual-reality environment as an aid to 3-D electromagnetic field computation

    SciTech Connect

    Turner, L.R.; Levine, D.; Huang, M.; Papka, M; Kettunen, L.

    1995-08-01

    One of the major problems in three-dimensional (3-D) field computation is visualizing the resulting 3-D field distributions. A virtual-reality environment, such as the CAVE, (CAVE Automatic Virtual Environment) is helping to overcome this problem, thus making the results of computation more usable for designers and users of magnets and other electromagnetic devices. As a demonstration of the capabilities of the CAVE, the elliptical multipole wiggler (EMW), an insertion device being designed for the Advanced Photon Source (APS) now being commissioned at Argonne National Laboratory (ANL), wa made visible, along with its fields and beam orbits. Other uses of the CAVE in preprocessing and postprocessing computation for electromagnetic applications are also discussed.

  4. Synesthetic art through 3-D projection: The requirements of a computer-based supermedium

    NASA Technical Reports Server (NTRS)

    Mallary, Robert

    1989-01-01

    A computer-based form of multimedia art is proposed that uses the computer to fuse aspects of painting, sculpture, dance, music, film, and other media into a one-to-one synthesia of image and sound for spatially synchronous 3-D projection. Called synesthetic art, this conversion of many varied media into an aesthetically unitary experience determines the character and requirements of the system and its software. During the start-up phase, computer stereographic systems are unsuitable for software development. Eventually, a new type of illusory-projective supermedium will be required to achieve the needed combination of large-format projection and convincing real life presence, and to handle the vast amount of 3-D visual and acoustic information required. The influence of the concept on the author's research and creative work is illustrated through two examples.

  5. Organ printing: computer-aided jet-based 3D tissue engineering.

    PubMed

    Mironov, Vladimir; Boland, Thomas; Trusk, Thomas; Forgacs, Gabor; Markwald, Roger R

    2003-04-01

    Tissue engineering technology promises to solve the organ transplantation crisis. However, assembly of vascularized 3D soft organs remains a big challenge. Organ printing, which we define as computer-aided, jet-based 3D tissue-engineering of living human organs, offers a possible solution. Organ printing involves three sequential steps: pre-processing or development of "blueprints" for organs; processing or actual organ printing; and postprocessing or organ conditioning and accelerated organ maturation. A cell printer that can print gels, single cells and cell aggregates has been developed. Layer-by-layer sequentially placed and solidified thin layers of a thermo-reversible gel could serve as "printing paper". Combination of an engineering approach with the developmental biology concept of embryonic tissue fluidity enables the creation of a new rapid prototyping 3D organ printing technology, which will dramatically accelerate and optimize tissue and organ assembly.

  6. Application of the ASP3D Computer Program to Unsteady Aerodynamic and Aeroelastic Analyses

    NASA Technical Reports Server (NTRS)

    Batina, John T.

    2006-01-01

    A new computer program has been developed called ASP3D (Advanced Small Perturbation - 3D), which solves the small perturbation potential flow equation in an advanced form including mass-consistent surface and trailing wake boundary conditions, and entropy, vorticity, and viscous effects. The purpose of the program is for unsteady aerodynamic and aeroelastic analyses, especially in the nonlinear transonic flight regime. The program exploits the simplicity of stationary Cartesian meshes with the movement or deformation of the configuration under consideration incorporated into the solution algorithm through a planar surface boundary condition. The paper presents unsteady aerodynamic and aeroelastic applications of ASP3D to assess the time dependent capability and demonstrate various features of the code.

  7. Computational study of 3-D hot-spot initiation in shocked insensitive high-explosive

    NASA Astrophysics Data System (ADS)

    Najjar, F. M.; Howard, W. M.; Fried, L. E.; Manaa, M. R.; Nichols, A., III; Levesque, G.

    2012-03-01

    High-explosive (HE) material consists of large-sized grains with micron-sized embedded impurities and pores. Under various mechanical/thermal insults, these pores collapse generating hightemperature regions leading to ignition. A hydrodynamic study has been performed to investigate the mechanisms of pore collapse and hot spot initiation in TATB crystals, employing a multiphysics code, ALE3D, coupled to the chemistry module, Cheetah. This computational study includes reactive dynamics. Two-dimensional high-resolution large-scale meso-scale simulations have been performed. The parameter space is systematically studied by considering various shock strengths, pore diameters and multiple pore configurations. Preliminary 3-D simulations are undertaken to quantify the 3-D dynamics.

  8. 3D Tomography of Ionospheric Perturbations Produced by Earthquakes Using Global Positioning System

    NASA Astrophysics Data System (ADS)

    Crespon, F.; Garcia, R.; Lognonné, P.; Murakami, M.

    2004-12-01

    The recent development of Global Positioning System led to establish dense regional networks of bistatic GPS receivers providing today a powerful ionospheric observing system. Now the ionosphere can be imaged by tomographic methods using GPS data. Therefore the ionospheric perturbations can be characterized by monitoring Total Electronic Content (TEC). These disturbances have multiple sources located adove and below ionospheric layers. The most known are the Travelling Ionospheric Disturbances (TID) produced by internal gravity waves. But some ionospheric disturbances are also due to infrasonic waves. We focus this study on ionospheric perturbations generated by infrasonic waves exited by seismic waves, resulting from the coupling between Earth and the atmosphere. We present a spectral analysis of TEC GPS data, the 3D tomographic method and its application to post-seismic perturbations. By removing background noise we are able to monitor acoustic post-seismic waves, generated by the rupture process and the seismic surface waves, that reach the ionosphere. Especially, we show the observations for the Denali earthquake of 3rd November 2002 and the Hokkaido earthquake of 25th September 2003 using respectively the Californian networks (SICGN) and the Japan network (GEONET). Both the horizontal and vertical propagation of the waves are vizualized in the 3D tomographic movies. The observed waves arrive with a timing and a propagation velocity coherent with expected waves and we purpose an interpretation in terms of infrasonic waves in the atmosphere, generated both near the epicenter and at further distance, at the level of the Rayleigh waves front. Finally we present the improvement of the 3D tomographic methods with the advent of the Galileo system and possible application in seismology.

  9. A 3-D liver segmentation method with parallel computing for selective internal radiation therapy.

    PubMed

    Goryawala, Mohammed; Guillen, Magno R; Cabrerizo, Mercedes; Barreto, Armando; Gulec, Seza; Barot, Tushar C; Suthar, Rekha R; Bhatt, Ruchir N; Mcgoron, Anthony; Adjouadi, Malek

    2012-01-01

    This study describes a new 3-D liver segmentation method in support of the selective internal radiation treatment as a treatment for liver tumors. This 3-D segmentation is based on coupling a modified k-means segmentation method with a special localized contouring algorithm. In the segmentation process, five separate regions are identified on the computerized tomography image frames. The merit of the proposed method lays in its potential to provide fast and accurate liver segmentation and 3-D rendering as well as in delineating tumor region(s), all with minimal user interaction. Leveraging of multicore platforms is shown to speed up the processing of medical images considerably, making this method more suitable in clinical settings. Experiments were performed to assess the effect of parallelization using up to 442 slices. Empirical results, using a single workstation, show a reduction in processing time from 4.5 h to almost 1 h for a 78% gain. Most important is the accuracy achieved in estimating the volumes of the liver and tumor region(s), yielding an average error of less than 2% in volume estimation over volumes generated on the basis of the current manually guided segmentation processes. Results were assessed using the analysis of variance statistical analysis.

  10. Analysis of 3-D images of dental imprints using computer vision

    NASA Astrophysics Data System (ADS)

    Aubin, Michele; Cote, Jean; Laurendeau, Denis; Poussart, Denis

    1992-05-01

    This paper addressed two important aspects of dental analysis: (1) location and (2) identification of the types of teeth by means of 3-D image acquisition and segmentation. The 3-D images of both maxillaries are acquired using a wax wafer as support. The interstices between teeth are detected by non-linear filtering of the 3-D and grey-level data. Two operators are presented: one for the detection of the interstices between incisors, canines, and premolars and one for those between molars. Teeth are then identified by mapping the imprint under analysis on the computer model of an 'ideal' imprint. For the mapping to be valid, a set of three reference points is detected on the imprint. Then, the points are put in correspondence with similar points on the model. Two such points are chosen based on a least-squares fit of a second-order polynomial of the 3-D data in the area of canines. This area is of particular interest since the canines show a very characteristic shape and are easily detected on the imprint. The mapping technique is described in detail in the paper as well as pre-processing of the 3-D profiles. Experimental results are presented for different imprints.

  11. Seeing a Mycobacterium-Infected Cell in Nanoscale 3D: Correlative Imaging by Light Microscopy and FIB/SEM Tomography.

    PubMed

    Beckwith, Marianne Sandvold; Beckwith, Kai Sandvold; Sikorski, Pawel; Skogaker, Nan Tostrup; Flo, Trude Helen; Halaas, Øyvind

    2015-01-01

    Mycobacteria pose a threat to the world health today, with pathogenic and opportunistic bacteria causing tuberculosis and non-tuberculous disease in large parts of the population. Much is still unknown about the interplay between bacteria and host during infection and disease, and more research is needed to meet the challenge of drug resistance and inefficient vaccines. This work establishes a reliable and reproducible method for performing correlative imaging of human macrophages infected with mycobacteria at an ultra-high resolution and in 3D. Focused Ion Beam/Scanning Electron Microscopy (FIB/SEM) tomography is applied, together with confocal fluorescence microscopy for localization of appropriately infected cells. The method is based on an Aclar poly(chloro-tri-fluoro)ethylene substrate, micropatterned into an advantageous geometry by a simple thermomoulding process. The platform increases the throughput and quality of FIB/SEM tomography analyses, and was successfully applied to detail the intracellular environment of a whole mycobacterium-infected macrophage in 3D.

  12. Seeing a Mycobacterium-Infected Cell in Nanoscale 3D: Correlative Imaging by Light Microscopy and FIB/SEM Tomography

    PubMed Central

    Beckwith, Marianne Sandvold; Beckwith, Kai Sandvold; Sikorski, Pawel; Skogaker, Nan Tostrup

    2015-01-01

    Mycobacteria pose a threat to the world health today, with pathogenic and opportunistic bacteria causing tuberculosis and non-tuberculous disease in large parts of the population. Much is still unknown about the interplay between bacteria and host during infection and disease, and more research is needed to meet the challenge of drug resistance and inefficient vaccines. This work establishes a reliable and reproducible method for performing correlative imaging of human macrophages infected with mycobacteria at an ultra-high resolution and in 3D. Focused Ion Beam/Scanning Electron Microscopy (FIB/SEM) tomography is applied, together with confocal fluorescence microscopy for localization of appropriately infected cells. The method is based on an Aclar poly(chloro-tri-fluoro)ethylene substrate, micropatterned into an advantageous geometry by a simple thermomoulding process. The platform increases the throughput and quality of FIB/SEM tomography analyses, and was successfully applied to detail the intracellular environment of a whole mycobacterium-infected macrophage in 3D. PMID:26406896

  13. Multi-hole seismic modeling in 3-D space and cross-hole seismic tomography analysis for boulder detection

    NASA Astrophysics Data System (ADS)

    Cheng, Fei; Liu, Jiangping; Wang, Jing; Zong, Yuquan; Yu, Mingyu

    2016-11-01

    A boulder stone, a common geological feature in south China, is referred to the remnant of a granite body which has been unevenly weathered. Undetected boulders could adversely impact the schedule and safety of subway construction when using tunnel boring machine (TBM) method. Therefore, boulder detection has always been a key issue demanded to be solved before the construction. Nowadays, cross-hole seismic tomography is a high resolution technique capable of boulder detection, however, the method can only solve for velocity in a 2-D slice between two wells, and the size and central position of the boulder are generally difficult to be accurately obtained. In this paper, the authors conduct a multi-hole wave field simulation and characteristic analysis of a boulder model based on the 3-D elastic wave staggered-grid finite difference theory, and also a 2-D imaging analysis based on first arrival travel time. The results indicate that (1) full wave field records could be obtained from multi-hole seismic wave simulations. Simulation results describe that the seismic wave propagation pattern in cross-hole high-velocity spherical geological bodies is more detailed and can serve as a basis for the wave field analysis. (2) When a cross-hole seismic section cuts through the boulder, the proposed method provides satisfactory cross-hole tomography results; however, when the section is closely positioned to the boulder, such high-velocity object in the 3-D space would impact on the surrounding wave field. The received diffracted wave interferes with the primary wave and in consequence the picked first arrival travel time is not derived from the profile, which results in a false appearance of high-velocity geology features. Finally, the results of 2-D analysis in 3-D modeling space are comparatively analyzed with the physical model test vis-a-vis the effect of high velocity body on the seismic tomographic measurements.

  14. Energy Dispersive X-ray Tomography for 3D Elemental Mapping of Individual Nanoparticles

    PubMed Central

    Slater, Thomas J. A.; Lewis, Edward A.; Haigh, Sarah J.

    2016-01-01

    Energy dispersive X-ray spectroscopy within the scanning transmission electron microscope (STEM) provides accurate elemental analysis with high spatial resolution, and is even capable of providing atomically resolved elemental maps. In this technique, a highly focused electron beam is incident upon a thin sample and the energy of emitted X-rays is measured in order to determine the atomic species of material within the beam path. This elementally sensitive spectroscopy technique can be extended to three dimensional tomographic imaging by acquiring multiple spectrum images with the sample tilted along an axis perpendicular to the electron beam direction. Elemental distributions within single nanoparticles are often important for determining their optical, catalytic and magnetic properties. Techniques such as X-ray tomography and slice and view energy dispersive X-ray mapping in the scanning electron microscope provide elementally sensitive three dimensional imaging but are typically limited to spatial resolutions of > 20 nm. Atom probe tomography provides near atomic resolution but preparing nanoparticle samples for atom probe analysis is often challenging. Thus, elementally sensitive techniques applied within the scanning transmission electron microscope are uniquely placed to study elemental distributions within nanoparticles of dimensions 10-100 nm. Here, energy dispersive X-ray (EDX) spectroscopy within the STEM is applied to investigate the distribution of elements in single AgAu nanoparticles. The surface segregation of both Ag and Au, at different nanoparticle compositions, has been observed. PMID:27403838

  15. Aquifer Characterization of the Boise Hydrogeophysical Research Site using 3-D Oscillatory Hydraulic Tomography

    NASA Astrophysics Data System (ADS)

    Bakhos, T.; Cardiff, M. A.; Hochstetler, D. L.; Zhou, Y.; Barrash, W.; Kitanidis, P. K.

    2014-12-01

    Hydraulic Tomography is a method of aquifer characterization that estimates hydraulic parameters related to the subsurface, such as hydraulic conductivity and storage, from measurements of hydraulic heads at numerous observation locations during a series of hydrologic tests, commonly pumping tests. Characterizing the subsurface is important for many hydrogeologic projects such as site remediation and groundwater resource exploration. Oscillatory Hydraulic Tomography (OHT) is a method of imaging that uses a tomographic analysis of periodic signals. These signals are generated at distinct locations by oscillatory pumping tests in which fluid is extracted for half a period then re-injected. The transmitted effects of these signals are recorded at observation wells. The resulting measurements can be used to reconstruct the spatial variation of hydraulic parameters by solving a nonlinear inverse problem, which we solve using the geostatistical approach. Oscillatory pumping test data were collected in the summer of 2013 in an extensive field campaign at the Boise Hydrogeophysical Research Site (BHRS), a moderately heterogeneous unconfined aquifer. We present results of OHT applied to the BHRS.

  16. Sub-millimeter resolution 3D optical imaging of living tissue using laminar optical tomography

    PubMed Central

    Hillman, Elizabeth M. C.; Burgess, Sean A.

    2009-01-01

    In-vivo imaging of optical contrast in living tissues can allow measurement of functional parameters such as blood oxygenation and detection of targeted and active fluorescent contrast agents. However, optical imaging must overcome the effects of light scattering, which limit the penetration depth and can affect quantitation and sensitivity. This article focuses on a technique for high-resolution, high-speed depth-resolved optical imaging of superficial living tissues called laminar optical tomography (LOT), which is capable of imaging absorbing and fluorescent contrast in living tissues to depths of 2–3 mm with 100–200 micron resolution. An overview of the advantages and challenges of in-vivo optical imaging is followed by a review of currently available techniques for high-resolution optical imaging of tissues. LOT is then described, including a description of the imaging system design and discussion of data analysis and image reconstruction approaches. Examples of recent applications of LOT are then provided and compared to other existing technologies. By measuring multiply-scattered light, Laminar Optical Tomography can probe beneath the surface of living tissues such as the skin and brain. PMID:19844595

  17. Analytic reconstruction approach for parallel translational computed tomography.

    PubMed

    Kong, Huihua; Yu, Hengyong

    2015-01-01

    To develop low-cost and low-dose computed tomography (CT) scanners for developing countries, recently a parallel translational computed tomography (PTCT) is proposed, and the source and detector are translated oppositely with respect to the imaging object without a slip-ring. In this paper, we develop an analytic filtered-backprojection (FBP)-type reconstruction algorithm for two dimensional (2D) fan-beam PTCT and extend it to three dimensional (3D) cone-beam geometry in a Feldkamp-type framework. Particularly, a weighting function is constructed to deal with data redundancy for multiple translations PTCT to eliminate image artifacts. Extensive numerical simulations are performed to validate and evaluate the proposed analytic reconstruction algorithms, and the results confirm their correctness and merits.

  18. User's guide to the NOZL3D and NOZLIC computer programs

    NASA Technical Reports Server (NTRS)

    Thomas, P. D.

    1980-01-01

    Complete FORTRAN listings and running instructions are given for a set of computer programs that perform an implicit numerical solution to the unsteady Navier-Stokes equations to predict the flow characteristics and performance of nonaxisymmetric nozzles. The set includes the NOZL3D program, which performs the flow computations; the NOZLIC program, which sets up the flow field initial conditions for general nozzle configurations, and also generates the computational grid for simple two dimensional and axisymmetric configurations; and the RGRIDD program, which generates the computational grid for complicated three dimensional configurations. The programs are designed specifically for the NASA-Langley CYBER 175 computer, and employ auxiliary disk files for primary data storage. Input instructions and computed results are given for four test cases that include two dimensional, three dimensional, and axisymmetric configurations.

  19. Computed tomography of nonanesthetized cats with upper airway obstruction.

    PubMed

    Stadler, Krystina; O'Brien, Robert

    2013-01-01

    Upper airway obstruction is a potentially life-threatening problem in cats and for which a noninvasive, sensitive method rapid diagnosis is needed. The purposes of this prospective study were to describe a computed tomography (CT) technique for nonanesthetized cats with upper airway obstruction, CT characteristics of obstructive diseases, and comparisons between CT findings and findings from other diagnostic tests. Ten cats with clinical signs of upper airway obstruction were recruited for the study. Four cats with no clinical signs of upper airway obstruction were recruited as controls. All cats underwent computed tomography imaging without sedation or anesthesia, using a 16-slice helical CT scanner and a previously described transparent positional device. Three-dimensional (3D) internal volume rendering was performed on all CT image sets and 3D external volume rendering was also performed on cats with evidence of mass lesions. Confirmation of upper airway obstruction was based on visual laryngeal examination, endoscopy, fine-needle aspirate, biopsy, or necropsy. Seven cats were diagnosed with intramural upper airway masses, two with laryngotracheitis, and one with laryngeal paralysis. The CT and 3D volume-rendered images identified lesions consistent with upper airway disease in all cats. In cats with mass lesions, CT accurately identified the mass and location. Findings from this study supported the use of CT imaging as an effective technique for diagnosing upper airway obstruction in nonanesthetized cats.

  20. Exploring 3D microstructural evolution in Li-Sulfur battery electrodes using in-situ X-ray tomography

    NASA Astrophysics Data System (ADS)

    Yermukhambetova, Assiya; Tan, Chun; Daemi, Sohrab R.; Bakenov, Zhumabay; Darr, Jawwad A.; Brett, Daniel J. L.; Shearing, Paul R.

    2016-10-01

    Lithium sulfur (Li-S) batteries offer higher theoretical specific capacity, lower cost and enhanced safety compared to current Li-ion battery technology. However, the multiple reactions and phase changes in the sulfur conversion cathode result in highly complex phenomena that significantly impact cycling life. For the first time to the authors’ knowledge, a multi-scale 3D in-situ tomography approach is used to characterize morphological parameters and track microstructural evolution of the sulfur cathode across multiple charge cycles. Here we show the uneven distribution of the sulfur phase fraction within the electrode thickness as a function of charge cycles, suggesting significant mass transport limitations within thick-film sulfur cathodes. Furthermore, we report a shift towards larger particle sizes and a decrease in volume specific surface area with cycling, suggesting sulfur agglomeration. Finally, we demonstrate the nano-scopic length-scale required for the features of the carbon binder domain to become discernible, confirming the need for future work on in-situ nano-tomography. We anticipate that X-ray tomography will be a powerful tool for optimization of electrode structures for Li-S batteries.

  1. Exploring 3D microstructural evolution in Li-Sulfur battery electrodes using in-situ X-ray tomography

    PubMed Central

    Yermukhambetova, Assiya; Tan, Chun; Daemi, Sohrab R.; Bakenov, Zhumabay; Darr, Jawwad A.; Brett, Daniel J. L.; Shearing, Paul R.

    2016-01-01

    Lithium sulfur (Li-S) batteries offer higher theoretical specific capacity, lower cost and enhanced safety compared to current Li-ion battery technology. However, the multiple reactions and phase changes in the sulfur conversion cathode result in highly complex phenomena that significantly impact cycling life. For the first time to the authors’ knowledge, a multi-scale 3D in-situ tomography approach is used to characterize morphological parameters and track microstructural evolution of the sulfur cathode across multiple charge cycles. Here we show the uneven distribution of the sulfur phase fraction within the electrode thickness as a function of charge cycles, suggesting significant mass transport limitations within thick-film sulfur cathodes. Furthermore, we report a shift towards larger particle sizes and a decrease in volume specific surface area with cycling, suggesting sulfur agglomeration. Finally, we demonstrate the nano-scopic length-scale required for the features of the carbon binder domain to become discernible, confirming the need for future work on in-situ nano-tomography. We anticipate that X-ray tomography will be a powerful tool for optimization of electrode structures for Li-S batteries. PMID:27748437

  2. Gust Acoustics Computation with a Space-Time CE/SE Parallel 3D Solver

    NASA Technical Reports Server (NTRS)

    Wang, X. Y.; Himansu, A.; Chang, S. C.; Jorgenson, P. C. E.; Reddy, D. R. (Technical Monitor)

    2002-01-01

    The benchmark Problem 2 in Category 3 of the Third Computational Aero-Acoustics (CAA) Workshop is solved using the space-time conservation element and solution element (CE/SE) method. This problem concerns the unsteady response of an isolated finite-span swept flat-plate airfoil bounded by two parallel walls to an incident gust. The acoustic field generated by the interaction of the gust with the flat-plate airfoil is computed by solving the 3D (three-dimensional) Euler equations in the time domain using a parallel version of a 3D CE/SE solver. The effect of the gust orientation on the far-field directivity is studied. Numerical solutions are presented and compared with analytical solutions, showing a reasonable agreement.

  3. The computer simulation of 3d gas dynamics in a gas centrifuge

    NASA Astrophysics Data System (ADS)

    Borman, V. D.; Bogovalov, S. V.; Borisevich, V. D.; Tronin, I. V.; Tronin, V. N.

    2016-09-01

    We argue on the basis of the results of 2D analysis of the gas flow in gas centrifuges that a reliable calculation of the circulation of the gas and gas content in the gas centrifuge is possible only in frameworks of 3D numerical simulation of gas dynamics in the gas centrifuge (hereafter GC). The group from National research nuclear university, MEPhI, has created a computer code for 3D simulation of the gas flow in GC. The results of the computer simulations of the gas flows in GC are presented. A model Iguassu centrifuge is explored for the simulations. A nonaxisymmetric gas flow is produced due to interaction of the hypersonic rotating flow with the scoops for extraction of the product and waste flows from the GC. The scoops produce shock waves penetrating into a working camera of the GC and form spiral waves there.

  4. SALE-3D: a simplified ALE computer program for calculating three-dimensional fluid flow

    SciTech Connect

    Amsden, A.A.; Ruppel, H.M.

    1981-11-01

    This report presents a simplified numerical fluid-dynamics computing technique for calculating time-dependent flows in three dimensions. An implicit treatment of the pressure equation permits calculation of flows far subsonic without stringent constraints on the time step. In addition, the grid vertices may be moved with the fluid in Lagrangian fashion or held fixed in an Eulerian manner, or moved in some prescribed manner to give a continuous rezoning capability. This report describes the combination of Implicit Continuous-fluid Eulerian (ICE) and Arbitrary Lagrangian-Eulerian (ALE) to form the ICEd-ALE technique in the framework of the Simplified-ALE (SALE-3D) computer program, for which a general flow diagram and complete FORTRAN listing are included. Sample problems show how to modify the code for a variety of applications. SALE-3D is patterned as closely as possible on the previously reported two-dimensional SALE program.

  5. Integration of 3D anatomical data obtained by CT imaging and 3D optical scanning for computer aided implant surgery

    PubMed Central

    2011-01-01

    Background A precise placement of dental implants is a crucial step to optimize both prosthetic aspects and functional constraints. In this context, the use of virtual guiding systems has been recognized as a fundamental tool to control the ideal implant position. In particular, complex periodontal surgeries can be performed using preoperative planning based on CT data. The critical point of the procedure relies on the lack of accuracy in transferring CT planning information to surgical field through custom-made stereo-lithographic surgical guides. Methods In this work, a novel methodology is proposed for monitoring loss of accuracy in transferring CT dental information into periodontal surgical field. The methodology is based on integrating 3D data of anatomical (impression and cast) and preoperative (radiographic template) models, obtained by both CT and optical scanning processes. Results A clinical case, relative to a fully edentulous jaw patient, has been used as test case to assess the accuracy of the various steps concurring in manufacturing surgical guides. In particular, a surgical guide has been designed to place implants in the bone structure of the patient. The analysis of the results has allowed the clinician to monitor all the errors, which have been occurring step by step manufacturing the physical templates. Conclusions The use of an optical scanner, which has a higher resolution and accuracy than CT scanning, has demonstrated to be a valid support to control the precision of the various physical models adopted and to point out possible error sources. A case study regarding a fully edentulous patient has confirmed the feasibility of the proposed methodology. PMID:21338504

  6. Automated in vivo 3D high-definition optical coherence tomography skin analysis system.

    PubMed

    Ai Ping Yow; Jun Cheng; Annan Li; Srivastava, Ruchir; Jiang Liu; Wong, Damon Wing Kee; Hong Liang Tey

    2016-08-01

    The in vivo assessment and visualization of skin structures can be performed through the use of high resolution optical coherence tomography imaging, also known as HD-OCT. However, the manual assessment of such images can be exhaustive and time consuming. In this paper, we present an analysis system to automatically identify and quantify the skin characteristics such as the topography of the surface of the skin and thickness of the epidermis in HD-OCT images. Comparison of this system with manual clinical measurements demonstrated its potential for automatic objective skin analysis and diseases diagnosis. To our knowledge, this is the first report of an automated system to process and analyse HD-OCT skin images.

  7. Effectiveness Evaluation of Force Protection Training Using Computer-Based Instruction and X3d Simulation

    DTIC Science & Technology

    2007-09-01

    to growing operational constraints accelerated by the Global War on Terror, the United States Navy is looking for alternative methods of training to...accomplished efficiently and effectively, saving the U.S. Navy time and resources while maintaining a high state of readiness. The goal of this thesis is...COMPUTER-BASED INSTRUCTION AND X3D SIMULATION Wilfredo Cruzbaez Lieutenant, United States Navy B.A., Norfolk State University, 2001 Submitted in

  8. Computer-aided planning and reconstruction of cranial 3D implants.

    PubMed

    Gall, Markus; Xing Li; Xiaojun Chen; Schmalstieg, Dieter; Egger, Jan

    2016-08-01

    In this contribution, a prototype for semiautomatic computer-aided planning and reconstruction of cranial 3D Implants is presented. The software prototype guides the user through the workflow, beginning with loading and mirroring the patient's head to obtain an initial curvature of the cranial implant. However, naïve mirroring is not sufficient for an implant, because human heads are in general too asymmetric. Thus, the user can perform Laplacian smoothing, followed by Delaunay triangulation, for generating an aesthetic looking and well-fitting implant. Finally, our software prototype allows to save the designed 3D model of the implant as a STL-file for 3D printing. The 3D printed implant can be used for further pre-interventional planning or even as the final implant for the patient. In summary, our findings show that a customized MeVisLab prototype can be an alternative to complex commercial planning software, which may not be available in a clinic.

  9. 3D animation of facial plastic surgery based on computer graphics

    NASA Astrophysics Data System (ADS)

    Zhang, Zonghua; Zhao, Yan

    2013-12-01

    More and more people, especial women, are getting desired to be more beautiful than ever. To some extent, it becomes true because the plastic surgery of face was capable in the early 20th and even earlier as doctors just dealing with war injures of face. However, the effect of post-operation is not always satisfying since no animation could be seen by the patients beforehand. In this paper, by combining plastic surgery of face and computer graphics, a novel method of simulated appearance of post-operation will be given to demonstrate the modified face from different viewpoints. The 3D human face data are obtained by using 3D fringe pattern imaging systems and CT imaging systems and then converted into STL (STereo Lithography) file format. STL file is made up of small 3D triangular primitives. The triangular mesh can be reconstructed by using hash function. Top triangular meshes in depth out of numbers of triangles must be picked up by ray-casting technique. Mesh deformation is based on the front triangular mesh in the process of simulation, which deforms interest area instead of control points. Experiments on face model show that the proposed 3D animation facial plastic surgery can effectively demonstrate the simulated appearance of post-operation.

  10. Mount Etna: 3-D and 4-D structure using seismic tomography

    NASA Astrophysics Data System (ADS)

    Nunn, C.; Julian, B. R.; Foulger, G. R.; Patanè, D.; Ibáñez, J. M.; Briole, P.; Mhanna, N.

    2015-12-01

    We investigate the time-varying structure of Etna, an active stratovolcano in eastern Sicily, using seismic tomography. In volcanic systems, it is thought that the presence of fluids, cracks and pressurized gases can rapidly and drastically change the elastic properties of the host rocks. Recent work suggests that changes beneath Etna are detectable with seismic methods, and that these changes can be linked to volcanic activity. Temporal changes to Earth structure are commonly investigated by carrying out separate tomographic inversions for different epochs. However, repeated inversions of the same area are expected to vary, even if the structure itself does not change. This is due to variations in the seismic ray distribution and to observational errors. Potentially, changes between epochs which are due to experimental limitations can be misinterpreted as changes to the structure of the volcano. Consequently, we use a new tomographic program, TOMO4D, that inverts multiple data sets simultaneously [Julian & Foulger, Time-dependent seismic tomography, GJI, 2010]. This code imposes constraints which minimise the differences calculated between two epochs. The remaining structural variations are thus truly required to fit the data, and reflect changes which almost certainly exist between the two epochs. We have selected and relocated ~400 local earthquakes with at least 5 P and 5 S observations. They cover a period which includes several eruptions, from 1st November 2000 to 31st December 2006. We divide our data into different epochs and invert two epochs simultaneously. The models show a seismically fast central region, surrounded by a slower outer region. This suggests a central system of dykes or sills surrounded by volcanic sediments and country rock. At depths of 0-4 km below sea level the seismically fast region is not below the summit crater but is offset to the southwest. By monitoring the changes to the elastic parameters of the host rocks we observe temporal

  11. THERM3D -- A boundary element computer program for transient heat conduction problems

    SciTech Connect

    Ingber, M.S.

    1994-02-01

    The computer code THERM3D implements the direct boundary element method (BEM) to solve transient heat conduction problems in arbitrary three-dimensional domains. This particular implementation of the BEM avoids performing time-consuming domain integrations by approximating a ``generalized forcing function`` in the interior of the domain with the use of radial basis functions. An approximate particular solution is then constructed, and the original problem is transformed into a sequence of Laplace problems. The code is capable of handling a large variety of boundary conditions including isothermal, specified flux, convection, radiation, and combined convection and radiation conditions. The computer code is benchmarked by comparisons with analytic and finite element results.

  12. Computation of an Underexpanded 3-D Rectangular Jet by the CE/SE Method

    NASA Technical Reports Server (NTRS)

    Loh, Ching Y.; Himansu, Ananda; Wang, Xiao Y.; Jorgenson, Philip C. E.

    2000-01-01

    Recently, an unstructured three-dimensional space-time conservation element and solution element (CE/SE) Euler solver was developed. Now it is also developed for parallel computation using METIS for domain decomposition and MPI (message passing interface). The method is employed here to numerically study the near-field of a typical 3-D rectangular under-expanded jet. For the computed case-a jet with Mach number Mj = 1.6. with a very modest grid of 1.7 million tetrahedrons, the flow features such as the shock-cell structures and the axis switching, are in good qualitative agreement with experimental results.

  13. Full 3-D OCT-based pseudophakic custom computer eye model

    PubMed Central

    Sun, M.; Pérez-Merino, P.; Martinez-Enriquez, E.; Velasco-Ocana, M.; Marcos, S.

    2016-01-01

    We compared measured wave aberrations in pseudophakic eyes implanted with aspheric intraocular lenses (IOLs) with simulated aberrations from numerical ray tracing on customized computer eye models, built using quantitative 3-D OCT-based patient-specific ocular geometry. Experimental and simulated aberrations show high correlation (R = 0.93; p<0.0001) and similarity (RMS for high order aberrations discrepancies within 23.58%). This study shows that full OCT-based pseudophakic custom computer eye models allow understanding the relative contribution of optical geometrical and surgically-related factors to image quality, and are an excellent tool for characterizing and improving cataract surgery. PMID:27231608

  14. Distributed network, wireless and cloud computing enabled 3-D ultrasound; a new medical technology paradigm.

    PubMed

    Meir, Arie; Rubinsky, Boris

    2009-11-19

    Medical technologies are indispensable to modern medicine. However, they have become exceedingly expensive and complex and are not available to the economically disadvantaged majority of the world population in underdeveloped as well as developed parts of the world. For example, according to the World Health Organization about two thirds of the world population does not have access to medical imaging. In this paper we introduce a new medical technology paradigm centered on wireless technology and cloud computing that was designed to overcome the problems of increasing health technology costs. We demonstrate the value of the concept with an example; the design of a wireless, distributed network and central (cloud) computing enabled three-dimensional (3-D) ultrasound system. Specifically, we demonstrate the feasibility of producing a 3-D high end ultrasound scan at a central computing facility using the raw data acquired at the remote patient site with an inexpensive low end ultrasound transducer designed for 2-D, through a mobile device and wireless connection link between them. Producing high-end 3D ultrasound images with simple low-end transducers reduces the cost of imaging by orders of magnitude. It also removes the requirement of having a highly trained imaging expert at the patient site, since the need for hand-eye coordination and the ability to reconstruct a 3-D mental image from 2-D scans, which is a necessity for high quality ultrasound imaging, is eliminated. This could enable relatively untrained medical workers in developing nations to administer imaging and a more accurate diagnosis, effectively saving the lives of people.

  15. Computer Tomography Analysis of Fastrac Composite Thrust Chamber Assemblies

    NASA Technical Reports Server (NTRS)

    Beshears, Ronald D.

    2000-01-01

    Computed tomography (CT) inspection has been integrated into the production process for NASA's Fastrac composite thrust chamber assemblies (TCAs). CT has been proven to be uniquely qualified to detect the known critical flaw for these nozzles, liner cracks that are adjacent to debonds between the liner and overwrap. CT is also being used as a process monitoring tool through analysis of low density indications in the nozzle overwraps. 3d reconstruction of CT images to produce models of flawed areas is being used to give program engineers better insight into the location and nature of nozzle flaws.

  16. A New Ionosphere Tomography Algorithm with Two-Grids Virtual Observations Constraints and 3D Velocity Profile

    NASA Astrophysics Data System (ADS)

    Kong, Jian; Yao, Yibin; Shum, Che-Kwan

    2014-05-01

    Due to the sparsity of world's GNSS stations and limitations of projection angles, GNSS-based ionosphere tomography is a typical ill-posed problem. There are two main ways to solve this problem. Firstly the joint inversion method combining multi-source data is one of the effective ways. Secondly using a priori or reference ionosphere models, e.g., IRI or GIM models, as the constraints to improve the state of normal equation is another effective approach. The traditional way for adding constraints with virtual observations can only solve the problem of sparse stations but the virtual observations still lack horizontal grid constraints therefore unable to fundamentally improve the near-singularity characteristic of the normal equation. In this paper, we impose a priori constraints by increasing the virtual observations in n-dimensional space, which can greatly reduce the condition number of the normal equation. Then after the inversion region is gridded, we can form a stable structure among the grids with loose constraints. We then further consider that the ionosphere indeed changes within certain temporal scale, e.g., two hours. In order to establish a more sophisticated and realistic ionosphere model and obtain the real time ionosphere electron density velocity (IEDV) information, we introduce the grid electron density velocity parameters, which can be estimated with electron density parameters simultaneously. The velocity parameters not only can enhance the temporal resolution of the ionosphere model thereby reflecting more elaborate structure (short-term disturbances) under ionosphere disturbances status, but also provide a new way for the real-time detection and prediction of ionosphere 3D changes. We applied the new algorithm to the GNSS data collected in Europe for tomography inversion for ionosphere electron density and velocity at 2-hour resolutions, which are consistent throughout the whole day variation. We then validate the resulting tomography model

  17. Panoramic cone beam computed tomography

    SciTech Connect

    Chang Jenghwa; Zhou Lili; Wang Song; Clifford Chao, K. S.

    2012-05-15

    Purpose: Cone-beam computed tomography (CBCT) is the main imaging tool for image-guided radiotherapy but its functionality is limited by a small imaging volume and restricted image position (imaged at the central instead of the treatment position for peripheral lesions to avoid collisions). In this paper, the authors present the concept of ''panoramic CBCT,'' which can image patients at the treatment position with an imaging volume as large as practically needed. Methods: In this novel panoramic CBCT technique, the target is scanned sequentially from multiple view angles. For each view angle, a half scan (180 deg. + {theta}{sub cone} where {theta}{sub cone} is the cone angle) is performed with the imaging panel positioned in any location along the beam path. The panoramic projection images of all views for the same gantry angle are then stitched together with the direct image stitching method (i.e., according to the reported imaging position) and full-fan, half-scan CBCT reconstruction is performed using the stitched projection images. To validate this imaging technique, the authors simulated cone-beam projection images of the Mathematical Cardiac Torso (MCAT) thorax phantom for three panoramic views. Gaps, repeated/missing columns, and different exposure levels were introduced between adjacent views to simulate imperfect image stitching due to uncertainties in imaging position or output fluctuation. A modified simultaneous algebraic reconstruction technique (modified SART) was developed to reconstruct CBCT images directly from the stitched projection images. As a gold standard, full-fan, full-scan (360 deg. gantry rotation) CBCT reconstructions were also performed using projection images of one imaging panel large enough to encompass the target. Contrast-to-noise ratio (CNR) and geometric distortion were evaluated to quantify the quality of reconstructed images. Monte Carlo simulations were performed to evaluate the effect of scattering on the image quality and

  18. Computed tomography in supratentorial hemangioblastoma.

    PubMed

    Romero, F J; Rovira, M; Ortega, A; Ibarra, B

    1984-01-01

    Supratentorial hemangioblastomas are rare. A 28-yr-old man with a solid tumor in the left temporal region is described. There was neither meningeal connection nor associated polycythemia or Von Hippel-Lindau disease. Contrast enhanced computerized tomography showed a hyperdense, homogeneous lesion and cerebral angiography demonstrated a nodular tumor blush. The microscopic appearance of the lesion is described with a review of previously reported cases.

  19. In-situ biofouling assessment in spacer filled channels using optical coherence tomography (OCT): 3D biofilm thickness mapping.

    PubMed

    Fortunato, Luca; Leiknes, TorOve

    2017-04-01

    Membrane systems for water purification can be seriously hampered by biofouling. The use of optical coherence tomography (OCT) to investigate biofilms in membrane systems has recently increased due to the ability to do the characterization in-situ and non-destructively. The OCT biofilm thickness map is presented for the first time as a tool to assess biofilm spatial distribution on a surface. The map allows the visualization and evaluation of the biofilm formation and growth in membrane filtration systems through the use of a false color scale. The biofilm development was monitored with OCT to evaluate the suitability of the proposed approach. A 3D time series analysis of biofilm development in a spacer filled channel representative of a spiral-wound membrane element was performed. The biofilm thickness map enables the time-resolved and spatial-resolved evaluation and visualization of the biofilm deposition pattern in-situ non-destructively.

  20. 3D histomorphometric quantification of trabecular bones by computed microtomography using synchrotron radiation.

    PubMed

    Nogueira, L P; Braz, D; Barroso, R C; Oliveira, L F; Pinheiro, C J G; Dreossi, D; Tromba, G

    2010-12-01

    Conventional bone histomorphometry is an important method for quantitative evaluation of bone microstructure. X-ray computed microtomography is a non-invasive technique, which can be used to evaluate histomorphometric indices in trabecular bones (BV/TV, BS/BV, Tb.N, Tb.Th, Tb.Sp). In this technique, 3D images are used to quantify the whole sample, differently from the conventional one, in which the quantification is performed in 2D slices and extrapolated for 3D case. In this work, histomorphometric quantification using synchrotron 3D X-ray computed microtomography was performed to quantify the bone structure at different skeletal sites as well as to investigate the effects of bone diseases on quantitative understanding of bone architecture. The images were obtained at Synchrotron Radiation for MEdical Physics (SYRMEP) beamline, at ELETTRA synchrotron radiation facility, Italy. Concerning the obtained results for normal and pathological bones from same skeletal sites and individuals, from our results, a certain declining bone volume fraction was achieved. The results obtained could be used in forming the basis for comparison of the bone microarchitecture and can be a valuable tool for predicting bone fragility.

  1. Design and highly accurate 3D displacement characterization of monolithic SMA microgripper using computer vision

    NASA Astrophysics Data System (ADS)

    Bellouard, Yves; Sulzmann, Armin; Jacot, Jacques; Clavel, Reymond

    1998-01-01

    In the robotics field, several grippers have been developed using SMA technologies, but, so far, SMA is only used as the actuating part of the mechanical device. However mechanical device requires assembly and in some cases this means friction. In the case of micro-grippers, this becomes a major problem due to the small size of the components. In this paper, a new monolithic concept of micro-gripper is presented. This concept is applied to the grasping of sub- millimeter optical elements such as Selfoc lenses and the fastening of optical fibers. Measurements are performed using a newly developed high precision 3D-computer vision tracking system to characterize the spatial positions of the micro-gripper in action. To characterize relative motion of the micro-gripper the natural texture of the micro-gripper is used to compute 3D displacement. The microscope image CCD receivers high frequency changes in light intensity from the surface of the ripper. Using high resolution camera calibration, passive auto focus algorithms and 2D object recognition, the position of the micro-gripper can be characterized in the 3D workspace and can be guided in future micro assembly tasks.

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

    SciTech Connect

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

    2010-12-02

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

  3. 3-D transient hydraulic tomography in unconfined aquifers with fast drainage response

    NASA Astrophysics Data System (ADS)

    Cardiff, M.; Barrash, W.

    2011-12-01

    We investigate, through numerical experiments, the viability of three-dimensional transient hydraulic tomography (3DTHT) for identifying the spatial distribution of groundwater flow parameters (primarily, hydraulic conductivity K) in permeable, unconfined aquifers. To invert the large amount of transient data collected from 3DTHT surveys, we utilize an iterative geostatistical inversion strategy in which outer iterations progressively increase the number of data points fitted and inner iterations solve the quasi-linear geostatistical formulas of Kitanidis. In order to base our numerical experiments around realistic scenarios, we utilize pumping rates, geometries, and test lengths similar to those attainable during 3DTHT field campaigns performed at the Boise Hydrogeophysical Research Site (BHRS). We also utilize hydrologic parameters that are similar to those observed at the BHRS and in other unconsolidated, unconfined fluvial aquifers. In addition to estimating K, we test the ability of 3DTHT to estimate both average storage values (specific storage Ss and specific yield Sy) as well as spatial variability in storage coefficients. The effects of model conceptualization errors during unconfined 3DTHT are investigated including: (1) assuming constant storage coefficients during inversion and (2) assuming stationary geostatistical parameter variability. Overall, our findings indicate that estimation of K is slightly degraded if storage parameters must be jointly estimated, but that this effect is quite small compared with the degradation of estimates due to violation of "structural" geostatistical assumptions. Practically, we find for our scenarios that assuming constant storage values during inversion does not appear to have a significant effect on K estimates or uncertainty bounds.

  4. Characterization of reactive transport by 3-D electrical resistivity tomography (ERT) under unsaturated conditions

    NASA Astrophysics Data System (ADS)

    Wehrer, Markus; Binley, Andrew; Slater, Lee D.

    2016-10-01

    The leaching of nitrate from intensively used arable soil is of major concern in many countries. In this study, we show how time lapse electrical resistivity tomography (ERT) can be used to characterize spatially heterogeneous processes of ion production, consumption, and transport in soils. A controlled release fertilizer was introduced into an undisturbed soil core in a laboratory lysimeter and subjected to infiltration events. The production of ions resulting from processes associated with nitrification and their transport through the soil core was observed by time lapse ERT and analysis of seepage water samples from a multicompartment sampler. ERT images show development and propagation of a high-conductivity plume from the fertilizer source zone. Molar amounts of nitrate produced in and exported from the soil core could be well reproduced by time lapse ERT using a spatial moment analysis. Furthermore, we observed that several shape measures of local breakthrough-curves (BTCs) of seepage water conductivity and nitrate derived by effluent analyses and BTCs of bulk conductivity derived by ERT are highly correlated, indicating the preservation of spatial differences of the plume breakthrough in the ERT data. Also differences between nitrate breakthrough and a conservative tracer breakthrough can be observed by ERT. However, the estimation of target ion concentrations by ERT is error bound and the smoothing algorithm of the inversion masks spatial conductivity differences. This results in difficulties reproducing spatial differences of ion source functions and variances of travel times. Despite the observed limitations, we conclude that time lapse ERT can be qualitatively and quantitatively informative with respect to processes affecting the fate of nitrate in arable soils.

  5. 3-D Transient Hydraulic Tomography in Unconfined Aquifers with Fast Drainage Response

    SciTech Connect

    Cardiff, Michael A.; Barrash, Warren

    2011-12-16

    We investigate, through numerical experiments, the viability of three-dimensional transient hydraulic tomography (3DTHT) for identifying the spatial distribution of groundwater flow parameters (primarily, hydraulic conductivity K) in permeable, unconfined aquifers. To invert the large amount of transient data collected from 3DTHT surveys, we utilize an iterative geostatistical inversion strategy in which outer iterations progressively increase the number of data points fitted and inner iterations solve the quasilinear geostatistical formulas of Kitanidis. In order to base our numerical experiments around realistic scenarios, we utilize pumping rates, geometries, and test lengths similar to those attainable during 3DTHT field campaigns performed at the Boise Hydrogeophysical Research Site (BHRS). We also utilize hydrologic parameters that are similar to those observed at the BHRS and in other unconsolidated, unconfined fluvial aquifers. In addition to estimating K, we test the ability of 3DTHT to estimate both average storage values (specific storage Ss and specific yield Sy) as well as spatial variability in storage coefficients. The effects of model conceptualization errors during unconfined 3DTHT are investigated including: (1) assuming constant storage coefficients during inversion and (2) assuming stationary geostatistical parameter variability. Overall, our findings indicate that estimation of K is slightly degraded if storage parameters must be jointly estimated, but that this effect is quite small compared with the degradation of estimates due to violation of ‘‘structural’’ geostatistical assumptions. Practically, we find for our scenarios that assuming constant storage values during inversion does not appear to have a significant effect on K estimates or uncertainty bounds.

  6. Realistic 3D computer model of the gerbil middle ear, featuring accurate morphology of bone and soft tissue structures.

    PubMed

    Buytaert, Jan A N; Salih, Wasil H M; Dierick, Manual; Jacobs, Patric; Dirckx, Joris J J

    2011-12-01

    In order to improve realism in middle ear (ME) finite-element modeling (FEM), comprehensive and precise morphological data are needed. To date, micro-scale X-ray computed tomography (μCT) recordings have been used as geometric input data for FEM models of the ME ossicles. Previously, attempts were made to obtain these data on ME soft tissue structures as well. However, due to low X-ray absorption of soft tissue, quality of these images is limited. Another popular approach is using histological sections as data for 3D models, delivering high in-plane resolution for the sections, but the technique is destructive in nature and registration of the sections is difficult. We combine data from high-resolution μCT recordings with data from high-resolution orthogonal-plane fluorescence optical-sectioning microscopy (OPFOS), both obtained on the same gerbil specimen. State-of-the-art μCT delivers high-resolution data on the 3D shape of ossicles and other ME bony structures, while the OPFOS setup generates data of unprecedented quality both on bone and soft tissue ME structures. Each of these techniques is tomographic and non-destructive and delivers sets of automatically aligned virtual sections. The datasets coming from different techniques need to be registered with respect to each other. By combining both datasets, we obtain a complete high-resolution morphological model of all functional components in the gerbil ME. The resulting 3D model can be readily imported in FEM software and is made freely available to the research community. In this paper, we discuss the methods used, present the resulting merged model, and discuss the morphological properties of the soft tissue structures, such as muscles and ligaments.

  7. Computer-assisted three-dimensional surgical planning: 3D virtual articulator: technical note.

    PubMed

    Ghanai, S; Marmulla, R; Wiechnik, J; Mühling, J; Kotrikova, B

    2010-01-01

    This study presents a computer-assisted planning system for dysgnathia treatment. It describes the process of information gathering using a virtual articulator and how the splints are constructed for orthognathic surgery. The deviation of the virtually planned splints is shown in six cases on the basis of conventionally planned cases. In all cases the plaster models were prepared and scanned using a 3D laser scanner. Successive lateral and posterior-anterior cephalometric images were used for reconstruction before surgery. By identifying specific points on the X-rays and marking them on the virtual models, it was possible to enhance the 2D images to create a realistic 3D environment and to perform virtual repositioning of the jaw. A hexapod was used to transfer the virtual planning to the real splints. Preliminary results showed that conventional repositioning could be replicated using the virtual articulator.

  8. Effect of Random Geometric Uncertainty on the Computational Design of a 3-D Flexible Wing

    NASA Technical Reports Server (NTRS)

    Gumbert, C. R.; Newman, P. A.; Hou, G. J.-W.

    2002-01-01

    The effect of geometric uncertainty due to statistically independent, random, normally distributed shape parameters is demonstrated in the computational design of a 3-D flexible wing. A first-order second-moment statistical approximation method is used to propagate the assumed input uncertainty through coupled Euler CFD aerodynamic / finite element structural codes for both analysis and sensitivity analysis. First-order sensitivity derivatives obtained by automatic differentiation are used in the input uncertainty propagation. These propagated uncertainties are then used to perform a robust design of a simple 3-D flexible wing at supercritical flow conditions. The effect of the random input uncertainties is shown by comparison with conventional deterministic design results. Sample results are shown for wing planform, airfoil section, and structural sizing variables.

  9. The 3D crustal structure of Northeastern Tibetan area from seismic tomography

    NASA Astrophysics Data System (ADS)

    Sun, Anhui

    2015-04-01

    The Northeastern Tibetan region is located in the border area of three sub-plates in China, i.e. the Tibetan plateau, North China block and Xinjiang block. Effected simultaneously by the extrusion driven by the India-Eurasia plat collision and the blockage of the Ordos basin, this area has complex geology, strong tectonics activities and suffered from several large historic earthquakes, such as the Haiyuan earthquake (M8.6) in 1920, the Gulang earthquake (M8.0) in 1927. To enhance our understanding of the crustal structure and the interaction between different tectonic blocks of this region, we conduct a three-dimensional (3D) tomographic study by using the arrival time date recorded by regional seismic network. We used 101101 P and 103313 S wave arrival times from 11650 local earthquakes during 1970 to 2013 recorded by 154 permanent seismic stations of the local Seismic Network, installed over five provinces in China, i.e. Gansu, Ningxia, Qinghai, Shanxi, Neimenggu. We first established a 1D primary crustal model from LITHO1.0, an updated crust and lithospheric model of the Earth by weighted averaging. To better performer ray tracing, our inversion involved three discontinuities (including the Moho) with depth variation over the mantle derived from LITHO1.0. Detailed three-dimensional seismic velocity (Vp and Vs) structures of the crust of the Northeastern Tibetan are determined with a horizontal resolution of about 35 km and a depth resolution of 6-20 km. The Poisson's ratio (σ) structure was also estimated after obtained Vp and Vs structures. We detected low-velocity anomalies in the lower crust and relative high-velocity anomalies in the upper crust beneath the Longmenshan faults zone, which are in good agreement with the results of most previous geophysical studies. Our results revealed clear different velocity variation beneath both sides of different tectonic blocks. In addition, we found the correlation between our tomographic result and previous

  10. Estimation of local stresses and elastic properties of a mortar sample by FFT computation of fields on a 3D image

    SciTech Connect

    Escoda, J.; Willot, F.; Jeulin, D.; Sanahuja, J.; Toulemonde, C.

    2011-05-15

    This study concerns the prediction of the elastic properties of a 3D mortar image, obtained by micro-tomography, using a combined image segmentation and numerical homogenization approach. The microstructure is obtained by segmentation of the 3D image into aggregates, voids and cement paste. Full-fields computations of the elastic response of mortar are undertaken using the Fast Fourier Transform method. Emphasis is made on highly-contrasted properties between aggregates and matrix, to anticipate needs for creep or damage computation. The representative volume element, i.e. the volume size necessary to compute the effective properties with a prescribed accuracy, is given. Overall, the volumes used in this work were sufficient to estimate the effective response of mortar with a precision of 5%, 6% and 10% for contrast ratios of 100, 1000 and 10,000, resp. Finally, a statistical and local characterization of the component of the stress field parallel to the applied loading is carried out.

  11. Calcaneal osteotomy preoperative planning system with 3D full-sized computer-assisted technology.

    PubMed

    Chou, Yi-Jiun; Sun, Shuh-Ping; Liu, Hsin-Hua

    2011-10-01

    In this study, we developed a CT-based computer-assisted pre-operative planning and simulating system for the calcaneal osteotomy by integrating different software's function. This system uses the full-scaled 3D reverse engineering technique in designing and developing preoperative planning modules for the calcaneal osteotomy surgery. The planning system presents a real-sized three-dimensional image of the calcaneus, and provides detailed interior measurements of the calcaneus from various cutting planes. This study applied computer-assisted technology to integrate different software's function to a surgical planning system. These functions include 3-D image model capturing, cutting, moving, rotating and measurement for relevant foot anatomy, and can be integrated as the user's function. Furthermore, the system is computer-based and computer-assisted technology. Surgeons can utilize it as part of preoperative planning to develop efficient operative procedures. This system also has a database that can be updated and extended and will provide the clinical cases to different users for experienced based learning.

  12. Master-slave interferometry for parallel spectral domain interferometry sensing and versatile 3D optical coherence tomography.

    PubMed

    Podoleanu, Adrian Gh; Bradu, Adrian

    2013-08-12

    Conventional spectral domain interferometry (SDI) methods suffer from the need of data linearization. When applied to optical coherence tomography (OCT), conventional SDI methods are limited in their 3D capability, as they cannot deliver direct en-face cuts. Here we introduce a novel SDI method, which eliminates these disadvantages. We denote this method as Master - Slave Interferometry (MSI), because a signal is acquired by a slave interferometer for an optical path difference (OPD) value determined by a master interferometer. The MSI method radically changes the main building block of an SDI sensor and of a spectral domain OCT set-up. The serially provided signal in conventional technology is replaced by multiple signals, a signal for each OPD point in the object investigated. This opens novel avenues in parallel sensing and in parallelization of signal processing in 3D-OCT, with applications in high- resolution medical imaging and microscopy investigation of biosamples. Eliminating the need of linearization leads to lower cost OCT systems and opens potential avenues in increasing the speed of production of en-face OCT images in comparison with conventional SDI.

  13. High-resolution 3-D P wave attenuation structure of the New Madrid Seismic Zone using local earthquake tomography

    NASA Astrophysics Data System (ADS)

    Bisrat, Shishay T.; DeShon, Heather R.; Pesicek, Jeremy; Thurber, Clifford

    2014-01-01

    A three-dimensional (3-D), high-resolution P wave seismic attenuation model for the New Madrid Seismic Zone (NMSZ) is determined using P wave path attenuation (t*) values of small-magnitude earthquakes (MD < 3.9). Events were recorded at 89 broadband and short-period seismometers of the Cooperative New Madrid Seismic Zone Network and 40 short-period seismometers of the Portable Array for Numerical Data Acquisition experiment. The amplitude spectra of all the earthquakes are simultaneously inverted for source, path (t*), and site parameters. The t* values are inverted for QP using local earthquake tomography methods and a known 3-D P wave velocity model for the region. The four major seismicity arms of the NMSZ exhibit reduced QP (higher attenuation) than the surrounding crust. The highest attenuation anomalies coincide with areas of previously reported high swarm activity attributed to fluid-rich fractures along the southeast extension of the Reelfoot fault. The QP results are consistent with previous attenuation studies in the region, which showed that active fault zones and fractured crust in the NMSZ are highly attenuating.

  14. Simultaneous real-time 3D photoacoustic tomography and EEG for neurovascular coupling study in an animal model of epilepsy

    NASA Astrophysics Data System (ADS)

    Wang, Bo; Xiao, Jiaying; Jiang, Huabei

    2014-08-01

    Objective. Neurovascular coupling in epilepsy is poorly understood; its study requires simultaneous monitoring of hemodynamic changes and neural activity in the brain. Approach. Here for the first time we present a combined real-time 3D photoacoustic tomography (PAT) and electrophysiology/electroencephalography (EEG) system for the study of neurovascular coupling in epilepsy, whose ability was demonstrated with a pentylenetetrazol (PTZ) induced generalized seizure model in rats. Two groups of experiments were carried out with different wavelengths to detect the changes of oxy-hemoglobin (HbO2) and deoxy-hemoglobin (HbR) signals in the rat brain. We extracted the average PAT signals of the superior sagittal sinus (SSS), and compared them with the EEG signal. Main results. Results showed that the seizure process can be divided into three stages. A ‘dip’ lasting for 1-2 min in the first stage and the following hyperfusion in the second stage were observed. The HbO2 signal and the HbR signal were generally negatively correlated. The change of blood flow was also estimated. All the acquired results here were in accordance with other published results. Significance. Compared to other existing functional neuroimaging tools, the method proposed here enables reliable tracking of hemodynamic signal with both high spatial and high temporal resolution in 3D, so it is more suitable for neurovascular coupling study of epilepsy.

  15. A novel iterative computation algorithm for Kinoform of 3D object

    NASA Astrophysics Data System (ADS)

    Jiang, Xiao-yu; Chuang, Pei; Wang, Xi; Zong, Yantao

    2012-11-01

    A novel method for computing kinoform of 3D object based on traditional iterate Fourier transform algorithm(IFTA) is proposed in this paper. Kinoform is a special kind of computer-generated holograms (CGH) which has very high diffraction efficiency since it only modulates the phase of illuminated light and doesn't have cross-interference from conjugate image. The traditional IFTA arithmetic assumes that reconstruction image is in infinity area(Fraunhofer diffraction region), and ignores the deepness of 3D object ,so it can only calculate two-dimensional kinoform. The proposed algorithm in this paper divides three-dimensional object into several object planes in deepness and treat every object plane as a target image then iterate computation is carried out between one input plane(kinoform) and multi-output planes(reconstruction images) .A space phase factor is added into iterate process to represent depth characters of 3D object, then reconstruction images is in Fresnel diffraction region. Optics reconstructed experiment of kinoform computed by this method is realized based on Liquid Crystals on Silicon (LCoS) Spatial Light Modulator(SLM). Mean Square Error(MSE) and Structure Similarity(SSIM) between original and reconstruction image is used to evaluate this method. The experimental result shows that this algorithm speed is fast and the result kinoform can reconstruct the object in different plane with high precision under the illumination of plane wave. The reconstruction images provide space sense of three-dimensional visual effect. At last, the influence of space and shelter between different object planes to reconstruction image is also discussed in the experiment.

  16. Constructing a starting 3D shear velocity model with sharp interfaces for SEM-based upper mantle tomography in North America

    NASA Astrophysics Data System (ADS)

    Calo, M.; Bodin, T.; Yuan, H.; Romanowicz, B. A.; Larmat, C. S.; Maceira, M.

    2013-12-01

    Seismic tomography is currently evolving towards 3D earth models that satisfy full seismic waveforms at increasingly high frequencies. This evolution is possible thanks to the advent of powerful numerical methods such as the Spectral Element Method (SEM) that allow accurate computation of the seismic wavefield in complex media, and the drastic increase of computational resources. However, the production of such models requires handling complex misfit functions with more than one local minimum. Standard linearized inversion methods (such as gradient methods) have two main drawbacks: 1) they produce solution models highly dependent on the starting model; 2) they do not provide a means of estimating true model uncertainties. However, these issues can be addressed with stochastic methods that can sample the space of possible solutions efficiently. Such methods are prohibitively challenging computationally in 3D, but increasingly accessible in 1D. In previous work (Yuan and Romanowicz, 2010; Yuan et al., 2011) we developed a continental scale anisotropic upper mantle model of north America based on a combination of long period seismic waveforms and SKS splitting measurements, showing the pervasive presence of layering of anisotropy in the cratonic lithosphere with significant variations in depth of the mid-lithospheric boundary. The radial anisotropy part of the model has been recently updated using the spectral element method for forward wavefield computations and waveform data from the latest deployments of USarray (Yuan and Romanowicz, 2013). However, the long period waveforms (periods > 40s) themselves only provide a relatively smooth view of the mantle if the starting model is smooth, and the mantle discontinuities necessary for geodynamical interpretation are not imaged. Increasing the frequency of the computations to constrain smaller scale features is possible, but challenging computationally, and at the risk of falling in local minima of the misfit function. In

  17. 3D registration of intravascular optical coherence tomography and cryo-image volumes for microscopic-resolution validation

    NASA Astrophysics Data System (ADS)

    Prabhu, David; Mehanna, Emile; Gargesha, Madhusudhana; Wen, Di; Brandt, Eric; van Ditzhuijzen, Nienke S.; Chamie, Daniel; Yamamoto, Hirosada; Fujino, Yusuke; Farmazilian, Ali; Patel, Jaymin; Costa, Marco; Bezerra, Hiram G.; Wilson, David L.

    2016-03-01

    High resolution, 100 frames/sec intravascular optical coherence tomography (IVOCT) can distinguish plaque types, but further validation is needed, especially for automated plaque characterization. We developed experimental and 3D registration methods, to provide validation of IVOCT pullback volumes using microscopic, brightfield and fluorescent cryoimage volumes, with optional, exactly registered cryo-histology. The innovation was a method to match an IVOCT pullback images, acquired in the catheter reference frame, to a true 3D cryo-image volume. Briefly, an 11-parameter, polynomial virtual catheter was initialized within the cryo-image volume, and perpendicular images were extracted, mimicking IVOCT image acquisition. Virtual catheter parameters were optimized to maximize cryo and IVOCT lumen overlap. Local minima were possible, but when we started within reasonable ranges, every one of 24 digital phantom cases converged to a good solution with a registration error of only +1.34+/-2.65μm (signed distance). Registration was applied to 10 ex-vivo cadaver coronary arteries (LADs), resulting in 10 registered cryo and IVOCT volumes yielding a total of 421 registered 2D-image pairs. Image overlays demonstrated high continuity between vascular and plaque features. Bland- Altman analysis comparing cryo and IVOCT lumen area, showed mean and standard deviation of differences as 0.01+/-0.43 mm2. DICE coefficients were 0.91+/-0.04. Finally, visual assessment on 20 representative cases with easily identifiable features suggested registration accuracy within one frame of IVOCT (+/-200μm), eliminating significant misinterpretations introduced by 1mm errors in the literature. The method will provide 3D data for training of IVOCT plaque algorithms and can be used for validation of other intravascular imaging modalities.

  18. 3D registration of intravascular optical coherence tomography and cryo-image volumes for microscopic-resolution validation

    PubMed Central

    Prabhu, David; Mehanna, Emile; Gargesha, Madhusudhana; Wen, Di; Brandt, Eric; van Ditzhuijzen, Nienke S.; Chamie, Daniel; Yamamoto, Hirosada; Fujino, Yusuke; Farmazilian, Ali; Patel, Jaymin; Costa, Marco; Bezerra, Hiram G.; Wilson, David L.

    2016-01-01

    High resolution, 100 frames/sec intravascular optical coherence tomography (IVOCT) can distinguish plaque types, but further validation is needed, especially for automated plaque characterization. We developed experimental and 3D registration methods, to provide validation of IVOCT pullback volumes using microscopic, brightfield and fluorescent cryo-image volumes, with optional, exactly registered cryo-histology. The innovation was a method to match an IVOCT pull-back images, acquired in the catheter reference frame, to a true 3D cryo-image volume. Briefly, an 11-parameter, polynomial virtual catheter was initialized within the cryo-image volume, and perpendicular images were extracted, mimicking IVOCT image acquisition. Virtual catheter parameters were optimized to maximize cryo and IVOCT lumen overlap. Local minima were possible, but when we started within reasonable ranges, every one of 24 digital phantom cases converged to a good solution with a registration error of only +1.34±2.65μm (signed distance). Registration was applied to 10 ex-vivo cadaver coronary arteries (LADs), resulting in 10 registered cryo and IVOCT volumes yielding a total of 421 registered 2D-image pairs. Image overlays demonstrated high continuity between vascular and plaque features. Bland-Altman analysis comparing cryo and IVOCT lumen area, showed mean and standard deviation of differences as 0.01±0.43 mm2. DICE coefficients were 0.91±0.04. Finally, visual assessment on 20 representative cases with easily identifiable features suggested registration accuracy within one frame of IVOCT (±200μm), eliminating significant misinterpretations introduced by 1mm errors in the literature. The method will provide 3D data for training of IVOCT plaque algorithms and can be used for validation of other intravascular imaging modalities. PMID:27162417

  19. Investigation of a slope endangered by rainfall-induced landslides using 3D resistivity tomography and geotechnical testing

    NASA Astrophysics Data System (ADS)

    Friedel, S.; Thielen, A.; Springman, S. M.

    2006-10-01

    Rainfall-induced landslides pose a common problem in areas with slopes steeper than the friction angle of the soil. A series of such landslides in North Switzerland inspired a detailed geophysical and geotechnical site investigation prior to a monitoring experiment. High-resolution 2D and 3D electrical resistivity tomography (ERT) was used to derive a detailed subsurface image, which was verified by direct penetration tests, boreholes and laboratory analysis of soil samples with respect to grain size distribution and plasticity. Resolution analysis of ERT configurations proved a combination of Wenner-, Schlumberger- and Dipole-Dipole data to be a reasonable compromise between measurement time and model accuracy. Furthermore, a statistical approach to reducing subjectivity in the interpretation of 3D resistivity models is suggested. Applying this classification scheme to field data yields a model in very good agreement with the geotechnical model. The 3D resistivity model is then interpreted quantitatively using laboratory data and a constitutive relation accounting for clay and silt contents. The dominant influence of saturation on resistivity predicted by this model is confirmed and exemplified during repeated surveys in a dry and a wet period. In wet summer 2004, a silty sand layer of high water saturation is confined between two less permeable layers, the sandstone bedrock below and a clayey sand layer on top. This layer may locally form an aquifer, which becomes rapidly saturated during heavy rainfalls and contributes to the risk of failure. The combined ERT and geotechnical survey helped to optimize the design of the forthcoming monitoring experiment and may be used as a guideline for the investigation of similar slope conditions.

  20. 3-D crustal structure along the North Anatolian Fault Zone in north-central Anatolia revealed by local earthquake tomography

    NASA Astrophysics Data System (ADS)

    Yolsal-Ćevikbilen, Seda; Biryol, C. Berk; Beck, Susan; Zandt, George; Taymaz, Tuncay; Adıyaman, Hande E.; Özacar, A. Arda

    2012-03-01

    3-D P-wave velocity structure and Vp/Vs variations in the crust along the North Anatolian Fault Zone (NAFZ) in north-central Anatolia were investigated by the inversion of local P- and S-wave traveltimes, to gain a better understanding of the seismological characteristics of the region. The 3-D local earthquake tomography inversions included 5444 P- and 3200 S-wave readings obtained from 168 well-located earthquakes between 2006 January and 2008 May. Dense ray coverage yields good resolution, particularly in the central part of the study area. The 3-D Vp and Vp/Vs tomographic images reveal clear correlations with both the surface geology and significant tectonic units in the region. We observed the lower limit of the seismogenic zone for north-central Anatolia at 15 km depth. Final earthquake locations display a distributed pattern throughout the study area, with most of the earthquakes occurring on the major splays of the NAFZ, rather than its master strand. We identify three major high-velocity blocks in the mid-crust separated by the İzmir-Ankara-Erzincan Suture and interpret these blocks to be continental basement fragments that were accreted onto the margin following the closure of Neo-Tethyan Ocean. These basement blocks may have in part influenced the rupture propagations of the historical 1939, 1942 and 1943 earthquakes. In addition, large variations in the Vp/Vs ratio in the mid-crust were observed and have been correlated with the varying fluid contents of the existing lithologies and related tectonic structures.

  1. Combined positron emission tomography and computed tomography to visualize and quantify fluid flow in sedimentary rocks

    NASA Astrophysics Data System (ADS)

    Fernø, M. A.; Gauteplass, J.; Hauge, L. P.; Abell, G. E.; Adamsen, T. C. H.; Graue, A.

    2015-09-01

    Here we show for the first time the combined positron emission tomography (PET) and computed tomography (CT) imaging of flow processes within porous rocks to quantify the development in local fluid saturations. The coupling between local rock structure and displacement fronts is demonstrated in exploratory experiments using this novel approach. We also compare quantification of 3-D temporal and spatial water saturations in two similar CO2 storage tests in sandstone imaged separately with PET and CT. The applicability of each visualization technique is evaluated for a range of displacement processes, and the favorable implementation of combining PET/CT for laboratory core analysis is discussed. We learn that the signal-to-noise ratio (SNR) is over an order of magnitude higher for PET compared with CT for the studied processes.

  2. A 3-D shear velocity model of the southern North American and Caribbean plates from ambient noise and earthquake tomography

    NASA Astrophysics Data System (ADS)

    Gaite, B.; Villaseñor, A.; Iglesias, A.; Herraiz, M.; Jiménez-Munt, I.

    2015-02-01

    We use group velocities from earthquake tomography together with group and phase velocities from ambient noise tomography (ANT) of Rayleigh waves to invert for the 3-D shear-wave velocity structure (5-70 km) of the Caribbean (CAR) and southern North American (NAM) plates. The lithospheric model proposed offers a complete image of the crust and uppermost-mantle with imprints of the tectonic evolution. One of the most striking features inferred is the main role of the Ouachita-Marathon-Sonora orogeny front on the crustal seismic structure of the NAM plate. A new imaged feature is the low crustal velocities along the USA-Mexico border. The model also shows a break of the east-west mantle velocity dichotomy of the NAM and CAR plates beneath the Isthmus of the Tehuantepec and the Yucatan Block. High upper-mantle velocities along the Mesoamerican Subduction Zone coincide with inactive volcanic areas while the lowest velocities correspond to active volcanic arcs and thin lithospheric mantle regions.

  3. 3D density model of the upper mantle of Asia based on inversion of gravity and seismic tomography data

    NASA Astrophysics Data System (ADS)

    Kaban, Mikhail K.; Stolk, Ward; Tesauro, Magdala; El Khrepy, Sami; Al-Arifi, Nassir; Beekman, Fred; Cloetingh, Sierd A. P. L.

    2016-11-01

    We construct a new-generation 3D density model of the upper mantle of Asia and its surrounding areas based on a joint interpretation of several data sets. A recent model of the crust combining nearly all available seismic data is employed to calculate the impact of the crust on the gravity anomalies and observed topography and to estimate the residual mantle anomalies and residual topography. These fields are jointly inverted to calculate the density variations in the lithosphere and upper mantle down to 325 km. As an initial approximation, we estimate density variations using a seismic tomography model. Seismic velocity variations are converted into temperatures and then to density variations based on mineral physics constraints. In the Occam-type inversion, we fit both the residual mantle gravity anomalies and residual topography by finding deviations to the initial model. The obtained corrections improve the resolution of the initial model and reflect important features of the mantle structure that are not well resolved by the seismic tomography. The most significant negative corrections of the upper mantle density, found in the Siberian and East European cratons, can be associated with depleted mantle material. The most pronounced positive density anomalies are found beneath the Tarim and South Caspian basins, Barents Sea, and Bay of Bengal. We attribute these anomalies to eclogites in the uppermost mantle, which have substantially affected the evolution of the basins. Furthermore, the obtained results provide evidence for the presence of eclogites in the oceanic subducting mantle lithosphere.

  4. Computed Tomography: Image and Dose Assessment

    SciTech Connect

    Valencia-Ortega, F.; Ruiz-Trejo, C.; Rodriguez-Villafuerte, M.; Buenfil, A. E.; Mora-Hernandez, L. A.

    2006-09-08

    In this work an experimental evaluation of image quality and dose imparted during a computed tomography study in a Public Hospital in Mexico City is presented; The measurements required the design and construction of two phantoms at the Institute of Physics, UNAM, according to the recommendations of American Association of Physicists in Medicine (AAPM). Image assessment was performed in terms the spatial resolution and image contrast. Dose measurements were carried out using LiF: Mg,Ti (TLD-100) dosemeters and pencil-shaped ionisation chamber; The results for a computed tomography head study in single and multiple detector modes are presented.

  5. Multidetector computed tomography angiography of the abdomen.

    PubMed

    Güven, Koray; Acunaş, Bülent

    2004-10-01

    Multidetector computed tomography (MDCT) angiography has provided excellent opportunities for advancement of computed tomography (CT) technology and clinical applications. It has a wide range of applications in the abdomen including vascular pathologies either occlusive or aneurysmal; enables the radiologist to produce vascular mapping that clearly show tumor invasion of vasculature and the relationship of vessels to mass lesions. MDCTA can be used in preoperative planning for hepatic resection, preoperative evaluation and planning for liver transplantation. MDCTA can also provide extremely valuable information in the evaluation of ischemic bowel disease, active Crohn disease, the extent and location of collateral vessels in cirrhosis.

  6. Computational Analysis of the Transonic Dynamics Tunnel Using FUN3D

    SciTech Connect

    Chwalowski, Pawel; Quon, Eliot; Brynildsen, Scott E.

    2016-01-04

    This paper presents results from an explanatory two-year effort of applying Computational Fluid Dynamics (CFD) to analyze the empty-tunnel flow in the NASA Langley Research Center Transonic Dynamics Tunnel (TDT). The TDT is a continuous-flow, closed circuit, 16- x 16-foot slotted-test-section wind tunnel, with capabilities to use air or heavy gas as a working fluid. In this study, experimental data acquired in the empty tunnel using the R-134a test medium was used to calibrate the computational data. The experimental calibration data includes wall pressures, boundary-layer profiles, and the tunnel centerline Mach number profiles. Subsonic and supersonic flow regimes were considered, focusing on Mach 0.5, 0.7 and Mach 1.1 in the TDT test section. This study discusses the computational domain, boundary conditions, and initial conditions selected in the resulting steady-state analyses using NASA's FUN3D CFD software.

  7. Computational Analysis of the Transonic Dynamics Tunnel Using FUN3D

    NASA Technical Reports Server (NTRS)

    Chwalowski, Pawel; Quon, Eliot; Brynildsen, Scott E.

    2016-01-01

    This paper presents results from an exploratory two-year effort of applying Computational Fluid Dynamics (CFD) to analyze the empty-tunnel flow in the NASA Langley Research Center Transonic Dynamics Tunnel (TDT). The TDT is a continuous-flow, closed circuit, 16- x 16-foot slotted-test-section wind tunnel, with capabilities to use air or heavy gas as a working fluid. In this study, experimental data acquired in the empty tunnel using the R-134a test medium was used to calibrate the computational data. The experimental calibration data includes wall pressures, boundary-layer profiles, and the tunnel centerline Mach number profiles. Subsonic and supersonic flow regimes were considered, focusing on Mach 0.5, 0.7 and Mach 1.1 in the TDT test section. This study discusses the computational domain, boundary conditions, and initial conditions selected and the resulting steady-state analyses using NASA's FUN3D CFD software.

  8. First direct 3D visualisation of microstructural evolutions during sintering through X-ray computed microtomography

    SciTech Connect

    Bernard, Dominique . E-mail: bernard@icmcb.u-bordeaux.fr; Gendron, Damien; Heintz, Jean-Marc; Bordere, Sylvie; Etourneau, Jean

    2005-01-03

    X-ray computed microtomography (XCMT) has been applied to ceramic samples of different materials to visualise, for the first time at this scale, real 3D microstructural evolutions during sintering. Using this technique, it has been possible to follow the whole sintering process of the same grains set. Two materials have been studied; a glass powder heat treated at 700 deg. C and a crystallised lithium borate (Li{sub 6}Gd(BO{sub 3}){sub 3}) powder heat treated at 720 deg. C. XCMT measurements have been done after different sintering times. For each material, a sub-volume was individualised and localised on the successive recordings and its 3D images numerically reconstructed. Description of the three-dimensional microstructures evolution is proposed. From the 3D experimental data, quantitative evolutions of parameters such as porosity and neck size are presented for the glass sample. Possibilities offered by this technique to study complex sintering processes, as for lithium borate, are illustrated.

  9. Computational-optical microscopy for 3D biological imaging beyond the diffraction limit

    NASA Astrophysics Data System (ADS)

    Grover, Ginni

    In recent years, super-resolution imaging has become an important fluorescent microscopy tool. It has enabled imaging of structures smaller than the optical diffraction limit with resolution less than 50 nm. Extension to high-resolution volume imaging has been achieved by integration with various optical techniques. In this thesis, development of a fluorescent microscope to enable high resolution, extended depth, three dimensional (3D) imaging is discussed; which is achieved by integration of computational methods with optical systems. In the first part of the thesis, point spread function (PSF) engineering for volume imaging is discussed. A class of PSFs, referred to as double-helix (DH) PSFs, is generated. The PSFs exhibit two focused spots in the image plane which rotate about the optical axis, encoding depth in rotation of the image. These PSFs extend the depth-of-field up to a factor of ˜5. Precision performance of the DH-PSFs, based on an information theoretical analysis, is compared with other 3D methods with conclusion that the DH-PSFs provide the best precision and the longest depth-of-field. Out of various possible DH-PSFs, a suitable PSF is obtained for super-resolution microscopy. The DH-PSFs are implemented in imaging systems, such as a microscope, with a special phase modulation at the pupil plane. Surface-relief elements which are polarization-insensitive and ˜90% light efficient are developed for phase modulation. The photon-efficient DH-PSF microscopes thus developed are used, along with optimal position estimation algorithms, for tracking and super-resolution imaging in 3D. Imaging at depths-of-field of up to 2.5 microm is achieved without focus scanning. Microtubules were imaged with 3D resolution of (6, 9, 39) nm, which is in close agreement with the theoretical limit. A quantitative study of co-localization of two proteins in volume was conducted in live bacteria. In the last part of the thesis practical aspects of the DH-PSF microscope are

  10. Multigrid Computations of 3-D Incompressible Internal and External Viscous Rotating Flows

    NASA Technical Reports Server (NTRS)

    Sheng, Chunhua; Taylor, Lafayette K.; Chen, Jen-Ping; Jiang, Min-Yee; Whitfield, David L.

    1996-01-01

    This report presents multigrid methods for solving the 3-D incompressible viscous rotating flows in a NASA low-speed centrifugal compressor and a marine propeller 4119. Numerical formulations are given in both the rotating reference frame and the absolute frame. Comparisons are made for the accuracy, efficiency, and robustness between the steady-state scheme and the time-accurate scheme for simulating viscous rotating flows for complex internal and external flow applications. Prospects for further increase in efficiency and accuracy of unsteady time-accurate computations are discussed.

  11. Computing 3-D steady supersonic flow via a new Lagrangian approach

    NASA Technical Reports Server (NTRS)

    Loh, C. Y.; Liou, M.-S.

    1993-01-01

    The new Lagrangian method introduced by Loh and Hui (1990) is extended for 3-D steady supersonic flow computation. Details of the conservation form, the implementation of the local Riemann solver, and the Godunov and the high resolution TVD schemes are presented. The new approach is robust yet accurate, capable of handling complicated geometry and reactions between discontinuous waves. It keeps all the advantages claimed in the 2-D method of Loh and Hui, e.g., crisp resolution for a slip surface (contact discontinuity) and automatic grid generation along the stream.

  12. Localization of Metal Electrodes in the Intact Rat Brain Using Registration of 3D Microcomputed Tomography Images to a Magnetic Resonance Histology Atlas1,2,3

    PubMed Central

    Borg, Jana Schaich; Vu, Mai-Anh; Badea, Cristian; Badea, Alexandra; Johnson, G. Allan

    2015-01-01

    Abstract Simultaneous neural recordings taken from multiple areas of the rodent brain are garnering growing interest because of the insight they can provide about spatially distributed neural circuitry. The promise of such recordings has inspired great progress in methods for surgically implanting large numbers of metal electrodes into intact rodent brains. However, methods for localizing the precise location of these electrodes have remained severely lacking. Traditional histological techniques that require slicing and staining of physical brain tissue are cumbersome and become increasingly impractical as the number of implanted electrodes increases. Here we solve these problems by describing a method that registers 3D computed tomography (CT) images of intact rat brains implanted with metal electrode bundles to a magnetic resonance imaging histology (MRH) atlas. Our method allows accurate visualization of each electrode bundle’s trajectory and location without removing the electrodes from the brain or surgically implanting external markers. In addition, unlike physical brain slices, once the 3D images of the electrode bundles and the MRH atlas are registered, it is possible to verify electrode placements from many angles by “reslicing” the images along different planes of view. Furthermore, our method can be fully automated and easily scaled to applications with large numbers of specimens. Our digital imaging approach to efficiently localizing metal electrodes offers a substantial addition to currently available methods, which, in turn, may help accelerate the rate at which insights are gleaned from rodent network neuroscience. PMID:26322331

  13. Use of cone beam computed tomography in periodontology.

    PubMed

    Acar, Buket; Kamburoğlu, Kıvanç

    2014-05-28

    Diagnosis of periodontal disease mainly depends on clinical signs and symptoms. However, in the case of bone destruction, radiographs are valuable diagnostic tools as an adjunct to the clinical examination. Two dimensional periapical and panoramic radiographs are routinely used for diagnosing periodontal bone levels. In two dimensional imaging, evaluation of bone craters, lamina dura and periodontal bone level is limited by projection geometry and superpositions of adjacent anatomical structures. Those limitations of 2D radiographs can be eliminated by three-dimensional imaging techniques such as computed tomography. Cone beam computed tomography (CBCT) generates 3D volumetric images and is also commonly used in dentistry. All CBCT units provide axial, coronal and sagittal multi-planar reconstructed images without magnification. Also, panoramic images without distortion and magnification can be generated with curved planar reformation. CBCT displays 3D images that are necessary for the diagnosis of intra bony defects, furcation involvements and buccal/lingual bone destructions. CBCT applications provide obvious benefits in periodontics, however; it should be used only in correct indications considering the necessity and the potential hazards of the examination.

  14. The occlusion-adjusted prefabricated 3D mirror image templates by computer simulation: the image-guided navigation system application in difficult cases of head and neck reconstruction.

    PubMed

    Cheng, Hsu-Tang; Wu, Chao-I; Tseng, Ching-Shiow; Chen, Hung-Chi; Lee, Wu-Song; Chen, Philip Kuo-Ting; Chang, Sophia Chia-Ning

    2009-11-01

    Computer applications in head and neck reconstruction are rapidly emerging and create not only a virtual environment for presurgical planning, but also help in image-guided navigational surgery. This study evaluates the use of prefabricated 3-dimensional (3D) mirror image templates made by computer-simulated adjusted occlusions to assist in microvascular prefabricated flap insertion during reconstructive surgery. Five patients underwent tumor ablation surgery in 1999 and survived for 8 years. Four of the patients with malignancy received radiation therapy. All patients in this study suffered from severe malocclusion causing trismus, headache, temporomandibular joint pain, an unsymmetrical face, and the inability of further osseointegrated teeth insertion. They underwent a 3D computer tomography examination and the nonprocessed raw data were sent for computer simulation in adjusting occlusion; thus, a mirror image template could be fabricated for microsurgical flap guidance. The computer simulated occlusion was acceptable and facial symmetry obtained. The use of the template resulted in a shorter operation time and recovery was as expected. The computer-simulated occlusion-adjusted 3D mirror image templates aid in the use of free vascularized bone flaps for restoring continuity to the mandible. The coordinated arch will help with further osseointegration teeth insertion.

  15. 3D surface reconstruction for laparoscopic computer-assisted interventions: comparison of state-of-the-art methods

    NASA Astrophysics Data System (ADS)

    Groch, A.; Seitel, A.; Hempel, S.; Speidel, S.; Engelbrecht, R.; Penne, J.; Höller, K.; Röhl, S.; Yung, K.; Bodenstedt, S.; Pflaum, F.; dos Santos, T. R.; Mersmann, S.; Meinzer, H.-P.; Hornegger, J.; Maier-Hein, L.

    2011-03-01

    One of the main challenges related to computer-assisted laparoscopic surgery is the accurate registration of pre-operative planning images with patient's anatomy. One popular approach for achieving this involves intraoperative 3D reconstruction of the target organ's surface with methods based on multiple view geometry. The latter, however, require robust and fast algorithms for establishing correspondences between multiple images of the same scene. Recently, the first endoscope based on Time-of-Flight (ToF) camera technique was introduced. It generates dense range images with high update rates by continuously measuring the run-time of intensity modulated light. While this approach yielded promising results in initial experiments, the endoscopic ToF camera has not yet been evaluated in the context of related work. The aim of this paper was therefore to compare its performance with different state-of-the-art surface reconstruction methods on identical objects. For this purpose, surface data from a set of porcine organs as well as organ phantoms was acquired with four different cameras: a novel Time-of-Flight (ToF) endoscope, a standard ToF camera, a stereoscope, and a High Definition Television (HDTV) endoscope. The resulting reconstructed partial organ surfaces were then compared to corresponding ground truth shapes extracted from computed tomography (CT) data using a set of local and global distance metrics. The evaluation suggests that the ToF technique has high potential as means for intraoperative endoscopic surface registration.

  16. "Let's get physical": advantages of a physical model over 3D computer models and textbooks in learning imaging anatomy.

    PubMed

    Preece, Daniel; Williams, Sarah B; Lam, Richard; Weller, Renate

    2013-01-01

    Three-dimensional (3D) information plays an important part in medical and veterinary education. Appreciating complex 3D spatial relationships requires a strong foundational understanding of anatomy and mental 3D visualization skills. Novel learning resources have been introduced to anatomy training to achieve this. Objective evaluation of their comparative efficacies remains scarce in the literature. This study developed and evaluated the use of a physical model in demonstrating the complex spatial relationships of the equine foot. It was hypothesized that the newly developed physical model would be more effective for students to learn magnetic resonance imaging (MRI) anatomy of the foot than textbooks or computer-based 3D models. Third year veterinary medicine students were randomly assigned to one of three teaching aid groups (physical model; textbooks; 3D computer model). The comparative efficacies of the three teaching aids were assessed through students' abilities to identify anatomical structures on MR images. Overall mean MRI assessment scores were significantly higher in students utilizing the physical model (86.39%) compared with students using textbooks (62.61%) and the 3D computer model (63.68%) (P < 0.001), with no significant difference between the textbook and 3D computer model groups (P = 0.685). Student feedback was also more positive in the physical model group compared with both the textbook and 3D computer model groups. Our results suggest that physical models may hold a significant advantage over alternative learning resources in enhancing visuospatial and 3D understanding of complex anatomical architecture, and that 3D computer models have significant limitations with regards to 3D learning.

  17. 3D virtual human atria: A computational platform for studying clinical atrial fibrillation.

    PubMed

    Aslanidi, Oleg V; Colman, Michael A; Stott, Jonathan; Dobrzynski, Halina; Boyett, Mark R; Holden, Arun V; Zhang, Henggui

    2011-10-01

    Despite a vast amount of experimental and clinical data on the underlying ionic, cellular and tissue substrates, the mechanisms of common atrial arrhythmias (such as atrial fibrillation, AF) arising from the functional interactions at the whole atria level remain unclear. Computational modelling provides a quantitative framework for integrating such multi-scale data and understanding the arrhythmogenic behaviour that emerges from the collective spatio-temporal dynamics in all parts of the heart. In this study, we have developed a multi-scale hierarchy of biophysically detailed computational models for the human atria--the 3D virtual human atria. Primarily, diffusion tensor MRI reconstruction of the tissue geometry and fibre orientation in the human sinoatrial node (SAN) and surrounding atrial muscle was integrated into the 3D model of the whole atria dissected from the Visible Human dataset. The anatomical models were combined with the heterogeneous atrial action potential (AP) models, and used to simulate the AP conduction in the human atria under various conditions: SAN pacemaking and atrial activation in the normal rhythm, break-down of regular AP wave-fronts during rapid atrial pacing, and the genesis of multiple re-entrant wavelets characteristic of AF. Contributions of different properties of the tissue to mechanisms of the normal rhythm and arrhythmogenesis were investigated. Primarily, the simulations showed that tissue heterogeneity caused the break-down of the normal AP wave-fronts at rapid pacing rates, which initiated a pair of re-entrant spiral waves; and tissue anisotropy resulted in a further break-down of the spiral waves into multiple meandering wavelets characteristic of AF. The 3D virtual atria model itself was incorporated into the torso model to simulate the body surface ECG patterns in the normal and arrhythmic conditions. Therefore, a state-of-the-art computational platform has been developed, which can be used for studying multi

  18. Variations in the vestibular cortical bone of permanent canine teeth in orthodontic patients. a comparative study: linear tomography vs. cbct (3d accuitomo).

    PubMed

    Mateu, María E; Martínez, M E; Dagum, H; Benítez Rogé, Sandra C; Bruno, Gabriela I; Hecht, Pedro; Folco, Alejandra A

    2014-01-01

    The aim of this study was to compare the results of measuring the height of the vestibular cortical bone of canine teeth by linear tomography (LT) and 3-D Accuitomo cone beam computed tomography (CBCT) before and after aligning dental arches by orthodontic treatment. LT and CBCT were performed before and after orthodontic alignment on 12 canines in three patients undergoing orthodontic treatment, and the height of the canine vestibular cortical bones measured in mm. Measurements were taken by double-blinded operators. The mean variation in height of the vestibular cortical bone with orthodontic treatment was - 0,33 mm} 0.233 standard error using CBCT and -0,08mm } 0.55 standard error using LT. Analysis of variance (ANOVA) was performed to compare the techniques, the patients and upper and lower canines. No significant difference was found for any of the cases. Using LT to evaluate vestibular crest cortical bone in canines is comparable in efficiency to using CBCT. Height in millimeters is less in LT because image resolution is lower and when it is very thin it is not appreciable by this method.

  19. Quick, Accurate, Smart: 3D Computer Vision Technology Helps Assessing Confined Animals' Behaviour.

    PubMed

    Barnard, Shanis; Calderara, Simone; Pistocchi, Simone; Cucchiara, Rita; Podaliri-Vulpiani, Michele; Messori, Stefano; Ferri, Nicola

    2016-01-01

    Mankind directly controls the environment and lifestyles of several domestic species for purposes ranging from production and research to conservation and companionship. These environments and lifestyles may not offer these animals the best quality of life. Behaviour is a direct reflection of how the animal is coping with its environment. Behavioural indicators are thus among the preferred parameters to assess welfare. However, behavioural recording (usually from video) can be very time consuming and the accuracy and reliability of the output rely on the experience and background of the observers. The outburst of new video technology and computer image processing gives the basis for promising solutions. In this pilot study, we present a new prototype software able to automatically infer the behaviour of dogs housed in kennels from 3D visual data and through structured machine learning frameworks. Depth information acquired through 3D features, body part detection and training are the key elements that allow the machine to recognise postures, trajectories inside the kennel and patterns of movement that can be later labelled at convenience. The main innovation of the software is its ability to automatically cluster frequently observed temporal patterns of movement without any pre-set ethogram. Conversely, when common patterns are defined through training, a deviation from normal behaviour in time or between individuals could be assessed. The software accuracy in correctly detecting the dogs' behaviour was checked through a validation process. An automatic behaviour recognition system, independent from human subjectivity, could add scientific knowledge on animals' quality of life in confinement as well as saving time and resources. This 3D framework was designed to be invariant to the dog's shape and size and could be extended to farm, laboratory and zoo quadrupeds in artificial housing. The computer vision technique applied to this software is innovative in non

  20. Quick, Accurate, Smart: 3D Computer Vision Technology Helps Assessing Confined Animals’ Behaviour

    PubMed Central

    Calderara, Simone; Pistocchi, Simone; Cucchiara, Rita; Podaliri-Vulpiani, Michele; Messori, Stefano; Ferri, Nicola

    2016-01-01

    Mankind directly controls the environment and lifestyles of several domestic species for purposes ranging from production and research to conservation and companionship. These environments and lifestyles may not offer these animals the best quality of life. Behaviour is a direct reflection of how the animal is coping with its environment. Behavioural indicators are thus among the preferred parameters to assess welfare. However, behavioural recording (usually from video) can be very time consuming and the accuracy and reliability of the output rely on the experience and background of the observers. The outburst of new video technology and computer image processing gives the basis for promising solutions. In this pilot study, we present a new prototype software able to automatically infer the behaviour of dogs housed in kennels from 3D visual data and through structured machine learning frameworks. Depth information acquired through 3D features, body part detection and training are the key elements that allow the machine to recognise postures, trajectories inside the kennel and patterns of movement that can be later labelled at convenience. The main innovation of the software is its ability to automatically cluster frequently observed temporal patterns of movement without any pre-set ethogram. Conversely, when common patterns are defined through training, a deviation from normal behaviour in time or between individuals could be assessed. The software accuracy in correctly detecting the dogs’ behaviour was checked through a validation process. An automatic behaviour recognition system, independent from human subjectivity, could add scientific knowledge on animals’ quality of life in confinement as well as saving time and resources. This 3D framework was designed to be invariant to the dog’s shape and size and could be extended to farm, laboratory and zoo quadrupeds in artificial housing. The computer vision technique applied to this software is innovative in non

  1. Nephrocutaneous fistula diagnosed by computed tomography.

    PubMed

    Cooper, S G; Richman, A H; Tager, M G

    1989-01-01

    We present an unusual case of isolated nephrocutaneous fistula secondary to renal calculi with perirenal infection. The usefulness of computed tomography (CT), with its depiction of the extent of involvement and its characterization of the disease process, is described and the literature is reviewed.

  2. Computed Tomography For Inspection Of Thermistors

    NASA Technical Reports Server (NTRS)

    Schaefer, Lloyd A.

    1991-01-01

    Computed tomography (CT) enables identification of cracked thermistors without disassembly of equipment containing them. CT unit used to scan equipment and locate thermistors. Further scans made in various radial orientations perpendicular to plane of devices to find cracks. Cracks invisible in conventional x-radiographs seen.

  3. Computed Tomography Analysis of NASA BSTRA Balls

    SciTech Connect

    Perry, R L; Schneberk, D J; Thompson, R R

    2004-10-12

    Fifteen 1.25 inch BSTRA balls were scanned with the high energy computed tomography system at LLNL. This system has a resolution limit of approximately 210 microns. A threshold of 238 microns (two voxels) was used, and no anomalies at or greater than this were observed.

  4. Cerebral computed tomography, 3rd Edition

    SciTech Connect

    Weisberg, L.; Nice, C.

    1988-01-01

    This book is an introduction to the utilization of computed tomography in evaluating patients with intracranial and orbital disorders. It features clinical correlations and provides an overview of general principles, performance, and normal anatomy of CT. It covers evaluation of specific neurologic signs and symptoms, including stroke, metastatic disease, increased intracranial pressure, head injury, pediatric conditions, and more.

  5. Bladder trauma: multidetector computed tomography cystography.

    PubMed

    Ishak, Charbel; Kanth, Nalini

    2011-08-01

    Multidetector computed tomography (MDCT) cystography is rapidly becoming the most recommended study for evaluation of the bladder for suspected trauma. This article reviews the bladder trauma with emphasis on the application of MDCT cystography to traumatic bladder injuries using a pictorial essay based on images collected in our level I trauma center.

  6. High performance computing approaches for 3D reconstruction of complex biological specimens.

    PubMed

    da Silva, M Laura; Roca-Piera, Javier; Fernández, José-Jesús

    2010-01-01

    Knowledge of the structure of specimens is crucial to determine the role that they play in cellular and molecular biology. To yield the three-dimensional (3D) reconstruction by means of tomographic reconstruction algorithms, we need the use of large projection images and high processing time. Therefore, we propose the use of the high performance computing (HPC) to cope with the huge computational demands of this problem. We have implemented a HPC strategy where the distribution of tasks follows the master-slave paradigm. The master processor distributes a slab of slices, a piece of the final 3D structure to reconstruct, among the slave processors and receives reconstructed slices of the volume. We have evaluated the performance of our HPC approach using different sizes of the slab. We have observed that it is possible to find out an optimal size of the slab for the number of processor used that minimize communications time while maintaining a reasonable grain of parallelism to be exploited by the set of processors.

  7. FaceWarehouse: a 3D facial expression database for visual computing.

    PubMed

    Cao, Chen; Weng, Yanlin; Zhou, Shun; Tong, Yiying; Zhou, Kun

    2014-03-01

    We present FaceWarehouse, a database of 3D facial expressions for visual computing applications. We use Kinect, an off-the-shelf RGBD camera, to capture 150 individuals aged 7-80 from various ethnic backgrounds. For each person, we captured the RGBD data of her different expressions, including the neutral expression and 19 other expressions such as mouth-opening, smile, kiss, etc. For every RGBD raw data record, a set of facial feature points on the color image such as eye corners, mouth contour, and the nose tip are automatically localized, and manually adjusted if better accuracy is required. We then deform a template facial mesh to fit the depth data as closely as possible while matching the feature points on the color image to their corresponding points on the mesh. Starting from these fitted face meshes, we construct a set of individual-specific expression blendshapes for each person. These meshes with consistent topology are assembled as a rank-3 tensor to build a bilinear face model with two attributes: identity and expression. Compared with previous 3D facial databases, for every person in our database, there is a much richer matching collection of expressions, enabling depiction of most human facial actions. We demonstrate the potential of FaceWarehouse for visual computing with four applications: facial image manipulation, face component transfer, real-time performance-based facial image animation, and facial animation retargeting from video to image.

  8. Planned development of a 3D computer based on free-space optical interconnects

    NASA Astrophysics Data System (ADS)

    Neff, John A.; Guarino, David R.

    1994-05-01

    Free-space optical interconnection has the potential to provide upwards of a million data channels between planes of electronic circuits. This may result in the planar board and backplane structures of today giving away to 3-D stacks of wafers or multi-chip modules interconnected via channels running perpendicular to the processor planes, thereby eliminating much of the packaging overhead. Three-dimensional packaging is very appealing for tightly coupled fine-grained parallel computing where the need for massive numbers of interconnections is severely taxing the capabilities of the planar structures. This paper describes a coordinated effort by four research organizations to demonstrate an operational fine-grained parallel computer that achieves global connectivity through the use of free space optical interconnects.

  9. Applying 3D measurements and computer matching algorithms to two firearm examination proficiency tests.

    PubMed

    Ott, Daniel; Thompson, Robert; Song, Junfeng

    2017-02-01

    In order for a crime laboratory to assess a firearms examiner's training, skills, experience, and aptitude, it is necessary for the examiner to participate in proficiency testing. As computer algorithms for comparisons of pattern evidence become more prevalent, it is of interest to test algorithm performance as well, using these same proficiency examinations. This article demonstrates the use of the Congruent Matching Cell (CMC) algorithm to compare 3D topography measurements of breech face impressions and firing pin impressions from a previously distributed firearms proficiency test. In addition, the algorithm is used to analyze the distribution of many comparisons from a collection of cartridge cases used to construct another recent set of proficiency tests. These results are provided along with visualizations that help to relate the features used in optical comparisons by examiners to the features used by computer comparison algorithms.

  10. A Guide to Computed Tomography System Specifications

    DTIC Science & Technology

    1990-08-01

    X - ray source and detectors and the mechanical handling equipment. The X - ray source could be as simple as a gamma- ray source; it could be a microfocus ...ABSTRACT (Continue on reverse if r cessary and identify by block number) The sensitivity to featu e and anomaly detection in industrial X - ray computed...SECURITY CLASSIFICATION OF THIS PAGE UNCLASSIFIED ABSTRACT The sensitivity to feature and anomaly detection in industrial X - ray computed tomography

  11. Computed tomography of the abnormal pericardium

    SciTech Connect

    Silverman, P.M.; Harell, G.S.; Korobkin, M.

    1983-06-01

    Computed tomographic (CT) findings in 18 patients with documented pericardial disease are reported. The pericardium appears as a thin, curvilinear, 1- to 2-mm-thick density best seen anterior to the right ventricular part of the heart. Pericardial abnormalities detected by CT include effusions, thickening, calcification, and cystic and solid masses. Computed tomography is complimentary to echocardiography in its ability to more accurately characterize pericardial effusions, masses, and pericardial thickening.

  12. Using Computer-Aided Design Software and 3D Printers to Improve Spatial Visualization

    ERIC Educational Resources Information Center

    Katsio-Loudis, Petros; Jones, Millie

    2015-01-01

    Many articles have been published on the use of 3D printing technology. From prefabricated homes and outdoor structures to human organs, 3D printing technology has found a niche in many fields, but especially education. With the introduction of AutoCAD technical drawing programs and now 3D printing, learners can use 3D printed models to develop…

  13. Fast 3D in vivo swept-source optical coherence tomography using a two-axis MEMS scanning micromirror

    NASA Astrophysics Data System (ADS)

    Kumar, Karthik; Condit, Jonathan C.; McElroy, Austin; Kemp, Nate J.; Hoshino, Kazunori; Milner, Thomas E.; Zhang, Xiaojing

    2008-04-01

    We report on a fibre-based forward-imaging swept-source optical coherence tomography system using a high-reflectivity two-axis microelectromechanical scanning mirror for high-speed 3D in vivo visualization of cellular-scale architecture of biological specimens. The scanning micromirrors, based on electrostatic staggered vertical comb drive actuators, can provide ± 9° of optical deflection on both rotation axes and uniform reflectivity of greater than 90% over the range of imaging wavelengths (1260-1360 nm), allowing for imaging turbid samples with good signal-to-noise ratio. The wavelength-swept laser, scanning over 100 nm spectrum at 20 kHz rate, enables fast image acquisition at 10.2 million voxels s-1 (for 3D imaging) or 40 frames s-1 (for 2D imaging with 500 transverse pixels per image) with 8.6 µm axial resolution. Lateral resolution of 12.5 µm over 3 mm field of view in each lateral direction is obtained using ZEMAX optical simulations for the lateral beam scanning system across the scanning angle range of the 500 µm × 700 µm micromirror. We successfully acquired en face and tomographic images of rigid structures (scanning micromirror), in vitro biological samples (onion peels and pickle slices) and in vivo images of human epidermis over 2 × 1 × 4 mm3 imaging volume in real time at faster-than-video 2D frame rates. The results indicate that our system framework may be suitable for image-guided minimally invasive examination of various diseased tissues.

  14. 3D ambient noise tomography across the Taiwan Strait: the structure of a magma-poor rifted margin

    NASA Astrophysics Data System (ADS)

    Kuo-Chen, Hao; Chen, Kai-Xun; Brown, Dennis; Li, Qiusheng; Ye, Zhuo; Liang, Wen-Tzong; Wang, Chien-Ying; Yao, Huajian

    2016-04-01

    Rifting along southeastern Eurasia in the Late Cenozoic led to the formation of a magma-poor rifted margin facing the South China Sea to the southeast and the Philippine Sea to the east. Further rifting along the outer part of the margin during the Middle to Late Miocene was accompanied by an extensive episode of intraplate flood volcanism that formed the Penghu Archipelago. Previous geophysical studies in the area of the Strait have focused primarily on the shallow structures of the rift basins and the depth to the Moho. In this study, we present the results of a joint Chinese and Taiwanese 3D ambient noise tomography study from which we calculate the regional-scale 3D S-wave structure of the Taiwan Strait. The S-wave model shows a thinning of the crust beneath the rift basins where, locally, thin high-velocity layers suggest the presence of intrusive bodies. The rift basins and, along the west coast of Taiwan, the foreland basin are imaged as c. 5 to 10 km thick low velocity zones that extend eastward beneath the Taiwan mountain belt. In the upper 10 km of the crust, the basaltic rocks of the Penghu Archipelago are imaged as a high velocity zone that, with depth, becomes a relatively low velocity zone. We interpret this low velocity zone in the lower crust and upper mantle beneath the Penghu Archipelago to image a thermal anomaly related to the still cooling magma feeding system and the melt reservoir area that fed the flood basalts at the surface.

  15. Multimodal photoacoustic and optical coherence tomography scanner using an all optical detection scheme for 3D morphological skin imaging.

    PubMed

    Zhang, Edward Z; Povazay, Boris; Laufer, Jan; Alex, Aneesh; Hofer, Bernd; Pedley, Barbara; Glittenberg, Carl; Treeby, Bradley; Cox, Ben; Beard, Paul; Drexler, Wolfgang

    2011-08-01

    A noninvasive, multimodal photoacoustic and optical coherence tomography (PAT/OCT) scanner for three-dimensional in vivo (3D) skin imaging is described. The system employs an integrated, all optical detection scheme for both modalities in backward mode utilizing a shared 2D optical scanner with a field-of-view of ~13 × 13 mm(2). The photoacoustic waves were detected using a Fabry Perot polymer film ultrasound sensor placed on the surface of the skin. The sensor is transparent in the spectral range 590-1200 nm. This permits the photoacoustic excitation beam (670-680 nm) and the OCT probe beam (1050 nm) to be transmitted through the sensor head and into the underlying tissue thus providing a backward mode imaging configuration. The respective OCT and PAT axial resolutions were 8 and 20 µm and the lateral resolutions were 18 and 50-100 µm. The system provides greater penetration depth than previous combined PA/OCT devices due to the longer wavelength of the OCT beam (1050 nm rather than 829-870 nm) and by operating in the tomographic rather than the optical resolution mode of photoacoustic imaging. Three-dimensional in vivo images of the vasculature and the surrounding tissue micro-morphology in murine and human skin were acquired. These studies demonstrated the complementary contrast and tissue information provided by each modality for high-resolution 3D imaging of vascular structures to depths of up to 5 mm. Potential applications include characterizing skin conditions such as tumors, vascular lesions, soft tissue damage such as burns and wounds, inflammatory conditions such as dermatitis and other superficial tissue abnormalities.

  16. Ground penetrating radar and microwave tomography 3D applications for the deck evaluation of the Musmeci bridge in Potenza, Italy

    NASA Astrophysics Data System (ADS)

    Bavusi, Massimo; Soldovieri, Francesco; Di Napoli, Rosario; Loperte, Antonio; Di Cesare, Antonio; Carlo Ponzo, Felice; Lapenna, Vincenzo

    2011-09-01

    An extensive experimental and numerical investigation has been carried out to assess the status of the 'Ponte sul Basento' (1967-1976), in the town of Potenza (Basilicata region, southern Italy), better known as the Musmeci bridge. Architecturally, the bridge is a considerable reinforced 20th century concrete structure that was designed and built by the Italian architect Sergio Musmeci (1926-1981). Moreover, the bridge represents an important element of the infrastructural network, linking the city centre to the Potenza-Sicignano highway, crossing the Basento river and the railway close to the main train station of the city. Recently, due to ageing and continuous and significant traffic, the bridge started to be affected by several problems such as water infiltration. Within the presented study, a widespread ground penetrating radar (GPR) survey has been designed to investigate the geometrical characteristics of the bridge deck (Gerber saddles, internal stiffening walls, pillar supports) and detect the presence of defects or damage due to water infiltration and traffic fatigue. Concerning this, a 900 MHz 3D GPR survey has been performed along a zone of one of the lanes on the road surface. Moreover, a second 1500 MHz 3D survey has been carried out at the bottom of the bridge deck in order to gain detailed information about an important structural element of the bridge, the Gerber saddle. Both results have been processed following two approaches: the first a classical time-domain processing session based on commercial software and the use of migration; the second in microwave tomography, an advanced frequency domain automatic PC-based inversion algorithm. In this paper, we present a comparative interpretation of both kinds of processed results, and provide considerations about the investigated structures.

  17. APPLICATION OF COMPUTER-AIDED TOMOGRAPHY TO VISUALIZE AND QUANTIFY BIOGENIC STRUCTURES IN MARINE SEDIMENTS

    EPA Science Inventory

    We used computer-aided tomography (CT) for 3D visualization and 2D analysis of

    marine sediment cores from 3 stations (at 10, 75 and 118 m depths) with different environmental

    impact. Biogenic structures such as tubes and burrows were quantified and compared among st...

  18. An Integrated Teaching Method of Gross Anatomy and Computed Tomography Radiology

    ERIC Educational Resources Information Center

    Murakami, Tohru; Tajika, Yuki; Ueno, Hitoshi; Awata, Sachiko; Hirasawa, Satoshi; Sugimoto, Maki; Kominato, Yoshihiko; Tsushima, Yoshito; Endo, Keigo; Yorifuji, Hiroshi

    2014-01-01

    It is essential for medical students to learn and comprehend human anatomy in three dimensions (3D). With this in mind, a new system was designed in order to integrate anatomical dissections with diagnostic computed tomography (CT) radiology. Cadavers were scanned by CT scanners, and students then consulted the postmortem CT images during cadaver…

  19. Proton computed tomography images with algebraic reconstruction

    NASA Astrophysics Data System (ADS)

    Bruzzi, M.; Civinini, C.; Scaringella, M.; Bonanno, D.; Brianzi, M.; Carpinelli, M.; Cirrone, G. A. P.; Cuttone, G.; Presti, D. Lo; Maccioni, G.; Pallotta, S.; Randazzo, N.; Romano, F.; Sipala, V.; Talamonti, C.; Vanzi, E.

    2017-02-01

    A prototype of proton Computed Tomography (pCT) system for hadron-therapy has been manufactured and tested in a 175 MeV proton beam with a non-homogeneous phantom designed to simulate high-contrast material. BI-SART reconstruction algorithms have been implemented with GPU parallelism, taking into account of most likely paths of protons in matter. Reconstructed tomography images with density resolutions r.m.s. down to 1% and spatial resolutions <1 mm, achieved within processing times of 15‧ for a 512×512 pixels image prove that this technique will be beneficial if used instead of X-CT in hadron-therapy.

  20. 3D printing in dentistry.

    PubMed

    Dawood, A; Marti Marti, B; Sauret-Jackson, V; Darwood, A

    2015-12-01

    3D printing has been hailed as a disruptive technology which will change manufacturing. Used in aerospace, defence, art and design, 3D printing is becoming a subject of great interest in surgery. The technology has a particular resonance with dentistry, and with advances in 3D imaging and modelling technologies such as cone beam computed tomography and intraoral scanning, and with the relatively long history of the use of CAD CAM technologies in dentistry, it will become of increasing importance. Uses of 3D printing include the production of drill guides for dental implants, the production of physical models for prosthodontics, orthodontics and surgery, the manufacture of dental, craniomaxillofacial and orthopaedic implants, and the fabrication of copings and frameworks for implant and dental restorations. This paper reviews the types of 3D printing technologies available and their various applications in dentistry and in maxillofacial surgery.

  1. Imaging mesenchymal stem cells containing single wall nanotube nanoprobes in a 3D scaffold using photo-thermal optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Connolly, Emma; Subhash, Hrebesh M.; Leahy, Martin; Rooney, Niall; Barry, Frank; Murphy, Mary; Barron, Valerie

    2014-02-01

    Despite the fact, that a range of clinically viable imaging modalities, such as magnetic resonance imaging (MRI), computed tomography (CT), photo emission tomography (PET), ultrasound and bioluminescence imaging are being optimised to track cells in vivo, many of these techniques are subject to limitations such as the levels of contrast agent required, toxic effects of radiotracers, photo attenuation of tissue and backscatter. With the advent of nanotechnology, nanoprobes are leading the charge to overcome these limitations. In particular, single wall nanotubes (SWNT) have been shown to be taken up by cells and as such are effective nanoprobes for cell imaging. Consequently, the main aim of this research is to employ mesenchymal stem cells (MSC) containing SWNT nanoprobes to image cell distribution in a 3D scaffold for cartilage repair. To this end, MSC were cultured in the presence of 32μg/ml SWNT in cell culture medium (αMEM, 10% FBS, 1% penicillin/streptomycin) for 24 hours. Upon confirmation of cell viability, the MSC containing SWNT were encapsulated in hyaluronic acid gels and loaded on polylactic acid polycaprolactone scaffolds. After 28 days in complete chondrogenic medium, with medium changes every 2 days, chondrogenesis was confirmed by the presence of glycosaminoglycan. Moreover, using photothermal optical coherence tomography (PT-OCT), the cells were seen to be distributed through the scaffold with high resolution. In summary, these data reveal that MSC containing SWNT nanoprobes in combination with PT-OCT offer an exciting opportunity for stem cell tracking in vitro for assessing seeding scaffolds and in vivo for determining biodistribution.

  2. The Effects of 3D Computer Modelling on Conceptual Change about Seasons and Phases of the Moon

    ERIC Educational Resources Information Center

    Kucukozer, Huseyin

    2008-01-01

    In this study, prospective science teachers' misconceptions about the seasons and the phases of the Moon were determined, and then the effects of 3D computer modelling on their conceptual changes were investigated. The topics were covered in two classes with a total of 76 students using a predict-observe-explain strategy supported by 3D computer…

  3. Computed tomography of the spine

    SciTech Connect

    Haughton, V.M.; Williams, A.L.

    1982-01-01

    The book describes the computed tomographic (CT) techniques for imaging the different elements comprising the spinal column and canal. The use of intravenous and intrathecal contrast enhancement and of xenon enhancement is briefly mentioned. Reconstruction techniques and special problems regarding CT of the spine are presented. CT of the spinal cord, meninges and subarachnoid space, epidural space, intervertebral discs, facet joints, and vertebrae present normal anatomy, and several common pathologic conditions. (KRM)

  4. 3D Cloud Tomography, Followed by Mean Optical and Microphysical Properties, with Multi-Angle/Multi-Pixel Data

    NASA Astrophysics Data System (ADS)

    Davis, A. B.; von Allmen, P. A.; Marshak, A.; Bal, G.

    2010-12-01

    -type model is used where the cloud surface "emits" either reflected (sunny-side) or transmitted (shady-side) light at different levels. As it turns out, the reflected/transmitted light ratio yields an approximate cloud optical thickness. Another approach is to invoke tomography techniques to define the volume occupied by the cloud using, as it were, cloud masks for each direction of observation. In the shape and opacity refinement phase, initial guesses along with solar and viewing geometry information are used to predict radiance in each pixel using a fast diffusion model for the 3D RT in MISR's non-absorbing red channel (275 m resolution). Refinement is constrained and stopped when optimal resolution is reached. Finally, multi-pixel/mono-angle MODIS data for the same cloud (at comparable 250 m resolution) reveals the desired droplet size information, hence the volume-averaged LWC. This is an ambitious remote sensing science project drawing on cross-disciplinary expertise gained in medical imaging using both X-ray and near-IR sources and detectors. It is high risk but with potentially high returns not only for the cloud modeling community but also aerosol and surface characterization in the presence of broken 3D clouds.

  5. A brain-computer interface method combined with eye tracking for 3D interaction.

    PubMed

    Lee, Eui Chul; Woo, Jin Cheol; Kim, Jong Hwa; Whang, Mincheol; Park, Kang Ryoung

    2010-07-15

    With the recent increase in the number of three-dimensional (3D) applications, the need for interfaces to these applications has increased. Although the eye tracking method has been widely used as an interaction interface for hand-disabled persons, this approach cannot be used for depth directional navigation. To solve this problem, we propose a new brain computer interface (BCI) method in which the BCI and eye tracking are combined to analyze depth navigation, including selection and two-dimensional (2D) gaze direction, respectively. The proposed method is novel in the following five ways compared to previous works. First, a device to measure both the gaze direction and an electroencephalogram (EEG) pattern is proposed with the sensors needed to measure the EEG attached to a head-mounted eye tracking device. Second, the reliability of the BCI interface is verified by demonstrating that there is no difference between the real and the imaginary movements for the same work in terms of the EEG power spectrum. Third, depth control for the 3D interaction interface is implemented by an imaginary arm reaching movement. Fourth, a selection method is implemented by an imaginary hand grabbing movement. Finally, for the independent operation of gazing and the BCI, a mode selection method is proposed that measures a user's concentration by analyzing the pupil accommodation speed, which is not affected by the operation of gazing and the BCI. According to experimental results, we confirmed the feasibility of the proposed 3D interaction method using eye tracking and a BCI.

  6. A study of 3D structure of nighttime electron density enhancement in the mid-latitude ionosphere by GPS tomography

    NASA Astrophysics Data System (ADS)

    Chen, C.; Saito, A.

    2011-12-01

    The mid-latitude summer nighttime anomaly (MSNA) is a feature that the nighttime electron density larger than that in the daytime mid-latitude ionosphere. This anomaly was first detected in the southern hemisphere five decades ago and observed in the northern hemisphere recently by ionosondes and satellites. Previous studies presented the electron density structure of MSNA by using COSMIC occultation data and found that MSNA is clearly seen around 300 km altitude during local summer. However, due to lack of observation, the day-to-day variation of MSNA was not investigated. A GPS tomography method by SPEL of Kyoto University using the total electron content (TEC) data measured by the ground-based GPS receiver network is employed in this study. The wide coverage and continuous observation of GPS receivers are suitable for investigating the spatial and day-to-day variations of ionospheric electron densities. The algorithm of the GPS tomography developed by SPEL of Kyoto University use a constraint condition that the gradient of election density tends to be smooth in the horizontal direction and steep in the vicinity of the F2 peak, instead of inputting the initial conditions. Therefore, the algorithm is independent of any ionospheric and plasmaspheric electron density distribution models. The dense ground-based GPS receiver network around European region is used to study the three dimensional (3D) structure of MSNA with GPS tomography. Results show that the MSNA usually appear around the geomagnetic mid-latitude region during local summer nighttime. The feature of MSNA is most obvious at the ionospheric F2-peak altitudes. The result also shows a day-to-day variation in the formation of MSNA, in terms of the occurrence time, intensity, and spatial extent. The tomographic results are compared with the ionosondes, satellites, and radar measurements. A theoretical model simulation, SAMI2, is also used to further discuss the mechanism of MSNA. The comparison with other

  7. Computational time analysis of the numerical solution of 3D electrostatic Poisson's equation

    NASA Astrophysics Data System (ADS)

    Kamboh, Shakeel Ahmed; Labadin, Jane; Rigit, Andrew Ragai Henri; Ling, Tech Chaw; Amur, Khuda Bux; Chaudhary, Muhammad Tayyab

    2015-05-01

    3D Poisson's equation is solved numerically to simulate the electric potential in a prototype design of electrohydrodynamic (EHD) ion-drag micropump. Finite difference method (FDM) is employed to discretize the governing equation. The system of linear equations resulting from FDM is solved iteratively by using the sequential Jacobi (SJ) and sequential Gauss-Seidel (SGS) methods, simulation results are also compared to examine the difference between the results. The main objective was to analyze the computational time required by both the methods with respect to different grid sizes and parallelize the Jacobi method to reduce the computational time. In common, the SGS method is faster than the SJ method but the data parallelism of Jacobi method may produce good speedup over SGS method. In this study, the feasibility of using parallel Jacobi (PJ) method is attempted in relation to SGS method. MATLAB Parallel/Distributed computing environment is used and a parallel code for SJ method is implemented. It was found that for small grid size the SGS method remains dominant over SJ method and PJ method while for large grid size both the sequential methods may take nearly too much processing time to converge. Yet, the PJ method reduces computational time to some extent for large grid sizes.

  8. Subsurface fault geometries in Southern California illuminated through Full-3D Seismic Waveform Tomography (F3DT)

    NASA Astrophysics Data System (ADS)

    Lee, En-Jui; Chen, Po

    2017-04-01

    More precise spatial descriptions of fault systems play an essential role in tectonic interpretations, deformation modeling, and seismic hazard assessments. The recent developed full-3D waveform tomography techniques provide high-resolution images and are able to image the material property differences across faults to assist the understanding of fault systems. In the updated seismic velocity model for Southern California, CVM-S4.26, many velocity gradients show consistency with surface geology and major faults defined in the Community Fault Model (CFM) (Plesch et al. 2007), which was constructed by using various geological and geophysical observations. In addition to faults in CFM, CVM-S4.26 reveals a velocity reversal mainly beneath the San Gabriel Mountain and Western Mojave Desert regions, which is correlated with the detachment structure that has also been found in other independent studies. The high-resolution tomographic images of CVM-S4.26 could assist the understanding of fault systems in Southern California and therefore benefit the development of fault models as well as other applications, such as seismic hazard analysis, tectonic reconstructions, and crustal deformation modeling.

  9. Intraoperative handheld probe for 3D imaging of pediatric benign vocal fold lesions using optical coherence tomography (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Benboujja, Fouzi; Garcia, Jordan; Beaudette, Kathy; Strupler, Mathias; Hartnick, Christopher J.; Boudoux, Caroline

    2016-02-01

    Excessive and repetitive force applied on vocal fold tissue can induce benign vocal fold lesions. Children affected suffer from chronic hoarseness. In this instance, the vibratory ability of the folds, a complex layered microanatomy, becomes impaired. Histological findings have shown that lesions produce a remodeling of sup-epithelial vocal fold layers. However, our understanding of lesion features and development is still limited. Indeed, conventional imaging techniques do not allow a non-invasive assessment of sub-epithelial integrity of the vocal fold. Furthermore, it remains challenging to differentiate these sub-epithelial lesions (such as bilateral nodules, polyps and cysts) from a clinical perspective, as their outer surfaces are relatively similar. As treatment strategy differs for each lesion type, it is critical to efficiently differentiate sub-epithelial alterations involved in benign lesions. In this study, we developed an optical coherence tomography (OCT) based handheld probe suitable for pediatric laryngological imaging. The probe allows for rapid three-dimensional imaging of vocal fold lesions. The system is adapted to allow for high-resolution intra-operative imaging. We imaged 20 patients undergoing direct laryngoscopy during which we looked at different benign pediatric pathologies such as bilateral nodules, cysts and laryngeal papillomatosis and compared them to healthy tissue. We qualitatively and quantitatively characterized laryngeal pathologies and demonstrated the added advantage of using 3D OCT imaging for lesion discrimination and margin assessment. OCT evaluation of the integrity of the vocal cord could yield to a better pediatric management of laryngeal diseases.

  10. High-resolution 3-D imaging of surface damage sites in fused silica with Optical Coherence Tomography

    SciTech Connect

    Guss, G; Bass, I; Hackel, R; Mailhiot, C; Demos, S G

    2007-10-30

    In this work, we present the first successful demonstration of a non-contact technique to precisely measure the 3D spatial characteristics of laser induced surface damage sites in fused silica for large aperture laser systems by employing Optical Coherence Tomography (OCT). What makes OCT particularly interesting in the characterization of optical materials for large aperture laser systems is that its axial resolution can be maintained with working distances greater than 5 cm, whether viewing through air or through the bulk of thick optics. Specifically, when mitigating surface damage sites against further growth by CO{sub 2} laser evaporation of the damage, it is important to know the depth of subsurface cracks below the damage site. These cracks are typically obscured by the damage rubble when imaged from above the surface. The results to date clearly demonstrate that OCT is a unique and valuable tool for characterizing damage sites before and after the mitigation process. We also demonstrated its utility as an in-situ diagnostic to guide and optimize our process when mitigating surface damage sites on large, high-value optics.

  11. Analyzing the Evolution of Membrane Fouling via a Novel Method Based on 3D Optical Coherence Tomography Imaging.

    PubMed

    Li, Weiyi; Liu, Xin; Wang, Yi-Ning; Chong, Tzyy Haur; Tang, Chuyang Y; Fane, Anthony G

    2016-07-05

    The development of novel tools for studying the fouling behavior during membrane processes is critical. This work explored optical coherence tomography (OCT) to quantitatively interpret the formation of a cake layer during a membrane process; the quantitative analysis was based on a novel image processing method that was able to precisely resolve the 3D structure of the cake layer on a micrometer scale. Fouling experiments were carried out with foulants having different physicochemical characteristics (silica nanoparticles and bentonite particles). The cake layers formed at a series of times were digitalized using the OCT-based characterization. The specific deposit (cake volume/membrane surface area) and surface coverage were evaluated as a function of time, which for the first time provided direct experimental evidence for the transition of various fouling mechanisms. Axial stripes were observed in the grayscale plots showing the deposit distribution in the scanned area; this interesting observation was in agreement with the instability analysis that correlated the polarized particle groups with the small disturbances in the boundary layer. This work confirms that the OCT-based characterization is able to provide deep insights into membrane fouling processes and offers a powerful tool for exploring membrane processes with enhanced performance.

  12. 3D noninvasive, high-resolution imaging using a photoacoustic tomography (PAT) system and rapid wavelength-cycling lasers

    NASA Astrophysics Data System (ADS)

    Sampathkumar, Ashwin; Gross, Daniel; Klosner, Marc; Chan, Gary; Wu, Chunbai; Heller, Donald F.

    2015-05-01

    Globally, cancer is a major health issue as advances in modern medicine continue to extend the human life span. Breast cancer ranks second as a cause of cancer death in women in the United States. Photoacoustic (PA) imaging (PAI) provides high molecular contrast at greater depths in tissue without the use of ionizing radiation. In this work, we describe the development of a PA tomography (PAT) system and a rapid wavelength-cycling Alexandrite laser designed for clinical PAI applications. The laser produces 450 mJ/pulse at 25 Hz to illuminate the entire breast, which eliminates the need to scan the laser source. Wavelength cycling provides a pulse sequence in which the output wavelength repeatedly alternates between 755 nm and 797 nm rapidly within milliseconds. We present imaging results of breast phantoms with inclusions of different sizes at varying depths, obtained with this laser source, a 5-MHz 128-element transducer and a 128-channel Verasonics system. Results include PA images and 3D reconstruction of the breast phantom at 755 and 797 nm, delineating the inclusions that mimic tumors in the breast.

  13. L- and Corner-arryas for 3D electric resistivity tomography: An alternative for geophysical surveys in urban zones

    NASA Astrophysics Data System (ADS)

    Chavez Segura, R. E.; Tejero-Andrade, A.; Delgado-Solorzano, C.; Cifuentes-Nava, G.; Hernández-Quintero, E.

    2011-12-01

    3D Electric Resitivity Tomography methods carried out on heavily urbanized areas become a difficult task, since buildings, houses or other type of obstacles do not allow parallel ERT arrays to be deployed. Therefore, insufficient information from the subsoil could be obtained. The present paper presents two new techniques, which allow acquiring information beneath a construction by simply surrounding the building or buildings to be studied by a series of ERT profiles. Apparent resistivities are obtained from L-shaped profiles, where alternations between current and potential electrodes along this array are carried out in an automatic way. Four L-arrays and four Corner-arrays are needed to cover the subsurface beneath the studied area. A field test was carried out on a small University of Mexico main Campus garden, where trees and other anthropogenic structures were the so called 'obstacles'. Geophysical work was performed employing parallel arrays (traditional methodology) and compared with this new method presented. Results show that the new method has a poor resolution towards the central portion of the area, mainly from anomalies produced by shallow structures as compared with the traditional grid method. However, the L- and Corner- arrays are more sensitive to anomalies produced by deeper objects, which cannot be observed in the traditional method. The final goal is to apply this method to study habitational complexes built on top of the ancient lake of Mexico City, where buildings are in constant risk due to fracturing and subsidence.

  14. Longitudinal imaging of HIV-1 spread in humanized mice with parallel 3D immunofluorescence and electron tomography

    PubMed Central

    Kieffer, Collin; Ladinsky, Mark S; Ninh, Allen; Galimidi, Rachel P; Bjorkman, Pamela J

    2017-01-01

    Dissemination of HIV-1 throughout lymphoid tissues leads to systemic virus spread following infection. We combined tissue clearing, 3D-immunofluorescence, and electron tomography (ET) to longitudinally assess early HIV-1 spread in lymphoid tissues in humanized mice. Immunofluorescence revealed peak infection density in gut at 10–12 days post-infection when blood viral loads were low. Human CD4+ T-cells and HIV-1–infected cells localized predominantly to crypts and the lower third of intestinal villi. Free virions and infected cells were not readily detectable by ET at 5-days post-infection, whereas HIV-1–infected cells surrounded by pools of free virions were present in ~10% of intestinal crypts by 10–12 days. ET of spleen revealed thousands of virions released by individual cells and discreet cytoplasmic densities near sites of prolific virus production. These studies highlight the importance of multiscale imaging of HIV-1–infected tissues and are adaptable to other animal models and human patient samples. DOI: http://dx.doi.org/10.7554/eLife.23282.001 PMID:28198699

  15. A study of internal structure in components made by additive manufacturing process using 3 D X-ray tomography

    SciTech Connect

    Raguvarun, K. Balasubramaniam, Krishnan Rajagopal, Prabhu; Palanisamy, Suresh; Nagarajah, Romesh; Kapoor, Ajay; Hoye, Nicholas; Curiri, Dominic

    2015-03-31

    Additive manufacturing methods are gaining increasing popularity for rapidly and efficiently manufacturing parts and components in the industrial context, as well as for domestic applications. However, except when used for prototyping or rapid visualization of components, industries are concerned with the load carrying capacity and strength achievable by additive manufactured parts. In this paper, the wire-arc additive manufacturing (AM) process based on gas tungsten arc welding (GTAW) has been examined for the internal structure and constitution of components generated by the process. High-resolution 3D X-ray tomography is used to gain cut-views through wedge-shaped parts created using this GTAW additive manufacturing process with titanium alloy materials. In this work, two different control conditions for the GTAW process are considered. The studies reveal clusters of porosities, located in periodic spatial intervals along the sample cross-section. Such internal defects can have a detrimental effect on the strength of the resulting AM components, as shown in destructive testing studies. Closer examination of this phenomenon shows that defect clusters are preferentially located at GTAW traversal path intervals. These results highlight the strong need for enhanced control of process parameters in ensuring components with minimal defects and higher strength.

  16. Computed tomography of the medulla

    SciTech Connect

    Daniels, D.L.; Williams, A.L.; Haughton, V.M.

    1982-10-01

    The medulla was studied in cadavers and in 100 patients both with and without the intrathecal administration of contrast material. The computed tomographic (CT) anatomy was correlated with the appearance on anatomic dissections. The pyramids, olives, and inferior cerebellar peduncles produced characteristic contours on cross sections of the medulla. The hypoglossal nerve by its location and course in the medullary cistern could be distinguished from the glossopharyngeal, vagal, and spinal accessory nerves. For optimal evaluation of the medulla, intrathecal administration of metrizamide and 5- and/or 1.5-mm-thick axial and coronal sections are recommended.

  17. Computational Study of 3-D Hot-Spot Initiation in Shocked Insensitive High-Explosive

    NASA Astrophysics Data System (ADS)

    Najjar, F. M.; Howard, W. M.; Fried, L. E.

    2011-06-01

    High explosive shock sensitivity is controlled by a combination of mechanical response, thermal properties, and chemical properties. The interplay of these physical phenomena in realistic condensed energetic materials is currently lacking. A multiscale computational framework is developed investigating hot spot (void) ignition in a single crystal of an insensitive HE, TATB. Atomistic MD simulations are performed to provide the key chemical reactions and these reaction rates are used in 3-D multiphysics simulations. The multiphysics code, ALE3D, is linked to the chemistry software, Cheetah, and a three-way coupled approach is pursued including hydrodynamics, thermal and chemical analyses. A single spherical air bubble is embedded in the insensitive HE and its collapse due to shock initiation is evolved numerically in time; while the ignition processes due chemical reactions are studied. Our current predictions showcase several interesting features regarding hot spot dynamics including the formation of a ``secondary'' jet. Results obtained with hydro-thermo-chemical processes leading to ignition growth will be discussed for various pore sizes and different shock pressures. LLNL-ABS-471438. This work performed under the auspices of the U.S. Department of Energy by LLNL under Contract DE-AC52-07NA27344.

  18. An improved version of NCOREL: A computer program for 3-D nonlinear supersonic potential flow computations

    NASA Technical Reports Server (NTRS)

    Siclari, Michael J.

    1988-01-01

    A computer code called NCOREL (for Nonconical Relaxation) has been developed to solve for supersonic full potential flows over complex geometries. The method first solves for the conical at the apex and then marches downstream in a spherical coordinate system. Implicit relaxation techniques are used to numerically solve the full potential equation at each subsequent crossflow plane. Many improvements have been made to the original code including more reliable numerics for computing wing-body flows with multiple embedded shocks, inlet flow through simulation, wake model and entropy corrections. Line relaxation or approximate factorization schemes are optionally available. Improved internal grid generation using analytic conformal mappings, supported by a simple geometric Harris wave drag input that was originally developed for panel methods and internal geometry package are some of the new features.

  19. The NCOREL computer program for 3D nonlinear supersonic potential flow computations

    NASA Technical Reports Server (NTRS)

    Siclari, M. J.

    1983-01-01

    An innovative computational technique (NCOREL) was established for the treatment of three dimensional supersonic flows. The method is nonlinear in that it solves the nonconservative finite difference analog of the full potential equation and can predict the formation of supercritical cross flow regions, embedded and bow shocks. The method implicitly computes a conical flow at the apex (R = 0) of a spherical coordinate system and uses a fully implicit marching technique to obtain three dimensional cross flow solutions. This implies that the radial Mach number must remain supersonic. The cross flow solutions are obtained by using type dependent transonic relaxation techniques with the type dependency linked to the character of the cross flow velocity (i.e., subsonic/supersonic). The spherical coordinate system and marching on spherical surfaces is ideally suited to the computation of wing flows at low supersonic Mach numbers due to the elimination of the subsonic axial Mach number problems that exist in other marching codes that utilize Cartesian transverse marching planes.

  20. A 3-D Computational Study of a Variable Camber Continuous Trailing Edge Flap (VCCTEF) Spanwise Segment

    NASA Technical Reports Server (NTRS)

    Kaul, Upender K.; Nguyen, Nhan T.

    2015-01-01

    Results of a computational study carried out to explore the effects of various elastomer configurations joining spanwise contiguous Variable Camber Continuous Trailing Edge Flap (VCCTEF) segments are reported here. This research is carried out as a proof-of-concept study that will seek to push the flight envelope in cruise with drag optimization as the objective. The cruise conditions can be well off design such as caused by environmental conditions, maneuvering, etc. To handle these off-design conditions, flap deflection is used so when the flap is deflected in a given direction, the aircraft angle of attack changes accordingly to maintain a given lift. The angle of attack is also a design parameter along with the flap deflection. In a previous 2D study,1 the effect of camber was investigated and the results revealed some insight into the relative merit of various camber settings of the VCCTEF. The present state of the art has not advanced sufficiently to do a full 3-D viscous analysis of the whole NASA Generic Transport Model (GTM) wing with VCCTEF deployed with elastomers. Therefore, this study seeks to explore the local effects of three contiguous flap segments on lift and drag of a model devised here to determine possible trades among various flap deflections to achieve desired lift and drag results. Although this approach is an approximation, it provides new insights into the "local" effects of the relative deflections of the contiguous spanwise flap systems and various elastomer segment configurations. The present study is a natural extension of the 2-D study to assess these local 3-D effects. Design cruise condition at 36,000 feet at free stream Mach number of 0.797 and a mean aerodynamic chord (MAC) based Reynolds number of 30.734x10(exp 6) is simulated for an angle of attack (AoA) range of 0 to 6 deg. In the previous 2-D study, the calculations revealed that the parabolic arc camber (1x2x3) and circular arc camber (VCCTEF222) offered the best L

  1. Computed tomography in the diagnosis of iliopsoas abscesses.

    PubMed

    Sykes, J T; Sage, M R; Burke, A M

    1984-04-14

    Two cases in which patients presented with lower back pain and bacteraemia, and in which the diagnosis of iliopsoas abscess was made by computed tomography, are reported. Before the introduction of computed tomography, this diagnosis was difficult to establish by means of clinical and radiological investigations. Computed tomography makes it possible to obtain a clear view of the retroperitoneum.

  2. Hyperspeed data acquisition for 3D computer vision metrology as applied to law enforcement

    NASA Astrophysics Data System (ADS)

    Altschuler, Bruce R.

    1997-02-01

    cycling at 1 millisecond, each pattern is projected and recorded in a cycle time of 1/500th second. An entire set of patterns can then be recorded within 1/60th second. This pattern set contains all the information necessary to calculate a 3-D map. The use of hyper-speed parallel video cameras in conjunction with high speed modulators enables video data rate acquisition of all data necessary to calculate numerical digital 3-D metrological surface data. Thus a 3-D video camera can operate at the rate of a conventional 2-D video camera. The speed of actual 3-D output information is a function of the speed of the computer, a parallel processor being preferred for the task. With video rate 3-D data acquisition law enforcement could survey crime scenes, obtain evidence, watch and record people, packages, suitcases, and record disaster scenes very rapidly.

  3. Development of complex 3D microstructures based on computer generated holography and their usage for biomedical applications

    NASA Astrophysics Data System (ADS)

    Palevicius, Arvydas; Grigaliunas, Viktoras; Janusas, Giedrius; Palevicius, Paulius; Sakalys, Rokas

    2016-04-01

    The main focus of the paper is the development of technological route of the production of complex 3D microstructure, from designing it by the method of computer generated holography till its physical 3D patterning by exploiting the process of electron beam lithography and thermal replication which is used for biomedical application. A phase data of a complex 3D microstructure was generated by using Gerchberg-Saxton algorithm which later was used to produce a computer generated hologram. Physical implementation of microstructure was done using a single layer polymethyl methacrylate (PMMA) as a basis for 3D microstructure, which was exposed using e-beam lithography system e-Line and replicated, using high frequency vibration. Manufactured 3D microstructure is used for designing micro sensor for biomedical applications.

  4. Roughness receptivity studies in a 3-D boundary layer - Flight tests and computations

    NASA Astrophysics Data System (ADS)

    Carpenter, Andrew L.; Saric, William S.; Reed, Helen L.

    The receptivity of 3-D boundary layers to micron-sized, spanwise-periodic Discrete Roughness Elements (DREs) was studied. The DREs were applied to the leading edge of a 30-degree swept-wing at the wavelength of the most unstable disturbance. In this case, calibrated, multi-element hotfilm sensors were used to measure disturbance wall shear stress. The roughness height was varied from 0 to 50 microns. Thus, the disturbance-shear-stress amplitude variations were determined as a function of modulated DRE heights. The computational work was conducted parallel to the flight experiments. The complete viscous flowfield over the O-2 aircraft with the SWIFT model mounted on the port wing store pylon was successfully modeled and validated with the flight data. This highly accurate basic-state solution was incorporated into linear stability calculations and the wave growth associated with the crossflow instability was calculated.

  5. Computation of a high-resolution MRI 3D stereotaxic atlas of the sheep brain.

    PubMed

    Ella, Arsène; Delgadillo, José A; Chemineau, Philippe; Keller, Matthieu

    2017-02-15

    The sheep model was first used in the fields of animal reproduction and veterinary sciences and then was utilized in fundamental and preclinical studies. For more than a decade, magnetic resonance (MR) studies performed on this model have been increasingly reported, especially in the field of neuroscience. To contribute to MR translational neuroscience research, a brain template and an atlas are necessary. We have recently generated the first complete T1-weighted (T1W) and T2W MR population average images (or templates) of in vivo sheep brains. In this study, we 1) defined a 3D stereotaxic coordinate system for previously established in vivo population average templates; 2) used deformation fields obtained during optimized nonlinear registrations to compute nonlinear tissues or prior probability maps (nlTPMs) of cerebrospinal fluid (CSF), gray matter (GM), and white matter (WM) tissues; 3) delineated 25 external and 28 internal sheep brain structures by segmenting both templates and nlTPMs; and 4) annotated and labeled these structures using an existing histological atlas. We built a quality high-resolution 3D atlas of average in vivo sheep brains linked to a reference stereotaxic space. The atlas and nlTPMs, associated with previously computed T1W and T2W in vivo sheep brain templates and nlTPMs, provide a complete set of imaging space that are able to be imported into other imaging software programs and could be used as standardized tools for neuroimaging studies or other neuroscience methods, such as image registration, image segmentation, identification of brain structures, implementation of recording devices, or neuronavigation. J. Comp. Neurol. 525:676-692, 2017. © 2016 Wiley Periodicals, Inc.

  6. Ceramic scaffolds produced by computer-assisted 3D printing and sintering: characterization and biocompatibility investigations.

    PubMed

    Warnke, Patrick H; Seitz, Hermann; Warnke, Frauke; Becker, Stephan T; Sivananthan, Sureshan; Sherry, Eugene; Liu, Qin; Wiltfang, Jörg; Douglas, Timothy

    2010-04-01

    Hydroxyapatite (HAP) and tricalcium phosphate (TCP) are two very common ceramic materials for bone replacement. However, in general HAP and TCP scaffolds are not tailored to the exact dimensions of the defect site and are mainly used as granules or beads. Some scaffolds are available as ordinary blocks, but cannot be customized for individual perfect fit. Using computer-assisted 3D printing, an emerging rapid prototyping technique, individual three-dimensional ceramic scaffolds can be built up from TCP or HAP powder layer by layer with subsequent sintering. These scaffolds have precise dimensions and highly defined and regular internal characteristics such as pore size. External shape and internal characteristics such as pore size can be fabricated using Computer Assisted Design (CAD) based on individual patient data. Thus, these scaffolds could be designed as perfect fit replacements to reconstruct the patient's skeleton. Before their use as bone replacement materials in vivo, in vitro testing of these scaffolds is necessary. In this study, the behavior of human osteoblasts on HAP and TCP scaffolds was investigated. The commonly used bone replacement material BioOss(R) served as control. Biocompatibility was assessed by scanning electron microscopy (SEM), fluorescence microscopy after staining for cell vitality with fluorescin diacetate (FDA) and propidium iodide (PI) and the MTT, LDH, and WST biocompatibility tests. Both versions were colonised by human osteoblasts, however more cells were seen on HAP scaffolds than TCP scaffolds. Cell vitality staining and MTT, LDH, and WST tests showed superior biocompatibility of HAP scaffolds to BioOss, while BioOss was more compatible than TCP. Further experiments are necessary to determine biocompatibility in vivo. Future modifications of 3D printed scaffolds offer advantageous features for Tissue Engineering. The integration of channels could allow for vascular and nerve ingrowth into the scaffold. Also the complex shapes

  7. Real-time computer-generated integral imaging and 3D image calibration for augmented reality surgical navigation.

    PubMed

    Wang, Junchen; Suenaga, Hideyuki; Liao, Hongen; Hoshi, Kazuto; Yang, Liangjing; Kobayashi, Etsuko; Sakuma, Ichiro

    2015-03-01

    Autostereoscopic 3D image overlay for augmented reality (AR) based surgical navigation has been studied and reported many times. For the purpose of surgical overlay, the 3D image is expected to have the same geometric shape as the original organ, and can be transformed to a specified location for image overlay. However, how to generate a 3D image with high geometric fidelity and quantitative evaluation of 3D image's geometric accuracy have not been addressed. This paper proposes a graphics processing unit (GPU) based computer-generated integral imaging pipeline for real-time autostereoscopic 3D display, and an automatic closed-loop 3D image calibration paradigm for displaying undistorted 3D images. Based on the proposed methods, a novel AR device for 3D image surgical overlay is presented, which mainly consists of a 3D display, an AR window, a stereo camera for 3D measurement, and a workstation for information processing. The evaluation on the 3D image rendering performance with 2560×1600 elemental image resolution shows the rendering speeds of 50-60 frames per second (fps) for surface models, and 5-8 fps for large medical volumes. The evaluation of the undistorted 3D image after the calibration yields sub-millimeter geometric accuracy. A phantom experiment simulating oral and maxillofacial surgery was also performed to evaluate the proposed AR overlay device in terms of the image registration accuracy, 3D image overlay accuracy, and the visual effects of the overlay. The experimental results show satisfactory image registration and image overlay accuracy, and confirm the system usability.

  8. FURN3D: A computer code for radiative heat transfer in pulverized coal furnaces

    SciTech Connect

    Ahluwalia, R.K.; Im, K.H.

    1992-08-01

    A computer code FURN3D has been developed for assessing the impact of burning different coals on heat absorption pattern in pulverized coal furnaces. The code is unique in its ability to conduct detailed spectral calculations of radiation tr