Science.gov

Sample records for 3d computer animation

  1. 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.…

  2. 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.

  3. 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

  4. 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

  5. 3D modeling method for computer animate based on modified weak structured light method

    NASA Astrophysics Data System (ADS)

    Xiong, Hanwei; Pan, Ming; Zhang, Xiangwei

    2010-11-01

    A simple and affordable 3D scanner is designed in this paper. Three-dimensional digital models are playing an increasingly important role in many fields, such as computer animate, industrial design, artistic design and heritage conservation. For many complex shapes, optical measurement systems are indispensable to acquiring the 3D information. In the field of computer animate, such an optical measurement device is too expensive to be widely adopted, and on the other hand, the precision is not as critical a factor in that situation. In this paper, a new cheap 3D measurement system is implemented based on modified weak structured light, using only a video camera, a light source and a straight stick rotating on a fixed axis. For an ordinary weak structured light configuration, one or two reference planes are required, and the shadows on these planes must be tracked in the scanning process, which destroy the convenience of this method. In the modified system, reference planes are unnecessary, and size range of the scanned objects is expanded widely. A new calibration procedure is also realized for the proposed method, and points cloud is obtained by analyzing the shadow strips on the object. A two-stage ICP algorithm is used to merge the points cloud from different viewpoints to get a full description of the object, and after a series of operations, a NURBS surface model is generated in the end. A complex toy bear is used to verify the efficiency of the method, and errors range from 0.7783mm to 1.4326mm comparing with the ground truth measurement.

  6. Teaching 3D computer animation to illustrators: the instructor as translator and technical director.

    PubMed

    Koning, Wobbe F

    2012-01-01

    An art instructor discusses the difficulties he's encountered teaching computer graphics skills to undergraduate art students. To help the students, he introduced an automated-rigging script for character animation. PMID:24806989

  7. 3-D Computer Animation vs. Live-Action Video: Differences in Viewers' Response to Instructional Vignettes

    ERIC Educational Resources Information Center

    Smith, Dennie; McLaughlin, Tim; Brown, Irving

    2012-01-01

    This study explored computer animation vignettes as a replacement for live-action video scenarios of classroom behavior situations previously used as an instructional resource in teacher education courses in classroom management strategies. The focus of the research was to determine if the embedded behavioral information perceived in a live-action…

  8. Development of 3D multimedia with advanced computer animation tools for outreach activities related to Meteor Science and Meteoritics

    NASA Astrophysics Data System (ADS)

    Madiedo, J. M.

    2012-09-01

    Documentaries related to Astronomy and Planetary Sciences are a common and very attractive way to promote the interest of the public in these areas. These educational tools can get benefit from new advanced computer animation software and 3D technologies, as these allow making these documentaries even more attractive. However, special care must be taken in order to guarantee that the information contained in them is serious and objective. In this sense, an additional value is given when the footage is produced by the own researchers. With this aim, a new documentary produced and directed by Prof. Madiedo has been developed. The documentary, which has been entirely developed by means of advanced computer animation tools, is dedicated to several aspects of Meteor Science and Meteoritics. The main features of this outreach and education initiative are exposed here.

  9. 3-D Animation of Typhoon Bopha

    NASA Video Gallery

    This 3-D animation of NASA's TRMM satellite data showed Typhoon Bopha tracking over the Philippines on Dec. 3 and moving into the Sulu Sea on Dec. 4, 2012. TRMM saw heavy rain (red) was falling at ...

  10. MOM3D/EM-ANIMATE - MOM3D WITH ANIMATION CODE

    NASA Technical Reports Server (NTRS)

    Shaeffer, J. F.

    1994-01-01

    MOM3D (LAR-15074) is a FORTRAN method-of-moments electromagnetic analysis algorithm for open or closed 3-D perfectly conducting or resistive surfaces. Radar cross section with plane wave illumination is the prime analysis emphasis; however, provision is also included for local port excitation for computing antenna gain patterns and input impedances. The Electric Field Integral Equation form of Maxwell's equations is solved using local triangle couple basis and testing functions with a resultant system impedance matrix. The analysis emphasis is not only for routine RCS pattern predictions, but also for phenomenological diagnostics: bistatic imaging, currents, and near scattered/total electric fields. The images, currents, and near fields are output in form suitable for animation. MOM3D computes the full backscatter and bistatic radar cross section polarization scattering matrix (amplitude and phase), body currents and near scattered and total fields for plane wave illumination. MOM3D also incorporates a new bistatic k space imaging algorithm for computing down range and down/cross range diagnostic images using only one matrix inversion. MOM3D has been made memory and cpu time efficient by using symmetric matrices, symmetric geometry, and partitioned fixed and variable geometries suitable for design iteration studies. MOM3D may be run interactively or in batch mode on 486 IBM PCs and compatibles, UNIX workstations or larger computers. A 486 PC with 16 megabytes of memory has the potential to solve a 30 square wavelength (containing 3000 unknowns) symmetric configuration. Geometries are described using a triangular mesh input in the form of a list of spatial vertex points and a triangle join connection list. The EM-ANIMATE (LAR-15075) program is a specialized visualization program that displays and animates the near-field and surface-current solutions obtained from an electromagnetics program, in particular, that from MOM3D. The EM-ANIMATE program is windows based and

  11. 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.

  12. Virtual reality and 3D animation in forensic visualization.

    PubMed

    Ma, Minhua; Zheng, Huiru; Lallie, Harjinder

    2010-09-01

    Computer-generated three-dimensional (3D) animation is an ideal media to accurately visualize crime or accident scenes to the viewers and in the courtrooms. Based upon factual data, forensic animations can reproduce the scene and demonstrate the activity at various points in time. The use of computer animation techniques to reconstruct crime scenes is beginning to replace the traditional illustrations, photographs, and verbal descriptions, and is becoming popular in today's forensics. This article integrates work in the areas of 3D graphics, computer vision, motion tracking, natural language processing, and forensic computing, to investigate the state-of-the-art in forensic visualization. It identifies and reviews areas where new applications of 3D digital technologies and artificial intelligence could be used to enhance particular phases of forensic visualization to create 3D models and animations automatically and quickly. Having discussed the relationships between major crime types and level-of-detail in corresponding forensic animations, we recognized that high level-of-detail animation involving human characters, which is appropriate for many major crime types but has had limited use in courtrooms, could be useful for crime investigation.

  13. Virtual reality and 3D animation in forensic visualization.

    PubMed

    Ma, Minhua; Zheng, Huiru; Lallie, Harjinder

    2010-09-01

    Computer-generated three-dimensional (3D) animation is an ideal media to accurately visualize crime or accident scenes to the viewers and in the courtrooms. Based upon factual data, forensic animations can reproduce the scene and demonstrate the activity at various points in time. The use of computer animation techniques to reconstruct crime scenes is beginning to replace the traditional illustrations, photographs, and verbal descriptions, and is becoming popular in today's forensics. This article integrates work in the areas of 3D graphics, computer vision, motion tracking, natural language processing, and forensic computing, to investigate the state-of-the-art in forensic visualization. It identifies and reviews areas where new applications of 3D digital technologies and artificial intelligence could be used to enhance particular phases of forensic visualization to create 3D models and animations automatically and quickly. Having discussed the relationships between major crime types and level-of-detail in corresponding forensic animations, we recognized that high level-of-detail animation involving human characters, which is appropriate for many major crime types but has had limited use in courtrooms, could be useful for crime investigation. PMID:20533989

  14. NASA TRMM Satellite 3-D Animation of Cyclone Mahasen Rainfall

    NASA Video Gallery

    This animation shows a simulated 3-D analysis of NASA's Tropical Rainfall Measuring Mission (TRMM) satellite's multisatellite Precipitation Analysis (TMPA). It shows rainfall that occurred with tro...

  15. Second Life, a 3-D Animated Virtual World: An Alternative Platform for (Art) Education

    ERIC Educational Resources Information Center

    Han, Hsiao-Cheng

    2011-01-01

    3-D animated virtual worlds are no longer only for gaming. With the advance of technology, animated virtual worlds not only are found on every computer, but also connect users with the internet. Today, virtual worlds are created not only by companies, but also through the collaboration of users. Online 3-D animated virtual worlds provide a new…

  16. Bringing macromolecular machinery to life using 3D animation.

    PubMed

    Iwasa, Janet H

    2015-04-01

    Over the past decade, there has been a rapid rise in the use of three-dimensional (3D) animation to depict molecular and cellular processes. Much of the growth in molecular animation has been in the educational arena, but increasingly, 3D animation software is finding its way into research laboratories. In this review, I will discuss a number of ways in which 3d animation software can play a valuable role in visualizing and communicating macromolecular structures and dynamics. I will also consider the challenges of using animation tools within the research sphere.

  17. Computer animation of clouds

    SciTech Connect

    Max, N.

    1994-01-28

    Computer animation of outdoor scenes is enhanced by realistic clouds. I will discuss several different modeling and rendering schemes for clouds, and show how they evolved in my animation work. These include transparency-textured clouds on a 2-D plane, smooth shaded or textured 3-D clouds surfaces, and 3-D volume rendering. For the volume rendering, I will present various illumination schemes, including the density emitter, single scattering, and multiple scattering models.

  18. [Computer-assisted 3D phonetography].

    PubMed

    Neuschaefer-Rube, C; Klajman, S

    1996-10-01

    Profiles of fundamental frequency sound pressure levels and voice duration are measured separately in clinical practice. It was the aim of the present study to combine the two examinations, in order to estimate the relationship between pitch, sound pressure level and voice duration and to develop a new computer-assisted graph. A three-dimensional (3D) wireframe phonogram was constructed based on SPL profiles to obtain a general view of the parameters recorded. We have termed this "phonetography". Variable further projections were selected for the analysis of different aspects of parametric relationships. The results in 21 healthy volunteers and 4 patients with hyperfunctional dysphonias demonstrated that there were three typical figures of the 3D phonograms produced, depending on the relationship between voice duration when soft ("piano") compared to loud ("forte"). In one-third of the healthy volunteers, the values of the piano voice duration were greater than those of forte for almost all pitches examined. In two-thirds of the healthy subjects the values of forte voice duration were partly greater, as were those of piano voice duration. All of the patients showed voice duration values greater for forte than for piano. The results of the study demonstrate that the 3D phonogram is a useful tool for obtaining new insights into various relationships of voice parameters.

  19. NASA's 3-D Animation of Tropical Storm Ulika from Space

    NASA Video Gallery

    An animated 3-D flyby of Tropical Storm Ulika using GPM's Radar data showed some strong convective storms inside the tropical storm were dropping precipitation at a rate of over 187 mm (7.4 inches)...

  20. Generating animated sequences from 3D whole-body scans

    NASA Astrophysics Data System (ADS)

    Pargas, Roy P.; Chhatriwala, Murtuza; Mulfinger, Daniel; Deshmukh, Pushkar; Vadhiyar, Sathish

    1999-03-01

    3D images of human subjects are, today, easily obtained using 3D wholebody scanners. 3D human images can provide static information about the physical characteristics of a person, information valuable to professionals such as clothing designers, anthropometrists, medical doctors, physical therapists, athletic trainers, and sculptors. Can 3D human images can be used to provide e more than static physical information. This research described in this paper attempts to answer the question by explaining a way that animated sequences may be generated from a single 3D scan. The process stars by subdividing the human image into segments and mapping the segments to those of a human model defined in a human-motion simulation package. The simulation software provides information used to display movement of the human image. Snapshots of the movement are captured and assembled to create an animated sequence. All of the postures and motion of the human images come from a single 3D scan. This paper describes the process involved in animating human figures from static 3D wholebody scans, presents an example of a generated animated sequence, and discusses possible applications of this approach.

  1. Use of Colour and Interactive Animation in Learning 3D Vectors

    ERIC Educational Resources Information Center

    Iskander, Wejdan; Curtis, Sharon

    2005-01-01

    This study investigated the effects of two computer-implemented techniques (colour and interactive animation) on learning 3D vectors. The participants were 43 female Saudi Arabian high school students. They were pre-tested on 3D vectors using a paper questionnaire that consisted of calculation and visualization types of questions. The students…

  2. Qualitative Assessment of a 3D Simulation Program: Faculty, Students, and Bio-Organic Reaction Animations

    ERIC Educational Resources Information Center

    Günersel, Adalet B.; Fleming, Steven A.

    2013-01-01

    Research shows that computer-based simulations and animations are especially helpful in fields such as chemistry where concepts are abstract and cannot be directly observed. Bio-Organic Reaction Animations (BioORA) is a freely available 3D visualization software program developed to help students understand the chemistry of biomolecular events.…

  3. 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.

  4. Markerless 3D motion capture for animal locomotion studies

    PubMed Central

    Sellers, William Irvin; Hirasaki, Eishi

    2014-01-01

    ABSTRACT Obtaining quantitative data describing the movements of animals is an essential step in understanding their locomotor biology. Outside the laboratory, measuring animal locomotion often relies on video-based approaches and analysis is hampered because of difficulties in calibration and often the limited availability of possible camera positions. It is also usually restricted to two dimensions, which is often an undesirable over-simplification given the essentially three-dimensional nature of many locomotor performances. In this paper we demonstrate a fully three-dimensional approach based on 3D photogrammetric reconstruction using multiple, synchronised video cameras. This approach allows full calibration based on the separation of the individual cameras and will work fully automatically with completely unmarked and undisturbed animals. As such it has the potential to revolutionise work carried out on free-ranging animals in sanctuaries and zoological gardens where ad hoc approaches are essential and access within enclosures often severely restricted. The paper demonstrates the effectiveness of video-based 3D photogrammetry with examples from primates and birds, as well as discussing the current limitations of this technique and illustrating the accuracies that can be obtained. All the software required is open source so this can be a very cost effective approach and provides a methodology of obtaining data in situations where other approaches would be completely ineffective. PMID:24972869

  5. Designing Multimedia Learning Application with Learning Theories: A Case Study on a Computer Science Subject with 2-D and 3-D Animated Versions

    ERIC Educational Resources Information Center

    Rias, Riaza Mohd; Zaman, Halimah Badioze

    2011-01-01

    Higher learning based instruction may be primarily concerned in most cases with the content of their academic lessons, and not very much with their instructional delivery. However, the effective application of learning theories and technology in higher education has an impact on student performance. With the rapid progress in the computer and…

  6. 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

  7. Parallel algorithm for computing 3-D reachable workspaces

    NASA Astrophysics Data System (ADS)

    Alameldin, Tarek K.; Sobh, Tarek M.

    1992-03-01

    The problem of computing the 3-D workspace for redundant articulated chains has applications in a variety of fields such as robotics, computer aided design, and computer graphics. The computational complexity of the workspace problem is at least NP-hard. The recent advent of parallel computers has made practical solutions for the workspace problem possible. Parallel algorithms for computing the 3-D workspace for redundant articulated chains with joint limits are presented. The first phase of these algorithms computes workspace points in parallel. The second phase uses workspace points that are computed in the first phase and fits a 3-D surface around the volume that encompasses the workspace points. The second phase also maps the 3- D points into slices, uses region filling to detect the holes and voids in the workspace, extracts the workspace boundary points by testing the neighboring cells, and tiles the consecutive contours with triangles. The proposed algorithms are efficient for computing the 3-D reachable workspace for articulated linkages, not only those with redundant degrees of freedom but also those with joint limits.

  8. Computer-aided 3D display system and its application in 3D vision test

    NASA Astrophysics Data System (ADS)

    Shen, XiaoYun; Ma, Lan; Hou, Chunping; Wang, Jiening; Tang, Da; Li, Chang

    1998-08-01

    The computer aided 3D display system, flicker-free field sequential stereoscopic image display system, is newly developed. This system is composed of personal computer, liquid crystal glasses driving card, stereoscopic display software and liquid crystal glasses. It can display field sequential stereoscopic images at refresh rate of 70 Hz to 120 Hz. A typical application of this system, 3D vision test system, is mainly discussed in this paper. This stereoscopic vision test system can test stereoscopic acuity, cross disparity, uncross disparity and dynamic stereoscopic vision quantitatively. We have taken the use of random-dot- stereograms as stereoscopic vision test charts. Through practical test experiment between Anaglyph Stereoscopic Vision Test Charts and this stereoscopic vision test system, the statistical figures and test result is given out.

  9. 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.

  10. Computational integral-imaging reconstruction-based 3-D volumetric target object recognition by using a 3-D reference object.

    PubMed

    Kim, Seung-Cheol; Park, Seok-Chan; Kim, Eun-Soo

    2009-12-01

    In this paper, we propose a novel computational integral-imaging reconstruction (CIIR)-based three-dimensional (3-D) image correlator system for the recognition of 3-D volumetric objects by employing a 3-D reference object. That is, a number of plane object images (POIs) computationally reconstructed from the 3-D reference object are used for the 3-D volumetric target recognition. In other words, simultaneous 3-D image correlations between two sets of target and reference POIs, which are depth-dependently reconstructed by using the CIIR method, are performed for effective recognition of 3-D volumetric objects in the proposed system. Successful experiments with this CIIR-based 3-D image correlator confirmed the feasibility of the proposed method.

  11. Error control in the set-up of stereo camera systems for 3d animal tracking

    NASA Astrophysics Data System (ADS)

    Cavagna, A.; Creato, C.; Del Castello, L.; Giardina, I.; Melillo, S.; Parisi, L.; Viale, M.

    2015-12-01

    Three-dimensional tracking of animal systems is the key to the comprehension of collective behavior. Experimental data collected via a stereo camera system allow the reconstruction of the 3d trajectories of each individual in the group. Trajectories can then be used to compute some quantities of interest to better understand collective motion, such as velocities, distances between individuals and correlation functions. The reliability of the retrieved trajectories is strictly related to the accuracy of the 3d reconstruction. In this paper, we perform a careful analysis of the most significant errors affecting 3d reconstruction, showing how the accuracy depends on the camera system set-up and on the precision of the calibration parameters.

  12. 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.

  13. Computations of Emissions Using a 3-D Combustor Program

    NASA Technical Reports Server (NTRS)

    Srivatsa, S. K.

    1983-01-01

    A general 3-D combustor performance program developed by Garrett was extended to predict soot and NOx emissions. The soot formation and oxidation rates were computed by quasi-global models, taking into account the influence of turbulence. Radiation heat transfer was computed by the six-flux radiation mode. The radiation properties include the influence of CO2 and H2O in addition to soot. NOx emissions were computed from a global four-step hydrocarbon oxidation scheme and a set of rate-controlled reactions involving radicals and nitrogen oxides.

  14. NASA's 3-D TRMM Satellite Animation of Tropical Storm Andrea

    NASA Video Gallery

    This 3-D view from the west was derived from TRMM Precipitation Radar (PR) data captured when Andrea was examined by the TRMM satellite with the June 5, 2234 UTC (6:34 p.m. EDT) orbit. It clearly s...

  15. A 3D- and 4D-ESR imaging system for small animals.

    PubMed

    Oikawa, K; Ogata, T; Togashi, H; Yokoyama, H; Ohya-Nishiguchi, H; Kamada, H

    1996-01-01

    A new version of in vivo ESR-CT system composed of custom-made 0.7 GHz ESR spectrometer, air-core magnet with a field-scanning coil, three field-gradient coils, and two computers enables up- and down-field, and rapid magnetic-field scanning linearly controlled by computer. 3D-pictures of distribution of nitroxide radicals injected in brains and livers of rats and mice were obtained in 1.5 min with resolution of 1 mm. We have also succeeded in obtaining spatial-time imagings of the animals.

  16. 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.

  17. V-Man Generation for 3-D Real Time Animation. Chapter 5

    NASA Technical Reports Server (NTRS)

    Nebel, Jean-Christophe; Sibiryakov, Alexander; Ju, Xiangyang

    2007-01-01

    The V-Man project has developed an intuitive authoring and intelligent system to create, animate, control and interact in real-time with a new generation of 3D virtual characters: The V-Men. It combines several innovative algorithms coming from Virtual Reality, Physical Simulation, Computer Vision, Robotics and Artificial Intelligence. Given a high-level task like "walk to that spot" or "get that object", a V-Man generates the complete animation required to accomplish the task. V-Men synthesise motion at runtime according to their environment, their task and their physical parameters, drawing upon its unique set of skills manufactured during the character creation. The key to the system is the automated creation of realistic V-Men, not requiring the expertise of an animator. It is based on real human data captured by 3D static and dynamic body scanners, which is then processed to generate firstly animatable body meshes, secondly 3D garments and finally skinned body meshes.

  18. Computer simulation on reconstruction of 3-D flame temperature distribution

    NASA Astrophysics Data System (ADS)

    Xu, Y.; Yung, K. L.; Wu, Z.; Li, T.

    To measure non-symmetric unsteady three dimensional temperature distribution in flame by simple, economic, fast and accurate means, and to apply a priori information to the measurement both sufficiently and efficiently, we conducted computer simulations. Simulation results proved that finite series-expansion reconstruction method is more suitable for measurement of temperature distribution in flame than transform method which is widely used in medical scanning and nondestructive testing. By comparing errors of simulations with different numbers of views, different domain shapes, different numbers of projections per view, different angles of views and different grid shapes, etc., we find that circle domain, triangular grid and sufficient number of projections per view, can improve the accuracy in the reconstruction of 3-D temperature distribution with limited views. With six views, errors caused by reconstruction computation are reduced, they are smaller than those caused by measurement. Therefore, a comparatively better means of measuring 3-D temperature distribution in flame with limited projection views by emission tomography is achieved. Experimental results also showed that the method we used was appropriate for measurement of 3-D temperature distribution with limited number of views [1].

  19. 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.

  20. Dynamic 3D computed tomography scanner for vascular imaging

    NASA Astrophysics Data System (ADS)

    Lee, Mark K.; Holdsworth, David W.; Fenster, Aaron

    2000-04-01

    A 3D dynamic computed-tomography (CT) scanner was developed for imaging objects undergoing periodic motion. The scanner system has high spatial and sufficient temporal resolution to produce quantitative tomographic/volume images of objects such as excised arterial samples perfused under physiological pressure conditions and enables the measurements of the local dynamic elastic modulus (Edyn) of the arteries in the axial and longitudinal directions. The system was comprised of a high resolution modified x-ray image intensifier (XRII) based computed tomographic system and a computer-controlled cardiac flow simulator. A standard NTSC CCD camera with a macro lens was coupled to the electro-optically zoomed XRII to acquire dynamic volumetric images. Through prospective cardiac gating and computer synchronized control, a time-resolved sequence of 20 mm thick high resolution volume images of porcine aortic specimens during one simulated cardiac cycle were obtained. Performance evaluation of the scanners illustrated that tomographic images can be obtained with resolution as high as 3.2 mm-1 with only a 9% decrease in the resolution for objects moving at velocities of 1 cm/s in 2D mode and static spatial resolution of 3.55 mm-1 with only a 14% decrease in the resolution in 3D mode for objects moving at a velocity of 10 cm/s. Application of the system for imaging of intact excised arterial specimens under simulated physiological flow/pressure conditions enabled measurements of the Edyn of the arteries with a precision of +/- kPa for the 3D scanner. Evaluation of the Edyn in the axial and longitudinal direction produced values of 428 +/- 35 kPa and 728 +/- 71 kPa, demonstrating the isotropic and homogeneous viscoelastic nature of the vascular specimens. These values obtained from the Dynamic CT systems were not statistically different (p less than 0.05) from the values obtained by standard uniaxial tensile testing and volumetric measurements.

  1. Femoroacetabular impingement with chronic acetabular rim fracture - 3D computed tomography, 3D magnetic resonance imaging and arthroscopic correlation

    PubMed Central

    Chhabra, Avneesh; Nordeck, Shaun; Wadhwa, Vibhor; Madhavapeddi, Sai; Robertson, William J

    2015-01-01

    Femoroacetabular impingement is uncommonly associated with a large rim fragment of bone along the superolateral acetabulum. We report an unusual case of femoroacetabular impingement (FAI) with chronic acetabular rim fracture. Radiographic, 3D computed tomography, 3D magnetic resonance imaging and arthroscopy correlation is presented with discussion of relative advantages and disadvantages of various modalities in the context of FAI. PMID:26191497

  2. 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.

  3. 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.

  4. Research on animation design of growing plant based on 3D MAX technology

    NASA Astrophysics Data System (ADS)

    Chen, Yineng; Fang, Kui; Bu, Weiqiong; Zhang, Xiaoling; Lei, Menglong

    In view of virtual plant has practical demands on quality, image and degree of realism animation in growing process of plant, this thesis design the animation based on mechanism and regularity of plant growth, and propose the design method based on 3D MAX technology. After repeated analysis and testing, it is concluded that there are modeling, rendering, animation fabrication and other key technologies in the animation design process. Based on this, designers can subdivid the animation into seed germination animation, plant growth prophase animation, catagen animation, later animation and blossom animation. This paper compounds the animation of these five stages by VP window to realize the completed 3D animation. Experimental result shows that the animation can realized rapid, visual and realistic simulatation the plant growth process.

  5. Flexible Animation Computer Program

    NASA Technical Reports Server (NTRS)

    Stallcup, Scott S.

    1990-01-01

    FLEXAN (Flexible Animation), computer program animating structural dynamics on Evans and Sutherland PS300-series graphics workstation with VAX/VMS host computer. Typical application is animation of spacecraft undergoing structural stresses caused by thermal and vibrational effects. Displays distortions in shape of spacecraft. Program displays single natural mode of vibration, mode history, or any general deformation of flexible structure. Written in FORTRAN 77.

  6. Parallelization of ARC3D with Computer-Aided Tools

    NASA Technical Reports Server (NTRS)

    Jin, Haoqiang; Hribar, Michelle; Yan, Jerry; Saini, Subhash (Technical Monitor)

    1998-01-01

    A series of efforts have been devoted to investigating methods of porting and parallelizing applications quickly and efficiently for new architectures, such as the SCSI Origin 2000 and Cray T3E. This report presents the parallelization of a CFD application, ARC3D, using the computer-aided tools, Cesspools. Steps of parallelizing this code and requirements of achieving better performance are discussed. The generated parallel version has achieved reasonably well performance, for example, having a speedup of 30 for 36 Cray T3E processors. However, this performance could not be obtained without modification of the original serial code. It is suggested that in many cases improving serial code and performing necessary code transformations are important parts for the automated parallelization process although user intervention in many of these parts are still necessary. Nevertheless, development and improvement of useful software tools, such as Cesspools, can help trim down many tedious parallelization details and improve the processing efficiency.

  7. 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.

  8. Software-based geometry operations for 3D computer graphics

    NASA Astrophysics Data System (ADS)

    Sima, Mihai; Iancu, Daniel; Glossner, John; Schulte, Michael; Mamidi, Suman

    2006-02-01

    In order to support a broad dynamic range and a high degree of precision, many of 3D renderings fundamental algorithms have been traditionally performed in floating-point. However, fixed-point data representation is preferable over floating-point representation in graphics applications on embedded devices where performance is of paramount importance, while the dynamic range and precision requirements are limited due to the small display sizes (current PDA's are 640 × 480 (VGA), while cell-phones are even smaller). In this paper we analyze the efficiency of a CORDIC-augmented Sandbridge processor when implementing a vertex processor in software using fixed-point arithmetic. A CORDIC-based solution for vertex processing exhibits a number of advantages over classical Multiply-and-Acumulate solutions. First, since a single primitive is used to describe the computation, the code can easily be vectorized and multithreaded, and thus fits the major Sandbridge architectural features. Second, since a CORDIC iteration consists of only a shift operation followed by an addition, the computation may be deeply pipelined. Initially, we outline the Sandbridge architecture extension which encompasses a CORDIC functional unit and the associated instructions. Then, we consider rigid-body rotation, lighting, exponentiation, vector normalization, and perspective division (which are some of the most important data-intensive 3D graphics kernels) and propose a scheme to implement them on the CORDIC-augmented Sandbridge processor. Preliminary results indicate that the performance improvement within the extended instruction set ranges from 3× to 10× (with the exception of rigid body rotation).

  9. Advances in animal ecology from 3D-LiDAR ecosystem mapping.

    PubMed

    Davies, Andrew B; Asner, Gregory P

    2014-12-01

    The advent and recent advances of Light Detection and Ranging (LiDAR) have enabled accurate measurement of 3D ecosystem structure. Here, we review insights gained through the application of LiDAR to animal ecology studies, revealing the fundamental importance of structure for animals. Structural heterogeneity is most conducive to increased animal richness and abundance, and increased complexity of vertical vegetation structure is more positively influential compared with traditionally measured canopy cover, which produces mixed results. However, different taxonomic groups interact with a variety of 3D canopy traits and some groups with 3D topography. To develop a better understanding of animal dynamics, future studies will benefit from considering 3D habitat effects in a wider variety of ecosystems and with more taxa.

  10. Advances in animal ecology from 3D-LiDAR ecosystem mapping.

    PubMed

    Davies, Andrew B; Asner, Gregory P

    2014-12-01

    The advent and recent advances of Light Detection and Ranging (LiDAR) have enabled accurate measurement of 3D ecosystem structure. Here, we review insights gained through the application of LiDAR to animal ecology studies, revealing the fundamental importance of structure for animals. Structural heterogeneity is most conducive to increased animal richness and abundance, and increased complexity of vertical vegetation structure is more positively influential compared with traditionally measured canopy cover, which produces mixed results. However, different taxonomic groups interact with a variety of 3D canopy traits and some groups with 3D topography. To develop a better understanding of animal dynamics, future studies will benefit from considering 3D habitat effects in a wider variety of ecosystems and with more taxa. PMID:25457158

  11. Special effects used in creating 3D animated scenes-part 1

    NASA Astrophysics Data System (ADS)

    Avramescu, A. M.

    2015-11-01

    In present, with the help of computer, we can create special effects that look so real that we almost don't perceive them as being different. These special effects are somehow hard to differentiate from the real elements like those on the screen. With the increasingly accesible 3D field that has more and more areas of application, the 3D technology goes easily from architecture to product designing. Real like 3D animations are used as means of learning, for multimedia presentations of big global corporations, for special effects and even for virtual actors in movies. Technology, as part of the movie art, is considered a prerequisite but the cinematography is the first art that had to wait for the correct intersection of technological development, innovation and human vision in order to attain full achievement. Increasingly more often, the majority of industries is using 3D sequences (three dimensional). 3D represented graphics, commercials and special effects from movies are all designed in 3D. The key for attaining real visual effects is to successfully combine various distinct elements: characters, objects, images and video scenes; like all these elements represent a whole that works in perfect harmony. This article aims to exhibit a game design from these days. Considering the advanced technology and futuristic vision of designers, nowadays we have different and multifarious game models. Special effects are decisively contributing in the creation of a realistic three-dimensional scene. These effects are essential for transmitting the emotional state of the scene. Creating the special effects is a work of finesse in order to achieve high quality scenes. Special effects can be used to get the attention of the onlooker on an object from a scene. Out of the conducted study, the best-selling game of the year 2010 was Call of Duty: Modern Warfare 2. This way, the article aims for the presented scene to be similar with many locations from this type of games, more

  12. 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

  13. Characteristics of visual fatigue under the effect of 3D animation.

    PubMed

    Chang, Yu-Shuo; Hsueh, Ya-Hsin; Tung, Kwong-Chung; Jhou, Fong-Yi; Lin, David Pei-Cheng

    2015-01-01

    Visual fatigue is commonly encountered in modern life. Clinical visual fatigue characteristics caused by 2-D and 3-D animations may be different, but have not been characterized in detail. This study tried to distinguish the differential effects on visual fatigue caused by 2-D and 3-D animations. A total of 23 volunteers were subjected to accommodation and vergence assessments, followed by a 40-min video game program designed to aggravate their asthenopic symptoms. The volunteers were then assessed for accommodation and vergence parameters again and directed to watch a 5-min 3-D video program, and then assessed again for the parameters. The results support that the 3-D animations caused similar characteristics in vision fatigue parameters in some specific aspects as compared to that caused by 2-D animations. Furthermore, 3-D animations may lead to more exhaustion in both ciliary and extra-ocular muscles, and such differential effects were more evident in the high demand of near vision work. The current results indicated that an arbitrary set of indexes may be promoted in the design of 3-D display or equipments.

  14. Computational MHD on 3D Unstructured Lagrangian Meshes

    NASA Astrophysics Data System (ADS)

    Rousculp, C. L.; Barnes, D. C.

    1999-11-01

    Lagrangian computational meshes are typically employed to model multi-material problems because they do not require costly interface tracking methods. Our algorithms, for ideal and non-ideal 3D MHD, are designed for use on such meshes composed of polyhedral cells with an arbitrary number of faces. This allows for mesh refinement during a calculation to prevent the well known problem of mesh tangling. The action of the magnetic vector potential, A \\cdot δ l, is centered on edges. For ideal and non-ideal flow, this maintains nabla \\cdot B = 0 to round-off error. Vertex forces are derived by the variation of magnetic energy with respect to vertex positions, F = - partial WB / partial r. This assures symmetry as well as magnetic flux, momentum, and energy conservation. The method is local so that parallelization by domain decomposition is natural for large meshes. The resistive diffusion part is calculated using the support operator method, to obtain energy conservation, symmetry. Implicit time difference equations are solved by preconditioned, conjugate gradient methods. Results of convergence tests are presented. Boundary conditions at plasma vaccuum interfaces have been incorporated. Initial results of an annular Z-pinch implosion problem are shown.

  15. 3D animations explaining the rotation, libration, and tides of planets

    NASA Astrophysics Data System (ADS)

    van Marcke de Lummen, J.; de Viron, O.; Dehant, V.; Defraigne, P.; Rosenblatt, P.; Karatekin, O.; van Hoolst, T.

    Space missions have always been appealing to the broad audience. In addition, the recent success of several experiments, revealing fascinating new information about the planets of the Solar System has had wide media coverage. For that reason, our team, involved in the preparation and analysis of missions such as Mars Express and BepiColombo is in contact with the press and with the public on a regular basis. It is not always an easy task to explain to a broad audience what we are doing on planets and why, because our science involves rather complicated computations of the deformations of the planet in response to gravitational forces, and of the variations of its orientation in space. Consequently, we decided to create computer animations to explain our work. These animations show how and why the rotations of the planets are not uniform and how and why the planets are changing their orientation in space. The films describe the precession, nutations, and polar motion, characteristics of the terrestrial planets such as the Earth and Mars, and the librations, characteristic of the terrestrial bodies such as Mercury and the icy satellites. The animations also describe the gravitational effects on a spacecraft orbiting around a planet as well as the tides induced by the Sun or the planets on the planets themselves. These films have the advantage of allowing the press and the public to have a correct and appealing representation of phenomena as complex as planetary tides, gravity perturbation on an ˇ orbit, precession, etcE The concept of the animations is a result of many discussions between scientists, and the movies have been generated on Blender, which is an open source software for 3D modeling, animation, rendering, post-production, interactive creation and playback (available on www.blender3D.org). Those movies have been shown very helpful when meeting the press (some of them aired on television), or the science decision makers, which fully justifies the work

  16. A small animal image guided irradiation system study using 3D dosimeters

    NASA Astrophysics Data System (ADS)

    Qian, Xin; Admovics, John; Wuu, Cheng-Shie

    2015-01-01

    In a high resolution image-guided small animal irradiation platform, a cone beam computed tomography (CBCT) is integrated with an irradiation unit for precise targeting. Precise quality assurance is essential for both imaging and irradiation components. The conventional commissioning techniques with films face major challenges due to alignment uncertainty and labour intensive film preparation and scanning. In addition, due to the novel design of this platform the mouse stage rotation for CBCT imaging is perpendicular to the gantry rotation for irradiation. Because these two rotations are associated with different mechanical systems, discrepancy between rotation isocenters exists. In order to deliver x-ray precisely, it is essential to verify coincidence of the imaging and the irradiation isocenters. A 3D PRESAGE dosimeter can provide an excellent tool for checking dosimetry and verifying coincidence of irradiation and imaging coordinates in one system. Dosimetric measurements were performed to obtain beam profiles and percent depth dose (PDD). Isocentricity and coincidence of the mouse stage and gantry rotations were evaluated with starshots acquired using PRESAGE dosimeters. A single PRESAGE dosimeter can provide 3 -D information in both geometric and dosimetric uncertainty, which is crucial for translational studies.

  17. Advances in animal ecology from 3D ecosystem mapping with LiDAR

    NASA Astrophysics Data System (ADS)

    Davies, A.; Asner, G. P.

    2015-12-01

    The advent and recent advances of Light Detection and Ranging (LiDAR) have enabled accurate measurement of 3D ecosystem structure. Although the use of LiDAR data is widespread in vegetation science, it has only recently (< 14 years) been applied to animal ecology. Despite such recent application, LiDAR has enabled new insights in the field and revealed the fundamental importance of 3D ecosystem structure for animals. We reviewed the studies to date that have used LiDAR in animal ecology, synthesising the insights gained. Structural heterogeneity is most conducive to increased animal richness and abundance, and increased complexity of vertical vegetation structure is more positively influential than traditionally measured canopy cover, which produces mixed results. However, different taxonomic groups interact with a variety of 3D canopy traits and some groups with 3D topography. LiDAR technology can be applied to animal ecology studies in a wide variety of environments to answer an impressive array of questions. Drawing on case studies from vastly different groups, termites and lions, we further demonstrate the applicability of LiDAR and highlight new understanding, ranging from habitat preference to predator-prey interactions, that would not have been possible from studies restricted to field based methods. We conclude with discussion of how future studies will benefit by using LiDAR to consider 3D habitat effects in a wider variety of ecosystems and with more taxa to develop a better understanding of animal dynamics.

  18. Comparison of traditional methods with 3D computer models in the instruction of hepatobiliary anatomy.

    PubMed

    Keedy, Alexander W; Durack, Jeremy C; Sandhu, Parmbir; Chen, Eric M; O'Sullivan, Patricia S; Breiman, Richard S

    2011-01-01

    This study was designed to determine whether an interactive three-dimensional presentation depicting liver and biliary anatomy is more effective for teaching medical students than a traditional textbook format presentation of the same material. Forty-six medical students volunteered for participation in this study. Baseline demographic information, spatial ability, and knowledge of relevant anatomy were measured. Participants were randomized into two groups and presented with a computer-based interactive learning module comprised of animations and still images to highlight various anatomical structures (3D group), or a computer-based text document containing the same images and text without animation or interactive features (2D group). Following each teaching module, students completed a satisfaction survey and nine-item anatomic knowledge post-test. The 3D group scored higher on the post-test than the 2D group, with a mean score of 74% and 64%, respectively; however, when baseline differences in pretest scores were accounted for, this difference was not statistically significant (P = 0.33). Spatial ability did not statistically significantly correlate with post-test scores for the 3D group or the 2D group. In the post-test satisfaction survey the 3D group expressed a statistically significantly higher overall satisfaction rating compared to students in the 2D control group (4.5 versus 3.7 out of 5, P = 0.02). While the interactive 3D multimedia module received higher satisfaction ratings from students, it neither enhanced nor inhibited learning of complex hepatobiliary anatomy compared to an informationally equivalent traditional textbook style approach. .

  19. Visualization of anthropometric measures of workers in computer 3D modeling of work place.

    PubMed

    Mijović, B; Ujević, D; Baksa, S

    2001-12-01

    In this work, 3D visualization of a work place by means of a computer-made 3D-machine model and computer animation of a worker have been performed. By visualization of 3D characters in inverse kinematic and dynamic relation with the operating part of a machine, the biomechanic characteristics of worker's body have been determined. The dimensions of a machine have been determined by an inspection of technical documentation as well as by direct measurements and recordings of the machine by camera. On the basis of measured body height of workers all relevant anthropometric measures have been determined by a computer program developed by the authors. By knowing the anthropometric measures, the vision fields and the scope zones while forming work places, exact postures of workers while performing technological procedures were determined. The minimal and maximal rotation angles and the translation of upper and lower arm which are basis for the analysis of worker burdening were analyzed. The dimensions of the seized space of a body are obtained by computer anthropometric analysis of movement, e.g. range of arms, position of legs, head, back. The influence of forming of a work place on correct postures of workers during work has been reconsidered and thus the consumption of energy and fatigue can be reduced to a minimum. PMID:11811295

  20. Animal testing using 3D microwave tomography system for breast cancer detection.

    PubMed

    Lee, Jong Moon; Son, Sung Ho; Kim, Hyuk Je; Kim, Bo Ra; Choi, Heyng Do; Jeon, Soon Ik

    2014-01-01

    The three dimensional microwave tomography (3D MT) system of the Electronics and Telecommunications Research Institute (ETRI) comprises an antenna array, transmitting receiving module, switch matrix module and a signal processing component. This system also includes a patient interface bed as well as a 3D reconstruction algorithm. Here, we perform a comparative analysis of image reconstruction results using the assembled system and MRI results, which is used to image the breasts of dogs. Microwave imaging reconstruction results (at 1,500 MHz) obtained using the ETRI 3D MT system are presented. The system provides computationally reliable diagnosis results from the reconstructed MT Image. PMID:25160233

  1. Evaluation of 3D reconstruction algorithms for a small animal PET camera

    SciTech Connect

    Johnson, C.A.; Gandler, W.R.; Seidel, J.

    1996-12-31

    The use of paired, opposing position-sensitive phototube scintillation cameras (SCs) operating in coincidence for small animal imaging with positron emitters is currently under study. Because of the low sensitivity of the system even in 3D mode and the need to produce images with high resolution, it was postulated that a 3D expectation maximization (EM) reconstruction algorithm might be well suited for this application. We investigated four reconstruction algorithms for the 3D SC PET camera: 2D filtered back-projection (FBP), 2D ordered subset EM (OSEM), 3D reprojection (3DRP), and 3D OSEM. Noise was assessed for all slices by the coefficient of variation in a simulated uniform cylinder. Resolution was assessed from a simulation of 15 point sources in the warm background of the uniform cylinder. At comparable noise levels, the resolution achieved with OSEM (0.9-mm to 1.2-mm) is significantly better than that obtained with FBP or 3DRP (1.5-mm to 2.0-mm.) Images of a rat skull labeled with {sup 18}F-fluoride suggest that 3D OSEM can improve image quality of a small animal PET camera.

  2. The effectiveness of 3D animations to enhance understanding of cranial cruciate ligament rupture.

    PubMed

    Clements, Dylan N; Broadhurst, Henry; Clarke, Stephen P; Farrell, Michael; Bennett, David; Mosley, John R; Mellanby, Richard J

    2013-01-01

    Cranial cruciate ligament (CCL) rupture is one of the most important orthopedic diseases taught to veterinary undergraduates. The complexity of the anatomy of the canine stifle joint combined with the plethora of different surgical interventions available for the treatment of the disease means that undergraduate veterinary students often have a poor understanding of the pathophysiology and treatment of CCL rupture. We designed, developed, and tested a three dimensional (3D) animation to illustrate the pertinent clinical anatomy of the stifle joint, the effects of CCL rupture, and the mechanisms by which different surgical techniques can stabilize the joint with CCL rupture. When compared with a non-animated 3D presentation, students' short-term retention of functional anatomy improved although they could not impart a better explanation of how different surgical techniques worked. More students found the animation useful than those who viewed a comparable non-animated 3D presentation. Multiple peer-review testing is required to maximize the usefulness of 3D animations during development. Free and open access to such tools should improve student learning and client understanding through wide-spread uptake and use. PMID:23475409

  3. Tools for 3D scientific visualization in computational aerodynamics at NASA Ames Research Center

    NASA Technical Reports Server (NTRS)

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

    1989-01-01

    Hardware, software, and techniques used by the Fluid Dynamics Division (NASA) for performing visualization of computational aerodynamics, which can be applied to the visualization of flow fields from computer simulations of fluid dynamics about the Space Shuttle, are discussed. Three visualization techniques applied, post-processing, tracking, and steering, are described, as well as the post-processing software packages used, PLOT3D, SURF (Surface Modeller), GAS (Graphical Animation System), and FAST (Flow Analysis software Toolkit). Using post-processing methods a flow simulation was executed on a supercomputer and, after the simulation was complete, the results were processed for viewing. It is shown that the high-resolution, high-performance three-dimensional workstation combined with specially developed display and animation software provides a good tool for analyzing flow field solutions obtained from supercomputers.

  4. Learning Projectile Motion with the Computer Game ``Scorched 3D``

    NASA Astrophysics Data System (ADS)

    Jurcevic, John S.

    2008-01-01

    For most of our students, video games are a normal part of their lives. We should take advantage of this medium to teach physics in a manner that is engrossing for our students. In particular, modern video games incorporate accurate physics in their game engines, and they allow us to visualize the physics through flashy and captivating graphics. I recently used the game "Scorched 3D" to help my students understand projectile motion.

  5. Computation of optimized arrays for 3-D electrical imaging surveys

    NASA Astrophysics Data System (ADS)

    Loke, M. H.; Wilkinson, P. B.; Uhlemann, S. S.; Chambers, J. E.; Oxby, L. S.

    2014-12-01

    3-D electrical resistivity surveys and inversion models are required to accurately resolve structures in areas with very complex geology where 2-D models might suffer from artefacts. Many 3-D surveys use a grid where the number of electrodes along one direction (x) is much greater than in the perpendicular direction (y). Frequently, due to limitations in the number of independent electrodes in the multi-electrode system, the surveys use a roll-along system with a small number of parallel survey lines aligned along the x-direction. The `Compare R' array optimization method previously used for 2-D surveys is adapted for such 3-D surveys. Offset versions of the inline arrays used in 2-D surveys are included in the number of possible arrays (the comprehensive data set) to improve the sensitivity to structures in between the lines. The array geometric factor and its relative error are used to filter out potentially unstable arrays in the construction of the comprehensive data set. Comparisons of the conventional (consisting of dipole-dipole and Wenner-Schlumberger arrays) and optimized arrays are made using a synthetic model and experimental measurements in a tank. The tests show that structures located between the lines are better resolved with the optimized arrays. The optimized arrays also have significantly better depth resolution compared to the conventional arrays.

  6. 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

  7. Computer-assisted three-dimensional surgical planning and simulation: 3D virtual osteotomy.

    PubMed

    Xia, J; Ip, H H; Samman, N; Wang, D; Kot, C S; Yeung, R W; Tideman, H

    2000-02-01

    A computer-assisted three-dimensional virtual osteotomy system for orthognathic surgery (CAVOS) is presented. The virtual reality workbench is used for surgical planning. The surgeon immerses in a virtual reality environment with stereo eyewear, holds a virtual "scalpel" (3D Mouse) and operates on a "real" patient (3D visualization) to obtain pre-surgical prediction (3D bony segment movements). Virtual surgery on a computer-generated 3D head model is simulated and can be visualized from any arbitrary viewing point in a personal computer system.

  8. ORPHEE 3D: Static and dynamic tridimensional BHA computer models

    SciTech Connect

    Birades, M.

    1986-01-01

    Elf Aquitaine, within an ARTEP research project granted by EEC, has developed two three-dimensional mathematical models to predict the directional behavior of bottom hole assemblies (BHAs). Both models simulate BHAs by finite element methods. The first model describes dynamically their transient behavior step by step during short time intervals which are continuously adjusted to attain the required precision. Displacements and lateral forces, computed for each step, integrate friction against the borehole wall through a sophisticated shock algorithm. The second model computes a static equilibrium of the BHA while assuming simplified friction forces at the contact points between the wellbore and the BHA. The lateral forces and displacements are found to be an average of the highly varying ones computed by the dynamic model and the static computer run is much faster.

  9. 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.

  10. The 3d International Workshop on Computational Electronics

    NASA Astrophysics Data System (ADS)

    Goodnick, Stephen M.

    1994-09-01

    The Third International Workshop on Computational Electronics (IWCE) was held at the Benson Hotel in downtown Portland, Oregon, on May 18, 19, and 20, 1994. The workshop was devoted to a broad range of topics in computational electronics related to the simulation of electronic transport in semiconductors and semiconductor devices, particularly those which use large computational resources. The workshop was supported by the National Science Foundation (NSF), the Office of Naval Research and the Army Research Office, as well as local support from the Oregon Joint Graduate Schools of Engineering and the Oregon Center for Advanced Technology Education. There were over 100 participants in the Portland workshop, of which more than one quarter represented research groups outside of the United States from Austria, Canada, France, Germany, Italy, Japan, Switzerland, and the United Kingdom. There were a total 81 papers presented at the workshop, 9 invited talks, 26 oral presentations and 46 poster presentations. The emphasis of the contributions reflected the interdisciplinary nature of computational electronics with researchers from the Chemistry, Computer Science, Mathematics, Engineering, and Physics communities participating in the workshop.

  11. 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 ...

  12. 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.

  13. 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.

  14. Requirements for mesh resolution in 3D computational hemodynamics.

    PubMed

    Prakash, S; Ethier, C R

    2001-04-01

    Computational techniques are widely used for studying large artery hemodynamics. Current trends favor analyzing flow in more anatomically realistic arteries. A significant obstacle to such analyses is generation of computational meshes that accurately resolve both the complex geometry and the physiologically relevant flow features. Here we examine, for a single arterial geometry, how velocity and wall shear stress patterns depend on mesh characteristics. A well-validated Navier-Stokes solver was used to simulate flow in an anatomically realistic human right coronary artery (RCA) using unstructured high-order tetrahedral finite element meshes. Velocities, wall shear stresses (WSS), and wall shear stress gradients were computed on a conventional "high-resolution" mesh series (60,000 to 160,000 velocity nodes) generated with a commercial meshing package. Similar calculations were then performed in a series of meshes generated through an adaptive mesh refinement (AMR) methodology. Mesh-independent velocity fields were not very difficult to obtain for both the conventional and adaptive mesh series. However, wall shear stress fields, and, in particular, wall shear stress gradient fields, were much more difficult to accurately resolve. The conventional (nonadaptive) mesh series did not show a consistent trend towards mesh-independence of WSS results. For the adaptive series, it required approximately 190,000 velocity nodes to reach an r.m.s. error in normalized WSS of less than 10 percent. Achieving mesh-independence in computed WSS fields requires a surprisingly large number of nodes, and is best approached through a systematic solution-adaptive mesh refinement technique. Calculations of WSS, and particularly WSS gradients, show appreciable errors even on meshes that appear to produce mesh-independent velocity fields.

  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. [3D computer-assisted ENT biopsies of the Iceman].

    PubMed

    Thumfart, W F; Freysinger, W; Gunkel, A R; Truppe, M J; Platzer, W

    1997-02-01

    The University of Innsbruck possesses a unique prehistoric, completely conserved 5300-year-old human cadaver. We report our experiences during which ENT specialists collected samples from various cavities inside the Iceman. Guidance of biopsy instruments was accomplished with computer-assisted navigation based on Interventional Video Tomography. This technology allows surgical guidance by interlinking currently available imaging modalities with live endoscopic video. The system operates without patient fixation and is practically free of external contact. Apart from sterility, special precautionary measures were necessary to avoid contamination with heavy metals or microorganisms. Visual inspection of the samples of mucosa from the nose, maxillary sinus and larynx revealed the typical patterns of a human cadaver without overt pathology.

  17. 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.

  18. 3D reconstruction of internal structure of animal body using near-infrared light

    NASA Astrophysics Data System (ADS)

    Tran, Trung Nghia; Yamamoto, Kohei; Namita, Takeshi; Kato, Yuji; Shimizu, Koichi

    2014-03-01

    To realize three-dimensional (3D) optical imaging of the internal structure of animal body, we have developed a new technique to reconstruct CT images from two-dimensional (2D) transillumination images. In transillumination imaging, the image is blurred due to the strong scattering in the tissue. We had developed a scattering suppression technique using the point spread function (PSF) for a fluorescent light source in the body. In this study, we have newly proposed a technique to apply this PSF for a light source to the image of unknown light-absorbing structure. The effectiveness of the proposed technique was examined in the experiments with a model phantom and a mouse. In the phantom experiment, the absorbers were placed in the tissue-equivalent medium to simulate the light-absorbing organs in mouse body. Near-infrared light was illuminated from one side of the phantom and the image was recorded with CMOS camera from another side. Using the proposed techniques, the scattering effect was efficiently suppressed and the absorbing structure can be visualized in the 2D transillumination image. Using the 2D images obtained in many different orientations, we could reconstruct the 3D image. In the mouse experiment, an anesthetized mouse was held in an acrylic cylindrical holder. We can visualize the internal organs such as kidneys through mouse's abdomen using the proposed technique. The 3D image of the kidneys and a part of the liver were reconstructed. Through these experimental studies, the feasibility of practical 3D imaging of the internal light-absorbing structure of a small animal was verified.

  19. Computer-generated hologram for 3D scene from multi-view images

    NASA Astrophysics Data System (ADS)

    Chang, Eun-Young; Kang, Yun-Suk; Moon, KyungAe; Ho, Yo-Sung; Kim, Jinwoong

    2013-05-01

    Recently, the computer generated hologram (CGH) calculated from real existing objects is more actively investigated to support holographic video and TV applications. In this paper, we propose a method of generating a hologram of the natural 3-D scene from multi-view images in order to provide motion parallax viewing with a suitable navigation range. After a unified 3-D point source set describing the captured 3-D scene is obtained from multi-view images, a hologram pattern supporting motion-parallax is calculated from the set using a point-based CGH method. We confirmed that 3-D scenes are faithfully reconstructed using numerical reconstruction.

  20. A 3D HIDAC-PET camera with sub-millimeter resolution for imaging small animals

    SciTech Connect

    Jeavons, A.P.; Chandler, R.A.; Dettmar, C.A.R.

    1999-06-01

    A HIDAC-PET camera consisting essentially of 5 million 0.5 mm gas avalanching detectors has been constructed for small-animal imaging. The particular HIDAC advantage--a high 3D spatial resolution--has been improved to 0.95 mm fwhm and to 0.7 mm fwhm when reconstructing with 3D-OSEM methods incorporating resolution recovery. A depth-of-interaction resolution of 2.5 mm is implicit, due to the laminar construction. Scatter-corrected sensitivity, at 8.9 cps/kBq (i.e. 0.9%) from a central point source, or 7.2 cps/kBq (543 cps/kBq/cm{sup 3}) from a distributed (40 mm diameter, 60 mm long) source is now much higher than previous, and other, work. A field-of-view of 100 mm (adjustable to 200 mm) diameter by 210 mm axially permits whole-body imaging of small animals, containing typically 4MBqs of activity, at 40 kcps of which 16% are random coincidences, with a typical scatter fraction of 44%. Throughout the field-of-view there are no positional distortions and relative quantitation is uniform to {+-} 3.5%, but some variation of spatial resolution is found. The performance demonstrates that HIDAC technology is quite appropriate for small-animal PET cameras.

  1. Sign Language for K-8 Mathematics by 3D Interactive Animation

    ERIC Educational Resources Information Center

    Adamo-Villani, Nicoletta; Doublestein, John; Martin, Zachary

    2005-01-01

    We present a new highly interactive computer animation tool to increase the mathematical skills of deaf children. We aim at increasing the effectiveness of (hearing) parents in teaching arithmetic to their deaf children, and the opportunity of deaf children to learn arithmetic via interactive media. Using state-of-the-art computer animation…

  2. Fraunhofer computer-generated hologram for diffused 3D scene in Fresnel region.

    PubMed

    Liu, Yuan-Zhi; Dong, Jian-Wen; Pu, Yi-Ying; He, He-Xiang; Chen, Bing-Chu; Wang, He-Zhou; Zheng, Huadong; Yu, Yingjie

    2011-06-01

    A Fraunhofer computer-generated hologram (CGH) is proved to be valid in display for three-dimensional (3D) objects from the Fresnel to the far-field region without a Fourier lens for reconstruction. To quickly compute large and complicated 3D objects that consist of slanted diffused surfaces in the Fresnel region, a Fraunhofer-based analytical approach using a basic-triangle tiling diffuser is developed. Both theoretical and experimental results reveal that Fraunhofer CGH can perform the same effects as Fresnel CGH but require less calculation time. Impressive 3D solid effects are achieved in the Fresnel region.

  3. Optimization Methods for Computer Animation.

    ERIC Educational Resources Information Center

    Donkin, John Caldwell

    Emphasizing the importance of economy and efficiency in the production of computer animation, this master's thesis outlines methodologies that can be used to develop animated sequences with the highest quality images for the least expenditure. It is assumed that if computer animators are to be able to fully exploit the available resources, they…

  4. A 3D character animation engine for multimodal interaction on mobile devices

    NASA Astrophysics Data System (ADS)

    Sandali, Enrico; Lavagetto, Fabio; Pisano, Paolo

    2005-03-01

    Talking virtual characters are graphical simulations of real or imaginary persons that enable natural and pleasant multimodal interaction with the user, by means of voice, eye gaze, facial expression and gestures. This paper presents an implementation of a 3D virtual character animation and rendering engine, compliant with the MPEG-4 standard, running on Symbian-based SmartPhones. Real-time animation of virtual characters on mobile devices represents a challenging task, since many limitations must be taken into account with respect to processing power, graphics capabilities, disk space and execution memory size. The proposed optimization techniques allow to overcome these issues, guaranteeing a smooth and synchronous animation of facial expressions and lip movements on mobile phones such as Sony-Ericsson's P800 and Nokia's 6600. The animation engine is specifically targeted to the development of new "Over The Air" services, based on embodied conversational agents, with applications in entertainment (interactive story tellers), navigation aid (virtual guides to web sites and mobile services), news casting (virtual newscasters) and education (interactive virtual teachers).

  5. Computer-Designed Splints for Surgical Transfer of 3D Orthognathic Planning.

    PubMed

    Zinser, Max; Zoeller, Joachim

    2015-10-01

    Advances in computers and imaging have permitted the adoption of three-dimensional (3D) planning protocols in orthognathic surgery, which may allow a paradigm shift when the computer-assisted planning can be transferred properly. The purpose of this investigation was to introduce an innovative clinical protocol using computer-aided designed and computer-aided manufactured (CAD/CAM) surgical splints for surgical transfer of 3D orthognathic planning compared with the classic technique using arbitrary occlusal splints. The clinical protocols consisted of computed tomography (CT) or cone-beam CT (CBCT) maxillofacial imaging, bone segmentation, 3D diagnosis, computer-assisted surgical treatment planning, and CAD/CAM surgical splints (group A) and manufacture of arbitrary occlusal splints (group B) for intraoperative surgical planning transfer. The observed patients underwent bimaxillary osteotomies and, if necessary, an additional genioplasty. Both techniques were evaluated by applying 13 hard tissue parameters to compare the 3D orthognathic planning (T0) with the postoperative result (T1) using 3D cephalometry. The CAD/CAM splints showed significant better precision for the maxilla (ΔT < 0.23 mm) and mandible (ΔT < 0.33 mm) compared with a maxillary deviation of 1.3 mm and a mandibular deviation of 1.8 mm when using the arbitrary splints. Computer-assisted diagnosis and preoperative surgical planning provide clinicians with valuable tools and allow 3D imagination. CAD/CAM splints provide a reliable, innovative, and precise approach for the transfer of 3D orthognathic planning, which is more precise compared with the conventional arbitrary occlusal splints.

  6. GeoBuilder: a geometric algorithm visualization and debugging system for 2D and 3D geometric computing.

    PubMed

    Wei, Jyh-Da; Tsai, Ming-Hung; Lee, Gen-Cher; Huang, Jeng-Hung; Lee, Der-Tsai

    2009-01-01

    Algorithm visualization is a unique research topic that integrates engineering skills such as computer graphics, system programming, database management, computer networks, etc., to facilitate algorithmic researchers in testing their ideas, demonstrating new findings, and teaching algorithm design in the classroom. Within the broad applications of algorithm visualization, there still remain performance issues that deserve further research, e.g., system portability, collaboration capability, and animation effect in 3D environments. Using modern technologies of Java programming, we develop an algorithm visualization and debugging system, dubbed GeoBuilder, for geometric computing. The GeoBuilder system features Java's promising portability, engagement of collaboration in algorithm development, and automatic camera positioning for tracking 3D geometric objects. In this paper, we describe the design of the GeoBuilder system and demonstrate its applications. PMID:19147888

  7. Estimating Mass Properties of Dinosaurs Using Laser Imaging and 3D Computer Modelling

    PubMed Central

    Bates, Karl T.; Manning, Phillip L.; Hodgetts, David; Sellers, William I.

    2009-01-01

    Body mass reconstructions of extinct vertebrates are most robust when complete to near-complete skeletons allow the reconstruction of either physical or digital models. Digital models are most efficient in terms of time and cost, and provide the facility to infinitely modify model properties non-destructively, such that sensitivity analyses can be conducted to quantify the effect of the many unknown parameters involved in reconstructions of extinct animals. In this study we use laser scanning (LiDAR) and computer modelling methods to create a range of 3D mass models of five specimens of non-avian dinosaur; two near-complete specimens of Tyrannosaurus rex, the most complete specimens of Acrocanthosaurus atokensis and Strutiomimum sedens, and a near-complete skeleton of a sub-adult Edmontosaurus annectens. LiDAR scanning allows a full mounted skeleton to be imaged resulting in a detailed 3D model in which each bone retains its spatial position and articulation. This provides a high resolution skeletal framework around which the body cavity and internal organs such as lungs and air sacs can be reconstructed. This has allowed calculation of body segment masses, centres of mass and moments or inertia for each animal. However, any soft tissue reconstruction of an extinct taxon inevitably represents a best estimate model with an unknown level of accuracy. We have therefore conducted an extensive sensitivity analysis in which the volumes of body segments and respiratory organs were varied in an attempt to constrain the likely maximum plausible range of mass parameters for each animal. Our results provide wide ranges in actual mass and inertial values, emphasizing the high level of uncertainty inevitable in such reconstructions. However, our sensitivity analysis consistently places the centre of mass well below and in front of hip joint in each animal, regardless of the chosen combination of body and respiratory structure volumes. These results emphasize that future

  8. Estimating mass properties of dinosaurs using laser imaging and 3D computer modelling.

    PubMed

    Bates, Karl T; Manning, Phillip L; Hodgetts, David; Sellers, William I

    2009-01-01

    Body mass reconstructions of extinct vertebrates are most robust when complete to near-complete skeletons allow the reconstruction of either physical or digital models. Digital models are most efficient in terms of time and cost, and provide the facility to infinitely modify model properties non-destructively, such that sensitivity analyses can be conducted to quantify the effect of the many unknown parameters involved in reconstructions of extinct animals. In this study we use laser scanning (LiDAR) and computer modelling methods to create a range of 3D mass models of five specimens of non-avian dinosaur; two near-complete specimens of Tyrannosaurus rex, the most complete specimens of Acrocanthosaurus atokensis and Strutiomimum sedens, and a near-complete skeleton of a sub-adult Edmontosaurus annectens. LiDAR scanning allows a full mounted skeleton to be imaged resulting in a detailed 3D model in which each bone retains its spatial position and articulation. This provides a high resolution skeletal framework around which the body cavity and internal organs such as lungs and air sacs can be reconstructed. This has allowed calculation of body segment masses, centres of mass and moments or inertia for each animal. However, any soft tissue reconstruction of an extinct taxon inevitably represents a best estimate model with an unknown level of accuracy. We have therefore conducted an extensive sensitivity analysis in which the volumes of body segments and respiratory organs were varied in an attempt to constrain the likely maximum plausible range of mass parameters for each animal. Our results provide wide ranges in actual mass and inertial values, emphasizing the high level of uncertainty inevitable in such reconstructions. However, our sensitivity analysis consistently places the centre of mass well below and in front of hip joint in each animal, regardless of the chosen combination of body and respiratory structure volumes. These results emphasize that future

  9. Estimating mass properties of dinosaurs using laser imaging and 3D computer modelling.

    PubMed

    Bates, Karl T; Manning, Phillip L; Hodgetts, David; Sellers, William I

    2009-01-01

    Body mass reconstructions of extinct vertebrates are most robust when complete to near-complete skeletons allow the reconstruction of either physical or digital models. Digital models are most efficient in terms of time and cost, and provide the facility to infinitely modify model properties non-destructively, such that sensitivity analyses can be conducted to quantify the effect of the many unknown parameters involved in reconstructions of extinct animals. In this study we use laser scanning (LiDAR) and computer modelling methods to create a range of 3D mass models of five specimens of non-avian dinosaur; two near-complete specimens of Tyrannosaurus rex, the most complete specimens of Acrocanthosaurus atokensis and Strutiomimum sedens, and a near-complete skeleton of a sub-adult Edmontosaurus annectens. LiDAR scanning allows a full mounted skeleton to be imaged resulting in a detailed 3D model in which each bone retains its spatial position and articulation. This provides a high resolution skeletal framework around which the body cavity and internal organs such as lungs and air sacs can be reconstructed. This has allowed calculation of body segment masses, centres of mass and moments or inertia for each animal. However, any soft tissue reconstruction of an extinct taxon inevitably represents a best estimate model with an unknown level of accuracy. We have therefore conducted an extensive sensitivity analysis in which the volumes of body segments and respiratory organs were varied in an attempt to constrain the likely maximum plausible range of mass parameters for each animal. Our results provide wide ranges in actual mass and inertial values, emphasizing the high level of uncertainty inevitable in such reconstructions. However, our sensitivity analysis consistently places the centre of mass well below and in front of hip joint in each animal, regardless of the chosen combination of body and respiratory structure volumes. These results emphasize that future

  10. Time- and Computation-Efficient Calibration of MEMS 3D Accelerometers and Gyroscopes

    PubMed Central

    Stančin, Sara; Tomažič, Sašo

    2014-01-01

    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. PMID:25123469

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

    PubMed

    Stančin, Sara; Tomažič, Sašo

    2014-01-01

    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.

  12. Investigation on reconstruction methods applied to 3D terahertz computed tomography.

    PubMed

    Recur, B; Younus, A; Salort, S; Mounaix, P; Chassagne, B; Desbarats, P; Caumes, J-P; Abraham, E

    2011-03-14

    3D terahertz computed tomography has been performed using a monochromatic millimeter wave imaging system coupled with an infrared temperature sensor. Three different reconstruction methods (standard back-projection algorithm and two iterative analysis) have been compared in order to reconstruct large size 3D objects. The quality (intensity, contrast and geometric preservation) of reconstructed cross-sectional images has been discussed together with the optimization of the number of projections. Final demonstration to real-life 3D objects has been processed to illustrate the potential of the reconstruction methods for applied terahertz tomography.

  13. 3D-SoftChip: A Novel Architecture for Next-Generation Adaptive Computing Systems

    NASA Astrophysics Data System (ADS)

    Kim, Chul; Rassau, Alex; Lachowicz, Stefan; Lee, Mike Myung-Ok; Eshraghian, Kamran

    2006-12-01

    This paper introduces a novel architecture for next-generation adaptive computing systems, which we term 3D-SoftChip. The 3D-SoftChip is a 3-dimensional (3D) vertically integrated adaptive computing system combining state-of-the-art processing and 3D interconnection technology. It comprises the vertical integration of two chips (a configurable array processor and an intelligent configurable switch) through an indium bump interconnection array (IBIA). The configurable array processor (CAP) is an array of heterogeneous processing elements (PEs), while the intelligent configurable switch (ICS) comprises a switch block, 32-bit dedicated RISC processor for control, on-chip program/data memory, data frame buffer, along with a direct memory access (DMA) controller. This paper introduces the novel 3D-SoftChip architecture for real-time communication and multimedia signal processing as a next-generation computing system. The paper further describes the advanced HW/SW codesign and verification methodology, including high-level system modeling of the 3D-SoftChip using SystemC, being used to determine the optimum hardware specification in the early design stage.

  14. 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.

  15. 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

  16. Computer-aided microtomography with true 3-D display in electron microscopy.

    PubMed

    Nelson, A C

    1986-01-01

    A novel research system has been designed to permit three-dimensional (3-D) viewing of high resolution image data from transmission electron microscopy (TEM) and scanning electron microscopy (SEM). The system consists of front-end primary data acquisition devices, such as TEM and SEM machines, which are equipped with computer-controlled specimen tilt stages. The output from these machines is in analogue form, where a video camera attached to the TEM provides the sequential analogue image output while the SEM direct video output is utilized. A 10 MHz digitizer transforms the video image to a digital array of 512 X 512 pixel units of 8 bits deep-stored in a frame buffer. Digital images from multiple projections are reconstructed into 3-D image boxes in a dedicated computer. Attached to the computer is a powerful true 3-D display device which has hardware for graphic manipulations including tilt and rotate on any axis and for probing the image with a 3-D cursor. Data editing and automatic contouring functions are used to enhance areas of interest, and specialized software is available for measurement of numbers, distances, areas, and volumes. With proper archiving of reconstructed image sequences, a dynamic 3-D presentation is possible. The microtomography system is highly versatile and can process image data on-line or from remote sites from which data records would typically be transported on computer tape, video tape, or floppy disk. PMID:3753610

  17. Computer-aided 3D-shape construction of hearts from CT images for rapid prototyping

    NASA Astrophysics Data System (ADS)

    Fukuzawa, Masayuki; Kato, Yutaro; Nakamori, Nobuyuki; Ozawa, Seiichiro; Shiraishi, Isao

    2012-03-01

    By developing a computer-aided modeling system, the 3D shapes of infant's heart have been constructed interactively from quality-limited CT images for rapid prototyping of biomodels. The 3D model was obtained by following interactive steps: (1) rough region cropping, (2) outline extraction in each slice with locally-optimized threshold, (3) verification and correction of outline overlap, (4) 3D surface generation of inside wall, (5) connection of inside walls, (6) 3D surface generation of outside wall, (7) synthesis of self-consistent 3D surface. The manufactured biomodels revealed characteristic 3D shapes of heart such as left atrium and ventricle, aortic arch and right auricle. Their real shape of cavity and vessel is suitable for surgery planning and simulation. It is a clear advantage over so-called "blood-pool" model which is massive and often found in 3D visualization of CT images as volume rendering perspective. The developed system contributed both to quality improvement and to modeling-time reduction, which may suggest a practical approach to establish a routine process for manufacturing heart biomodels. Further study on the system performance is now still in progress.

  18. Enhancement of 3D modeling and classification of microcalcifications in breast computed tomography (BCT)

    NASA Astrophysics Data System (ADS)

    Alquran, Hiam; Shaheen, Eman; O'Connor, J. Michael; Mahd, Mufeed

    2014-03-01

    Current computer aided diagnosis (CADx) software for digital mammography relies mainly on 2D techniques. With the emergence of three-dimensional (3D) breast imaging modalities such as breast Computed Tomography (BCT), there is an opportunity to analyze 3D features in the classification of calcifications. We previously reported our initial work on automated 3D feature detection and classification based on morphological descriptions for single microcalcifications within clusters [1]. In this work, we propose the expansion of the 3D classification methods to include novel microcalcification morphological feature detection such as including more morphological classes and replacing the 2D Radon transform by a 3D Radon transform. Results show that the classification rate improved compared to the previously reported results from a total of 546 to 559 consistently classified calcifications out of 635 total calcifications. This slight improvement is due to the use of the 3D Radon transform and incorporating methods to detect two classes not previously implemented. Future work will focus on adding feature detection and classification of cluster patterns.

  19. Software Development: 3D Animations and Creating User Interfaces for Realistic Simulations

    NASA Technical Reports Server (NTRS)

    Gordillo, Orlando Enrique

    2015-01-01

    My fall 2015 semester was spent at the Lyndon B. Johnson Space Center working in the Integrated Graphics, Operations, and Analysis Laboratory (IGOAL). My first project was to create a video animation that could tell the story of OMICS. OMICS is a term being used in the field of biomedical science to describe the collective technologies that study biological systems, such as what makes up a cell and how it functions with other systems. In the IGOAL I used a large 23 inch Wacom monitor to draw storyboards, graphics, and line art animations. I used Blender as the 3D environment to sculpt, shape, cut or modify the several scenes and models for the video. A challenge creating this video was to take a term used in biomedical science and describe it in such a way that an 8th grade student can understand. I used a line art style because it would visually set the tone for what we thought was an educational style. In order to get a handle on the perspective and overall feel for the animation without overloading my workspace, I split up the 2 minute animation into several scenes. I used Blender's python scripting capabilities which allowed for the addition of plugins to add or modify tools. The scripts can also directly interact with the objects to create naturalistic patterns or movements. After collecting the rendered scenes, I used Blender's built-in video editing workspace to output the animation. My second project was to write software that emulates a physical system's interface. The interface was to simulate a boat, ROV, and winch system. Simulations are a time and cost effective way to test complicated data and provide training for operators without having to use expensive hardware. We created the virtual controls with 3-D Blender models and 2-D graphics, and then add functionality in C# using the Unity game engine. The Unity engine provides several essential behaviors of a simulator, such as the start and update functions. A framework for Unity, which was developed in

  20. Three-Dimensional Reconstructions Come to Life – Interactive 3D PDF Animations in Functional Morphology

    PubMed Central

    van de Kamp, Thomas; dos Santos Rolo, Tomy; Vagovič, Patrik; Baumbach, Tilo; Riedel, Alexander

    2014-01-01

    Digital surface mesh models based on segmented datasets have become an integral part of studies on animal anatomy and functional morphology; usually, they are published as static images, movies or as interactive PDF files. We demonstrate the use of animated 3D models embedded in PDF documents, which combine the advantages of both movie and interactivity, based on the example of preserved Trigonopterus weevils. The method is particularly suitable to simulate joints with largely deterministic movements due to precise form closure. We illustrate the function of an individual screw-and-nut type hip joint and proceed to the complex movements of the entire insect attaining a defence position. This posture is achieved by a specific cascade of movements: Head and legs interlock mutually and with specific features of thorax and the first abdominal ventrite, presumably to increase the mechanical stability of the beetle and to maintain the defence position with minimal muscle activity. The deterministic interaction of accurately fitting body parts follows a defined sequence, which resembles a piece of engineering. PMID:25029366

  1. Three-dimensional reconstructions come to life--interactive 3D PDF animations in functional morphology.

    PubMed

    van de Kamp, Thomas; dos Santos Rolo, Tomy; Vagovič, Patrik; Baumbach, Tilo; Riedel, Alexander

    2014-01-01

    Digital surface mesh models based on segmented datasets have become an integral part of studies on animal anatomy and functional morphology; usually, they are published as static images, movies or as interactive PDF files. We demonstrate the use of animated 3D models embedded in PDF documents, which combine the advantages of both movie and interactivity, based on the example of preserved Trigonopterus weevils. The method is particularly suitable to simulate joints with largely deterministic movements due to precise form closure. We illustrate the function of an individual screw-and-nut type hip joint and proceed to the complex movements of the entire insect attaining a defence position. This posture is achieved by a specific cascade of movements: Head and legs interlock mutually and with specific features of thorax and the first abdominal ventrite, presumably to increase the mechanical stability of the beetle and to maintain the defence position with minimal muscle activity. The deterministic interaction of accurately fitting body parts follows a defined sequence, which resembles a piece of engineering. PMID:25029366

  2. 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.

  3. Computer-Generated, Three-Dimensional Character Animation: A Report and Analysis.

    ERIC Educational Resources Information Center

    Kingsbury, Douglas Lee

    This master's thesis details the experience gathered in the production "Snoot and Muttly," a short character animation with 3-D computer generated images, and provides an analysis of the computer-generated 3-D character animation system capabilities. Descriptions are provided of the animation environment at the Ohio State University Computer…

  4. 3D computer data capture and imaging applied to the face and jaws.

    PubMed

    Spencer, R; Hathaway, R; Speculand, B

    1996-02-01

    There have been few attempts in the past at 3D computer modelling of facial deformity because of the difficulties with generating accurate three-dimensional data and subsequent image regeneration and manipulation. We report the application of computer aided engineering techniques to the study of jaw deformity. The construction of a 3D image of the mandible using a Ferranti co-ordinate measuring machine for data capture and the 'DUCT5' surface modelling programme for image regeneration is described. The potential application of this work will be discussed. PMID:8645664

  5. 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.

  6. Computer-Assisted 3D Kinematic Analysis of All Leg Joints in Walking Insects

    PubMed Central

    Bender, John A.; Simpson, Elaine M.; Ritzmann, Roy E.

    2010-01-01

    High-speed video can provide fine-scaled analysis of animal behavior. However, extracting behavioral data from video sequences is a time-consuming, tedious, subjective task. These issues are exacerbated where accurate behavioral descriptions require analysis of multiple points in three dimensions. We describe a new computer program written to assist a user in simultaneously extracting three-dimensional kinematics of multiple points on each of an insect's six legs. Digital video of a walking cockroach was collected in grayscale at 500 fps from two synchronized, calibrated cameras. We improved the legs' visibility by painting white dots on the joints, similar to techniques used for digitizing human motion. Compared to manual digitization of 26 points on the legs over a single, 8-second bout of walking (or 106,496 individual 3D points), our software achieved approximately 90% of the accuracy with 10% of the labor. Our experimental design reduced the complexity of the tracking problem by tethering the insect and allowing it to walk in place on a lightly oiled glass surface, but in principle, the algorithms implemented are extensible to free walking. Our software is free and open-source, written in the free language Python and including a graphical user interface for configuration and control. We encourage collaborative enhancements to make this tool both better and widely utilized. PMID:21049024

  7. Models the Electromagnetic Response of a 3D Distribution using MP COMPUTERS

    1999-05-01

    EM3D models the electromagnetic response of a 3D distribution of conductivity, dielectric permittivity and magnetic permeability within the earth for geophysical applications using massively parallel computers. The simulations are carried out in the frequency domain for either electric or magnetic sources for either scattered or total filed formulations of Maxwell''s equations. The solution is based on the method of finite differences and includes absorbing boundary conditions so that responses can be modeled up into themore » radar range where wave propagation is dominant. Recent upgrades in the software include the incorporation of finite size sources, that in addition to dipolar source fields, and a low induction number preconditioner that can significantly reduce computational run times. A graphical user interface (GUI) is bundled with the software so that complicated 3D models can be easily constructed and simulated with the software. The GUI also allows for plotting of the output.« less

  8. 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.

  9. 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,…

  10. 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...

  11. 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.

  12. 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…

  13. 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.

  14. 3D image fusion and guidance for computer-assisted bronchoscopy

    NASA Astrophysics Data System (ADS)

    Higgins, W. E.; Rai, L.; Merritt, S. A.; Lu, K.; Linger, N. T.; Yu, K. C.

    2005-11-01

    The standard procedure for diagnosing lung cancer involves two stages. First, the physician evaluates a high-resolution three-dimensional (3D) computed-tomography (CT) chest image to produce a procedure plan. Next, the physician performs bronchoscopy on the patient, which involves navigating the the bronchoscope through the airways to planned biopsy sites. Unfortunately, the physician has no link between the 3D CT image data and the live video stream provided during bronchoscopy. In addition, these data sources differ greatly in what they physically give, and no true 3D planning tools exist for planning and guiding procedures. This makes it difficult for the physician to translate a CT-based procedure plan to the video domain of the bronchoscope. Thus, the physician must essentially perform biopsy blindly, and the skill levels between different physicians differ greatly. We describe a system that enables direct 3D CT-based procedure planning and provides direct 3D guidance during bronchoscopy. 3D CT-based information on biopsy sites is provided interactively as the physician moves the bronchoscope. Moreover, graphical information through a live fusion of the 3D CT data and bronchoscopic video is provided during the procedure. This information is coupled with a series of computer-graphics tools to give the physician a greatly augmented reality of the patient's interior anatomy during a procedure. Through a series of controlled tests and studies with human lung-cancer patients, we have found that the system not only reduces the variation in skill level between different physicians, but also increases biopsy success rate.

  15. Function of pretribosphenic and tribosphenic mammalian molars inferred from 3D animation.

    PubMed

    Schultz, Julia A; Martin, Thomas

    2014-10-01

    Appearance of the tribosphenic molar in the Late Jurassic (160 Ma) is a crucial innovation for food processing in mammalian evolution. This molar type is characterized by a protocone, a talonid basin and a two-phased chewing cycle, all of which are apomorphic. In this functional study on the teeth of Late Jurassic Dryolestes leiriensis and the living marsupial Monodelphis domestica, we demonstrate that pretribosphenic and tribosphenic molars show fundamental differences of food reduction strategies, representing a shift in dental function during the transition of tribosphenic mammals. By using the Occlusal Fingerprint Analyser (OFA), we simulated the chewing motions of the pretribosphenic Dryolestes that represents an evolutionary precursor condition to such tribosphenic mammals as Monodelphis. Animation of chewing path and detection of collisional contacts between virtual models of teeth suggests that Dryolestes differs from the classical two-phased chewing movement of tribosphenidans, due to the narrowing of the interdental space in cervical (crown-root transition) direction, the inclination angle of the hypoflexid groove, and the unicuspid talonid. The pretribosphenic chewing cycle is equivalent to phase I of the tribosphenic chewing cycle, but the former lacks phase II of the tribosphenic chewing. The new approach can analyze the chewing cycle of the jaw by using polygonal 3D models of tooth surfaces, in a way that is complementary to the electromyography and strain gauge studies of muscle function of living animals. The technique allows alignment and scaling of isolated fossil teeth and utilizes the wear facet orientation and striation of the teeth to reconstruct the chewing path of extinct mammals.

  16. Function of pretribosphenic and tribosphenic mammalian molars inferred from 3D animation

    NASA Astrophysics Data System (ADS)

    Schultz, Julia A.; Martin, Thomas

    2014-10-01

    Appearance of the tribosphenic molar in the Late Jurassic (160 Ma) is a crucial innovation for food processing in mammalian evolution. This molar type is characterized by a protocone, a talonid basin and a two-phased chewing cycle, all of which are apomorphic. In this functional study on the teeth of Late Jurassic Dryolestes leiriensis and the living marsupial Monodelphis domestica, we demonstrate that pretribosphenic and tribosphenic molars show fundamental differences of food reduction strategies, representing a shift in dental function during the transition of tribosphenic mammals. By using the Occlusal Fingerprint Analyser (OFA), we simulated the chewing motions of the pretribosphenic Dryolestes that represents an evolutionary precursor condition to such tribosphenic mammals as Monodelphis. Animation of chewing path and detection of collisional contacts between virtual models of teeth suggests that Dryolestes differs from the classical two-phased chewing movement of tribosphenidans, due to the narrowing of the interdental space in cervical (crown-root transition) direction, the inclination angle of the hypoflexid groove, and the unicuspid talonid. The pretribosphenic chewing cycle is equivalent to phase I of the tribosphenic chewing cycle, but the former lacks phase II of the tribosphenic chewing. The new approach can analyze the chewing cycle of the jaw by using polygonal 3D models of tooth surfaces, in a way that is complementary to the electromyography and strain gauge studies of muscle function of living animals. The technique allows alignment and scaling of isolated fossil teeth and utilizes the wear facet orientation and striation of the teeth to reconstruct the chewing path of extinct mammals.

  17. 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.

  18. Efficient 3D geometric and Zernike moments computation from unstructured surface meshes.

    PubMed

    Pozo, José María; Villa-Uriol, Maria-Cruz; Frangi, Alejandro F

    2011-03-01

    This paper introduces and evaluates a fast exact algorithm and a series of faster approximate algorithms for the computation of 3D geometric moments from an unstructured surface mesh of triangles. Being based on the object surface reduces the computational complexity of these algorithms with respect to volumetric grid-based algorithms. In contrast, it can only be applied for the computation of geometric moments of homogeneous objects. This advantage and restriction is shared with other proposed algorithms based on the object boundary. The proposed exact algorithm reduces the computational complexity for computing geometric moments up to order N with respect to previously proposed exact algorithms, from N(9) to N(6). The approximate series algorithm appears as a power series on the rate between triangle size and object size, which can be truncated at any desired degree. The higher the number and quality of the triangles, the better the approximation. This approximate algorithm reduces the computational complexity to N(3). In addition, the paper introduces a fast algorithm for the computation of 3D Zernike moments from the computed geometric moments, with a computational complexity N(4), while the previously proposed algorithm is of order N(6). The error introduced by the proposed approximate algorithms is evaluated in different shapes and the cost-benefit ratio in terms of error, and computational time is analyzed for different moment orders. PMID:20714011

  19. 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.

  20. 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.

  1. 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. PMID:12679063

  2. 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.

  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. Performance assessment of KORAT-3D on the ANL IBM-SP computer

    SciTech Connect

    Alexeyev, A.V.; Zvenigorodskaya, O.A.; Shagaliev, R.M.; Taiwo, T.A.

    1999-09-01

    The TENAR code is currently being developed at the Russian Federal Nuclear Center (VNIIEF) as a coupled dynamics code for the simulation of transients in VVER and RBMK systems and other nuclear systems. The neutronic module in this code system is KORAT-3D. This module is also one of the most computationally intensive components of the code system. A parallel version of KORAT-3D has been implemented to achieve the goal of obtaining transient solutions in reasonable computational time, particularly for RBMK calculations that involve the application of >100,000 nodes. An evaluation of the KORAT-3D code performance was recently undertaken on the Argonne National Laboratory (ANL) IBM ScalablePower (SP) parallel computer located in the Mathematics and Computer Science Division of ANL. At the time of the study, the ANL IBM-SP computer had 80 processors. This study was conducted under the auspices of a technical staff exchange program sponsored by the International Nuclear Safety Center (INSC).

  5. Computational optical-sectioning microscopy for 3D quantization of cell motion: results and challenges

    NASA Astrophysics Data System (ADS)

    McNally, James G.

    1994-09-01

    How cells move and navigate within a 3D tissue mass is of central importance in such diverse problems as embryonic development, wound healing and metastasis. This locomotion can now be visualized and quantified by using computation optical-sectioning microscopy. In this approach, a series of 2D images at different depths in a specimen are stacked to construct a 3D image, and then with a knowledge of the microscope's point-spread function, the actual distribution of fluorescent intensity in the specimen is estimated via computation. When coupled with wide-field optics and a cooled CCD camera, this approach permits non-destructive 3D imaging of living specimens over long time periods. With these techniques, we have observed a complex diversity of motile behaviors in a model embryonic system, the cellular slime mold Dictyostelium. To understand the mechanisms which control these various behaviors, we are examining motion in various Dictyostelium mutants with known defects in proteins thought to be essential for signal reception, cell-cell adhesion or locomotion. This application of computational techniques to analyze 3D cell locomotion raises several technical challenges. Image restoration techniques must be fast enough to process numerous 1 Gbyte time-lapse data sets (16 Mbytes per 3D image X 60 time points). Because some cells are weakly labeled and background intensity is often high due to unincorporated dye, the SNR in some of these images is poor. Currently, the images are processed by a regularized linear least- squares restoration method, and occasionally by a maximum-likelihood method. Also required for these studies are accurate automated- tracking procedures to generate both 3D trajectories for individual cells and 3D flows for a group of cells. Tracking is currently done independently for each cell, using a cell's image as a template to search for a similar image at the next time point. Finally, sophisticated visualization techniques are needed to view the

  6. 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.

  7. Computer animation challenges for computational fluid dynamics

    NASA Astrophysics Data System (ADS)

    Vines, Mauricio; Lee, Won-Sook; Mavriplis, Catherine

    2012-07-01

    Computer animation requirements differ from those of traditional computational fluid dynamics (CFD) investigations in that visual plausibility and rapid frame update rates trump physical accuracy. We present an overview of the main techniques for fluid simulation in computer animation, starting with Eulerian grid approaches, the Lattice Boltzmann method, Fourier transform techniques and Lagrangian particle introduction. Adaptive grid methods, precomputation of results for model reduction, parallelisation and computation on graphical processing units (GPUs) are reviewed in the context of accelerating simulation computations for animation. A survey of current specific approaches for the application of these techniques to the simulation of smoke, fire, water, bubbles, mixing, phase change and solid-fluid coupling is also included. Adding plausibility to results through particle introduction, turbulence detail and concentration on regions of interest by level set techniques has elevated the degree of accuracy and realism of recent animations. Basic approaches are described here. Techniques to control the simulation to produce a desired visual effect are also discussed. Finally, some references to rendering techniques and haptic applications are mentioned to provide the reader with a complete picture of the challenges of simulating fluids in computer animation.

  8. 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.

  9. Computer-generated animal model stimuli.

    PubMed

    Woo, Kevin L

    2007-01-01

    Communication between animals is diverse and complex. Animals may communicate using auditory, seismic, chemosensory, electrical, or visual signals. In particular, understanding the constraints on visual signal design for communication has been of great interest. Traditional methods for investigating animal interactions have used basic observational techniques, staged encounters, or physical manipulation of morphology. Less intrusive methods have tried to simulate conspecifics using crude playback tools, such as mirrors, still images, or models. As technology has become more advanced, video playback has emerged as another tool in which to examine visual communication (Rosenthal, 2000). However, to move one step further, the application of computer-animation now allows researchers to specifically isolate critical components necessary to elicit social responses from conspecifics, and manipulate these features to control interactions. Here, I provide detail on how to create an animation using the Jacky dragon as a model, but this process may be adaptable for other species. In building the animation, I elected to use Lightwave 3D to alter object morphology, add texture, install bones, and provide comparable weight shading that prevents exaggerated movement. The animation is then matched to select motor patterns to replicate critical movement features. Finally, the sequence must rendered into an individual clip for presentation. Although there are other adaptable techniques, this particular method had been demonstrated to be effective in eliciting both conspicuous and social responses in staged interactions.

  10. Visual presentation and computer animation

    SciTech Connect

    Wang, Hua.

    1991-01-01

    This paper presents an assessment of the current computer graphics and video technologies as they applied to the fields of visual presentation and computer animation, including a discussion of inherent incompatibilities between computer graphics and video systems. The near-term technology trend is directed towards the integration of sound, video and computer graphics into a multimedia, desktop presentation system. With the forthcoming High-Definition Television (HDTV) standard, it can be predicted that computer graphics and video will eventually be integrated to a desktop video system. Recent advances in technology development to achieve these goals are described. 3 tabs.

  11. NOTE: A 3D MRI sequence for computer assisted surgery of the lumbar spine

    NASA Astrophysics Data System (ADS)

    Hoad, C. L.; Martel, A. L.; Kerslake, R.; Grevitt, M.

    2001-08-01

    The aim of this research was to develop a magnetic resonance (MR) sequence capable of producing images suitable for use with computer assisted surgery (CAS) of the lumbar spine. These images needed good tissue contrast between bone and soft tissue to allow for image segmentation and generation of a 3D-surface model of the bone for surface registration. A 3D double echo fast gradient echo sequence was designed. Images were filtered for noise and non-uniformity and combined into a single data set. Registration experiments were carried out to directly compare segmentation of MR and computed tomography (CT) images using a physical model of a spine. These experiments showed the MR data produced adequate surface registration in 90% of the experiments compared to 100% with CT data. The MR images acquired using the sequence and processing described in this article are suitable to be used with CAS of the spine.

  12. 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.

  13. 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.

  14. Confocal 3D DNA Cytometry: Assessment of Required Coefficient of Variation by Computer Simulation

    PubMed Central

    Ploeger, Lennert S.; Beliën, Jeroen A.M.; Poulin, Neal M.; Grizzle, William; van Diest, Paul J.

    2004-01-01

    Background: Confocal Laser Scanning Microscopy (CLSM) provides the opportunity to perform 3D DNA content measurements on intact cells in thick histological sections. So far, sample size has been limited by the time consuming nature of the technology. Since the power of DNA histograms to resolve different stemlines depends on both the sample size and the coefficient of variation (CV) of histogram peaks, interpretation of 3D CLSM DNA histograms might be hampered by both a small sample size and a large CV. The aim of this study was to analyze the required CV for 3D CLSM DNA histograms given a realistic sample size. Methods: By computer simulation, virtual histograms were composed for sample sizes of 20000, 10000, 5000, 1000, and 273 cells and CVs of 30, 25, 20, 15, 10 and 5%. By visual inspection, the histogram quality with respect to resolution of G0/1 and G2/M peaks of a diploid stemline was assessed. Results: As expected, the interpretability of DNA histograms deteriorated with decreasing sample sizes and higher CVs. For CVs of 15% and lower, a clearly bimodal peak pattern with well distinguishable G0/1 and G2/M peaks were still seen at a sample size of 273 cells, which is our current average sample size with 3D CLSM DNA cytometry. Conclusions: For unambiguous interpretation of DNA histograms obtained using 3D CLSM, a CV of at most 15% is tolerable at currently achievable sample sizes. To resolve smaller near diploid stemlines, a CV of 10% or better should be aimed at. With currently available 3D imaging technology, this CV is achievable. PMID:15371645

  15. 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

  16. 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.

  17. Effectiveness of Applying 2D Static Depictions and 3D Animations to Orthographic Views Learning in Graphical Course

    ERIC Educational Resources Information Center

    Wu, Chih-Fu; Chiang, Ming-Chin

    2013-01-01

    This study provides experiment results as an educational reference for instructors to help student obtain a better way to learn orthographic views in graphical course. A visual experiment was held to explore the comprehensive differences between 2D static and 3D animation object features; the goal was to reduce the possible misunderstanding…

  18. 3D reservoir visualization

    SciTech Connect

    Van, B.T.; Pajon, J.L.; Joseph, P. )

    1991-11-01

    This paper shows how some simple 3D computer graphics tools can be combined to provide efficient software for visualizing and analyzing data obtained from reservoir simulators and geological simulations. The animation and interactive capabilities of the software quickly provide a deep understanding of the fluid-flow behavior and an accurate idea of the internal architecture of a reservoir.

  19. 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.

  20. CELSS-3D: a broad computer model simulating a controlled ecological life support system.

    PubMed

    Schneegurt, M A; Sherman, L A

    1997-01-01

    CELSS-3D is a dynamic, deterministic, and discrete computer simulation of a controlled ecological life support system (CELSS) focusing on biological issues. A series of linear difference equations within a graphic-based modeling environment, the IThink program, was used to describe a modular CELSS system. The overall model included submodels for crop growth chambers, food storage reservoirs, the human crew, a cyanobacterial growth chamber, a waste processor, fixed nitrogen reservoirs, and the atmospheric gases, CO, O2, and N2. The primary process variable was carbon, although oxygen and nitrogen flows were also modeled. Most of the input data used in CELSS-3D were from published sources. A separate linear optimization program, What'sBest!, was used to compare options for the crew's vegetarian diet. CELSS-3D simulations were run for the equivalent of 3 years with a 1-h time interval. Output from simulations run under nominal conditions was used to illustrate dynamic changes in the concentrations of atmospheric gases. The modular design of CELSS-3D will allow other configurations and various failure scenarios to be tested and compared.

  1. CELSS-3D: a broad computer model simulating a controlled ecological life support system.

    PubMed

    Schneegurt, M A; Sherman, L A

    1997-01-01

    CELSS-3D is a dynamic, deterministic, and discrete computer simulation of a controlled ecological life support system (CELSS) focusing on biological issues. A series of linear difference equations within a graphic-based modeling environment, the IThink program, was used to describe a modular CELSS system. The overall model included submodels for crop growth chambers, food storage reservoirs, the human crew, a cyanobacterial growth chamber, a waste processor, fixed nitrogen reservoirs, and the atmospheric gases, CO, O2, and N2. The primary process variable was carbon, although oxygen and nitrogen flows were also modeled. Most of the input data used in CELSS-3D were from published sources. A separate linear optimization program, What'sBest!, was used to compare options for the crew's vegetarian diet. CELSS-3D simulations were run for the equivalent of 3 years with a 1-h time interval. Output from simulations run under nominal conditions was used to illustrate dynamic changes in the concentrations of atmospheric gases. The modular design of CELSS-3D will allow other configurations and various failure scenarios to be tested and compared. PMID:11540449

  2. 3D fast adaptive correlation imaging for large-scale gravity data based on GPU computation

    NASA Astrophysics Data System (ADS)

    Chen, Z.; Meng, X.; Guo, L.; Liu, G.

    2011-12-01

    In recent years, large scale gravity data sets have been collected and employed to enhance gravity problem-solving abilities of tectonics studies in China. Aiming at the large scale data and the requirement of rapid interpretation, previous authors have carried out a lot of work, including the fast gradient module inversion and Euler deconvolution depth inversion ,3-D physical property inversion using stochastic subspaces and equivalent storage, fast inversion using wavelet transforms and a logarithmic barrier method. So it can be say that 3-D gravity inversion has been greatly improved in the last decade. Many authors added many different kinds of priori information and constraints to deal with nonuniqueness using models composed of a large number of contiguous cells of unknown property and obtained good results. However, due to long computation time, instability and other shortcomings, 3-D physical property inversion has not been widely applied to large-scale data yet. In order to achieve 3-D interpretation with high efficiency and precision for geological and ore bodies and obtain their subsurface distribution, there is an urgent need to find a fast and efficient inversion method for large scale gravity data. As an entirely new geophysical inversion method, 3D correlation has a rapid development thanks to the advantage of requiring no a priori information and demanding small amount of computer memory. This method was proposed to image the distribution of equivalent excess masses of anomalous geological bodies with high resolution both longitudinally and transversely. In order to tranform the equivalence excess masses into real density contrasts, we adopt the adaptive correlation imaging for gravity data. After each 3D correlation imaging, we change the equivalence into density contrasts according to the linear relationship, and then carry out forward gravity calculation for each rectangle cells. Next, we compare the forward gravity data with real data, and

  3. Full 3-D OCT-based pseudophakic custom computer eye model.

    PubMed

    Sun, M; Pérez-Merino, P; Martinez-Enriquez, E; Velasco-Ocana, M; Marcos, S

    2016-03-01

    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

  4. 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

  5. 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.

  6. Noninvasive CT to Iso-C3D registration for improved intraoperative visualization in computer assisted orthopedic surgery

    NASA Astrophysics Data System (ADS)

    Rudolph, Tobias; Ebert, Lars; Kowal, Jens

    2006-03-01

    Supporting surgeons in performing minimally invasive surgeries can be considered as one of the major goals of computer assisted surgery. Excellent intraoperative visualization is a prerequisite to achieve this aim. The Siremobil Iso-C 3D has become a widely used imaging device, which, in combination with a navigation system, enables the surgeon to directly navigate within the acquired 3D image volume without any extra registration steps. However, the image quality is rather low compared to a CT scan and the volume size (approx. 12 cm 3) limits its application. A regularly used alternative in computer assisted orthopedic surgery is to use of a preoperatively acquired CT scan to visualize the operating field. But, the additional registration step, necessary in order to use CT stacks for navigation is quite invasive. Therefore the objective of this work is to develop a noninvasive registration technique. In this article a solution is being proposed that registers a preoperatively acquired CT scan to the intraoperatively acquired Iso-C 3D image volume, thereby registering the CT to the tracked anatomy. The procedure aligns both image volumes by maximizing the mutual information, an algorithm that has already been applied to similar registration problems and demonstrated good results. Furthermore the accuracy of such a registration method was investigated in a clinical setup, integrating a navigated Iso-C 3D in combination with an tracking system. Initial tests based on cadaveric animal bone resulted in an accuracy ranging from 0.63mm to 1.55mm mean error.

  7. 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.

  8. 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

  9. Multiscale segmentation method for small inclusion detection in 3D industrial computed tomography

    NASA Astrophysics Data System (ADS)

    Zauner, G.; Harrer, B.; Angermaier, D.; Reiter, M.; Kastner, J.

    2007-06-01

    In this paper a new segmentation method for highly precise inclusion detection in 3D X-ray computed tomography (CT), based on multiresolution denoising methods, is presented. The aim of this work is the automatic 3D-segmentation of small graphite inclusions in cast iron samples. Industrial X-ray computed tomography of metallic samples often suffers from imaging artifacts (e.g. cupping effects) which result in unwanted background image structures, making automated segmentation a difficult task. Additionally, small spatial structures (inclusions and voids) are generally difficult to detect e.g. by standard region based methods like watershed segmentation. Finally, image noise (assuming a Poisson noise characteristic) and the large amount of 3D data have to be considered to obtain good results. The approach presented is based on image subtraction of two different representations of the image under consideration. The first image represents the low spatial frequency content derived by means of wavelet filtering based on the 'a trous' algorithm (i.e. the 'background' content) assuming standard Gaussian noise. The second image is derived by applying a multiresolution denoising scheme based on 'platelet'-filtering, which can produce highly accurate intensity and density estimates assuming Poisson noise. It is shown that the resulting arithmetic difference between these two images can give highly accurate segmentation results with respect to finding small spatial structures in heavily cluttered background structures. Experimental results of industrial CT measurements are presented showing the practicability and reliability of this approach for the proposed task.

  10. The RNA 3D Motif Atlas: Computational methods for extraction, organization and evaluation of RNA motifs.

    PubMed

    Parlea, Lorena G; Sweeney, Blake A; Hosseini-Asanjan, Maryam; Zirbel, Craig L; Leontis, Neocles B

    2016-07-01

    RNA 3D motifs occupy places in structured RNA molecules that correspond to the hairpin, internal and multi-helix junction "loops" of their secondary structure representations. As many as 40% of the nucleotides of an RNA molecule can belong to these structural elements, which are distinct from the regular double helical regions formed by contiguous AU, GC, and GU Watson-Crick basepairs. With the large number of atomic- or near atomic-resolution 3D structures appearing in a steady stream in the PDB/NDB structure databases, the automated identification, extraction, comparison, clustering and visualization of these structural elements presents an opportunity to enhance RNA science. Three broad applications are: (1) identification of modular, autonomous structural units for RNA nanotechnology, nanobiology and synthetic biology applications; (2) bioinformatic analysis to improve RNA 3D structure prediction from sequence; and (3) creation of searchable databases for exploring the binding specificities, structural flexibility, and dynamics of these RNA elements. In this contribution, we review methods developed for computational extraction of hairpin and internal loop motifs from a non-redundant set of high-quality RNA 3D structures. We provide a statistical summary of the extracted hairpin and internal loop motifs in the most recent version of the RNA 3D Motif Atlas. We also explore the reliability and accuracy of the extraction process by examining its performance in clustering recurrent motifs from homologous ribosomal RNA (rRNA) structures. We conclude with a summary of remaining challenges, especially with regard to extraction of multi-helix junction motifs. PMID:27125735

  11. A Computational Model for Suspended Large Rigid Bodies in 3D Unsteady Viscous Flows

    NASA Astrophysics Data System (ADS)

    Xiao, Feng

    1999-11-01

    A 3D numerical model for computing large rigid objects suspended in fluid flow has been developed. Rather than calculating the surface pressure upon the solid body, we evaluate the net force and torque based on a volume force formulation. The total effective force is obtained by summing up the forces at the Eulerian grids occupied by the rigid body. The effects of the moving bodies are coupled to the fluid flow by imposing the velocity field of the bodies to the fluid. A Poisson equation is used to compute the pressure over the whole domain. The objects are identified by color functions and calculated by the PPM scheme and a tangent function transformation which scales the transition region of the computed interface to a compact thickness. The model is then implemented on a parallel computer of distributed memory and validated with Stokes and low Reynolds number flows.

  12. 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.

  13. User's manual for PELE3D: a computer code for three-dimensional incompressible fluid dynamics

    SciTech Connect

    McMaster, W H

    1982-05-07

    The PELE3D code is a three-dimensional semi-implicit Eulerian hydrodynamics computer program for the solution of incompressible fluid flow coupled to a structure. The fluid and coupling algorithms have been adapted from the previously developed two-dimensional code PELE-IC. The PELE3D code is written in both plane and cylindrical coordinates. The coupling algorithm is general enough to handle a variety of structural shapes. The free surface algorithm is able to accommodate a top surface and several independent bubbles. The code is in a developmental status since all the intended options have not been fully implemented and tested. Development of this code ended in 1980 upon termination of the contract with the Nuclear Regulatory Commission.

  14. 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.

  15. Parallel Adaptive Computation of Blood Flow in a 3D ``Whole'' Body Model

    NASA Astrophysics Data System (ADS)

    Zhou, M.; Figueroa, C. A.; Taylor, C. A.; Sahni, O.; Jansen, K. E.

    2008-11-01

    Accurate numerical simulations of vascular trauma require the consideration of a larger portion of the vasculature than previously considered, due to the systemic nature of the human body's response. A patient-specific 3D model composed of 78 connected arterial branches extending from the neck to the lower legs is constructed to effectively represent the entire body. Recently developed outflow boundary conditions that appropriately represent the downstream vasculature bed which is not included in the 3D computational domain are applied at 78 outlets. In this work, the pulsatile blood flow simulations are started on a fairly uniform, unstructured mesh that is subsequently adapted using a solution-based approach to efficiently resolve the flow features. The adapted mesh contains non-uniform, anisotropic elements resulting in resolution that conforms with the physical length scales present in the problem. The effects of the mesh resolution on the flow field are studied, specifically on relevant quantities of pressure, velocity and wall shear stress.

  16. Effect of 3D animation videos over 2D video projections in periodontal health education among dental students

    PubMed Central

    Dhulipalla, Ravindranath; Marella, Yamuna; Katuri, Kishore Kumar; Nagamani, Penupothu; Talada, Kishore; Kakarlapudi, Anusha

    2015-01-01

    Background: There is limited evidence about the distinguished effect of 3D oral health education videos over conventional 2 dimensional projections in improving oral health knowledge. This randomized controlled trial was done to test the effect of 3 dimensional oral health educational videos among first year dental students. Materials and Methods: 80 first year dental students were enrolled and divided into two groups (test and control). In the test group, 3D animation and in the control group, regular 2D video projections pertaining to periodontal anatomy, etiology, presenting conditions, preventive measures and treatment of periodontal problems were shown. Effect of 3D animation was evaluated by using a questionnaire consisting of 10 multiple choice questions given to all participants at baseline, immediately after and 1month after the intervention. Clinical parameters like Plaque Index (PI), Gingival Bleeding Index (GBI), and Oral Hygiene Index Simplified (OHI-S) were measured at baseline and 1 month follow up. Results: A significant difference in the post intervention knowledge scores was found between the groups as assessed by unpaired t-test (p<0.001) at baseline, immediate and after 1 month. At baseline, all the clinical parameters in the both the groups were similar and showed a significant reduction (p<0.001)p after 1 month, whereas no significant difference was noticed post intervention between the groups. Conclusion: 3D animation videos are more effective over 2D videos in periodontal disease education and knowledge recall. The application of 3D animation results also demonstrate a better visual comprehension for students and greater health care outcomes. PMID:26759805

  17. Computational 3D reconstructions by optimization for cryo-electron microscopy

    NASA Astrophysics Data System (ADS)

    Yin, Zhye; Zheng, Yili; Doerschuk, Peter C.; Johnson, John E.

    2003-06-01

    An algorithm for the simultaneous 3-D reconstruction of several types of object, where each type of object may possibly have a rotational symmetry, from 2-D projection images, where for each image the type of object imaged, the projection orientation used to create the image, and the location of the object in the image are unknown, is described. The motivating application is the determination of the 3-D structure of small spherical viruses from cryo electron microscopy images. The algorithm is a maximum likelihood estimator which is computed by expectation maximization (EM). Due to the structure of the statistical model, the maximization step of EM can be easily computed but the expectation step requires 5-D numerical quadrature. The computational burden of the quadratures necessitates parallel computation and three different implementations of two different types of parallelism have been developed using pthreads (for shared memory processors) and MPI (for distributed memory processors). An example applying one of the MPI implementations, running on a 32 node PC cluster, to experimental images of Flock House Virus with comparison to the x-ray crystal diffraction structure of the virus is described.

  18. Development of computer program NAS3D using Vector processing for geometric nonlinear analysis of structures

    NASA Technical Reports Server (NTRS)

    Mangalgiri, P. D.; Prabhakaran, R.

    1986-01-01

    An algorithm for vectorized computation of stiffness matrices of an 8 noded isoparametric hexahedron element for geometric nonlinear analysis was developed. This was used in conjunction with the earlier 2-D program GAMNAS to develop the new program NAS3D for geometric nonlinear analysis. A conventional, modified Newton-Raphson process is used for the nonlinear analysis. New schemes for the computation of stiffness and strain energy release rates is presented. The organization the program is explained and some results on four sample problems are given. The study of CPU times showed that savings by a factor of 11 to 13 were achieved when vectorized computation was used for the stiffness instead of the conventional scalar one. Finally, the scheme of inputting data is explained.

  19. 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.

  20. 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

  1. Traveltime computation and imaging from rugged topography in 3D TTI media

    NASA Astrophysics Data System (ADS)

    Liu, Shaoyong; Wang, Huazhong; Yang, Qinyong; Fang, Wubao

    2014-02-01

    Foothill areas with rugged topography are of great potential for oil and gas seismic exploration, but subsurface imaging in these areas is very challenging. Seismic acquisition with larger offset and wider azimuth is necessary for seismic imaging in complex areas. However, the scale anisotropy in this case must be taken into account. To generalize the pre-stack depth migration (PSDM) to 3D transversely isotropic media with vertical symmetry axes (VTI) and tilted symmetry axes (TTI) from rugged topography, a new dynamic programming approach for the first-arrival traveltime computation method is proposed. The first-arrival time on every uniform mesh point is calculated based on Fermat's principle with simple calculus techniques and a systematic mapping scheme. In order to calculate the minimum traveltime, a set of nonlinear equations is solved on each mesh point, where the group velocity is determined by the group angle. Based on the new first-arrival time calculation method, the corresponding PSDM and migration velocity analysis workflow for 3D anisotropic media from rugged surface is developed. Numerical tests demonstrate that the proposed traveltime calculation method is effective in both VTI and TTI media. The migration results for 3D field data show that it is necessary to choose a smooth datum to remove the high wavenumber move-out components for PSDM with rugged topography and take anisotropy into account to achieve better images.

  2. Generic camera model and its calibration for computational integral imaging and 3D reconstruction.

    PubMed

    Li, Weiming; Li, Youfu

    2011-03-01

    Integral imaging (II) is an important 3D imaging technology. To reconstruct 3D information of the viewed objects, modeling and calibrating the optical pickup process of II are necessary. This work focuses on the modeling and calibration of an II system consisting of a lenslet array, an imaging lens, and a charge-coupled device camera. Most existing work on such systems assumes a pinhole array model (PAM). In this work, we explore a generic camera model that accommodates more generality. This model is an empirical model based on measurements, and we constructed a setup for its calibration. Experimental results show a significant difference between the generic camera model and the PAM. Images of planar patterns and 3D objects were computationally reconstructed with the generic camera model. Compared with the images reconstructed using the PAM, the images present higher fidelity and preserve more high spatial frequency components. To the best of our knowledge, this is the first attempt in applying a generic camera model to an II system.

  3. Knowledge-based system for computer-aided process planning of laser sensor 3D digitizing

    NASA Astrophysics Data System (ADS)

    Bernard, Alain; Davillerd, Stephane; Sidot, Benoit

    1999-11-01

    This paper introduces some results of a research work carried out on the automation of digitizing process of complex part using a precision 3D-laser sensor. Indeed, most of the operations are generally still manual to perform digitalization. In fact, redundancies, lacks or forgetting in point acquisition are possible. Moreover, digitization time of a part, i.e. immobilization of the machine, is thus not optimized overall. So, it is important, for time- compression during product development, to minimize time consuming of reverse engineering step. A new way to scan automatically a complex 3D part is presented to order to measure and to compare the acquired data with the reference CAD model. After introducing digitization, the environment used for the experiments is presented, based on a CMM machine and a plane laser sensor. Then the proposed strategy is introduced for the adaptation of this environment to a robotic CAD software in order to be able to simulate and validate 3D-laser-scanning paths. The CAPP (Computer Aided Process Planning) system used for the automatic generation of the laser scanning process is also presented.

  4. 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

  5. Topological evolutionary computing in the optimal design of 2D and 3D structures

    NASA Astrophysics Data System (ADS)

    Burczynski, T.; Poteralski, A.; Szczepanik, M.

    2007-10-01

    An application of evolutionary algorithms and the finite-element method to the topology optimization of 2D structures (plane stress, bending plates, and shells) and 3D structures is described. The basis of the topological evolutionary optimization is the direct control of the density material distribution (or thickness for 2D structures) by the evolutionary algorithm. The structures are optimized for stress, mass, and compliance criteria. The numerical examples demonstrate that this method is an effective technique for solving problems in computer-aided optimal design.

  6. 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.

  7. "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.

  8. 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.

  9. 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. PMID:20865517

  10. Computer-aided assessment of anomalies in the scoliotic spine in 3-D MRI images.

    PubMed

    Jäger, Florian; Hornegger, Joachim; Schwab, Siegfried; Janka, Rolf

    2009-01-01

    The assessment of anomalies in the scoliotic spine using Magnetic Resonance Imaging (MRI) is an essential task during the planning phase of a patient's treatment and operations. Due to the pathologic bending of the spine, this is an extremely time consuming process as an orthogonal view onto every vertebra is required. In this article we present a system for computer-aided assessment (CAA) of anomalies in 3-D MRI images of the spine relying on curved planar reformations (CPR). We introduce all necessary steps, from the pre-processing of the data to the visualization component. As the core part of the framework is based on a segmentation of the spinal cord we focus on this. The proposed segmentation method is an iterative process. In every iteration the segmentation is updated by an energy based scheme derived from Markov random field (MRF) theory. We evaluate the segmentation results on public available clinical relevant 3-D MRI data sets of scoliosis patients. In order to assess the quality of the segmentation we use the angle between automatically computed planes through the vertebra and planes estimated by medical experts. This results in a mean angle difference of less than six degrees.

  11. Denoising of high resolution small animal 3D PET data using the non-subsampled Haar wavelet transform

    NASA Astrophysics Data System (ADS)

    Ochoa Domínguez, Humberto de Jesús; Máynez, Leticia O.; Vergara Villegas, Osslan O.; Mederos, Boris; Mejía, José M.; Cruz Sánchez, Vianey G.

    2015-06-01

    PET allows functional imaging of the living tissue. However, one of the most serious technical problems affecting the reconstructed data is the noise, particularly in images of small animals. In this paper, a method for high-resolution small animal 3D PET data is proposed with the aim to reduce the noise and preserve details. The method is based on the estimation of the non-subsampled Haar wavelet coefficients by using a linear estimator. The procedure is applied to the volumetric images, reconstructed without correction factors (plane reconstruction). Results show that the method preserves the structures and drastically reduces the noise that contaminates the image.

  12. 3D Flow Visualization Using Texture Advection

    NASA Technical Reports Server (NTRS)

    Kao, David; Zhang, Bing; Kim, Kwansik; Pang, Alex; Moran, Pat (Technical Monitor)

    2001-01-01

    Texture advection is an effective tool for animating and investigating 2D flows. In this paper, we discuss how this technique can be extended to 3D flows. In particular, we examine the use of 3D and 4D textures on 3D synthetic and computational fluid dynamics flow fields.

  13. 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…

  14. A new 3-D integral code for computation of accelerator magnets

    SciTech Connect

    Turner, L.R.; Kettunen, L.

    1991-01-01

    For computing accelerator magnets, integral codes have several advantages over finite element codes; far-field boundaries are treated automatically, and computed field in the bore region satisfy Maxwell's equations exactly. A new integral code employing edge elements rather than nodal elements has overcome the difficulties associated with earlier integral codes. By the use of field integrals (potential differences) as solution variables, the number of unknowns is reduced to one less than the number of nodes. Two examples, a hollow iron sphere and the dipole magnet of Advanced Photon Source injector synchrotron, show the capability of the code. The CPU time requirements are comparable to those of three-dimensional (3-D) finite-element codes. Experiments show that in practice it can realize much of the potential CPU time saving that parallel processing makes possible. 8 refs., 4 figs., 1 tab.

  15. 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. PMID:26409422

  16. 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.

  17. Parallel I/O and computation for 3D post-stack depth migration

    NASA Astrophysics Data System (ADS)

    Mosher, Charles C.; Joyner, Calvin L.

    1994-09-01

    Scalable parallel algorithms for seismic imaging remain a significant challenge for the oil and gas industry. Scalability must address both the computational and the input/output portions of the algorithm in question. These issues are addressed by the ARCO Seismic Benchmark Suite, a public domain software system that provides an environment for development and performance analysis of parallel seismic processing algorithm. We illustrate some of the issues in the design of scalable parallel imaging algorithms with an example process, 3D post-stack depth migration. The algorithm used is based on an implicit finite difference formulation described by Zhiming Li. Scalability is obtained by designing computation, communication between processors, and input/output as parallel operations. The resulting application runs efficiently on both distributed memory and shared memory hardware platforms with processor counts from 1 - 128 nodes.

  18. Grooving in Trenchtown (computer animation)

    NASA Technical Reports Server (NTRS)

    2004-01-01

    This image is a screenshot from a computer-generated animation showing the Mars Exploration Rover Opportunity's arm exploring the trench dug by one of its wheels. The rover's arm, or instrument deployment device, holds a suite of scientific instruments designed to examine rocks and soil for signs of past water on Mars. One of these instruments, the alpha particle X-ray spectrometer, is shown here investigating the trench. The movie was generated from data taken by the rover's onboard sensors.

  19. Animation Strategies for Smooth Transformations Between Discrete Lods of 3d Building Models

    NASA Astrophysics Data System (ADS)

    Kada, Martin; Wichmann, Andreas; Filippovska, Yevgeniya; Hermes, Tobias

    2016-06-01

    The cartographic 3D visualization of urban areas has experienced tremendous progress over the last years. An increasing number of applications operate interactively in real-time and thus require advanced techniques to improve the quality and time response of dynamic scenes. The main focus of this article concentrates on the discussion of strategies for smooth transformation between two discrete levels of detail (LOD) of 3D building models that are represented as restricted triangle meshes. Because the operation order determines the geometrical and topological properties of the transformation process as well as its visual perception by a human viewer, three different strategies are proposed and subsequently analyzed. The simplest one orders transformation operations by the length of the edges to be collapsed, while the other two strategies introduce a general transformation direction in the form of a moving plane. This plane either pushes the nodes that need to be removed, e.g. during the transformation of a detailed LOD model to a coarser one, towards the main building body, or triggers the edge collapse operations used as transformation paths for the cartographic generalization.

  20. Fully 3D-computations of submarine turbid surges : comparison with flume experiments

    NASA Astrophysics Data System (ADS)

    Cayocca, F.; Le Hir, P.

    2003-04-01

    Most numerical models of submarine gravity currents use layer-averaged equations. The description of the flow properties then requires the use of empirical terms to include 1) water entrainment at the surface of the dense layer and 2) entrainment of sediment by erosion of the seafloor. SiAM3D is a three-dimensional numerical model based on the hydrostatic approximation to solve the mass and momentum conservation equations for highly concentrated mixtures. Stratification turbulence damping, hindered settling and increase of molecular viscosity with concentration (which can lead to a visco-plastic behaviour) are included. Water entrainment results here from the turbulent behaviour of the flow and does not require empirical coefficients as in vertically integrated models. A mixing length turbulence closure is also used to compute bottom friction. Erosion and deposition can be taken into account. The model is used to simulate slope-failure-induced submarine turbid surges. It is compared with data from flume experiments carried out with saline or sediment laden flows. Front velocity, length and concentration of the flow can therefore be validated for various values of slope angle, surge volume and initial density. The hard bottoms used in the experiments found in the literature do not allow the validation of erosion computations. 3D computations were carried out to simulate the submarine landslide generated by the collapse of Nice airport landfill in 1979. Large computation times do not allow simulations long enough for the flow to reach distances where data are available. However the results compare well with simulations produced by a more complex model, the results of which were validated by observed hydraulic effects in front of the airport (landslide-generated tsunami).

  1. Creating photo-realistic works in a 3D scene using layers styles to create an animation

    NASA Astrophysics Data System (ADS)

    Avramescu, A. M.

    2015-11-01

    Creating realist objects in a 3D scene is not an easy work. We have to be very careful to make the creation very detailed. If we don't know how to make these photo-realistic works, by using the techniques and a good reference photo we can create an amazing amount of detail and realism. For example, in this article there are some of these detailed methods from which we can learn the techniques necessary to make beautiful and realistic objects in a scene. More precisely, in this paper, we present how to create a 3D animated scene, mainly using the Pen Tool and Blending Options. Indeed, this work is based on teaching some simple ways of using the Layer Styles to create some great shadows, lights, textures and a realistic sense of 3 Dimension. The present work involves also showing how some interesting ways of using the illuminating and rendering options can create a realistic effect in a scene. Moreover, this article shows how to create photo realistic 3D models from a digital image. The present work proposes to present how to use Illustrator paths, texturing, basic lighting and rendering, how to apply textures and how to parent the building and objects components. We also propose to use this proposition to recreate smaller details or 3D objects from a 2D image. After a critic art stage, we are able now to present in this paper the architecture of a design method that proposes to create an animation. The aim is to create a conceptual and methodological tutorial to address this issue both scientifically and in practice. This objective also includes proposing, on strong scientific basis, a model that gives the possibility of a better understanding of the techniques necessary to create a realistic animation.

  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. Computer-assisted 3D design software for teaching neuro-ophthalmology of the oculomotor system and training new retinal surgery techniques

    NASA Astrophysics Data System (ADS)

    Glittenberg, Carl; Binder, Susanne

    2004-07-01

    Purpose: To create a more effective method of demonstrating complex subject matter in ophthalmology with the use of high end, 3-D, computer aided animation and interactive multimedia technologies. Specifically, to explore the possibilities of demonstrating the complex nature of the neuroophthalmological basics of the human oculomotor system in a clear and non confusing way, and to demonstrate new forms of retinal surgery in a manner that makes the procedures easier to understand for other retinal surgeons. Methods and Materials: Using Reflektions 4.3, Monzoom Pro 4.5, Cinema 4D XL 5.03, Cinema 4D XL 8 Studio Bundle, Mediator 4.0, Mediator Pro 5.03, Fujitsu-Siemens Pentium III and IV, Gericom Webgine laptop, M.G.I. Video Wave 1.0 and 5, Micrografix Picture Publisher 6.0 and 8, Amorphium 1.0, and Blobs for Windows, we created 3-D animations showing the origin, insertion, course, main direction of pull, and auxiliary direction of pull of the six extra-ocular eye muscles. We created 3-D animations that (a) show the intra-cranial path of the relevant oculomotor cranial nerves and which muscles are supplied by them, (b) show which muscles are active in each of the ten lines of sight, (c) demonstrate the various malfunctions of oculomotor systems, as well as (d) show the surgical techniques and the challenges in radial optic neurotomies and subretinal surgeries. Most of the 3-D animations were integrated in interactive multimedia teaching programs. Their effectiveness was compared to conventional teaching methods in a comparative study performed at the University of Vienna. We also performed a survey to examine the response of students being taught with the interactive programs. We are currently in the process of placing most of the animations in an interactive web site in order to make them freely available to everyone who is interested. Results: Although learning how to use complex 3-D computer animation and multimedia authoring software can be very time consuming and

  4. Computer modeling of 3D structures of cytochrome P450s.

    PubMed

    Chang, Y T; Stiffelman, O B; Loew, G H

    1996-01-01

    The understanding of structure-function relationship of enzymes requires detailed information of their three-dimensional structure. Protein structure determination by X-ray and NMR methods, the two most frequently used experimental procedures, are often difficult and time-consuming. Thus computer modeling of protein structures has become an increasingly active and attractive option for obtaining predictive models of three-dimensional protein structures. Specifically, for the ubiquitous metabolizing heme proteins, the cytochrome P450s, the X-ray structures of four isozymes of bacterial origin, P450cam, P450terp, P450BM-3 and P450eryF have now been determined. However, attempts to obtain the structure of mammalian forms by experimental means have thus far not been successful. Thus, there have been numerous attempts to construct models of mammalian P450s using homology modeling methods in which the known structures have been used to various extents and in various strategies to build models of P450 isozymes. In this paper, we review these efforts and then describe a strategy for structure building and assessment of 3D models of P450s recently developed in our laboratory that corrects many of the weaknesses in the previous procedures. The results are 3D models that for the first time are stable to unconstrained molecular dynamics simulations. The use of this method is demonstrated by the construction and validation of a 3D model for rabbit liver microsomal P450 isozyme 2B4, responsible for the oxidative metabolism of diverse xenobiotics including widely used inhalation anesthetics. Using this 2B4 model, the substrate access channel, substrate binding site and plausible surface regions for binding with P450 redox partners were identified. PMID:9010606

  5. 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.

  6. 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.

  7. 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.

  8. e-LEA3D: a computational-aided drug design web server.

    PubMed

    Douguet, Dominique

    2010-07-01

    e-LEA3D web server integrates three complementary tools to perform computer-aided drug design based on molecular fragments. In drug discovery projects, there is a considerable interest in identifying novel and diverse molecular scaffolds to enhance chances of success. The de novo drug design tool is used to invent new ligands to optimize a user-specified scoring function. The composite scoring function includes both structure- and ligand-based evaluations. The de novo approach is an alternative to a blind virtual screening of large compound collections. A heuristic based on a genetic algorithm rapidly finds which fragments or combination of fragments fit a QSAR model or the binding site of a protein. While the approach is ideally suited for scaffold-hopping, this module also allows a scan for possible substituents to a user-specified scaffold. The second tool offers a traditional virtual screening and filtering of an uploaded library of compounds. The third module addresses the combinatorial library design that is based on a user-drawn scaffold and reactants coming, for example, from a chemical supplier. The e-LEA3D server is available at: http://bioinfo.ipmc.cnrs.fr/lea.html.

  9. e-LEA3D: a computational-aided drug design web server

    PubMed Central

    Douguet, Dominique

    2010-01-01

    e-LEA3D web server integrates three complementary tools to perform computer-aided drug design based on molecular fragments. In drug discovery projects, there is a considerable interest in identifying novel and diverse molecular scaffolds to enhance chances of success. The de novo drug design tool is used to invent new ligands to optimize a user-specified scoring function. The composite scoring function includes both structure- and ligand-based evaluations. The de novo approach is an alternative to a blind virtual screening of large compound collections. A heuristic based on a genetic algorithm rapidly finds which fragments or combination of fragments fit a QSAR model or the binding site of a protein. While the approach is ideally suited for scaffold-hopping, this module also allows a scan for possible substituents to a user-specified scaffold. The second tool offers a traditional virtual screening and filtering of an uploaded library of compounds. The third module addresses the combinatorial library design that is based on a user-drawn scaffold and reactants coming, for example, from a chemical supplier. The e-LEA3D server is available at: http://bioinfo.ipmc.cnrs.fr/lea.html. PMID:20444867

  10. Using Gabor filter banks and temporal-spatial constraints to compute 3D myocardium strain.

    PubMed

    Chen, Ting; Axel, Leon

    2006-01-01

    In this paper, we describe a new approach for reconstructing 3D strains in the myocardium using tagged MR images. We first segment the myocardium using a 3D deformable model driven by image gradients and Gabor filter responses. Tags are automatically detected and tracked as deformable thin plates during systole and early diastole. To keep the tracking results more stable and consistent, we use a combination of gradient information, an intensity probabilistic model, the phase information, and a temporal-spatial smoothness constraint. Based on the tag deformation, we compute a dense displacement in the myocardium around both ventricles. The displacements in x-, y-, and z- directions are calculated separately and are combined to form the final displacement maps. We do not use the information outside the segmented surface of the myocardium to avoid displacement errors caused by noises, artifacts, and correlations between different regions in the myocardium. The strain in the myocardium during the heart cycle is derived from the displacement. This method accepts images of either a tag grid or separate horizontal and vertical tag lines as its input. Experimental results on phantom and real data demonstrate good performance of this method in calculating the myocardial strain.

  11. Automated Computed Tomography-Ultrasound Cross-Modality 3-D Contouring Algorithm for Prostate.

    PubMed

    Ermacora, Denis; Pesente, Silvia; Pascoli, Francesco; Raducci, Sebastian; Mauro, Rudy; Rumeileh, Imad Abu; Verhaegen, Frank; Fontanarosa, Davide

    2015-10-01

    A novel fully automated algorithm is introduced for 3-D cross-modality image segmentation of the prostate, based on the simultaneous use of co-registered computed tomography (CT) and 3-D ultrasound (US) images. By use of a Gabor feature detector, the algorithm can outline in three dimensions and in cross-modality the prostate, and it can be trained and optimized on specific patient populations. We applied it to 16 prostate cancer patients and evaluated the conformity between the automatically segmented prostate contours and the contours manually outlined by an experienced physician, on the CT-US fusion, using the mean distance to conformity (MDC) index. When only the CT scans were used, the average MDC value was 4.5 ± 1.7 mm (maximum value = 9.0 mm). When the US scans also were considered, the mean ± standard deviation was reduced to 3.9 ± 0.7 mm (maximum value = 5.5 mm). The cross-modality approach acted on all the largest distance values, reducing them to acceptable discrepancies.

  12. 3D robust Chan-Vese model for industrial computed tomography volume data segmentation

    NASA Astrophysics Data System (ADS)

    Liu, Linghui; Zeng, Li; Luan, Xiao

    2013-11-01

    Industrial computed tomography (CT) has been widely applied in many areas of non-destructive testing (NDT) and non-destructive evaluation (NDE). In practice, CT volume data to be dealt with may be corrupted by noise. This paper addresses the segmentation of noisy industrial CT volume data. Motivated by the research on the Chan-Vese (CV) model, we present a region-based active contour model that draws upon intensity information in local regions with a controllable scale. In the presence of noise, a local energy is firstly defined according to the intensity difference within a local neighborhood. Then a global energy is defined to integrate local energy with respect to all image points. In a level set formulation, this energy is represented by a variational level set function, where a surface evolution equation is derived for energy minimization. Comparative analysis with the CV model indicates the comparable performance of the 3D robust Chan-Vese (RCV) model. The quantitative evaluation also shows the segmentation accuracy of 3D RCV. In addition, the efficiency of our approach is validated under several types of noise, such as Poisson noise, Gaussian noise, salt-and-pepper noise and speckle noise.

  13. 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.

  14. More effective antimicrobial mastoparan derivatives, generated by 3D-QSAR-Almond and computational mutagenesis.

    PubMed

    Avram, Speranta; Buiu, Catalin; Borcan, Florin; Milac, Adina-Luminita

    2012-02-01

    Antimicrobial peptides are drugs used against a wide range of pathogens which present a great advantage: in contrast with antibiotics they do not develop resistance. The wide spectrum of antimicrobial peptides advertises them in the research and pharmaceutical industry as attractive starting points for obtaining new, more effective analogs. Here we predict the antimicrobial activity against Bacillus subtilis (expressed as minimal inhibitory concentration values) for 33 mastoparan analogs and their new derivatives by a non-aligned 3D-QSAR (quantitative structure-activity relationship) method. We establish the contribution to antimicrobial activity of molecular descriptors (hydrophobicity, hydrogen bond donor and steric), correlated with contributions from the membrane environment (sodium, potassium, chloride). Our best QSAR models show significant cross-validated correlation q(2) (0.55-0.75), fitted correlation r(2) (greater than 0.90) coefficients and standard error of prediction SDEP (less than 0.250). Moreover, based on our most accurate 3D-QSAR models, we propose nine new mastoparan analogs, obtained by computational mutagenesis, some of them predicted to have significantly improved antimicrobial activity compared to the parent compound.

  15. Automatic segmentation of pulmonary fissures in computed tomography images using 3D surface features.

    PubMed

    Yu, Mali; Liu, Hong; Gong, Jianping; Jin, Renchao; Han, Ping; Song, Enmin

    2014-02-01

    Pulmonary interlobar fissures are important anatomic structures in human lungs and are useful in locating and classifying lung abnormalities. Automatic segmentation of fissures is a difficult task because of their low contrast and large variability. We developed a fully automatic training-free approach for fissure segmentation based on the local bending degree (LBD) and the maximum bending index (MBI). The LBD is determined by the angle between the eigenvectors of two Hessian matrices for a pair of adjacent voxels. It is used to construct a constraint to extract the candidate surfaces in three-dimensional (3D) space. The MBI is a measure to discriminate cylindrical surfaces from planar surfaces in 3D space. Our approach for segmenting fissures consists of five steps, including lung segmentation, plane-like structure enhancement, surface extraction with LBD, initial fissure identification with MBI, and fissure extension based on local plane fitting. When applying our approach to 15 chest computed tomography (CT) scans, the mean values of the positive predictive value, the sensitivity, the root-mean square (RMS) distance, and the maximal RMS are 91 %, 88 %, 1.01 ± 0.99 mm, and 11.56 mm, respectively, which suggests that our algorithm can efficiently segment fissures in chest CT scans.

  16. 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

  17. 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.

  18. Computer-aided detection of clustered microcalcifications in digital breast tomosynthesis: A 3D approach

    PubMed Central

    Sahiner, Berkman; Chan, Heang-Ping; Hadjiiski, Lubomir M.; Helvie, Mark A.; Wei, Jun; Zhou, Chuan; Lu, Yao

    2012-01-01

    Purpose: To design a computer-aided detection (CADe) system for clustered microcalcifications in reconstructed digital breast tomosynthesis (DBT) volumes and to perform a preliminary evaluation of the CADe system. Methods: IRB approval and informed consent were obtained in this study. A data set of two-view DBT of 72 breasts containing microcalcification clusters was collected from 72 subjects who were scheduled to undergo breast biopsy. Based on tissue sampling results, 17 cases had breast cancer and 55 were benign. A separate data set of two-view DBT of 38 breasts free of clustered microcalcifications from 38 subjects was collected to independently estimate the number of false-positives (FPs) generated by the CADe system. A radiologist experienced in breast imaging marked the biopsied cluster of microcalcifications with a 3D bounding box using all available clinical and imaging information. A CADe system was designed to detect microcalcification clusters in the reconstructed volume. The system consisted of prescreening, clustering, and false-positive reduction stages. In the prescreening stage, the conspicuity of microcalcification-like objects was increased by an enhancement-modulated 3D calcification response function. An iterative thresholding and 3D object growing method was used to detect cluster seed objects, which were used as potential centers of microcalcification clusters. In the cluster detection stage, microcalcification candidates were identified using a second iterative thresholding procedure, which was applied to the signal-to-noise ratio (SNR) enhanced image voxels with a positive calcification response. Starting with each cluster seed object as the initial cluster center, a dynamic clustering algorithm formed a cluster candidate by including microcalcification candidates within a 3D neighborhood of the cluster seed object that satisfied the clustering criteria. The number, size, and SNR of the microcalcifications in a cluster candidate and the

  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. 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.

  1. 3-D reconstruction of an ancient Egyptian mummy using X-ray computer tomography.

    PubMed

    Baldock, C; Hughes, S W; Whittaker, D K; Taylor, J; Davis, R; Spencer, A J; Tonge, K; Sofat, A

    1994-12-01

    Computer tomography has been used to image and reconstruct in 3-D an Egyptian mummy from the collection of the British Museum. This study of Tjentmutengebtiu, a priestess from the 22nd dynasty (945-715 BC) revealed invaluable information of a scientific, Egyptological and palaeopathological nature without mutilation and destruction of the painted cartonnage case or linen wrappings. Precise details on the removal of the brain through the nasal cavity and the viscera from the abdominal cavity were obtained. The nature and composition of the false eyes were investigated. The detailed analysis of the teeth provided a much closer approximation of age at death. The identification of materials used for the various amulets including that of the figures placed in the viscera was graphically demonstrated using this technique.

  2. 3-D reconstruction of an ancient Egyptian mummy using X-ray computer tomography.

    PubMed Central

    Baldock, C; Hughes, S W; Whittaker, D K; Taylor, J; Davis, R; Spencer, A J; Tonge, K; Sofat, A

    1994-01-01

    Computer tomography has been used to image and reconstruct in 3-D an Egyptian mummy from the collection of the British Museum. This study of Tjentmutengebtiu, a priestess from the 22nd dynasty (945-715 BC) revealed invaluable information of a scientific, Egyptological and palaeopathological nature without mutilation and destruction of the painted cartonnage case or linen wrappings. Precise details on the removal of the brain through the nasal cavity and the viscera from the abdominal cavity were obtained. The nature and composition of the false eyes were investigated. The detailed analysis of the teeth provided a much closer approximation of age at death. The identification of materials used for the various amulets including that of the figures placed in the viscera was graphically demonstrated using this technique. Images Figure 1. Figure 2. Figure 3. Figure 4. Figure 5. PMID:7853321

  3. SU-E-T-376: 3-D Commissioning for An Image-Guided Small Animal Micro- Irradiation Platform

    SciTech Connect

    Qian, X; Wuu, C; Admovics, J

    2014-06-01

    Purpose: A 3-D radiochromic plastic dosimeter has been used to cross-test the isocentricity of a high resolution image-guided small animal microirradiation platform. In this platform, the mouse stage rotating for cone beam CT imaging is perpendicular to the gantry rotation for sub-millimeter radiation delivery. A 3-D dosimeter can be used to verify both imaging and irradiation coordinates. Methods: A 3-D dosimeter and optical CT scanner were used in this study. In the platform, both mouse stage and gantry can rotate 360° with rotation axis perpendicular to each other. Isocentricity and coincidence of mouse stage and gantry rotations were evaluated using star patterns. A 3-D dosimeter was placed on mouse stage with center at platform isocenter approximately. For CBCT isocentricity, with gantry moved to 90°, the mouse stage rotated horizontally while the x-ray was delivered to the dosimeter at certain angles. For irradiation isocentricity, the gantry rotated 360° to deliver beams to the dosimeter at certain angles for star patterns. The uncertainties and agreement of both CBCT and irradiation isocenters can be determined from the star patterns. Both procedures were repeated 3 times using 3 dosimeters to determine short-term reproducibility. Finally, dosimeters were scanned using optical CT scanner to obtain the results. Results: The gantry isocentricity is 0.9 ± 0.1 mm and mouse stage rotation isocentricity is about 0.91 ± 0.11 mm. Agreement between the measured isocenters of irradiation and imaging coordinates was determined. The short-term reproducibility test yielded 0.5 ± 0.1 mm between the imaging isocenter and the irradiation isocenter, with a maximum displacement of 0.7 ± 0.1 mm. Conclusion: The 3-D dosimeter can be very useful in precise verification of targeting for a small animal irradiation research. In addition, a single 3-D dosimeter can provide information in both geometric and dosimetric uncertainty, which is crucial for translational studies.

  4. A 3D computer-aided design system applied to diagnosis and treatment planning in orthodontics and orthognathic surgery.

    PubMed

    Motohashi, N; Kuroda, T

    1999-06-01

    The purpose of this article is to describe a newly developed 3D computer-aided design (CAD) system for the diagnostic set-up of casts in orthodontic diagnosis and treatment planning, and its preliminary clinical applications. The system comprises a measuring unit which obtains 3D information from the dental model using laser scanning, and a personal computer to generate the 3D graphics. When measuring the 3D shape of the model, to minimize blind sectors, the model is scanned from two different directions with the slit-ray laser beam by rotating the mounting angle of the model on the measuring device. For computed simulation of tooth movement, the representative planes, defined by the anatomical reference points, are formed for each individual tooth and are arranged along a guideline descriptive of the individual arch form. Subsequently, the 3D shape is imparted to each of the teeth arranged on the representative plane to form an arrangement of the 3D profile. When necessary, orthognathic surgery can be simulated by moving the mandibular dental arch three-dimensionally to establish the optimum occlusal relationship. Compared with hand-made set-up models, the computed diagnostic cast has advantages such as high-speed processing and quantitative evaluation on the amount of 3D movement of the individual tooth relative to the craniofacial plane. Trial clinical applications demonstrated that the use of this system facilitated the otherwise complicated and time-consuming mock surgery for treatment planning in orthognathic surgery.

  5. 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

  6. 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

  7. Linear traveltime perturbation interpolation: a novel method to compute 3-D traveltimes

    NASA Astrophysics Data System (ADS)

    Zhang, Jianzhong; Shi, Junjie; Song, Lin-Ping; Zhou, Hua-wei

    2015-10-01

    The linear traveltime interpolation has been a routine method to compute first arrivals of seismic waves and trace rays in complex media. The method assumes that traveltimes follow a linear distribution on each boundary of cells. The linearity assumption of traveltimes facilitates the numerical implementation but its violation may result in large computational errors. In this paper, we propose a new way to mitigate the potential shortcoming hidden in the linear traveltime interpolation. We use the vertex traveltimes in a calculated cell to introduce an equivalent homogeneous medium that is specific to the cell boundary from a source. Therefore, we can decompose the traveltime at a point on the cell boundary into two parts: (1) a reference traveltime propagating in the equivalent homogeneous medium and (2) a perturbation traveltime that is defined as the difference between the original and reference traveltimes. We now treat that the traveltime perturbation is linear along each boundary of cells instead of the traveltime. With the new assumption, we carry out the bilinear interpolation over traveltime perturbation to complete traveltime computation in a 3-D heterogeneous model. The numerical experiments show that the new method, the linear traveltime perturbation interpolation, is able to achieve much higher accuracy than that based on the linear traveltime interpolation.

  8. Enabling 3D-Liver Perfusion Mapping from MR-DCE Imaging Using Distributed Computing.

    PubMed

    Leporq, Benjamin; Camarasu-Pop, Sorina; Davila-Serrano, Eduardo E; Pilleul, Frank; Beuf, Olivier

    2013-01-01

    An MR acquisition protocol and a processing method using distributed computing on the European Grid Infrastructure (EGI) to allow 3D liver perfusion parametric mapping after Magnetic Resonance Dynamic Contrast Enhanced (MR-DCE) imaging are presented. Seven patients (one healthy control and six with chronic liver diseases) were prospectively enrolled after liver biopsy. MR-dynamic acquisition was continuously performed in free-breathing during two minutes after simultaneous intravascular contrast agent (MS-325 blood pool agent) injection. Hepatic capillary system was modeled by a 3-parameters one-compartment pharmacokinetic model. The processing step was parallelized and executed on the EGI. It was modeled and implemented as a grid workflow using the Gwendia language and the MOTEUR workflow engine. Results showed good reproducibility in repeated processing on the grid. The results obtained from the grid were well correlated with ROI-based reference method ran locally on a personal computer. The speed-up range was 71 to 242 with an average value of 126. In conclusion, distributed computing applied to perfusion mapping brings significant speed-up to quantification step to be used for further clinical studies in a research context. Accuracy would be improved with higher image SNR accessible on the latest 3T MR systems available today.

  9. 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 transport in furnaces fully accounting for the size distributions of char, soot and ash particles, ash content, and ash composition. The code uses a hybrid technique of solving the three-dimensional radiation transport equation for absorbing, emitting and anisotropically scattering media. The technique achieves an optimal mix of computational speed and accuracy by combining the discrete ordinate method (S[sub 4]), modified differential approximation (MDA) and P, approximation in different range of optical thicknesses. The code uses spectroscopic data for estimating the absorption coefficients of participating gases C0[sub 2], H[sub 2]0 and CO. It invokes Mie theory for determining the extinction and scattering coefficients of combustion particulates. The optical constants of char, soot and ash are obtained from dispersion relations derived from reflectivity, transmissivity and extinction measurements. A control-volume formulation is adopted for determining the temperature field inside the furnace. A simple char burnout model is employed for estimating heat release and evolution of particle size distribution. The code is written in Fortran 77, has modular form, and is machine-independent. The computer memory required by the code depends upon the number of grid points specified and whether the transport calculations are performed on spectral or gray basis.

  10. 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 transport in furnaces fully accounting for the size distributions of char, soot and ash particles, ash content, and ash composition. The code uses a hybrid technique of solving the three-dimensional radiation transport equation for absorbing, emitting and anisotropically scattering media. The technique achieves an optimal mix of computational speed and accuracy by combining the discrete ordinate method (S{sub 4}), modified differential approximation (MDA) and P, approximation in different range of optical thicknesses. The code uses spectroscopic data for estimating the absorption coefficients of participating gases C0{sub 2}, H{sub 2}0 and CO. It invokes Mie theory for determining the extinction and scattering coefficients of combustion particulates. The optical constants of char, soot and ash are obtained from dispersion relations derived from reflectivity, transmissivity and extinction measurements. A control-volume formulation is adopted for determining the temperature field inside the furnace. A simple char burnout model is employed for estimating heat release and evolution of particle size distribution. The code is written in Fortran 77, has modular form, and is machine-independent. The computer memory required by the code depends upon the number of grid points specified and whether the transport calculations are performed on spectral or gray basis.

  11. Interaction of 3d transition metal atoms with charged ion projectiles from Electron Nuclear Dynamics computation

    NASA Astrophysics Data System (ADS)

    Hagelberg, Frank

    2003-03-01

    Computational results on atomic scattering between charged projectiles and transition metal target atoms are presented. This work aims at obtaining detailed information about charge, spin and energy transfer processes that occur between the interacting particles. An in-depth understanding of these phenomena is expected to provide a theoretical basis for the interpretation of various types of ion beam experiments, ranging from gas phase chromatography to spectroscopic observations of fast ions in ferromagnetic media. This contribution focuses on the scattering of light projectiles ranging from He to O, that are prepared in various initial charge states, by 3d transition metal atoms. The presented computations are performed in the framework of Electron Nuclear Dynamics (END)^1 theory which incorporates the coupling between electronic and nuclear degrees of freedom without reliance on the computationally cumbersome and frequently intractable determination of potential energy surfaces. In the present application of END theory to ion - transition metal atom scattering, a supermolecule approach is utilized in conjunction with a spin-unrestricted single determinantal wave function describing the electronic system. Integral scattering, charge and spin exchange cross sections are discussed as functions of the elementary parameters of the problem, such as projectile and target atomic numbers as well as projectile charge and initial kinetic energy. ^1 E.Deumens, A.Diz, R.Longo, Y.Oehrn, Rev.Mod.Phys. 66, 917 (1994)

  12. Automated Lung Segmentation and Image Quality Assessment for Clinical 3-D/4-D-Computed Tomography

    PubMed Central

    Li, Guang

    2014-01-01

    4-D-computed tomography (4DCT) provides not only a new dimension of patient-specific information for radiation therapy planning and treatment, but also a challenging scale of data volume to process and analyze. Manual analysis using existing 3-D tools is unable to keep up with vastly increased 4-D data volume, automated processing and analysis are thus needed to process 4DCT data effectively and efficiently. In this paper, we applied ideas and algorithms from image/signal processing, computer vision, and machine learning to 4DCT lung data so that lungs can be reliably segmented in a fully automated manner, lung features can be visualized and measured on the fly via user interactions, and data quality classifications can be computed in a robust manner. Comparisons of our results with an established treatment planning system and calculation by experts demonstrated negligible discrepancies (within ±2%) for volume assessment but one to two orders of magnitude performance enhancement. An empirical Fourier-analysis-based quality measure-delivered performances closely emulating human experts. Three machine learners are inspected to justify the viability of machine learning techniques used to robustly identify data quality of 4DCT images in the scalable manner. The resultant system provides a toolkit that speeds up 4-D tasks in the clinic and facilitates clinical research to improve current clinical practice. PMID:25621194

  13. A Fast Full Tensor Gravity computation algorithm for High Resolution 3D Geologic Interpretations

    NASA Astrophysics Data System (ADS)

    Jayaram, V.; Crain, K.; Keller, G. R.

    2011-12-01

    We present an algorithm to rapidly calculate the vertical gravity and full tensor gravity (FTG) values due to a 3-D geologic model. This algorithm can be implemented on single, multi-core CPU and graphical processing units (GPU) architectures. Our technique is based on the line element approximation with a constant density within each grid cell. This type of parameterization is well suited for high-resolution elevation datasets with grid size typically in the range of 1m to 30m. The large high-resolution data grids in our studies employ a pre-filtered mipmap pyramid type representation for the grid data known as the Geometry clipmap. The clipmap was first introduced by Microsoft Research in 2004 to do fly-through terrain visualization. This method caches nested rectangular extents of down-sampled data layers in the pyramid to create view-dependent calculation scheme. Together with the simple grid structure, this allows the gravity to be computed conveniently on-the-fly, or stored in a highly compressed format. Neither of these capabilities has previously been available. Our approach can perform rapid calculations on large topographies including crustal-scale models derived from complex geologic interpretations. For example, we used a 1KM Sphere model consisting of 105000 cells at 10m resolution with 100000 gravity stations. The line element approach took less than 90 seconds to compute the FTG and vertical gravity on an Intel Core i7 CPU at 3.07 GHz utilizing just its single core. Also, unlike traditional gravity computational algorithms, the line-element approach can calculate gravity effects at locations interior or exterior to the model. The only condition that must be met is the observation point cannot be located directly above the line element. Therefore, we perform a location test and then apply appropriate formulation to those data points. We will present and compare the computational performance of the traditional prism method versus the line element

  14. Precise Animated 3-D Displays Of The Heart Constructed From X-Ray Scatter Fields

    NASA Astrophysics Data System (ADS)

    McInerney, J. J.; Herr, M. D.; Copenhaver, G. L.

    1986-01-01

    A technique, based upon the interrogation of x-ray scatter, has been used to construct precise animated displays of the three-dimensional surface of the heart throughout the cardiac cycle. With the selection of motion amplification, viewing orientation, beat rate, and repetitive playbacks of isolated segments of the cardiac cycle, these displays are used to directly visualize epicardial surface velocity and displacement patterns, to construct regional maps of old or new myocardial infarction, and to visualize diastolic stiffening of the ventricle associated with acute ischemia. The procedure is non-invasive. Cut-downs or injections are not required.

  15. A supervisor for the successive 3D computations of magnetic, mechanical and acoustic quantities in power oil inductors and transformers

    SciTech Connect

    Reyne, G.; Magnin, H.; Berliat, G.; Clerc, C.

    1994-09-01

    A supervisor has been developed so as to allow successive 3D computations of different quantities by different softwares on the same physical problem. Noise of a given power oil transformer can be deduced from the surface vibrations of the tank. These vibrations are obtained through a mechanic computation whose Inputs are the electromagnetic forces provided . by an electromagnetic computation. Magnetic, mechanic and acoustic experimental data are compared with the results of the 3D computations. Stress Is put on the main characteristics of the supervisor such as the transfer of a given quantity from one mesh to the other.

  16. Potential hazards of viewing 3-D stereoscopic television, cinema and computer games: a review.

    PubMed

    Howarth, Peter A

    2011-03-01

    The visual stimulus provided by a 3-D stereoscopic display differs from that of the real world because the image provided to each eye is produced on a flat surface. The distance from the screen to the eye remains fixed, providing a single focal distance, but the introduction of disparity between the images allows objects to be located geometrically in front of, or behind, the screen. Unlike in the real world, the stimulus to accommodation and the stimulus to convergence do not match. Although this mismatch is used positively in some forms of Orthoptic treatment, a number of authors have suggested that it could negatively lead to the development of asthenopic symptoms. From knowledge of the zone of clear, comfortable, single binocular vision one can predict that, for people with normal binocular vision, adverse symptoms will not be present if the discrepancy is small, but are likely if it is large, and that what constitutes 'large' and 'small' are idiosyncratic to the individual. The accommodation-convergence mismatch is not, however, the only difference between the natural and the artificial stimuli. In the former case, an object located in front of, or behind, a fixated object will not only be perceived as double if the images fall outside Panum's fusional areas, but it will also be defocused and blurred. In the latter case, however, it is usual for the producers of cinema, TV or computer game content to provide an image that is in focus over the whole of the display, and as a consequence diplopic images will be sharply in focus. The size of Panum's fusional area is spatial frequency-dependent, and because of this the high spatial frequencies present in the diplopic 3-D image will provide a different stimulus to the fusion system from that found naturally.

  17. 3-D Computational Modelling of Oblique Continental Collision near South Island, New Zealand

    NASA Astrophysics Data System (ADS)

    Karatun, L.; Pysklywec, R. N.

    2015-12-01

    The research explores the highly oblique continental convergence at the South Island of New Zealand, considering the fundamental geodynamic mechanisms of sub-crustal lithospheric deformation during the orogenesis. In addition to the high velocity of along-strike plate motion, the oppositely verging subduction zones bounding the collision make the problem inherently three-dimensional. To study such factors during orogenesis, we conduct 3D computational modelling and present the results of a series of new experiments configured for the oblique South Island collision. The geodynamic modelling uses ASPECT - a robust highly-scalable and extendable geodynamic code featuring adaptive mesh refinement and complex rheologies. The model domain is defined by a box with prescribed velocities on the left and right faces with varied ratio of convergent versus strike-slip components, periodic boundary conditions for the front and back faces, free surface on top, and free slip at the bottom. Two different rheology types are used: brittle (pressure-, strain rate-, and material strength-dependent) for crust and visco-plastic (temperature-, pressure- and strain rate-dependent) for mantle. The obtained results provide insight into the behaviour of the lithosphere under the situation of young oblique convergence. We focus on the development of the mantle lithosphere, considering how the morphology of the sub-crustal orogenic root evolves during the convergent/strike-slip plate motions. The numerical experiments explore the dependence of this process on such factors as ratio of convergent versus strike-slip motion at the plate boundary, and rheological parameters of crust and mantle. The behaviour of the crust is also tracked to determine how the deep 3D tectonics may manifest at the surface.

  18. Parallel computing simulation of electrical excitation and conduction in the 3D human heart.

    PubMed

    Di Yu; Dongping Du; Hui Yang; Yicheng Tu

    2014-01-01

    A correctly beating heart is important to ensure adequate circulation of blood throughout the body. Normal heart rhythm is produced by the orchestrated conduction of electrical signals throughout the heart. Cardiac electrical activity is the resulted function of a series of complex biochemical-mechanical reactions, which involves transportation and bio-distribution of ionic flows through a variety of biological ion channels. Cardiac arrhythmias are caused by the direct alteration of ion channel activity that results in changes in the AP waveform. In this work, we developed a whole-heart simulation model with the use of massive parallel computing with GPGPU and OpenGL. The simulation algorithm was implemented under several different versions for the purpose of comparisons, including one conventional CPU version and two GPU versions based on Nvidia CUDA platform. OpenGL was utilized for the visualization / interaction platform because it is open source, light weight and universally supported by various operating systems. The experimental results show that the GPU-based simulation outperforms the conventional CPU-based approach and significantly improves the speed of simulation. By adopting modern computer architecture, this present investigation enables real-time simulation and visualization of electrical excitation and conduction in the large and complicated 3D geometry of a real-world human heart.

  19. Parallel 3D computation of unsteady wake flows with complex geometries and fluid-structure interactions

    NASA Astrophysics Data System (ADS)

    Osawa, Yasuo

    New powerful parallel computational tools are developed for 3D simulation of unsteady wake flows with complex geometries and fluid-structure interactions. The base method for flow simulation is a finite element formulation for the Navier-Stokes equations. The finite element formulation is based on the streamline-upwind/Petrov-Galerkin (SUPG) and pressure-stabilizing/Petrov-Galerkin (PSPG) techniques. These stabilization techniques facilitate simulation of flows with high Reynolds numbers, and allow us to use equal-order interpolation functions for velocity and pressure without generating numerical oscillations. A multi-domain computational method is developed to simulate wake flow both in the near and far downstream. The formulations lead to coupled nonlinear equation systems which are solved, at every time step, with the Newton-Raphson method. The overall formulation and solution techniques are implemented on parallel platforms such as the CRAY T3E and SGI PowerChallenge. Two phases of vortex shedding for flow past a cylinder is simulated to verify the accuracy of this method. The Enhanced-Discretization Interface Capturing Technique (EDICT) is utilized to simulate wake flow accurately. Fluid-structure coupling solution method based on the Deforming-Spatial-Domain/Stabilized Space-Time (DSD/SST) formulation is applied to simulate a parachute behavior in the unsteady wake.

  20. Toward virtual anatomy: a stereoscopic 3-D interactive multimedia computer program for cranial osteology.

    PubMed

    Trelease, R B

    1996-01-01

    Advances in computer visualization and user interface technologies have enabled development of "virtual reality" programs that allow users to perceive and to interact with objects in artificial three-dimensional environments. Such technologies were used to create an image database and program for studying the human skull, a specimen that has become increasingly expensive and scarce. Stereoscopic image pairs of a museum-quality skull were digitized from multiple views. For each view, the stereo pairs were interlaced into a single, field-sequential stereoscopic picture using an image processing program. The resulting interlaced image files are organized in an interactive multimedia program. At run-time, gray-scale 3-D images are displayed on a large-screen computer monitor and observed through liquid-crystal shutter goggles. Users can then control the program and change views with a mouse and cursor to point-and-click on screen-level control words ("buttons"). For each view of the skull, an ID control button can be used to overlay pointers and captions for important structures. Pointing and clicking on "hidden buttons" overlying certain structures triggers digitized audio spoken word descriptions or mini lectures.

  1. PLOT3D user's manual

    NASA Technical Reports Server (NTRS)

    Walatka, Pamela P.; Buning, Pieter G.; Pierce, Larry; Elson, Patricia A.

    1990-01-01

    PLOT3D is a computer graphics program designed to visualize the grids and solutions of computational fluid dynamics. Seventy-four functions are available. Versions are available for many systems. PLOT3D can handle multiple grids with a million or more grid points, and can produce varieties of model renderings, such as wireframe or flat shaded. Output from PLOT3D can be used in animation programs. The first part of this manual is a tutorial that takes the reader, keystroke by keystroke, through a PLOT3D session. The second part of the manual contains reference chapters, including the helpfile, data file formats, advice on changing PLOT3D, and sample command files.

  2. A Computational Framework for 3D Mechanical Modeling of Plant Morphogenesis with Cellular Resolution

    PubMed Central

    Gilles, Benjamin; Hamant, Olivier; Boudaoud, Arezki; Traas, Jan; Godin, Christophe

    2015-01-01

    The link between genetic regulation and the definition of form and size during morphogenesis remains largely an open question in both plant and animal biology. This is partially due to the complexity of the process, involving extensive molecular networks, multiple feedbacks between different scales of organization and physical forces operating at multiple levels. Here we present a conceptual and modeling framework aimed at generating an integrated understanding of morphogenesis in plants. This framework is based on the biophysical properties of plant cells, which are under high internal turgor pressure, and are prevented from bursting because of the presence of a rigid cell wall. To control cell growth, the underlying molecular networks must interfere locally with the elastic and/or plastic extensibility of this cell wall. We present a model in the form of a three dimensional (3D) virtual tissue, where growth depends on the local modulation of wall mechanical properties and turgor pressure. The model shows how forces generated by turgor-pressure can act both cell autonomously and non-cell autonomously to drive growth in different directions. We use simulations to explore lateral organ formation at the shoot apical meristem. Although different scenarios lead to similar shape changes, they are not equivalent and lead to different, testable predictions regarding the mechanical and geometrical properties of the growing lateral organs. Using flower development as an example, we further show how a limited number of gene activities can explain the complex shape changes that accompany organ outgrowth. PMID:25569615

  3. A computational framework for 3D mechanical modeling of plant morphogenesis with cellular resolution.

    PubMed

    Boudon, Frédéric; Chopard, Jérôme; Ali, Olivier; Gilles, Benjamin; Hamant, Olivier; Boudaoud, Arezki; Traas, Jan; Godin, Christophe

    2015-01-01

    The link between genetic regulation and the definition of form and size during morphogenesis remains largely an open question in both plant and animal biology. This is partially due to the complexity of the process, involving extensive molecular networks, multiple feedbacks between different scales of organization and physical forces operating at multiple levels. Here we present a conceptual and modeling framework aimed at generating an integrated understanding of morphogenesis in plants. This framework is based on the biophysical properties of plant cells, which are under high internal turgor pressure, and are prevented from bursting because of the presence of a rigid cell wall. To control cell growth, the underlying molecular networks must interfere locally with the elastic and/or plastic extensibility of this cell wall. We present a model in the form of a three dimensional (3D) virtual tissue, where growth depends on the local modulation of wall mechanical properties and turgor pressure. The model shows how forces generated by turgor-pressure can act both cell autonomously and non-cell autonomously to drive growth in different directions. We use simulations to explore lateral organ formation at the shoot apical meristem. Although different scenarios lead to similar shape changes, they are not equivalent and lead to different, testable predictions regarding the mechanical and geometrical properties of the growing lateral organs. Using flower development as an example, we further show how a limited number of gene activities can explain the complex shape changes that accompany organ outgrowth.

  4. A computational framework for 3D mechanical modeling of plant morphogenesis with cellular resolution.

    PubMed

    Boudon, Frédéric; Chopard, Jérôme; Ali, Olivier; Gilles, Benjamin; Hamant, Olivier; Boudaoud, Arezki; Traas, Jan; Godin, Christophe

    2015-01-01

    The link between genetic regulation and the definition of form and size during morphogenesis remains largely an open question in both plant and animal biology. This is partially due to the complexity of the process, involving extensive molecular networks, multiple feedbacks between different scales of organization and physical forces operating at multiple levels. Here we present a conceptual and modeling framework aimed at generating an integrated understanding of morphogenesis in plants. This framework is based on the biophysical properties of plant cells, which are under high internal turgor pressure, and are prevented from bursting because of the presence of a rigid cell wall. To control cell growth, the underlying molecular networks must interfere locally with the elastic and/or plastic extensibility of this cell wall. We present a model in the form of a three dimensional (3D) virtual tissue, where growth depends on the local modulation of wall mechanical properties and turgor pressure. The model shows how forces generated by turgor-pressure can act both cell autonomously and non-cell autonomously to drive growth in different directions. We use simulations to explore lateral organ formation at the shoot apical meristem. Although different scenarios lead to similar shape changes, they are not equivalent and lead to different, testable predictions regarding the mechanical and geometrical properties of the growing lateral organs. Using flower development as an example, we further show how a limited number of gene activities can explain the complex shape changes that accompany organ outgrowth. PMID:25569615

  5. 3D printing meets computational astrophysics: deciphering the structure of η Carinae's inner colliding winds

    NASA Astrophysics Data System (ADS)

    Madura, T. I.; Clementel, N.; Gull, T. R.; Kruip, C. J. H.; Paardekooper, J.-P.

    2015-06-01

    We present the first 3D prints of output from a supercomputer simulation of a complex astrophysical system, the colliding stellar winds in the massive (≳120 M⊙), highly eccentric (e ˜ 0.9) binary star system η Carinae. We demonstrate the methodology used to incorporate 3D interactive figures into a PDF (Portable Document Format) journal publication and the benefits of using 3D visualization and 3D printing as tools to analyse data from multidimensional numerical simulations. Using a consumer-grade 3D printer (MakerBot Replicator 2X), we successfully printed 3D smoothed particle hydrodynamics simulations of η Carinae's inner (r ˜ 110 au) wind-wind collision interface at multiple orbital phases. The 3D prints and visualizations reveal important, previously unknown `finger-like' structures at orbital phases shortly after periastron (φ ˜ 1.045) that protrude radially outwards from the spiral wind-wind collision region. We speculate that these fingers are related to instabilities (e.g. thin-shell, Rayleigh-Taylor) that arise at the interface between the radiatively cooled layer of dense post-shock primary-star wind and the fast (3000 km s-1), adiabatic post-shock companion-star wind. The success of our work and easy identification of previously unrecognized physical features highlight the important role 3D printing and interactive graphics can play in the visualization and understanding of complex 3D time-dependent numerical simulations of astrophysical phenomena.

  6. A new approach of building 3D visualization framework for multimodal medical images display and computed assisted diagnosis

    NASA Astrophysics Data System (ADS)

    Li, Zhenwei; Sun, Jianyong; Zhang, Jianguo

    2012-02-01

    As more and more CT/MR studies are scanning with larger volume of data sets, more and more radiologists and clinician would like using PACS WS to display and manipulate these larger data sets of images with 3D rendering features. In this paper, we proposed a design method and implantation strategy to develop 3D image display component not only with normal 3D display functions but also with multi-modal medical image fusion as well as compute-assisted diagnosis of coronary heart diseases. The 3D component has been integrated into the PACS display workstation of Shanghai Huadong Hospital, and the clinical practice showed that it is easy for radiologists and physicians to use these 3D functions such as multi-modalities' (e.g. CT, MRI, PET, SPECT) visualization, registration and fusion, and the lesion quantitative measurements. The users were satisfying with the rendering speeds and quality of 3D reconstruction. The advantages of the component include low requirements for computer hardware, easy integration, reliable performance and comfortable application experience. With this system, the radiologists and the clinicians can manipulate with 3D images easily, and use the advanced visualization tools to facilitate their work with a PACS display workstation at any time.

  7. 3-D visualization and identification of biological microorganisms using partially temporal incoherent light in-line computational holographic imaging.

    PubMed

    Moon, Inkyu; Javidi, Bahram

    2008-12-01

    We present a new method for three-dimensional (3-D) visualization and identification of biological microorganisms using partially temporal incoherent light in-line (PTILI) computational holographic imaging and multivariate statistical methods. For 3-D data acquisition of biological microorganisms, the band-pass filtered white light is used to illuminate a biological sample. The transversely and longitudinally diffracted pattern of the biological sample is magnified by microscope objective (MO) and is optically recorded with an image sensor array interfaced with a computer. Three-dimensional reconstruction of the biological sample from the diffraction pattern is accomplished by using computational Fresnel propagation method. Principal components analysis and nonparametric inference algorithms are applied to the 3-D complex amplitude biological sample for identification purposes. Experiments indicate that the proposed system can be useful for identifying biological microorganisms. To the best of our knowledge, this is the first report on using PTILI computational holographic microscopy for identification of biological microorganisms.

  8. 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. PMID:27622416

  9. Real-time 3D computed tomographic reconstruction using commodity graphics hardware

    NASA Astrophysics Data System (ADS)

    Xu, Fang; Mueller, Klaus

    2007-07-01

    The recent emergence of various types of flat-panel x-ray detectors and C-arm gantries now enables the construction of novel imaging platforms for a wide variety of clinical applications. Many of these applications require interactive 3D image generation, which cannot be satisfied with inexpensive PC-based solutions using the CPU. We present a solution based on commodity graphics hardware (GPUs) to provide these capabilities. While GPUs have been employed for CT reconstruction before, our approach provides significant speedups by exploiting the various built-in hardwired graphics pipeline components for the most expensive CT reconstruction task, backprojection. We show that the timings so achieved are superior to those obtained when using the GPU merely as a multi-processor, without a drop in reconstruction quality. In addition, we also show how the data flow across the graphics pipeline can be optimized, by balancing the load among the pipeline components. The result is a novel streaming CT framework that conceptualizes the reconstruction process as a steady flow of data across a computing pipeline, updating the reconstruction result immediately after the projections have been acquired. Using a single PC equipped with a single high-end commodity graphics board (the Nvidia 8800 GTX), our system is able to process clinically-sized projection data at speeds meeting and exceeding the typical flat-panel detector data production rates, enabling throughput rates of 40-50 projections s-1 for the reconstruction of 5123 volumes.

  10. GBM Volumetry using the 3D Slicer Medical Image Computing Platform

    PubMed Central

    Egger, Jan; Kapur, Tina; Fedorov, Andriy; Pieper, Steve; Miller, James V.; Veeraraghavan, Harini; Freisleben, Bernd; Golby, Alexandra J.; Nimsky, Christopher; Kikinis, Ron

    2013-01-01

    Volumetric change in glioblastoma multiforme (GBM) over time is a critical factor in treatment decisions. Typically, the tumor volume is computed on a slice-by-slice basis using MRI scans obtained at regular intervals. (3D)Slicer – a free platform for biomedical research – provides an alternative to this manual slice-by-slice segmentation process, which is significantly faster and requires less user interaction. In this study, 4 physicians segmented GBMs in 10 patients, once using the competitive region-growing based GrowCut segmentation module of Slicer, and once purely by drawing boundaries completely manually on a slice-by-slice basis. Furthermore, we provide a variability analysis for three physicians for 12 GBMs. The time required for GrowCut segmentation was on an average 61% of the time required for a pure manual segmentation. A comparison of Slicer-based segmentation with manual slice-by-slice segmentation resulted in a Dice Similarity Coefficient of 88.43 ± 5.23% and a Hausdorff Distance of 2.32 ± 5.23 mm. PMID:23455483

  11. 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.

  12. Detectability of hepatic tumors during 3D post-processed ultrafast cone-beam computed tomography

    NASA Astrophysics Data System (ADS)

    Paul, Jijo; Vogl, Thomas J.; Chacko, Annamma

    2015-10-01

    To evaluate hepatic tumor detection using ultrafast cone-beam computed tomography (UCBCT) cross-sectional and 3D post-processed image datasets. 657 patients were examined using UCBCT during hepatic transarterial chemoembolization (TACE), and data were collected retrospectively from January 2012 to September 2014. Tumor detectability, diagnostic ability, detection accuracy and sensitivity were examined for different hepatic tumors using UCBCT cross-sectional, perfusion blood volume (PBV) and UCBCT-MRI (magnetic resonance imaging) fused image datasets. Appropriate statistical tests were used to compare collected sample data. Fused image data showed the significantly higher (all P  <  0.05) diagnostic ability for hepatic tumors compared to UCBCT or PBV image data. The detectability of small hepatic tumors (<5 mm) was significantly reduced (all P  <  0.05) using UCBCT cross-sectional images compared to MRI or fused image data; however, PBV improved tumor detectability using a color display. Fused image data produced 100% tumor sensitivity due to the simultaneous availability of MRI and UCBCT information during tumor diagnosis. Fused image data produced excellent hepatic tumor sensitivity, detectability and diagnostic ability compared to other datasets assessed. Fused image data is extremely reliable and useful compared to UCBCT cross-sectional or PBV image datasets to depict hepatic tumors during TACE. Partial anatomical visualization on cross-sectional images was compensated by fused image data during tumor diagnosis.

  13. Auto-masked 2D/3D image registration and its validation with clinical cone-beam computed tomography

    NASA Astrophysics Data System (ADS)

    Steininger, P.; Neuner, M.; Weichenberger, H.; Sharp, G. C.; Winey, B.; Kametriser, G.; Sedlmayer, F.; Deutschmann, H.

    2012-07-01

    Image-guided alignment procedures in radiotherapy aim at minimizing discrepancies between the planned and the real patient setup. For that purpose, we developed a 2D/3D approach which rigidly registers a computed tomography (CT) with two x-rays by maximizing the agreement in pixel intensity between the x-rays and the corresponding reconstructed radiographs from the CT. Moreover, the algorithm selects regions of interest (masks) in the x-rays based on 3D segmentations from the pre-planning stage. For validation, orthogonal x-ray pairs from different viewing directions of 80 pelvic cone-beam CT (CBCT) raw data sets were used. The 2D/3D results were compared to corresponding standard 3D/3D CBCT-to-CT alignments. Outcome over 8400 2D/3D experiments showed that parametric errors in root mean square were <0.18° (rotations) and <0.73 mm (translations), respectively, using rank correlation as intensity metric. This corresponds to a mean target registration error, related to the voxels of the lesser pelvis, of <2 mm in 94.1% of the cases. From the results we conclude that 2D/3D registration based on sequentially acquired orthogonal x-rays of the pelvis is a viable alternative to CBCT-based approaches if rigid alignment on bony anatomy is sufficient, no volumetric intra-interventional data set is required and the expected error range fits the individual treatment prescription.

  14. Computation of neutron fluxes in clusters of fuel pins arranged in hexagonal assemblies (2D and 3D)

    SciTech Connect

    Prabha, H.; Marleau, G.

    2012-07-01

    For computations of fluxes, we have used Carvik's method of collision probabilities. This method requires tracking algorithms. An algorithm to compute tracks (in 2D and 3D) has been developed for seven hexagonal geometries with cluster of fuel pins. This has been implemented in the NXT module of the code DRAGON. The flux distribution in cluster of pins has been computed by using this code. For testing the results, they are compared when possible with the EXCELT module of the code DRAGON. Tracks are plotted in the NXT module by using MATLAB, these plots are also presented here. Results are presented with increasing number of lines to show the convergence of these results. We have numerically computed volumes, surface areas and the percentage errors in these computations. These results show that 2D results converge faster than 3D results. The accuracy on the computation of fluxes up to second decimal is achieved with fewer lines. (authors)

  15. Images of Soft-bodied Animals with External Hard Shell: 3D Visualization of the Embedded Soft Tissue

    SciTech Connect

    Rao, Donepudi V.; Akatsuka, Takao; Tromba, Giuliana

    2004-05-12

    Images of soft-bodied animals (snails) of various types with external hard shell are obtained for 25, 27 and 29 keV synchrotron X-rays. The SYRMEP facility at Elettra,Trieste, Italy and the associated detection system has been used for the image acquisition. The interior properties of the embedded soft tissue are analysed utilizing the software. From the reconstructed images, the soft tissue distribution, void spaces associated with the soft tissue and external hard shell are identified. 3D images are reconstructed at these energies and optimum energy is chosen based on the quality of the image for further analysis. The optimum energy allowed us to visualize the visibility of low absorbing details and interior microstructure of the embedded soft tissue.

  16. Validation of computational fluid dynamics methods with anatomically exact, 3D printed MRI phantoms and 4D pcMRI.

    PubMed

    Anderson, Jeff R; Diaz, Orlando; Klucznik, Richard; Zhang, Y Jonathan; Britz, Gavin W; Grossman, Robert G; Lv, Nan; Huang, Qinghai; Karmonik, Christof

    2014-01-01

    A new concept of rapid 3D prototyping was implemented using cost-effective 3D printing for creating anatomically correct replica of cerebral aneurysms. With a dedicated flow loop set-up in a full body human MRI scanner, flow measurements were performed using 4D phase contrast magnetic resonance imaging to visualize and quantify intra-aneurysmal flow patterns. Ultrashort TE sequences were employed to obtain high-resolution 3D image data to visualize the lumen inside the plastic replica. In-vitro results were compared with retrospectively obtained in-vivo data and results from computational fluid dynamics simulations (CFD). Rapid prototyping of anatomically realistic 3D models may have future impact in treatment planning, design of image acquisition methods for MRI and angiographic systems and for the design and testing of advanced image post-processing technologies.

  17. Computer numerical control (CNC) lithography: light-motion synchronized UV-LED lithography for 3D microfabrication

    NASA Astrophysics Data System (ADS)

    Kim, Jungkwun; Yoon, Yong-Kyu; Allen, Mark G.

    2016-03-01

    This paper presents a computer-numerical-controlled ultraviolet light-emitting diode (CNC UV-LED) lithography scheme for three-dimensional (3D) microfabrication. The CNC lithography scheme utilizes sequential multi-angled UV light exposures along with a synchronized switchable UV light source to create arbitrary 3D light traces, which are transferred into the photosensitive resist. The system comprises a switchable, movable UV-LED array as a light source, a motorized tilt-rotational sample holder, and a computer-control unit. System operation is such that the tilt-rotational sample holder moves in a pre-programmed routine, and the UV-LED is illuminated only at desired positions of the sample holder during the desired time period, enabling the formation of complex 3D microstructures. This facilitates easy fabrication of complex 3D structures, which otherwise would have required multiple manual exposure steps as in the previous multidirectional 3D UV lithography approach. Since it is batch processed, processing time is far less than that of the 3D printing approach at the expense of some reduction in the degree of achievable 3D structure complexity. In order to produce uniform light intensity from the arrayed LED light source, the UV-LED array stage has been kept rotating during exposure. UV-LED 3D fabrication capability was demonstrated through a plurality of complex structures such as V-shaped micropillars, micropanels, a micro-‘hi’ structure, a micro-‘cat’s claw,’ a micro-‘horn,’ a micro-‘calla lily,’ a micro-‘cowboy’s hat,’ and a micro-‘table napkin’ array.

  18. 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.

  19. 3D printing of preclinical X-ray computed tomographic data sets.

    PubMed

    Doney, Evan; Krumdick, Lauren A; Diener, Justin M; Wathen, Connor A; Chapman, Sarah E; Stamile, Brian; Scott, Jeremiah E; Ravosa, Matthew J; Van Avermaete, Tony; Leevy, W Matthew

    2013-01-01

    Three-dimensional printing allows for the production of highly detailed objects through a process known as additive manufacturing. Traditional, mold-injection methods to create models or parts have several limitations, the most important of which is a difficulty in making highly complex products in a timely, cost-effective manner.(1) However, gradual improvements in three-dimensional printing technology have resulted in both high-end and economy instruments that are now available for the facile production of customized models.(2) These printers have the ability to extrude high-resolution objects with enough detail to accurately represent in vivo images generated from a preclinical X-ray CT scanner. With proper data collection, surface rendering, and stereolithographic editing, it is now possible and inexpensive to rapidly produce detailed skeletal and soft tissue structures from X-ray CT data. Even in the early stages of development, the anatomical models produced by three-dimensional printing appeal to both educators and researchers who can utilize the technology to improve visualization proficiency. (3, 4) The real benefits of this method result from the tangible experience a researcher can have with data that cannot be adequately conveyed through a computer screen. The translation of pre-clinical 3D data to a physical object that is an exact copy of the test subject is a powerful tool for visualization and communication, especially for relating imaging research to students, or those in other fields. Here, we provide a detailed method for printing plastic models of bone and organ structures derived from X-ray CT scans utilizing an Albira X-ray CT system in conjunction with PMOD, ImageJ, Meshlab, Netfabb, and ReplicatorG software packages. PMID:23542702

  20. 3D printing of preclinical X-ray computed tomographic data sets.

    PubMed

    Doney, Evan; Krumdick, Lauren A; Diener, Justin M; Wathen, Connor A; Chapman, Sarah E; Stamile, Brian; Scott, Jeremiah E; Ravosa, Matthew J; Van Avermaete, Tony; Leevy, W Matthew

    2013-03-22

    Three-dimensional printing allows for the production of highly detailed objects through a process known as additive manufacturing. Traditional, mold-injection methods to create models or parts have several limitations, the most important of which is a difficulty in making highly complex products in a timely, cost-effective manner.(1) However, gradual improvements in three-dimensional printing technology have resulted in both high-end and economy instruments that are now available for the facile production of customized models.(2) These printers have the ability to extrude high-resolution objects with enough detail to accurately represent in vivo images generated from a preclinical X-ray CT scanner. With proper data collection, surface rendering, and stereolithographic editing, it is now possible and inexpensive to rapidly produce detailed skeletal and soft tissue structures from X-ray CT data. Even in the early stages of development, the anatomical models produced by three-dimensional printing appeal to both educators and researchers who can utilize the technology to improve visualization proficiency. (3, 4) The real benefits of this method result from the tangible experience a researcher can have with data that cannot be adequately conveyed through a computer screen. The translation of pre-clinical 3D data to a physical object that is an exact copy of the test subject is a powerful tool for visualization and communication, especially for relating imaging research to students, or those in other fields. Here, we provide a detailed method for printing plastic models of bone and organ structures derived from X-ray CT scans utilizing an Albira X-ray CT system in conjunction with PMOD, ImageJ, Meshlab, Netfabb, and ReplicatorG software packages.

  1. Development, Verification and Use of Gust Modeling in the NASA Computational Fluid Dynamics Code FUN3D

    NASA Technical Reports Server (NTRS)

    Bartels, Robert E.

    2012-01-01

    This paper presents the implementation of gust modeling capability in the CFD code FUN3D. The gust capability is verified by computing the response of an airfoil to a sharp edged gust. This result is compared with the theoretical result. The present simulations will be compared with other CFD gust simulations. This paper also serves as a users manual for FUN3D gust analyses using a variety of gust profiles. Finally, the development of an Auto-Regressive Moving-Average (ARMA) reduced order gust model using a gust with a Gaussian profile in the FUN3D code is presented. ARMA simulated results of a sequence of one-minus-cosine gusts is shown to compare well with the same gust profile computed with FUN3D. Proper Orthogonal Decomposition (POD) is combined with the ARMA modeling technique to predict the time varying pressure coefficient increment distribution due to a novel gust profile. The aeroelastic response of a pitch/plunge airfoil to a gust environment is computed with a reduced order model, and compared with a direct simulation of the system in the FUN3D code. The two results are found to agree very well.

  2. A new method for combining live action and computer graphics in stereoscopic 3D

    NASA Astrophysics Data System (ADS)

    Rupkalvis, John A.; Gillen, Ron

    2008-02-01

    A primary requirement when elements are to be combined stereoscopically, is that homologous points in each eye view of each element have identical parallax separation at any point of interaction. If this is not done, the image parts on one element will appear to be at a different distance from the corresponding or associated parts on the other element. This results in a visual discontinuity that appears very unnatural. For example, if a live actor were to appear to "shake hands" with a cartoon character, a very natural appearing juncture may appear to be the case when seen in 2-D, but their hands may appear to miss when seen in 3-D. Previous efforts to compensate, or correct these errors have involved painstaking time-consuming trial-and-error tests. In the area of pure animation, efforts to make cartoon characters appear more realistic were developed. A "motion tracking" technique was developed. This involves an actor wearing a special suit with indicator marks at various points on their body. The actor walks through the scene, then the animator tracks the points using motion capture software. Because live action and CG elements can interact or change at several different points and levels within a scene, additional requirements must also be addressed. "Occlusions" occur when one object passes in front of another. A particular tracking point may appear in one eye-view, and not the other. When Z-axis differentials are to be considered in the live action as well as the CG elements, and both are to interact with each other, both eye-views must be tracked, especially at points of occlusion. A new approach would be to generate a three dimensional grid, within which the action is to take place. This grid can be projected, onto the stage where the live action part is to take place. When differential occlusions occur, the grid may be seen and CG elements plotted in reference to it. Because of the capability of precisely locating points in a digital image, a pixel

  3. 3D reconstructions with pixel-based images are made possible by digitally clearing plant and animal tissue

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Reconstruction of 3D images from a series of 2D images has been restricted by the limited capacity to decrease the opacity of surrounding tissue. Commercial software that allows color-keying and manipulation of 2D images in true 3D space allowed us to produce 3D reconstructions from pixel based imag...

  4. User's Guide for Subroutine PLOT3D. Physical Processes in Terrestrial and Aquatic Ecosystems, Computer Programs and Graphics Capabilities.

    ERIC Educational Resources Information Center

    Gales, Larry

    This module is part of a series designed to be used by life science students for instruction in the application of physical theory to ecosystem operation. Most modules contain computer programs which are built around a particular application of a physical process. PLOT3D is a subroutine package which generates a variety of three dimensional hidden…

  5. DEVELOPMENT OF 3-D COMPUTER MODELS OF HUMAN LUNG MORPHOLOGY FOR IMPROOVED RISK ASSESSMENT OF INHALED PARTICULATE MATTER

    EPA Science Inventory

    DEVELOPMENT OF 3-D COMPUTER MODELS OF HUMAN LUNG MORPHOLOGY FOR IMPROVED RISK ASSESSMENT OF INHALED PARTICULATE MATTER

    Jeffry D. Schroeter, Curriculum in Toxicology, University of North Carolina, Chapel Hill, NC 27599; Ted B. Martonen, ETD, NHEERL, USEPA, RTP, NC 27711; Do...

  6. Programmer's Guide for Subroutine PRNT3D. Physical Processes in Terrestrial and Aquatic Ecosystems, Computer Programs and Graphics Capabilities.

    ERIC Educational Resources Information Center

    Gales, Larry

    These materials were designed to be used by life science students for instruction in the application of physical theory to ecosystem operation. Most modules contain computer programs which are built around a particular application of a physical process. PRNT3D is a subroutine package which generates a variety of printed plot displays. The displays…

  7. User's Guide for Subroutine PRNT3D. Physical Processes in Terrestrial and Aquatic Ecosystems, Computer Programs and Graphics Capabilities.

    ERIC Educational Resources Information Center

    Gales, Larry

    These materials were designed to be used by life science students for instruction in the application of physical theory to ecosystem operation. Most modules contain computer programs which are built around a particular application of a physical process. PRNT3D is a subroutine package which generates a variety of printer plot displays. The displays…

  8. Programmer's Guide for Subroutine PLOT3D. Physical Processes in Terrestrial and Aquatic Ecosystems, Computer Programs and Graphics Capabilities.

    ERIC Educational Resources Information Center

    Gales, Larry

    This module is part of a series designed to be used by life science students for instruction in the application of physical theory to ecosystem operation. Most modules contain computer programs which are built around a particular application of a physical process. PLOT3D is a subroutine package which generates a variety of three-dimensional hidden…

  9. A collaborative computing framework of cloud network and WBSN applied to fall detection and 3-D motion reconstruction.

    PubMed

    Lai, Chin-Feng; Chen, Min; Pan, Jeng-Shyang; Youn, Chan-Hyun; Chao, Han-Chieh

    2014-03-01

    As cloud computing and wireless body sensor network technologies become gradually developed, ubiquitous healthcare services prevent accidents instantly and effectively, as well as provides relevant information to reduce related processing time and cost. This study proposes a co-processing intermediary framework integrated cloud and wireless body sensor networks, which is mainly applied to fall detection and 3-D motion reconstruction. In this study, the main focuses includes distributed computing and resource allocation of processing sensing data over the computing architecture, network conditions and performance evaluation. Through this framework, the transmissions and computing time of sensing data are reduced to enhance overall performance for the services of fall events detection and 3-D motion reconstruction.

  10. Estimation of bisphenol A-Human toxicity by 3D cell culture arrays, high throughput alternatives to animal tests.

    PubMed

    Lee, Dong Woo; Oh, Woo-Yeon; Yi, Sang Hyun; Ku, Bosung; Lee, Moo-Yeal; Cho, Yoon Hee; Yang, Mihi

    2016-09-30

    Bisphenol A (BPA) has been widely used for manufacturing polycarbonate plastics and epoxy resins and has been extensively tested in animals to predict human toxicity. In order to reduce the use of animals for toxicity assessment and provide further accurate information on BPA toxicity in humans, we encapsulated Hep3B human hepatoma cells in alginate and cultured them in three dimensions (3D) on a micropillar chip coupled to a panel of metabolic enzymes on a microwell chip. As a result, we were able to assess the toxicity of BPA under various metabolic enzyme conditions using a high-throughput and micro assay; sample volumes were nearly 2,000 times less than that required for a 96-well plate. We applied a total of 28 different enzymes to each chip, including 10 cytochrome P450s (CYP450s), 10 UDP-glycosyltransferases (UGTs), 3 sulfotransferases (SULTs), alcohol dehydrogenase (ADH), and aldehyde dehydrogenase 2 (ALDH2). Phase I enzyme mixtures, phase II enzyme mixtures, and a combination of phase I and phase II enzymes were also applied to the chip. BPA toxicity was higher in samples containing CYP2E1 than controls, which contained no enzymes (IC50, 184±16μM and 270±25.8μM, respectively, p<0.01). However, BPA-induced toxicity was alleviated in the presence of ADH (IC50, 337±17.9μM), ALDH2 (335±13.9μM), and SULT1E1 (318±17.7μM) (p<0.05). CYP2E1-mediated cytotoxicity was confirmed by quantifying unmetabolized BPA using HPLC/FD. Therefore, we suggest the present micropillar/microwell chip platform as an effective alternative to animal testing for estimating BPA toxicity via human metabolic systems. PMID:27491884

  11. 3D Printing Meets Computational Astrophysics: Deciphering the Structure of Eta Carinae’s Colliding Winds Using 3D Prints of Smoothed Particle Hydrodynamics Simulations

    NASA Astrophysics Data System (ADS)

    Madura, Thomas; Gull, Theodore R.; Clementel, Nicola; Paardekooper, Jan-Pieter; Kruip, Chael; Corcoran, Michael F.; Hamaguchi, Kenji; Teodoro, Mairan

    2015-01-01

    We present the first 3D prints of output from a supercomputer simulation of a complex astrophysical system, the colliding stellar winds in the massive (>120 MSun), highly eccentric (e ~ 0.9) binary Eta Carinae. Using a consumer-grade 3D printer (Makerbot Replicator 2X), we successfully printed 3D smoothed particle hydrodynamics simulations of Eta Carinae's inner (r ~110 AU) wind-wind collision interface at multiple orbital phases. These 3D prints reveal important, previously unknown 'finger-like' structures at orbital phases shortly after periastron (φ ~1.045) that protrude radially outward from the spiral wind-wind collision region. We speculate that these fingers are related to instabilities (e.g. Rayleigh-Taylor) that arise at the interface between the radiatively-cooled layer of dense post-shock primary-star wind and the hot, adiabatic post-shock companion-star wind. The success of our work and easy identification of previously unknown physical features highlight the important role 3D printing can play in the visualization and understanding of complex 3D time-dependent numerical simulations of astrophysical phenomena.

  12. Comparison of Computational Aeroacoustics Prediction of Acoustic Transmission Through a 3D Stator with Experiment

    NASA Technical Reports Server (NTRS)

    Hixon, Ray; Envia, Edmane; Dahl, Milo; Sutliff, Daniel

    2014-01-01

    In this paper, numerical predictions of acoustic transmission through a 3D stator obtained using the NASA BASS code are compared with experimentally measured data. The influence of vane count and stagger as well as frequency and mode order on the transmission loss is investigated. The data-theory comparisons indicate that BASS can predict all the important trends observed in the experimental data.

  13. Comparison of Computational Aeroacoustics Prediction of Acoustic Transmission Through a 3D Stator With Experiment

    NASA Technical Reports Server (NTRS)

    Hixon, Ray; Envia, Edmane; Dahl, Milo; Sutliff, Daniel L.

    2014-01-01

    In this paper, numerical predictions of acoustic transmission through a 3D stator obtained using the NASA BASS code are compared with experimentally measured data. The influence of vane count and stagger as well as frequency and mode order on the transmission loss is investigated. The data-theory comparisons indicate that BASS can predict all the important trends observed in the experimental data.

  14. Grid-Adapted FUN3D Computations for the Second High Lift Prediction Workshop

    NASA Technical Reports Server (NTRS)

    Lee-Rausch, E. M.; Rumsey, C. L.; Park, M. A.

    2014-01-01

    Contributions of the unstructured Reynolds-averaged Navier-Stokes code FUN3D to the 2nd AIAA CFD High Lift Prediction Workshop are described, and detailed comparisons are made with experimental data. Using workshop-supplied grids, results for the clean wing configuration are compared with results from the structured code CFL3D Using the same turbulence model, both codes compare reasonably well in terms of total forces and moments, and the maximum lift is similarly over-predicted for both codes compared to experiment. By including more representative geometry features such as slat and flap brackets and slat pressure tube bundles, FUN3D captures the general effects of the Reynolds number variation, but under-predicts maximum lift on workshop-supplied grids in comparison with the experimental data, due to excessive separation. However, when output-based, off-body grid adaptation in FUN3D is employed, results improve considerably. In particular, when the geometry includes both brackets and the pressure tube bundles, grid adaptation results in a more accurate prediction of lift near stall in comparison with the wind-tunnel data. Furthermore, a rotation-corrected turbulence model shows improved pressure predictions on the outboard span when using adapted grids.

  15. TBIEM3D: A Computer Program for Predicting Ducted Fan Engine Noise. Version 1.1

    NASA Technical Reports Server (NTRS)

    Dunn, M. H.

    1997-01-01

    This document describes the usage of the ducted fan noise prediction program TBIEM3D (Thin duct - Boundary Integral Equation Method - 3 Dimensional). A scattering approach is adopted in which the acoustic pressure field is split into known incident and unknown scattered parts. The scattering of fan-generated noise by a finite length circular cylinder in a uniform flow field is considered. The fan noise is modeled by a collection of spinning point thrust dipoles. The program, based on a Boundary Integral Equation Method (BIEM), calculates circumferential modal coefficients of the acoustic pressure at user-specified field locations. The duct interior can be of the hard wall type or lined. The duct liner is axisymmetric, locally reactive, and can be uniform or axially segmented. TBIEM3D is written in the FORTRAN programming language. Input to TBIEM3D is minimal and consists of geometric and kinematic parameters. Discretization and numerical parameters are determined automatically by the code. Several examples are presented to demonstrate TBIEM3D capabilities.

  16. Computer-aided diagnosis of pulmonary nodules on CT scans: Segmentation and classification using 3D active contours

    PubMed Central

    Way, Ted W.; Hadjiiski, Lubomir M.; Sahiner, Berkman; Chan, Heang-Ping; Cascade, Philip N.; Kazerooni, Ella A.; Bogot, Naama; Zhou, Chuan

    2009-01-01

    We are developing a computer-aided diagnosis (CAD) system to classify malignant and benign lung nodules found on CT scans. A fully automated system was designed to segment the nodule from its surrounding structured background in a local volume of interest (VOI) and to extract image features for classification. Image segmentation was performed with a three-dimensional (3D) active contour (AC) method. A data set of 96 lung nodules (44 malignant, 52 benign) from 58 patients was used in this study. The 3D AC model is based on two-dimensional AC with the addition of three new energy components to take advantage of 3D information: (1) 3D gradient, which guides the active contour to seek the object surface, (2) 3D curvature, which imposes a smoothness constraint in the z direction, and (3) mask energy, which penalizes contours that grow beyond the pleura or thoracic wall. The search for the best energy weights in the 3D AC model was guided by a simplex optimization method. Morphological and gray-level features were extracted from the segmented nodule. The rubber band straightening transform (RBST) was applied to the shell of voxels surrounding the nodule. Texture features based on run-length statistics were extracted from the RBST image. A linear discriminant analysis classifier with stepwise feature selection was designed using a second simplex optimization to select the most effective features. Leave-one-case-out resampling was used to train and test the CAD system. The system achieved a test area under the receiver operating characteristic curve (Az) of 0.83±0.04. Our preliminary results indicate that use of the 3D AC model and the 3D texture features surrounding the nodule is a promising approach to the segmentation and classification of lung nodules with CAD. The segmentation performance of the 3D AC model trained with our data set was evaluated with 23 nodules available in the Lung Image Database Consortium (LIDC). The lung nodule volumes segmented by the 3D AC

  17. Generating 3D anatomically detailed models of the retina from OCT data sets: implications for computational modelling

    NASA Astrophysics Data System (ADS)

    Shalbaf, Farzaneh; Dokos, Socrates; Lovell, Nigel H.; Turuwhenua, Jason; Vaghefi, Ehsan

    2015-12-01

    Retinal prosthesis has been proposed to restore vision for those suffering from the retinal pathologies that mainly affect the photoreceptors layer but keep the inner retina intact. Prior to costly risky experimental studies computational modelling of the retina will help to optimize the device parameters and enhance the outcomes. Here, we developed an anatomically detailed computational model of the retina based on OCT data sets. The consecutive OCT images of individual were subsequently segmented to provide a 3D representation of retina in the form of finite elements. Thereafter, the electrical properties of the retina were modelled by implementing partial differential equation on the 3D mesh. Different electrode configurations, that is bipolar and hexapolar configurations, were implemented and the results were compared with the previous computational and experimental studies. Furthermore, the possible effects of the curvature of retinal layers on the current steering through the retina were proposed and linked to the clinical observations.

  18. A review of computer-aided body surface area determination: SAGE II and EPRI's 3D Burn Vision.

    PubMed

    Neuwalder, J M; Sampson, C; Breuing, K H; Orgill, D P

    2002-01-01

    Estimates of percent body surface area (%BSA) burns correlate well with fluid needs, nutritional requirements, and prognosis. Most burn centers rely on the Lund Browder chart and "rule of nines," to calculate the %BSA. Computer-based methods may improve precision and data analysis. We studied two new methods of determining %BSA: a two-dimensional Web-based program (Sage II) and a three-dimensional computer-aided design program (EPRI 3D Burn Vision). Members of our burn team found the Sage II program easy to use and found many of the features useful for patient care. The EPRI program has the advantage of 3D images and different body morphologies but required training to use. Computer-aided methods offer the potential for improved precision and data analysis of %BSA measurements.

  19. Technical Note: Guidelines for the digital computation of 2D and 3D enamel thickness in hominoid teeth.

    PubMed

    Benazzi, Stefano; Panetta, Daniele; Fornai, Cinzia; Toussaint, Michel; Gruppioni, Giorgio; Hublin, Jean-Jacques

    2014-02-01

    The study of enamel thickness has received considerable attention in regard to the taxonomic, phylogenetic and dietary assessment of human and non-human primates. Recent developments based on two-dimensional (2D) and three-dimensional (3D) digital techniques have facilitated accurate analyses, preserving the original object from invasive procedures. Various digital protocols have been proposed. These include several procedures based on manual handling of the virtual models and technical shortcomings, which prevent other scholars from confidently reproducing the entire digital protocol. There is a compelling need for standard, reproducible, and well-tailored protocols for the digital analysis of 2D and 3D dental enamel thickness. In this contribution we provide essential guidelines for the digital computation of 2D and 3D enamel thickness in hominoid molars, premolars, canines and incisors. We modify previous techniques suggested for 2D analysis and we develop a new approach for 3D analysis that can also be applied to premolars and anterior teeth. For each tooth class, the cervical line should be considered as the fundamental morphological feature both to isolate the crown from the root (for 3D analysis) and to define the direction of the cross-sections (for 2D analysis).

  20. A computational model that recovers the 3D shape of an object from a single 2D retinal representation.

    PubMed

    Li, Yunfeng; Pizlo, Zygmunt; Steinman, Robert M

    2009-05-01

    Human beings perceive 3D shapes veridically, but the underlying mechanisms remain unknown. The problem of producing veridical shape percepts is computationally difficult because the 3D shapes have to be recovered from 2D retinal images. This paper describes a new model, based on a regularization approach, that does this very well. It uses a new simplicity principle composed of four shape constraints: viz., symmetry, planarity, maximum compactness and minimum surface. Maximum compactness and minimum surface have never been used before. The model was tested with random symmetrical polyhedra. It recovered their 3D shapes from a single randomly-chosen 2D image. Neither learning, nor depth perception, was required. The effectiveness of the maximum compactness and the minimum surface constraints were measured by how well the aspect ratio of the 3D shapes was recovered. These constraints were effective; they recovered the aspect ratio of the 3D shapes very well. Aspect ratios recovered by the model were compared to aspect ratios adjusted by four human observers. They also adjusted aspect ratios very well. In those rare cases, in which the human observers showed large errors in adjusted aspect ratios, their errors were very similar to the errors made by the model. PMID:18621410

  1. Computer-aided multiple-head 3D printing system for printing of heterogeneous organ/tissue constructs

    NASA Astrophysics Data System (ADS)

    Jung, Jin Woo; Lee, Jung-Seob; Cho, Dong-Woo

    2016-02-01

    Recently, much attention has focused on replacement or/and enhancement of biological tissues via the use of cell-laden hydrogel scaffolds with an architecture that mimics the tissue matrix, and with the desired three-dimensional (3D) external geometry. However, mimicking the heterogeneous tissues that most organs and tissues are formed of is challenging. Although multiple-head 3D printing systems have been proposed for fabricating heterogeneous cell-laden hydrogel scaffolds, to date only the simple exterior form has been realized. Here we describe a computer-aided design and manufacturing (CAD/CAM) system for this application. We aim to develop an algorithm to enable easy, intuitive design and fabrication of a heterogeneous cell-laden hydrogel scaffolds with a free-form 3D geometry. The printing paths of the scaffold are automatically generated from the 3D CAD model, and the scaffold is then printed by dispensing four materials; i.e., a frame, two kinds of cell-laden hydrogel and a support. We demonstrated printing of heterogeneous tissue models formed of hydrogel scaffolds using this approach, including the outer ear, kidney and tooth tissue. These results indicate that this approach is particularly promising for tissue engineering and 3D printing applications to regenerate heterogeneous organs and tissues with tailored geometries to treat specific defects or injuries.

  2. 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.

  3. Computer-aided multiple-head 3D printing system for printing of heterogeneous organ/tissue constructs.

    PubMed

    Jung, Jin Woo; Lee, Jung-Seob; Cho, Dong-Woo

    2016-01-01

    Recently, much attention has focused on replacement or/and enhancement of biological tissues via the use of cell-laden hydrogel scaffolds with an architecture that mimics the tissue matrix, and with the desired three-dimensional (3D) external geometry. However, mimicking the heterogeneous tissues that most organs and tissues are formed of is challenging. Although multiple-head 3D printing systems have been proposed for fabricating heterogeneous cell-laden hydrogel scaffolds, to date only the simple exterior form has been realized. Here we describe a computer-aided design and manufacturing (CAD/CAM) system for this application. We aim to develop an algorithm to enable easy, intuitive design and fabrication of a heterogeneous cell-laden hydrogel scaffolds with a free-form 3D geometry. The printing paths of the scaffold are automatically generated from the 3D CAD model, and the scaffold is then printed by dispensing four materials; i.e., a frame, two kinds of cell-laden hydrogel and a support. We demonstrated printing of heterogeneous tissue models formed of hydrogel scaffolds using this approach, including the outer ear, kidney and tooth tissue. These results indicate that this approach is particularly promising for tissue engineering and 3D printing applications to regenerate heterogeneous organs and tissues with tailored geometries to treat specific defects or injuries. PMID:26899876

  4. Computer-aided multiple-head 3D printing system for printing of heterogeneous organ/tissue constructs

    PubMed Central

    Jung, Jin Woo; Lee, Jung-Seob; Cho, Dong-Woo

    2016-01-01

    Recently, much attention has focused on replacement or/and enhancement of biological tissues via the use of cell-laden hydrogel scaffolds with an architecture that mimics the tissue matrix, and with the desired three-dimensional (3D) external geometry. However, mimicking the heterogeneous tissues that most organs and tissues are formed of is challenging. Although multiple-head 3D printing systems have been proposed for fabricating heterogeneous cell-laden hydrogel scaffolds, to date only the simple exterior form has been realized. Here we describe a computer-aided design and manufacturing (CAD/CAM) system for this application. We aim to develop an algorithm to enable easy, intuitive design and fabrication of a heterogeneous cell-laden hydrogel scaffolds with a free-form 3D geometry. The printing paths of the scaffold are automatically generated from the 3D CAD model, and the scaffold is then printed by dispensing four materials; i.e., a frame, two kinds of cell-laden hydrogel and a support. We demonstrated printing of heterogeneous tissue models formed of hydrogel scaffolds using this approach, including the outer ear, kidney and tooth tissue. These results indicate that this approach is particularly promising for tissue engineering and 3D printing applications to regenerate heterogeneous organs and tissues with tailored geometries to treat specific defects or injuries. PMID:26899876

  5. Computer-aided multiple-head 3D printing system for printing of heterogeneous organ/tissue constructs.

    PubMed

    Jung, Jin Woo; Lee, Jung-Seob; Cho, Dong-Woo

    2016-02-22

    Recently, much attention has focused on replacement or/and enhancement of biological tissues via the use of cell-laden hydrogel scaffolds with an architecture that mimics the tissue matrix, and with the desired three-dimensional (3D) external geometry. However, mimicking the heterogeneous tissues that most organs and tissues are formed of is challenging. Although multiple-head 3D printing systems have been proposed for fabricating heterogeneous cell-laden hydrogel scaffolds, to date only the simple exterior form has been realized. Here we describe a computer-aided design and manufacturing (CAD/CAM) system for this application. We aim to develop an algorithm to enable easy, intuitive design and fabrication of a heterogeneous cell-laden hydrogel scaffolds with a free-form 3D geometry. The printing paths of the scaffold are automatically generated from the 3D CAD model, and the scaffold is then printed by dispensing four materials; i.e., a frame, two kinds of cell-laden hydrogel and a support. We demonstrated printing of heterogeneous tissue models formed of hydrogel scaffolds using this approach, including the outer ear, kidney and tooth tissue. These results indicate that this approach is particularly promising for tissue engineering and 3D printing applications to regenerate heterogeneous organs and tissues with tailored geometries to treat specific defects or injuries.

  6. 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.

  7. Computer animations stimulate contagious yawning in chimpanzees

    PubMed Central

    Campbell, Matthew W.; Carter, J. Devyn; Proctor, Darby; Eisenberg, Michelle L.; de Waal, Frans B. M.

    2009-01-01

    People empathize with fictional displays of behaviour, including those of cartoons and computer animations, even though the stimuli are obviously artificial. However, the extent to which other animals also may respond empathetically to animations has yet to be determined. Animations provide a potentially useful tool for exploring non-human behaviour, cognition and empathy because computer-generated stimuli offer complete control over variables and the ability to program stimuli that could not be captured on video. Establishing computer animations as a viable tool requires that non-human subjects identify with and respond to animations in a way similar to the way they do to images of actual conspecifics. Contagious yawning has been linked to empathy and poses a good test of involuntary identification and motor mimicry. We presented 24 chimpanzees with three-dimensional computer-animated chimpanzees yawning or displaying control mouth movements. The apes yawned significantly more in response to the yawn animations than to the controls, implying identification with the animations. These results support the phenomenon of contagious yawning in chimpanzees and suggest an empathic response to animations. Understanding how chimpanzees connect with animations, to both empathize and imitate, may help us to understand how humans do the same. PMID:19740888

  8. Computer-aided diagnosis for osteoporosis using chest 3D CT images

    NASA Astrophysics Data System (ADS)

    Yoneda, K.; Matsuhiro, M.; Suzuki, H.; Kawata, Y.; Niki, N.; Nakano, Y.; Ohmatsu, H.; Kusumoto, M.; Tsuchida, T.; Eguchi, K.; Kaneko, M.

    2016-03-01

    The patients of osteoporosis comprised of about 13 million people in Japan and it is one of the problems the aging society has. In order to prevent the osteoporosis, it is necessary to do early detection and treatment. Multi-slice CT technology has been improving the three dimensional (3-D) image analysis with higher body axis resolution and shorter scan time. The 3-D image analysis using multi-slice CT images of thoracic vertebra can be used as a support to diagnose osteoporosis and at the same time can be used for lung cancer diagnosis which may lead to early detection. We develop automatic extraction and partitioning algorithm for spinal column by analyzing vertebral body structure, and the analysis algorithm of the vertebral body using shape analysis and a bone density measurement for the diagnosis of osteoporosis. Osteoporosis diagnosis support system obtained high extraction rate of the thoracic vertebral in both normal and low doses.

  9. A Pipeline for 3D Multimodality Image Integration and Computer-assisted Planning in Epilepsy Surgery.

    PubMed

    Nowell, Mark; Rodionov, Roman; Zombori, Gergely; Sparks, Rachel; Rizzi, Michele; Ourselin, Sebastien; Miserocchi, Anna; McEvoy, Andrew; Duncan, John

    2016-01-01

    Epilepsy surgery is challenging and the use of 3D multimodality image integration (3DMMI) to aid presurgical planning is well-established. Multimodality image integration can be technically demanding, and is underutilised in clinical practice. We have developed a single software platform for image integration, 3D visualization and surgical planning. Here, our pipeline is described in step-by-step fashion, starting with image acquisition, proceeding through image co-registration, manual segmentation, brain and vessel extraction, 3D visualization and manual planning of stereoEEG (SEEG) implantations. With dissemination of the software this pipeline can be reproduced in other centres, allowing other groups to benefit from 3DMMI. We also describe the use of an automated, multi-trajectory planner to generate stereoEEG implantation plans. Preliminary studies suggest this is a rapid, safe and efficacious adjunct for planning SEEG implantations. Finally, a simple solution for the export of plans and models to commercial neuronavigation systems for implementation of plans in the operating theater is described. This software is a valuable tool that can support clinical decision making throughout the epilepsy surgery pathway.

  10. A Pipeline for 3D Multimodality Image Integration and Computer-assisted Planning in Epilepsy Surgery.

    PubMed

    Nowell, Mark; Rodionov, Roman; Zombori, Gergely; Sparks, Rachel; Rizzi, Michele; Ourselin, Sebastien; Miserocchi, Anna; McEvoy, Andrew; Duncan, John

    2016-01-01

    Epilepsy surgery is challenging and the use of 3D multimodality image integration (3DMMI) to aid presurgical planning is well-established. Multimodality image integration can be technically demanding, and is underutilised in clinical practice. We have developed a single software platform for image integration, 3D visualization and surgical planning. Here, our pipeline is described in step-by-step fashion, starting with image acquisition, proceeding through image co-registration, manual segmentation, brain and vessel extraction, 3D visualization and manual planning of stereoEEG (SEEG) implantations. With dissemination of the software this pipeline can be reproduced in other centres, allowing other groups to benefit from 3DMMI. We also describe the use of an automated, multi-trajectory planner to generate stereoEEG implantation plans. Preliminary studies suggest this is a rapid, safe and efficacious adjunct for planning SEEG implantations. Finally, a simple solution for the export of plans and models to commercial neuronavigation systems for implementation of plans in the operating theater is described. This software is a valuable tool that can support clinical decision making throughout the epilepsy surgery pathway. PMID:27286266

  11. A Pipeline for 3D Multimodality Image Integration and Computer-assisted Planning in Epilepsy Surgery

    PubMed Central

    Nowell, Mark; Rodionov, Roman; Zombori, Gergely; Sparks, Rachel; Rizzi, Michele; Ourselin, Sebastien; Miserocchi, Anna; McEvoy, Andrew; Duncan, John

    2016-01-01

    Epilepsy surgery is challenging and the use of 3D multimodality image integration (3DMMI) to aid presurgical planning is well-established. Multimodality image integration can be technically demanding, and is underutilised in clinical practice. We have developed a single software platform for image integration, 3D visualization and surgical planning. Here, our pipeline is described in step-by-step fashion, starting with image acquisition, proceeding through image co-registration, manual segmentation, brain and vessel extraction, 3D visualization and manual planning of stereoEEG (SEEG) implantations. With dissemination of the software this pipeline can be reproduced in other centres, allowing other groups to benefit from 3DMMI. We also describe the use of an automated, multi-trajectory planner to generate stereoEEG implantation plans. Preliminary studies suggest this is a rapid, safe and efficacious adjunct for planning SEEG implantations. Finally, a simple solution for the export of plans and models to commercial neuronavigation systems for implementation of plans in the operating theater is described. This software is a valuable tool that can support clinical decision making throughout the epilepsy surgery pathway. PMID:27286266

  12. Computational Identification of Genomic Features That Influence 3D Chromatin Domain Formation

    PubMed Central

    Mourad, Raphaël; Cuvier, Olivier

    2016-01-01

    Recent advances in long-range Hi-C contact mapping have revealed the importance of the 3D structure of chromosomes in gene expression. A current challenge is to identify the key molecular drivers of this 3D structure. Several genomic features, such as architectural proteins and functional elements, were shown to be enriched at topological domain borders using classical enrichment tests. Here we propose multiple logistic regression to identify those genomic features that positively or negatively influence domain border establishment or maintenance. The model is flexible, and can account for statistical interactions among multiple genomic features. Using both simulated and real data, we show that our model outperforms enrichment test and non-parametric models, such as random forests, for the identification of genomic features that influence domain borders. Using Drosophila Hi-C data at a very high resolution of 1 kb, our model suggests that, among architectural proteins, BEAF-32 and CP190 are the main positive drivers of 3D domain borders. In humans, our model identifies well-known architectural proteins CTCF and cohesin, as well as ZNF143 and Polycomb group proteins as positive drivers of domain borders. The model also reveals the existence of several negative drivers that counteract the presence of domain borders including P300, RXRA, BCL11A and ELK1. PMID:27203237

  13. Ligand mapping on protein surfaces by the 3D-RISM theory: toward computational fragment-based drug design.

    PubMed

    Imai, Takashi; Oda, Koji; Kovalenko, Andriy; Hirata, Fumio; Kidera, Akinori

    2009-09-01

    In line with the recent development of fragment-based drug design, a new computational method for mapping of small ligand molecules on protein surfaces is proposed. The method uses three-dimensional (3D) spatial distribution functions of the atomic sites of the ligand calculated using the molecular theory of solvation, known as the 3D reference interaction site model (3D-RISM) theory, to identify the most probable binding modes of ligand molecules. The 3D-RISM-based method is applied to the binding of several small organic molecules to thermolysin, in order to show its efficiency and accuracy in detecting binding sites. The results demonstrate that our method can reproduce the major binding modes found by X-ray crystallographic studies with sufficient precision. Moreover, the method can successfully identify some binding modes associated with a known inhibitor, which could not be detected by X-ray analysis. The dependence of ligand-binding modes on the ligand concentration, which essentially cannot be treated with other existing computational methods, is also investigated. The results indicate that some binding modes are readily affected by the ligand concentration, whereas others are not significantly altered. In the former case, it is the subtle balance in the binding affinity between the ligand and water that determines the dominant ligand-binding mode.

  14. Validation of a 3D computational fluid-structure interaction model simulating flow through an elastic aperture

    PubMed Central

    Quaini, A.; Canic, S.; Glowinski, R.; Igo, S.; Hartley, C.J.; Zoghbi, W.; Little, S.

    2011-01-01

    This work presents a validation of a fluid-structure interaction computational model simulating the flow conditions in an in vitro mock heart chamber modeling mitral valve regurgitation during the ejection phase during which the trans-valvular pressure drop and valve displacement are not as large. The mock heart chamber was developed to study the use of 2D and 3D color Doppler techniques in imaging the clinically relevant complex intra-cardiac flow events associated with mitral regurgitation. Computational models are expected to play an important role in supporting, refining, and reinforcing the emerging 3D echocardiographic applications. We have developed a 3D computational fluid-structure interaction algorithm based on a semi-implicit, monolithic method, combined with an arbitrary Lagrangian-Eulerian approach to capture the fluid domain motion. The mock regurgitant mitral valve corresponding to an elastic plate with a geometric orifice, was modeled using 3D elasticity, while the blood flow was modeled using the 3D Navier-Stokes equations for an incompressible, viscous fluid. The two are coupled via the kinematic and dynamic conditions describing the two-way coupling. The pressure, the flow rate, and orifice plate displacement were measured and compared with numerical simulation results. In-line flow meter was used to measure the flow, pressure transducers were used to measure the pressure, and a Doppler method developed by one of the authors was used to measure the axial displacement of the orifice plate. The maximum recorded difference between experiment and numerical simulation for the flow rate was 4%, the pressure 3.6%, and for the orifice displacement 15%, showing excellent agreement between the two. PMID:22138194

  15. Computer-aided segmentation and 3D analysis of in vivo MRI examinations of the human vocal tract during phonation

    NASA Astrophysics Data System (ADS)

    Wismüller, Axel; Behrends, Johannes; Hoole, Phil; Leinsinger, Gerda L.; Meyer-Baese, Anke; Reiser, Maximilian F.

    2008-03-01

    We developed, tested, and evaluated a 3D segmentation and analysis system for in vivo MRI examinations of the human vocal tract during phonation. For this purpose, six professionally trained speakers, age 22-34y, were examined using a standardized MRI protocol (1.5 T, T1w FLASH, ST 4mm, 23 slices, acq. time 21s). The volunteers performed a prolonged (>=21s) emission of sounds of the German phonemic inventory. Simultaneous audio tape recording was obtained to control correct utterance. Scans were made in axial, coronal, and sagittal planes each. Computer-aided quantitative 3D evaluation included (i) automated registration of the phoneme-specific data acquired in different slice orientations, (ii) semi-automated segmentation of oropharyngeal structures, (iii) computation of a curvilinear vocal tract midline in 3D by nonlinear PCA, (iv) computation of cross-sectional areas of the vocal tract perpendicular to this midline. For the vowels /a/,/e/,/i/,/o/,/ø/,/u/,/y/, the extracted area functions were used to synthesize phoneme sounds based on an articulatory-acoustic model. For quantitative analysis, recorded and synthesized phonemes were compared, where area functions extracted from 2D midsagittal slices were used as a reference. All vowels could be identified correctly based on the synthesized phoneme sounds. The comparison between synthesized and recorded vowel phonemes revealed that the quality of phoneme sound synthesis was improved for phonemes /a/ and /y/, if 3D instead of 2D data were used, as measured by the average relative frequency shift between recorded and synthesized vowel formants (p<0.05, one-sided Wilcoxon rank sum test). In summary, the combination of fast MRI followed by subsequent 3D segmentation and analysis is a novel approach to examine human phonation in vivo. It unveils functional anatomical findings that may be essential for realistic modelling of the human vocal tract during speech production.

  16. Analysis of cardiac development in the turtle Emys orbicularis (Testudines: Emidydae) using 3-D computer modeling from histological sections.

    PubMed

    Bertens, Laura M F; Richardson, M K; Verbeek, F J

    2010-07-01

    In this article we present a 3-D modeling study of cardiac development in the European pond turtle, Emys orbicularis (of the reptilian order Testudines). The study is aimed at elucidating the embryonic development of the horizontal septum in the ventricle and underscoring the importance of 3-D reconstructions in studying morphogenesis. Turtles possess one common ventricle, partly divided into three cava by a vertical and a horizontal septum, of which the embryonic origins have so far not been described. We used serial sectioning and computerized high-resolution 3-D reconstructions of different developmental stages to create a chronological overview of cardiogenesis, in order to study this process. This has yielded a new understanding of the development of the horizontal septum and (directly related) the looping of the heart tube. This looping is found to be markedly different from that in the human heart, with the turtle having two clear bends in the part of the heart tube leaving the primitive ventricle, as opposed to one in humans. It is this particular looping that is responsible for the formation of the horizontal septum. In addition to our findings on the ventricular septation this study has also yielded new insights into the developmental origins of the pulmonary vein. The 3-D reconstructions were built using our platform TDR-3-D base and enabled us to study the developmental processes in specific parts of the turtle heart separately and in three dimensions, over time. The complete 3-D reconstructions have been made available to the reader via internet using our 3-D model browser application, which allows interactive viewing of the models. The browser application can be found on bio-imaging.liacs.nl/galleries/emysorbicularis/TurtleGallery.html, along with additional images of both models and histological sections and animation sequences of the models. By allowing the reader to view the material in such an interactive way, we hope to make optimal use of the

  17. An interactive 3D visualization and manipulation tool for effective assessment of angiogenesis and arteriogenesis using computed tomographic angiography

    NASA Astrophysics Data System (ADS)

    Shen, Li; Gao, Ling; Zhuang, Zhenwu; DeMuinck, Ebo; Huang, Heng; Makedon, Fillia; Pearlman, Justin

    2005-04-01

    This paper presents IVM, an Interactive Vessel Manipulation tool that can help make effective and efficient assessment of angiogenesis and arteriogenesis in computed tomographic angiography (CTA) studies. IVM consists of three fundamental components: (1) a visualization component, (2) a tracing component, and (3) a measurement component. Given a user-specified threshold, IVM can create a 3D surface visualization based on it. Since vessels are thin and tubular structures, using standard isosurface extraction techniques usually cannot yield satisfactory reconstructions. Instead, IVM directly renders the surface of a derived binary 3D image. The image volumes collected in CTA studies often have a relatively high resolution. Thus, compared with more complicated vessel extraction and visualization techniques, rendering the binary image surface has the advantages of being effective, simple and fast. IVM employs a semi-automatic approach to determine the threshold: a user can adjust the threshold by checking the corresponding 3D surface reconstruction and make the choice. Typical tracing software often defines ROIs on 3D image volumes using three orthogonal views. The tracing component in IVM takes one step further: it can perform tracing not only on image slices but also in a 3D view. We observe that directly operating on a 3D view can help a tracer identify ROIs more easily. After setting a threshold and tracing an ROI, a user can use IVM's measurement component to estimate the volume and other parameters of vessels in the ROI. The effectiveness of the IVM tool is demonstrated on rat vessel/bone images collected in a previous CTA study.

  18. Isoparametric 3-D Finite Element Mesh Generation Using Interactive Computer Graphics

    NASA Technical Reports Server (NTRS)

    Kayrak, C.; Ozsoy, T.

    1985-01-01

    An isoparametric 3-D finite element mesh generator was developed with direct interface to an interactive geometric modeler program called POLYGON. POLYGON defines the model geometry in terms of boundaries and mesh regions for the mesh generator. The mesh generator controls the mesh flow through the 2-dimensional spans of regions by using the topological data and defines the connectivity between regions. The program is menu driven and the user has a control of element density and biasing through the spans and can also apply boundary conditions, loads interactively.

  19. 3D-computation of a thermal process in a superconducting coil

    SciTech Connect

    Netter, D.; Leveque, J.; Rezzoug, A.; Caron, J.P.; Sargos, F.M.

    1995-11-01

    This study deals with the resistive zone propagation in a superconducting coil during a quench, taking into account both the flux density distribution and the anisotropy of the thermal parameters. A Finite Difference Method is used to solve the heat diffusion equation and the flux density is calculated by means of a semi-analytical method. The 3-D model is suitable to describe the quench of thick coils and it can be applied to the study of thermal stability. As an application, a 10 kJ-solenoid is studied.

  20. Implementation of Headtracking and 3D Stereo with Unity and VRPN for Computer Simulations

    NASA Technical Reports Server (NTRS)

    Noyes, Matthew A.

    2013-01-01

    This paper explores low-cost hardware and software methods to provide depth cues traditionally absent in monocular displays. The use of a VRPN server in conjunction with a Microsoft Kinect and/or Nintendo Wiimote to provide head tracking information to a Unity application, and NVIDIA 3D Vision for retinal disparity support, is discussed. Methods are suggested to implement this technology with NASA's EDGE simulation graphics package, along with potential caveats. Finally, future applications of this technology to astronaut crew training, particularly when combined with an omnidirectional treadmill for virtual locomotion and NASA's ARGOS system for reduced gravity simulation, are discussed.

  1. Scanning transmission and computer-aided volumic electron microscopy: 3-D modeling of entire cells by electronic imaging

    NASA Astrophysics Data System (ADS)

    Bron, Christophe; Gremillet, Philip; Launay, D.; Jourlin, Michel; Gautschi, H. P.; Baechi, Thomas; Schuepbach, Joerg

    1990-05-01

    The digital processing of electron microscopic images from serial sections containing laser-induced topographical references allows a 3-D reconstruction at a depth resolution of 30 to 40 nm of entire cells by the use of image analysis methods, as already demonstrated for Transmission Electron Microscopy (TEM) coupled with a video camera. We decided to use a Scanning Transmission Electron Microscope (STEM) to get higher contrast and better resolution at medium magnification. The scanning of our specimens at video frequencies is an attractive and easy way to link a STEM with an image processing system but the hysteresis of the electronic spools responsible for the magnetic deviation of the scanning electron beam induces deformations of images which have to be modelized and corrected before registration. Computer algorithms developed for image analysis and treatment correct the artifacts caused by the use of STEM and by serial sectioning to automatically reconstruct the third dimension of the cells. They permit the normalization of the images through logarithmic processing of the original grey level infonnation. The automatic extraction of cell limits allows to link the image analysis and treatments with image synthesis methods by minimal human intervention. The surface representation and the registered images provide an ultrastructural data base from which quantitative 3-D morphological parameters, as well as otherwise impossible visualizations, can be computed. This 3-D image processing named C.A.V.U.M. for Computer Aided Volumic Ultra-Microscopy offers a new tool for the documentation and analysis of cell ultrastructure and for 3-D morphometric studies at EM magnifications. Further, a virtual observer can be computed in such a way as to simulate a visit of the reconstructed object.

  2. Computing and monitoring potential of public spaces by shading analysis using 3d lidar data and advanced image analysis

    NASA Astrophysics Data System (ADS)

    Zwolinski, A.; Jarzemski, M.

    2015-04-01

    The paper regards specific context of public spaces in "shadow" of tall buildings located in European cities. Majority of tall buildings in European cities were built in last 15 years. Tall buildings appear mainly in city centres, directly at important public spaces being viable environment for inhabitants with variety of public functions (open spaces, green areas, recreation places, shops, services etc.). All these amenities and services are under direct impact of extensive shading coming from the tall buildings. The paper focuses on analyses and representation of impact of shading from tall buildings on various public spaces in cities using 3D city models. Computer environment of 3D city models in cityGML standard uses 3D LiDAR data as one of data types for definition of 3D cities. The structure of cityGML allows analytic applications using existing computer tools, as well as developing new techniques to estimate extent of shading coming from high-risers, affecting life in public spaces. These measurable shading parameters in specific time are crucial for proper functioning, viability and attractiveness of public spaces - finally it is extremely important for location of tall buildings at main public spaces in cities. The paper explores impact of shading from tall buildings in different spatial contexts on the background of using cityGML models based on core LIDAR data to support controlled urban development in sense of viable public spaces. The article is prepared within research project 2TaLL: Application of 3D Virtual City Models in Urban Analyses of Tall Buildings, realized as a part of Polish-Norway Grants.

  3. Novel low-cost 2D/3D switchable autostereoscopic system for notebook computers and other portable devices

    NASA Astrophysics Data System (ADS)

    Eichenlaub, Jesse B.

    1995-03-01

    Mounting a lenticular lens in front of a flat panel display is a well known, inexpensive, and easy way to create an autostereoscopic system. Such a lens produces half resolution 3D images because half the pixels on the LCD are seen by the left eye and half by the right eye. This may be acceptable for graphics, but it makes full resolution text, as displayed by common software, nearly unreadable. Very fine alignment tolerances normally preclude the possibility of removing and replacing the lens in order to switch between 2D and 3D applications. Lenticular lens based displays are therefore limited to use as dedicated 3D devices. DTI has devised a technique which removes this limitation, allowing switching between full resolution 2D and half resolution 3D imaging modes. A second element, in the form of a concave lenticular lens array whose shape is exactly the negative of the first lens, is mounted on a hinge so that it can be swung down over the first lens array. When so positioned the two lenses cancel optically, allowing the user to see full resolution 2D for text or numerical applications. The two lenses, having complementary shapes, naturally tend to nestle together and snap into perfect alignment when pressed together--thus obviating any need for user operated alignment mechanisms. This system represents an ideal solution for laptop and notebook computer applications. It was devised to meet the stringent requirements of a laptop computer manufacturer including very compact size, very low cost, little impact on existing manufacturing or assembly procedures, and compatibility with existing full resolution 2D text- oriented software as well as 3D graphics. Similar requirements apply to high and electronic calculators, several models of which now use LCDs for the display of graphics.

  4. 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.

  5. FastScript3D - A Companion to Java 3D

    NASA Technical Reports Server (NTRS)

    Koenig, Patti

    2005-01-01

    FastScript3D is a computer program, written in the Java 3D(TM) programming language, that establishes an alternative language that helps users who lack expertise in Java 3D to use Java 3D for constructing three-dimensional (3D)-appearing graphics. The FastScript3D language provides a set of simple, intuitive, one-line text-string commands for creating, controlling, and animating 3D models. The first word in a string is the name of a command; the rest of the string contains the data arguments for the command. The commands can also be used as an aid to learning Java 3D. Developers can extend the language by adding custom text-string commands. The commands can define new 3D objects or load representations of 3D objects from files in formats compatible with such other software systems as X3D. The text strings can be easily integrated into other languages. FastScript3D facilitates communication between scripting languages [which enable programming of hyper-text markup language (HTML) documents to interact with users] and Java 3D. The FastScript3D language can be extended and customized on both the scripting side and the Java 3D side.

  6. 3D Quantification of Mandibular Asymmetry through Cone Beam Computed Tomography

    PubMed Central

    Cevidanes, Lucia H.S.; Alhadidi, Abeer; Paniagua, Beatriz; Styner, Martin; Ludlow, John; Mol, Andre; Turvey, Timothy; Proffit, William R.; Rossouw, Paul Emile

    2011-01-01

    Objective To determine if 3D shape analysis precisely diagnoses right and left differences in asymmetry patients Study Design Cone-beam CT data was acquired pretreatment from 20 patients with mandibular asymmetry. 3D shape analysis was used to localize and quantify the extent of virtually simulated asymmetry. Two approaches were used: (1) mirroring on the midsagittal plane determined from landmarks and (2) mirroring on an arbitrary plane, then registering on the cranial base of the original image. The validation presented in this study used simulated data and has been applied to three clinical cases. Results For mirroring on the midsagittal plane there was a >99% probability that the difference between measured and simulated asymmetry was less than 0.5 mm. For mirroring with cranial base registration, there was a >84% probability of differences less than 0.5 mm. Conclusions Mandibular asymmetry can be precisely quantified with both mirroring methods. Cranial base registration has the potential to be used for patients with trauma situations or when key landmarks are unreliable or absent. PMID:21497527

  7. Fabrication of computationally designed scaffolds by low temperature 3D printing.

    PubMed

    Castilho, Miguel; Dias, Marta; Gbureck, Uwe; Groll, Jürgen; Fernandes, Paulo; Pires, Inês; Gouveia, Barbara; Rodrigues, Jorge; Vorndran, Elke

    2013-09-01

    The development of artificial bone substitutes that mimic the properties of bone and simultaneously promote the desired tissue regeneration is a current issue in bone tissue engineering research. An approach to create scaffolds with such characteristics is based on the combination of novel design and additive manufacturing processes. The objective of this work is to characterize the microstructural and the mechanical properties of scaffolds developed by coupling both topology optimization and a low temperature 3D printing process. The scaffold design was obtained using a topology optimization approach to maximize the permeability with constraints on the mechanical properties. This procedure was studied to be suitable for the fabrication of a cage prototype for tibial tuberosity advancement application, which is one of the most recent and promising techniques to treat cruciate ligament rupture in dogs. The microstructural and mechanical properties of the scaffolds manufactured by reacting α/β-tricalcium phosphate with diluted phosphoric acid were then assessed experimentally and the scaffolds strength reliability was determined. The results demonstrate that the low temperature 3D printing process is a reliable option to create synthetic scaffolds with tailored properties, and when coupled with topology optimization design it can be a powerful tool for the fabrication of patient-specific bone implants. PMID:23887064

  8. Computation of elastic properties of 3D digital cores from the Longmaxi shale

    NASA Astrophysics Data System (ADS)

    Zhang, Wen-Hui; Fu, Li-Yun; Zhang, Yan; Jin, Wei-Jun

    2016-06-01

    The dependence of elastic moduli of shales on the mineralogy and microstructure of shales is important for the prediction of sweet spots and shale gas production. Based on 3D digital images of the microstructure of Longmaxi black shale samples using X-ray CT, we built detailed 3D digital images of cores with porosity properties and mineral contents. Next, we used finite-element (FE) methods to derive the elastic properties of the samples. The FE method can accurately model the shale mineralogy. Particular attention is paid to the derived elastic properties and their dependence on porosity and kerogen. The elastic moduli generally decrease with increasing porosity and kerogen, and there is a critical porosity (0.75) and kerogen content (ca. ≤3%) over which the elastic moduli decrease rapidly and slowly, respectively. The derived elastic moduli of gas- and oil-saturated digital cores differ little probably because of the low porosity (4.5%) of the Longmaxi black shale. Clearly, the numerical experiments demonstrated the feasibility of combining microstructure images of shale samples with elastic moduli calculations to predict shale properties.

  9. Modeling and Analysis of a Lunar Space Reactor with the Computer Code RELAP5-3D/ATHENA

    SciTech Connect

    Carbajo, Juan J; Qualls, A L

    2008-01-01

    The transient analysis 3-dimensional (3-D) computer code RELAP5-3D/ATHENA has been employed to model and analyze a space reactor of 180 kW(thermal), 40 kW (net, electrical) with eight Stirling engines (SEs). Each SE will generate over 6 kWe; the excess power will be needed for the pumps and other power management devices. The reactor will be cooled by NaK (a eutectic mixture of sodium and potassium which is liquid at ambient temperature). This space reactor is intended to be deployed over the surface of the Moon or Mars. The reactor operating life will be 8 to 10 years. The RELAP5-3D/ATHENA code is being developed and maintained by Idaho National Laboratory. The code can employ a variety of coolants in addition to water, the original coolant employed with early versions of the code. The code can also use 3-D volumes and 3-D junctions, thus allowing for more realistic representation of complex geometries. A combination of 3-D and 1-D volumes is employed in this study. The space reactor model consists of a primary loop and two secondary loops connected by two heat exchangers (HXs). Each secondary loop provides heat to four SEs. The primary loop includes the nuclear reactor with the lower and upper plena, the core with 85 fuel pins, and two vertical heat exchangers (HX). The maximum coolant temperature of the primary loop is 900 K. The secondary loops also employ NaK as a coolant at a maximum temperature of 877 K. The SEs heads are at a temperature of 800 K and the cold sinks are at a temperature of ~400 K. Two radiators will be employed to remove heat from the SEs. The SE HXs surrounding the SE heads are of annular design and have been modeled using 3-D volumes. These 3-D models have been used to improve the HX design by optimizing the flows of coolant and maximizing the heat transferred to the SE heads. The transients analyzed include failure of one or more Stirling engines, trip of the reactor pump, and trips of the secondary loop pumps feeding the HXs of the

  10. Improved Algorithms and Methods for Solving Strongly Variable-Viscosity 3D Stokes flow and Strongly Variable Permeability 3D D’Arcy flow on a Parallel Computer

    NASA Astrophysics Data System (ADS)

    Morgan, J. P.; Hasenclever, J.; Shi, C.

    2009-12-01

    Computational studies of mantle convection face large challenges to obtain fast and accurate solutions for variable viscosity 3d flow. Recently we have been using parallel (MPI-based) MATLAB to more thoroughly explore possible pitfalls and algorithmic improvements to current ‘best-practice’ variable viscosity Stokes and D’Arcy flow solvers. Here we focus on study of finite-element solvers based on a decomposition of the equations for incompressible Stokes flow: Ku + Gp = f and G’u = 0 (K-velocity stiffness matrix, G-discretized gradient operator, G’=transpose(G)-discretized divergence operator) into a single equation for pressure Sp==G’K^-1Gp =G’K^-1f, in which the velocity is also updated as part of each pressure iteration. The outer pressure iteration is solved with preconditioned conjugate gradients (CG) (Maday and Patera, 1989), with a multigrid-preconditioned CG solver for the z=K^-1 (Gq) step of each pressure iteration. One fairly well-known pitfall (Fortin, 1985) is that constant-pressure elements can generate a spurious non-zero flow under a constant body force within non-rectangular geometries. We found a new pitfall when using an iterative method to solve the Kz=y operation in evaluating each G’K^-1Gq product -- even if the residual of the outer pressure equation converges to zero, the discrete divergence of this equation does not correspondingly converge; the error in the incompressibility depends on roughly the square of the tolerance used to solve each Kz=y velocity-like subproblem. Our current best recipe is: (1) Use flexible CG (cf. Notay, 2001) to solve the outer pressure problem. This is analogous to GMRES for a symmetric positive definite problem. It allows use of numerically unsymmetric and/or inexact preconditioners with CG. (2) In this outer-iteration, use an ‘alpha-bar’ technique to find the appropriate magnitude alpha to change the solution in each search direction. This improvement allows a similar iterative tolerance of

  11. Implementation of a 3D mixing layer code on parallel computers

    NASA Technical Reports Server (NTRS)

    Roe, K.; Thakur, R.; Dang, T.; Bogucz, E.

    1995-01-01

    This paper summarizes our progress and experience in the development of a Computational-Fluid-Dynamics code on parallel computers to simulate three-dimensional spatially-developing mixing layers. In this initial study, the three-dimensional time-dependent Euler equations are solved using a finite-volume explicit time-marching algorithm. The code was first programmed in Fortran 77 for sequential computers. The code was then converted for use on parallel computers using the conventional message-passing technique, while we have not been able to compile the code with the present version of HPF compilers.

  12. Computer assisted surgery with 3D robot models and visualisation of the telesurgical action.

    PubMed

    Rovetta, A

    2000-01-01

    This paper deals with the support of virtual reality computer action in the procedures of surgical robotics. Computer support gives a direct representation of the surgical theatre. The modelization of the procedure in course and in development gives a psychological reaction towards safety and reliability. Robots similar to the ones used by the manufacturing industry can be used with little modification as very effective surgical tools. They have high precision, repeatability and are versatile in integrating with the medical instrumentation. Now integrated surgical rooms, with computer and robot-assisted intervention, are operating. The computer is the element for a decision taking aid, and the robot works as a very effective tool.

  13. Coupling 2-D cylindrical and 3-D x-y-z transport computations

    SciTech Connect

    Abu-Shumays, I.K.; Yehnert, C.E.; Pitcairn, T.N.

    1998-06-30

    This paper describes a new two-dimensional (2-D) cylindrical geometry to three-dimensional (3-D) rectangular x-y-z splice option for multi-dimensional discrete ordinates solutions to the neutron (photon) transport equation. Of particular interest are the simple transformations developed and applied in order to carry out the required spatial and angular interpolations. The spatial interpolations are linear and equivalent to those applied elsewhere. The angular interpolations are based on a high order spherical harmonics representation of the angular flux. Advantages of the current angular interpolations over previous work are discussed. An application to an intricate streaming problem is provided to demonstrate the advantages of the new method for efficient and accurate prediction of particle behavior in complex geometries.

  14. CasimirSim - A Tool to Compute Casimir Polder Forces for Nontrivial 3D Geometries

    SciTech Connect

    Sedmik, Rene; Tajmar, Martin

    2007-01-30

    The so-called Casimir effect is one of the most interesting macro-quantum effects. Being negligible on the macro-scale it becomes a governing factor below structure sizes of 1 {mu}m where it accounts for typically 100 kN m-2. The force does not depend on gravity, or electric charge but solely on the materials properties, and geometrical shape. This makes the effect a strong candidate for micro(nano)-mechanical devices M(N)EMS. Despite a long history of research the theory lacks a uniform description valid for arbitrary geometries which retards technical application. We present an advanced state-of-the-art numerical tool overcoming all the usual geometrical restrictions, capable of calculating arbitrary 3D geometries by utilizing the Casimir Polder approximation for the Casimir force.

  15. 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.

  16. 3-D parallel program for numerical calculation of gas dynamics problems with heat conductivity on distributed memory computational systems (CS)

    SciTech Connect

    Sofronov, I.D.; Voronin, B.L.; Butnev, O.I.

    1997-12-31

    The aim of the work performed is to develop a 3D parallel program for numerical calculation of gas dynamics problem with heat conductivity on distributed memory computational systems (CS), satisfying the condition of numerical result independence from the number of processors involved. Two basically different approaches to the structure of massive parallel computations have been developed. The first approach uses the 3D data matrix decomposition reconstructed at temporal cycle and is a development of parallelization algorithms for multiprocessor CS with shareable memory. The second approach is based on using a 3D data matrix decomposition not reconstructed during a temporal cycle. The program was developed on 8-processor CS MP-3 made in VNIIEF and was adapted to a massive parallel CS Meiko-2 in LLNL by joint efforts of VNIIEF and LLNL staffs. A large number of numerical experiments has been carried out with different number of processors up to 256 and the efficiency of parallelization has been evaluated in dependence on processor number and their parameters.

  17. Progress in off-plane computer-generated waveguide holography for near-to-eye 3D display

    NASA Astrophysics Data System (ADS)

    Jolly, Sundeep; Savidis, Nickolaos; Datta, Bianca; Bove, V. Michael; Smalley, Daniel

    2016-03-01

    Waveguide holography refers to the use of holographic techniques for the control of guided-wave light in integrated optical devices (e.g., off-plane grating couplers and in-plane distributed Bragg gratings for guided-wave optical filtering). Off-plane computer-generated waveguide holography (CGWH) has also been employed in the generation of simple field distributions for image display. We have previously depicted the design and fabrication of a binary-phase CGWH operating in the Raman-Nath regime for the purposes of near-to-eye 3-D display and as a precursor to a dynamic, transparent flat-panel guided-wave holographic video display. In this paper, we describe design algorithms and fabrication techniques for multilevel phase CGWHs for near-to-eye 3-D display.

  18. 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.

  19. 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.

  20. Illustrating Language through Computer Generated Animation.

    ERIC Educational Resources Information Center

    Withrow, Margaret

    1979-01-01

    Originally part of a symposium on educational media for the deaf, the paper discusses the use of animated sequences which illustrate linguistic principles. The work of the Computer Graphics Research Group at Ohio State University is highlighted. It has been discovered that computer-assisted instructional systems enhance learning through greater…

  1. Computers as Teachers: Learning from Animations.

    ERIC Educational Resources Information Center

    Lilienfield, Lawrence S.; Broering, Naomi C.

    1994-01-01

    Describes the use of an interactive multimedia computer program in the study of cardiovascular physiology. Scores on tests given immediately after completion of a two-hour animation program on the Cardiac Cycle and Introduction to Electrocardiography were significantly higher than pretest scores. Students who used the computer program achieved…

  2. Viscous Incompressible Flow Computations for 3-D Steady and Unsteady Flows

    NASA Technical Reports Server (NTRS)

    Kwak, Dochan

    2001-01-01

    This viewgraph presentation gives an overview of viscous incompressible flow computations for three-dimensional steady and unsteady flows. Details are given on the use of computational fluid dynamics (CFD) as an engineering tool, solution methods for incompressible Navier-Stokes equations, numerical and physical characteristics of the primitive variable approach, and the role of CFD in the past and in current engineering and research applications.

  3. Computational modeling of RNA 3D structures, with the aid of experimental restraints

    PubMed Central

    Magnus, Marcin; Matelska, Dorota; Łach, Grzegorz; Chojnowski, Grzegorz; Boniecki, Michal J; Purta, Elzbieta; Dawson, Wayne; Dunin-Horkawicz, Stanislaw; Bujnicki, Janusz M

    2014-01-01

    In addition to mRNAs whose primary function is transmission of genetic information from DNA to proteins, numerous other classes of RNA molecules exist, which are involved in a variety of functions, such as catalyzing biochemical reactions or performing regulatory roles. In analogy to proteins, the function of RNAs depends on their structure and dynamics, which are largely determined by the ribonucleotide sequence. Experimental determination of high-resolution RNA structures is both laborious and difficult, and therefore, the majority of known RNAs remain structurally uncharacterized. To address this problem, computational structure prediction methods were developed that simulate either the physical process of RNA structure formation (“Greek science” approach) or utilize information derived from known structures of other RNA molecules (“Babylonian science” approach). All computational methods suffer from various limitations that make them generally unreliable for structure prediction of long RNA sequences. However, in many cases, the limitations of computational and experimental methods can be overcome by combining these two complementary approaches with each other. In this work, we review computational approaches for RNA structure prediction, with emphasis on implementations (particular programs) that can utilize restraints derived from experimental analyses. We also list experimental approaches, whose results can be relatively easily used by computational methods. Finally, we describe case studies where computational and experimental analyses were successfully combined to determine RNA structures that would remain out of reach for each of these approaches applied separately. PMID:24785264

  4. A 3-D admittance-level computational model of a rat hippocampus for improving prosthetic design.

    PubMed

    Gilbert, Andrew; Loizos, Kyle; RamRakhyani, Anil Kumar; Hendrickson, Phillip; Lazzi, Gianluca; Berger, Theodore W

    2015-01-01

    Hippocampal prosthetic devices have been developed to bridge the gap between functioning portions of the hippocampus, in order to restore lost memory functionality in those suffering from brain injury or diseases. One approach taken in recent neuroprosthetic design is to use a multi-input, multi-output device that reads data from the CA3 in the hippocampus and electrically stimulates the CA1 in an attempt to mimic the appropriate firing pattern that would occur naturally between the two areas. However, further study needs to be conducted in order to optimize electrode placement, pulse magnitude, and shape for creating the appropriate firing pattern. This paper describes the creation and implementation of an anatomically correct 3D model of the hippocampus to simulate the electric field patterns and axonal activation from electrical stimulation due to an implanted electrode array. The activating function was applied to the voltage results to determine the firing patterns in possible axon locations within the CA1. PMID:26736751

  5. Geometric Neural Computing for 2D Contour and 3D Surface Reconstruction

    NASA Astrophysics Data System (ADS)

    Rivera-Rovelo, Jorge; Bayro-Corrochano, Eduardo; Dillmann, Ruediger

    In this work we present an algorithm to approximate the surface of 2D or 3D objects combining concepts from geometric algebra and artificial neural networks. Our approach is based on the self-organized neural network called Growing Neural Gas (GNG), incorporating versors of the geometric algebra in its neural units; such versors are the transformations that will be determined during the training stage and then applied to a point to approximate the surface of the object. We also incorporate the information given by the generalized gradient vector flow to select automatically the input patterns, and also in the learning stage in order to improve the performance of the net. Several examples using medical images are presented, as well as images of automatic visual inspection. We compared the results obtained using snakes against the GSOM incorporating the gradient information and using versors. Such results confirm that our approach is very promising. As a second application, a kind of morphing or registration procedure is shown; namely the algorithm can be used when transforming one model at time t 1 into another at time t 2. We include also examples applying the same procedure, now extended to models based on spheres.

  6. Computer-based automatic identification of neurons in gigavoxel-sized 3D human brain images.

    PubMed

    Soda, Paolo; Acciai, Ludovica; Cordelli, Ermanno; Costantini, Irene; Sacconi, Leonardo; Pavone, Francesco Saverio; Conti, Valerio; Guerrini, Renzo; Frasconi, Paolo; Iannello, Giulio

    2015-01-01

    Achieving a comprehensive knowledge of the human brain cytoarchitecture is a fundamental step to understand how the nervous system works, i.e., one of the greatest challenge of 21(st) century science. The recent development of biological tissue labeling and automated microscopic imaging systems has permitted to acquire images at the micro-resolution, which produce a huge quantity of data that cannot be manually analyzed. In case of mammals brain, automatic methods to extract objective information at the microscale have been applied until now to mice, macaque and cat 3D volume images. Here we report a method to automatically localize neurons in a sample of human brain removed during a surgical procedure for the treatments of drug resistant epilepsy in a child with hemimegalencephaly, whose neurons and neurites were fluorescence labelled and finally imaged using the two-photon fluorescence microscope. The method provides the map of both parvalbuminergic neurons and all other cells nuclei with a satisfactory f-score measured using more than two thousand human labelled soma. PMID:26738082

  7. High performance computing for a 3-D optical diffraction tomographic application in fluid velocimetry.

    PubMed

    Lobera, Julia; Ortega, Gloria; García, Inmaculada; Arroyo, María del Pilar; Garzón, Ester M

    2015-02-23

    Optical Diffraction Tomography has been recently introduced in fluid velocimetry to provide three dimensional information of seeding particle locations. In general, image reconstruction methods at visible wavelengths have to account for diffraction. Linear approximation has been used for three-dimensional image reconstruction, but a non-linear and iterative reconstruction method is required when multiple scattering is not negligible. Non-linear methods require the solution of the Helmholtz equation, computationally highly demanding due to the size of the problem. The present work shows the results of a non-linear method customized for spherical particle location using GPU computing and a made-to-measure storing format.

  8. COMPUTER SIMULATIONS OF SPRAY RETENTION BY A 3D BARLEY PLANT: EFFECT OF FORMULATION SURFACE TENSION.

    PubMed

    Massinon, M; De Cock, N; Salah, S Ouled Taleb; Lebeau, F

    2015-01-01

    A spray retention model was used in this study to explore theoretically the effect of a range of mixture surface tension on the spray retention and the variability of deposits. The spray retention model was based on an algorithm that tested whether droplets from a virtual nozzle intercepted a 3D plant model. If so, the algorithm determined the contribution of the droplet to the overall retention depending on the droplet impact behaviour on the leaf; adhesion, rebound or splashing. The impact outcome probabilities, function of droplet impact energy, were measured using high-speed imaging on an excised indoor grown barley leaf (BBCH12) both for pure water (surface tension of 0.072 N/m) and a non-ionic super spreader (static surface tension of 0.021 N/m) depending on the surface orientation. The modification of spray mixture properties in the simulations was performed by gradually changing the spray the droplet impact probabilities between pure water and a solution with non-ionic surfactant exhibiting super spreading properties. The plant architecture was measured using a structured light scanner. The final retention was expressed as the volume of liquid retained by the whole plant relative to the projected leaf surface area in the main spray direction. One hundred simulations were performed at different volumes per hectare and flat-fan nozzles for each formulation surface tension. The coefficient of variation was used as indicator of variability of deposits. The model was able to discriminate between mixture surface tension. The spray retention increased as the mixture surface tension decreased. The variability of deposits also decreased as the surface tension decreased. The proposed modelling approach provides a suited tool for sensitivity analysis: nozzle kind, pressure, volume per hectare applied, spray mixture physicochemical properties, plant species, growth stage could be screened to determine the best spraying characteristics maximizing the retention. The

  9. A computational model for estimating tumor margins in complementary tactile and 3D ultrasound images

    NASA Astrophysics Data System (ADS)

    Shamsil, Arefin; Escoto, Abelardo; Naish, Michael D.; Patel, Rajni V.

    2016-03-01

    Conventional surgical methods are effective for treating lung tumors; however, they impose high trauma and pain to patients. Minimally invasive surgery is a safer alternative as smaller incisions are required to reach the lung; however, it is challenging due to inadequate intraoperative tumor localization. To address this issue, a mechatronic palpation device was developed that incorporates tactile and ultrasound sensors capable of acquiring surface and cross-sectional images of palpated tissue. Initial work focused on tactile image segmentation and fusion of position-tracked tactile images, resulting in a reconstruction of the palpated surface to compute the spatial locations of underlying tumors. This paper presents a computational model capable of analyzing orthogonally-paired tactile and ultrasound images to compute the surface circumference and depth margins of a tumor. The framework also integrates an error compensation technique and an algebraic model to align all of the image pairs and to estimate the tumor depths within the tracked thickness of a palpated tissue. For validation, an ex vivo experimental study was conducted involving the complete palpation of 11 porcine liver tissues injected with iodine-agar tumors of varying sizes and shapes. The resulting tactile and ultrasound images were then processed using the proposed model to compute the tumor margins and compare them to fluoroscopy based physical measurements. The results show a good negative correlation (r = -0.783, p = 0.004) between the tumor surface margins and a good positive correlation (r = 0.743, p = 0.009) between the tumor depth margins.

  10. Computational 3D structures of drug-targeting proteins in the 2009-H1N1 influenza A virus

    NASA Astrophysics Data System (ADS)

    Du, Qi-Shi; Wang, Shu-Qing; Huang, Ri-Bo; Chou, Kuo-Chen

    2010-01-01

    The neuraminidase (NA) and M2 proton channel of influenza virus are the drug-targeting proteins, based on which several drugs were developed. However these once powerful drugs encountered drug-resistant problem to the H5N1 and H1N1 flu. To address this problem, the computational 3D structures of NA and M2 proteins of 2009-H1N1 influenza virus were built using the molecular modeling technique and computational chemistry method. Based on the models the structure features of NA and M2 proteins were analyzed, the docking structures of drug-protein complexes were computed, and the residue mutations were annotated. The results may help to solve the drug-resistant problem and stimulate designing more effective drugs against 2009-H1N1 influenza pandemic.

  11. 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.

  12. How computer science can help in understanding the 3D genome architecture.

    PubMed

    Shavit, Yoli; Merelli, Ivan; Milanesi, Luciano; Lio', Pietro

    2016-09-01

    Chromosome conformation capture techniques are producing a huge amount of data about the architecture of our genome. These data can provide us with a better understanding of the events that induce critical regulations of the cellular function from small changes in the three-dimensional genome architecture. Generating a unified view of spatial, temporal, genetic and epigenetic properties poses various challenges of data analysis, visualization, integration and mining, as well as of high performance computing and big data management. Here, we describe the critical issues of this new branch of bioinformatics, oriented at the comprehension of the three-dimensional genome architecture, which we call 'Nucleome Bioinformatics', looking beyond the currently available tools and methods, and highlight yet unaddressed challenges and the potential approaches that could be applied for tackling them. Our review provides a map for researchers interested in using computer science for studying 'Nucleome Bioinformatics', to achieve a better understanding of the biological processes that occur inside the nucleus.

  13. A 3D-PNS computer code for the calculation of supersonic combusting flows

    NASA Technical Reports Server (NTRS)

    Chitsomboon, Tawit; Northam, G. Burton

    1988-01-01

    A computer code has been developed based on the three-dimensional parabolized Navier-Stokes (PNS) equations which govern the supersonic combusting flow of the hydrogen-air system. The finite difference algorithm employed was a hybrid of the Schiff-Steger algorithm and the Vigneron, et al., algorithm which is fully implicit and fully coupled. The combustion of hydrogen and air was modeled by the finite-rate two-step combustion model of Rogers-Chinitz. A new dependent variable vector was introduced to simplify the numerical algorithm. Robustness of the algorithm was considerably enhanced by introducing an adjustable parameter. The computer code was used to solve a premixed shock-induced combustion problem and the results were compared with those of a full Navier-Stokes code. Reasonably good agreement was obtained at a fraction of the cost of the full Navier-Stokes procedure.

  14. High-Performance Computation of Distributed-Memory Parallel 3D Voronoi and Delaunay Tessellation

    SciTech Connect

    Peterka, Tom; Morozov, Dmitriy; Phillips, Carolyn

    2014-11-14

    Computing a Voronoi or Delaunay tessellation from a set of points is a core part of the analysis of many simulated and measured datasets: N-body simulations, molecular dynamics codes, and LIDAR point clouds are just a few examples. Such computational geometry methods are common in data analysis and visualization; but as the scale of simulations and observations surpasses billions of particles, the existing serial and shared-memory algorithms no longer suffice. A distributed-memory scalable parallel algorithm is the only feasible approach. The primary contribution of this paper is a new parallel Delaunay and Voronoi tessellation algorithm that automatically determines which neighbor points need to be exchanged among the subdomains of a spatial decomposition. Other contributions include periodic and wall boundary conditions, comparison of our method using two popular serial libraries, and application to numerous science datasets.

  15. 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

  16. Computer-aided determination of occlusal contact points for dental 3-D CAD.

    PubMed

    Maruyama, Tomoaki; Nakamura, Yasuo; Hayashi, Toyohiko; Kato, Kazumasa

    2006-05-01

    Present dental CAD systems enable us to design functional occlusal tooth surfaces which harmonize with the patient's stomatognathic function. In order to avoid occlusal interferences during tooth excursions, currently available systems usually use the patient's functional occlusal impressions for the design of occlusal contact points. Previous interfere-free design, however, has been done on a trial-and-error basis by using visual inspection. To improve this time-consuming procedure, this paper proposes a computer-aided system for assisting in the determination of the occlusal contact points by visualizing the appropriate regions of the opposing surface. The system can designate such regions from data of the opposing occlusal surfaces and their relative movements can be simulated by using a virtual articulator. Experiments for designing the crown of a lower first molar demonstrated that all contact points selected within the designated regions completely satisfied the required contact or separation during tooth excursions, confirming the effectiveness of our computer-aided procedure.

  17. 3D chemical imaging in the laboratory by hyperspectral X-ray computed tomography.

    PubMed

    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

  18. A shell element for computing 3D eddy currents -- Applications to transformers

    SciTech Connect

    Guerin, C.; Tanneau, G.; Meunier, G.; Labie, P.; Ngnegueu, T.; Sacotte, M.

    1995-05-01

    A skin depth-independent shell element to model thin conducting sheets is described in a finite element context. This element takes into account the field variation through depth due to skin effect. The finite element formulation is first described, then boundary conditions at the edge of conducting shells and the possibility of describing non conducting line gaps and holes are discussed. Finally, a computation of an earthing transformer model with an aluminium shield modelled with shell elements is presented.

  19. The 3D computation of single-expansion-ramp and scramjet nozzles

    NASA Technical Reports Server (NTRS)

    Lai, H. T.

    1991-01-01

    A description of the computations for three-dimensional nonaxisymmetric nozzles and an analysis of the flowfields are presented. Two different types of nozzles are investigated for compressible flows at high Reynolds numbers. These are the single-expansion-ramp and scramjet nozzles. The computation for the single-expansion-ramp nozzle focuses on the condition of low pressure ratio, which requires the simulation for turbulent flow that is not needed at high pressure ratios. The flowfield contains the external quiescent air, and the internal regions of subsonic and low supersonic flows. The second type is the scramjet nozzle, which typically has a very large area ratio and is designed to operate at high speeds and pressure ratios. The freestream external flow has a Mach number of 6, and the internal flow leaving the combustion chamber is at a Mach number of 1.62. The flowfield is mostly supersonic except in the viscous region near walls. The computed results from both cases are compared with experimental data for the surface pressure distributions.

  20. Computation of stationary 3D halo currents in fusion devices with accuracy control

    SciTech Connect

    Bettini, Paolo; Specogna, Ruben

    2014-09-15

    This paper addresses the calculation of the resistive distribution of halo currents in three-dimensional structures of large magnetic confinement fusion machines. A Neumann electrokinetic problem is solved on a geometry so complicated that complementarity is used to monitor the discretization error. An irrotational electric field is obtained by a geometric formulation based on the electric scalar potential, whereas three geometric formulations are compared to obtain a solenoidal current density: a formulation based on the electric vector potential and two geometric formulations inspired from mixed and mixed-hybrid Finite Elements. The electric vector potential formulation is usually considered impractical since an enormous computing power is wasted by the topological pre-processing it requires. To solve this challenging problem, we present novel algorithms based on lazy cohomology generators that enable to save orders of magnitude computational time with respect to all other state-of-the-art solutions proposed in literature. Believing that our results are useful in other fields of scientific computing, the proposed algorithm is presented as a detailed pseudocode in such a way that it can be easily implemented.

  1. Computer-generated 3D ultrasound images of the carotid artery

    NASA Technical Reports Server (NTRS)

    Selzer, Robert H.; Lee, Paul L.; Lai, June Y.; Frieden, Howard J.; Blankenhorn, David H.

    1989-01-01

    A method is under development to measure carotid artery lesions from a computer-generated three-dimensional ultrasound image. For each image, the position of the transducer in six coordinates (x, y, z, azimuth, elevation, and roll) is recorded and used to position each B-mode picture element in its proper spatial position in a three-dimensional memory array. After all B-mode images have been assembled in the memory, the three-dimensional image is filtered and resampled to produce a new series of parallel-plane two-dimensional images from which arterial boundaries are determined using edge tracking methods.

  2. Computer-generated 3D ultrasound images of the carotid artery

    NASA Astrophysics Data System (ADS)

    Selzer, Robert H.; Lee, Paul L.; Lai, June Y.; Frieden, Howard J.; Blankenhorn, David H.

    A method is under development to measure carotid artery lesions from a computer-generated three-dimensional ultrasound image. For each image, the position of the transducer in six coordinates (x, y, z, azimuth, elevation, and roll) is recorded and used to position each B-mode picture element in its proper spatial position in a three-dimensional memory array. After all B-mode images have been assembled in the memory, the three-dimensional image is filtered and resampled to produce a new series of parallel-plane two-dimensional images from which arterial boundaries are determined using edge tracking methods.

  3. Computational studies of hard-body and 3-D effects in plume flows

    NASA Technical Reports Server (NTRS)

    Venkatapathy, Ethiraj; Feiereisen, William J.; Obayashi, Shigeru

    1989-01-01

    Axisymmetric and three-dimensional, multi-nozzle plume flows around generic rocket geometries are investigated with a three-dimensional Navier-Stokes solver to study the interactive effects between hard body and the plume. Time-asymptotic, laminar, ideal-gas solutions obtained with a two-factor, flux-split scheme and a diagonal, upwind scheme are presented. Computed solutions to three-dimensional, multi-nozzle problems and single-nozzle, axisymmetric problems demonstrate flow field features including three-dimensionality and hard-body effects. Geometry and three-dimensional effects are shown to be significant in multi-nozzle flows.

  4. Endocranial features of Australopithecus africanus revealed by 2- and 3-D computed tomography.

    PubMed

    Conroy, G C; Vannier, M W; Tobias, P V

    1990-02-16

    The earliest hominid from South Africa, Australopithecus africanus, is known from only six specimens in which accurate assessment of endocranial capacity and cranial venous outflow pattern can be obtained. This places a severe limit on a number of hypotheses concerning early hominid evolution, particularly those involving brain-body size relationships and adaptations of the circulatory system to evolving upright posture. Advances in high-resolution two- and three-dimensional computed tomography (CT) now allow the inclusion of another important specimen to this list, MLD 37/38 from Makapansgat. A new computer imaging technique is described that "reconstructs" the missing portions of the endocranial cavity in order to determine endocranial capacity. In addition, CT evaluation allows assessment of cranial venous outflow pattern even in cases where the endocranial cavity is completely filled with stone matrix. Results show that endocranial capacity in this specimen is less than originally proposed and also support the view that gracile and robust australopithecines evolved different cranial venous outflow patterns in response to upright postures. PMID:2305255

  5. Computation of electric and magnetic stimulation in human head using the 3-D impedance method.

    PubMed

    Nadeem, Mohammad; Thorlin, Thorleif; Gandhi, Om P; Persson, Mikael

    2003-07-01

    A comparative, computational study of the modeling of transcranial magnetic stimulation (TMS) and electroconvulsive therapy (ECT) is presented using a human head model. The magnetic fields from a typical TMS coil of figure-eight type is modeled using the Biot-Savart law. The TMS coil is placed in a position used clinically for treatment of depression. Induced current densities and electric field distributions are calculated in the model using the impedance method. The calculations are made using driving currents and wave forms typical in the clinical setting. The obtained results are compared and contrasted with the corresponding ECT results. In the ECT case, a uniform current density is injected on one side of the head and extracted from the equal area on the opposite side of the head. The area of the injected currents corresponds to the electrode placement used in the clinic. The currents and electric fields, thus, produced within the model are computed using the same three-dimensional impedance method as used for the TMS case. The ECT calculations are made using currents and wave forms typical in the clinic. The electrical tissue properties are obtained from a 4-Cole-Cole model. The numerical results obtained are shown on a two-dimenaional cross section of the model. In this study, we find that the current densities and electric fields in the ECT case are stronger and deeper penetrating than the corresponding TMS quantities but both methods show biologically interesting current levels deep inside the brain. PMID:12848358

  6. 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.

  7. Semi-automatic 3D segmentation of carotid lumen in contrast-enhanced computed tomography angiography images.

    PubMed

    Hemmati, Hamidreza; Kamli-Asl, Alireza; Talebpour, Alireza; Shirani, Shapour

    2015-12-01

    The atherosclerosis disease is one of the major causes of the death in the world. Atherosclerosis refers to the hardening and narrowing of the arteries by plaques. Carotid stenosis is a narrowing or constriction of carotid artery lumen usually caused by atherosclerosis. Carotid artery stenosis can increase risk of brain stroke. Contrast-enhanced Computed Tomography Angiography (CTA) is a minimally invasive method for imaging and quantification of the carotid plaques. Manual segmentation of carotid lumen in CTA images is a tedious and time consuming procedure which is subjected to observer variability. As a result, there is a strong and growing demand for developing computer-aided carotid segmentation procedures. In this study, a novel method is presented for carotid artery lumen segmentation in CTA data. First, the mean shift smoothing is used for uniformity enhancement of gray levels. Then with the help of three seed points, the centerlines of the arteries are extracted by a 3D Hessian based fast marching shortest path algorithm. Finally, a 3D Level set function is performed for segmentation. Results on 14 CTA volumes data show 85% of Dice similarity and 0.42 mm of mean absolute surface distance measures. Evaluation shows that the proposed method requires minimal user intervention, low dependence to gray levels changes in artery path, resistance to extreme changes in carotid diameter and carotid branch locations. The proposed method has high accuracy and can be used in qualitative and quantitative evaluation. PMID:26429385

  8. Multigrid acceleration and turbulence models for computations of 3D turbulent jets in crossflow

    NASA Technical Reports Server (NTRS)

    Demuren, A. O.

    1991-01-01

    A multigrid method is presented for the calculation of three-dimensional turbulent jets in crossflow. Turbulence closure is achieved with either the standard k-epsilon model or a Reynolds Stress Model (RSM). Multigrid acceleration enables convergence rates which are far superior to that for a single grid method. With the k-epsilon model the rate approaches that for laminar flow, but with RSM it is somewhat slower. The increased stiffness of the system of equations in the latter may be responsible. Computed results with both turbulence models are compared with experimental data for a pair of opposed jets in crossflow. Both models yield reasonable agreement with mean flow velocity but RSM yields better prediction of the Reynolds stresses.

  9. Towards increased speed computations in 3D moving eddy current finite element modelling

    SciTech Connect

    Allen, N.; Rodger, D.; Coles, P.C.; Street, S.; Leonard, P.J.

    1995-11-01

    Attractive and drag forces on such devices as magnetically levitated (MAGLEV) vehicles and magnetic bearings are crucially dependent on induced eddy currents. Here, a finite element scheme used to model eddy current problems with motional velocity is described here. The formulation is a variation on the A {minus} {psi} method. An additional Minkowski-transformation term is required to take into account the velocity. However, computational instability arises when the velocity increases to the point that the first order velocity terms severely dominate the second order diffusion terms. The method presented here uses upwinding to help regain stability. An additional degree of stability is inserted at higher speeds by using a lower speed result as an initial vector. This leads to a reduced permeability in saturated regions which counter-balances to some extent the increase in velocity. The method is validated by experimental measurement.

  10. Large-scale Parallel Unstructured Mesh Computations for 3D High-lift Analysis

    NASA Technical Reports Server (NTRS)

    Mavriplis, Dimitri J.; Pirzadeh, S.

    1999-01-01

    A complete "geometry to drag-polar" analysis capability for the three-dimensional high-lift configurations is described. The approach is based on the use of unstructured meshes in order to enable rapid turnaround for complicated geometries that arise in high-lift configurations. Special attention is devoted to creating a capability for enabling analyses on highly resolved grids. Unstructured meshes of several million vertices are initially generated on a work-station, and subsequently refined on a supercomputer. The flow is solved on these refined meshes on large parallel computers using an unstructured agglomeration multigrid algorithm. Good prediction of lift and drag throughout the range of incidences is demonstrated on a transport take-off configuration using up to 24.7 million grid points. The feasibility of using this approach in a production environment on existing parallel machines is demonstrated, as well as the scalability of the solver on machines using up to 1450 processors.

  11. Users manual for CAFE-3D : a computational fluid dynamics fire code.

    SciTech Connect

    Khalil, Imane; Lopez, Carlos; Suo-Anttila, Ahti Jorma

    2005-03-01

    The Container Analysis Fire Environment (CAFE) computer code has been developed to model all relevant fire physics for predicting the thermal response of massive objects engulfed in large fires. It provides realistic fire thermal boundary conditions for use in design of radioactive material packages and in risk-based transportation studies. The CAFE code can be coupled to commercial finite-element codes such as MSC PATRAN/THERMAL and ANSYS. This coupled system of codes can be used to determine the internal thermal response of finite element models of packages to a range of fire environments. This document is a user manual describing how to use the three-dimensional version of CAFE, as well as a description of CAFE input and output parameters. Since this is a user manual, only a brief theoretical description of the equations and physical models is included.

  12. An efficient algorithm for mapping imaging data to 3D unstructured grids in computational biomechanics.

    PubMed

    Einstein, Daniel R; Kuprat, Andrew P; Jiao, Xiangmin; Carson, James P; Einstein, David M; Jacob, Richard E; Corley, Richard A

    2013-01-01

    Geometries for organ scale and multiscale simulations of organ function are now routinely derived from imaging data. However, medical images may also contain spatially heterogeneous information other than geometry that are relevant to such simulations either as initial conditions or in the form of model parameters. In this manuscript, we present an algorithm for the efficient and robust mapping of such data to imaging-based unstructured polyhedral grids in parallel. We then illustrate the application of our mapping algorithm to three different mapping problems: (i) the mapping of MRI diffusion tensor data to an unstructured ventricular grid; (ii) the mapping of serial cyrosection histology data to an unstructured mouse brain grid; and (iii) the mapping of computed tomography-derived volumetric strain data to an unstructured multiscale lung grid. Execution times and parallel performance are reported for each case. PMID:23293066

  13. Performance Modeling for 3D Visualization in a Heterogeneous Computing Environment

    SciTech Connect

    Bowman, Ian; Shalf, John; Ma, Kwan-Liu; Bethel, Wes

    2004-06-30

    The visualization of large, remotely located data sets necessitates the development of a distributed computing pipeline in order to reduce the data, in stages, to a manageable size. The required baseline infrastructure for launching such a distributed pipeline is becoming available, but few services support even marginally optimal resource selection and partitioning of the data analysis workflow. We explore a methodology for building a model of overall application performance using a composition of the analytic models of individual components that comprise the pipeline. The analytic models are shown to be accurate on a testbed of distributed heterogeneous systems. The prediction methodology will form the foundation of a more robust resource management service for future Grid-based visualization applications.

  14. On a 3-D singularity element for computation of combined mode stress intensities

    NASA Technical Reports Server (NTRS)

    Atluri, S. N.; Kathiresan, K.

    1976-01-01

    A special three-dimensional singularity element is developed for the computation of combined modes 1, 2, and 3 stress intensity factors, which vary along an arbitrarily curved crack front in three dimensional linear elastic fracture problems. The finite element method is based on a displacement-hybrid finite element model, based on a modified variational principle of potential energy, with arbitrary element interior displacements, interelement boundary displacements, and element boundary tractions as variables. The special crack-front element used in this analysis contains the square root singularity in strains and stresses, where the stress-intensity factors K(1), K(2), and K(3) are quadratically variable along the crack front and are solved directly along with the unknown nodal displacements.

  15. 3D Reconstruction of Chick Embryo Vascular Geometries Using Non-invasive High-Frequency Ultrasound for Computational Fluid Dynamics Studies.

    PubMed

    Tan, Germaine Xin Yi; Jamil, Muhammad; Tee, Nicole Gui Zhen; Zhong, Liang; Yap, Choon Hwai

    2015-11-01

    Recent animal studies have provided evidence that prenatal blood flow fluid mechanics may play a role in the pathogenesis of congenital cardiovascular malformations. To further these researches, it is important to have an imaging technique for small animal embryos with sufficient resolution to support computational fluid dynamics studies, and that is also non-invasive and non-destructive to allow for subject-specific, longitudinal studies. In the current study, we developed such a technique, based on ultrasound biomicroscopy scans on chick embryos. Our technique included a motion cancelation algorithm to negate embryonic body motion, a temporal averaging algorithm to differentiate blood spaces from tissue spaces, and 3D reconstruction of blood volumes in the embryo. The accuracy of the reconstructed models was validated with direct stereoscopic measurements. A computational fluid dynamics simulation was performed to model fluid flow in the generated construct of a Hamburger-Hamilton (HH) stage 27 embryo. Simulation results showed that there were divergent streamlines and a low shear region at the carotid duct, which may be linked to the carotid duct's eventual regression and disappearance by HH stage 34. We show that our technique has sufficient resolution to produce accurate geometries for computational fluid dynamics simulations to quantify embryonic cardiovascular fluid mechanics.

  16. 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)

  17. Separation efficiency of a hydrodynamic separator using a 3D computational fluid dynamics multiscale approach.

    PubMed

    Schmitt, Vivien; Dufresne, Matthieu; Vazquez, Jose; Fischer, Martin; Morin, Antoine

    2014-01-01

    The aim of this study is to investigate the use of computational fluid dynamics (CFD) to predict the solid separation efficiency of a hydrodynamic separator. The numerical difficulty concerns the discretization of the geometry to simulate both the global behavior and the local phenomena that occur near the screen. In this context, a CFD multiscale approach was used: a global model (at the scale of the device) is used to observe the hydrodynamic behavior within the device; a local model (portion of the screen) is used to determine the local phenomena that occur near the screen. The Eulerian-Lagrangian approach was used to model the particle trajectories in both models. The global model shows the influence of the particles' characteristics on the trapping efficiency. A high density favors the sedimentation. In contrast, particles with small densities (1,040 kg/m(3)) are steered by the hydrodynamic behavior and can potentially be trapped by the separator. The use of the local model allows us to observe the particle trajectories near the screen. A comparison between two types of screens (perforated plate vs expanded metal) highlights the turbulent effects created by the shape of the screen.

  18. 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

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

    PubMed

    Shih, Tian-Yu; Wu, Jay; 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

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

    PubMed

    Shih, Tian-Yu; Wu, Jay; 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.

  1. Supermodeled sabercat, predatory behavior in Smilodon fatalis revealed by high-resolution 3D computer simulation.

    PubMed

    McHenry, Colin R; Wroe, Stephen; Clausen, Philip D; Moreno, Karen; Cunningham, Eleanor

    2007-10-01

    The American sabercat Smilodon fatalis is among the most charismatic of fossil carnivores. Despite broad agreement that its extraordinary anatomy reflects unique hunting techniques, after >150 years of study, many questions remain concerning its predatory behavior. Were the "sabers" used to take down large prey? Were prey killed with an eviscerating bite to the abdomen? Was its bite powerful or weak compared with that of modern big cats? Here we quantitatively assess the sabercat's biomechanical performance using the most detailed computer reconstructions yet developed for the vertebrate skull. Our results demonstrate that bite force driven by jaw muscles was relatively weak in S. fatalis, one-third that of a lion (Panthera leo) of comparable size, and its skull was poorly optimized to resist the extrinsic loadings generated by struggling prey. Its skull is better optimized for bites on restrained prey where the bite is augmented by force from the cervical musculature. We conclude that prey were brought to ground and restrained before a killing bite, driven in large part by powerful cervical musculature. Because large prey is easier to restrain if its head is secured, the killing bite was most likely directed to the neck. We suggest that the more powerful jaw muscles of P. leo may be required for extended, asphyxiating bites and that the relatively low bite forces in S. fatalis might reflect its ability to kill large prey more quickly, avoiding the need for prolonged bites.

  2. A computationally efficient hybrid 2D/3D thin film dislocation model

    NASA Astrophysics Data System (ADS)

    Sarrafan, Siavash

    Substantial research has been devoted to attempting to understand how dislocation structures evolve and how they affect device properties. However, current dislocation simulation methods are only able to model highly idealized systems accurately. The three-dimensional discrete dislocation dynamics models, in particular, are too computationally intensive for modelling high dislocation densities and their resultant deformations that are observed in some real applications. In this thesis, we propose a novel method to exploit the quasi-two-dimensional nature of three-dimensional dislocation loops in a thin film to model their behaviors. For most film configurations, simulation performance can be greatly enhanced by implementing a hybrid two-dimensional/three-dimensional model without losing significant fidelity. In this technique, misfits stress fields are modeled by superposing multiple two-dimensional models. Threads are modeled with a more traditional three-dimensional implementation as they move through the misfit stress field. Using this innovative technique, much higher strains and/or dislocation densities could be studied.

  3. 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.

  4. Efficient computational methods for electromagnetic imaging with applications to 3D magnetotellurics

    NASA Astrophysics Data System (ADS)

    Kordy, Michal Adam

    The motivation for this work is the forward and inverse problem for magnetotellurics, a frequency domain electromagnetic remote-sensing geophysical method used in mineral, geothermal, and groundwater exploration. The dissertation consists of four papers. In the first paper, we prove the existence and uniqueness of a representation of any vector field in H(curl) by a vector lying in H(curl) and H(div). It allows us to represent electric or magnetic fields by another vector field, for which nodal finite element approximation may be used in the case of non-constant electromagnetic properties. With this approach, the system matrix does not become ill-posed for low-frequency. In the second paper, we consider hexahedral finite element approximation of an electric field for the magnetotelluric forward problem. The near-null space of the system matrix for low frequencies makes the numerical solution unstable in the air. We show that the proper solution may obtained by applying a correction on the null space of the curl. It is done by solving a Poisson equation using discrete Helmholtz decomposition. We parallelize the forward code on multicore workstation with large RAM. In the next paper, we use the forward code in the inversion. Regularization of the inversion is done by using the second norm of the logarithm of conductivity. The data space Gauss-Newton approach allows for significant savings in memory and computational time. We show the efficiency of the method by considering a number of synthetic inversions and we apply it to real data collected in Cascade Mountains. The last paper considers a cross-frequency interpolation of the forward response as well as the Jacobian. We consider Pade approximation through model order reduction and rational Krylov subspace. The interpolating frequencies are chosen adaptively in order to minimize the maximum error of interpolation. Two error indicator functions are compared. We prove a theorem of almost always lucky failure in the

  5. Large-scale computer-generated absorption holograms of 3D objects: I. Theoretical background and visual concepts

    NASA Astrophysics Data System (ADS)

    Cameron, Colin D.; Payne, Douglas A.; Sheerin, David T.; Slinger, Christopher W.; Phillips, Nicholas J.; Dodd, Adrian K.

    1999-03-01

    Over many years, the subject of computer generation of holograms has been visited in various guises. Historically, the obvious restrictions imposed by computational power and computer generated hologram (CGH) fabrication techniques have placed limits on what can be taken seriously in terms of image complexity. Modern advances in computational hardware and electro-optic systems now permit both the calculation and the manufacture of CGH's of complex 3D objects which fill a significant volume of space. New methods permit the recording to be made within a reasonable timescale. In addition to advancing fixed CGH generation techniques, the motivation for the work reported here includes assessment of design algorithms, modulation strategies and image quality metrics. These results are of relevance for a novel electroholography system, currently under development at DERA Malvern. This paper describes a complete process of data generation, computation, data manipulation and recording leading to practical techniques for the creation of large area CGH's. As a support to the advances in theoretical understanding and computational methods, we describe (in Part II) a new laser plotter technique that enables, in principle, an unlimited size of pixel array to be plotted efficiently with a rigorous estimate of duration of the plot run time. The results reported here are limited to 2048 X 2048 pixels. In this example, the novel switching techniques employed on the laser plotter permit the pixel array to be printed in approximately 1 hour. However, paths towards easily raising the pixel count and its associated printing rate are presented for both the computational engine and laser plotting processes.

  6. Computational hologram synthesis and representation on spatial light modulators for real-time 3D holographic imaging

    NASA Astrophysics Data System (ADS)

    Reichelt, Stephan; Leister, Norbert

    2013-02-01

    In dynamic computer-generated holography that utilizes spatial light modulators, both hologram synthesis and hologram representation are essential in terms of fast computation and high reconstruction quality. For hologram synthesis, i.e. the computation step, Fresnel transform based or point-source based raytracing methods can be applied. In the encoding step, the complex wave-field has to be optimally represented by the SLM with its given modulation capability. For proper hologram reconstruction that implies a simultaneous and independent amplitude and phase modulation of the input wave-field by the SLM. In this paper, we discuss full complex hologram representation methods on SLMs by considering inherent SLM parameter such as modulation type and bit depth on their reconstruction performance such as diffraction efficiency and SNR. We review the three implementation schemes of Burckhardt amplitude-only representation, phase-only macro-pixel representation, and two-phase interference representation. Besides the optical performance we address their hardware complexity and required computational load. Finally, we experimentally demonstrate holographic reconstructions of different representation schemes as obtained by functional prototypes utilizing SeeReal's viewing-window holographic display technology. The proposed hardware implementations enable a fast encoding of complex-valued hologram data and thus will pave the way for commercial real-time holographic 3D imaging in the near future.

  7. Computation of Flow Over a Drag Prediction Workshop Wing/Body Transport Configuration Using CFL3D

    NASA Technical Reports Server (NTRS)

    Rumsey, Christopher L.; Biedron, Robert T.

    2001-01-01

    A Drag Prediction Workshop was held in conjunction with the 19th AIAA Applied Aerodynamics Conference in June 2001. The purpose of the workshop was to assess the prediction of drag by computational methods for a wing/body configuration (DLR-F4) representative of subsonic transport aircraft. This report details computed results submitted to this workshop using the Reynolds-averaged Navier-Stokes code CFL3D. Two supplied grids were used: a point-matched 1-to-1 multi-block grid, and an overset multi-block grid. The 1-to-1 grid, generally of much poorer quality and with less streamwise resolution than the overset grid, is found to be too coarse to adequately resolve the surface pressures. However, the global forces and moments are nonetheless similar to those computed using the overset grid. The effect of three different turbulence models is assessed using the 1-to-1 grid. Surface pressures are very similar overall, and the drag variation due to turbulence model is 18 drag counts. Most of this drag variation is in the friction component, and is attributed in part to insufficient grid resolution of the 1-to-1 grid. The misnomer of 'fully turbulent' computations is discussed; comparisons are made using different transition locations and their effects on the global forces and moments are quantified. Finally, the effect of two different versions of a widely used one-equation turbulence model is explored.

  8. Petrophysical analysis of limestone rocks by nuclear logging and 3D high-resolution X-ray computed microtomography

    NASA Astrophysics Data System (ADS)

    Oliveira, M. F. S.; Lima, I.; Ferrucio, P. L.; Abreu, C. J.; Borghi, L.; Lopes, R. T.

    2011-10-01

    This study presents the pore-space system analysis of the 2-ITAB-1-RJ well cores, which were drilled in the São José do Itaboraí Basin, in the state of Rio de Janeiro, Brasil. The analysis presented herein has been developed based on two techniques: nuclear logging and 3D high-resolution X-ray computed microtomography. Nuclear logging has been proven to be the technique that provides better quality and more quantitative information about the porosity using radioactive sources. The Density Gamma Probe and the Neutron Sonde used in this work provide qualitative information about bulk density variations and compensated porosity of the geological formation. The samples obtained from the well cores were analyzed by microtomography. The use of this technique in sedimentary rocks allows quantitative evaluation of pore system and generates high-resolution 3D images (˜microns order). The images and data obtained by microtomography were integrated with the response obtained by nuclear logging. The results obtained by these two techniques allow the understanding of the pore-size distribution and connectivity, as well as the porosity values. Both techniques are important and they complement each other.

  9. 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.

  10. 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.

  11. Applying and evaluating computer-animated tutors

    NASA Astrophysics Data System (ADS)

    Massaro, Dominic W.; Bosseler, Alexis; Stone, Patrick S.; Connors, Pamela

    2002-05-01

    We have developed computer-assisted speech and language tutors for deaf, hard of hearing, and autistic children. Our language-training program utilizes our computer-animated talking head, Baldi, as the conversational agent, who guides students through a variety of exercises designed to teach vocabulary and grammer, to improve speech articulation, and to develop linguistic and phonological awareness. Baldi is an accurate three-dimensional animated talking head appropriately aligned with either synthesized or natural speech. Baldi has a tongue and palate, which can be displayed by making his skin transparent. Two specific language-training programs have been evaluated to determine if they improve word learning and speech articulation. The results indicate that the programs are effective in teaching receptive and productive language. Advantages of utilizing a computer-animated agent as a language tutor are the popularity of computers and embodied conversational agents with autistic kids, the perpetual availability of the program, and individualized instruction. Students enjoy working with Baldi because he offers extreme patience, he doesn't become angry, tired, or bored, and he is in effect a perpetual teaching machine. The results indicate that the psychology and technology of Baldi holds great promise in language learning and speech therapy. [Work supported by NSF Grant Nos. CDA-9726363 and BCS-9905176 and Public Health Service Grant No. PHS R01 DC00236.

  12. The DANTE Boltzmann transport solver: An unstructured mesh, 3-D, spherical harmonics algorithm compatible with parallel computer architectures

    SciTech Connect

    McGhee, J.M.; Roberts, R.M.; Morel, J.E.

    1997-06-01

    A spherical harmonics research code (DANTE) has been developed which is compatible with parallel computer architectures. DANTE provides 3-D, multi-material, deterministic, transport capabilities using an arbitrary finite element mesh. The linearized Boltzmann transport equation is solved in a second order self-adjoint form utilizing a Galerkin finite element spatial differencing scheme. The core solver utilizes a preconditioned conjugate gradient algorithm. Other distinguishing features of the code include options for discrete-ordinates and simplified spherical harmonics angular differencing, an exact Marshak boundary treatment for arbitrarily oriented boundary faces, in-line matrix construction techniques to minimize memory consumption, and an effective diffusion based preconditioner for scattering dominated problems. Algorithm efficiency is demonstrated for a massively parallel SIMD architecture (CM-5), and compatibility with MPP multiprocessor platforms or workstation clusters is anticipated.

  13. Voxelization algorithms for geospatial applications: Computational methods for voxelating spatial datasets of 3D city models containing 3D surface, curve and point data models.

    PubMed

    Nourian, Pirouz; Gonçalves, Romulo; Zlatanova, Sisi; Ohori, Ken Arroyo; Vu Vo, Anh

    2016-01-01

    Voxel representations have been used for years in scientific computation and medical imaging. The main focus of our research is to provide easy access to methods for making large-scale voxel models of built environment for environmental modelling studies while ensuring they are spatially correct, meaning they correctly represent topological and semantic relations among objects. In this article, we present algorithms that generate voxels (volumetric pixels) out of point cloud, curve, or surface objects. The algorithms for voxelization of surfaces and curves are a customization of the topological voxelization approach [1]; we additionally provide an extension of this method for voxelization of point clouds. The developed software has the following advantages:•It provides easy management of connectivity levels in the resulting voxels.•It is not dependant on any external library except for primitive types and constructs; therefore, it is easy to integrate them in any application.•One of the algorithms is implemented in C++ and C for platform independence and efficiency.

  14. Voxelization algorithms for geospatial applications: Computational methods for voxelating spatial datasets of 3D city models containing 3D surface, curve and point data models.

    PubMed

    Nourian, Pirouz; Gonçalves, Romulo; Zlatanova, Sisi; Ohori, Ken Arroyo; Vu Vo, Anh

    2016-01-01

    Voxel representations have been used for years in scientific computation and medical imaging. The main focus of our research is to provide easy access to methods for making large-scale voxel models of built environment for environmental modelling studies while ensuring they are spatially correct, meaning they correctly represent topological and semantic relations among objects. In this article, we present algorithms that generate voxels (volumetric pixels) out of point cloud, curve, or surface objects. The algorithms for voxelization of surfaces and curves are a customization of the topological voxelization approach [1]; we additionally provide an extension of this method for voxelization of point clouds. The developed software has the following advantages:•It provides easy management of connectivity levels in the resulting voxels.•It is not dependant on any external library except for primitive types and constructs; therefore, it is easy to integrate them in any application.•One of the algorithms is implemented in C++ and C for platform independence and efficiency. PMID:27408832

  15. A full-field and real-time 3D surface imaging augmented DOT system for in-vivo small animal studies

    NASA Astrophysics Data System (ADS)

    Yi, Steven X.; Yang, Bingcheng; Yin, Gongjie

    2010-02-01

    A crucial parameter in Diffuse Optical Tomography (DOT) is the construction of an accurate forward model, which greatly depends on tissue boundary. Since photon propagation is a three-dimensional volumetric problem, extraction and subsequent modeling of three-dimensional boundaries is essential. Original experimental demonstration of the feasibility of DOT to reconstruct absorbers, scatterers and fluorochromes used phantoms or tissues confined appropriately to conform to easily modeled geometries such as a slab or a cylinder. In later years several methods have been developed to model photon propagation through diffuse media with complex boundaries using numerical solutions of the diffusion or transport equation (finite elements or differences) or more recently analytical methods based on the tangent-plane method . While optical examinations performed simultaneously with anatomical imaging modalities such as MRI provide well-defined boundaries, very limited progress has been done so far in extracting full-field (360 degree) boundaries for in-vivo three-dimensional DOT stand-alone imaging. In this paper, we present a desktop multi-spectrum in-vivo 3D DOT system for small animal imaging. This system is augmented with Technest's full-field 3D cameras. The built system has the capability of acquiring 3D object surface profiles in real time and registering 3D boundary with diffuse tomography. Extensive experiments are performed on phantoms and small animals by our collaborators at the Center for Molecular Imaging Research (CMIR) at Massachusetts General Hospital (MGH) and Harvard Medical School. Data has shown successful reconstructed DOT data with improved accuracy.

  16. In vivo 3D analysis of systemic effects after local heavy-ion beam irradiation in an animal model

    PubMed Central

    Nagata, Kento; Hashimoto, Chika; Watanabe-Asaka, Tomomi; Itoh, Kazusa; Yasuda, Takako; Ohta, Kousaku; Oonishi, Hisako; Igarashi, Kento; Suzuki, Michiyo; Funayama, Tomoo; Kobayashi, Yasuhiko; Nishimaki, Toshiyuki; Katsumura, Takafumi; Oota, Hiroki; Ogawa, Motoyuki; Oga, Atsunori; Ikemoto, Kenzo; Itoh, Hiroshi; Kutsuna, Natsumaro; Oda, Shoji; Mitani, Hiroshi

    2016-01-01

    Radiotherapy is widely used in cancer treatment. In addition to inducing effects in the irradiated area, irradiation may induce effects on tissues close to and distant from the irradiated area. Japanese medaka, Oryzias latipes, is a small teleost fish and a model organism for evaluating the environmental effects of radiation. In this study, we applied low-energy carbon-ion (26.7 MeV/u) irradiation to adult medaka to a depth of approximately 2.2 mm from the body surface using an irradiation system at the National Institutes for Quantum and Radiological Science and Technology. We histologically evaluated the systemic alterations induced by irradiation using serial sections of the whole body, and conducted a heart rate analysis. Tissues from the irradiated side showed signs of serious injury that corresponded with the radiation dose. A 3D reconstruction analysis of the kidney sections showed reductions in the kidney volume and blood cell mass along the irradiated area, reflecting the precise localization of the injuries caused by carbon-beam irradiation. Capillary aneurysms were observed in the gill in both ventrally and dorsally irradiated fish, suggesting systemic irradiation effects. The present study provides an in vivo model for further investigation of the effects of irradiation beyond the locally irradiated area. PMID:27345436

  17. Internal structures of scaffold-free 3D cell cultures visualized by synchrotron radiation-based micro-computed tomography

    NASA Astrophysics Data System (ADS)

    Saldamli, Belma; Herzen, Julia; Beckmann, Felix; Tübel, Jutta; Schauwecker, Johannes; Burgkart, Rainer; Jürgens, Philipp; Zeilhofer, Hans-Florian; Sader, Robert; Müller, Bert

    2008-08-01

    Recently the importance of the third dimension in cell biology has been better understood, resulting in a re-orientation towards three-dimensional (3D) cultivation. Yet adequate tools for their morphological characterization have to be established. Synchrotron radiation-based micro computed tomography (SRμCT) allows visualizing such biological systems with almost isotropic micrometer resolution, non-destructively. We have applied SRμCT for studying the internal morphology of human osteoblast-derived, scaffold-free 3D cultures, termed histoids. Primary human osteoblasts, isolated from femoral neck spongy bone, were grown as 2D culture in non-mineralizing osteogenic medium until a rather thick, multi-cellular membrane was formed. This delicate system was intentionally released to randomly fold itself. The folded cell cultures were grown to histoids of cubic milli- or centimeter size in various combinations of mineralizing and non-mineralizing osteogenic medium for a total period of minimum 56 weeks. The SRμCT-measurements were performed in the absorption contrast mode at the beamlines BW 2 and W 2 (HASYLAB at DESY, Hamburg, Germany), operated by the GKSS-Research Center. To investigate the entire volume of interest several scans were performed under identical conditions and registered to obtain one single dataset of each sample. The histoids grown under different conditions exhibit similar external morphology of globular or ovoid shape. The SRμCT-examination revealed the distinctly different morphological structures inside the histoids. One obtains details of the histoids that permit to identify and select the most promising slices for subsequent histological characterization.

  18. Computer-aided detection of lung nodules: false positive reduction using a 3D gradient field method

    NASA Astrophysics Data System (ADS)

    Ge, Zhanyu; Sahiner, Berkman; Chan, Heang-Ping; Hadjiiski, Lubomir M.; Wei, Jun; Bogot, Naama; Cascade, Philip N.; Kazerooni, Ella A.; Zhou, Chuan

    2004-05-01

    We are developing a computer-aided detection system to aid radiologists in diagnosing lung cancer in thoracic computed tomographic (CT) images. The purpose of this study was to improve the false-positive (FP) reduction stage of our algorithm by developing and incorporating a gradient field technique. This technique extracts 3D shape information from the gray-scale values within a volume of interest. The gradient field feature values are higher for spherical objects, and lower for elongated and irregularly-shaped objects. A data set of 55 thin CT scans from 40 patients was used to evaluate the usefulness of the gradient field technique. After initial nodule candidate detection and rule-based first stage FP reduction, there were 3487 FP and 65 true positive (TP) objects in our data set. Linear discriminant classifiers with and without the gradient field feature were designed for the second stage FP reduction. The accuracy of these classifiers was evaluated using the area Az under the receiver operating characteristic (ROC) curve. The Az values were 0.93 and 0.91 with and without the gradient field feature, respectively. The improvement with the gradient field feature was statistically significant (p=0.01).

  19. Taming supersymmetric defects in 3d-3d correspondence

    NASA Astrophysics Data System (ADS)

    Gang, Dongmin; Kim, Nakwoo; Romo, Mauricio; Yamazaki, Masahito

    2016-07-01

    We study knots in 3d Chern-Simons theory with complex gauge group {SL}(N,{{C}}), in the context of its relation with 3d { N }=2 theory (the so-called 3d-3d correspondence). The defect has either co-dimension 2 or co-dimension 4 inside the 6d (2,0) theory, which is compactified on a 3-manifold \\hat{M}. We identify such defects in various corners of the 3d-3d correspondence, namely in 3d {SL}(N,{{C}}) CS theory, in 3d { N }=2 theory, in 5d { N }=2 super Yang-Mills theory, and in the M-theory holographic dual. We can make quantitative checks of the 3d-3d correspondence by computing partition functions at each of these theories. This Letter is a companion to a longer paper [1], which contains more details and more results.

  20. The Intercomparison of 3D Radiation Codes (I3RC): Showcasing Mathematical and Computational Physics in a Critical Atmospheric Application

    NASA Astrophysics Data System (ADS)

    Davis, A. B.; Cahalan, R. F.

    2001-05-01

    The Intercomparison of 3D Radiation Codes (I3RC) is an on-going initiative involving an international group of over 30 researchers engaged in the numerical modeling of three-dimensional radiative transfer as applied to clouds. Because of their strong variability and extreme opacity, clouds are indeed a major source of uncertainty in the Earth's local radiation budget (at GCM grid scales). Also 3D effects (at satellite pixel scales) invalidate the standard plane-parallel assumption made in the routine of cloud-property remote sensing at NASA and NOAA. Accordingly, the test-cases used in I3RC are based on inputs and outputs which relate to cloud effects in atmospheric heating rates and in real-world remote sensing geometries. The main objectives of I3RC are to (1) enable participants to improve their models, (2) publish results as a community, (3) archive source code, and (4) educate. We will survey the status of I3RC and its plans for the near future with a special emphasis on the mathematical models and computational approaches. We will also describe some of the prime applications of I3RC's efforts in climate models, cloud-resolving models, and remote-sensing observations of clouds, or that of the surface in their presence. In all these application areas, computational efficiency is the main concern and not accuracy. One of I3RC's main goals is to document the performance of as wide a variety as possible of three-dimensional radiative transfer models for a small but representative number of ``cases.'' However, it is dominated by modelers working at the level of linear transport theory (i.e., they solve the radiative transfer equation) and an overwhelming majority of these participants use slow-but-robust Monte Carlo techniques. This means that only a small portion of the efficiency vs. accuracy vs. flexibility domain is currently populated by I3RC participants. To balance this natural clustering the present authors have organized a systematic outreach towards

  1. Visualizing Infrared (IR) Spectroscopy with Computer Animation

    NASA Technical Reports Server (NTRS)

    Abrams, Charles B.; Fine, Leonard W.

    1996-01-01

    IR Tutor, an interactive, animated infrared (IR) spectroscopy tutorial has been developed for Macintosh and IBM-compatible computers. Using unique color animation, complicated vibrational modes can be introduced to beginning students. Rules governing the appearance of IR absorption bands become obvious because the vibrational modes can be visualized. Each peak in the IR spectrum is highlighted, and the animation of the corresponding normal mode can be shown. Students can study each spectrum stepwise, or click on any individual peak to see its assignment. Important regions of each spectrum can be expanded and spectra can be overlaid for comparison. An introduction to the theory of IR spectroscopy is included, making the program a complete instructional package. Our own success in using this software for teaching and research in both academic and industrial environments will be described. IR Tutor consists of three sections: (1) The 'Introduction' is a review of basic principles of spectroscopy. (2) 'Theory' begins with the classical model of a simple diatomic molecule and is expanded to include larger molecules by introducing normal modes and group frequencies. (3) 'Interpretation' is the heart of the tutorial. Thirteen IR spectra are analyzed in detail, covering the most important functional groups. This section features color animation of each normal mode, full interactivity, overlay of related spectra, and expansion of important regions. This section can also be used as a reference.

  2. Modeling Warm Dense Matter Experiments using the 3D ALE-AMR Code and the Move Toward Exascale Computing

    SciTech Connect

    Koniges, A; Eder, E; Liu, W; Barnard, J; Friedman, A; Logan, G; Fisher, A; Masers, N; Bertozzi, A

    2011-11-04

    The Neutralized Drift Compression Experiment II (NDCX II) is an induction accelerator planned for initial commissioning in 2012. The final design calls for a 3 MeV, Li+ ion beam, delivered in a bunch with characteristic pulse duration of 1 ns, and transverse dimension of order 1 mm. The NDCX II will be used in studies of material in the warm dense matter (WDM) regime, and ion beam/hydrodynamic coupling experiments relevant to heavy ion based inertial fusion energy. We discuss recent efforts to adapt the 3D ALE-AMR code to model WDM experiments on NDCX II. The code, which combines Arbitrary Lagrangian Eulerian (ALE) hydrodynamics with Adaptive Mesh Refinement (AMR), has physics models that include ion deposition, radiation hydrodynamics, thermal diffusion, anisotropic material strength with material time history, and advanced models for fragmentation. Experiments at NDCX-II will explore the process of bubble and droplet formation (two-phase expansion) of superheated metal solids using ion beams. Experiments at higher temperatures will explore equation of state and heavy ion fusion beam-to-target energy coupling efficiency. Ion beams allow precise control of local beam energy deposition providing uniform volumetric heating on a timescale shorter than that of hydrodynamic expansion. The ALE-AMR code does not have any export control restrictions and is currently running at the National Energy Research Scientific Computing Center (NERSC) at LBNL and has been shown to scale well to thousands of CPUs. New surface tension models that are being implemented and applied to WDM experiments. Some of the approaches use a diffuse interface surface tension model that is based on the advective Cahn-Hilliard equations, which allows for droplet breakup in divergent velocity fields without the need for imposed perturbations. Other methods require seeding or other methods for droplet breakup. We also briefly discuss the effects of the move to exascale computing and related

  3. Computation of load performance and other parameters of extra high speed modified Lundell alternators from 3D-FE magnetic field solutions

    NASA Technical Reports Server (NTRS)

    Wang, R.; Demerdash, N. A.

    1992-01-01

    The combined magnetic vector potential - magnetic scalar potential method of computation of 3D magnetic fields by finite elements, introduced in a companion paper, in combination with state modeling in the abc-frame of reference, are used for global 3D magnetic field analysis and machine performance computation under rated load and overload condition in an example 14.3 kVA modified Lundell alternator. The results vividly demonstrate the 3D nature of the magnetic field in such machines, and show how this model can be used as an excellent tool for computation of flux density distributions, armature current and voltage waveform profiles and harmonic contents, as well as computation of torque profiles and ripples. Use of the model in gaining insight into locations of regions in the magnetic circuit with heavy degrees of saturation is demonstrated. Experimental results which correlate well with the simulations of the load case are given.

  4. 'Towers in the Tempest' Computer Animation Submission

    NASA Technical Reports Server (NTRS)

    Shirah, Greg

    2008-01-01

    The following describes a computer animation that has been submitted to the ACM/SIGGRAPH 2008 computer graphics conference: 'Towers in the Tempest' clearly communicates recent scientific research into how hurricanes intensify. This intensification can be caused by a phenomenon called a 'hot tower.' For the first time, research meteorologists have run complex atmospheric simulations at a very fine temporal resolution of 3 minutes. Combining this simulation data with satellite observations enables detailed study of 'hot towers.' The science of 'hot towers' is described using: satellite observation data, conceptual illustrations, and a volumetric atmospheric simulation data. The movie starts by showing a 'hot tower' observed by NASA's Tropical Rainfall Measuring Mission (TRMM) spacecraft's three dimensional precipitation radar data of Hurricane Bonnie. Next, the dynamics of a hurricane and the formation of 'hot towers' are briefly explained using conceptual illustrations. Finally, volumetric cloud, wind, and vorticity data from a supercomputer simulation of Hurricane Bonnie are shown using volume techniques such as ray marching.

  5. Rapid Reconstitution Packages (RRPs) implemented by integration of computational fluid dynamics (CFD) and 3D printed microfluidics.

    PubMed

    Chi, Albert; Curi, Sebastian; Clayton, Kevin; Luciano, David; Klauber, Kameron; Alexander-Katz, Alfredo; D'hers, Sebastian; Elman, Noel M

    2014-08-01

    Rapid Reconstitution Packages (RRPs) are portable platforms that integrate microfluidics for rapid reconstitution of lyophilized drugs. Rapid reconstitution of lyophilized drugs using standard vials and syringes is an error-prone process. RRPs were designed using computational fluid dynamics (CFD) techniques to optimize fluidic structures for rapid mixing and integrating physical properties of targeted drugs and diluents. Devices were manufactured using stereo lithography 3D printing for micrometer structural precision and rapid prototyping. Tissue plasminogen activator (tPA) was selected as the initial model drug to test the RRPs as it is unstable in solution. tPA is a thrombolytic drug, stored in lyophilized form, required in emergency settings for which rapid reconstitution is of critical importance. RRP performance and drug stability were evaluated by high-performance liquid chromatography (HPLC) to characterize release kinetics. In addition, enzyme-linked immunosorbent assays (ELISAs) were performed to test for drug activity after the RRPs were exposed to various controlled temperature conditions. Experimental results showed that RRPs provided effective reconstitution of tPA that strongly correlated with CFD results. Simulation and experimental results show that release kinetics can be adjusted by tuning the device structural dimensions and diluent drug physical parameters. The design of RRPs can be tailored for a number of applications by taking into account physical parameters of the active pharmaceutical ingredients (APIs), excipients, and diluents. RRPs are portable platforms that can be utilized for reconstitution of emergency drugs in time-critical therapies.

  6. A Real-Time Magnetoencephalography Brain-Computer Interface Using Interactive 3D Visualization and the Hadoop Ecosystem.

    PubMed

    McClay, Wilbert A; Yadav, Nancy; Ozbek, Yusuf; Haas, Andy; Attias, Hagaii T; Nagarajan, Srikantan S

    2015-09-30

    Ecumenically, the fastest growing segment of Big Data is human biology-related data and the annual data creation is on the order of zetabytes. The implications are global across industries, of which the treatment of brain related illnesses and trauma could see the most significant and immediate effects. The next generation of health care IT and sensory devices are acquiring and storing massive amounts of patient related data. An innovative Brain-Computer Interface (BCI) for interactive 3D visualization is presented utilizing the Hadoop Ecosystem for data analysis and storage. The BCI is an implementation of Bayesian factor analysis algorithms that can distinguish distinct thought actions using magneto encephalographic (MEG) brain signals. We have collected data on five subjects yielding 90% positive performance in MEG mid- and post-movement activity. We describe a driver that substitutes the actions of the BCI as mouse button presses for real-time use in visual simulations. This process has been added into a flight visualization demonstration. By thinking left or right, the user experiences the aircraft turning in the chosen direction. The driver components of the BCI can be compiled into any software and substitute a user's intent for specific keyboard strikes or mouse button presses. The BCI's data analytics OPEN ACCESS Brain. Sci. 2015, 5 420 of a subject's MEG brainwaves and flight visualization performance are stored and analyzed using the Hadoop Ecosystem as a quick retrieval data warehouse.

  7. A Real-Time Magnetoencephalography Brain-Computer Interface Using Interactive 3D Visualization and the Hadoop Ecosystem.

    PubMed

    McClay, Wilbert A; Yadav, Nancy; Ozbek, Yusuf; Haas, Andy; Attias, Hagaii T; Nagarajan, Srikantan S

    2015-01-01

    Ecumenically, the fastest growing segment of Big Data is human biology-related data and the annual data creation is on the order of zetabytes. The implications are global across industries, of which the treatment of brain related illnesses and trauma could see the most significant and immediate effects. The next generation of health care IT and sensory devices are acquiring and storing massive amounts of patient related data. An innovative Brain-Computer Interface (BCI) for interactive 3D visualization is presented utilizing the Hadoop Ecosystem for data analysis and storage. The BCI is an implementation of Bayesian factor analysis algorithms that can distinguish distinct thought actions using magneto encephalographic (MEG) brain signals. We have collected data on five subjects yielding 90% positive performance in MEG mid- and post-movement activity. We describe a driver that substitutes the actions of the BCI as mouse button presses for real-time use in visual simulations. This process has been added into a flight visualization demonstration. By thinking left or right, the user experiences the aircraft turning in the chosen direction. The driver components of the BCI can be compiled into any software and substitute a user's intent for specific keyboard strikes or mouse button presses. The BCI's data analytics OPEN ACCESS Brain. Sci. 2015, 5 420 of a subject's MEG brainwaves and flight visualization performance are stored and analyzed using the Hadoop Ecosystem as a quick retrieval data warehouse. PMID:26437432

  8. Rational Design of Prevascularized Large 3D Tissue Constructs Using Computational Simulations and Biofabrication of Geometrically Controlled Microvessels.

    PubMed

    Arrigoni, Chiara; Bongio, Matilde; Talò, Giuseppe; Bersini, Simone; Enomoto, Junko; Fukuda, Junji; Moretti, Matteo

    2016-07-01

    A major challenge in the development of clinically relevant 3D tissue constructs is the formation of vascular networks for oxygenation, nutrient supply, and waste removal. To this end, this study implements a multimodal approach for the promotion of vessel-like structures formation in stiff fibrin hydrogels. Computational simulations have been performed to identify the easiest microchanneled configuration assuring normoxic conditions throughout thick cylindrical hydrogels (8 mm height, 6 mm ∅), showing that in our configuration a minimum of three microchannels (600 μm ∅), placed in a non-planar disposition, is required. Using small hydrogel bricks with oxygen distribution equal to the microchanneled configuration, this study demonstrates that among different culture conditions, co-culture of mesenchymal and endothelial cells supplemented with ANG-1 and VEGF leads to the most developed vascular network. Microchanneled hydrogels have been then cultured in the same conditions both statically and in a bioreactor for 7 d. Unexpectedly, the combination between shear forces and normoxic conditions is unable to promote microvascular networks formation in three-channeled hydrogels. Differently, application of either shear forces or normoxic conditions alone results in microvessels outgrowth. These results suggest that to induce angiogenesis in engineered constructs, complex interactions between several biochemical and biophysical parameters have to be modulated.

  9. A Real-Time Magnetoencephalography Brain-Computer Interface Using Interactive 3D Visualization and the Hadoop Ecosystem

    PubMed Central

    McClay, Wilbert A.; Yadav, Nancy; Ozbek, Yusuf; Haas, Andy; Attias, Hagaii T.; Nagarajan, Srikantan S.

    2015-01-01

    Ecumenically, the fastest growing segment of Big Data is human biology-related data and the annual data creation is on the order of zetabytes. The implications are global across industries, of which the treatment of brain related illnesses and trauma could see the most significant and immediate effects. The next generation of health care IT and sensory devices are acquiring and storing massive amounts of patient related data. An innovative Brain-Computer Interface (BCI) for interactive 3D visualization is presented utilizing the Hadoop Ecosystem for data analysis and storage. The BCI is an implementation of Bayesian factor analysis algorithms that can distinguish distinct thought actions using magneto encephalographic (MEG) brain signals. We have collected data on five subjects yielding 90% positive performance in MEG mid- and post-movement activity. We describe a driver that substitutes the actions of the BCI as mouse button presses for real-time use in visual simulations. This process has been added into a flight visualization demonstration. By thinking left or right, the user experiences the aircraft turning in the chosen direction. The driver components of the BCI can be compiled into any software and substitute a user’s intent for specific keyboard strikes or mouse button presses. The BCI’s data analytics of a subject’s MEG brainwaves and flight visualization performance are stored and analyzed using the Hadoop Ecosystem as a quick retrieval data warehouse. PMID:26437432

  10. The 3D MHD code GOEMHD3 for astrophysical plasmas with large Reynolds numbers. Code description, verification, and computational performance

    NASA Astrophysics Data System (ADS)

    Skála, J.; Baruffa, F.; Büchner, J.; Rampp, M.

    2015-08-01

    Context. The numerical simulation of turbulence and flows in almost ideal astrophysical plasmas with large Reynolds numbers motivates the implementation of magnetohydrodynamical (MHD) computer codes with low resistivity. They need to be computationally efficient and scale well with large numbers of CPU cores, allow obtaining a high grid resolution over large simulation domains, and be easily and modularly extensible, for instance, to new initial and boundary conditions. Aims: Our aims are the implementation, optimization, and verification of a computationally efficient, highly scalable, and easily extensible low-dissipative MHD simulation code for the numerical investigation of the dynamics of astrophysical plasmas with large Reynolds numbers in three dimensions (3D). Methods: The new GOEMHD3 code discretizes the ideal part of the MHD equations using a fast and efficient leap-frog scheme that is second-order accurate in space and time and whose initial and boundary conditions can easily be modified. For the investigation of diffusive and dissipative processes the corresponding terms are discretized by a DuFort-Frankel scheme. To always fulfill the Courant-Friedrichs-Lewy stability criterion, the time step of the code is adapted dynamically. Numerically induced local oscillations are suppressed by explicit, externally controlled diffusion terms. Non-equidistant grids are implemented, which enhance the spatial resolution, where needed. GOEMHD3 is parallelized based on the hybrid MPI-OpenMP programing paradigm, adopting a standard two-dimensional domain-decomposition approach. Results: The ideal part of the equation solver is verified by performing numerical tests of the evolution of the well-understood Kelvin-Helmholtz instability and of Orszag-Tang vortices. The accuracy of solving the (resistive) induction equation is tested by simulating the decay of a cylindrical current column. Furthermore, we show that the computational performance of the code scales very

  11. GRID2D/3D: A computer program for generating grid systems in complex-shaped two- and three-dimensional spatial domains. Part 1: Theory and method

    NASA Technical Reports Server (NTRS)

    Shih, T. I.-P.; Bailey, R. T.; Nguyen, H. L.; Roelke, R. J.

    1990-01-01

    An efficient computer program, called GRID2D/3D was developed to generate single and composite grid systems within geometrically complex two- and three-dimensional (2- and 3-D) spatial domains that can deform with time. GRID2D/3D generates single grid systems by using algebraic grid generation methods based on transfinite interpolation in which the distribution of grid points within the spatial domain is controlled by stretching functions. All single grid systems generated by GRID2D/3D can have grid lines that are continuous and differentiable everywhere up to the second-order. Also, grid lines can intersect boundaries of the spatial domain orthogonally. GRID2D/3D generates composite grid systems by patching together two or more single grid systems. The patching can be discontinuous or continuous. For continuous composite grid systems, the grid lines are continuous and differentiable everywhere up to the second-order except at interfaces where different single grid systems meet. At interfaces where different single grid systems meet, the grid lines are only differentiable up to the first-order. For 2-D spatial domains, the boundary curves are described by using either cubic or tension spline interpolation. For 3-D spatial domains, the boundary surfaces are described by using either linear Coon's interpolation, bi-hyperbolic spline interpolation, or a new technique referred to as 3-D bi-directional Hermite interpolation. Since grid systems generated by algebraic methods can have grid lines that overlap one another, GRID2D/3D contains a graphics package for evaluating the grid systems generated. With the graphics package, the user can generate grid systems in an interactive manner with the grid generation part of GRID2D/3D. GRID2D/3D is written in FORTRAN 77 and can be run on any IBM PC, XT, or AT compatible computer. In order to use GRID2D/3D on workstations or mainframe computers, some minor modifications must be made in the graphics part of the program; no

  12. 3D computed tomographic evaluation of the upper airway space of patients undergoing mandibular distraction osteogenesis for micrognathia.

    PubMed

    Bianchi, A; Betti, E; Badiali, G; Ricotta, F; Marchetti, C; Tarsitano, A

    2015-10-01

    Mandibular distraction osteogenesis (MDO) is currently an accepted method of treatment for patients requiring reconstruction of hypoplastic mandibles. To date one of the unsolved problems is how to assess the quantitative increase of mandible length needed to achieve a significant change in the volume of the posterior airway space (PAS) in children with mandibular micrognathia following distraction osteogenesis. The purpose of this study is to present quantitative volumetric evaluation of PAS in young patients having distraction osteogenesis for micrognathia using 3D-CT data sets and compare it with pre-operative situation. In this observational retrospective study, we report our experience in five consecutive patients who underwent MDO in an attempt to relieve severe upper airway obstruction. Each patient was evaluated before treatment (T0) and at the end of distraction procedure (T1) with computer tomography (CT) in axial, coronal, and sagittal planes and three-dimensional CT of the facial bones and upper airway. Using parameters to extract only data within anatomic constraints, a digital set of the edited upper airway volume was obtained. The volume determination was used for volumetric qualification of upper airway. The computed tomographic digital data were used to evaluate the upper airway volumes both pre-distraction and post-distraction. The mean length of distraction was 23 mm. Quantitative assessment of upper airway volume before and after distraction demonstrated increased volumes ranging from 84% to 3,087% with a mean of 536%. In conclusion, our study seems to show that DO can significantly increase the volume of the PAS in patients with upper airway obstruction following micrognathia, by an average of 5 times. Furthermore, the worse is the starting volume, the greater the increase in PAS to equal distraction.

  13. Comparison of 3D Maximum A Posteriori and Filtered Backprojection algorithms for high resolution animal imaging in microPET

    SciTech Connect

    Chatziioannou, A.; Qi, J.; Moore, A.; Annala, A.; Nguyen, K.; Leahy, R.M.; Cherry, S.R.

    2000-01-01

    We have evaluated the performance of two three dimensional reconstruction algorithms with data acquired from microPET, a high resolution tomograph dedicated to small animal imaging. The first was a linear filtered-backprojection algorithm (FBP) with reprojection of the missing data and the second was a statistical maximum-aposteriori probability algorithm (MAP). The two algorithms were evaluated in terms of their resolution performance, both in phantoms and in vivo. Sixty independent realizations of a phantom simulating the brain of a baby monkey were acquired, each containing 3 million counts. Each of these realizations was reconstructed independently with both algorithms. The ensemble of the sixty reconstructed realizations was used to estimate the standard deviation as a measure of the noise for each reconstruction algorithm. More detail was recovered in the MAP reconstruction without an increase in noise relative to FBP. Studies in a simple cylindrical compartment phantom demonstrated improved recovery of known activity ratios with MAP. Finally in vivo studies also demonstrated a clear improvement in spatial resolution using the MAP algorithm. The quantitative accuracy of the MAP reconstruction was also evaluated by comparison with autoradiography and direct well counting of tissue samples and was shown to be superior.

  14. High resolution cone beam X-ray computed tomography of 3D-microstructures of cast Al-alloys

    SciTech Connect

    Kastner, Johann; Harrer, Bernhard; Degischer, H. Peter

    2011-01-15

    X-ray computed tomography (XCT) has become a very important method for non-destructive 3D-characterisation of materials. XCT systems with cone beam geometry, micro- or nano-focus tubes and matrix detectors are increasingly used in research and non-destructive testing. Spatial resolutions down to 1 {mu}m can be reached with such XCT-systems for heterogeneities in metals with high absorption contrast. High resolution cone beam XCT is applied to five different Al-alloys: AlMg5Si7, AlCu4Mg1, AlZn6Mg2Cu2, AlZn8Mg2Cu2 and AlSi12Ni1. Up to four different types of inhomogeneities are segmented in one alloy using voxel sizes between (0.4 {mu}m){sup 3} and (2.3 {mu}m){sup 3}. Target metallography and elemental analysis by energy dispersive X-ray analysis are used to identify the inhomogeneities. The possibilities and restrictions of XCT applied to Al-alloys are discussed. AlMg5Si7 XCT-data with a voxel size of (0.4 {mu}m){sup 3} show inhomogeneities with brighter grey-values than the Al-matrix identified as elongated Fe-aluminides, and those with lower grey-values identified as pores and Mg{sub 2}Si-particles with a 'Chinese script-like' structure. Higher-absorbing interdendritic Al-Al{sub 2}Cu-eutectic regions appear brighter than the Al-dendrites in the CT-data of AlCu4Mg1 with (1.1 {mu}m){sup 3}/voxel, whereas pores > 4 {mu}m appear darker than the Al-matrix. The size and the 3D-structure of the {alpha}-Al dendrite arms with a diameter of 50-100 {mu}m are determined in samples from chill cast billets of AlCu4Mg1 and AlZn6Mg2Cu2 alloys. The irregular interdendritic regions containing eutectic segregations with Cu- and Zn-rich phases are > 5 {mu}m wide. Equally absorbing primary equi-axed Al{sub 3}(Sc, Zr) particles > 5 {mu}m are distinguished in the centres of the dendrites by the level of sphericity values. The distribution of Ni- and Fe-aluminides in a squeeze cast AlSi12Ni1-alloy is imaged with (0.4 {mu}m){sup 3}/voxel, but the Si-phase cannot be segmented.

  15. Computational Design of Animated Mechanical Characters

    NASA Astrophysics Data System (ADS)

    Coros, Stelian; Thomaszewski, Bernhard; DRZ Team Team

    2014-03-01

    A factor key to the appeal of modern CG movies and video-games is that the virtual worlds they portray place no bounds on what can be imagined. Rapid manufacturing devices hold the promise of bringing this type of freedom to our own world, by enabling the fabrication of physical objects whose appearance, deformation behaviors and motions can be precisely specified. In order to unleash the full potential of this technology however, computational design methods that create digital content suitable for fabrication need to be developed. In recent work, we presented a computational design system that allows casual users to create animated mechanical characters. Given an articulated character as input, the user designs the animated character by sketching motion curves indicating how they should move. For each motion curve, our framework creates an optimized mechanism that reproduces it as closely as possible. The resulting mechanisms are attached to the character and then connected to each other using gear trains, which are created in a semi-automated fashion. The mechanical assemblies generated with our system can be driven with a single input driver, such as a hand-operated crank or an electric motor, and they can be fabricated using rapid prototyping devices.

  16. The polyGeVero® software for fast and easy computation of 3D radiotherapy dosimetry data

    NASA Astrophysics Data System (ADS)

    Kozicki, Marek; Maras, Piotr

    2015-01-01

    The polyGeVero® software package was elaborated for calculations of 3D dosimetry data such as the polymer gel dosimetry. It comprises four workspaces designed for: i) calculating calibrations, ii) storing calibrations in a database, iii) calculating dose distribution 3D cubes, iv) comparing two datasets e.g. a measured one with a 3D dosimetry with a calculated one with the aid of a treatment planning system. To accomplish calculations the software was equipped with a number of tools such as the brachytherapy isotopes database, brachytherapy dose versus distance calculation based on the line approximation approach, automatic spatial alignment of two 3D dose cubes for comparison purposes, 3D gamma index, 3D gamma angle, 3D dose difference, Pearson's coefficient, histograms calculations, isodoses superimposition for two datasets, and profiles calculations in any desired direction. This communication is to briefly present the main functions of the software and report on the speed of calculations performed by polyGeVero®.

  17. Automatic reconstruction of 3D urban landscape by computing connected regions and assigning them an average altitude from LiDAR point cloud image

    NASA Astrophysics Data System (ADS)

    Kawata, Yoshiyuki; Koizumi, Kohei

    2014-10-01

    The demand of 3D city modeling has been increasing in many applications such as urban planing, computer gaming with realistic city environment, car navigation system with showing 3D city map, virtual city tourism inviting future visitors to a virtual city walkthrough and others. We proposed a simple method for reconstructing a 3D urban landscape from airborne LiDAR point cloud data. The automatic reconstruction method of a 3D urban landscape was implemented by the integration of all connected regions, which were extracted and extruded from the altitude mask images. These mask images were generated from the gray scale LiDAR image by the altitude threshold ranges. In this study we demonstrated successfully in the case of Kanazawa city center scene by applying the proposed method to the airborne LiDAR point cloud data.

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

    SciTech Connect

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

    2015-01-13

    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 512{sup 3} to 8192{sup 3} 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 H{sup t} (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.

  19. SU-C-BRE-01: 3D Conformal Micro Irradiation Results of Four Treatment Sites for Preclinical Small Animal and Clinical Treatment Plans

    SciTech Connect

    Price, S; Yaddanapudi, S; Rangaraj, D; Izaguirre, E

    2014-06-15

    Purpose: Small animal irradiation can provide preclinical insights necessary for clinical advancement. In order to provide clinically relevant data, these small animal irradiations must be designed such that the treatment methods and results are comparable to clinical protocols, regardless of variations in treatment size and modality. Methods: Small animal treatments for four treatment sites (brain, liver, lung and spine) were investigated, accounting for change in treatment energy and target size. Up to five orthovoltage (300kVp) beams were used in the preclinical treatments, using circular, square, and conformal tungsten apertures, based on the treatment site. Treatments were delivered using the image guided micro irradiator (microIGRT). The plans were delivered to a mouse sized phantom and dose measurements in axial and coronal planes were performed using radiochromic film. The results of the clinical and preclinical protocols were characterized in terms of conformality number, CTV coverage, dose nonuniformity ratio, and organ at risk sparing. Results: Preclinical small animal treatment conformality was within 1–16% of clinical results for all treatment sites. The volume of the CTV receiving 100% of the prescription dose was typically within 10% of clinical values. The dose non-uniformity was consistently higher for preclinical treatments compared to clinical treatments, indicating hot spots in the target. The ratios of the mean dose in the target to the mean dose in an organ at risk were comparable if not better for preclinical versus clinical treatments. Finally, QUANTEC dose constraints were applied and the recommended morbidity limits were satisfied in each small animal treatment site. Conclusion: We have shown that for four treatment sites, preclinical 3D conformal small animal treatments can be clinically comparable if clinical protocols are followed. Using clinical protocols as the standard, preclinical irradiation methods can be altered and iteratively

  20. SRS Computer Animation and Drive Train System

    NASA Technical Reports Server (NTRS)

    Arthun, Daniel; Schachner, Christian

    2001-01-01

    The spinning rocket simulator (SRS) is an ongoing project at Oral Roberts University. The goal of the SRS is to gather crucial data concerning a spinning rocket under thrust for the purpose of analysis and correction of the coning motion experienced by this type of spacecraft maneuver. The computer animation simulates a virtual, scale model of the component of the SRS that represents the spacecraft itself. This component is known as the (VSM), or virtual spacecraft model. During actual physical simulation, this component of the SRS will experience a coning. The goal of the animation is to cone the VSM within that range to accurately represent the motion of the actual simulator. The drive system of the SRS is the apparatus that turns the actual simulator. It consists of a drive motor, motor mount and chain to power the simulator into motion. The motor mount is adjustable and rigid for high torque application. A digital stepper motor controller actuates the main drive motor for linear acceleration. The chain transfers power from the motor to the simulator via sprockets on both ends.

  1. Computer animation of Phanerozoic plate motions

    SciTech Connect

    Scotese, C.R. . Dept. of Geology)

    1992-01-01

    Since 1985, the PALEOMAP Project, in collaboration with research groups both in the US and abroad, has assembled a digital model that describes global plate motions during the last 600 million years. In this paper the authors present a series of computer animations that dynamically illustrates the movement of continents and terranes, and the evolution of the ocean basins since the breakup of the late Precambrian supercontinent. These animations depict the motion of the plates from both equatorial and polar perspectives. Mesozoic and Cenozoic plate tectonic reconstructions are based on a synthesis of linear magnetic anomalies, fracture zone locations, intracontinental rifts, collision and thrust belts, and zones of strike-slip. Paleozoic plate reconstructions, though more speculative, are based on evidence of past subduction, continental collision, and inferred sea floor spreading. The relative longitudinal positions of the continents during the Paleozoic and the width of intervening oceans have been adjusted to best explain changing biogeographic and paleoclimatic patterns. A new paleomagnetic/hot spot reference frame has been constructed that combines paleomagnetic data compiled by Rob Van der Voo (1992) with inferred motion relative to a fixed frame of hot spots. Using probable Early Mesozoic and Paleozoic hot spot tracks on the major continents, the authors have extended plate motions relative to the hot spot reference frame back to 400 million years.

  2. A Smart Cage With Uniform Wireless Power Distribution in 3D for Enabling Long-Term Experiments With Freely Moving Animals.

    PubMed

    Mirbozorgi, S Abdollah; Bahrami, Hadi; Sawan, Mohamad; Gosselin, Benoit

    2016-04-01

    This paper presents a novel experimental chamber with uniform wireless power distribution in 3D for enabling long-term biomedical experiments with small freely moving animal subjects. The implemented power transmission chamber prototype is based on arrays of parallel resonators and multicoil inductive links, to form a novel and highly efficient wireless power transmission system. The power transmitter unit includes several identical resonators enclosed in a scalable array of overlapping square coils which are connected in parallel to provide uniform power distribution along x and y. Moreover, the proposed chamber uses two arrays of primary resonators, facing each other, and connected in parallel to achieve uniform power distribution along the z axis. Each surface includes 9 overlapped coils connected in parallel and implemented into two layers of FR4 printed circuit board. The chamber features a natural power localization mechanism, which simplifies its implementation and ease its operation by avoiding the need for active detection and control mechanisms. A single power surface based on the proposed approach can provide a power transfer efficiency (PTE) of 69% and a power delivered to the load (PDL) of 120 mW, for a separation distance of 4 cm, whereas the complete chamber prototype provides a uniform PTE of 59% and a PDL of 100 mW in 3D, everywhere inside the chamber with a size of 27×27×16 cm(3). PMID:26011866

  3. A Smart Cage With Uniform Wireless Power Distribution in 3D for Enabling Long-Term Experiments With Freely Moving Animals.

    PubMed

    Mirbozorgi, S Abdollah; Bahrami, Hadi; Sawan, Mohamad; Gosselin, Benoit

    2016-04-01

    This paper presents a novel experimental chamber with uniform wireless power distribution in 3D for enabling long-term biomedical experiments with small freely moving animal subjects. The implemented power transmission chamber prototype is based on arrays of parallel resonators and multicoil inductive links, to form a novel and highly efficient wireless power transmission system. The power transmitter unit includes several identical resonators enclosed in a scalable array of overlapping square coils which are connected in parallel to provide uniform power distribution along x and y. Moreover, the proposed chamber uses two arrays of primary resonators, facing each other, and connected in parallel to achieve uniform power distribution along the z axis. Each surface includes 9 overlapped coils connected in parallel and implemented into two layers of FR4 printed circuit board. The chamber features a natural power localization mechanism, which simplifies its implementation and ease its operation by avoiding the need for active detection and control mechanisms. A single power surface based on the proposed approach can provide a power transfer efficiency (PTE) of 69% and a power delivered to the load (PDL) of 120 mW, for a separation distance of 4 cm, whereas the complete chamber prototype provides a uniform PTE of 59% and a PDL of 100 mW in 3D, everywhere inside the chamber with a size of 27×27×16 cm(3).

  4. Audio-visual perception of 3D cinematography: an fMRI study using condition-based and computation-based analyses.

    PubMed

    Ogawa, Akitoshi; Bordier, Cecile; Macaluso, Emiliano

    2013-01-01

    The use of naturalistic stimuli to probe sensory functions in the human brain is gaining increasing interest. Previous imaging studies examined brain activity associated with the processing of cinematographic material using both standard "condition-based" designs, as well as "computational" methods based on the extraction of time-varying features of the stimuli (e.g. motion). Here, we exploited both approaches to investigate the neural correlates of complex visual and auditory spatial signals in cinematography. In the first experiment, the participants watched a piece of a commercial movie presented in four blocked conditions: 3D vision with surround sounds (3D-Surround), 3D with monaural sound (3D-Mono), 2D-Surround, and 2D-Mono. In the second experiment, they watched two different segments of the movie both presented continuously in 3D-Surround. The blocked presentation served for standard condition-based analyses, while all datasets were submitted to computation-based analyses. The latter assessed where activity co-varied with visual disparity signals and the complexity of auditory multi-sources signals. The blocked analyses associated 3D viewing with the activation of the dorsal and lateral occipital cortex and superior parietal lobule, while the surround sounds activated the superior and middle temporal gyri (S/MTG). The computation-based analyses revealed the effects of absolute disparity in dorsal occipital and posterior parietal cortices and of disparity gradients in the posterior middle temporal gyrus plus the inferior frontal gyrus. The complexity of the surround sounds was associated with activity in specific sub-regions of S/MTG, even after accounting for changes of sound intensity. These results demonstrate that the processing of naturalistic audio-visual signals entails an extensive set of visual and auditory areas, and that computation-based analyses can track the contribution of complex spatial aspects characterizing such life-like stimuli. PMID

  5. Computational design of soft materials for the capture of Cs-137 in contaminated environments: From 2D covalent cucurbituril networks to 3D supramolecular materials

    NASA Astrophysics Data System (ADS)

    Pichierri, Fabio

    2016-08-01

    Using computational quantum chemistry methods we design novel 2D and 3D soft materials made of cucurbituril macrocycles covalently connected with each other via rigid linkers. Such covalent cucurbituril networks might be useful for the capture of radioactive Cs-137 (present as Cs+) in the contaminated environment.

  6. A 3-D finite-element computation of eddy currents and losses in laminated iron cores allowing for electric and magnetic anisotropy

    SciTech Connect

    Silva, V.C.; Meunier, G.; Foggia, A.

    1995-05-01

    A 3-D scheme based on the Finite Element Method, which takes electric and magnetic anisotropy into consideration, has been developed for computing eddy-current losses caused by stray magnetic fields in laminated iron cores of large transformers and generators. The model is applied to some laminated iron-core samples and compared with equivalent solid-iron cases.

  7. Precise 3D dimensional metrology using high-resolution x-ray computed tomography (μCT)

    NASA Astrophysics Data System (ADS)

    Brunke, Oliver; Santillan, Javier; Suppes, Alexander

    2010-09-01

    Over the past decade computed tomography (CT) with conventional x-ray sources has evolved from an imaging method in medicine to a well established technology for industrial applications in fields such as material science, light metals and plastics processing, microelectronics and geology. By using modern microfocus and nanofocus X-ray tubes, parts can be scanned with sub-micrometer resolutions. Currently, micro-CT is a technology increasingly used for metrology applications in the automotive industry. CT offers big advantages compared with conventional tactile or optical coordinate measuring machines (CMMs). This is of greater importance if complex parts with hidden or difficult accessible surfaces have to be measured. In these cases, CT offers the advantage of a high density of measurement points and a non-destructive and fast capturing of the sample's complete geometry. When using this growing technology the question arises how precise a μCT based CMM can measure as compared to conventional and established methods for coordinate measurements. For characterizing the metrological capabilities of a tactile or optical CMM, internationally standardized parameters like length measurement error and probing error are defined and used. To increase the acceptance of CT as a metrological method, our work seeks to clarify the definition and usage of parameters used in the field of metrology as these apply to CT. In this paper, an overview of the process chain in CT based metrology will be given and metrological characteristics will be described. For the potential user of CT as 3D metrology tool it is important to show the measurement accuracy and repeatability on realistic samples. Following a discussion of CT metrology techniques, two samples are discussed. The first compares a measured CT Data set to CAD data using CMM data as a standard for comparison of results. The second data second realistic data set will compare the results of applying both the CMM method of

  8. Bootstrapping 3D fermions

    DOE PAGES

    Iliesiu, Luca; Kos, Filip; Poland, David; Pufu, Silviu S.; Simmons-Duffin, David; Yacoby, Ran

    2016-03-17

    We study the conformal bootstrap for a 4-point function of fermions <ψψψψ> in 3D. We first introduce an embedding formalism for 3D spinors and compute the conformal blocks appearing in fermion 4-point functions. Using these results, we find general bounds on the dimensions of operators appearing in the ψ × ψ OPE, and also on the central charge CT. We observe features in our bounds that coincide with scaling dimensions in the GrossNeveu models at large N. Finally, we also speculate that other features could coincide with a fermionic CFT containing no relevant scalar operators.

  9. Audio-Visual Perception of 3D Cinematography: An fMRI Study Using Condition-Based and Computation-Based Analyses

    PubMed Central

    Ogawa, Akitoshi; Bordier, Cecile; Macaluso, Emiliano

    2013-01-01

    The use of naturalistic stimuli to probe sensory functions in the human brain is gaining increasing interest. Previous imaging studies examined brain activity associated with the processing of cinematographic material using both standard “condition-based” designs, as well as “computational” methods based on the extraction of time-varying features of the stimuli (e.g. motion). Here, we exploited both approaches to investigate the neural correlates of complex visual and auditory spatial signals in cinematography. In the first experiment, the participants watched a piece of a commercial movie presented in four blocked conditions: 3D vision with surround sounds (3D-Surround), 3D with monaural sound (3D-Mono), 2D-Surround, and 2D-Mono. In the second experiment, they watched two different segments of the movie both presented continuously in 3D-Surround. The blocked presentation served for standard condition-based analyses, while all datasets were submitted to computation-based analyses. The latter assessed where activity co-varied with visual disparity signals and the complexity of auditory multi-sources signals. The blocked analyses associated 3D viewing with the activation of the dorsal and lateral occipital cortex and superior parietal lobule, while the surround sounds activated the superior and middle temporal gyri (S/MTG). The computation-based analyses revealed the effects of absolute disparity in dorsal occipital and posterior parietal cortices and of disparity gradients in the posterior middle temporal gyrus plus the inferior frontal gyrus. The complexity of the surround sounds was associated with activity in specific sub-regions of S/MTG, even after accounting for changes of sound intensity. These results demonstrate that the processing of naturalistic audio-visual signals entails an extensive set of visual and auditory areas, and that computation-based analyses can track the contribution of complex spatial aspects characterizing such life-like stimuli

  10. Combined magnetic vector-scalar potential finite element computation of 3D magnetic field and performance of modified Lundell alternators in Space Station applications. Ph.D. Thesis

    NASA Technical Reports Server (NTRS)

    Wang, Ren H.

    1991-01-01

    A method of combined use of magnetic vector potential (MVP) based finite element (FE) formulations and magnetic scalar potential (MSP) based FE formulations for computation of three-dimensional (3D) magnetostatic fields is developed. This combined MVP-MSP 3D-FE method leads to considerable reduction by nearly a factor of 3 in the number of unknowns in comparison to the number of unknowns which must be computed in global MVP based FE solutions. This method allows one to incorporate portions of iron cores sandwiched in between coils (conductors) in current-carrying regions. Thus, it greatly simplifies the geometries of current carrying regions (in comparison with the exclusive MSP based methods) in electric machinery applications. A unique feature of this approach is that the global MSP solution is single valued in nature, that is, no branch cut is needed. This is again a superiority over the exclusive MSP based methods. A Newton-Raphson procedure with a concept of an adaptive relaxation factor was developed and successfully used in solving the 3D-FE problem with magnetic material anisotropy and nonlinearity. Accordingly, this combined MVP-MSP 3D-FE method is most suited for solution of large scale global type magnetic field computations in rotating electric machinery with very complex magnetic circuit geometries, as well as nonlinear and anisotropic material properties.

  11. Role of the Animator in the Generation of 3-Dimensional Computer Generated Animation.

    ERIC Educational Resources Information Center

    Wedge, John Christian

    This master's thesis investigates the relationship between the traditional animator and the computer as computer animation systems allow them to apply traditional skills with a high degree of success. The advantages and disadvantages of traditional animation as a medium for expressing motion and character are noted, and it is argued that the…

  12. Hybrid 3-D rocket trajectory program. Part 1: Formulation and analysis. Part 2: Computer programming and user's instruction. [computerized simulation using three dimensional motion analysis

    NASA Technical Reports Server (NTRS)

    Huang, L. C. P.; Cook, R. A.

    1973-01-01

    Models utilizing various sub-sets of the six degrees of freedom are used in trajectory simulation. A 3-D model with only linear degrees of freedom is especially attractive, since the coefficients for the angular degrees of freedom are the most difficult to determine and the angular equations are the most time consuming for the computer to evaluate. A computer program is developed that uses three separate subsections to predict trajectories. A launch rail subsection is used until the rocket has left its launcher. The program then switches to a special 3-D section which computes motions in two linear and one angular degrees of freedom. When the rocket trims out, the program switches to the standard, three linear degrees of freedom model.

  13. PLOT3D/AMES, UNIX SUPERCOMPUTER AND SGI IRIS VERSION (WITHOUT TURB3D)

    NASA Technical Reports Server (NTRS)

    Buning, P.

    1994-01-01

    calculations on a supercomputer, the Supercomputer/IRIS implementation of PLOT3D offers advanced 3-D, view manipulation, and animation capabilities. Shading and hidden line/surface removal can be used to enhance depth perception and other aspects of the graphical displays. A mouse can be used to translate, rotate, or zoom in on views. Files for several types of output can be produced. Two animation options are available. Simple animation sequences can be created on the IRIS, or,if an appropriately modified version of ARCGRAPH (ARC-12350) is accesible on the supercomputer, files can be created for use in GAS (Graphics Animation System, ARC-12379), an IRIS program which offers more complex rendering and animation capabilities and options for recording images to digital disk, video tape, or 16-mm film. The version 3.6b+ Supercomputer/IRIS implementations of PLOT3D (ARC-12779) and PLOT3D/TURB3D (ARC-12784) are suitable for use on CRAY 2/UNICOS, CONVEX, and ALLIANT computers with a remote Silicon Graphics IRIS 2xxx/3xxx or IRIS 4D workstation. These programs are distributed on .25 inch magnetic tape cartridges in IRIS TAR format. Customers purchasing one implementation version of PLOT3D or PLOT3D/TURB3D will be given a $200 discount on each additional implementation version ordered at the same time. Version 3.6b+ of PLOT3D and PLOT3D/TURB3D are also supported for the following computers and graphics libraries: (1) Silicon Graphics IRIS 2xxx/3xxx or IRIS 4D workstations (ARC-12783, ARC-12782); (2) VAX computers running VMS Version 5.0 and DISSPLA Version 11.0 (ARC12777, ARC-12781); (3) generic UNIX and DISSPLA Version 11.0 (ARC-12788, ARC-12778); and (4) Apollo computers running UNIX and GMR3D Version 2.0 (ARC-12789, ARC-12785 - which have no capabilities to put text on plots). Silicon Graphics Iris, IRIS 4D, and IRIS 2xxx/3xxx are trademarks of Silicon Graphics Incorporated. VAX and VMS are trademarks of Digital Electronics Corporation. DISSPLA is a trademark of Computer Associates

  14. PLOT3D/AMES, UNIX SUPERCOMPUTER AND SGI IRIS VERSION (WITH TURB3D)

    NASA Technical Reports Server (NTRS)

    Buning, P.

    1994-01-01

    calculations on a supercomputer, the Supercomputer/IRIS implementation of PLOT3D offers advanced 3-D, view manipulation, and animation capabilities. Shading and hidden line/surface removal can be used to enhance depth perception and other aspects of the graphical displays. A mouse can be used to translate, rotate, or zoom in on views. Files for several types of output can be produced. Two animation options are available. Simple animation sequences can be created on the IRIS, or,if an appropriately modified version of ARCGRAPH (ARC-12350) is accesible on the supercomputer, files can be created for use in GAS (Graphics Animation System, ARC-12379), an IRIS program which offers more complex rendering and animation capabilities and options for recording images to digital disk, video tape, or 16-mm film. The version 3.6b+ Supercomputer/IRIS implementations of PLOT3D (ARC-12779) and PLOT3D/TURB3D (ARC-12784) are suitable for use on CRAY 2/UNICOS, CONVEX, and ALLIANT computers with a remote Silicon Graphics IRIS 2xxx/3xxx or IRIS 4D workstation. These programs are distributed on .25 inch magnetic tape cartridges in IRIS TAR format. Customers purchasing one implementation version of PLOT3D or PLOT3D/TURB3D will be given a $200 discount on each additional implementation version ordered at the same time. Version 3.6b+ of PLOT3D and PLOT3D/TURB3D are also supported for the following computers and graphics libraries: (1) Silicon Graphics IRIS 2xxx/3xxx or IRIS 4D workstations (ARC-12783, ARC-12782); (2) VAX computers running VMS Version 5.0 and DISSPLA Version 11.0 (ARC12777, ARC-12781); (3) generic UNIX and DISSPLA Version 11.0 (ARC-12788, ARC-12778); and (4) Apollo computers running UNIX and GMR3D Version 2.0 (ARC-12789, ARC-12785 - which have no capabilities to put text on plots). Silicon Graphics Iris, IRIS 4D, and IRIS 2xxx/3xxx are trademarks of Silicon Graphics Incorporated. VAX and VMS are trademarks of Digital Electronics Corporation. DISSPLA is a trademark of Computer Associates

  15. Animation graphic interface for the space shuttle onboard computer

    NASA Technical Reports Server (NTRS)

    Wike, Jeffrey; Griffith, Paul

    1989-01-01

    Graphics interfaces designed to operate on space qualified hardware challenge software designers to display complex information under processing power and physical size constraints. Under contract to Johnson Space Center, MICROEXPERT Systems is currently constructing an intelligent interface for the LASER DOCKING SENSOR (LDS) flight experiment. Part of this interface is a graphic animation display for Rendezvous and Proximity Operations. The displays have been designed in consultation with Shuttle astronauts. The displays show multiple views of a satellite relative to the shuttle, coupled with numeric attitude information. The graphics are generated using position data received by the Shuttle Payload and General Support Computer (PGSC) from the Laser Docking Sensor. Some of the design considerations include crew member preferences in graphic data representation, single versus multiple window displays, mission tailoring of graphic displays, realistic 3D images versus generic icon representations of real objects, the physical relationship of the observers to the graphic display, how numeric or textual information should interface with graphic data, in what frame of reference objects should be portrayed, recognizing conditions of display information-overload, and screen format and placement consistency.

  16. Coupling of PIES 3-D Equilibrium Code and NIFS Bootstrap Code with Applications to the Computation of Stellarator Equilibria

    NASA Astrophysics Data System (ADS)

    Monticello, D. A.; Reiman, A. H.; Watanabe, K. Y.; Nakajima, N.; Okamoto, M.

    1997-11-01

    The existence of bootstrap currents in both tokamaks and stellarators was confirmed, experimentally, more than ten years ago. Such currents can have significant effects on the equilibrium and stability of these MHD devices. In addition, stellarators, with the notable exception of W7-X, are predicted to have such large bootstrap currents that reliable equilibrium calculations require the self-consistent evaluation of bootstrap currents. Modeling of discharges which contain islands requires an algorithm that does not assume good surfaces. Only one of the two 3-D equilibrium codes that exist, PIES( Reiman, A. H., Greenside, H. S., Compt. Phys. Commun. 43), (1986)., can easily be modified to handle bootstrap current. Here we report on the coupling of the PIES 3-D equilibrium code and NIFS bootstrap code(Watanabe, K., et al., Nuclear Fusion 35) (1995), 335.

  17. 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.

  18. Neutron detection and characterization for non-proliferation applications using 3D computer optical memories [Use of 3D optical computer memory for radiation detectors/dosimeters. Final progress report

    SciTech Connect

    Gary W. Phillips

    2000-12-20

    We have investigated 3-dimensional optical random access memory (3D-ORAM) materials for detection and characterization of charged particles of neutrons by detecting tracks left by the recoil charged particles produced by the neutrons. We have characterized the response of these materials to protons, alpha particles and carbon-12 nuclei as a functions of dose and energy. We have observed individual tracks using scanning electron microscopy and atomic force microscopy. We are investigating the use of neural net analysis to characterize energetic neutron fields from their track structure in these materials.

  19. The New 3D Printed Left Atrial Appendage Closure with a Novel Holdfast Device: A Pre-Clinical Feasibility Animal Study

    PubMed Central

    Brzeziński, M.; Bury, K.; Dąbrowski, L.; Holak, P.; Sejda, A.; Pawlak, M.; Jagielak, D.; Adamiak, Z.; Rogowski, J.

    2016-01-01

    surrounding tissues. No pericarditis or macroscopic signs of inflammation at the site of the device were found. All pigs were in good condition with normal weight gain and no other clinical symptoms. Conclusion This novel 3D printed left atrial appendage closure technique with a novel holdfast device was proven to be safe and feasible in all pigs. A benign healing process without inflammation and damage to the surrounding structures or evidence of new thrombi formation was observed. Moreover, the uncomplicated survival and full LAA exclusion in all animals demonstrate the efficacy of this novel and relatively cheap device. Further clinical evaluation and implementation studies should be performed to introduce this new technology into clinical practice. PMID:27219618

  20. 3-D structural modeling of humic acids through experimental characterization, computer assisted structure elucidation and atomistic simulations 1. Chelsea soil humic acid.

    SciTech Connect

    Gassman, Paul; Hatcher, Patrick G.; Faulon, Jean-Loup Michel; Simpson, Andre; Goddard, William A., III; Diallo, Mamadou S.; Johnson, James H. Jr.

    2003-07-01

    This paper describes an integrated experimental and computational framework for developing 3-D structural models for humic acids (HAs). This approach combines experimental characterization, computer assisted structure elucidation (CASE), and atomistic simulations to generate all 3-D structural models or a representative sample of these models consistent with the analytical data and bulk thermodynamic/structural properties of HAs. To illustrate this methodology, structural data derived from elemental analysis, diffuse reflectance FT-IR spectroscopy, 1-D/2-D {sup 1}H and {sup 13}C solution NMR spectroscopy, and electrospray ionization quadrupole time-of-flight mass spectrometry (ESI QqTOF MS) are employed as input to the CASE program SIGNATURE to generate all 3-D structural models for Chelsea soil humic acid (HA). These models are subsequently used as starting 3-D structures to carry out constant temperature-constant pressure molecular dynamics simulations to estimate their bulk densities and Hildebrand solubility parameters. Surprisingly, only a few model isomers are found to exhibit molecular compositions and bulk thermodynamic properties consistent with the experimental data. The simulated {sup 13}C NMR spectrum of an equimolar mixture of these model isomers compares favorably with the measured spectrum of Chelsea soil HA.

  1. Developing and Using Conceptual Computer Animations for Chemistry Instruction

    NASA Astrophysics Data System (ADS)

    Burke, K. A.; Greenbowe, Thomas J.; Windschitl, Mark A.

    1998-12-01

    Multimedia technology has advanced rapidly within the past two years providing an opportunity for chemistry instructors to develop and use their own computer animations. Conceptual computer animations are designed to help students understand the basic concept or principle of a dynamic chemical process. This paper discusses several issues surrounding the development and use of instructional conceptual computer animations. If possible, an animation sequence should be linked to a lecture demonstration, thereby assisting in the presentation of all three levels of representation: microscopic, macroscopic and symbolic. Computer animations provide instructors with a vehicle for presenting topics from the particulate nature of matter view and a technique for teaching for conceptual understanding. A design team consisting of individuals who have knowledge or expertise in the content area, instructional design, computer animation techniques, and graphic and sound production should work with the chemistry instructor to develop and produce the animation sequences. Various software tools for drawing, animating, and incorporating audio tracks along with the animation are discussed. Aspects of effective computer anmation are listed. Techniques for 24-hour student access to instructional computer animations through the internet via the World Wide Web, as well as to a local file servers through the intranet are mentioned. Chemistry instructors who develop computer animations or multimedia presentations must be aware of copyright laws pertaining to the educational use and distribution of images, pictures, illustrations, and sounds. Using computer animations does take additonal time in lecture. However instructors must decide whether they want to "cover" or "uncover" material. The inclusion of computer animations is consistent with reports from the ACS task force that emphasizes "less is more" in terms of curriculum reform.

  2. Validity of computational hemodynamics in human arteries based on 3D time-of-flight MR angiography and 2D electrocardiogram gated phase contrast images

    NASA Astrophysics Data System (ADS)

    Yu, Huidan (Whitney); Chen, Xi; Chen, Rou; Wang, Zhiqiang; Lin, Chen; Kralik, Stephen; Zhao, Ye

    2015-11-01

    In this work, we demonstrate the validity of 4-D patient-specific computational hemodynamics (PSCH) based on 3-D time-of-flight (TOF) MR angiography (MRA) and 2-D electrocardiogram (ECG) gated phase contrast (PC) images. The mesoscale lattice Boltzmann method (LBM) is employed to segment morphological arterial geometry from TOF MRA, to extract velocity profiles from ECG PC images, and to simulate fluid dynamics on a unified GPU accelerated computational platform. Two healthy volunteers are recruited to participate in the study. For each volunteer, a 3-D high resolution TOF MRA image and 10 2-D ECG gated PC images are acquired to provide the morphological geometry and the time-varying flow velocity profiles for necessary inputs of the PSCH. Validation results will be presented through comparisons of LBM vs. 4D Flow Software for flow rates and LBM simulation vs. MRA measurement for blood flow velocity maps. Indiana University Health (IUH) Values Fund.

  3. Improved integral imaging based image copyright protection algorithm using 3-D computational integral imaging pickup and super-resolution reconstruction technique

    NASA Astrophysics Data System (ADS)

    Li, Xiao Wei; Lee, In-Kwon; Kim, Seok Tae

    2014-11-01

    Cellular automata transform (CAT) based watermarking method can provide multi-transform planes for embedding watermark. In this paper, to overcome conventional transform-based watermarking methods have only one transform plane for watermark embedding, we propose a CAT-based watermarking system, in which the three-dimensional (3-D) watermark data is decomposed by the computational integral imaging (CII) technique and be embedded into the CAT domain. However, in the 3-D watermark reconstruction process, the computational integral imaging reconstruction (CIIR) technique in CII system that can degrade the quality of the extracted watermark due to the pixel overlapping. We introduce the super-resolution reconstruction technique that can effectively improve this problem. Some experiments are carried out to verify the performance of the CAT-based watermarking scheme. From the experimental results, the proposed watermarking system can provide good imperceptibility and high robustness.

  4. PLOT3D/AMES, DEC VAX VMS VERSION USING DISSPLA (WITH TURB3D)

    NASA Technical Reports Server (NTRS)

    Buning, P.

    1994-01-01

    well as 2-D and 3-D lines, but does not support graphics features requiring 3-D polygons (shading and hidden line removal, for example). Views can be manipulated using keyboard commands. This version of PLOT3D is potentially able to produce files for a variety of output devices; however, site-specific capabilities will vary depending on the device drivers supplied with the user's DISSPLA library. If ARCGRAPH (ARC-12350) is installed on the user's VAX, the VMS/DISSPLA version of PLOT3D can also be used to create files for use in GAS (Graphics Animation System, ARC-12379), an IRIS program capable of animating and recording images on film. The version 3.6b+ VMS/DISSPLA implementations of PLOT3D (ARC-12777) and PLOT3D/TURB3D (ARC-12781) were developed for use on VAX computers running VMS Version 5.0 and DISSPLA Version 11.0. The standard distribution media for each of these programs is a 9-track, 6250 bpi magnetic tape in DEC VAX BACKUP format. Customers purchasing one implementation version of PLOT3D or PLOT3D/TURB3D will be given a $200 discount on each additional implementation version ordered at the same time. Version 3.6b+ of PLOT3D and PLOT3D/TURB3D are also supported for the following computers and graphics libraries: (1) generic UNIX Supercomputer and IRIS, suitable for CRAY 2/UNICOS, CONVEX, and Alliant with remote IRIS 2xxx/3xxx or IRIS 4D (ARC-12779, ARC-12784); (2) Silicon Graphics IRIS 2xxx/3xxx or IRIS 4D (ARC-12783, ARC12782); (3) generic UNIX and DISSPLA Version 11.0 (ARC-12788, ARC-12778); and (4) Apollo computers running UNIX and GMR3D Version 2.0 (ARC-12789, ARC-12785 which have no capabilities to put text on plots). Silicon Graphics Iris, IRIS 4D, and IRIS 2xxx/3xxx are trademarks of Silicon Graphics Incorporated. VAX and VMS are trademarks of Digital Electronics Corporation. DISSPLA is a trademark of Computer Associates. CRAY 2 and UNICOS are trademarks of CRAY Research, Incorporated. CONVEX is a trademark of Convex Computer Corporation. Alliant is a

  5. PLOT3D/AMES, DEC VAX VMS VERSION USING DISSPLA (WITHOUT TURB3D)

    NASA Technical Reports Server (NTRS)

    Buning, P. G.

    1994-01-01

    well as 2-D and 3-D lines, but does not support graphics features requiring 3-D polygons (shading and hidden line removal, for example). Views can be manipulated using keyboard commands. This version of PLOT3D is potentially able to produce files for a variety of output devices; however, site-specific capabilities will vary depending on the device drivers supplied with the user's DISSPLA library. If ARCGRAPH (ARC-12350) is installed on the user's VAX, the VMS/DISSPLA version of PLOT3D can also be used to create files for use in GAS (Graphics Animation System, ARC-12379), an IRIS program capable of animating and recording images on film. The version 3.6b+ VMS/DISSPLA implementations of PLOT3D (ARC-12777) and PLOT3D/TURB3D (ARC-12781) were developed for use on VAX computers running VMS Version 5.0 and DISSPLA Version 11.0. The standard distribution media for each of these programs is a 9-track, 6250 bpi magnetic tape in DEC VAX BACKUP format. Customers purchasing one implementation version of PLOT3D or PLOT3D/TURB3D will be given a $200 discount on each additional implementation version ordered at the same time. Version 3.6b+ of PLOT3D and PLOT3D/TURB3D are also supported for the following computers and graphics libraries: (1) generic UNIX Supercomputer and IRIS, suitable for CRAY 2/UNICOS, CONVEX, and Alliant with remote IRIS 2xxx/3xxx or IRIS 4D (ARC-12779, ARC-12784); (2) Silicon Graphics IRIS 2xxx/3xxx or IRIS 4D (ARC-12783, ARC12782); (3) generic UNIX and DISSPLA Version 11.0 (ARC-12788, ARC-12778); and (4) Apollo computers running UNIX and GMR3D Version 2.0 (ARC-12789, ARC-12785 which have no capabilities to put text on plots). Silicon Graphics Iris, IRIS 4D, and IRIS 2xxx/3xxx are trademarks of Silicon Graphics Incorporated. VAX and VMS are trademarks of Digital Electronics Corporation. DISSPLA is a trademark of Computer Associates. CRAY 2 and UNICOS are trademarks of CRAY Research, Incorporated. CONVEX is a trademark of Convex Computer Corporation. Alliant is a

  6. PLOT3D/AMES, SGI IRIS VERSION (WITH TURB3D)

    NASA Technical Reports Server (NTRS)

    Buning, P.

    1994-01-01

    advanced features which aid visualization efforts. Shading and hidden line/surface removal can be used to enhance depth perception and other aspects of the graphical displays. A mouse can be used to translate, rotate, or zoom in on views. Files for several types of output can be produced. Two animation options are even offered: creation of simple animation sequences without the need for other software; and, creation of files for use in GAS (Graphics Animation System, ARC-12379), an IRIS program which offers more complex rendering and animation capabilities and can record images to digital disk, video tape, or 16-mm film. The version 3.6b+ SGI implementations of PLOT3D (ARC-12783) and PLOT3D/TURB3D (ARC-12782) were developed for use on Silicon Graphics IRIS 2xxx/3xxx or IRIS 4D workstations. These programs are each distributed on one .25 inch magnetic tape cartridge in IRIS TAR format. Customers purchasing one implementation version of PLOT3D or PLOT3D/TURB3D will be given a $200 discount on each additional implementation version ordered at the same time. Version 3.6b+ of PLOT3D and PLOT3D/TURB3D are also supported for the following computers and graphics libraries: (1) generic UNIX Supercomputer and IRIS, suitable for CRAY 2/UNICOS, CONVEX, and Alliant with remote IRIS 2xxx/3xxx or IRIS 4D (ARC-12779, ARC-12784); (2) VAX computers running VMS Version 5.0 and DISSPLA Version 11.0 (ARC-12777,ARC-12781); (3) generic UNIX and DISSPLA Version 11.0 (ARC-12788, ARC-12778); and (4) Apollo computers running UNIX and GMR3D Version 2.0 (ARC-12789, ARC-12785 which have no capabilities to put text on plots). Silicon Graphics Iris, IRIS 4D, and IRIS 2xxx/3xxx are trademarks of Silicon Graphics Incorporated. VAX and VMS are trademarks of Digital Electronics Corporation. DISSPLA is a trademark of Computer Associates. CRAY 2 and UNICOS are trademarks of CRAY Research, Incorporated. CONVEX is a trademark of Convex Computer Corporation. Alliant is a trademark of Alliant. Apollo and GMR3D are

  7. PLOT3D/AMES, SGI IRIS VERSION (WITHOUT TURB3D)

    NASA Technical Reports Server (NTRS)

    Buning, P.

    1994-01-01

    advanced features which aid visualization efforts. Shading and hidden line/surface removal can be used to enhance depth perception and other aspects of the graphical displays. A mouse can be used to translate, rotate, or zoom in on views. Files for several types of output can be produced. Two animation options are even offered: creation of simple animation sequences without the need for other software; and, creation of files for use in GAS (Graphics Animation System, ARC-12379), an IRIS program which offers more complex rendering and animation capabilities and can record images to digital disk, video tape, or 16-mm film. The version 3.6b+ SGI implementations of PLOT3D (ARC-12783) and PLOT3D/TURB3D (ARC-12782) were developed for use on Silicon Graphics IRIS 2xxx/3xxx or IRIS 4D workstations. These programs are each distributed on one .25 inch magnetic tape cartridge in IRIS TAR format. Customers purchasing one implementation version of PLOT3D or PLOT3D/TURB3D will be given a $200 discount on each additional implementation version ordered at the same time. Version 3.6b+ of PLOT3D and PLOT3D/TURB3D are also supported for the following computers and graphics libraries: (1) generic UNIX Supercomputer and IRIS, suitable for CRAY 2/UNICOS, CONVEX, and Alliant with remote IRIS 2xxx/3xxx or IRIS 4D (ARC-12779, ARC-12784); (2) VAX computers running VMS Version 5.0 and DISSPLA Version 11.0 (ARC-12777,ARC-12781); (3) generic UNIX and DISSPLA Version 11.0 (ARC-12788, ARC-12778); and (4) Apollo computers running UNIX and GMR3D Version 2.0 (ARC-12789, ARC-12785 which have no capabilities to put text on plots). Silicon Graphics Iris, IRIS 4D, and IRIS 2xxx/3xxx are trademarks of Silicon Graphics Incorporated. VAX and VMS are trademarks of Digital Electronics Corporation. DISSPLA is a trademark of Computer Associates. CRAY 2 and UNICOS are trademarks of CRAY Research, Incorporated. CONVEX is a trademark of Convex Computer Corporation. Alliant is a trademark of Alliant. Apollo and GMR3D are

  8. Real time 3D scanner: investigations and results

    NASA Astrophysics Data System (ADS)

    Nouri, Taoufik; Pflug, Leopold

    1993-12-01

    This article presents a concept of reconstruction of 3-D objects using non-invasive and touch loss techniques. The principle of this method is to display parallel interference optical fringes on an object and then to record the object under two angles of view. According to an appropriated treatment one reconstructs the 3-D object even when the object has no symmetrical plan. The 3-D surface data is available immediately in digital form for computer- visualization and for analysis software tools. The optical set-up for recording the 3-D object, the 3-D data extraction and treatment, as well as the reconstruction of the 3-D object are reported and commented on. This application is dedicated for reconstructive/cosmetic surgery, CAD, animation and research purposes.

  9. A 3-D CE/SE Navier-Stokes Solver With Unstructured Hexahedral Grid for Computation of Near Field Jet Screech Noise

    NASA Technical Reports Server (NTRS)

    Loh, Ching Y.; Himansu, Ananda; Hultgren, Lennart S.

    2003-01-01

    A 3-D space-time CE/SE Navier-Stokes solver using an unstructured hexahedral grid is described and applied to a circular jet screech noise computation. The present numerical results for an underexpanded jet, corresponding to a fully expanded Mach number of 1.42, capture the dominant and nonaxisymmetric 'B' screech mode and are generally in good agreement with existing experiments.

  10. 3D volume assessment techniques and computer-aided design and manufacturing for preoperative fabrication of implants in head and neck reconstruction.

    PubMed

    Patel, Ashish; Otterburn, David; Saadeh, Pierre; Levine, Jamie; Hirsch, David L

    2011-11-01

    Cases in subdisciplines of craniomaxillofacial surgery--corrective jaw surgery, maxillofacial trauma, temporomandibular joint/skull base, jaw reconstruction, and postablative reconstruction-illustrate the ease of use, cost effectiveness, and superior results that can be achieved when using computer-assisted design and 3D volumetric analysis in preoperative surgical planning. This article discusses the materials and methods needed to plan cases, illustrates implementation of guides and implants, and describes postoperative analysis in relation to the virtually planned surgery.

  11. X-38 research aircraft deorbit - computer animation

    NASA Technical Reports Server (NTRS)

    1997-01-01

    with the parafoil. Intermediate parafoil tests at the Army Yuma Proving Grounds in Arizona enabled the project to resolve these problems and resume flight research. In the drop tests, the X-38 vehicles have been autonomous after airlaunch from the B-52. After they deploy the parafoil, they have remained autonomous, but there is also a manual mode that allows control from the ground. The X-38 vehicles (designated V131 and V132) are each 24.5 feet long. The actual CRV to be flown in space is expected to be 30 feet long. This is short 16-second computer animation clip showing the X-38 vehicle performing a deorbit engine burn, bringing the vehicle around 180 degrees and then jettisoning the solid rocket pack to reduce its re-entry weight.

  12. X-38 research aircraft landing - computer animation

    NASA Technical Reports Server (NTRS)

    1997-01-01

    been some problems with the parafoil. Intermediate parafoil tests at the Army Yuma Proving Grounds in Arizona enabled the project to resolve these problems and resume flight research. In the drop tests, the X-38 vehicles have been autonomous after air launch from the B-52. After they deploy the parafoil, they have remained autonomous, but there is also a manual mode that allows control from the ground. The X-38 vehicles (designated V131 and V132) are each 24.5 feet long. The actual CRV to be flown in space is expected to be 30 feet long. This is a 21-second computer animation clip showing the X-38 vehicle under its main parachute gliding in for a Global Positioning System-guided landing on a dry desert lakebed.

  13. WebRASP: a server for computing energy scores to assess the accuracy and stability of RNA 3D structures

    PubMed Central

    Norambuena, Tomas; Cares, Jorge F.; Capriotti, Emidio; Melo, Francisco

    2013-01-01

    Summary: The understanding of the biological role of RNA molecules has changed. Although it is widely accepted that RNAs play important regulatory roles without necessarily coding for proteins, the functions of many of these non-coding RNAs are unknown. Thus, determining or modeling the 3D structure of RNA molecules as well as assessing their accuracy and stability has become of great importance for characterizing their functional activity. Here, we introduce a new web application, WebRASP, that uses knowledge-based potentials for scoring RNA structures based on distance-dependent pairwise atomic interactions. This web server allows the users to upload a structure in PDB format, select several options to visualize the structure and calculate the energy profile. The server contains online help, tutorials and links to other related resources. We believe this server will be a useful tool for predicting and assessing the quality of RNA 3D structures. Availability and implementation: The web server is available at http://melolab.org/webrasp. It has been tested on the most popular web browsers and requires Java plugin for Jmol visualization. Contact: fmelo@bio.puc.cl PMID:23929030

  14. Development of a locally mass flux conservative computer code for calculating 3-D viscous flow in turbomachines

    NASA Technical Reports Server (NTRS)

    Walitt, L.

    1982-01-01

    The VANS successive approximation numerical method was extended to the computation of three dimensional, viscous, transonic flows in turbomachines. A cross-sectional computer code, which conserves mass flux at each point of the cross-sectional surface of computation was developed. In the VANS numerical method, the cross-sectional computation follows a blade-to-blade calculation. Numerical calculations were made for an axial annular turbine cascade and a transonic, centrifugal impeller with splitter vanes. The subsonic turbine cascade computation was generated in blade-to-blade surface to evaluate the accuracy of the blade-to-blade mode of marching. Calculated blade pressures at the hub, mid, and tip radii of the cascade agreed with corresponding measurements. The transonic impeller computation was conducted to test the newly developed locally mass flux conservative cross-sectional computer code. Both blade-to-blade and cross sectional modes of calculation were implemented for this problem. A triplet point shock structure was computed in the inducer region of the impeller. In addition, time-averaged shroud static pressures generally agreed with measured shroud pressures. It is concluded that the blade-to-blade computation produces a useful engineering flow field in regions of subsonic relative flow; and cross-sectional computation, with a locally mass flux conservative continuity equation, is required to compute the shock waves in regions of supersonic relative flow.

  15. Developing Educational Computer Animation Based on Human Personality Types

    ERIC Educational Resources Information Center

    Musa, Sajid; Ziatdinov, Rushan; Sozcu, Omer Faruk; Griffiths, Carol

    2015-01-01

    Computer animation in the past decade has become one of the most noticeable features of technology-based learning environments. By its definition, it refers to simulated motion pictures showing movement of drawn objects, and is often defined as the art in movement. Its educational application known as educational computer animation is considered…

  16. Using a Computer Animation to Teach High School Molecular Biology

    ERIC Educational Resources Information Center

    Rotbain, Yosi; Marbach-Ad, Gili; Stavy, Ruth

    2008-01-01

    We present an active way to use a computer animation in secondary molecular genetics class. For this purpose we developed an activity booklet that helps students to work interactively with a computer animation which deals with abstract concepts and processes in molecular biology. The achievements of the experimental group were compared with those…

  17. 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.

  18. A 3D finite-element computation of eddy currents and losses in the stator end laminations of large synchronous machines

    SciTech Connect

    Silva, V.C.; Meunier, G.; Foggia, A.

    1996-05-01

    Eddy current losses due to axial fluxes are computed in the stator end laminations of a salient-pole synchronous machine at open-circuit operating condition. The calculation is carried out with the aid of a 3D finite-element package which uses a linear T-{phi} formulation. The domain spans a full pole pitch of the machine. The flux densities computed in the end region at points outside the stator core are compared with experimental measurements. The results and the limitations of the model are discussed.

  19. 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

  20. Computational fluid dynamics modeling and analysis of the effect of 3-D distortion of the human aortic arch.

    PubMed

    Mori, Daisuke; Yamaguchi, Takami

    2002-06-01

    An idealized CFD model and a realistic one were used to investigate the effect of the 3-D distortion of the aortic arch on the blood flow and its pathophysiological significance with respect to the pathogenesis of the aortic aneurysm. From the results of the flow simulations, the distortion of the centerline of the pipe was shown to affect significantly the flow structure. A right-handed vortex at the descending arch, and a left-handed one at the end of the arch tended to develop in the realistic model. But the secondary flow did not become a single helix. The top of the arch was the region where complex spatial and temporal WSS distributed. It was also observed that the direction of WSS had a significant circumferential component at the top of the arch.

  1. Computer animation and improved student comprehension of basic science concepts.

    PubMed

    Thatcher, Jack D

    2006-01-01

    Many medical students have difficulty learning basic science, either because they find the material challenging to comprehend or because they believe it has limited clinical application. Computer-assisted instruction (CAI)--ie, computer animation--can clarify instruction by allowing students to visualize complex, dynamic processes in an interesting presentation. At West Virginia School of Osteopathic Medicine (WVSOM) in Lewisburg, a series of computer animations have been developed to present concepts in molecular and cellular biology. The author conducted an investigation to compare the efficacy of one representative computer animation with that of traditional textbook material. The subjects were 22 students who had been admitted to WVSOM but who had not yet begun classes. The experimental design of the study consisted of a prelesson test, a lesson, and a postlesson test. The lesson explained the process of deoxyribonucleic acid (DNA) replication using either a computer animation (n=12) or a chapter from a textbook (n=10). Lesson comprehension as measured by the tests was significantly higher for subjects who used the computer animation than for subjects who used the textbook (P<.01). Furthermore, reviewing the text after studying with the computer animation did not raise test scores, suggesting that the animation was sufficient for learning and the text was unnecessary. After the study, a majority of subjects indicated a preference for the animation over the text. These results demonstrate that CAI can be an effective tool for relating basic science to medical students by improving comprehension and eliciting interest in the lessons.

  2. Computer animation and improved student comprehension of basic science concepts.

    PubMed

    Thatcher, Jack D

    2006-01-01

    Many medical students have difficulty learning basic science, either because they find the material challenging to comprehend or because they believe it has limited clinical application. Computer-assisted instruction (CAI)--ie, computer animation--can clarify instruction by allowing students to visualize complex, dynamic processes in an interesting presentation. At West Virginia School of Osteopathic Medicine (WVSOM) in Lewisburg, a series of computer animations have been developed to present concepts in molecular and cellular biology. The author conducted an investigation to compare the efficacy of one representative computer animation with that of traditional textbook material. The subjects were 22 students who had been admitted to WVSOM but who had not yet begun classes. The experimental design of the study consisted of a prelesson test, a lesson, and a postlesson test. The lesson explained the process of deoxyribonucleic acid (DNA) replication using either a computer animation (n=12) or a chapter from a textbook (n=10). Lesson comprehension as measured by the tests was significantly higher for subjects who used the computer animation than for subjects who used the textbook (P<.01). Furthermore, reviewing the text after studying with the computer animation did not raise test scores, suggesting that the animation was sufficient for learning and the text was unnecessary. After the study, a majority of subjects indicated a preference for the animation over the text. These results demonstrate that CAI can be an effective tool for relating basic science to medical students by improving comprehension and eliciting interest in the lessons. PMID:16428683

  3. Comparison of the LLNL ALE3D and AKTS Thermal Safety Computer Codes for Calculating Times to Explosion in ODTX and STEX Thermal Cookoff Experiments

    SciTech Connect

    Wemhoff, A P; Burnham, A K

    2006-04-05

    Cross-comparison of the results of two computer codes for the same problem provides a mutual validation of their computational methods. This cross-validation exercise was performed for LLNL's ALE3D code and AKTS's Thermal Safety code, using the thermal ignition of HMX in two standard LLNL cookoff experiments: the One-Dimensional Time to Explosion (ODTX) test and the Scaled Thermal Explosion (STEX) test. The chemical kinetics model used in both codes was the extended Prout-Tompkins model, a relatively new addition to ALE3D. This model was applied using ALE3D's new pseudospecies feature. In addition, an advanced isoconversional kinetic approach was used in the AKTS code. The mathematical constants in the Prout-Tompkins code were calibrated using DSC data from hermetically sealed vessels and the LLNL optimization code Kinetics05. The isoconversional kinetic parameters were optimized using the AKTS Thermokinetics code. We found that the Prout-Tompkins model calculations agree fairly well between the two codes, and the isoconversional kinetic model gives very similar results as the Prout-Tompkins model. We also found that an autocatalytic approach in the beta-delta phase transition model does affect the times to explosion for some conditions, especially STEX-like simulations at ramp rates above 100 C/hr, and further exploration of that effect is warranted.

  4. PLOT3D/AMES, APOLLO UNIX VERSION USING GMR3D (WITHOUT TURB3D)

    NASA Technical Reports Server (NTRS)

    Buning, P.

    1994-01-01

    PLOT3D is an interactive graphics program designed to help scientists visualize computational fluid dynamics (CFD) grids and solutions. Today, supercomputers and CFD algorithms can provide scientists with simulations of such highly complex phenomena that obtaining an understanding of the simulations has become a major problem. Tools which help the scientist visualize the simulations can be of tremendous aid. PLOT3D/AMES offers more functions and features, and has been adapted for more types of computers than any other CFD graphics program. Version 3.6b+ is supported for five computers and graphic libraries. Using PLOT3D, CFD physicists can view their computational models from any angle, observing the physics of problems and the quality of solutions. As an aid in designing aircraft, for example, PLOT3D's interactive computer graphics can show vortices, temperature, reverse flow, pressure, and dozens of other characteristics of air flow during flight. As critical areas become obvious, they can easily be studied more closely using a finer grid. PLOT3D is part of a computational fluid dynamics software cycle. First, a program such as 3DGRAPE (ARC-12620) helps the scientist generate computational grids to model an object and its surrounding space. Once the grids have been designed and parameters such as the angle of attack, Mach number, and Reynolds number have been specified, a "flow-solver" program such as INS3D (ARC-11794 or COS-10019) solves the system of equations governing fluid flow, usually on a supercomputer. Grids sometimes have as many as two million points, and the "flow-solver" produces a solution file which contains density, x- y- and z-momentum, and stagnation energy for each grid point. With such a solution file and a grid file containing up to 50 grids as input, PLOT3D can calculate and graphically display any one of 74 functions, including shock waves, surface pressure, velocity vectors, and particle traces. PLOT3D's 74 functions are organized into

  5. PLOT3D/AMES, APOLLO UNIX VERSION USING GMR3D (WITH TURB3D)

    NASA Technical Reports Server (NTRS)

    Buning, P.

    1994-01-01

    PLOT3D is an interactive graphics program designed to help scientists visualize computational fluid dynamics (CFD) grids and solutions. Today, supercomputers and CFD algorithms can provide scientists with simulations of such highly complex phenomena that obtaining an understanding of the simulations has become a major problem. Tools which help the scientist visualize the simulations can be of tremendous aid. PLOT3D/AMES offers more functions and features, and has been adapted for more types of computers than any other CFD graphics program. Version 3.6b+ is supported for five computers and graphic libraries. Using PLOT3D, CFD physicists can view their computational models from any angle, observing the physics of problems and the quality of solutions. As an aid in designing aircraft, for example, PLOT3D's interactive computer graphics can show vortices, temperature, reverse flow, pressure, and dozens of other characteristics of air flow during flight. As critical areas become obvious, they can easily be studied more closely using a finer grid. PLOT3D is part of a computational fluid dynamics software cycle. First, a program such as 3DGRAPE (ARC-12620) helps the scientist generate computational grids to model an object and its surrounding space. Once the grids have been designed and parameters such as the angle of attack, Mach number, and Reynolds number have been specified, a "flow-solver" program such as INS3D (ARC-11794 or COS-10019) solves the system of equations governing fluid flow, usually on a supercomputer. Grids sometimes have as many as two million points, and the "flow-solver" produces a solution file which contains density, x- y- and z-momentum, and stagnation energy for each grid point. With such a solution file and a grid file containing up to 50 grids as input, PLOT3D can calculate and graphically display any one of 74 functions, including shock waves, surface pressure, velocity vectors, and particle traces. PLOT3D's 74 functions are organized into

  6. Computer-aided classification of liver tumors in 3D ultrasound images with combined deformable model segmentation and support vector machine

    NASA Astrophysics Data System (ADS)

    Lee, Myungeun; Kim, Jong Hyo; Park, Moon Ho; Kim, Ye-Hoon; Seong, Yeong Kyeong; Cho, Baek Hwan; Woo, Kyoung-Gu

    2014-03-01

    In this study, we propose a computer-aided classification scheme of liver tumor in 3D ultrasound by using a combination of deformable model segmentation and support vector machine. For segmentation of tumors in 3D ultrasound images, a novel segmentation model was used which combined edge, region, and contour smoothness energies. Then four features were extracted from the segmented tumor including tumor edge, roundness, contrast, and internal texture. We used a support vector machine for the classification of features. The performance of the developed method was evaluated with a dataset of 79 cases including 20 cysts, 20 hemangiomas, and 39 hepatocellular carcinomas, as determined by the radiologist's visual scoring. Evaluation of the results showed that our proposed method produced tumor boundaries that were equal to or better than acceptable in 89.8% of cases, and achieved 93.7% accuracy in classification of cyst and hemangioma.

  7. 3-D Structural Modeling of Humic Acids through Experimental Characterization, Computer Assisted Structure Elucidation and Atomistic Simulations. 1. Chelsea Soil Humic Acid

    SciTech Connect

    Diallo, Mamadou S.; Simpson, Andre; Gassman, Paul L.; Faulon, Jean Loup; Johnson, Jr., James H.; Goddard, III, William A.; Hatcher, Patrick G.

    2003-05-01

    This paper describes an integrated experimental and computational framework for developing 3-D structural models for humic acids (HAs). This approach combines experimental characterization, computer assisted structure elucidation (CASE), and atomistic simulations to generate all 3-D structural models or a representative sample of these models consistent with the analytical data and bulk thermodynamic/structural properties of HAs. To illustrate this methodology, structural data derived from elemental analysis, diffuse reflectance FT-IR spectroscopy, 1-D/2-D | 1H and 13C solution NMR spectroscopy, and electrospray ionization quadrupole time-of-flight mass spectrometry (ESI QqTOF MS) are employed as input to the CASE program SIGNATURE to generate all 3-D structural models for Chelsea soil humic acid (HA). These models are subsequently used as starting 3-D structures to carry out constant temperature-constant pressure molecular dynamics simulations to estimate their bulk densities and Hildebrand solubility parameters. Surprisingly, only a few model isomers are found to exhibit molecular compositions and bulk thermodynamic properties consistent with the experimental data. The simulated 13C NMR spectrum of * Corresponding author phone: (626)395-2730; fax: (626)585-0918; e-mail: diallo@wag.caltech.edu and mdiallo@howard.edu. Present address: Materials and Process Simulation Center,BeckmanInstitute 139-74, California Institute of Technology, Pasadena, CA 91125. † California Institute of Technology. ‡ Howard University. § University of Toronto. Pacific Northwest National Laboratory. ^ Sandia National Laboratories. # The Ohio State University. ã xxxx American Chemical Society PAGE EST: 11 10.1021/es0259638 CCC: $25.00 Published on Web 00/00/0000 an equimolar mixture of these model isomers compares favorably with the measured spectrum of Chelsea soil HA.

  8. High-resolution 3D imaging of osteocytes and computational modelling in mechanobiology: insights on bone development, ageing, health and disease.

    PubMed

    Goggin, P M; Zygalakis, K C; Oreffo, R O; Schneider, P

    2016-05-22

    Osteocytes are involved in mechanosensation and mechanotransduction in bone and hence, are key to bone adaptation in response to development, ageing and disease. Thus, detailed knowledge of the three-dimensional (3D) structure of the osteocyte network (ON) and the surrounding lacuno-canalicular network (LCN) is essential. Enhanced understanding of the ON&LCN will contribute to a better understanding of bone mechanics on cellular and sub-cellular scales, for instance through improved computational models of bone mechanotransduction. Until now, the location of the ON within the hard bone matrix and the sub-µm dimensions of the ON&LCN have posed significant challenges for 3D imaging. This review identifies relevant microstructural phenotypes of the ON&LCN in health and disease and summarises how light microscopy, electron microscopy and X-ray imaging techniques have been used in studies of osteocyte anatomy, pathology and mechanobiology to date. In this review, we assess the requirements for ON&LCN imaging and examine the state of the art in the fields of imaging and computational modelling as well as recent advances in high-resolution 3D imaging. Suggestions for future investigations using volume electron microscopy are indicated and we present new data on the ON&LCN using serial block-face scanning electron microscopy. A correlative approach using these high-resolution 3D imaging techniques in conjunction with in silico modelling in bone mechanobiology will increase understanding of osteocyte function and, ultimately, lead to improved pathways for diagnosis and treatment of bone diseases such as osteoporosis.

  9. In vivo MRI-Based 3D FSI RV/LV Models for Human Right Ventricle and Patch Design for Potential Computer-Aided Surgery Optimization.

    PubMed

    Yang, Chun; Tang, Dalin; Haber, Idith; Geva, Tal; Del Nido, Pedro J

    2007-01-01

    Right ventricular dysfunction is one of the more common causes of heart failure in patients with congenital heart defects. Use of computer-assisted procedures is becoming more popular in clinical decision making process and computer-aided surgeries. A 3D in vivo MRI-based RV/LV combination model with fluid-structure interaction (FSI), RV-LV interaction, and RV-patch interaction was introduced to perform mechanical analysis for human right ventricle with potential clinical applications. Patient-specific RV/LV morphologies were acquired by using planar tagged MRI. The 3D RV/LV FSI model was solved using a commercial finite element package ADINA. Our results indicated that flow and stress/strain distributions in the right ventricle are closely related to RV morphology, material properties and blood pressure conditions. Patches with material properties better matching RV tissue properties and smaller size lead to better RV function recoveries. Computational RV volumes showed very good agreement with MRI data (error < 3%). More patient studies are needed to establish baseline database so that computational simulations can be used to replace empirical and often risky clinical experimentation to examine the efficiency and suitability of various reconstructive procedures in diseased hearts and optimal design can be found.

  10. A Longitudinal Study of Remodeling in a Revised Peripheral Artery Bypass Graft Using 3D Ultrasound Imaging and Computational Hemodynamics

    PubMed Central

    Leotta, Daniel F.; Beach, Kirk W.; Riley, James J.; Aliseda, Alberto

    2011-01-01

    We report a study of the role of hemodynamic shear stress in the remodeling and failure of a peripheral artery bypass graft. Three separate scans of a femoral to popliteal above-knee bypass graft were taken over the course of a 16 month period following a revision of the graft. The morphology of the lumen is reconstructed from data obtained by a custom 3D ultrasound system. Numerical simulations are performed with the patient-specific geometries and physiologically realistic flow rates. The ultrasound reconstructions reveal two significant areas of remodeling: a stenosis with over 85% reduction in area, which ultimately caused graft failure, and a poststenotic dilatation or widening of the lumen. Likewise, the simulations reveal a complicated hemodynamic environment within the graft. Preliminary comparisons with in vivo velocimetry also showed qualitative agreement with the flow dynamics observed in the simulations. Two distinct flow features are discerned and are hypothesized to directly initiate the observed in vivo remodeling. First, a flow separation occurs at the stenosis. A low shear recirculation region subsequently develops distal to the stenosis. The low shear region is thought to be conducive to smooth muscle cell proliferation and intimal growth. A poststenotic jet issues from the stenosis and subsequently impinges onto the lumen wall. The lumen dilation is thought to be a direct result of the high shear stress and high frequency pressure fluctuations associated with the jet impingement. PMID:21428682

  11. A 3D interactive method for estimating body segmental parameters in animals: application to the turning and running performance of Tyrannosaurus rex.

    PubMed

    Hutchinson, John R; Ng-Thow-Hing, Victor; Anderson, Frank C

    2007-06-21

    We developed a method based on interactive B-spline solids for estimating and visualizing biomechanically important parameters for animal body segments. Although the method is most useful for assessing the importance of unknowns in extinct animals, such as body contours, muscle bulk, or inertial parameters, it is also useful for non-invasive measurement of segmental dimensions in extant animals. Points measured directly from bodies or skeletons are digitized and visualized on a computer, and then a B-spline solid is fitted to enclose these points, allowing quantification of segment dimensions. The method is computationally fast enough so that software implementations can interactively deform the shape of body segments (by warping the solid) or adjust the shape quantitatively (e.g., expanding the solid boundary by some percentage or a specific distance beyond measured skeletal coordinates). As the shape changes, the resulting changes in segment mass, center of mass (CM), and moments of inertia can be recomputed immediately. Volumes of reduced or increased density can be embedded to represent lungs, bones, or other structures within the body. The method was validated by reconstructing an ostrich body from a fleshed and defleshed carcass and comparing the estimated dimensions to empirically measured values from the original carcass. We then used the method to calculate the segmental masses, centers of mass, and moments of inertia for an adult Tyrannosaurus rex, with measurements taken directly from a complete skeleton. We compare these results to other estimates, using the model to compute the sensitivities of unknown parameter values based upon 30 different combinations of trunk, lung and air sac, and hindlimb dimensions. The conclusion that T. rex was not an exceptionally fast runner remains strongly supported by our models-the main area of ambiguity for estimating running ability seems to be estimating fascicle lengths, not body dimensions. Additionally, the

  12. Spatial Pattern Dynamics of 3D Stem Cell Loss of Pluripotency via Rules-Based Computational Modeling

    PubMed Central

    White, Douglas E.; Kinney, Melissa A.; McDevitt, Todd C.; Kemp, Melissa L.

    2013-01-01

    powerful tool to predict stem cell behavior under a number of culture conditions that emulate characteristics of 3D stem cell niches. PMID:23516345

  13. Computer simulated screening of dentin bonding primer monomers through analysis of their chemical functions and their spatial 3D alignment.

    PubMed

    Vaidyanathan, J; Vaidyanathan, T K; Ravichandran, S

    2009-02-01

    Binding interactions between dentin bonding primer monomers and dentinal collagen were studied by an analysis of their chemical functions and their spatial 3D alignment. A trial set of 12 monomers used as primers in dentin adhesives was characterized to assess them for binding to a complementary target. HipHop utility in the Catalyst software from Accelrys was used for the study. Ten hypotheses were generated by HipHop procedures involving (a) conformational generation using a poling technique to promote conformational variation, (b) extraction of functions to remodel ligands as function-based structures, and (c) identification of common patterns of functional alignment displayed by low energy conformations. The hypotheses, designated as pharmacaphores, were also scored and ranked. Analysis of pharmacaphore models through mapping of ligands revealed important differences between ligands. Top-ranked poses from direct docking simulations using type 1 collagen target were mapped in a rigid manner to the highest ranked pharmacophore model. The visual match observed in mapping and associated fit values suggest a strong correspondence between direct and indirect docking simulations. The results elegantly demonstrate that an indirect approach used to identify pharmacaphore models from adhesive ligands without a target may be a simple and viable approach to assess their intermolecular interactions with an intended target. Inexpensive indirect/direct virtual screening of hydrophilic monomer candidates may be a practical way to assess their initial promise for dentin primer use well before additional experimental evaluation of their priming/bonding efficacy. This is also of value in the search/design of new compounds for priming dentin. PMID:18546179

  14. Computer simulated screening of dentin bonding primer monomers through analysis of their chemical functions and their spatial 3D alignment.

    PubMed

    Vaidyanathan, J; Vaidyanathan, T K; Ravichandran, S

    2009-02-01

    Binding interactions between dentin bonding primer monomers and dentinal collagen were studied by an analysis of their chemical functions and their spatial 3D alignment. A trial set of 12 monomers used as primers in dentin adhesives was characterized to assess them for binding to a complementary target. HipHop utility in the Catalyst software from Accelrys was used for the study. Ten hypotheses were generated by HipHop procedures involving (a) conformational generation using a poling technique to promote conformational variation, (b) extraction of functions to remodel ligands as function-based structures, and (c) identification of common patterns of functional alignment displayed by low energy conformations. The hypotheses, designated as pharmacaphores, were also scored and ranked. Analysis of pharmacaphore models through mapping of ligands revealed important differences between ligands. Top-ranked poses from direct docking simulations using type 1 collagen target were mapped in a rigid manner to the highest ranked pharmacophore model. The visual match observed in mapping and associated fit values suggest a strong correspondence between direct and indirect docking simulations. The results elegantly demonstrate that an indirect approach used to identify pharmacaphore models from adhesive ligands without a target may be a simple and viable approach to assess their intermolecular interactions with an intended target. Inexpensive indirect/direct virtual screening of hydrophilic monomer candidates may be a practical way to assess their initial promise for dentin primer use well before additional experimental evaluation of their priming/bonding efficacy. This is also of value in the search/design of new compounds for priming dentin.

  15. 3D Audio System

    NASA Technical Reports Server (NTRS)

    1992-01-01

    Ames Research Center research into virtual reality led to the development of the Convolvotron, a high speed digital audio processing system that delivers three-dimensional sound over headphones. It consists of a two-card set designed for use with a personal computer. The Convolvotron's primary application is presentation of 3D audio signals over headphones. Four independent sound sources are filtered with large time-varying filters that compensate for motion. The perceived location of the sound remains constant. Possible applications are in air traffic control towers or airplane cockpits, hearing and perception research and virtual reality development.

  16. Quantitative 3-D Imaging, Segmentation and Feature Extraction of the Respiratory System in Small Mammals for Computational Biophysics Simulations

    SciTech Connect

    Trease, Lynn L.; Trease, Harold E.; Fowler, John

    2007-03-15

    One of the critical steps toward performing computational biology simulations, using mesh based integration methods, is in using topologically faithful geometry derived from experimental digital image data as the basis for generating the computational meshes. Digital image data representations contain both the topology of the geometric features and experimental field data distributions. The geometric features that need to be captured from the digital image data are three-dimensional, therefore the process and tools we have developed work with volumetric image data represented as data-cubes. This allows us to take advantage of 2D curvature information during the segmentation and feature extraction process. The process is basically: 1) segmenting to isolate and enhance the contrast of the features that we wish to extract and reconstruct, 2) extracting the geometry of the features in an isosurfacing technique, and 3) building the computational mesh using the extracted feature geometry. “Quantitative” image reconstruction and feature extraction is done for the purpose of generating computational meshes, not just for producing graphics "screen" quality images. For example, the surface geometry that we extract must represent a closed water-tight surface.

  17. 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...

  18. Surface impedance for 3D non-linear eddy current problems -- Application to loss computation in transformers

    SciTech Connect

    Guerin, C.; Meunier, G.; Tanneau, G.

    1996-05-01

    A method based on surface impedance and the limit theory using a rectangular B(H) curve has been developed. The method, as well as the finite element formulation is first described. A computation on a three-phase three-limb 100 MVA transformer is then presented.

  19. Use of 3D X-ray Computed Microtomography to Observe in situ Sediment Structure and Colloidal Zirconia Deposits at the Pore Scale

    NASA Astrophysics Data System (ADS)

    Chen, C.; Packman, A. I.; Keane, D. T.; Gaillard, J.

    2006-12-01

    We are using X-ray Micro-Tomography (XMT) to study in situ sediment structure using the facilities of the DuPont-Northwestern-Dow Collaborative Access Team (DND-CAT), Advanced Photon Source (APS), Argonne National Laboratory. Images of a sediment sample are taken at a number of different angles as the incident x- ray beam passes through it, and a three-dimensional view of the interior of the sample is then reconstructed from these maps using Computed Tomography (CT). These 3D images allow us to observe sediment structure with near-micron-scale resolution. We are also using difference tomography to resolve the distribution of zirconium in sediment cores. Column experiments were performed to observe the deposition of colloidal zirconia (Zr) particles in porous media composed of glass beads. Reconstructed 3D maps of Zr deposition demonstrate strong pore-scale heterogeneity. Most zirconia particles accumulated at the upstream sides of collector beads and in narrow pore throats. Statistical analysis of deposition clusters reveals the average, large-scale filtration behavior. Reconstructed 3D pore structure data were used to investigate scale dependency and the effects of local variation within the porous medium. Statistical representative elementary volumes were calculated for quantities such as porosity, specific surface area, and permeability. Finally, preliminary experiments in flume were conducted in order to investigate zirconia deposition in streambeds at the scale of characteristic topographic features (bedforms).

  20. Development and evaluation of a new 3-D digitization and computer graphic system to study the anatomic tissue and restoration surfaces.

    PubMed

    Dastane, A; Vaidyanathan, T K; Vaidyanathan, J; Mehra, R; Hesby, R

    1996-01-01

    It is necessary to visualize and reconstruct tissue anatomic surfaces accurately for a variety of oral rehabilitation applications such as surface wear characterization and automated fabrication of dental restorations, accuracy of reproduction of impression and die materials, etc. In this investigation, a 3-D digitization and computer-graphic system was developed for surface characterization. The hardware consists of a profiler assembly for digitization in an MTS biomechanical test system with an artificial mouth, an IBM PS/2 computer model 70 for data processing and a Hewlett-Packard laser printer for hardcopy outputs. The software used includes a commercially available Surfer 3-D graphics package, a public domain data-fitting alignment software and an inhouse Pascal program for intercommunication plus some other limited tasks. Surfaces were digitized before and after rotation by angular displacement, the digital data were interpolated by Surfer to provide a data grid and the surfaces were computer graphically reconstructed: Misaligned surfaces were aligned by the data-fitting alignment software under different choices of parameters. The effect of different interpolation parameters (e.g. grid size, method of interpolation) and extent of rotation on the alignment accuracy was determined. The results indicate that improved alignment accuracy results from optimization of interpolation parameters and minimization of the initial misorientation between the digitized surfaces. The method provides important advantages for surface reconstruction and visualization, such as overlay of sequentially generated surfaces and accurate alignment of pairs of surfaces with small misalignment.

  1. Instability due to a two recirculation pump trip in a BWR using RAMONA-4B computer code with 3D neutron kinetics

    SciTech Connect

    Cheng, H.S.; Rohatgi, U.S.

    1993-06-01

    An investigation was made of the potential for thermal-hydraulic instabilities coupled to neutronic feedback in a BWR due to a two recirculation pump trip event using the RAMONA-4B computer code with 3D neutron kinetics. It is concluded that a high-power (100%) and low-flow (75%) initial condition would most likely lead to in-phase density wave oscillations after the tripping of both recirculation pumps, and that RAMONA-4B is capable of predicting such thermal-hydraulic instabilities coupled to neutronic feedback in BWR and in SBWR.

  2. A Computer-Assisted 3D Model for Analyzing the Aggregation of Tumorigenic Cells Reveals Specialized Behaviors and Unique Cell Types that Facilitate Aggregate Coalescence

    PubMed Central

    Scherer, Amanda; Kuhl, Spencer; Wessels, Deborah; Lusche, Daniel F.; Hanson, Brett; Ambrose, Joseph; Voss, Edward; Fletcher, Emily; Goldman, Charles; Soll, David R.

    2015-01-01

    We have developed a 4D computer-assisted reconstruction and motion analysis system, J3D-DIAS 4.1, and applied it to the reconstruction and motion analysis of tumorigenic cells in a 3D matrix. The system is unique in that it is fast, high-resolution, acquires optical sections using DIC microscopy (hence there is no associated photoxicity), and is capable of long-term 4D reconstruction. Specifically, a z-series at 5 μm increments can be acquired in less than a minute on tissue samples embedded in a 1.5 mm thick 3D Matrigel matrix. Reconstruction can be repeated at intervals as short as every minute and continued for 30 days or longer. Images are converted to mathematical representations from which quantitative parameters can be derived. Application of this system to cancer cells from established lines and fresh tumor tissue has revealed unique behaviors and cell types not present in non-tumorigenic lines. We report here that cells from tumorigenic lines and tumors undergo rapid coalescence in 3D, mediated by specific cell types that we have named “facilitators” and “probes.” A third cell type, the “dervish”, is capable of rapid movement through the gel and does not adhere to it. These cell types have never before been described. Our data suggest that tumorigenesis in vitro is a developmental process involving coalescence facilitated by specialized cells that culminates in large hollow spheres with complex architecture. The unique effects of select monoclonal antibodies on these processes demonstrate the usefulness of the model for analyzing the mechanisms of anti-cancer drugs. PMID:25790299

  3. The use of 3D computed tomography reconstruction in medico-legal testimony regarding injuries in living victims - Risks and benefits.

    PubMed

    Borowska-Solonynko, Aleksandra; Solonynko, Bohdan

    2015-02-01

    Forensic pathologists are often called upon to determine the mechanism and severity of injuries in living individuals. Such expert testimony is often based solely on hand-written clinical notes. The victims' injuries may also be visualized via three-dimensional (3D) reconstruction of computed tomography (CT) images. This method has certain benefits but is not free from limitations. This paper presents two case reports. The first case is that of a female who was brought to the hospital with a knife thrust into her body. The prosecutor's questions focused on the wound channel. The information obtained from the patient's medical records was very general with many contradictory statements. A re-evaluation of the available CT scan data and a subsequent 3D reconstruction helped determine the exact course of the wound channel. The other case was that of a young male, hospitalized based on CT evidence of bilateral rib fractions, who claimed to have been assaulted by police officers. Court expert witnesses were already in possession of a 3D reconstruction showing symmetrical fractures of the patient's lower ribs with bone fragment displacement. An expert witness in radiology definitively excluded the presence of any actual fractures, and explained their apparent visibility in the three-dimensionally reconstructed image as a motion artifact. These two cases suggest that a professionally conducted 3D CT reconstruction is a very useful tool in providing expert testimony on injuries in living victims. However, the deceptive simplicity of conducting such a reconstruction may encourage inexperienced individuals to undertake it, and thus lead to erroneous conclusions. PMID:25623187

  4. 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.

  5. Computer-controlled multi-parameter mapping of 3D compressible flowfields using planar laser-induced iodine fluorescence

    NASA Technical Reports Server (NTRS)

    Donohue, James M.; Victor, Kenneth G.; Mcdaniel, James C., Jr.

    1993-01-01

    A computer-controlled technique, using planar laser-induced iodine fluorescence, for measuring complex compressible flowfields is presented. A new laser permits the use of a planar two-line temperature technique so that all parameters can be measured with the laser operated narrowband. Pressure and temperature measurements in a step flowfield show agreement within 10 percent of a CFD model except in regions close to walls. Deviation of near wall temperature measurements from the model was decreased from 21 percent to 12 percent compared to broadband planar temperature measurements. Computer-control of the experiment has been implemented, except for the frequency tuning of the laser. Image data storage and processing has been improved by integrating a workstation into the experimental setup reducing the data reduction time by a factor of 50.

  6. 3-D components of a biological neural network visualized in computer generated imagery. II - Macular neural network organization

    NASA Technical Reports Server (NTRS)

    Ross, Muriel D.; Meyer, Glenn; Lam, Tony; Cutler, Lynn; Vaziri, Parshaw

    1990-01-01

    Computer-assisted reconstructions of small parts of the macular neural network show how the nerve terminals and receptive fields are organized in 3-dimensional space. This biological neural network is anatomically organized for parallel distributed processing of information. Processing appears to be more complex than in computer-based neural network, because spatiotemporal factors figure into synaptic weighting. Serial reconstruction data show anatomical arrangements which suggest that (1) assemblies of cells analyze and distribute information with inbuilt redundancy, to improve reliability; (2) feedforward/feedback loops provide the capacity for presynaptic modulation of output during processing; (3) constrained randomness in connectivities contributes to adaptability; and (4) local variations in network complexity permit differing analyses of incoming signals to take place simultaneously. The last inference suggests that there may be segregation of information flow to central stations subserving particular functions.

  7. FACET: a radiation view factor computer code for axisymmetric, 2D planar, and 3D geometries with shadowing

    SciTech Connect

    Shapiro, A.B.

    1983-08-01

    The computer code FACET calculates the radiation geometric view factor (alternatively called shape factor, angle factor, or configuration factor) between surfaces for axisymmetric, two-dimensional planar and three-dimensional geometries with interposed third surface obstructions. FACET was developed to calculate view factors for input to finite-element heat-transfer analysis codes. The first section of this report is a brief review of previous radiation-view-factor computer codes. The second section presents the defining integral equation for the geometric view factor between two surfaces and the assumptions made in its derivation. Also in this section are the numerical algorithms used to integrate this equation for the various geometries. The third section presents the algorithms used to detect self-shadowing and third-surface shadowing between the two surfaces for which a view factor is being calculated. The fourth section provides a user's input guide followed by several example problems.

  8. An adaptive grid method for computing the high speed 3D viscous flow about a re-entry vehicle

    NASA Technical Reports Server (NTRS)

    Bockelie, Michael J.; Smith, Robert E.

    1992-01-01

    An algebraic solution adaptive grid generation method that allows adapting the grid in all three coordinate directions is presented. Techniques are described that maintain the integrity of the original vehicle definition for grid point movement on the vehicle surface and that avoid grid cross over in the boundary layer portion of the grid lying next to the vehicle surface. The adaptive method is tested by computing the Mach 6 hypersonic three dimensional viscous flow about a proposed Martian entry vehicle.

  9. A System for Computer-Assisted Design of Stent-Grafts for Aortic Aneurysms Using 3-D Morphological Models

    SciTech Connect

    Imai, Yasuhiro; Urayama, Shin-ich; Uyama, Chikao; Inoue, Kanji; Ueno, Katsuya; Kuribayashi, Sachio; Takamiya, Makoto; Hamada, Seiki; Hirane, Yoshihisa

    2001-07-15

    A three-dimensional model was constructed from helical CT images for abdominal aortic aneurysm (AAA) and thoracic aortic aneurysm (TAA). A stent-graft was designed and positioned endoluminally on the computer. One hundred and nine stent-grafts for 101 patients were designed by this method and deployed well in all patients. The design time was reduced from 4 to 0.5 hr.

  10. GRID3D-v2: An updated version of the GRID2D/3D computer program for generating grid systems in complex-shaped three-dimensional spatial domains

    NASA Technical Reports Server (NTRS)

    Steinthorsson, E.; Shih, T. I-P.; Roelke, R. J.

    1991-01-01

    In order to generate good quality systems for complicated three-dimensional spatial domains, the grid-generation method used must be able to exert rather precise controls over grid-point distributions. Several techniques are presented that enhance control of grid-point distribution for a class of algebraic grid-generation methods known as the two-, four-, and six-boundary methods. These techniques include variable stretching functions from bilinear interpolation, interpolating functions based on tension splines, and normalized K-factors. The techniques developed in this study were incorporated into a new version of GRID3D called GRID3D-v2. The usefulness of GRID3D-v2 was demonstrated by using it to generate a three-dimensional grid system in the coolent passage of a radial turbine blade with serpentine channels and pin fins.

  11. 3-D components of a biological neural network visualized in computer generated imagery. I - Macular receptive field organization

    NASA Technical Reports Server (NTRS)

    Ross, Muriel D.; Cutler, Lynn; Meyer, Glenn; Lam, Tony; Vaziri, Parshaw

    1990-01-01

    Computer-assisted, 3-dimensional reconstructions of macular receptive fields and of their linkages into a neural network have revealed new information about macular functional organization. Both type I and type II hair cells are included in the receptive fields. The fields are rounded, oblong, or elongated, but gradations between categories are common. Cell polarizations are divergent. Morphologically, each calyx of oblong and elongated fields appears to be an information processing site. Intrinsic modulation of information processing is extensive and varies with the kind of field. Each reconstructed field differs in detail from every other, suggesting that an element of randomness is introduced developmentally and contributes to endorgan adaptability.

  12. 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. PMID:26657435

  13. 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.

  14. A non-CFD modeling system for computing 3D wind and concentration fields in urban environments

    SciTech Connect

    Nelson, Matthew A; Brown, Michael J; Williams, Michael D; Gowardhan, Akshay; Pardyjak, Eric R

    2010-01-01

    The Quick Urban & Industrial Complex (QUIC) Dispersion Modeling System has been developed to rapidly compute the transport and dispersion of toxic agent releases in the vicinity of buildings. It is composed of an empirical-diagnostic wind solver, an 'urbanized' Lagrangian random-walk model, and a graphical user interface. The code has been used for homeland security and environmental air pollution applications. In this paper, we discuss the wind solver methodology and improvements made to the original Roeckle schemes in order to better capture flow fields in dense built-up areas. The mode1-computed wind and concentration fields are then compared to measurements from several field experiments. Improvements to the QUIC Dispersion Modeling System have been made to account for the inhomogeneous and complex building layouts found in large cities. The logic that has been introduced into the code is described and comparisons of model output to full-scale outdoor urban measurements in Oklahoma City and New York City are given. Although far from perfect, the model agreed fairly well with measurements and in many cases performed equally to CFD codes.

  15. Assessment of the 3-D Thermal-Hydraulic Nuclear Core Computer Code FLICA-IV on Rod Bundle Experiments

    SciTech Connect

    Bergeron, Andre; Caruge, Daniel; Clement, Philippe

    2001-04-15

    The physical validation compared with the hydraulic and two-phase flow experiments of the thermal-hydraulic FLICA-IV nuclear core computer code, in the case of a pressurized water reactor is presented. This three-dimensional two-phase flow code is devoted to steady state and transient thermal-hydraulic analysis of nuclear reactor cores. The four balance equations used by the code and the closure relationships are first presented. Then, the facilities employed for the code validation are described. They are the ones that use either laser velocimetry techniques in the case of hydraulic validation to measure accurately the flow field around rods or isokinetic sampling to carry out the qualities and the axial mass velocities at the outlet of a rod bundle in the case of two-phase flow validation. Comparisons between experimental and computed values are then presented for the axial flow blockage simulation, inlet assemblies flow mixing, axial flow spacer grid disturbance, and an outlet rod bundle map of qualities and axial mass velocities.

  16. Computer-assisted three-dimensional surgical planing and simulation. 3D soft tissue planning and prediction.

    PubMed

    Xia, J; Samman, N; Yeung, R W; Wang, D; Shen, S G; Ip, H H; Tideman, H

    2000-08-01

    The purpose of this paper is to report a new technique for three-dimensional facial soft-tissue-change prediction after simulated orthognathic surgical planning. A scheme for soft tissue deformation, "Computer-assisted three-dimensional virtual reality soft tissue planning and prediction for orthognathic surgery (CASP)", is presented. The surgical planning was based on three-dimensional reconstructed CT visualization. Soft tissue changes were predicted by two newly devised algorithms: Surface Normal-based Model Deformation Algorithm and Ray Projection-based Model Deformation Algorithm. A three-dimensional color facial texture-mapping technique was also used for generating the color photo-realistic facial model. As a final result, a predicted and simulated patient's color facial model can be visualized from arbitrary viewing points.

  17. Development of microgravity, full body functional reach envelope using 3-D computer graphic models and virtual reality technology

    NASA Technical Reports Server (NTRS)

    Lindsey, Patricia F.

    1994-01-01

    In microgravity conditions mobility is greatly enhanced and body stability is difficult to achieve. Because of these difficulties, optimum placement and accessibility of objects and controls can be critical to required tasks on board shuttle flights or on the proposed space station. Anthropometric measurement of the maximum reach of occupants of a microgravity environment provide knowledge about maximum functional placement for tasking situations. Calculations for a full body, functional reach envelope for microgravity environments are imperative. To this end, three dimensional computer modeled human figures, providing a method of anthropometric measurement, were used to locate the data points that define the full body, functional reach envelope. Virtual reality technology was utilized to enable an occupant of the microgravity environment to experience movement within the reach envelope while immersed in a simulated microgravity environment.

  18. An Exploratory Study of Apache Middle School Students' Computer Animation.

    ERIC Educational Resources Information Center

    Stokrocki, Mary; Buckpitt, Marcia

    The paper describes a participant observation study of a 3 week summer art program for Apache middle school students on the White Mountain Reservation. Computer art skills, specifically animation using a menu-driven computer paint program, were the focus of the investigation. Because it was in the context of a summer program, instruction was…

  19. Production of Computer Animated Movies for Educational Purposes.

    ERIC Educational Resources Information Center

    Elberg, H. H.

    A detailed account is given in this paper of the procedures and the equipment used in producing six computer-animated instructional movies. First, the sequence of events were described in a script, which, together with the analytical expressions that were dealt with, formed the basis of a program. Then, the program was run on a computer and the…

  20. Cardiovascular Physiology Teaching: Computer Simulations vs. Animal Demonstrations.

    ERIC Educational Resources Information Center

    Samsel, Richard W.; And Others

    1994-01-01

    At the introductory level, the computer provides an effective alternative to using animals for laboratory teaching. Computer software can simulate the operation of multiple organ systems. Advantages of software include alteration of variables that are not easily changed in vivo, repeated interventions, and cost-effective hands-on student access.…

  1. [3-D ultrasound in gastroenterology].

    PubMed

    Zoller, W G; Liess, H

    1994-06-01

    Three-dimensional (3D) sonography represents a development of noninvasive diagnostic imaging by real-time two-dimensional (2D) sonography. The use of transparent rotating scans, comparable to a block of glass, generates a 3D effect. The objective of the present study was to optimate 3D presentation of abdominal findings. Additional investigations were made with a new volumetric program to determine the volume of selected findings of the liver. The results were compared with the estimated volumes of 2D sonography and 2D computer tomography (CT). For the processing of 3D images, typical parameter constellations were found for the different findings, which facilitated processing of 3D images. In more than 75% of the cases examined we found an optimal 3D presentation of sonographic findings with respect to the evaluation criteria developed by us for the 3D imaging of processed data. Great differences were found for the estimated volumes of the findings of the liver concerning the three different techniques applied. 3D ultrasound represents a valuable method to judge morphological appearance in abdominal findings. The possibility of volumetric measurements enlarges its potential diagnostic significance. Further clinical investigations are necessary to find out if definite differentiation between benign and malign findings is possible.

  2. Confirmatory analysis of the AP1000 passive residual heat removal heat exchanger with 3-D computational fluid dynamic analysis

    SciTech Connect

    Schwall, James R.; Karim, Naeem U.; Thakkar, Jivan G.; Taylor, Creed; Schulz, Terry; Wright, Richard F.

    2006-07-01

    The AP1000 is an 1100 MWe advanced nuclear power plant that uses passive safety features to enhance plant safety and to provide significant and measurable improvements in plant simplification, reliability, investment protection and plant costs. The AP1000 received final design approval from the US-NRC in 2004. The AP1000 design is based on the AP600 design that received final design approval in 1999. Wherever possible, the AP1000 plant configuration and layout was kept the same as AP600 to take advantage of the maturity of the design and to minimize new design efforts. As a result, the two-loop configuration was maintained for AP1000, and the containment vessel diameter was kept the same. It was determined that this significant power up-rate was well within the capability of the passive safety features, and that the safety margins for AP1000 were greater than those of operating PWRs. A key feature of the passive core cooling system is the passive residual heat removal heat exchanger (PRHR HX) that provides decay heat removal for postulated LOCA and non-LOCA events. The PRHR HX is a C-tube heat exchanger located in the in-containment refueling water storage tank (IRWST) above the core promoting natural circulation heat removal between the reactor cooling system and the tank. Component testing was performed for the AP600 PRHR HX to determine the heat transfer characteristics and to develop correlations to be used for the AP1000 safety analysis codes. The data from these tests were confirmed by subsequent integral tests at three separate facilities including the ROSA facility in Japan. Owing to the importance of this component, an independent analysis has been performed using the ATHOS-based computational fluid dynamics computer code PRHRCFD. Two separate models of the PRHR HX and IRWST have been developed representing the ROSA test geometry and the AP1000 plant geometry. Confirmation of the ROSA test results were used to validate PRHRCFD, and the AP1000 plant model

  3. 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.

  4. 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

  5. Regional seismic wavefield computation on a 3-D heterogeneous Earth model by means of coupled traveling wave synthesis

    USGS Publications Warehouse

    Pollitz, F.F.

    2002-01-01

    I present a new algorithm for calculating seismic wave propagation through a three-dimensional heterogeneous medium using the framework of mode coupling theory originally developed to perform very low frequency (f < ???0.01-0.05 Hz) seismic wavefield computation. It is a Greens function approach for multiple scattering within a defined volume and employs a truncated traveling wave basis set using the locked mode approximation. Interactions between incident and scattered wavefields are prescribed by mode coupling theory and account for the coupling among surface waves, body waves, and evanescent waves. The described algorithm is, in principle, applicable to global and regional wave propagation problems, but I focus on higher frequency (typically f ??????0.25 Hz) applications at regional and local distances where the locked mode approximation is best utilized and which involve wavefields strongly shaped by propagation through a highly heterogeneous crust. Synthetic examples are shown for P-SV-wave propagation through a semi-ellipsoidal basin and SH-wave propagation through a fault zone.

  6. 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.

  7. Algorithms for Haptic Rendering of 3D Objects

    NASA Technical Reports Server (NTRS)

    Basdogan, Cagatay; Ho, Chih-Hao; Srinavasan, Mandayam

    2003-01-01

    Algorithms have been developed to provide haptic rendering of three-dimensional (3D) objects in virtual (that is, computationally simulated) environments. The goal of haptic rendering is to generate tactual displays of the shapes, hardnesses, surface textures, and frictional properties of 3D objects in real time. Haptic rendering is a major element of the emerging field of computer haptics, which invites comparison with computer graphics. We have already seen various applications of computer haptics in the areas of medicine (surgical simulation, telemedicine, haptic user interfaces for blind people, and rehabilitation of patients with neurological disorders), entertainment (3D painting, character animation, morphing, and sculpting), mechanical design (path planning and assembly sequencing), and scientific visualization (geophysical data analysis and molecular manipulation).

  8. Generation of a suite of 3D computer-generated breast phantoms from a limited set of human subject data

    SciTech Connect

    Hsu, Christina M. L.; Palmeri, Mark L.; Segars, W. Paul; Veress, Alexander I.; Dobbins, James T. III

    2013-04-15

    Purpose: The authors previously reported on a three-dimensional computer-generated breast phantom, based on empirical human image data, including a realistic finite-element based compression model that was capable of simulating multimodality imaging data. The computerized breast phantoms are a hybrid of two phantom generation techniques, combining empirical breast CT (bCT) data with flexible computer graphics techniques. However, to date, these phantoms have been based on single human subjects. In this paper, the authors report on a new method to generate multiple phantoms, simulating additional subjects from the limited set of original dedicated breast CT data. The authors developed an image morphing technique to construct new phantoms by gradually transitioning between two human subject datasets, with the potential to generate hundreds of additional pseudoindependent phantoms from the limited bCT cases. The authors conducted a preliminary subjective assessment with a limited number of observers (n= 4) to illustrate how realistic the simulated images generated with the pseudoindependent phantoms appeared. Methods: Several mesh-based geometric transformations were developed to generate distorted breast datasets from the original human subject data. Segmented bCT data from two different human subjects were used as the 'base' and 'target' for morphing. Several combinations of transformations were applied to morph between the 'base' and 'target' datasets such as changing the breast shape, rotating the glandular data, and changing the distribution of the glandular tissue. Following the morphing, regions of skin and fat were assigned to the morphed dataset in order to appropriately assign mechanical properties during the compression simulation. The resulting morphed breast was compressed using a finite element algorithm and simulated mammograms were generated using techniques described previously. Sixty-two simulated mammograms, generated from morphing three human

  9. Europeana and 3D

    NASA Astrophysics Data System (ADS)

    Pletinckx, D.

    2011-09-01

    The current 3D hype creates a lot of interest in 3D. People go to 3D movies, but are we ready to use 3D in our homes, in our offices, in our communication? Are we ready to deliver real 3D to a general public and use interactive 3D in a meaningful way to enjoy, learn, communicate? The CARARE project is realising this for the moment in the domain of monuments and archaeology, so that real 3D of archaeological sites and European monuments will be available to the general public by 2012. There are several aspects to this endeavour. First of all is the technical aspect of flawlessly delivering 3D content over all platforms and operating systems, without installing software. We have currently a working solution in PDF, but HTML5 will probably be the future. Secondly, there is still little knowledge on how to create 3D learning objects, 3D tourist information or 3D scholarly communication. We are still in a prototype phase when it comes to integrate 3D objects in physical or virtual museums. Nevertheless, Europeana has a tremendous potential as a multi-facetted virtual museum. Finally, 3D has a large potential to act as a hub of information, linking to related 2D imagery, texts, video, sound. We describe how to create such rich, explorable 3D objects that can be used intuitively by the generic Europeana user and what metadata is needed to support the semantic linking.

  10. The three-dimensional Event-Driven Graphics Environment (3D-EDGE)

    NASA Technical Reports Server (NTRS)

    Freedman, Jeffrey; Hahn, Roger; Schwartz, David M.

    1993-01-01

    Stanford Telecom developed the Three-Dimensional Event-Driven Graphics Environment (3D-EDGE) for NASA GSFC's (GSFC) Communications Link Analysis and Simulation System (CLASS). 3D-EDGE consists of a library of object-oriented subroutines which allow engineers with little or no computer graphics experience to programmatically manipulate, render, animate, and access complex three-dimensional objects.

  11. Automotive Underhood Thermal Management Analysis Using 3-D Coupled Thermal-Hydrodynamic Computer Models: Thermal Radiation Modeling

    SciTech Connect

    Pannala, S; D'Azevedo, E; Zacharia, T

    2002-02-26

    The goal of the radiation modeling effort was to develop and implement a radiation algorithm that is fast and accurate for the underhood environment. As part of this CRADA, a net-radiation model was chosen to simulate radiative heat transfer in an underhood of a car. The assumptions (diffuse-gray and uniform radiative properties in each element) reduce the problem tremendously and all the view factors for radiation thermal calculations can be calculated once and for all at the beginning of the simulation. The cost for online integration of heat exchanges due to radiation is found to be less than 15% of the baseline CHAD code and thus very manageable. The off-line view factor calculation is constructed to be very modular and has been completely integrated to read CHAD grid files and the output from this code can be read into the latest version of CHAD. Further integration has to be performed to accomplish the same with STAR-CD. The main outcome of this effort is to obtain a highly scalable and portable simulation capability to model view factors for underhood environment (for e.g. a view factor calculation which took 14 hours on a single processor only took 14 minutes on 64 processors). The code has also been validated using a simple test case where analytical solutions are available. This simulation capability gives underhood designers in the automotive companies the ability to account for thermal radiation - which usually is critical in the underhood environment and also turns out to be one of the most computationally expensive components of underhood simulations. This report starts off with the original work plan as elucidated in the proposal in section B. This is followed by Technical work plan to accomplish the goals of the project in section C. In section D, background to the current work is provided with references to the previous efforts this project leverages on. The results are discussed in section 1E. This report ends with conclusions and future scope of

  12. Induction of social behavior in zebrafish: live versus computer animated fish as stimuli.

    PubMed

    Qin, Meiying; Wong, Albert; Seguin, Diane; Gerlai, Robert

    2014-06-01

    The zebrafish offers an excellent compromise between system complexity and practical simplicity and has been suggested as a translational research tool for the analysis of human brain disorders associated with abnormalities of social behavior. Unlike laboratory rodents zebrafish are diurnal, thus visual cues may be easily utilized in the analysis of their behavior and brain function. Visual cues, including the sight of conspecifics, have been employed to induce social behavior in zebrafish. However, the method of presentation of these cues and the question of whether computer animated images versus live stimulus fish have differential effects have not been systematically analyzed. Here, we compare the effects of five stimulus presentation types: live conspecifics in the experimental tank or outside the tank, playback of video-recorded live conspecifics, computer animated images of conspecifics presented by two software applications, the previously employed General Fish Animator, and a new application Zebrafish Presenter. We report that all stimuli were equally effective and induced a robust social response (shoaling) manifesting as reduced distance between stimulus and experimental fish. We conclude that presentation of live stimulus fish, or 3D images, is not required and 2D computer animated images are sufficient to induce robust and consistent social behavioral responses in zebrafish.

  13. 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

  14. A 3-D finite-element model for computation of temperature profiles and regions of thermal damage during focused ultrasound surgery exposures.

    PubMed

    Meaney, P M; Clarke, R L; ter Haar, G R; Rivens, I H

    1998-11-01

    Although there have been numerous models implemented for modeling thermal diffusion effects during focused ultrasound surgery (FUS), most have limited themselves to representing simple situations for which analytical solutions and the use of cylindrical geometries sufficed. For modeling single lesion formation and the heating patterns from a single exposure, good results were achieved in comparison with experimental results for predicting lesion size, shape and location. However, these types of approaches are insufficient when considering the heating of multiple sites with FUS exposures when the time interval between exposures is short. In such cases, the heat dissipation patterns from initial exposures in the lesion array formation can play a significant role in the heating patterns for later exposures. Understanding the effects of adjacent lesion formation, such as this, requires a three-dimensional (3-D) representation of the bioheat equation. Thus, we have developed a 3-D finite-element representation for modeling the thermal diffusion effects during FUS exposures in clinically relevant tissue volumes. The strength of this approach over past methods is its ability to represent arbitrarily shaped 3-D situations. Initial simulations have allowed calculation of the temperature distribution as a function of time for adjacent FUS exposures in excised bovine liver, with the individually computed point temperatures comparing favorably with published measurements. In addition to modeling these temperature distributions, the model was implemented in conjunction with an algorithm for calculating the thermal dose as a way of predicting lesion shape. Although used extensively in conventional hyperthermia applications, this thermal dose criterion has only been applied in a limited number of simulations in FUS for comparison with experimental measurements. In this study, simulations were run for focal depths 2 and 3 cm below the surface of pig's liver, using multiple

  15. A precise and non-destructive method to calculate the surface area in living scleractinian corals using X-ray computed tomography and 3D modeling

    NASA Astrophysics Data System (ADS)

    Laforsch, C.; Christoph, E.; Glaser, C.; Naumann, M.; Wild, C.; Niggl, W.

    2008-12-01

    The surface area of corals represents a major reference parameter for the standardization of flux rates, for coral growth investigations, and for investigations of coral metabolism. The methods currently used to determine the surface area of corals are rather approximate approaches lacking accuracy, or are invasive and often destructive methods that are inapplicable for experiments involving living corals. This study introduces a novel precise and non-destructive technique to quantify surface area in living coral colonies by applying computed tomography (CT) and subsequent 3D reconstruction. Living coral colonies of different taxa were scanned by conventional medical CT either in air or in sea water. Resulting data volumes were processed by 3D modeling software providing realistic 3D coral skeleton surface reconstructions, thus enabling surface area measurements. Comparisons of CT datasets obtained from calibration bodies and coral colonies proved the accuracy of the surface area determination. Surface area quantifications derived from two different surface rendering techniques applied for scanning living coral colonies showed congruent results (mean deviation ranging from 1.32 to 2.03%). The validity of surface area measurement was verified by repeated measurements of the same coral colonies by three test persons. No significant differences between all test persons in all coral genera and in both surface rendering techniques were found (independent sample t-test: all n.s.). Data analysis of a single coral colony required approximately 15 to 30 min for a trained user using the isosurface technique regardless of the complexity and growth form of the latter, rendering the method presented in this study as a time-saving and accurate method to quantify surface areas in both living coral colonies and bare coral skeletons.

  16. Developing and Evaluating of Non-Realistic Three-Dimensional (3d-Nr) and Two-Dimensional (2d) Talking-Head Animation Courseware

    ERIC Educational Resources Information Center

    Hamdan, Mohd Najib; Ali, Ahmad Zamzuri Mohamad

    2015-01-01

    The talking-head animation is an instructional animation capable of improving the communication skills through enhancing the pronunciation skills; whereby a word is pronounced correctly and accurately. This had been proven by several researches, which indicate that learning with interactive animation is much more advantageous than conventional…

  17. Software to compute elastostatic Green's functions for sources in 3D homogeneous elastic layers above a (visco)elastic halfspace

    NASA Astrophysics Data System (ADS)

    Bradley, A. M.; Segall, P.

    2012-12-01

    . Let \\bar A be the matrix after scaling its columns to unit infinity norm and \\bar x the scaled x. If \\bar A is well conditioned, as it often is in (visco)elastostatic problems, then using determinants is unnecessary. Multiply each side of A x = b by a propagator matrix to the computation depth zcd prior to storing the matrix in finite precision. zcd is determined by the rule that zr and zcd must be on opposite sides of zs. Let the resulting matrix be A(zcd). Three facts imply that this rule controls the NWRE in \\hat x: 1. Diagonally scaling a matrix changes the accuracy of an element of the solution by about one ULP (unit in the last place). 2. If the NWRE of \\bar x is small, then the largest elements are accurate. 3. zcd controls the magnitude of elements in \\bar x. In step 4, to avoid numerically Fourier transforming the (nearly) non-square-integrable functions that arise when the receiver and source depths are (nearly) the same, a function is divided into an analytical part and a numerical part that goes quickly to 0 as k -> ∞ . Our poster will describe these calculations, present a preliminary interface to a C-language package in development, and show some physical results.

  18. Increasing the impact of medical image computing using community-based open-access hackathons: The NA-MIC and 3D Slicer experience.

    PubMed

    Kapur, Tina; Pieper, Steve; Fedorov, Andriy; Fillion-Robin, J-C; Halle, Michael; O'Donnell, Lauren; Lasso, Andras; Ungi, Tamas; Pinter, Csaba; Finet, Julien; Pujol, Sonia; Jagadeesan, Jayender; Tokuda, Junichi; Norton, Isaiah; Estepar, Raul San Jose; Gering, David; Aerts, Hugo J W L; Jakab, Marianna; Hata, Nobuhiko; Ibanez, Luiz; Blezek, Daniel; Miller, Jim; Aylward, Stephen; Grimson, W Eric L; Fichtinger, Gabor; Wells, William M; Lorensen, William E; Schroeder, Will; Kikinis, Ron

    2016-10-01

    The National Alliance for Medical Image Computing (NA-MIC) was launched in 2004 with the goal of investigating and developing an open source software infrastructure for the extraction of information and knowledge from medical images using computational methods. Several leading research and engineering groups participated in this effort that was funded by the US National Institutes of Health through a variety of infrastructure grants. This effort transformed 3D Slicer from an internal, Boston-based, academic research software application into a professionally maintained, robust, open source platform with an international leadership and developer and user communities. Critical improvements to the widely used underlying open source libraries and tools-VTK, ITK, CMake, CDash, DCMTK-were an additional consequence of this effort. This project has contributed to close to a thousand peer-reviewed publications and a growing portfolio of US and international funded efforts expanding the use of these tools in new medical computing applications every year. In this editorial, we discuss what we believe are gaps in the way medical image computing is pursued today; how a well-executed research platform can enable discovery, innovation and reproducible science ("Open Science"); and how our quest to build such a software platform has evolved into a productive and rewarding social engineering exercise in building an open-access community with a shared vision.

  19. Increasing the impact of medical image computing using community-based open-access hackathons: The NA-MIC and 3D Slicer experience.

    PubMed

    Kapur, Tina; Pieper, Steve; Fedorov, Andriy; Fillion-Robin, J-C; Halle, Michael; O'Donnell, Lauren; Lasso, Andras; Ungi, Tamas; Pinter, Csaba; Finet, Julien; Pujol, Sonia; Jagadeesan, Jayender; Tokuda, Junichi; Norton, Isaiah; Estepar, Raul San Jose; Gering, David; Aerts, Hugo J W L; Jakab, Marianna; Hata, Nobuhiko; Ibanez, Luiz; Blezek, Daniel; Miller, Jim; Aylward, Stephen; Grimson, W Eric L; Fichtinger, Gabor; Wells, William M; Lorensen, William E; Schroeder, Will; Kikinis, Ron

    2016-10-01

    The National Alliance for Medical Image Computing (NA-MIC) was launched in 2004 with the goal of investigating and developing an open source software infrastructure for the extraction of information and knowledge from medical images using computational methods. Several leading research and engineering groups participated in this effort that was funded by the US National Institutes of Health through a variety of infrastructure grants. This effort transformed 3D Slicer from an internal, Boston-based, academic research software application into a professionally maintained, robust, open source platform with an international leadership and developer and user communities. Critical improvements to the widely used underlying open source libraries and tools-VTK, ITK, CMake, CDash, DCMTK-were an additional consequence of this effort. This project has contributed to close to a thousand peer-reviewed publications and a growing portfolio of US and international funded efforts expanding the use of these tools in new medical computing applications every year. In this editorial, we discuss what we believe are gaps in the way medical image computing is pursued today; how a well-executed research platform can enable discovery, innovation and reproducible science ("Open Science"); and how our quest to build such a software platform has evolved into a productive and rewarding social engineering exercise in building an open-access community with a shared vision. PMID:27498015

  20. Accuracy and Computational Efficiency in 3D Dispersion via Lattice-Boltzmann:. Models for Dispersion in Rough Fractures and Double-Diffusive Fingering

    NASA Astrophysics Data System (ADS)

    Stockman, Harlan W.; Glass, Robert J.; Cooper, Clay; Rajaram, Harihar

    In the presence of buoyancy, multiple diffusion coefficients, and porous media, the dispersion of solutes can be remarkably complex. The lattice-Boltzmann (LB) method is ideal for modeling dispersion in flow through complex geometries; yet, LB models of solute fingers or slugs can suffer from peculiar numerical conditions (e.g., denormal generation) that degrade computational performance by factors of 6 or more. Simple code optimizations recover performance and yield simulation rates up to ~3 million site updates per second on inexpensive, single-CPU systems. Two examples illustrate limits of the methods: (1) Dispersion of solute in a thin duct is often approximated with dispersion between infinite parallel plates. However, Doshi, Daiya and Gill (DDG) showed that for a smooth-walled duct, this approximation is in error by a factor of ~8. But in the presence of wall roughness (found in all real fractures), the DDG phenomenon can be diminished. (2) Double-diffusive convection drives "salt-fingering", a process for mixing of fresh-cold and warm-salty waters in many coastal regions. Fingering experiments are typically performed in Hele-Shaw cells, and can be modeled with the 2D (pseudo-3D) LB method with velocity-proportional drag forces. However, the 2D models cannot capture Taylor-Aris dispersion from the cell walls. We compare 2D and true 3D fingering models against observations from laboratory experiments.

  1. Integrated computational tools for identification of CCR5 antagonists as potential HIV-1 entry inhibitors: homology modeling, virtual screening, molecular dynamics simulations and 3D QSAR analysis.

    PubMed

    Moonsamy, Suri; Dash, Radha Charan; Soliman, Mahmoud E S

    2014-04-23

    Using integrated in-silico computational techniques, including homology modeling, structure-based and pharmacophore-based virtual screening, molecular dynamic simulations, per-residue energy decomposition analysis and atom-based 3D-QSAR analysis, we proposed ten novel compounds as potential CCR5-dependent HIV-1 entry inhibitors. Via validated docking calculations, binding free energies revealed that novel leads demonstrated better binding affinities with CCR5 compared to maraviroc, an FDA-approved HIV-1 entry inhibitor and in clinical use. Per-residue interaction energy decomposition analysis on the averaged MD structure showed that hydrophobic active residues Trp86, Tyr89 and Tyr108 contributed the most to inhibitor binding. The validated 3D-QSAR model showed a high cross-validated rcv2 value of 0.84 using three principal components and non-cross-validated r2 value of 0.941. It was also revealed that almost all compounds in the test set and training set yielded a good predicted value. Information gained from this study could shed light on the activity of a new series of lead compounds as potential HIV entry inhibitors and serve as a powerful tool in the drug design and development machinery.

  2. Investigation and optimization of a finite element simulation of transducer array systems for 3D ultrasound computer tomography with respect to electrical impedance characteristics

    NASA Astrophysics Data System (ADS)

    Kohout, B.; Pirinen, J.; Ruiter, N. V.

    2012-03-01

    The established standard screening method to detect breast cancer is X-ray mammography. However X-ray mammography often has low contrast for tumors located within glandular tissue. A new approach is 3D Ultrasound Computer Tomography (USCT), which is expected to detect small tumors at an early stage. This paper describes the development, improvement and the results of Finite Element Method (FEM) simulations of the Transducer Array System (TAS) used in our 3D USCT. The focus of this work is on researching the influence of meshing and material parameters on the electrical impedance curves. Thereafter, these findings are used to optimize the simulation model. The quality of the simulation was evaluated by comparing simulated impedance characteristics with measured data of the real TAS. The resulting FEM simulation model is a powerful tool to analyze and optimize transducer array systems applied for USCT. With this simulation model, the behavior of TAS for different geometry modifications was researched. It provides a means to understand the acoustical performances inside of any ultrasound transducer represented by its electrical impedance characteristic.

  3. A multiscale 0-D/3-D approach to patient-specific adaptation of a cerebral autoregulation model for computational fluid dynamics studies of cardiopulmonary bypass.

    PubMed

    Neidlin, Michael; Steinseifer, Ulrich; Kaufmann, Tim A S

    2014-06-01

    Neurological complication often occurs during cardiopulmonary bypass (CPB). One of the main causes is hypoperfusion of the cerebral tissue affected by the position of the cannula tip and diminished cerebral autoregulation (CA). Recently, a lumped parameter approach could describe the baroreflex, one of the main mechanisms of cerebral autoregulation, in a computational fluid dynamics (CFD) study of CPB. However, the cerebral blood flow (CBF) was overestimated and the physiological meaning of the variables and their impact on the model was unknown. In this study, we use a 0-D control circuit representation of the Baroreflex mechanism, to assess the parameters with respect to their physiological meaning and their influence on CBF. Afterwards the parameters are transferred to 3D-CFD and the static and dynamic behavior of cerebral autoregulation is investigated. The parameters of the baroreflex mechanism can reproduce normotensive, hypertensive and impaired autoregulation behavior. Further on, the proposed model can mimic the effects of anesthetic agents and other factors controlling dynamic CA. The CFD simulations deliver similar results of static and dynamic CBF as the 0-D control circuit. This study shows the feasibility of a multiscale 0-D/3-D approach to include patient-specific cerebral autoregulation into CFD studies. PMID:24746017

  4. A task-based parallelism and vectorized approach to 3D Method of Characteristics (MOC) reactor simulation for high performance computing architectures

    NASA Astrophysics Data System (ADS)

    Tramm, John R.; Gunow, Geoffrey; He, Tim; Smith, Kord S.; Forget, Benoit; Siegel, Andrew R.

    2016-05-01

    In this study we present and analyze a formulation of the 3D Method of Characteristics (MOC) technique applied to the simulation of full core nuclear reactors. Key features of the algorithm include a task-based parallelism model that allows independent MOC tracks to be assigned to threads dynamically, ensuring load balancing, and a wide vectorizable inner loop that takes advantage of modern SIMD computer architectures. The algorithm is implemented in a set of highly optimized proxy applications in order to investigate its performance characteristics on CPU, GPU, and Intel Xeon Phi architectures. Speed, power, and hardware cost efficiencies are compared. Additionally, performance bottlenecks are identified for each architecture in order to determine the prospects for continued scalability of the algorithm on next generation HPC architectures.

  5. Accepting the T3D

    SciTech Connect

    Rich, D.O.; Pope, S.C.; DeLapp, J.G.

    1994-10-01

    In April, a 128 PE Cray T3D was installed at Los Alamos National Laboratory`s Advanced Computing Laboratory as part of the DOE`s High-Performance Parallel Processor Program (H4P). In conjunction with CRI, the authors implemented a 30 day acceptance test. The test was constructed in part to help them understand the strengths and weaknesses of the T3D. In this paper, they briefly describe the H4P and its goals. They discuss the design and implementation of the T3D acceptance test and detail issues that arose during the test. They conclude with a set of system requirements that must be addressed as the T3D system evolves.

  6. Techniques for animation of CFD results. [computational fluid dynamics

    NASA Technical Reports Server (NTRS)

    Horowitz, Jay; Hanson, Jeffery C.

    1992-01-01

    Video animation is becoming increasingly vital to the computational fluid dynamics researcher, not just for presentation, but for recording and comparing dynamic visualizations that are beyond the current capabilities of even the most powerful graphic workstation. To meet these needs, Lewis Research Center has recently established a facility to provide users with easy access to advanced video animation capabilities. However, producing animation that is both visually effective and scientifically accurate involves various technological and aesthetic considerations that must be understood both by the researcher and those supporting the visualization process. These considerations include: scan conversion, color conversion, and spatial ambiguities.

  7. 3d-3d correspondence revisited

    NASA Astrophysics Data System (ADS)

    Chung, Hee-Joong; Dimofte, Tudor; Gukov, Sergei; Sułkowski, Piotr

    2016-04-01

    In fivebrane compactifications on 3-manifolds, we point out the importance of all flat connections in the proper definition of the effective 3d {N}=2 theory. The Lagrangians of some theories with the desired properties can be constructed with the help of homological knot invariants that categorify colored Jones polynomials. Higgsing the full 3d theories constructed this way recovers theories found previously by Dimofte-Gaiotto-Gukov. We also consider the cutting and gluing of 3-manifolds along smooth boundaries and the role played by all flat connections in this operation.

  8. 3d-3d correspondence revisited

    DOE PAGES

    Chung, Hee -Joong; Dimofte, Tudor; Gukov, Sergei; Sułkowski, Piotr

    2016-04-21

    In fivebrane compactifications on 3-manifolds, we point out the importance of all flat connections in the proper definition of the effective 3d N = 2 theory. The Lagrangians of some theories with the desired properties can be constructed with the help of homological knot invariants that categorify colored Jones polynomials. Higgsing the full 3d theories constructed this way recovers theories found previously by Dimofte-Gaiotto-Gukov. As a result, we also consider the cutting and gluing of 3-manifolds along smooth boundaries and the role played by all flat connections in this operation.

  9. 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

  10. Benzimidazole derivatives. 3. 3D-QSAR/CoMFA model and computational simulation for the recognition of 5-HT(4) receptor antagonists.

    PubMed

    López-Rodríguez, María L; Murcia, Marta; Benhamú, Bellinda; Viso, Alma; Campillo, Mercedes; Pardo, Leonardo

    2002-10-24

    A three-dimensional quantitative structure-affinity relationship study (3D-QSAR), using the comparative molecular field analysis (CoMFA) method, and subsequent computational simulation of ligand recognition have been successfully applied to explain the binding affinities for the 5-HT(4) receptor (5-HT(4)R) of a series of benzimidazole-4-carboxamides and carboxylates derivatives 1-24. The K(i) values of these compounds are in the range from 0.11 to 10 000 nM. The derived 3D-QSAR model shows high predictive ability (q(2) = 0.789 and r(2) = 0.997). Steric (contribution of 43.5%) and electrostatic (50.3%) fields and solvation energy (6.1%) of this novel class of 5-HT(4)R antagonists are relevant descriptors for structure-activity relationships. Computational simulation of the complexes between the benzimidazole-4-carboxamide UCM-21195 (5) and the carboxylate UCM-26995 (21) and a 3D model of the transmembrane domain of the 5-HT(4)R, constructed using the reported crystal structure of rhodopsin, have allowed us to define the molecular details of the ligand-receptor interaction that includes (i) the ionic interaction between the NH group of the protonated piperidine of the ligand and the carboxylate group of Asp(3.32), (ii) the hydrogen bond between the carbonyl oxygen of the ligand and the hydroxyl group of Ser(5.43), (iii) the hydrogen bond between the NH group of Asn(6.55) and the aromatic ring of carboxamides or the ether oxygen of carboxylates, (iv) the interaction of the electron-rich clouds of the aromatic ring of Phe(6.51) and the electron-poor hydrogens of the carbon atoms adjacent to the protonated piperidine nitrogen of the ligand, and (v) the pi-sigma stacking interaction between the benzimidazole system of the ligand and the benzene ring of Tyr(5.38). Moreover, the noticeable increase in potency at the 5-HT(4)R sites, by the introduction of a chloro or bromo atom at the 6-position of the aromatic ring, is attributed to the additional electrostatic and van der

  11. 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, a