Science.gov

Sample records for 3d tomographic reconstruction

  1. Recovery and Visualization of 3D Structure of Chromosomes from Tomographic Reconstruction Images

    NASA Astrophysics Data System (ADS)

    Babu, Sabarish; Liao, Pao-Chuan; Shin, Min C.; Tsap, Leonid V.

    2006-12-01

    The objectives of this work include automatic recovery and visualization of a 3D chromosome structure from a sequence of 2D tomographic reconstruction images taken through the nucleus of a cell. Structure is very important for biologists as it affects chromosome functions, behavior of the cell, and its state. Analysis of chromosome structure is significant in the detection of diseases, identification of chromosomal abnormalities, study of DNA structural conformation, in-depth study of chromosomal surface morphology, observation of in vivo behavior of the chromosomes over time, and in monitoring environmental gene mutations. The methodology incorporates thresholding based on a histogram analysis with a polyline splitting algorithm, contour extraction via active contours, and detection of the 3D chromosome structure by establishing corresponding regions throughout the slices. Visualization using point cloud meshing generates a 3D surface. The 3D triangular mesh of the chromosomes provides surface detail and allows a user to interactively analyze chromosomes using visualization software.

  2. Recovery and Visualization of 3D Structure of Chromosomes from Tomographic Reconstruction Images

    SciTech Connect

    Babu, S; Liao, P; Shin, M C; Tsap, L V

    2004-04-28

    The objectives of this work include automatic recovery and visualization of a 3D chromosome structure from a sequence of 2D tomographic reconstruction images taken through the nucleus of a cell. Structure is very important for biologists as it affects chromosome functions, behavior of the cell and its state. Chromosome analysis is significant in the detection of deceases and in monitoring environmental gene mutations. The algorithm incorporates thresholding based on a histogram analysis with a polyline splitting algorithm, contour extraction via active contours, and detection of the 3D chromosome structure by establishing corresponding regions throughout the slices. Visualization using point cloud meshing generates a 3D surface. The 3D triangular mesh of the chromosomes provides surface detail and allows a user to interactively analyze chromosomes using visualization software.

  3. Evaluation of a 3D point cloud tetrahedral tomographic reconstruction method

    PubMed Central

    Pereira, N F; Sitek, A

    2011-01-01

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

  4. Comparison of 3D-OP-OSEM and 3D-FBP reconstruction algorithms for High-Resolution Research Tomograph studies: effects of randoms estimation methods

    NASA Astrophysics Data System (ADS)

    van Velden, Floris H. P.; Kloet, Reina W.; van Berckel, Bart N. M.; Wolfensberger, Saskia P. A.; Lammertsma, Adriaan A.; Boellaard, Ronald

    2008-06-01

    The High-Resolution Research Tomograph (HRRT) is a dedicated human brain positron emission tomography (PET) scanner. Recently, a 3D filtered backprojection (3D-FBP) reconstruction method has been implemented to reduce bias in short duration frames, currently observed in 3D ordinary Poisson OSEM (3D-OP-OSEM) reconstructions. Further improvements might be expected using a new method of variance reduction on randoms (VRR) based on coincidence histograms instead of using the delayed window technique (DW) to estimate randoms. The goal of this study was to evaluate VRR in combination with 3D-OP-OSEM and 3D-FBP reconstruction techniques. To this end, several phantom studies and a human brain study were performed. For most phantom studies, 3D-OP-OSEM showed higher accuracy of observed activity concentrations with VRR than with DW. However, both positive and negative deviations in reconstructed activity concentrations and large biases of grey to white matter contrast ratio (up to 88%) were still observed as a function of scan statistics. Moreover 3D-OP-OSEM+VRR also showed bias up to 64% in clinical data, i.e. in some pharmacokinetic parameters as compared with those obtained with 3D-FBP+VRR. In the case of 3D-FBP, VRR showed similar results as DW for both phantom and clinical data, except that VRR showed a better standard deviation of 6-10%. Therefore, VRR should be used to correct for randoms in HRRT PET studies.

  5. BOX SPLINE BASED 3D TOMOGRAPHIC RECONSTRUCTION OF DIFFUSION PROPAGATORS FROM MRI DATA.

    PubMed

    Ye, Wenxing; Portnoy, Sharon; Entezari, Alireza; Vemuri, Baba C; Blackband, Stephen J

    2011-06-09

    This paper introduces a tomographic approach for reconstruction of diffusion propagators, P( r ), in a box spline framework. Box splines are chosen as basis functions for high-order approximation of P( r ) from the diffusion signal. Box splines are a generalization of B-splines to multivariate setting that are particularly useful in the context of tomographic reconstruction. The X-Ray or Radon transform of a (tensor-product B-spline or a non-separable) box spline is a box spline - the space of box splines is closed under the Radon transform.We present synthetic and real multi-shell diffusion-weighted MR data experiments that demonstrate the increased accuracy of P( r ) reconstruction as the order of basis functions is increased.

  6. Post-processing methods of rendering and visualizing 3-D reconstructed tomographic images

    SciTech Connect

    Wong, S.T.C.

    1997-02-01

    The purpose of this presentation is to discuss the computer processing techniques of tomographic images, after they have been generated by imaging scanners, for volume visualization. Volume visualization is concerned with the representation, manipulation, and rendering of volumetric data. Since the first digital images were produced from computed tomography (CT) scanners in the mid 1970s, applications of visualization in medicine have expanded dramatically. Today, three-dimensional (3D) medical visualization has expanded from using CT data, the first inherently digital source of 3D medical data, to using data from various medical imaging modalities, including magnetic resonance scanners, positron emission scanners, digital ultrasound, electronic and confocal microscopy, and other medical imaging modalities. We have advanced from rendering anatomy to aid diagnosis and visualize complex anatomic structures to planning and assisting surgery and radiation treatment. New, more accurate and cost-effective procedures for clinical services and biomedical research have become possible by integrating computer graphics technology with medical images. This trend is particularly noticeable in current market-driven health care environment. For example, interventional imaging, image-guided surgery, and stereotactic and visualization techniques are now stemming into surgical practice. In this presentation, we discuss only computer-display-based approaches of volumetric medical visualization. That is, we assume that the display device available is two-dimensional (2D) in nature and all analysis of multidimensional image data is to be carried out via the 2D screen of the device. There are technologies such as holography and virtual reality that do provide a {open_quotes}true 3D screen{close_quotes}. To confine the scope, this presentation will not discuss such approaches.

  7. GPU-based rapid reconstruction of cellular 3D refractive index maps from tomographic phase microscopy (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Dardikman, Gili; Shaked, Natan T.

    2016-03-01

    We present highly parallel and efficient algorithms for real-time reconstruction of the quantitative three-dimensional (3-D) refractive-index maps of biological cells without labeling, as obtained from the interferometric projections acquired by tomographic phase microscopy (TPM). The new algorithms are implemented on the graphic processing unit (GPU) of the computer using CUDA programming environment. The reconstruction process includes two main parts. First, we used parallel complex wave-front reconstruction of the TPM-based interferometric projections acquired at various angles. The complex wave front reconstructions are done on the GPU in parallel, while minimizing the calculation time of the Fourier transforms and phase unwrapping needed. Next, we implemented on the GPU in parallel the 3-D refractive index map retrieval using the TPM filtered-back projection algorithm. The incorporation of algorithms that are inherently parallel with a programming environment such as Nvidia's CUDA makes it possible to obtain real-time processing rate, and enables high-throughput platform for label-free, 3-D cell visualization and diagnosis.

  8. Dynamic 3D reconstructions of the heart wall from tomographic imaging

    NASA Astrophysics Data System (ADS)

    Lange, Joerg; von Smekal, Alexander

    1994-05-01

    We present a dynamic reconstruction of the left ventricle (LV) of the human heart. LV surface is represented by a set of points. The coordinates of these points are iterated by an artificial neural network while optimizing the match between the reconstruction based on these coordinates and the signal data. The input for the network are the segment's positions which represent the surface within the original data. The output is a set of real-valued coordinates quantifying the location of the LV surface points. The reconstruction is simultaneously developed in 3-D space and temporal domain. A topological constraint during training of the network gives corresponding vertices in space and time with global correctness. At any phase of the heart beat the network develops a map among the surface points which is highly ordered. This results in very regular wire-frames, that can be displayed rapidly on even small graphic workstations. Without time and third dimension this is very similar to Durbin's algorithm for solving the traveling salesman problem (TSP). To achieve a smooth representation we keep our network from developing the full TSP optimal solution.

  9. Microcomputer-based technique for 3-D reconstruction and volume measurement of computer tomographic images. Part 1: Phantom studies.

    PubMed

    Albright, R E; Fram, E K

    1988-12-01

    This paper presents a microcomputer-based technique that accurately quantifies volumes from computed tomographic (CT) scans of irregularly shaped objects as well as displaying 3-D reconstructions. The method uses standard CT film, allowing analysis of previous or outside CT studies. The planimetry method showed less than 5% error in measuring irregular 2-D areas larger than 6 mm2. The method is demonstrated to be significantly more accurate than spherical, ellipsoid, or rectangular geometric models in quantifying object volume by CT (P less than .001). With a single gantry angle, planimetry showed a two standard deviation error under 10% in measuring the volume of irregular objects compared with an error over 30% for ellipsoid models. The inaccuracy of the spherical model (80% error) and the rectangular prism model (192% error) renders them impractical to provide quantitative object volume. Microcomputer planimetry provides an accurate and versatile means to measure the volume and produce 3-D reconstructions of objects scanned with CT, and it has potential application in quantifying tumor response with CT and magnetic resonance imaging.

  10. Understanding the 3D morphology of the Jovian aurora using Juno-UVS observations: simulations and tomographic reconstruction

    NASA Astrophysics Data System (ADS)

    Bonfond, B.; Gladstone, R.

    2012-12-01

    The aurora at Jupiter is a spectacular signature of the many processes taking place in the Jovian magnetosphere, such as magnetic reconnection, large scale electric currents, moon-magnetosphere interactions, etc. As a consequence, this aurora is extremely complex and dynamic, powered by a variety of phenomena that we have only begun to unravel. The 3D morphology of the aurora can provide a way to untangle the different processes at play. As a polar orbiter, Juno will provide unprecedented global and close-up views of Jupiter's auroral emissions. As it flies at low altitude over auroral curtains, spots and patches, it will provide views of these features from multiple points, allowing the retrieval of their 3D structure. The ultraviolet spectrograph on board Juno (Juno-UVS) is designed to observe auroral emissions in the 68 to 210 nm range. It is equipped with a scan mirror targeting up to +/-30 degrees off axis of the spacecraft rotation plane. We have built a planning tool to determine which auroral targets of interest, such as a satellite footprint for example, is observable by the instrument at any time during the mission. We have also built a simulation tool that allows us to generate realistic views of the Jovian aurora as observed by Juno-UVS. The purpose of this tool is to 1) fine-tune the selection algorithm to identify the most valuable data in the harsh radiation environment encountered around Jupiter, and 2) serve as a test bed for adapting tomographic algorithms to the Juno-UVS dataset. Tomographic reconstruction will allow estimation of the position and horizontal extent of the auroral regions of interest, as well as their vertical emission structure, which may be used to characterize the energy distribution of the precipitating particles responsible for the features.

  11. Tomographic 3D-PIV and Applications

    NASA Astrophysics Data System (ADS)

    Elsinga, Gerrit E.; Wieneke, Bernhard; Scarano, Fulvio; Schröder, Andreas

    Tomographic particle image velocimetry is a 3D PIV technique based on the illumination, recording, reconstruction and analysis of tracer-particle motion within a three-dimensional measurement volume. The recently developed technique makes use of several simultaneous views of the illuminated particles, typically 4, and their three-dimensional reconstruction as a light-intensity distribution by means of optical tomography. The reconstruction is performed with the MART algorithm (multiplicative algebraic reconstruction technique), yielding a 3D distribution of light intensity discretized over an array of voxels. The reconstructed tomogram pair is then analyzed by means of 3D crosscorrelation with an iterative multigrid volume-deformation technique, returning the three-component velocity vector distribution over the measurement volume. The implementation of the tomographic technique in time-resolved mode by means of high repetition rate PIV hardware has the capability to yield 4D velocity information. The first part of the chapter describes the operation principles and gives a detailed assessment of the tomographic reconstruction algorithm performance based upon a computer-simulated experiment. The second part of the chapter proposes four applications on two flow cases: 1. the transitional wake behind a circular cylinder; 2. the turbulent boundary layer developing over a flat plate. For the first case, experiments in air at ReD = 2700 are described together with the experimental assessment of the tomographic reconstruction accuracy. In this experiment a direct comparison is made between the results obtained by tomographic PIV and stereo-PIV. Experiments conducted in a water facility on the cylinder wake shows the extension of the technique to time-resolved measurements in water at ReD = 540 by means of a low repetition rate PIV system. A high data yield is obtained using high-resolution cameras (2k × 2k pixels) returning 650k vectors per volume. Measurements of the

  12. Tomographic reconstruction of circularly polarized high-harmonic fields: 3D attosecond metrology.

    PubMed

    Chen, Cong; Tao, Zhensheng; Hernández-García, Carlos; Matyba, Piotr; Carr, Adra; Knut, Ronny; Kfir, Ofer; Zusin, Dimitry; Gentry, Christian; Grychtol, Patrik; Cohen, Oren; Plaja, Luis; Becker, Andreas; Jaron-Becker, Agnieszka; Kapteyn, Henry; Murnane, Margaret

    2016-02-01

    Bright, circularly polarized, extreme ultraviolet (EUV) and soft x-ray high-harmonic beams can now be produced using counter-rotating circularly polarized driving laser fields. Although the resulting circularly polarized harmonics consist of relatively simple pairs of peaks in the spectral domain, in the time domain, the field is predicted to emerge as a complex series of rotating linearly polarized bursts, varying rapidly in amplitude, frequency, and polarization. We extend attosecond metrology techniques to circularly polarized light by simultaneously irradiating a copper surface with circularly polarized high-harmonic and linearly polarized infrared laser fields. The resulting temporal modulation of the photoelectron spectra carries essential phase information about the EUV field. Utilizing the polarization selectivity of the solid surface and by rotating the circularly polarized EUV field in space, we fully retrieve the amplitude and phase of the circularly polarized harmonics, allowing us to reconstruct one of the most complex coherent light fields produced to date.

  13. Tomographic reconstruction of circularly polarized high-harmonic fields: 3D attosecond metrology

    PubMed Central

    Chen, Cong; Tao, Zhensheng; Hernández-García, Carlos; Matyba, Piotr; Carr, Adra; Knut, Ronny; Kfir, Ofer; Zusin, Dimitry; Gentry, Christian; Grychtol, Patrik; Cohen, Oren; Plaja, Luis; Becker, Andreas; Jaron-Becker, Agnieszka; Kapteyn, Henry; Murnane, Margaret

    2016-01-01

    Bright, circularly polarized, extreme ultraviolet (EUV) and soft x-ray high-harmonic beams can now be produced using counter-rotating circularly polarized driving laser fields. Although the resulting circularly polarized harmonics consist of relatively simple pairs of peaks in the spectral domain, in the time domain, the field is predicted to emerge as a complex series of rotating linearly polarized bursts, varying rapidly in amplitude, frequency, and polarization. We extend attosecond metrology techniques to circularly polarized light by simultaneously irradiating a copper surface with circularly polarized high-harmonic and linearly polarized infrared laser fields. The resulting temporal modulation of the photoelectron spectra carries essential phase information about the EUV field. Utilizing the polarization selectivity of the solid surface and by rotating the circularly polarized EUV field in space, we fully retrieve the amplitude and phase of the circularly polarized harmonics, allowing us to reconstruct one of the most complex coherent light fields produced to date. PMID:26989782

  14. 3D tomographic reconstruction of the internal velocity field of an immiscible drop in a shear flow

    NASA Astrophysics Data System (ADS)

    Kerdraon, Paul; Dalziel, Stuart B.; Goldstein, Raymond E.; Landel, Julien R.; Peaudecerf, Francois J.

    2015-11-01

    We study experimentally the internal flow of a drop attached to a flat substrate and immersed in an immiscible shear flow. Transport inside the drop can play a crucial role in cleaning applications. Internal advection can enhance the mass transfer across the drop surface, thus increasing the cleaning rate. We used microlitre water-glycerol drops on a hydrophobic substrate. The drops were spherical and did not deform significantly under the shear flow. An oil phase of relative viscosity 0.01 to 1 was flowed over the drop. Typical Reynolds numbers inside the drops were of the order of 0.1 to 10. Using confocal microscopy, we performed 3D tomographic reconstruction of the flow field in the drop. The in-plane velocity field was measured using micro-PIV, and the third velocity component was computed from incompressibility. To our knowledge, this study gives the first experimental measurement of the three-dimensional internal velocity field of a drop in a shear flow. Numerical simulations and theoretical models published in the past 30 years predict a toroidal internal recirculation flow, for which the entire surface flows streamwise. However, our measurements reveal a qualitatively different picture with a two-lobed recirculation, featuring two stagnation points at the surface and a reverse surface flow closer to the substrate. This finding appears to be independent of Reynolds number and viscosity ratio in the ranges studied; we conjecture that the observed flow is due to the effect of surfactants at the drop surface.

  15. Kinky tomographic reconstruction

    SciTech Connect

    Hanson, K.M.; Cunningham, G.S.; Bilisoly, R.L.

    1996-05-01

    We address the issue of how to make decisions about the degree of smoothness demanded of a flexible contour used to model the boundary of a 2D object. We demonstrate the use of a Bayesian approach to set the strength of the smoothness prior for a tomographic reconstruction problem. The Akaike Information Criterion is used to determine whether to allow a kink in the contour.

  16. Investigation of the performance of the General Electric ADVANCE positron emission tomograph in 3D mode

    SciTech Connect

    Lewellen, T.K.; Kohlmyer, S.G.; Miyaoka, R.S.; Kaplan, M.S.; Stearns, C.W.; Schubert, S.F.

    1996-08-01

    Performance measurements of the General Electric ADVANCE Positron Emission Tomograph operating with the septa retracted (3D mode) were made. All reconstructions were performed with the GE ADVANCE 3D package. Performance tests were carried out with: the NEMA phantoms; a 3D Hoffman phantom; a Data Spectrum torso phantom with lung and cardiac inserts; and the Utah 3D evaluation phantom. Data collected included: transaxial and axial resolution, uniformity, recovery coefficients, count rate performance, dead time accuracy, and effect of scatter correction.

  17. Microcomputer-based technique for 3-D reconstruction and volume measurement of computed tomographic images. Part 2: Anaplastic primary brain tumors.

    PubMed

    Albright, R E; Fram, E K

    1988-12-01

    Serial computed tomography (CT) plays an integral part in monitoring effects of therapy for primary anaplastic brain tumors. Despite advances in CT technology, clinicians often cannot obtain accurate quantitative volume information to complement the qualitative assessment of tumor change. This paper presents a microcomputer-based method that provides both quantitative volume measurements and 3-D reconstructions of primary anaplastic brain tumors based on their hard copy CT or magnetic resonance imaging studies. The findings of this study demonstrate that planimetry is feasible for routine clinical use and is superior in accuracy to the spherical geometric model, which is shown to significantly overestimate tumor volume. The findings of 62 quantitative tumor studies (17 patients) showed a direct relationship between the total tumor volume and the volume of the hypodense intratumor core. There was no evidence of a relationship between the total tumor volume and the amount of peritumor low density (edema).

  18. X-Ray Tomographic Reconstruction

    SciTech Connect

    Bonnie Schmittberger

    2010-08-25

    Tomographic scans have revolutionized imaging techniques used in medical and biological research by resolving individual sample slices instead of several superimposed images that are obtained from regular x-ray scans. X-Ray fluorescence computed tomography, a more specific tomography technique, bombards the sample with synchrotron x-rays and detects the fluorescent photons emitted from the sample. However, since x-rays are attenuated as they pass through the sample, tomographic scans often produce images with erroneous low densities in areas where the x-rays have already passed through most of the sample. To correct for this and correctly reconstruct the data in order to obtain the most accurate images, a program employing iterative methods based on the inverse Radon transform was written. Applying this reconstruction method to a tomographic image recovered some of the lost densities, providing a more accurate image from which element concentrations and internal structure can be determined.

  19. Fast 3-d tomographic microwave imaging for breast cancer detection.

    PubMed

    Grzegorczyk, Tomasz M; Meaney, Paul M; Kaufman, Peter A; diFlorio-Alexander, Roberta M; Paulsen, Keith D

    2012-08-01

    Microwave breast imaging (using electromagnetic waves of frequencies around 1 GHz) has mostly remained at the research level for the past decade, gaining little clinical acceptance. The major hurdles limiting patient use are both at the hardware level (challenges in collecting accurate and noncorrupted data) and software level (often plagued by unrealistic reconstruction times in the tens of hours). In this paper we report improvements that address both issues. First, the hardware is able to measure signals down to levels compatible with sub-centimeter image resolution while keeping an exam time under 2 min. Second, the software overcomes the enormous time burden and produces similarly accurate images in less than 20 min. The combination of the new hardware and software allows us to produce and report here the first clinical 3-D microwave tomographic images of the breast. Two clinical examples are selected out of 400+ exams conducted at the Dartmouth Hitchcock Medical Center (Lebanon, NH). The first example demonstrates the potential usefulness of our system for breast cancer screening while the second example focuses on therapy monitoring.

  20. 3D Image Reconstruction: Determination of Pattern Orientation

    SciTech Connect

    Blankenbecler, Richard

    2003-03-13

    The problem of determining the euler angles of a randomly oriented 3-D object from its 2-D Fraunhofer diffraction patterns is discussed. This problem arises in the reconstruction of a positive semi-definite 3-D object using oversampling techniques. In such a problem, the data consists of a measured set of magnitudes from 2-D tomographic images of the object at several unknown orientations. After the orientation angles are determined, the object itself can then be reconstructed by a variety of methods using oversampling, the magnitude data from the 2-D images, physical constraints on the image and then iteration to determine the phases.

  1. Practical pseudo-3D registration for large tomographic images

    NASA Astrophysics Data System (ADS)

    Liu, Xuan; Laperre, Kjell; Sasov, Alexander

    2014-09-01

    Image registration is a powerful tool in various tomographic applications. Our main focus is on microCT applications in which samples/animals can be scanned multiple times under different conditions or at different time points. For this purpose, a registration tool capable of handling fairly large volumes has been developed, using a novel pseudo-3D method to achieve fast and interactive registration with simultaneous 3D visualization. To reduce computation complexity in 3D registration, we decompose it into several 2D registrations, which are applied to the orthogonal views (transaxial, sagittal and coronal) sequentially and iteratively. After registration in each view, the next view is retrieved with the new transformation matrix for registration. This reduces the computation complexity significantly. For rigid transform, we only need to search for 3 parameters (2 shifts, 1 rotation) in each of the 3 orthogonal views instead of 6 (3 shifts, 3 rotations) for full 3D volume. In addition, the amount of voxels involved is also significantly reduced. For the proposed pseudo-3D method, image-based registration is employed, with Sum of Square Difference (SSD) as the similarity measure. The searching engine is Powell's conjugate direction method. In this paper, only rigid transform is used. However, it can be extended to affine transform by adding scaling and possibly shearing to the transform model. We have noticed that more information can be used in the 2D registration if Maximum Intensity Projections (MIP) or Parallel Projections (PP) is used instead of the orthogonal views. Also, other similarity measures, such as covariance or mutual information, can be easily incorporated. The initial evaluation on microCT data shows very promising results. Two application examples are shown: dental samples before and after treatment and structural changes in materials before and after compression. Evaluation on registration accuracy between pseudo-3D method and true 3D method has

  2. Forensic 3D scene reconstruction

    NASA Astrophysics Data System (ADS)

    Little, Charles Q.; Small, Daniel E.; Peters, Ralph R.; Rigdon, J. B.

    2000-05-01

    Traditionally law enforcement agencies have relied on basic measurement and imaging tools, such as tape measures and cameras, in recording a crime scene. A disadvantage of these methods is that they are slow and cumbersome. The development of a portable system that can rapidly record a crime scene with current camera imaging, 3D geometric surface maps, and contribute quantitative measurements such as accurate relative positioning of crime scene objects, would be an asset to law enforcement agents in collecting and recording significant forensic data. The purpose of this project is to develop a fieldable prototype of a fast, accurate, 3D measurement and imaging system that would support law enforcement agents to quickly document and accurately record a crime scene.

  3. Forensic 3D Scene Reconstruction

    SciTech Connect

    LITTLE,CHARLES Q.; PETERS,RALPH R.; RIGDON,J. BRIAN; SMALL,DANIEL E.

    1999-10-12

    Traditionally law enforcement agencies have relied on basic measurement and imaging tools, such as tape measures and cameras, in recording a crime scene. A disadvantage of these methods is that they are slow and cumbersome. The development of a portable system that can rapidly record a crime scene with current camera imaging, 3D geometric surface maps, and contribute quantitative measurements such as accurate relative positioning of crime scene objects, would be an asset to law enforcement agents in collecting and recording significant forensic data. The purpose of this project is to develop a feasible prototype of a fast, accurate, 3D measurement and imaging system that would support law enforcement agents to quickly document and accurately record a crime scene.

  4. Simultaneous high-speed 3D flame front detection and tomographic PIV

    NASA Astrophysics Data System (ADS)

    Ebi, Dominik; Clemens, Noel T.

    2016-03-01

    A technique capable of detecting the instantaneous, time-resolved, 3D flame topography is successfully demonstrated in a lean-premixed swirl flame undergoing flashback. A simultaneous measurement of the volumetric velocity field is possible without the need for additional hardware. Droplets which vaporize in the preheat zone of the flame serve as the marker for the flame front. The droplets are illuminated with a laser and imaged from four different views followed by a tomographic reconstruction to obtain the volumetric particle field. Void regions in the reconstructed particle field, which correspond to regions of burnt gas, are detected with a series of image processing steps. The interface separating the void region from regions filled with particles is defined as the flame surface. The velocity field in the unburnt gas is measured using tomographic PIV. The resulting data include the simultaneous 3D flame front and 3D volumetric velocity field at 5 kHz. The technique is applied to a lean-premixed (ϕ  =  0.8), swirling methane-air flame and validated against simultaneously acquired planar measurements. The mean error associated with the reconstructed 3D flame topography is about 0.4 mm, which is smaller than the flame thickness under the studied conditions. The mean error associated with the volumetric velocity field is about 0.2 m s-1.

  5. Double-frame 3D-PTV using a tomographic predictor

    NASA Astrophysics Data System (ADS)

    Fuchs, Thomas; Hain, Rainer; Kähler, Christian J.

    2016-11-01

    Thanks to the technological progress, 3D velocimetry techniques are becoming more popular. In particular, the time-resolved flow analysis by means of particle tracking is very attractive. Compared to double-frame recordings, higher seeding concentrations are feasible, yielding high spatial resolution results without bias errors due to strong velocity gradients. However, hardware restrictions still limit time-resolved measurements to rather small flow velocities and low magnifications. In aerodynamics, especially, this is a drawback, since often higher flow velocities are of interest. To conduct reliable 3D-PTV measurements from double-frame recordings, the well-established techniques tomographic particle imaging and 3D-PTV are employed for a novel processing approach. In this combined approach, the tomographic reconstruction is used as a predictor for the sensor locations of the corresponding particle images of the reconstructed particles. Furthermore, the reconstruction helps to identify and reject non-corresponding sets of particle images, reducing the amount of ghost particles to a minimum. A probabilistic tracking algorithm is then applied to estimate the flow field.

  6. Accuracy of 3-D reconstruction with occlusions.

    PubMed

    Begon, Mickaël; Lacouture, Patrick

    2010-02-01

    A marker has to be seen by at least two cameras for its three-dimensional (3-D) reconstruction, and the accuracy can be improved with more cameras. However, a change in the set of cameras used in the reconstruction can alter the kinematics. The purpose of this study was to quantify the harmful effect of occlusions on two-dimensional (2-D) images and to make recommendations about the signal processing. A reference kinematics data set was collected for a three degree-of-freedom linkage with three cameras of a commercial motion analysis system without any occlusion on the 2-D images. In the 2-D images, some occlusions were artificially created based on trials of real cyclic motions. An interpolation of 2-D trajectories before the 3-D reconstruction and two filters (Savitsky-Golay and Butterworth filters) after reconstruction were successively applied to minimize the effect of the 2-D occlusions. The filter parameters were optimized by minimizing the root mean square error between the reference and the filtered data. The optimal parameters of the filters were marker dependent, whereas no filter was necessary after a 2-D interpolation. As the occlusions cause systematic error in the 3-D reconstruction, the interpolation of the 2-D trajectories is more appropriate than filtering the 3-D trajectories.

  7. Model-based 3D SAR reconstruction

    NASA Astrophysics Data System (ADS)

    Knight, Chad; Gunther, Jake; Moon, Todd

    2014-06-01

    Three dimensional scene reconstruction with synthetic aperture radar (SAR) is desirable for target recognition and improved scene interpretability. The vertical aperture, which is critical to reconstruct 3D SAR scenes, is almost always sparsely sampled due to practical limitations, which creates an underdetermined problem. This papers explores 3D scene reconstruction using a convex model-based approach. The approach developed is demonstrated on 3D scenes, but can be extended to SAR reconstruction of sparsely sampled signals in the spatial and, or, frequency domains. The model-based approach enables knowledge-aided image formation (KAIF) by incorporating spatial, aspect, and sparsity magnitude terms into the image reconstruction. The incorporation of these terms, which are based on prior scene knowledge, will demonstrate improved results compared to traditional image formation algorithms. The SAR image formation problem is formulated as a second order cone program (SOCP) and the results are demonstrated on 3D scenes using simulated data and data from the GOTCHA data collect.1 The model-based results are contrasted against traditional backprojected images.

  8. Deformable 3D-2D registration for CT and its application to low dose tomographic fluoroscopy

    NASA Astrophysics Data System (ADS)

    Flach, Barbara; Brehm, Marcus; Sawall, Stefan; Kachelrieß, Marc

    2014-12-01

    Many applications in medical imaging include image registration for matching of images from the same or different modalities. In the case of full data sampling, the respective reconstructed images are usually of such a good image quality that standard deformable volume-to-volume (3D-3D) registration approaches can be applied. But research in temporal-correlated image reconstruction and dose reductions increases the number of cases where rawdata are available from only few projection angles. Here, deteriorated image quality leads to non-acceptable deformable volume-to-volume registration results. Therefore a registration approach is required that is robust against a decreasing number of projections defining the target position. We propose a deformable volume-to-rawdata (3D-2D) registration method that aims at finding a displacement vector field maximizing the alignment of a CT volume and the acquired rawdata based on the sum of squared differences in rawdata domain. The registration is constrained by a regularization term in accordance with a fluid-based diffusion. Both cost function components, the rawdata fidelity and the regularization term, are optimized in an alternating manner. The matching criterion is optimized by a conjugate gradient descent for nonlinear functions, while the regularization is realized by convolution of the vector fields with Gaussian kernels. We validate the proposed method and compare it to the demons algorithm, a well-known 3D-3D registration method. The comparison is done for a range of 4-60 target projections using datasets from low dose tomographic fluoroscopy as an application example. The results show a high correlation to the ground truth target position without introducing artifacts even in the case of very few projections. In particular the matching in the rawdata domain is improved compared to the 3D-3D registration for the investigated range. The proposed volume-to-rawdata registration increases the robustness regarding sparse

  9. Deformable 3D-2D registration for CT and its application to low dose tomographic fluoroscopy.

    PubMed

    Flach, Barbara; Brehm, Marcus; Sawall, Stefan; Kachelrieß, Marc

    2014-12-21

    Many applications in medical imaging include image registration for matching of images from the same or different modalities. In the case of full data sampling, the respective reconstructed images are usually of such a good image quality that standard deformable volume-to-volume (3D-3D) registration approaches can be applied. But research in temporal-correlated image reconstruction and dose reductions increases the number of cases where rawdata are available from only few projection angles. Here, deteriorated image quality leads to non-acceptable deformable volume-to-volume registration results. Therefore a registration approach is required that is robust against a decreasing number of projections defining the target position. We propose a deformable volume-to-rawdata (3D-2D) registration method that aims at finding a displacement vector field maximizing the alignment of a CT volume and the acquired rawdata based on the sum of squared differences in rawdata domain. The registration is constrained by a regularization term in accordance with a fluid-based diffusion. Both cost function components, the rawdata fidelity and the regularization term, are optimized in an alternating manner. The matching criterion is optimized by a conjugate gradient descent for nonlinear functions, while the regularization is realized by convolution of the vector fields with Gaussian kernels. We validate the proposed method and compare it to the demons algorithm, a well-known 3D-3D registration method. The comparison is done for a range of 4-60 target projections using datasets from low dose tomographic fluoroscopy as an application example. The results show a high correlation to the ground truth target position without introducing artifacts even in the case of very few projections. In particular the matching in the rawdata domain is improved compared to the 3D-3D registration for the investigated range. The proposed volume-to-rawdata registration increases the robustness regarding sparse

  10. Reproducibility of 3D chromatin configuration reconstructions

    PubMed Central

    Segal, Mark R.; Xiong, Hao; Capurso, Daniel; Vazquez, Mariel; Arsuaga, Javier

    2014-01-01

    It is widely recognized that the three-dimensional (3D) architecture of eukaryotic chromatin plays an important role in processes such as gene regulation and cancer-driving gene fusions. Observing or inferring this 3D structure at even modest resolutions had been problematic, since genomes are highly condensed and traditional assays are coarse. However, recently devised high-throughput molecular techniques have changed this situation. Notably, the development of a suite of chromatin conformation capture (CCC) assays has enabled elicitation of contacts—spatially close chromosomal loci—which have provided insights into chromatin architecture. Most analysis of CCC data has focused on the contact level, with less effort directed toward obtaining 3D reconstructions and evaluating the accuracy and reproducibility thereof. While questions of accuracy must be addressed experimentally, questions of reproducibility can be addressed statistically—the purpose of this paper. We use a constrained optimization technique to reconstruct chromatin configurations for a number of closely related yeast datasets and assess reproducibility using four metrics that measure the distance between 3D configurations. The first of these, Procrustes fitting, measures configuration closeness after applying reflection, rotation, translation, and scaling-based alignment of the structures. The others base comparisons on the within-configuration inter-point distance matrix. Inferential results for these metrics rely on suitable permutation approaches. Results indicate that distance matrix-based approaches are preferable to Procrustes analysis, not because of the metrics per se but rather on account of the ability to customize permutation schemes to handle within-chromosome contiguity. It has recently been emphasized that the use of constrained optimization approaches to 3D architecture reconstruction are prone to being trapped in local minima. Our methods of reproducibility assessment provide a

  11. EFIT 3D Reconstruction and Recent Developments

    NASA Astrophysics Data System (ADS)

    Lao, L. L.; Chu, M. S.; St. John, H. E.; Strait, E. J.; Turnbull, A. D.; Ren, Q.; Jeon, Y. M.; Flannagan, D.

    2007-11-01

    Recent 3D extension of the EFIT equilibrium reconstruction code to model toroidally asymmetric effects due to error and externally applied perturbation magnetic fields and other developments are presented. The 3D extension is based on an expansion of the MHD equations. Other developments include a new computational structure based on Fortran 90/95 with a unified interface that can conveniently accommodate different tokamak devices and grid sizes, as well as a Python-based GUI. New computational links that allow easy integration with transport and stability physics modules to facilitate kinetic reconstruction and stability analysis are also being developed. A new more complete uncertainty matrix for magnetic diagnostics based on knowledge about their fabrication, installation, calibration, and operation has also been implemented into EFIT and tested. Reconstructions with the new magnetic uncertainty matrix yield results similar to those using the existing one but with more realistic fitting merit figures.

  12. Progress Update on Iterative Reconstruction of Neutron Tomographic Images

    SciTech Connect

    Hausladen, Paul; Gregor, Jens

    2016-09-15

    This report satisfies the fiscal year 2016 technical deliverable to report on progress in development of fast iterative reconstruction algorithms for project OR16-3DTomography-PD2Jb, "3D Tomography and Image Processing Using Fast Neutrons." This project has two overall goals. The first of these goals is to extend associated-particle fast neutron transmission and, particularly, induced-reaction tomographic imaging algorithms to three dimensions. The second of these goals is to automatically segment the resultant tomographic images into constituent parts, and then extract information about the parts, such as the class of shape and potentially shape parameters. This report addresses of the component of the project concerned with three-dimensional (3D) image reconstruction.

  13. The PRISM3D paleoenvironmental reconstruction

    USGS Publications Warehouse

    Dowsett, H.; Robinson, M.; Haywood, A.M.; Salzmann, U.; Hill, Daniel; Sohl, L.E.; Chandler, M.; Williams, Mark; Foley, K.; Stoll, D.K.

    2010-01-01

    The Pliocene Research, Interpretation and Synoptic Mapping (PRISM) paleoenvironmental reconstruction is an internally consistent and comprehensive global synthesis of a past interval of relatively warm and stable climate. It is regularly used in model studies that aim to better understand Pliocene climate, to improve model performance in future climate scenarios, and to distinguish model-dependent climate effects. The PRISM reconstruction is constantly evolving in order to incorporate additional geographic sites and environmental parameters, and is continuously refined by independent research findings. The new PRISM three dimensional (3D) reconstruction differs from previous PRISM reconstructions in that it includes a subsurface ocean temperature reconstruction, integrates geochemical sea surface temperature proxies to supplement the faunal-based temperature estimates, and uses numerical models for the first time to augment fossil data. Here we describe the components of PRISM3D and describe new findings specific to the new reconstruction. Highlights of the new PRISM3D reconstruction include removal of Hudson Bay and the Great Lakes and creation of open waterways in locations where the current bedrock elevation is less than 25m above modern sea level, due to the removal of the West Antarctic Ice Sheet and the reduction of the East Antarctic Ice Sheet. The mid-Piacenzian oceans were characterized by a reduced east-west temperature gradient in the equatorial Pacific, but PRISM3D data do not imply permanent El Niño conditions. The reduced equator-to-pole temperature gradient that characterized previous PRISM reconstructions is supported by significant displacement of vegetation belts toward the poles, is extended into the Arctic Ocean, and is confirmed by multiple proxies in PRISM3D. Arctic warmth coupled with increased dryness suggests the formation of warm and salty paleo North Atlantic Deep Water (NADW) and a more vigorous thermohaline circulation system that may

  14. Automated Serial Sectioning for 3D Reconstruction

    NASA Technical Reports Server (NTRS)

    Alkemper, Jen; Voorhees, Peter W.

    2003-01-01

    Some aspects of an apparatus and method for automated serial sectioning of a specimen of a solder, aluminum, or other relatively soft opaque material are discussed. The apparatus includes a small milling machine (micromiller) that takes precise, shallow cuts (increments of depth as small as 1 micron) to expose successive sections. A microscope equipped with an electronic camera, mounted in a fixed position on the micromiller, takes pictures of the newly exposed specimen surface at each increment of depth. The images are digitized, and the resulting data are subsequently processed to reconstruct three-dimensional (3D) features of the specimen.

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

    SciTech Connect

    Glaeser, R.M.

    1997-02-01

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

  16. 3D reconstruction of tensors and vectors

    SciTech Connect

    Defrise, Michel; Gullberg, Grant T.

    2005-02-17

    Here we have developed formulations for the reconstruction of 3D tensor fields from planar (Radon) and line-integral (X-ray) projections of 3D vector and tensor fields. Much of the motivation for this work is the potential application of MRI to perform diffusion tensor tomography. The goal is to develop a theory for the reconstruction of both Radon planar and X-ray or line-integral projections because of the flexibility of MRI to obtain both of these type of projections in 3D. The development presented here for the linear tensor tomography problem provides insight into the structure of the nonlinear MRI diffusion tensor inverse problem. A particular application of tensor imaging in MRI is the potential application of cardiac diffusion tensor tomography for determining in vivo cardiac fiber structure. One difficulty in the cardiac application is the motion of the heart. This presents a need for developing future theory for tensor tomography in a motion field. This means developing a better understanding of the MRI signal for diffusion processes in a deforming media. The techniques developed may allow the application of MRI tensor tomography for the study of structure of fiber tracts in the brain, atherosclerotic plaque, and spine in addition to fiber structure in the heart. However, the relations presented are also applicable to other fields in medical imaging such as diffraction tomography using ultrasound. The mathematics presented can also be extended to exponential Radon transform of tensor fields and to other geometric acquisitions such as cone beam tomography of tensor fields.

  17. 3D flame topography obtained by tomographic chemiluminescence with direct comparison to planar Mie scattering measurements.

    PubMed

    Xu, Wenjiang; Wickersham, A J; Wu, Yue; He, Fan; Ma, Lin

    2015-03-20

    This work reports the measurements of 3D flame topography using tomographic chemiluminescence and its validation by direct comparison against planar Mie scattering measurements. Tomographic measurements of the 3D topography of various well-controlled laboratory flames were performed using projections measured by seven cameras, and a simultaneous Mie scattering measurement was performed to measure a 2D cross section of the 3D flame topography. The tomographic measurements were based on chemiluminescence emissions from the flame, and the Mie scattering measurements were based on micrometer-size oil droplets seeded into the flow. The flame topography derived from the 3D tomographic and the Mie scattering measurement was then directly compared. The results show that the flame topography obtained from tomographic chemiluminescence and the Mie measurement agreed qualitatively (i.e., both methods yielded the same profile of the flame fronts), but a quantitative difference on the order of millimeters was observed between these two methods. These results are expected to be useful for understanding the capabilities and limitations of the 3D tomographic and Mie scattering techniques in combustion diagnostics.

  18. Adapting 3D Equilibrium Reconstruction to Reconstruct Weakly 3D H-mode Tokamaks

    NASA Astrophysics Data System (ADS)

    Cianciosa, M. R.; Hirshman, S. P.; Seal, S. K.; Unterberg, E. A.; Wilcox, R. S.; Wingen, A.; Hanson, J. D.

    2015-11-01

    The application of resonant magnetic perturbations for edge localized mode (ELM) mitigation breaks the toroidal symmetry of tokamaks. In these scenarios, the axisymmetric assumptions of the Grad-Shafranov equation no longer apply. By extension, equilibrium reconstruction tools, built around these axisymmetric assumptions, are insufficient to fully reconstruct a 3D perturbed equilibrium. 3D reconstruction tools typically work on systems where the 3D components of signals are a significant component of the input signals. In nominally axisymmetric systems, applied field perturbations can be on the order of 1% of the main field or less. To reconstruct these equilibria, the 3D component of signals must be isolated from the axisymmetric portions to provide the necessary information for reconstruction. This presentation will report on the adaptation to V3FIT for application on DIII-D H-mode discharges with applied resonant magnetic perturbations (RMPs). Newly implemented motional stark effect signals and modeling of electric field effects will also be discussed. Work supported under U.S. DOE Cooperative Agreement DE-AC05-00OR22725.

  19. Photogrammetric 3D reconstruction using mobile imaging

    NASA Astrophysics Data System (ADS)

    Fritsch, Dieter; Syll, Miguel

    2015-03-01

    In our paper we demonstrate the development of an Android Application (AndroidSfM) for photogrammetric 3D reconstruction that works on smartphones and tablets likewise. The photos are taken with mobile devices, and can thereafter directly be calibrated using standard calibration algorithms of photogrammetry and computer vision, on that device. Due to still limited computing resources on mobile devices, a client-server handshake using Dropbox transfers the photos to the sever to run AndroidSfM for the pose estimation of all photos by Structure-from-Motion and, thereafter, uses the oriented bunch of photos for dense point cloud estimation by dense image matching algorithms. The result is transferred back to the mobile device for visualization and ad-hoc on-screen measurements.

  20. Geometric effects in tomographic reconstruction

    SciTech Connect

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

    1990-01-08

    In x-ray and ion-beam computerized tomography, there are a number of reconstruction effects, manifested as artifacts, that can be attributed to the geometry of the experimental setup and of the object being scanned. In this work, we will examine four geometric effects that are common to first-and third-generation (parallel beam, 180 degree) computerized tomography (CT) scanners and suggest solutions for each problem. The geometric effects focused on in this paper are: X-pattern'' artifacts (believed to be caused by several errors), edge-generated ringing artifacts (due to improper choice of the reconstruction filter and cutoff frequency), circular-ring artifacts (caused by employing uncalibrated detectors), and tuning-fork artifacts (generated by an incorrectly specified center-of-rotation). Examples of four effects are presented. The X-pattern and edge-generated ringing artifacts are presented with actual experimental data introducing the artifact. given the source of the artifact, we present simulated data designed to replicate the artifact. Finally, we suggest ways to reduce or completely remove these artifacts. The circular-ring and tuning-fork artifacts are introduced with actual experimental data as well, while digital signal processing solutions are employed to remove the artifacts from the data. 15 refs., 12 figs.

  1. Rational approximations for tomographic reconstructions

    NASA Astrophysics Data System (ADS)

    Reynolds, Matthew; Beylkin, Gregory; Monzón, Lucas

    2013-06-01

    We use optimal rational approximations of projection data collected in x-ray tomography to improve image resolution. Under the assumption that the object of interest is described by functions with jump discontinuities, for each projection we construct its rational approximation with a small (near optimal) number of terms for a given accuracy threshold. This allows us to augment the measured data, i.e., double the number of available samples in each projection or, equivalently, extend (double) the domain of their Fourier transform. We also develop a new, fast, polar coordinate Fourier domain algorithm which uses our nonlinear approximation of projection data in a natural way. Using augmented projections of the Shepp-Logan phantom, we provide a comparison between the new algorithm and the standard filtered back-projection algorithm. We demonstrate that the reconstructed image has improved resolution without additional artifacts near sharp transitions in the image.

  2. Model-based Tomographic Reconstruction Literature Search

    SciTech Connect

    Chambers, D H; Lehman, S K

    2005-11-30

    In the process of preparing a proposal for internal research funding, a literature search was conducted on the subject of model-based tomographic reconstruction (MBTR). The purpose of the search was to ensure that the proposed research would not replicate any previous work. We found that the overwhelming majority of work on MBTR which used parameterized models of the object was theoretical in nature. Only three researchers had applied the technique to actual data. In this note, we summarize the findings of the literature search.

  3. Dense velocity reconstruction from tomographic PTV with material derivatives

    NASA Astrophysics Data System (ADS)

    Schneiders, Jan F. G.; Scarano, Fulvio

    2016-09-01

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

  4. 3D Surface Reconstruction and Automatic Camera Calibration

    NASA Technical Reports Server (NTRS)

    Jalobeanu, Andre

    2004-01-01

    Illustrations in this view-graph presentation are presented on a Bayesian approach to 3D surface reconstruction and camera calibration.Existing methods, surface analysis and modeling,preliminary surface reconstruction results, and potential applications are addressed.

  5. Infrared tomographic PIV and 3D motion tracking system applied to aquatic predator-prey interaction

    NASA Astrophysics Data System (ADS)

    Adhikari, Deepak; Longmire, Ellen K.

    2013-02-01

    Infrared tomographic PIV and 3D motion tracking are combined to measure evolving volumetric velocity fields and organism trajectories during aquatic predator-prey interactions. The technique was used to study zebrafish foraging on both non-evasive and evasive prey species. Measurement volumes of 22.5 mm × 10.5 mm × 12 mm were reconstructed from images captured on a set of four high-speed cameras. To obtain accurate fluid velocity vectors within each volume, fish were first masked out using an automated visual hull method. Fish and prey locations were identified independently from the same image sets and tracked separately within the measurement volume. Experiments demonstrated that fish were not influenced by the infrared laser illumination or the tracer particles. Results showed that the zebrafish used different strategies, suction and ram feeding, for successful capture of non-evasive and evasive prey, respectively. The two strategies yielded different variations in fluid velocity between the fish mouth and the prey. In general, the results suggest that the local flow field, the direction of prey locomotion with respect to the predator and the relative accelerations and speeds of the predator and prey may all be significant in determining predation success.

  6. [Potentials of 3D-modeling in reconstructive orbital surgery].

    PubMed

    Butsan, S B; Khokhlachev, S B; Ĭigitaliev, Sh N; Zaiakin, Ia A

    2012-01-01

    A technique of bone reconstructive surgery of orbitofrontonasomalar region using 3D-modeling based on multispiral computer tomography data is presented. The efficacy of intraoperative templates created using 3D-modeling was showed for harvesting and modeling of bone calvarial autografts. The steps of reconstructive procedure are explained in details for repair of medial and inferior orbital fractures.

  7. Development and Testing of EFIT 3D Equilibrium Reconstruction Capability

    NASA Astrophysics Data System (ADS)

    Lao, L. L.; Ferraro, N. M.; Strait, E. J.; Turnbull, A. D.; King, J. D.

    2014-10-01

    Recent development and testing of EFIT capability to reconstruct tokamak 3D perturbed equilibrium are described. The 3D extension is based on an expansion of the MHD equations to account for the 3D effects. EFIT uses the cylindrical coordinate system and can include magnetic island and stochastic effects. Several linearization schemes are being explored to improve the EFIT 3D perturbed solutions. Algorithms are also being developed to allow EFIT to reconstruct 3D perturbed equilibria directly making use of plasma response to 3D perturbations from the MARS or M3D-C1 MHD codes. Other efforts include testing of the new EFIT 3D capability using simulated magnetic data based on response calculations from MARS and M3D-C1, and performing detailed benchmarking calculations against other 3D codes such as VMEC/V3FIT. Reconstruction examples using EFIT and the new DIII-D 3D magnetic measurements to reconstruct 3D perturbed experimental equilibria using well-diagnosed discharges from DIII-D error field, RWM, and RMP experiments will be presented. Work supported by the US DOE under DE-FC02-04ER54698 and DE-FG02-95ER54309.

  8. Time-dependent tomographic reconstruction of the solar corona

    NASA Astrophysics Data System (ADS)

    Vibert, D.; Peillon, C.; Lamy, P.; Frazin, R. A.; Wojak, J.

    2016-10-01

    Solar rotational tomography (SRT) applied to white-light coronal images observed at multiple aspect angles has been the preferred approach for determining the three-dimensional (3D) electron density structure of the solar corona. However, it is seriously hampered by the restrictive assumption that the corona is time-invariant which introduces significant errors in the reconstruction. We first explore several methods to mitigate the temporal variation of the corona by decoupling the "fast-varying" inner corona from the "slow-moving" outer corona using multiple masking (either by juxtaposition or recursive combination) and radial weighting. Weighting with a radial exponential profile provides some improvement over a classical reconstruction but only beyond ≈ 3R⊙. We next consider a full time-dependent tomographic reconstruction involving spatio-temporal regularization and further introduce a co-rotating regularization aimed at preventing concentration of reconstructed density in the plane of the sky. Crucial to testing our procedure and properly tuning the regularization parameters is the introduction of a time-dependent MHD model of the corona based on observed magnetograms to build a time-series of synthetic images of the corona. Our procedure, which successfully reproduces the time-varying model corona, is finally applied to a set of 53 LASCO-C2 pB images roughly evenly spaced in time from 15 to 29 March 2009. Our procedure paves the way to a time-dependent tomographic reconstruction of the coronal electron density to the whole set of LASCO-C2 images presently spanning 20 years.

  9. Mini gamma cameras for intra-operative nuclear tomographic reconstruction.

    PubMed

    Matthies, Philipp; Gardiazabal, José; Okur, Aslı; Vogel, Jakob; Lasser, Tobias; Navab, Nassir

    2014-12-01

    Nuclear imaging modalities like PET or SPECT are in extensive use in medical diagnostics. In a move towards personalized therapy, we present a flexible nuclear tomographic imaging system to enable intra-operative SPECT-like 3D imaging. The system consists of a miniaturized gamma camera mounted on a robot arm for flexible positioning, while spatio-temporal localization is provided by an optical tracking system. To facilitate statistical tomographic reconstruction of the radiotracer distribution using a maximum likelihood approach, a precise model of the mini gamma camera is generated by measurements. The entire system is evaluated in a series of experiments using a hot spot phantom, with a focus on criteria relevant for the intra-operative workflow, namely the number of required imaging positions as well as the required imaging time. The results show that high quality reconstructed images of simple hot spot configurations with positional errors of less than one millimeter are possible within acquisition times as short as 15s.

  10. 3D scene reconstruction based on 3D laser point cloud combining UAV images

    NASA Astrophysics Data System (ADS)

    Liu, Huiyun; Yan, Yangyang; Zhang, Xitong; Wu, Zhenzhen

    2016-03-01

    It is a big challenge capturing and modeling 3D information of the built environment. A number of techniques and technologies are now in use. These include GPS, and photogrammetric application and also remote sensing applications. The experiment uses multi-source data fusion technology for 3D scene reconstruction based on the principle of 3D laser scanning technology, which uses the laser point cloud data as the basis and Digital Ortho-photo Map as an auxiliary, uses 3DsMAX software as a basic tool for building three-dimensional scene reconstruction. The article includes data acquisition, data preprocessing, 3D scene construction. The results show that the 3D scene has better truthfulness, and the accuracy of the scene meet the need of 3D scene construction.

  11. 3D Equilibrium Reconstructions in DIII-D

    NASA Astrophysics Data System (ADS)

    Lao, L. L.; Ferraro, N. W.; Strait, E. J.; Turnbull, A. D.; King, J. D.; Hirshman, H. P.; Lazarus, E. A.; Sontag, A. C.; Hanson, J.; Trevisan, G.

    2013-10-01

    Accurate and efficient 3D equilibrium reconstruction is needed in tokamaks for study of 3D magnetic field effects on experimentally reconstructed equilibrium and for analysis of MHD stability experiments with externally imposed magnetic perturbations. A large number of new magnetic probes have been recently installed in DIII-D to improve 3D equilibrium measurements and to facilitate 3D reconstructions. The V3FIT code has been in use in DIII-D to support 3D reconstruction and the new magnetic diagnostic design. V3FIT is based on the 3D equilibrium code VMEC that assumes nested magnetic surfaces. V3FIT uses a pseudo-Newton least-square algorithm to search for the solution vector. In parallel, the EFIT equilibrium reconstruction code is being extended to allow for 3D effects using a perturbation approach based on an expansion of the MHD equations. EFIT uses the cylindrical coordinate system and can include the magnetic island and stochastic effects. Algorithms are being developed to allow EFIT to reconstruct 3D perturbed equilibria directly making use of plasma response to 3D perturbations from the GATO, MARS-F, or M3D-C1 MHD codes. DIII-D 3D reconstruction examples using EFIT and V3FIT and the new 3D magnetic data will be presented. Work supported in part by US DOE under DE-FC02-04ER54698, DE-FG02-95ER54309 and DE-AC05-06OR23100.

  12. Reconstruction-based 3D/2D image registration.

    PubMed

    Tomazevic, Dejan; Likar, Bostjan; Pernus, Franjo

    2005-01-01

    In this paper we present a novel 3D/2D registration method, where first, a 3D image is reconstructed from a few 2D X-ray images and next, the preoperative 3D image is brought into the best possible spatial correspondence with the reconstructed image by optimizing a similarity measure. Because the quality of the reconstructed image is generally low, we introduce a novel asymmetric mutual information similarity measure, which is able to cope with low image quality as well as with different imaging modalities. The novel 3D/2D registration method has been evaluated using standardized evaluation methodology and publicly available 3D CT, 3DRX, and MR and 2D X-ray images of two spine phantoms, for which gold standard registrations were known. In terms of robustness, reliability and capture range the proposed method outperformed the gradient-based method and the method based on digitally reconstructed radiographs (DRRs).

  13. Research in Image Understanding as Applied to 3-D Microwave Tomographic Imaging with Near Optical Resolution.

    DTIC Science & Technology

    1986-03-10

    Severe Clutter .... ........ 1I-i III . Optical Implementation of the HopfieldModel .I -? .- . ." Model........................ . . BY...can be employed in future broad-band imaging radar networks capable of providing 3-D projective or . - tomographic images of remote aerospace targets...We expect the results of this effort to tell us how to achieve centimeter resolution on remote aerospace objects cost-effectively using microwave

  14. 3D Building Reconstruction Using Dense Photogrammetric Point Cloud

    NASA Astrophysics Data System (ADS)

    Malihi, S.; Valadan Zoej, M. J.; Hahn, M.; Mokhtarzade, M.; Arefi, H.

    2016-06-01

    Three dimensional models of urban areas play an important role in city planning, disaster management, city navigation and other applications. Reconstruction of 3D building models is still a challenging issue in 3D city modelling. Point clouds generated from multi view images of UAV is a novel source of spatial data, which is used in this research for building reconstruction. The process starts with the segmentation of point clouds of roofs and walls into planar groups. By generating related surfaces and using geometrical constraints plus considering symmetry, a 3d model of building is reconstructed. In a refinement step, dormers are extracted, and their models are reconstructed. The details of the 3d reconstructed model are in LoD3 level, with respect to modelling eaves, fractions of roof and dormers.

  15. Mapping 3D Large-Scale Structure at z ˜2 with Lyman-α Forest Tomographic Mapping

    NASA Astrophysics Data System (ADS)

    Lee, Khee-Gan; Hennawi, J. F.; White, M.; Croft, R. A.; Prochaska, J. X.; Schlegel, D. J.; Suzuki, N.; Kneib, J.; Bailey, S. J.; Spergel, D. N.; Rix, H.; Strauss, M. A.

    2014-01-01

    The Lyman-α (Lyα) forest absorption at z>2 traces the underlying dark-matter distribution, and with a sufficient density of background sightlines can be used to create 3D tomographic maps of large-scale structure. Since the useful Lyα forest in each sightline spans ˜400-500 h-1Mpc, Lyα forest tomography can efficiently map out large-scale structure at z˜2. The Cosmic Lyman-Alpha Program for the Tomographic Reconstruction of Absorption Probes (CLAPTRAP) will be the first survey to attempt this technique. We aim to obtain spectra for a background grid of faint quasars and bright LBGs at 23D map with similar 3 h-1Mpc resolution to be reconstructed from the data. In a recent paper, we have found that spectra with S/N ˜ 4 per Å are sufficient to make excellent-quality tomographic maps that clearly trace the underlying dark-matter distribution at overdensities of order unity. This requires integrations of several hours on moderate-resolution spectrographs mounted on existing 8-10m telescopes, such as LRIS on the Keck-I telescope and VIMOS on the Very Large Telescopes. We aim to observe ˜1500-2000 background sources over 1 sq deg of the COSMOS field with Lyα forest coverage over 2.0tomographic maps will be the first 3D maps of large-scale structure at z>1. In conjunction with the rich multi-wavelength data from the COSMOS survey, these maps will facilitate the study of galaxies in the context of the large-scale environment, reveal the topology of large-scale structure at high-redshifts, and allow the direct detection of galaxy protoclusters at the intersections of the cosmic web. The

  16. Interior Reconstruction Using the 3d Hough Transform

    NASA Astrophysics Data System (ADS)

    Dumitru, R.-C.; Borrmann, D.; Nüchter, A.

    2013-02-01

    Laser scanners are often used to create accurate 3D models of buildings for civil engineering purposes, but the process of manually vectorizing a 3D point cloud is time consuming and error-prone (Adan and Huber, 2011). Therefore, the need to characterize and quantify complex environments in an automatic fashion arises, posing challenges for data analysis. This paper presents a system for 3D modeling by detecting planes in 3D point clouds, based on which the scene is reconstructed at a high architectural level through removing automatically clutter and foreground data. The implemented software detects openings, such as windows and doors and completes the 3D model by inpainting.

  17. DCT and DST Based Image Compression for 3D Reconstruction

    NASA Astrophysics Data System (ADS)

    Siddeq, Mohammed M.; Rodrigues, Marcos A.

    2017-03-01

    This paper introduces a new method for 2D image compression whose quality is demonstrated through accurate 3D reconstruction using structured light techniques and 3D reconstruction from multiple viewpoints. The method is based on two discrete transforms: (1) A one-dimensional Discrete Cosine Transform (DCT) is applied to each row of the image. (2) The output from the previous step is transformed again by a one-dimensional Discrete Sine Transform (DST), which is applied to each column of data generating new sets of high-frequency components followed by quantization of the higher frequencies. The output is then divided into two parts where the low-frequency components are compressed by arithmetic coding and the high frequency ones by an efficient minimization encoding algorithm. At decompression stage, a binary search algorithm is used to recover the original high frequency components. The technique is demonstrated by compressing 2D images up to 99% compression ratio. The decompressed images, which include images with structured light patterns for 3D reconstruction and from multiple viewpoints, are of high perceptual quality yielding accurate 3D reconstruction. Perceptual assessment and objective quality of compression are compared with JPEG and JPEG2000 through 2D and 3D RMSE. Results show that the proposed compression method is superior to both JPEG and JPEG2000 concerning 3D reconstruction, and with equivalent perceptual quality to JPEG2000.

  18. Towards a 3-D tomographic retrieval for the air-borne limb-imager GLORIA

    NASA Astrophysics Data System (ADS)

    Ungermann, J.; Kaufmann, M.; Hoffmann, L.; Preusse, P.; Oelhaf, H.; Friedl-Vallon, F.; Riese, M.

    2010-11-01

    GLORIA (Gimballed Limb Observer for Radiance Imaging of the Atmosphere) is a new remote sensing instrument essentially combining a Fourier transform infrared spectrometer with a two-dimensional (2-D) detector array in combination with a highly flexible gimbal mount. It will be housed in the belly pod of the German research aircraft HALO (High Altitude and Long Range Research Aircraft). It is unique in its combination of high spatial and state-of-the art spectral resolution. Furthermore, the horizontal view angle with respect to the aircraft flight direction can be varied from 45° to 135°. This allows for tomographic measurements of mesoscale events for a wide variety of atmospheric constituents. In this paper, a tomographic retrieval scheme is presented, which is able to fully exploit the manifold radiance observations of the GLORIA limb sounder. The algorithm is optimized for massive 3-D retrievals of several hundred thousands of measurements and atmospheric constituents on common hardware. The new scheme is used to explore the capabilities of GLORIA to sound the atmosphere in full 3-D with respect to the choice of the flightpath and to different measurement modes of the instrument using ozone as a test species. It is demonstrated that the achievable resolution should approach 200 m vertically and 20 km-30 km horizontally. Finally, a comparison of the 3-D inversion with conventional 1-D inversions using the assumption of a horizontally homogeneous atmosphere is performed.

  19. Towards a 3-D tomographic retrieval for the Air-borne Limb-imager GLORIA

    NASA Astrophysics Data System (ADS)

    Ungermann, J.; Kaufmann, M.; Hoffmann, L.; Preusse, P.; Oelhaf, H.; Friedl-Vallon, F.; Riese, M.

    2010-07-01

    GLORIA (Gimballed Limb Observer for Radiance Imaging of the Atmosphere) is a new remote sensing instrument essentially combining a Fourier transform infrared spectrometer with two two-dimensional (2-D) detector arrays in combination with a highly flexible gimbal mount. It will be housed in the belly pod of the German research aircraft HALO (High Altitude and Long Range Research Aircraft). It is unique in its high spatial and spectral resolution. Furthermore, the horizontal view angle with respect to the aircraft can be varied from 45° to 135°. This allows for tomographic measurements of mesoscale events for a wide variety of atmospheric constituents. In this paper, a fast tomographic retrieval scheme is presented, which is able to fully exploit the high-resolution radiance observations of the GLORIA limb sounder. The algorithm is optimized for massive 3-D retrievals of several hundred thousands of measurements and atmospheric constituents on common hardware. The new scheme is used to explore the capabilities of GLORIA to sound the atmosphere in full 3-D with respect to the choice of the flightpath and to different measurement modes of the instrument using ozone as a test species. It is demonstrated that the achievable resolution should approach 200 m vertically and 20 km-30 km horizontally. Finally, a comparison of the 3-D inversion with conventional 1-D inversions using the assumption of a horizontally homogeneous atmosphere is performed.

  20. 3-D flame temperature field reconstruction with multiobjective neural network

    NASA Astrophysics Data System (ADS)

    Wan, Xiong; Gao, Yiqing; Wang, Yuanmei

    2003-02-01

    A novel 3-D temperature field reconstruction method is proposed in this paper, which is based on multiwavelength thermometry and Hopfield neural network computed tomography. A mathematical model of multi-wavelength thermometry is founded, and a neural network algorithm based on multiobjective optimization is developed. Through computer simulation and comparison with the algebraic reconstruction technique (ART) and the filter back-projection algorithm (FBP), the reconstruction result of the new method is discussed in detail. The study shows that the new method always gives the best reconstruction results. At last, temperature distribution of a section of four peaks candle flame is reconstructed with this novel method.

  1. Light field display and 3D image reconstruction

    NASA Astrophysics Data System (ADS)

    Iwane, Toru

    2016-06-01

    Light field optics and its applications become rather popular in these days. With light field optics or light field thesis, real 3D space can be described in 2D plane as 4D data, which we call as light field data. This process can be divided in two procedures. First, real3D scene is optically reduced with imaging lens. Second, this optically reduced 3D image is encoded into light field data. In later procedure we can say that 3D information is encoded onto a plane as 2D data by lens array plate. This transformation is reversible and acquired light field data can be decoded again into 3D image with the arrayed lens plate. "Refocusing" (focusing image on your favorite point after taking a picture), light-field camera's most popular function, is some kind of sectioning process from encoded 3D data (light field data) to 2D image. In this paper at first I show our actual light field camera and our 3D display using acquired and computer-simulated light field data, on which real 3D image is reconstructed. In second I explain our data processing method whose arithmetic operation is performed not in Fourier domain but in real domain. Then our 3D display system is characterized by a few features; reconstructed image is of finer resolutions than density of arrayed lenses and it is not necessary to adjust lens array plate to flat display on which light field data is displayed.

  2. HeinzelCluster: accelerated reconstruction for FORE and OSEM3D.

    PubMed

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

    2002-08-07

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

  3. A distributed multi-GPU system for high speed electron microscopic tomographic reconstruction.

    PubMed

    Zheng, Shawn Q; Branlund, Eric; Kesthelyi, Bettina; Braunfeld, Michael B; Cheng, Yifan; Sedat, John W; Agard, David A

    2011-07-01

    Full resolution electron microscopic tomographic (EMT) reconstruction of large-scale tilt series requires significant computing power. The desire to perform multiple cycles of iterative reconstruction and realignment dramatically increases the pressing need to improve reconstruction performance. This has motivated us to develop a distributed multi-GPU (graphics processing unit) system to provide the required computing power for rapid constrained, iterative reconstructions of very large three-dimensional (3D) volumes. The participating GPUs reconstruct segments of the volume in parallel, and subsequently, the segments are assembled to form the complete 3D volume. Owing to its power and versatility, the CUDA (NVIDIA, USA) platform was selected for GPU implementation of the EMT reconstruction. For a system containing 10 GPUs provided by 5 GTX295 cards, 10 cycles of SIRT reconstruction for a tomogram of 4096(2) × 512 voxels from an input tilt series containing 122 projection images of 4096(2) pixels (single precision float) takes a total of 1845 s of which 1032 s are for computation with the remainder being the system overhead. The same system takes only 39 s total to reconstruct 1024(2) × 256 voxels from 122 1024(2) pixel projections. While the system overhead is non-trivial, performance analysis indicates that adding extra GPUs to the system would lead to steadily enhanced overall performance. Therefore, this system can be easily expanded to generate superior computing power for very large tomographic reconstructions and especially to empower iterative cycles of reconstruction and realignment.

  4. A Distributed Multi-GPU System for High Speed Electron Microscopic Tomographic Reconstruction

    PubMed Central

    Zheng, Shawn Q.; Branlund, Eric; Kesthelyi, Bettina; Braunfeld, Michael B.; Cheng, Yifan; Sedat, John W.; Agard, David A.

    2011-01-01

    Full resolution electron microscopic tomographic (EMT) reconstruction of large-scale tilt series requires significant computing power. The desire to perform multiple cycles of iterative reconstruction and realignment dramatically increases the pressing need to improve reconstruction performance. This has motivated us to develop a distributed multi-GPU (graphics processing unit) system to provide the required computing power for rapid constrained, iterative reconstructions of very large three-dimensional (3D) volumes. The participating GPUs reconstruct segments of the volume in parallel, and subsequently, the segments are assembled to form the complete 3D volume. Owing to its power and versatility, the CUDA (NVIDIA, USA) platform was selected for GPU implementation of the EMT reconstruction. For a system containing 10 GPUs provided by 5 GTX295 cards, 10 cycles of SIRT reconstruction for a tomogram of 40962 × 512 voxels from an input tilt series containing 122 projection images of 40962 pixels (single precision float) takes a total of 1845 seconds of which 1032 seconds are for computation with the remainder being the system overhead. The same system takes only 39 seconds total to reconstruct 10242 × 256 voxels from 122 10242 pixel projections. While the system overhead is non-trivial, performance analysis indicates that adding extra GPUs to the system would lead to steadily enhanced overall performance. Therefore, this system can be easily expanded to generate superior computing power for very large tomographic reconstructions and especially to empower iterative cycles of reconstruction and realignment. PMID:21741915

  5. Improving automated 3D reconstruction methods via vision metrology

    NASA Astrophysics Data System (ADS)

    Toschi, Isabella; Nocerino, Erica; Hess, Mona; Menna, Fabio; Sargeant, Ben; MacDonald, Lindsay; Remondino, Fabio; Robson, Stuart

    2015-05-01

    This paper aims to provide a procedure for improving automated 3D reconstruction methods via vision metrology. The 3D reconstruction problem is generally addressed using two different approaches. On the one hand, vision metrology (VM) systems try to accurately derive 3D coordinates of few sparse object points for industrial measurement and inspection applications; on the other, recent dense image matching (DIM) algorithms are designed to produce dense point clouds for surface representations and analyses. This paper strives to demonstrate a step towards narrowing the gap between traditional VM and DIM approaches. Efforts are therefore intended to (i) test the metric performance of the automated photogrammetric 3D reconstruction procedure, (ii) enhance the accuracy of the final results and (iii) obtain statistical indicators of the quality achieved in the orientation step. VM tools are exploited to integrate their main functionalities (centroid measurement, photogrammetric network adjustment, precision assessment, etc.) into the pipeline of 3D dense reconstruction. Finally, geometric analyses and accuracy evaluations are performed on the raw output of the matching (i.e. the point clouds) by adopting a metrological approach. The latter is based on the use of known geometric shapes and quality parameters derived from VDI/VDE guidelines. Tests are carried out by imaging the calibrated Portable Metric Test Object, designed and built at University College London (UCL), UK. It allows assessment of the performance of the image orientation and matching procedures within a typical industrial scenario, characterised by poor texture and known 3D/2D shapes.

  6. 3D Equilibrium Reconstruction in Stellarators and Tokamaks with STELLOPT

    NASA Astrophysics Data System (ADS)

    Lazerson, Samuel; Pablant, Novimir; Gates, David; Neilson, Hutch; Nazikian, Raffi; Suzuki, Yasuhiro; Watanabe, Kiyomasa; Ida, Katsumi; Sakakibara, Satoru

    2012-10-01

    The ability to model and predict the behavior of stellarators and tokamaks requires an ability to match simulation parameters with experimental measurements. This process, known as experimental reconstruction, has been used extensively with 2D axisymmetric codes for Tokamaks. These codes, such as EFIT, lack the ability to model the 3D nature of stellarators and the emerging 3D nature of Tokamaks. Phenomena such as, shielding of islands by neoclassical flows and the suppression of edge localized modes through application of 3D fields, highlight the need for such 3D tools. The stellarator optimizer code STELLOPT has been modified to match 3D VMEC equilibria to experimental measurements. This has allowed 3D experimental reconstructions to be preformed on W7-AS, LHD, and DIII-D devices. The free boundary VMEC equilibria are matched to Thomson profiles (ne and Te), charge exchange measurements (Ti), MSE (polarization angle), and magnetic diagnostics (B-probes, flux loops, Rogowski coils). Three dimensional reconstructed equilibria are presented alongside confidence metrics for the reconstruction process.

  7. Bound constrained bundle adjustment for reliable 3D reconstruction

    PubMed Central

    Gong, Yuanzheng; Meng, De; Seibel, Eric J.

    2015-01-01

    Bundle adjustment (BA) is a common estimation algorithm that is widely used in machine vision as the last step in a feature-based three-dimensional (3D) reconstruction algorithm. BA is essentially a non-convex non-linear least-square problem that can simultaneously solve the 3D coordinates of all the feature points describing the scene geometry, as well as the parameters of the camera. The conventional BA takes a parameter either as a fixed value or as an unconstrained variable based on whether the parameter is known or not. In cases where the known parameters are inaccurate but constrained in a range, conventional BA results in an incorrect 3D reconstruction by using these parameters as fixed values. On the other hand, these inaccurate parameters can be treated as unknown variables, but this does not exploit the knowledge of the constraints, and the resulting reconstruction can be erroneous since the BA optimization halts at a dramatically incorrect local minimum due to its non-convexity. In many practical 3D reconstruction applications, unknown variables with range constraints are usually available, such as a measurement with a range of uncertainty or a bounded estimate. Thus to better utilize these pre-known, constrained, but inaccurate parameters, a bound constrained bundle adjustment (BCBA) algorithm is proposed, developed and tested in this study. A scanning fiber endoscope (the camera) is used to capture a sequence of images above a surgery phantom (the object) of known geometry. 3D virtual models are reconstructed based on these images and then compared with the ground truth. The experimental results demonstrate BCBA can achieve a more reliable, rapid, and accurate 3D reconstruction than conventional bundle adjustment. PMID:25969115

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  9. 3D confocal reconstruction of gene expression in mouse.

    PubMed

    Hecksher-Sørensen, J; Sharpe, J

    2001-01-01

    Three-dimensional computer reconstructions of gene expression data will become a valuable tool in biomedical research in the near future. However, at present the process of converting in situ expression data into 3D models is a highly specialized and time-consuming procedure. Here we present a method which allows rapid reconstruction of whole-mount in situ data from mouse embryos. Mid-gestation embryos were stained with the alkaline phosphotase substrate Fast Red, which can be detected using confocal laser scanning microscopy (CLSM), and cut into 70 microm sections. Each section was then scanned and digitally reconstructed. Using this method it took two days to section, digitize and reconstruct the full expression pattern of Shh in an E9.5 embryo (a 3D model of this embryo can be seen at genex.hgu.mrc.ac.uk). Additionally we demonstrate that this technique allows gene expression to be studied at the single cell level in intact tissue.

  10. Strategies to reconstruct 3D Coffea arabica L. plant structure.

    PubMed

    Matsunaga, Fabio Takeshi; Tosti, Jonas Barbosa; Androcioli-Filho, Armando; Brancher, Jacques Duílio; Costes, Evelyne; Rakocevic, Miroslava

    2016-01-01

    Accurate model of structural elements is necessary to model the foliage and fruit distributions in cultivated plants, both of them being key parameters for yield prediction. However, the level of details in architectural data collection could vary, simplifying the data collection when plants get older and because of the high time cost required. In the present study, we aimed at reconstructing and analyzing plant structure, berry distributions and yield in Coffea arabica (Arabica coffee), by using both detailed or partial morphological information and probabilistic functions. Different datasets of coffee plant architectures were available with different levels of detail depending on the tree age. Three scales of decomposition-plant, axes and metamers were used reconstruct the plant architectures. CoffePlant3D, a software which integrates a series of mathematical, computational and statistical methods organized in three newly developed modules, AmostraCafe3D, VirtualCafe3D and Cafe3D, was developed to accurately reconstruct coffee plants in 3D, whatever the level of details available. The number of metamers of the 2nd order axes was shown to be linearly proportional to that of the orthotropic trunk, and the number of berries per metamer was modeled as a Gaussian function within a specific zone along the plagiotropic axes. This ratio of metamer emission rhythm between the orthotropic trunk and plagiotropic axes represents the pillar of botanical events in the C. arabica development and was central in our modeling approach, especially to reconstruct missing data. The methodology proposed for reconstructing coffee plants under the CoffePlant3D was satisfactorily validated across dataset available and could be performed for any other Arabica coffee variety.

  11. 3-D Tomographic Imaging of the Chicxulub Impact Crater: Preliminary Results From EW#0501

    NASA Astrophysics Data System (ADS)

    Surendra, A. T.; Barton, P. J.; Vermeesch, P. M.; Morgan, J. V.; Warner, M. R.; Gulick, S. P.; Christeson, G. L.; Urrutia-Fucugauchi, J.; Rebolledo-Vieyra, M.; Melosh, H. J.; McDonald, M. A.; Goldin, T.; Mendoza, K.

    2005-05-01

    The Chicxulub impact structure provides a unique opportunity to investigate the sub-surface morphology of large craters on Earth and other planets. The structure of the crater interior is still poorly known and there is much uncertainty over the sequence of events by which these large craters form and the magnitude of the subsequent catastrophic environmental effects. In early 2005, a reflection-refraction survey aboard the R/V Maurice Ewing imaged the deep structure of the Chicxulub impact. We present wide-angle data collected by a 3-D grid of 50 ocean bottom seismometers (OBSs), 86 three-component land stations and a 6 km long hydrophone streamer. The OBS grid, designed to image the peak ring and underlying structure of the northwestern quadrant of the crater, recorded shots from several seismic profiles in various orientations. Many of these profiles extended past the crater rim imaging to the base of the crust. Travel-time picks from this dataset, combined with existing 1996 data, will be inverted using the JIVE3-D tomographic inversion program to create a fully 3-D velocity model of the crater interior. The interpretation of the velocity model will focus on the morphology of the peak ring and the central uplift, and the distribution of breccia and suevite (an impact related breccia/melt) in the centre of the crater. We will calculate the Poisson's ratio for different areas of the crater using both the P-wave velocity model and S-wave arrivals, including those from the 1996 land station data. Comparisons of these values with measurements on the Yaxcopoil-1 core taken from within the crater provide ground-truth for our tomographic model. The contrast in Poisson's ratio between areas of suevite and the surrounding rock further constrain the distribution of breccia and suevite.

  12. New Reconstruction Accuracy Metric for 3D PIV

    NASA Astrophysics Data System (ADS)

    Bajpayee, Abhishek; Techet, Alexandra

    2015-11-01

    Reconstruction for 3D PIV typically relies on recombining images captured from different viewpoints via multiple cameras/apertures. Ideally, the quality of reconstruction dictates the accuracy of the derived velocity field. A reconstruction quality parameter Q is commonly used as a measure of the accuracy of reconstruction algorithms. By definition, a high Q value requires intensity peak levels and shapes in the reconstructed and reference volumes to be matched. We show that accurate velocity fields rely only on the peak locations in the volumes and not on intensity peak levels and shapes. In synthetic aperture (SA) PIV reconstructions, the intensity peak shapes and heights vary with the number of cameras and due to spatial/temporal particle intensity variation respectively. This lowers Q but not the accuracy of the derived velocity field. We introduce a new velocity vector correlation factor Qv as a metric to assess the accuracy of 3D PIV techniques, which provides a better indication of algorithm accuracy. For SAPIV, the number of cameras required for a high Qv are lower than that for a high Q. We discuss Qv in the context of 3D PIV and also present a preliminary comparison of the performance of TomoPIV and SAPIV based on Qv.

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

    PubMed Central

    Lukeneder, Alexander

    2012-01-01

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

  14. 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.

  15. 3D Medical Volume Reconstruction Using Web Services

    PubMed Central

    Kooper, Rob; Shirk, Andrew; Lee, Sang-Chul; Lin, Amy; Folberg, Robert; Bajcsy, Peter

    2008-01-01

    We address the problem of 3D medical volume reconstruction using web services. The use of proposed web services is motivated by the fact that the problem of 3D medical volume reconstruction requires significant computer resources and human expertise in medical and computer science areas. Web services are implemented as an additional layer to a dataflow framework called Data to Knowledge. In the collaboration between UIC and NCSA, pre-processed input images at NCSA are made accessible to medical collaborators for registration. Every time UIC medical collaborators inspected images and selected corresponding features for registration, the web service at NCSA is contacted and the registration processing query is executed using the Image to Knowledge library of registration methods. Co-registered frames are returned for verification by medical collaborators in a new window. In this paper, we present 3D volume reconstruction problem requirements and the architecture of the developed prototype system at http://isda.ncsa.uiuc.edu/MedVolume. We also explain the tradeoffs of our system design and provide experimental data to support our system implementation. The prototype system has been used for multiple 3D volume reconstructions of blood vessels and vasculogenic mimicry patterns in histological sections of uveal melanoma studied by fluorescent confocal laser scanning microscope. PMID:18336808

  16. 3D multifocus astigmatism and compressed sensing (3D MACS) based superresolution reconstruction

    PubMed Central

    Huang, Jiaqing; Sun, Mingzhai; Gumpper, Kristyn; Chi, Yuejie; Ma, Jianjie

    2015-01-01

    Single molecule based superresolution techniques (STORM/PALM) achieve nanometer spatial resolution by integrating the temporal information of the switching dynamics of fluorophores (emitters). When emitter density is low for each frame, they are located to the nanometer resolution. However, when the emitter density rises, causing significant overlapping, it becomes increasingly difficult to accurately locate individual emitters. This is particularly apparent in three dimensional (3D) localization because of the large effective volume of the 3D point spread function (PSF). The inability to precisely locate the emitters at a high density causes poor temporal resolution of localization-based superresolution technique and significantly limits its application in 3D live cell imaging. To address this problem, we developed a 3D high-density superresolution imaging platform that allows us to precisely locate the positions of emitters, even when they are significantly overlapped in three dimensional space. Our platform involves a multi-focus system in combination with astigmatic optics and an ℓ1-Homotopy optimization procedure. To reduce the intrinsic bias introduced by the discrete formulation of compressed sensing, we introduced a debiasing step followed by a 3D weighted centroid procedure, which not only increases the localization accuracy, but also increases the computation speed of image reconstruction. We implemented our algorithms on a graphic processing unit (GPU), which speeds up processing 10 times compared with central processing unit (CPU) implementation. We tested our method with both simulated data and experimental data of fluorescently labeled microtubules and were able to reconstruct a 3D microtubule image with 1000 frames (512×512) acquired within 20 seconds. PMID:25798314

  17. Automated 3D reconstruction of interiors with multiple scan views

    NASA Astrophysics Data System (ADS)

    Sequeira, Vitor; Ng, Kia C.; Wolfart, Erik; Goncalves, Joao G. M.; Hogg, David C.

    1998-12-01

    This paper presents two integrated solutions for realistic 3D model acquisition and reconstruction; an early prototype, in the form of a push trolley, and a later prototype in the form of an autonomous robot. The systems encompass all hardware and software required, from laser and video data acquisition, processing and output of texture-mapped 3D models in VRML format, to batteries for power supply and wireless network communications. The autonomous version is also equipped with a mobile platform and other sensors for the purpose of automatic navigation. The applications for such a system range from real estate and tourism (e.g., showing a 3D computer model of a property to a potential buyer or tenant) or as tool for content creation (e.g., creating 3D models of heritage buildings or producing broadcast quality virtual studios). The system can also be used in industrial environments as a reverse engineering tool to update the design of a plant, or as a 3D photo-archive for insurance purposes. The system is Internet compatible: the photo-realistic models can be accessed via the Internet and manipulated interactively in 3D using a common Web browser with a VRML plug-in. Further information and example reconstructed models are available on- line via the RESOLV web-page at http://www.scs.leeds.ac.uk/resolv/.

  18. Automating 3D reconstruction using a probabilistic grammar

    NASA Astrophysics Data System (ADS)

    Xiong, Hanwei; Xu, Jun; Xu, Chenxi; Pan, Ming

    2015-10-01

    3D reconstruction of objects from point clouds with a laser scanner is still a laborious task in many applications. Automating 3D process is an ongoing research topic and suffers from the complex structure of the data. The main difficulty is due to lack of knowledge of real world objects structure. In this paper, we accumulate such structure knowledge by a probabilistic grammar learned from examples in the same category. The rules of the grammar capture compositional structures at different levels, and a feature dependent probability function is attached for every rule. The learned grammar can be used to parse new 3D point clouds, organize segment patches in a hierarchal way, and assign them meaningful labels. The parsed semantics can be used to guide the reconstruction algorithms automatically. Some examples are given to explain the method.

  19. Estimation of the thermal conductivity of hemp based insulation material from 3D tomographic images

    NASA Astrophysics Data System (ADS)

    El-Sawalhi, R.; Lux, J.; Salagnac, P.

    2016-08-01

    In this work, we are interested in the structural and thermal characterization of natural fiber insulation materials. The thermal performance of these materials depends on the arrangement of fibers, which is the consequence of the manufacturing process. In order to optimize these materials, thermal conductivity models can be used to correlate some relevant structural parameters with the effective thermal conductivity. However, only a few models are able to take into account the anisotropy of such material related to the fibers orientation, and these models still need realistic input data (fiber orientation distribution, porosity, etc.). The structural characteristics are here directly measured on a 3D tomographic image using advanced image analysis techniques. Critical structural parameters like porosity, pore and fiber size distribution as well as local fiber orientation distribution are measured. The results of the tested conductivity models are then compared with the conductivity tensor obtained by numerical simulation on the discretized 3D microstructure, as well as available experimental measurements. We show that 1D analytical models are generally not suitable for assessing the thermal conductivity of such anisotropic media. Yet, a few anisotropic models can still be of interest to relate some structural parameters, like the fiber orientation distribution, to the thermal properties. Finally, our results emphasize that numerical simulations on 3D realistic microstructure is a very interesting alternative to experimental measurements.

  20. Reconstruction and 3D visualisation based on objective real 3D based documentation.

    PubMed

    Bolliger, Michael J; Buck, Ursula; Thali, Michael J; Bolliger, Stephan A

    2012-09-01

    Reconstructions based directly upon forensic evidence alone are called primary information. Historically this consists of documentation of findings by verbal protocols, photographs and other visual means. Currently modern imaging techniques such as 3D surface scanning and radiological methods (computer tomography, magnetic resonance imaging) are also applied. Secondary interpretation is based on facts and the examiner's experience. Usually such reconstructive expertises are given in written form, and are often enhanced by sketches. However, narrative interpretations can, especially in complex courses of action, be difficult to present and can be misunderstood. In this report we demonstrate the use of graphic reconstruction of secondary interpretation with supporting pictorial evidence, applying digital visualisation (using 'Poser') or scientific animation (using '3D Studio Max', 'Maya') and present methods of clearly distinguishing between factual documentation and examiners' interpretation based on three cases. The first case involved a pedestrian who was initially struck by a car on a motorway and was then run over by a second car. The second case involved a suicidal gunshot to the head with a rifle, in which the trigger was pushed with a rod. The third case dealt with a collision between two motorcycles. Pictorial reconstruction of the secondary interpretation of these cases has several advantages. The images enable an immediate overview, give rise to enhanced clarity, and compel the examiner to look at all details if he or she is to create a complete image.

  1. 3D morphological measurement of whole slide histological vasculature reconstructions

    NASA Astrophysics Data System (ADS)

    Xu, Yiwen; Pickering, J. G.; Nong, Zengxuan; Ward, Aaron D.

    2016-03-01

    Properties of the microvasculature that contribute to tissue perfusion can be assessed using immunohistochemistry on 2D histology sections. However, the vasculature is inherently 3D and the ability to measure and visualize the vessel wall components in 3D will aid in detecting focal pathologies. Our objectives were (1) to develop a method for 3D measurement and visualization of microvasculature in 3D, (2) to compare the normal and regenerated post-ischemia mouse hind limb microvasculature, and (3) to compare the 2D and 3D vessel morphology measures. Vessels were stained for smooth muscle using 3,3'-Diaminobenzidine (DAB) immunostain for both normal (n = 6 mice) and regenerated vasculature (n = 5 mice). 2D vessel segmentations were reconstructed into 3D using landmark based registration. No substantial bias was found in the 2D measurements relative to 3D, but larger differences were observed for individual vessels oriented non-orthogonally to the plane of sectioning. A larger value of area, perimeter, and vessel wall thickness was found in the normal vasculature as compared to the regenerated vasculature, for both the 2D and 3D measurements (p < 0.01). Aggregated 2D measurements are sufficient for identifying morphological differences between groups of mice; however, one must interpret individual 2D measurements with caution if the vessel centerline direction is unknown. Visualization of 3D measurements permits the detection of localized vessel morphology aberrations that are not revealed by 2D measurements. With vascular measure visualization methodologies in 3D, we are now capable of locating focal pathologies on a whole slide level.

  2. Electrochemical fields within 3D reconstructed microstructures of mixed ionic and electronic conducting devices

    NASA Astrophysics Data System (ADS)

    Zhang, Yanxiang; Chen, Yu; Lin, Ye; Yan, Mufu; Harris, William M.; Chiu, Wilson K. S.; Ni, Meng; Chen, Fanglin

    2016-11-01

    The performance and stability of the mixed ionic and electronic conducting (MIEC) membrane devices, such as solid oxide cells (SOCs) and oxygen separation membranes (OSMs) interplay tightly with the transport properties and the three-dimensional (3D) microstructure of the membrane. However, development of the MIEC devices is hindered by the limited knowledge about the distribution of electrochemical fields within the 3D local microstructures, especially at surface and interface. In this work, a generic model conforming to local thermodynamic equilibrium is developed to calculate the electrochemical fields, such as electric potential and oxygen chemical potential, within the 3D microstructure of the MIEC membrane. Stability of the MIEC membrane is evaluated by the distribution of oxygen partial pressure. The cell-level performance such as polarization resistance and voltage vs. current curve can be further calculated. Case studies are performed to demonstrate the capability of the framework by using X-ray computed tomography reconstructed 3D microstructures of a SOC and an OSM. The calculation method demonstrates high computational efficiency for large size 3D tomographic microstructures, and permits parallel calculation. The framework can serve as a powerful tool for correlating the transport properties and the 3D microstructure to the performance and the stability of MIEC devices.

  3. Ring artifacts correction in compressed sensing tomographic reconstruction

    PubMed Central

    Paleo, Pierre; Mirone, Alessandro

    2015-01-01

    Ring artifacts are a very common problem in tomographic reconstruction, and numerous methods exist to either pre-process the sinogram or correct the reconstructed slice. A novel approach to perform the correction as part of the reconstruction process is presented. It is shown that for iterative techniques, which amount to optimizing an objective function, the ring artifacts correction can be easily integrated in the formalism, enabling simultaneous slice reconstruction and ring artifacts correction. This method is tested and compared with mainstream correction techniques for both simulated and experimental data. Results show that the correction is efficient, especially for undersampled datasets. This technique is included in the PyHST2 code which is used at the European Synchrotron Radiation Facility for tomographic reconstruction. PMID:26289279

  4. Exposing digital image forgeries by 3D reconstruction technology

    NASA Astrophysics Data System (ADS)

    Wang, Yongqiang; Xu, Xiaojing; Li, Zhihui; Liu, Haizhen; Li, Zhigang; Huang, Wei

    2009-11-01

    Digital images are easy to tamper and edit due to availability of powerful image processing and editing software. Especially, forged images by taking from a picture of scene, because of no manipulation was made after taking, usual methods, such as digital watermarks, statistical correlation technology, can hardly detect the traces of image tampering. According to image forgery characteristics, a method, based on 3D reconstruction technology, which detect the forgeries by discriminating the dimensional relationship of each object appeared on image, is presented in this paper. This detection method includes three steps. In the first step, all the parameters of images were calibrated and each crucial object on image was chosen and matched. In the second step, the 3D coordinates of each object were calculated by bundle adjustment. In final step, the dimensional relationship of each object was analyzed. Experiments were designed to test this detection method; the 3D reconstruction and the forged image 3D reconstruction were computed independently. Test results show that the fabricating character in digital forgeries can be identified intuitively by this method.

  5. Adaptive 3D Face Reconstruction from Unconstrained Photo Collections.

    PubMed

    Roth, Joseph; Tong, Yiying; Liu, Xiaoming

    2016-12-07

    Given a photo collection of "unconstrained" face images of one individual captured under a variety of unknown pose, expression, and illumination conditions, this paper presents a method for reconstructing a 3D face surface model of the individual along with albedo information. Unlike prior work on face reconstruction that requires large photo collections, we formulate an approach to adapt to photo collections with a high diversity in both the number of images and the image quality. To achieve this, we incorporate prior knowledge about face shape by fitting a 3D morphable model to form a personalized template, following by using a novel photometric stereo formulation to complete the fine details, under a coarse-to-fine scheme. Our scheme incorporates a structural similarity-based local selection step to help identify a common expression for reconstruction while discarding occluded portions of faces. The evaluation of reconstruction performance is through a novel quality measure, in the absence of ground truth 3D scans. Superior large-scale experimental results are reported on synthetic, Internet, and personal photo collections.

  6. 3D/3D registration of coronary CTA and biplane XA reconstructions for improved image guidance

    SciTech Connect

    Dibildox, Gerardo Baka, Nora; Walsum, Theo van; Punt, Mark; Aben, Jean-Paul; Schultz, Carl; Niessen, Wiro

    2014-09-15

    Purpose: The authors aim to improve image guidance during percutaneous coronary interventions of chronic total occlusions (CTO) by providing information obtained from computed tomography angiography (CTA) to the cardiac interventionist. To this end, the authors investigate a method to register a 3D CTA model to biplane reconstructions. Methods: The authors developed a method for registering preoperative coronary CTA with intraoperative biplane x-ray angiography (XA) images via 3D models of the coronary arteries. The models are extracted from the CTA and biplane XA images, and are temporally aligned based on CTA reconstruction phase and XA ECG signals. Rigid spatial alignment is achieved with a robust probabilistic point set registration approach using Gaussian mixture models (GMMs). This approach is extended by including orientation in the Gaussian mixtures and by weighting bifurcation points. The method is evaluated on retrospectively acquired coronary CTA datasets of 23 CTO patients for which biplane XA images are available. Results: The Gaussian mixture model approach achieved a median registration accuracy of 1.7 mm. The extended GMM approach including orientation was not significantly different (P > 0.1) but did improve robustness with regards to the initialization of the 3D models. Conclusions: The authors demonstrated that the GMM approach can effectively be applied to register CTA to biplane XA images for the purpose of improving image guidance in percutaneous coronary interventions.

  7. Implementation of a fully 3D system model for brain SPECT with fan- beam-collimator OSEM reconstruction with 3D total variation regularization

    NASA Astrophysics Data System (ADS)

    Ye, Hongwei; Krol, Andrzej; Lipson, Edward D.; Lu, Yao; Xu, Yuesheng; Lee, Wei; Feiglin, David H.

    2007-03-01

    In order to improve tomographically reconstructed image quality, we have implemented a fully 3D reconstruction, using an ordered subsets expectation maximization (OSEM) algorithm for fan-beam collimator (FBC) SPECT, along with a volumetric system model-fan-volume system model (FVSM), a modified attenuation compensation, a 3D depth- and angle-dependent resolution and sensitivity correction, and a 3D total variation (TV) regularization. SPECT data were acquired in a 128x64 matrix, in 120 views with a circular orbit. The numerical Zubal brain phantom was used to simulate a FBC HMPAO Tc-99m brain SPECT scan, and a low noise and scatter-free projection dataset was obtained using the SimSET Monte Carlo package. A SPECT scan for a mini-Defrise phantom and brain HMPAO SPECT scans for five patients were acquired with a triple-head gamma camera (Triad 88) equipped with a low-energy high-resolution (LEHR) FBC. The reconstructed images, obtained using clinical filtered back projection (FBP), OSEM with a line-length system model (LLSM) and 3D TV regularization, and OSEM with FVSM and 3D TV regularization were quantitatively studied. Overall improvement in the image quality has been observed, including better axial and transaxial resolution, better integral uniformity, higher contrast-to-noise ration between the gray matter and the white matter, and better accuracy and lower bias in OSEM-FVSM, compared with OSEM-LLSM and clinical FBP.

  8. [Optimized study technic in meniscopathies by NMR tomographic 3D imaging at 1.5 tesla].

    PubMed

    Skalej, M; Klose, U; Küper, K

    1988-02-01

    Traumatic and degenerative changes in the meniscus can be demonstrated well by MRT, but the small size and complex anatomical structure of the menisci present practical problems. A correct understanding is only possible by images in several planes and good resolution, making the examination a lengthy procedure. A technique is therefore described using 3-D images and reconstruction of high-resolution films, which allows rapid examination of the menisci in optimal planes.

  9. Possibilities and limitations of the ART-Sample algorithm for reconstruction of 3D temperature fields and the influence of opaque obstacles.

    PubMed

    Li, Yuanyang; Herman, Cila

    2013-07-01

    The need for the measurement of complex, unsteady, three-dimensional (3D) temperature distributions arises in a variety of engineering applications, and tomographic techniques are applied to accomplish this goal. Holographic interferometry (HI), one of the optical methods used for visualizing temperature fields, combined with tomographic reconstruction techniques requires multi-directional interferometric data to recover the 3D information. However, the presence of opaque obstacles (such as solid objects in the flow field and heaters) in the measurement volume, prevents the probing light beams from traversing the entire measurement volume. As a consequence, information on the average value of the field variable will be lost in regions located in the shade of the obstacle. The capability of the ART-Sample tomographic reconstruction method to recover 3D temperature distributions both in unobstructed temperature fields and in the presence of opaque obstacles is discussed in this paper. A computer code for tomographic reconstruction of 3D temperature fields from 2D projections was developed. In the paper, the reconstruction accuracy is discussed quantitatively both without and with obstacles in the measurement volume for a set of phantom functions mimicking realistic temperature distributions. The reconstruction performance is optimized while minimizing the number of irradiation directions (experimental hardware requirements) and computational effort. For the smooth temperature field both with and without obstacles, the reconstructions produced by this algorithm are good, both visually and using quantitative criteria. The results suggest that the location and the size of the obstacle and the number of viewing directions will affect the reconstruction of the temperature field. When the best performance parameters of the ART-Sample algorithm identified in this paper are used to reconstruct the 3D temperature field, the 3D reconstructions with and without obstacle are

  10. Multi-sensor 3D volumetric reconstruction using CUDA

    NASA Astrophysics Data System (ADS)

    Aliakbarpour, Hadi; Almeida, Luis; Menezes, Paulo; Dias, Jorge

    2011-12-01

    This paper presents a full-body volumetric reconstruction of a person in a scene using a sensor network, where some of them can be mobile. The sensor network is comprised of couples of camera and inertial sensor (IS). Taking advantage of IS, the 3D reconstruction is performed using no planar ground assumption. Moreover, IS in each couple is used to define a virtual camera whose image plane is horizontal and aligned with the earth cardinal directions. The IS is furthermore used to define a set of inertial planes in the scene. The image plane of each virtual camera is projected onto this set of parallel-horizontal inertial-planes, using some adapted homography functions. A parallel processing architecture is proposed in order to perform human real-time volumetric reconstruction. The real-time characteristic is obtained by implementing the reconstruction algorithm on a graphics processing unit (GPU) using Compute Unified Device Architecture (CUDA). In order to show the effectiveness of the proposed algorithm, a variety of the gestures of a person acting in the scene is reconstructed and demonstrated. Some analyses have been carried out to measure the performance of the algorithm in terms of processing time. The proposed framework has potential to be used by different applications such as smart-room, human behavior analysis and 3D teleconference. [Figure not available: see fulltext.

  11. On detailed 3D reconstruction of large indoor environments

    NASA Astrophysics Data System (ADS)

    Bondarev, Egor

    2015-03-01

    In this paper we present techniques for highly detailed 3D reconstruction of extra large indoor environments. We discuss the benefits and drawbacks of low-range, far-range and hybrid sensing and reconstruction approaches. The proposed techniques for low-range and hybrid reconstruction, enabling the reconstruction density of 125 points/cm3 on large 100.000 m3 models, are presented in detail. The techniques tackle the core challenges for the above requirements, such as a multi-modal data fusion (fusion of a LIDAR data with a Kinect data), accurate sensor pose estimation, high-density scanning and depth data noise filtering. Other important aspects for extra large 3D indoor reconstruction are the point cloud decimation and real-time rendering. In this paper, we present a method for planar-based point cloud decimation, allowing for reduction of a point cloud size by 80-95%. Besides this, we introduce a method for online rendering of extra large point clouds enabling real-time visualization of huge cloud spaces in conventional web browsers.

  12. 3D reconstruction methods of coronal structures by radio observations

    NASA Technical Reports Server (NTRS)

    Aschwanden, Markus J.; Bastian, T. S.; White, Stephen M.

    1992-01-01

    The ability to carry out the three dimensional (3D) reconstruction of structures in the solar corona would represent a major advance in the study of the physical properties in active regions and in flares. Methods which allow a geometric reconstruction of quasistationary coronal structures (for example active region loops) or dynamic structures (for example flaring loops) are described: stereoscopy of multi-day imaging observations by the VLA (Very Large Array); tomography of optically thin emission (in radio or soft x-rays); multifrequency band imaging by the VLA; and tracing of magnetic field lines by propagating electron beams.

  13. Advances in the calibration of atom probe tomographic reconstruction

    SciTech Connect

    Gault, Baptiste; Moody, Michael P.; La Fontaine, Alexandre; Stephenson, Leigh T.; Haley, Daniel; Ringer, Simon P.; Geuser, Frederic de; Tsafnat, Guy

    2009-02-01

    Modern wide field-of-view atom probes permit observation of a wide range of crystallographic features that can be used to calibrate the tomographic reconstruction of the analyzed volume. In this study, methodologies to determine values of the geometric parameters involved in the tomographic reconstruction of atom probe data sets are presented and discussed. The influence of the tip to electrode distance and specimen temperature on these parameters is explored. Significantly, their influence is demonstrated to be very limited, indicating a relatively wide regime of experimental parameters space for sound atom probe tomography (APT) experiments. These methods have been used on several specimens and material types, and the results indicate that the reconstruction parameters are specific to each specimen. Finally, it is shown how an accurate calibration of the reconstruction enables improvements to the quality and reliability of the microscopy and microanalysis capabilities of the atom probe.

  14. Optical Sensors and Methods for Underwater 3D Reconstruction

    PubMed Central

    Massot-Campos, Miquel; Oliver-Codina, Gabriel

    2015-01-01

    This paper presents a survey on optical sensors and methods for 3D reconstruction in underwater environments. The techniques to obtain range data have been listed and explained, together with the different sensor hardware that makes them possible. The literature has been reviewed, and a classification has been proposed for the existing solutions. New developments, commercial solutions and previous reviews in this topic have also been gathered and considered. PMID:26694389

  15. Postoperative 3D spine reconstruction by navigating partitioning manifolds

    SciTech Connect

    Kadoury, Samuel; Labelle, Hubert Parent, Stefan

    2016-03-15

    Purpose: The postoperative evaluation of scoliosis patients undergoing corrective treatment is an important task to assess the strategy of the spinal surgery. Using accurate 3D geometric models of the patient’s spine is essential to measure longitudinal changes in the patient’s anatomy. On the other hand, reconstructing the spine in 3D from postoperative radiographs is a challenging problem due to the presence of instrumentation (metallic rods and screws) occluding vertebrae on the spine. Methods: This paper describes the reconstruction problem by searching for the optimal model within a manifold space of articulated spines learned from a training dataset of pathological cases who underwent surgery. The manifold structure is implemented based on a multilevel manifold ensemble to structure the data, incorporating connections between nodes within a single manifold, in addition to connections between different multilevel manifolds, representing subregions with similar characteristics. Results: The reconstruction pipeline was evaluated on x-ray datasets from both preoperative patients and patients with spinal surgery. By comparing the method to ground-truth models, a 3D reconstruction accuracy of 2.24 ± 0.90 mm was obtained from 30 postoperative scoliotic patients, while handling patients with highly deformed spines. Conclusions: This paper illustrates how this manifold model can accurately identify similar spine models by navigating in the low-dimensional space, as well as computing nonlinear charts within local neighborhoods of the embedded space during the testing phase. This technique allows postoperative follow-ups of spinal surgery using personalized 3D spine models and assess surgical strategies for spinal deformities.

  16. Comparing 3D virtual methods for hemimandibular body reconstruction.

    PubMed

    Benazzi, Stefano; Fiorenza, Luca; Kozakowski, Stephanie; Kullmer, Ottmar

    2011-07-01

    Reconstruction of fractured, distorted, or missing parts in human skeleton presents an equal challenge in the fields of paleoanthropology, bioarcheology, forensics, and medicine. This is particularly important within the disciplines such as orthodontics and surgery, when dealing with mandibular defects due to tumors, developmental abnormalities, or trauma. In such cases, proper restorations of both form (for esthetic purposes) and function (restoration of articulation, occlusion, and mastication) are required. Several digital approaches based on three-dimensional (3D) digital modeling, computer-aided design (CAD)/computer-aided manufacturing techniques, and more recently geometric morphometric methods have been used to solve this problem. Nevertheless, comparisons among their outcomes are rarely provided. In this contribution, three methods for hemimandibular body reconstruction have been tested. Two bone defects were virtually simulated in a 3D digital model of a human hemimandible. Accordingly, 3D digital scaffolds were obtained using the mirror copy of the unaffected hemimandible (Method 1), the thin plate spline (TPS) interpolation (Method 2), and the combination between TPS and CAD techniques (Method 3). The mirror copy of the unaffected hemimandible does not provide a suitable solution for bone restoration. The combination between TPS interpolation and CAD techniques (Method 3) produces an almost perfect-fitting 3D digital model that can be used for biocompatible custom-made scaffolds generated by rapid prototyping technologies.

  17. Structured Light-Based 3D Reconstruction System for Plants.

    PubMed

    Nguyen, Thuy Tuong; Slaughter, David C; Max, Nelson; Maloof, Julin N; Sinha, Neelima

    2015-07-29

    Camera-based 3D reconstruction of physical objects is one of the most popular computer vision trends in recent years. Many systems have been built to model different real-world subjects, but there is lack of a completely robust system for plants. This paper presents a full 3D reconstruction system that incorporates both hardware structures (including the proposed structured light system to enhance textures on object surfaces) and software algorithms (including the proposed 3D point cloud registration and plant feature measurement). This paper demonstrates the ability to produce 3D models of whole plants created from multiple pairs of stereo images taken at different viewing angles, without the need to destructively cut away any parts of a plant. The ability to accurately predict phenotyping features, such as the number of leaves, plant height, leaf size and internode distances, is also demonstrated. Experimental results show that, for plants having a range of leaf sizes and a distance between leaves appropriate for the hardware design, the algorithms successfully predict phenotyping features in the target crops, with a recall of 0.97 and a precision of 0.89 for leaf detection and less than a 13-mm error for plant size, leaf size and internode distance.

  18. Structured Light-Based 3D Reconstruction System for Plants

    PubMed Central

    Nguyen, Thuy Tuong; Slaughter, David C.; Max, Nelson; Maloof, Julin N.; Sinha, Neelima

    2015-01-01

    Camera-based 3D reconstruction of physical objects is one of the most popular computer vision trends in recent years. Many systems have been built to model different real-world subjects, but there is lack of a completely robust system for plants.This paper presents a full 3D reconstruction system that incorporates both hardware structures (including the proposed structured light system to enhance textures on object surfaces) and software algorithms (including the proposed 3D point cloud registration and plant feature measurement). This paper demonstrates the ability to produce 3D models of whole plants created from multiple pairs of stereo images taken at different viewing angles, without the need to destructively cut away any parts of a plant. The ability to accurately predict phenotyping features, such as the number of leaves, plant height, leaf size and internode distances, is also demonstrated. Experimental results show that, for plants having a range of leaf sizes and a distance between leaves appropriate for the hardware design, the algorithms successfully predict phenotyping features in the target crops, with a recall of 0.97 and a precision of 0.89 for leaf detection and less than a 13-mm error for plant size, leaf size and internode distance. PMID:26230701

  19. An automated 3D reconstruction method of UAV images

    NASA Astrophysics Data System (ADS)

    Liu, Jun; Wang, He; Liu, Xiaoyang; Li, Feng; Sun, Guangtong; Song, Ping

    2015-10-01

    In this paper a novel fully automated 3D reconstruction approach based on low-altitude unmanned aerial vehicle system (UAVs) images will be presented, which does not require previous camera calibration or any other external prior knowledge. Dense 3D point clouds are generated by integrating orderly feature extraction, image matching, structure from motion (SfM) and multi-view stereo (MVS) algorithms, overcoming many of the cost, time limitations of rigorous photogrammetry techniques. An image topology analysis strategy is introduced to speed up large scene reconstruction by taking advantage of the flight-control data acquired by UAV. Image topology map can significantly reduce the running time of feature matching by limiting the combination of images. A high-resolution digital surface model of the study area is produced base on UAV point clouds by constructing the triangular irregular network. Experimental results show that the proposed approach is robust and feasible for automatic 3D reconstruction of low-altitude UAV images, and has great potential for the acquisition of spatial information at large scales mapping, especially suitable for rapid response and precise modelling in disaster emergency.

  20. Determination of three-dimensional atomic positions from tomographic reconstruction using ensemble empirical mode decomposition

    NASA Astrophysics Data System (ADS)

    Li, Po-Nan; Wu, Zong-Han; Hsiao, Chien-Nan; Lee, Ting-Kuo; Chen, Chien-Chun

    2016-08-01

    Tomographic reconstruction from a tilt series of electron micrographs has raised great interest in materials, chemical, and condensed matters science because of its capability of revealing 3D local atomic structures within nanomaterials. Previous breakthroughs have demonstrated that the positions of individual atoms can not only be visualized but also determined by combining a scanning transmission electron microscope with a high-angle annular dark-field detector, equally sloped tomography, and the filtering/denoising method. However, the filtering/denoising approach—whether imposed on 2D projections or 3D reconstruction—raises concerns regarding the robustness of image processing, the accuracy of atomic positions, and the artificial atoms introduced during filtering. In this article, we report a general method that overcomes these limitations. By removing unphysical oscillations in 2D projections through ensemble empirical mode decomposition and applying a standard Wiener filter to the 3D reconstruction, we are able to determine atomic structures with higher accuracy.

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

    PubMed Central

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

    2008-01-01

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

  2. 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.

  3. 3D reconstruction of light flux distribution on arbitrary surfaces from 2D multi-photographic images.

    PubMed

    Chen, Xueli; Gao, Xinbo; Chen, Duofang; Ma, Xiaopeng; Zhao, Xiaohui; Shen, Man; Li, Xiangsi; Qu, Xiaochao; Liang, Jimin; Ripoll, Jorge; Tian, Jie

    2010-09-13

    Optical tomography can demonstrate accurate three-dimensional (3D) imaging that recovers the 3D spatial distribution and concentration of the luminescent probes in biological tissues, compared with planar imaging. However, the tomographic approach is extremely difficult to implement due to the complexity in the reconstruction of 3D surface flux distribution from multi-view two dimensional (2D) measurements on the subject surface. To handle this problem, a novel and effective method is proposed in this paper to determine the surface flux distribution from multi-view 2D photographic images acquired by a set of non-contact detectors. The method is validated with comparison experiments involving both regular and irregular surfaces. Reconstruction of the inside probes based on the reconstructed surface flux distribution further demonstrates the potential of the proposed method in its application in optical tomography.

  4. Optimization of tomographic reconstruction workflows on geographically distributed resources

    DOE PAGES

    Bicer, Tekin; Gursoy, Doga; Kettimuthu, Rajkumar; ...

    2016-01-01

    New technological advancements in synchrotron light sources enable data acquisitions at unprecedented levels. This emergent trend affects not only the size of the generated data but also the need for larger computational resources. Although beamline scientists and users have access to local computational resources, these are typically limited and can result in extended execution times. Applications that are based on iterative processing as in tomographic reconstruction methods require high-performance compute clusters for timely analysis of data. Here, time-sensitive analysis and processing of Advanced Photon Source data on geographically distributed resources are focused on. Two main challenges are considered: (i) modelingmore » of the performance of tomographic reconstruction workflows and (ii) transparent execution of these workflows on distributed resources. For the former, three main stages are considered: (i) data transfer between storage and computational resources, (i) wait/queue time of reconstruction jobs at compute resources, and (iii) computation of reconstruction tasks. These performance models allow evaluation and estimation of the execution time of any given iterative tomographic reconstruction workflow that runs on geographically distributed resources. For the latter challenge, a workflow management system is built, which can automate the execution of workflows and minimize the user interaction with the underlying infrastructure. The system utilizes Globus to perform secure and efficient data transfer operations. The proposed models and the workflow management system are evaluated by using three high-performance computing and two storage resources, all of which are geographically distributed. Workflows were created with different computational requirements using two compute-intensive tomographic reconstruction algorithms. Experimental evaluation shows that the proposed models and system can be used for selecting the optimum resources, which in

  5. Optimization of tomographic reconstruction workflows on geographically distributed resources

    PubMed Central

    Bicer, Tekin; Gürsoy, Doǧa; Kettimuthu, Rajkumar; De Carlo, Francesco; Foster, Ian T.

    2016-01-01

    New technological advancements in synchrotron light sources enable data acquisitions at unprecedented levels. This emergent trend affects not only the size of the generated data but also the need for larger computational resources. Although beamline scientists and users have access to local computational resources, these are typically limited and can result in extended execution times. Applications that are based on iterative processing as in tomographic reconstruction methods require high-performance compute clusters for timely analysis of data. Here, time-sensitive analysis and processing of Advanced Photon Source data on geographically distributed resources are focused on. Two main challenges are considered: (i) modeling of the performance of tomographic reconstruction workflows and (ii) transparent execution of these workflows on distributed resources. For the former, three main stages are considered: (i) data transfer between storage and computational resources, (i) wait/queue time of reconstruction jobs at compute resources, and (iii) computation of reconstruction tasks. These performance models allow evaluation and estimation of the execution time of any given iterative tomographic reconstruction workflow that runs on geographically distributed resources. For the latter challenge, a workflow management system is built, which can automate the execution of workflows and minimize the user interaction with the underlying infrastructure. The system utilizes Globus to perform secure and efficient data transfer operations. The proposed models and the workflow management system are evaluated by using three high-performance computing and two storage resources, all of which are geographically distributed. Workflows were created with different computational requirements using two compute-intensive tomographic reconstruction algorithms. Experimental evaluation shows that the proposed models and system can be used for selecting the optimum resources, which in turn can

  6. 3D Reconstruction of Coronary Artery Vascular Smooth Muscle Cells

    PubMed Central

    Luo, Tong; Chen, Huan; Kassab, Ghassan S.

    2016-01-01

    Aims The 3D geometry of individual vascular smooth muscle cells (VSMCs), which are essential for understanding the mechanical function of blood vessels, are currently not available. This paper introduces a new 3D segmentation algorithm to determine VSMC morphology and orientation. Methods and Results A total of 112 VSMCs from six porcine coronary arteries were used in the analysis. A 3D semi-automatic segmentation method was developed to reconstruct individual VSMCs from cell clumps as well as to extract the 3D geometry of VSMCs. A new edge blocking model was introduced to recognize cell boundary while an edge growing was developed for optimal interpolation and edge verification. The proposed methods were designed based on Region of Interest (ROI) selected by user and interactive responses of limited key edges. Enhanced cell boundary features were used to construct the cell’s initial boundary for further edge growing. A unified framework of morphological parameters (dimensions and orientations) was proposed for the 3D volume data. Virtual phantom was designed to validate the tilt angle measurements, while other parameters extracted from 3D segmentations were compared with manual measurements to assess the accuracy of the algorithm. The length, width and thickness of VSMCs were 62.9±14.9μm, 4.6±0.6μm and 6.2±1.8μm (mean±SD). In longitudinal-circumferential plane of blood vessel, VSMCs align off the circumferential direction with two mean angles of -19.4±9.3° and 10.9±4.7°, while an out-of-plane angle (i.e., radial tilt angle) was found to be 8±7.6° with median as 5.7°. Conclusions A 3D segmentation algorithm was developed to reconstruct individual VSMCs of blood vessel walls based on optical image stacks. The results were validated by a virtual phantom and manual measurement. The obtained 3D geometries can be utilized in mathematical models and leads a better understanding of vascular mechanical properties and function. PMID:26882342

  7. An Automatic 3-D Reconstruction of Coronary Arteries by Stereopsis.

    PubMed

    Cetin, Mufit; Iskurt, Ali

    2016-04-01

    Stereopsis of X-ray images can produce 3D tree of coronary arteries up to a certain accuracy level with a lower dose of radiation when compared to computer tomography (CT). In this study, a novel and complete automatic system is designed that covers preprocessing, segmentation, matching and reconstruction steps for that purpose. First, an automatic and novel pattern recognition technique is applied for extraction of the bifurcation points with their diameters recorded in a map. Then, a novel optimization algorithm is run for matching the branches efficiently which is based on that map and the epipolar geometry of stereopsis. Finally, cut branches are fixed one by one at the bifurcations for completing the 3D reconstruction. This method prevails the similar ones in the literature with this novelty since it automatically and inherently prevents the wrong overlapping of branches. Other essential problems like correct detection of the bifurcations and accurate calibration parameters and fast overlapping of matched branches are addressed at acceptable levels. The accuracy of bifurcation extraction is high at 90 % with 96 % sensitivity. Accuracy of vessel centerlines has rootmean-square (rms) error smaller than 0.57 mm for 20 different patients. For phantom model, rms error is 0.75 ± 0.8 mm in 3D localization.

  8. 3D temperature field reconstruction using ultrasound sensing system

    NASA Astrophysics Data System (ADS)

    Liu, Yuqian; Ma, Tong; Cao, Chengyu; Wang, Xingwei

    2016-04-01

    3D temperature field reconstruction is of practical interest to the power, transportation and aviation industries and it also opens up opportunities for real time control or optimization of high temperature fluid or combustion process. In our paper, a new distributed optical fiber sensing system consisting of a series of elements will be used to generate and receive acoustic signals. This system is the first active temperature field sensing system that features the advantages of the optical fiber sensors (distributed sensing capability) and the acoustic sensors (non-contact measurement). Signals along multiple paths will be measured simultaneously enabled by a code division multiple access (CDMA) technique. Then a proposed Gaussian Radial Basis Functions (GRBF)-based approach can approximate the temperature field as a finite summation of space-dependent basis functions and time-dependent coefficients. The travel time of the acoustic signals depends on the temperature of the media. On this basis, the Gaussian functions are integrated along a number of paths which are determined by the number and distribution of sensors. The inversion problem to estimate the unknown parameters of the Gaussian functions can be solved with the measured times-of-flight (ToF) of acoustic waves and the length of propagation paths using the recursive least square method (RLS). The simulation results show an approximation error less than 2% in 2D and 5% in 3D respectively. It demonstrates the availability and efficiency of our proposed 3D temperature field reconstruction mechanism.

  9. Real-Time Camera Guidance for 3d Scene Reconstruction

    NASA Astrophysics Data System (ADS)

    Schindler, F.; Förstner, W.

    2012-07-01

    We propose a framework for operator guidance during the image acquisition process for reliable multi-view stereo reconstruction. Goal is to achieve full coverage of the object and sufficient overlap. Multi-view stereo is a commonly used method to reconstruct both camera trajectory and 3D object shape. After determining an initial solution, a globally optimal reconstruction is usually obtained by executing a bundle adjustment involving all images. Acquiring suitable images, however, still requires an experienced operator to ensure accuracy and completeness of the final solution. We propose an interactive framework for guiding unexperienced users or possibly an autonomous robot. Using approximate camera orientations and object points we estimate point uncertainties within a sliding bundle adjustment and suggest appropriate camera movements. A visual feedback system communicates the decisions to the user in an intuitive way. We demonstrate the suitability of our system with a virtual image acquisition simulation as well as in real-world scenarios. We show that when following the camera movements suggested by our system, the proposed framework is able to generate good approximate values for the bundle adjustment, leading to accurate results compared to ground truth after few iterations. Possible applications are non-professional 3D acquisition systems on low-cost platforms like mobile phones, autonomously navigating robots as well as online flight planning of unmanned aerial vehicles.

  10. Facial-paralysis diagnostic system based on 3D reconstruction

    NASA Astrophysics Data System (ADS)

    Khairunnisaa, Aida; Basah, Shafriza Nisha; Yazid, Haniza; Basri, Hassrizal Hassan; Yaacob, Sazali; Chin, Lim Chee

    2015-05-01

    The diagnostic process of facial paralysis requires qualitative assessment for the classification and treatment planning. This result is inconsistent assessment that potential affect treatment planning. We developed a facial-paralysis diagnostic system based on 3D reconstruction of RGB and depth data using a standard structured-light camera - Kinect 360 - and implementation of Active Appearance Models (AAM). We also proposed a quantitative assessment for facial paralysis based on triangular model. In this paper, we report on the design and development process, including preliminary experimental results. Our preliminary experimental results demonstrate the feasibility of our quantitative assessment system to diagnose facial paralysis.

  11. Fully automated, high speed, tomographic phase object reconstruction using the transport of intensity equation in transmission and reflection configurations.

    PubMed

    Nguyen, Thanh; Nehmetallah, George; Tran, Dat; Darudi, Ahmad; Soltani, Peyman

    2015-12-10

    While traditional transport of intensity equation (TIE) based phase retrieval of a phase object is performed through axial translation of the CCD, in this work a tunable lens TIE is employed in both transmission and reflection configurations. These configurations are extended to a 360° tomographic 3D reconstruction through multiple illuminations from different angles by a custom fabricated rotating assembly of the phase object. Synchronization circuitry is developed to control the CCD camera and the Arduino board, which in its turn controls the tunable lens and the stepper motor to automate the tomographic reconstruction process. Finally, a MATLAB based user friendly graphical user interface is developed to control the whole system and perform tomographic reconstruction using both multiplicative and inverse radon based techniques.

  12. Expediting model-based optoacoustic reconstructions with tomographic symmetries

    SciTech Connect

    Lutzweiler, Christian; Deán-Ben, Xosé Luís; Razansky, Daniel

    2014-01-15

    Purpose: Image quantification in optoacoustic tomography implies the use of accurate forward models of excitation, propagation, and detection of optoacoustic signals while inversions with high spatial resolution usually involve very large matrices, leading to unreasonably long computation times. The development of fast and memory efficient model-based approaches represents then an important challenge to advance on the quantitative and dynamic imaging capabilities of tomographic optoacoustic imaging. Methods: Herein, a method for simplification and acceleration of model-based inversions, relying on inherent symmetries present in common tomographic acquisition geometries, has been introduced. The method is showcased for the case of cylindrical symmetries by using polar image discretization of the time-domain optoacoustic forward model combined with efficient storage and inversion strategies. Results: The suggested methodology is shown to render fast and accurate model-based inversions in both numerical simulations andpost mortem small animal experiments. In case of a full-view detection scheme, the memory requirements are reduced by one order of magnitude while high-resolution reconstructions are achieved at video rate. Conclusions: By considering the rotational symmetry present in many tomographic optoacoustic imaging systems, the proposed methodology allows exploiting the advantages of model-based algorithms with feasible computational requirements and fast reconstruction times, so that its convenience and general applicability in optoacoustic imaging systems with tomographic symmetries is anticipated.

  13. Hydrodynamic Simulations and Tomographic Reconstructions of the Intergalactic Medium

    NASA Astrophysics Data System (ADS)

    Stark, Casey William

    discuss differences in their convergence behavior, their overall agreement, and the implications for cosmological constraints. In the second part of my thesis, I present a tomographic reconstruction method that allows us to make 3D maps of the IGM with Mpc resolution. In order to make reconstructions of large surveys computationally feasible, I developed a new Wiener Filter application with an algorithm specialized to our problem, which significantly reduces the space and time complexity compared to previous implementations. I explore two scientific applications of the maps: finding protoclusters by searching the maps for large, contiguous regions of low flux and finding cosmic voids by searching the maps for regions of high flux. Using a large N-body simulation, I identify and characterize both protoclusters and voids at z = 2.5, in the middle of the redshift range being mapped by ongoing surveys. I provide simple methods for identifying protocluster and void candidates in the tomographic flux maps, and then test them on mock surveys and reconstructions. I present forecasts for sample purity and completeness and other scientific applications of these large, high-redshift objects.

  14. 3D x-ray reconstruction using lightfield imaging

    NASA Astrophysics Data System (ADS)

    Saha, Sajib; Tahtali, Murat; Lambert, Andrew; Pickering, Mark R.

    2014-09-01

    Existing Computed Tomography (CT) systems require full 360° rotation projections. Using the principles of lightfield imaging, only 4 projections under ideal conditions can be sufficient when the object is illuminated with multiple-point Xray sources. The concept was presented in a previous work with synthetically sampled data from a synthetic phantom. Application to real data requires precise calibration of the physical set up. This current work presents the calibration procedures along with experimental findings for the reconstruction of a physical 3D phantom consisting of simple geometric shapes. The crucial part of this process is to determine the effective distances of the X-ray paths, which are not possible or very difficult by direct measurements. Instead, they are calculated by tracking the positions of fiducial markers under prescribed source and object movements. Iterative algorithms are used for the reconstruction. Customized backprojection is used to ensure better initial guess for the iterative algorithms to start with.

  15. Reconstruction of 3D angiography data using the algebraic reconstruction technique (ART)

    NASA Astrophysics Data System (ADS)

    Hampton, Carnell J.; Hemler, Paul F.

    2001-07-01

    Three-dimensional angiographic reconstrcution has emerged as an alternative to the traditional depiction of aneurysm angioarchitecture provided by 2-D perspective projections acquired by digital subtraction angiography (DSA) and fluoroscopy. One clinical application of research involving 3-D angiographic reconstruction is intraoperative localization and visualization during aneurysm embolization procedures. For this procedure, reconstruction quality is important for the 3-D reconstruction of anatomy as well as for the reconstrucution of intraaneurysm coils imaged endovascularly and subsequently rendered within an existing 3-D anatomic representation. Rotational angiography involves the acquisition of a series of 2-D, cone-beam projections of intracranial anatomy by a rotating x-ray gantry following a single injection of contrast media. Our investigation focuses on the practicality of using methods that employ algebraic reconstruction techniques (ART) to reconstruct 3-D data from 2-D cone-beam projections acquired using rotational angiography during embolization procedures. Important to our investigation are issues that arise within the implementation of the projection, correction and backprojection steps of the reconstruction algorithm that affect reconstruction quality. Several methods are discussed to perform accurate voxel grid projection and backprojection. Various parameters of the reconstruction algorithm implementation are also investigated. Preliminary results indicating that quality 3-D reconstructions from 2-D projections of synthetic volumes are presented. Further modifications to our implementation hold the promise of achieving accurate reconstruction results with a lower computation cost than the algorithm implemention used for this study. We have concluded that methods to extend the traditional ART algorithm for cone-beam projection acquisition produce quality 3-D reconstructions.

  16. Projected restarted framework for tomographic reconstruction

    NASA Astrophysics Data System (ADS)

    He, Wei; Zhang, Guanglei; Pu, Huangsheng; Liu, Fei; Cao, Xu; Bai, Jing; Luo, Jianwen

    2014-09-01

    Fluorescence molecular tomography (FMT) is an important molecular imaging modality developed to reveal the three-dimensional distribution of fluorescent targets using fluorescent measurements and appropriate image reconstruction methods. During the past years, many efforts have been devoted to the development of efficient inverse reconstruction methods for FMT. In this study, a projected restarted framework is proposed, using an inner-outer iteration scheme to compute the nonnegative solutions of the ill-posed non-square linear systems in FMT. In the inner iteration, conventional inverse reconstruction methods are employed to obtain a solution for the residual equation of the original linear system. In the outer iteration, the solution of the original linear system is updated using the results obtained in the inner iteration. Two kinds of projected restarted methods are obtained based on Tikhonov regularization (TR) and Generalized Minimal RESidual (GMRES). Both simulation and phantom studies are carried out to evaluate the performance of the proposed methods in the situation of limited projections, which is very helpful for reducing the acquisition time of fluorescent measurements and suitable for resolving fast biological processes in vivo. Compared with the conventional TR and GMRES needing 36 or even more projections, the projected restarted methods can maintain the image quality when limited projections (n>=4) are employed in the reconstruction. In addition, satisfactory reconstruction results based on the projected restarted methods can be obtained even when high noise level (SNR=20 dB) or closely adjacent targets (edge-to-edge distance between two targets is 0.4 cm) are encountered.

  17. Fast vision-based catheter 3D reconstruction.

    PubMed

    Moradi Dalvand, Mohsen; Nahavandi, Saeid; Howe, Robert D

    2016-07-21

    Continuum robots offer better maneuverability and inherent compliance and are well-suited for surgical applications as catheters, where gentle interaction with the environment is desired. However, sensing their shape and tip position is a challenge as traditional sensors can not be employed in the way they are in rigid robotic manipulators. In this paper, a high speed vision-based shape sensing algorithm for real-time 3D reconstruction of continuum robots based on the views of two arbitrary positioned cameras is presented. The algorithm is based on the closed-form analytical solution of the reconstruction of quadratic curves in 3D space from two arbitrary perspective projections. High-speed image processing algorithms are developed for the segmentation and feature extraction from the images. The proposed algorithms are experimentally validated for accuracy by measuring the tip position, length and bending and orientation angles for known circular and elliptical catheter shaped tubes. Sensitivity analysis is also carried out to evaluate the robustness of the algorithm. Experimental results demonstrate good accuracy (maximum errors of  ±0.6 mm and  ±0.5 deg), performance (200 Hz), and robustness (maximum absolute error of 1.74 mm, 3.64 deg for the added noises) of the proposed high speed algorithms.

  18. Fast vision-based catheter 3D reconstruction

    NASA Astrophysics Data System (ADS)

    Moradi Dalvand, Mohsen; Nahavandi, Saeid; Howe, Robert D.

    2016-07-01

    Continuum robots offer better maneuverability and inherent compliance and are well-suited for surgical applications as catheters, where gentle interaction with the environment is desired. However, sensing their shape and tip position is a challenge as traditional sensors can not be employed in the way they are in rigid robotic manipulators. In this paper, a high speed vision-based shape sensing algorithm for real-time 3D reconstruction of continuum robots based on the views of two arbitrary positioned cameras is presented. The algorithm is based on the closed-form analytical solution of the reconstruction of quadratic curves in 3D space from two arbitrary perspective projections. High-speed image processing algorithms are developed for the segmentation and feature extraction from the images. The proposed algorithms are experimentally validated for accuracy by measuring the tip position, length and bending and orientation angles for known circular and elliptical catheter shaped tubes. Sensitivity analysis is also carried out to evaluate the robustness of the algorithm. Experimental results demonstrate good accuracy (maximum errors of  ±0.6 mm and  ±0.5 deg), performance (200 Hz), and robustness (maximum absolute error of 1.74 mm, 3.64 deg for the added noises) of the proposed high speed algorithms.

  19. Digital 3D facial reconstruction of George Washington

    NASA Astrophysics Data System (ADS)

    Razdan, Anshuman; Schwartz, Jeff; Tocheri, Mathew; Hansford, Dianne

    2006-02-01

    PRISM is a focal point of interdisciplinary research in geometric modeling, computer graphics and visualization at Arizona State University. Many projects in the last ten years have involved laser scanning, geometric modeling and feature extraction from such data as archaeological vessels, bones, human faces, etc. This paper gives a brief overview of a recently completed project on the 3D reconstruction of George Washington (GW). The project brought together forensic anthropologists, digital artists and computer scientists in the 3D digital reconstruction of GW at 57, 45 and 19 including detailed heads and bodies. Although many other scanning projects such as the Michelangelo project have successfully captured fine details via laser scanning, our project took it a step further, i.e. to predict what that individual (in the sculpture) might have looked like both in later and earlier years, specifically the process to account for reverse aging. Our base data was GWs face mask at Morgan Library and Hudons bust of GW at Mount Vernon, both done when GW was 53. Additionally, we scanned the statue at the Capitol in Richmond, VA; various dentures, and other items. Other measurements came from clothing and even portraits of GW. The digital GWs were then milled in high density foam for a studio to complete the work. These will be unveiled at the opening of the new education center at Mt Vernon in fall 2006.

  20. Superiorization of incremental optimization algorithms for statistical tomographic image reconstruction

    NASA Astrophysics Data System (ADS)

    Helou, E. S.; Zibetti, M. V. W.; Miqueles, E. X.

    2017-04-01

    We propose the superiorization of incremental algorithms for tomographic image reconstruction. The resulting methods follow a better path in its way to finding the optimal solution for the maximum likelihood problem in the sense that they are closer to the Pareto optimal curve than the non-superiorized techniques. A new scaled gradient iteration is proposed and three superiorization schemes are evaluated. Theoretical analysis of the methods as well as computational experiments with both synthetic and real data are provided.

  1. Fusion of terrestrial LiDAR and tomographic mapping data for 3D karst landform investigation

    NASA Astrophysics Data System (ADS)

    Höfle, B.; Forbriger, M.; Siart, C.; Nowaczinski, E.

    2012-04-01

    Highly detailed topographic information has gained in importance for studying Earth surface landforms and processes. LiDAR has evolved into the state-of-the-art technology for 3D data acquisition on various scales. This multi-sensor system can be operated on several platforms such as airborne LS (ALS), mobile LS (MLS) from moving vehicles or stationary on ground (terrestrial LS, TLS). In karst research the integral investigation of surface and subsurface components of solution depressions (e.g. sediment-filled dolines) is required to gather and quantify the linked geomorphic processes such as sediment flux and limestone dissolution. To acquire the depth of the different subsurface layers, a combination of seismic refraction tomography (SRT) and electrical resistivity tomography (ERT) is increasingly applied. This multi-method approach allows modeling the extension of different subsurface media (i.e. colluvial fill, epikarst zone and underlying basal bedrock). Subsequent fusion of the complementary techniques - LiDAR surface and tomographic subsurface data - first-time enables 3D prospection and visualization as well as quantification of geomorphometric parameters (e.g. depth, volume, slope and aspect). This study introduces a novel GIS-based method for semi-automated fusion of TLS and geophysical data. The study area is located in the Dikti Mountains of East Crete and covers two adjacent dolines. The TLS data was acquired with a Riegl VZ-400 scanner from 12 scan positions located mainly at the doline divide. The scan positions were co-registered using the iterative closest point (ICP) algorithm of RiSCAN PRO. For the digital elevation rasters a resolution of 0.5 m was defined. The digital surface model (DSM) of the study was derived by moving plane interpolation of all laser points (including objects) using the OPALS software. The digital terrain model (DTM) was generated by iteratively "eroding" objects in the DSM by minimum filter, which additionally accounts for

  2. Imaging of 3-D seismic velocity structure of Southern Sumatra region using double difference tomographic method

    NASA Astrophysics Data System (ADS)

    Lestari, Titik; Nugraha, Andri Dian

    2015-04-01

    Southern Sumatra region has a high level of seismicity due to the influence of the subduction system, Sumatra fault, Mentawai fault and stretching zone activities. The seismic activities of Southern Sumatra region are recorded by Meteorological Climatological and Geophysical Agency (MCGA's) Seismograph network. In this study, we used earthquake data catalog compiled by MCGA for 3013 events from 10 seismic stations around Southern Sumatra region for time periods of April 2009 - April 2014 in order to invert for the 3-D seismic velocities structure (Vp, Vs, and Vp/Vs ratio). We applied double-difference seismic tomography method (tomoDD) to determine Vp, Vs and Vp/Vs ratio with hypocenter adjustment. For the inversion procedure, we started from the initial 1-D seismic velocity model of AK135 and constant Vp/Vs of 1.73. The synthetic travel time from source to receiver was calculated using ray pseudo-bending technique, while the main tomographic inversion was applied using LSQR method. The resolution model was evaluated using checkerboard test and Derivative Weigh Sum (DWS). Our preliminary results show low Vp and Vs anomalies region along Bukit Barisan which is may be associated with weak zone of Sumatran fault and migration of partial melted material. Low velocity anomalies at 30-50 km depth in the fore arc region may indicated the hydrous material circulation because the slab dehydration. We detected low seismic seismicity in the fore arc region that may be indicated as seismic gap. It is coincides contact zone of high and low velocity anomalies. And two large earthquakes (Jambi and Mentawai) also occurred at the contact of contrast velocity.

  3. Imaging of 3-D seismic velocity structure of Southern Sumatra region using double difference tomographic method

    SciTech Connect

    Lestari, Titik; Nugraha, Andri Dian

    2015-04-24

    Southern Sumatra region has a high level of seismicity due to the influence of the subduction system, Sumatra fault, Mentawai fault and stretching zone activities. The seismic activities of Southern Sumatra region are recorded by Meteorological Climatological and Geophysical Agency (MCGA’s) Seismograph network. In this study, we used earthquake data catalog compiled by MCGA for 3013 events from 10 seismic stations around Southern Sumatra region for time periods of April 2009 – April 2014 in order to invert for the 3-D seismic velocities structure (Vp, Vs, and Vp/Vs ratio). We applied double-difference seismic tomography method (tomoDD) to determine Vp, Vs and Vp/Vs ratio with hypocenter adjustment. For the inversion procedure, we started from the initial 1-D seismic velocity model of AK135 and constant Vp/Vs of 1.73. The synthetic travel time from source to receiver was calculated using ray pseudo-bending technique, while the main tomographic inversion was applied using LSQR method. The resolution model was evaluated using checkerboard test and Derivative Weigh Sum (DWS). Our preliminary results show low Vp and Vs anomalies region along Bukit Barisan which is may be associated with weak zone of Sumatran fault and migration of partial melted material. Low velocity anomalies at 30-50 km depth in the fore arc region may indicated the hydrous material circulation because the slab dehydration. We detected low seismic seismicity in the fore arc region that may be indicated as seismic gap. It is coincides contact zone of high and low velocity anomalies. And two large earthquakes (Jambi and Mentawai) also occurred at the contact of contrast velocity.

  4. From Tls Point Clouds to 3d Models of Trees: a Comparison of Existing Algorithms for 3d Tree Reconstruction

    NASA Astrophysics Data System (ADS)

    Bournez, E.; Landes, T.; Saudreau, M.; Kastendeuch, P.; Najjar, G.

    2017-02-01

    3D models of tree geometry are important for numerous studies, such as for urban planning or agricultural studies. In climatology, tree models can be necessary for simulating the cooling effect of trees by estimating their evapotranspiration. The literature shows that the more accurate the 3D structure of a tree is, the more accurate microclimate models are. This is the reason why, since 2013, we have been developing an algorithm for the reconstruction of trees from terrestrial laser scanner (TLS) data, which we call TreeArchitecture. Meanwhile, new promising algorithms dedicated to tree reconstruction have emerged in the literature. In this paper, we assess the capacity of our algorithm and of two others -PlantScan3D and SimpleTree- to reconstruct the 3D structure of trees. The aim of this reconstruction is to be able to characterize the geometric complexity of trees, with different heights, sizes and shapes of branches. Based on a specific surveying workflow with a TLS, we have acquired dense point clouds of six different urban trees, with specific architectures, before reconstructing them with each algorithm. Finally, qualitative and quantitative assessments of the models are performed using reference tree reconstructions and field measurements. Based on this assessment, the advantages and the limits of every reconstruction algorithm are highlighted. Anyway, very satisfying results can be reached for 3D reconstructions of tree topology as well as of tree volume.

  5. Tomographic reconstruction of time-bin-entangled qudits

    NASA Astrophysics Data System (ADS)

    Nowierski, Samantha J.; Oza, Neal N.; Kumar, Prem; Kanter, Gregory S.

    2016-10-01

    We describe an experimental implementation to generate and measure high-dimensional time-bin-entangled qudits. Two-photon time-bin entanglement is generated via spontaneous four-wave mixing in single-mode fiber. Unbalanced Mach-Zehnder interferometers transform selected time bins to polarization entanglement, allowing standard polarization-projective measurements to be used for complete quantum state tomographic reconstruction. Here we generate maximally entangled qubits (d =2 ) , qutrits (d =3 ) , and ququarts (d =4 ) , as well as other phase-modulated nonmaximally entangled qubits and qutrits. We reconstruct and verify all generated states using maximum-likelihood estimation tomography.

  6. Three-dimensional tomographic reconstruction through two-dimensional multiresolution backprojection steps according to Marr's method

    NASA Astrophysics Data System (ADS)

    Stephanakis, Ioannis M.; Anastassopoulos, George C.

    2009-03-01

    A novel algorithm for 3-D tomographic reconstruction is proposed. The proposed algorithm is based on multiresolution techniques for local inversion of the 3-D Radon transform in confined subvolumes within the entire object space. Directional wavelet functions of the form ψm,nj(x)=2j/2ψ(2jwm,nx) are employed in a sequel of double filtering and 2-D backprojection operations performed on vertical and horizontal reconstruction planes using the method suggested by Marr and others. The densities of the 3-D object are found initially as backprojections of coarse wavelet functions of this form at directions on vertical and horizontal planes that intersect the object. As the algorithm evolves, finer planar wavelets intersecting a subvolume of medical interest within the original object may be used to reconstruct its details by double backprojection steps on vertical and horizontal planes in a similar fashion. Reduction in the complexity of the reconstruction algorithm is achieved due to the good localization properties of planar wavelets that render the details of the projections with small errors. Experimental results that illustrate multiresolution reconstruction at four successive levels of resolution are given for wavelets belonging to the Daubechies family.

  7. Colored 3D surface reconstruction using Kinect sensor

    NASA Astrophysics Data System (ADS)

    Guo, Lian-peng; Chen, Xiang-ning; Chen, Ying; Liu, Bin

    2015-03-01

    A colored 3D surface reconstruction method which effectively fuses the information of both depth and color image using Microsoft Kinect is proposed and demonstrated by experiment. Kinect depth images are processed with the improved joint-bilateral filter based on region segmentation which efficiently combines the depth and color data to improve its quality. The registered depth data are integrated to achieve a surface reconstruction through the colored truncated signed distance fields presented in this paper. Finally, the improved ray casting for rendering full colored surface is implemented to estimate color texture of the reconstruction object. Capturing the depth and color images of a toy car, the improved joint-bilateral filter based on region segmentation is used to improve the quality of depth images and the peak signal-to-noise ratio (PSNR) is approximately 4.57 dB, which is better than 1.16 dB of the joint-bilateral filter. The colored construction results of toy car demonstrate the suitability and ability of the proposed method.

  8. Optimization of tomographic reconstruction workflows on geographically distributed resources

    SciTech Connect

    Bicer, Tekin; Gursoy, Doga; Kettimuthu, Rajkumar; De Carlo, Francesco; Foster, Ian T.

    2016-01-01

    New technological advancements in synchrotron light sources enable data acquisitions at unprecedented levels. This emergent trend affects not only the size of the generated data but also the need for larger computational resources. Although beamline scientists and users have access to local computational resources, these are typically limited and can result in extended execution times. Applications that are based on iterative processing as in tomographic reconstruction methods require high-performance compute clusters for timely analysis of data. Here, time-sensitive analysis and processing of Advanced Photon Source data on geographically distributed resources are focused on. Two main challenges are considered: (i) modeling of the performance of tomographic reconstruction workflows and (ii) transparent execution of these workflows on distributed resources. For the former, three main stages are considered: (i) data transfer between storage and computational resources, (i) wait/queue time of reconstruction jobs at compute resources, and (iii) computation of reconstruction tasks. These performance models allow evaluation and estimation of the execution time of any given iterative tomographic reconstruction workflow that runs on geographically distributed resources. For the latter challenge, a workflow management system is built, which can automate the execution of workflows and minimize the user interaction with the underlying infrastructure. The system utilizes Globus to perform secure and efficient data transfer operations. The proposed models and the workflow management system are evaluated by using three high-performance computing and two storage resources, all of which are geographically distributed. Workflows were created with different computational requirements using two compute-intensive tomographic reconstruction algorithms. Experimental evaluation shows that the proposed models and system can be used for selecting the optimum

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

    NASA Astrophysics Data System (ADS)

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

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

  10. Ensemble Neuron Tracer for 3D Neuron Reconstruction.

    PubMed

    Wang, Ching-Wei; Lee, Yu-Ching; Pradana, Hilmil; Zhou, Zhi; Peng, Hanchuan

    2017-02-09

    Tracing of neuron paths is important in neuroscience. Recent studies have shown that it is possible to segment and reconstruct three-dimensional morphology of axons and dendrites using fully automatic neuron tracing methods. A specific tracer may be better than others for a specific dataset, but another tracer could perform better for some other datasets. Ensemble of learners is an effective way to improve learning accuracy in machine learning. We developed automatic ensemble neuron tracers, which consistently perform well on 57 datasets of 5 species collected from 7 laboratories worldwide. Quantitative evaluation based on the data generated by human annotators shows that the proposed ensemble tracers are valuable for 3D neuron tracing and can be widely applied to different datasets.

  11. 3D Lunar Terrain Reconstruction from Apollo Images

    NASA Technical Reports Server (NTRS)

    Broxton, Michael J.; Nefian, Ara V.; Moratto, Zachary; Kim, Taemin; Lundy, Michael; Segal, Alkeksandr V.

    2009-01-01

    Generating accurate three dimensional planetary models is becoming increasingly important as NASA plans manned missions to return to the Moon in the next decade. This paper describes a 3D surface reconstruction system called the Ames Stereo Pipeline that is designed to produce such models automatically by processing orbital stereo imagery. We discuss two important core aspects of this system: (1) refinement of satellite station positions and pose estimates through least squares bundle adjustment; and (2) a stochastic plane fitting algorithm that generalizes the Lucas-Kanade method for optimal matching between stereo pair images.. These techniques allow us to automatically produce seamless, highly accurate digital elevation models from multiple stereo image pairs while significantly reducing the influence of image noise. Our technique is demonstrated on a set of 71 high resolution scanned images from the Apollo 15 mission

  12. Robust 3D reconstruction with an RGB-D camera.

    PubMed

    Wang, Kangkan; Zhang, Guofeng; Bao, Hujun

    2014-11-01

    We present a novel 3D reconstruction approach using a low-cost RGB-D camera such as Microsoft Kinect. Compared with previous methods, our scanning system can work well in challenging cases where there are large repeated textures and significant depth missing problems. For robust registration, we propose to utilize both visual and geometry features and combine SFM technique to enhance the robustness of feature matching and camera pose estimation. In addition, a novel prior-based multicandidates RANSAC is introduced to efficiently estimate the model parameters and significantly speed up the camera pose estimation under multiple correspondence candidates. Even when serious depth missing occurs, our method still can successfully register all frames together. Loop closure also can be robustly detected and handled to eliminate the drift problem. The missing geometry can be completed by combining multiview stereo and mesh deformation techniques. A variety of challenging examples demonstrate the effectiveness of the proposed approach.

  13. Tomographic Reconstruction of Neopterous Carboniferous Insect Nymphs

    PubMed Central

    Garwood, Russell; Ross, Andrew; Sotty, Daniel; Chabard, Dominique; Charbonnier, Sylvain; Sutton, Mark; Withers, Philip J.

    2012-01-01

    Two new polyneopteran insect nymphs from the Montceau-les-Mines Lagerstätte of France are presented. Both are preserved in three dimensions, and are imaged with the aid of X-ray micro-tomography, allowing their morphology to be recovered in unprecedented detail. One–Anebos phrixos gen. et sp. nov.–is of uncertain affinities, and preserves portions of the antennae and eyes, coupled with a heavily spined habitus. The other is a roachoid with long antennae and chewing mouthparts very similar in form to the most generalized mandibulate mouthparts of extant orthopteroid insects. Computer reconstructions reveal limbs in both specimens, allowing identification of the segments and annulation in the tarsus, while poorly developed thoracic wing pads suggest both are young instars. This work describes the morphologically best-known Palaeozoic insect nymphs, allowing a better understanding of the juveniles’ palaeobiology and palaeoecology. We also consider the validity of evidence from Palaeozoic juvenile insects in wing origin theories. The study of juvenile Palaeozoic insects is currently a neglected field, yet these fossils provide direct evidence on the evolution of insect development. It is hoped this study will stimulate a renewed interest in such work. PMID:23049858

  14. The new CORIMP CME catalog & 3D reconstructions

    NASA Astrophysics Data System (ADS)

    Byrne, Jason; Morgan, Huw; Gallagher, Peter; Habbal, Shadia; Davies, Jackie

    2015-04-01

    A new coronal mass ejection catalog has been built from a unique set of coronal image processing techniques, called CORIMP, that overcomes many of the limitations of current catalogs in operation. An online database has been produced for the SOHO/LASCO data and event detections therein; providing information on CME onset time, position angle, angular width, speed, acceleration, and mass, along with kinematic plots and observation movies. The high-fidelity and robustness of these methods and derived CME structure and kinematics will lead to an improved understanding of the dynamics of CMEs, and a realtime version of the algorithm has been implemented to provide CME detection alerts to the interested space weather community. Furthermore, STEREO data has been providing the ability to perform 3D reconstructions of CMEs that are observed in multipoint observations. This allows a determination of the 3D kinematics and morphologies of CMEs characterised in STEREO data via the 'elliptical tie-pointing' technique. The associated observations of SOHO, SDO and PROBA2 (and intended use of K-Cor) provide additional measurements and constraints on the CME analyses in order to improve their accuracy.

  15. 3D imaging reconstruction and impacted third molars: case reports

    PubMed Central

    Tuzi, Andrea; Di Bari, Roberto; Cicconetti, Andrea

    2012-01-01

    Summary There is a debate in the literature about the need for Computed Tomagraphy (CT) before removing third molars, even if positive radiographic signs are present. In few cases, the third molar is so close to the inferior alveolar nerve that its extraction might expose patients to the risk of post-operative neuro-sensitive alterations of the skin and the mucosa of the homolateral lower lip and chin. Thus, the injury of the inferior alveolar nerve may represent a serious, though infrequent, neurologic complication in the surgery of the third molars rendering necessary a careful pre-operative evaluation of their anatomical relationship with the inferior alveolar nerve by means of radiographic imaging techniques. This contribution presents two case reports showing positive radiographic signs, which are the hallmarks of a possible close relationship between the inferior alveolar nerve and the third molars. We aim at better defining the relationship between third molars and the mandibular canal using Dental CT Scan, DICOM image acquisition and 3D reconstruction with a dedicated software. By our study we deduce that 3D images are not indispensable, but they can provide a very agreeable assistance in the most complicated cases. PMID:23386934

  16. Tomographic reconstruction of tissue properties and temperature increase for high-intensity focused ultrasound applications.

    PubMed

    Yin, Lu; Gudur, Madhu Sudhan Reddy; Hsiao, Yi-Sing; Kumon, Ronald E; Deng, Cheri X; Jiang, Huabei

    2013-10-01

    The acoustic and thermal properties as well as the temperature change within a tissue volume during high-intensity focused ultrasound ablation are critically important for treatment planning and monitoring. Described in this article is a tomographic reconstruction method used to determine the tissue properties and increase in temperature in a 3-D volume. On the basis of the iterative finite-element solution to the bioheat equation coupled with Tikhonov regularization techniques, our reconstruction algorithm solves the inverse problem of bioheat transfer and uses the time-dependent temperature measured on a tissue surface to obtain the acoustic absorption coefficient, thermal diffusivity and temperature increase within the subsurface volume. Numerical simulations were performed to validate the reconstruction algorithm. The method was initially conducted in ex vivo experiments in which time-dependent temperature on a tissue surface was measured using high-resolution, non-invasive infrared thermography.

  17. TOMOGRAPHIC RECONSTRUCTION OF TISSUE PROPERTIES AND TEMPERATURE INCREASE FOR HIGH-INTENSITY FOCUSED ULTRASOUND APPLICATIONS

    PubMed Central

    Yin, Lu; Gudur, Madhu Sudhan Reddy; Hsiao, Yi-Sing; Kumon, Ronald E.; Deng, Cheri X.; Jiang, Huabei

    2013-01-01

    The acoustic and thermal properties as well as the temperature change within a tissue volume during high-intensity focused ultrasound ablation are critically important for treatment planning and monitoring. Described in this article is a tomographic reconstruction method used to determine the tissue properties and increase in temperature in a 3-D volume. On the basis of the iterative finite-element solution to the bioheat equation coupled with Tikhonov regularization techniques, our reconstruction algorithm solves the inverse problem of bioheat transfer and uses the time-dependent temperature measured on a tissue surface to obtain the acoustic absorption coefficient, thermal diffusivity and temperature increase within the subsurface volume. Numerical simulations were performed to validate the reconstruction algorithm. The method was initially conducted in ex vivo experiments in which time-dependent temperature on a tissue surface was measured using high-resolution, non-invasive infrared thermography. PMID:23849388

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

    PubMed

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

    2013-12-01

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

  19. 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.

  20. Accurate stochastic reconstruction of heterogeneous microstructures by limited x-ray tomographic projections.

    PubMed

    Li, Hechao; Kaira, Shashank; Mertens, James; Chawla, Nikhilesh; Jiao, Yang

    2016-12-01

    An accurate knowledge of the complex microstructure of a heterogeneous material is crucial for its performance prediction, prognosis and optimization. X-ray tomography has provided a nondestructive means for microstructure characterization in 3D and 4D (i.e. structural evolution over time), in which a material is typically reconstructed from a large number of tomographic projections using filtered-back-projection (FBP) method or algebraic reconstruction techniques (ART). Here, we present in detail a stochastic optimization procedure that enables one to accurately reconstruct material microstructure from a small number of absorption contrast x-ray tomographic projections. This discrete tomography reconstruction procedure is in contrast to the commonly used FBP and ART, which usually requires thousands of projections for accurate microstructure rendition. The utility of our stochastic procedure is first demonstrated by reconstructing a wide class of two-phase heterogeneous materials including sandstone and hard-particle packing from simulated limited-angle projections in both cone-beam and parallel beam projection geometry. It is then applied to reconstruct tailored Sn-sphere-clay-matrix systems from limited-angle cone-beam data obtained via a lab-scale tomography facility at Arizona State University and parallel-beam synchrotron data obtained at Advanced Photon Source, Argonne National Laboratory. In addition, we examine the information content of tomography data by successively incorporating larger number of projections and quantifying the accuracy of the reconstructions. We show that only a small number of projections (e.g. 20-40, depending on the complexity of the microstructure of interest and desired resolution) are necessary for accurate material reconstructions via our stochastic procedure, which indicates its high efficiency in using limited structural information. The ramifications of the stochastic reconstruction procedure in 4D materials science are also

  1. 3D-MSCT imaging of bullet trajectory in 3D crime scene reconstruction: two case reports.

    PubMed

    Colard, T; Delannoy, Y; Bresson, F; Marechal, C; Raul, J S; Hedouin, V

    2013-11-01

    Postmortem investigations are increasingly assisted by three-dimensional multi-slice computed tomography (3D-MSCT) and have become more available to forensic pathologists over the past 20years. In cases of ballistic wounds, 3D-MSCT can provide an accurate description of the bullet location, bone fractures and, more interestingly, a clear visual of the intracorporeal trajectory (bullet track). These forensic medical examinations can be combined with tridimensional bullet trajectory reconstructions created by forensic ballistic experts. These case reports present the implementation of tridimensional methods and the results of 3D crime scene reconstruction in two cases. The authors highlight the value of collaborations between police forensic experts and forensic medicine institutes through the incorporation of 3D-MSCT data in a crime scene reconstruction, which is of great interest in forensic science as a clear visual communication tool between experts and the court.

  2. Proposal of fault-tolerant tomographic image reconstruction

    NASA Astrophysics Data System (ADS)

    Kudo, Hiroyuki; Takaki, Keita; Yamazaki, Fukashi; Nemoto, Takuya

    2016-10-01

    This paper deals with tomographic image reconstruction under the situation where some of projection data bins are contaminated with abnormal data. Such situations occur in various instances of tomography. We propose a new reconstruction algorithm called the Fault-Tolerant reconstruction outlined as follows. The least-squares (L2- norm) error function || Ax- b||22 used in ordinary iterative reconstructions is sensitive to the existence of abnormal data. The proposed algorithm utilizes the L1-norm error function || Ax- b||11 instead of the L2-norm, and we develop a row-action-type iterative algorithm using the proximal splitting framework in convex optimization fields. We also propose an improved version of the L1-norm reconstruction called the L1-TV reconstruction, in which a weak Total Variation (TV) penalty is added to the cost function. Simulation results demonstrate that reconstructed images with the L2-norm were severely damaged by the effect of abnormal bins, whereas images with the L1-norm and L1-TV reconstructions were robust to the existence of abnormal bins.

  3. Cone beam 3D reconstruction with double circular trajectory

    SciTech Connect

    Rizo, P. CEA Centre d'Etudes Nucleaires de Grenoble, 38 . Lab. d'Electronique et de Technologie de l'Informatique); Grangeat, P.; Sire, P.; Lemasson, P. . Lab. d'Electronique et de Technologie de l'Informatique); Delageniere, S. )

    1990-11-01

    In x-ray cone beam tomography the only planar source trajectory which do not produce incomplete data is the infinite line. This kind of source trajectory is not experimentally doable. To ensure a complete data acquisition with cone beam radiographs, a set of non planar trajectory has been studied. Among the trajectories proposed in the literature a simple one is the set of 2 circular trajectories with intersection of the two circular trajectories with intersection of the two trajectory axis. The angle between the two axis is related to the maximum aperture of the cone beam. We propose here an exact method to perform this reconstruction using the 3D radon transform of the object. The modulation transfer function (MTF) of this algorithm remain identical to the MTF on the central slice of reconstruction with single circular trajectory. The density relative mean square error stays within 2% for an aperture of {plus minus}30{degree}. With single circular trajectory the relative mean square error may reach 20% at the same aperture. With double circular trajectory, horizontal artifacts are almost suppressed. 12 refs., 5 figs.

  4. Plasma tomographic reconstruction from tangentially viewing camera with background subtraction

    SciTech Connect

    Odstrčil, M.; Mlynář, J.; Weinzettl, V.; Háček, P.; Verdoolaege, G.; Berta, M.

    2014-01-15

    Light reflections are one of the main and often underestimated issues of plasma emissivity reconstruction in visible light spectral range. Metallic and other specular components of tokamak generate systematic errors in the optical measurements that could lead to wrong interpretation of data. Our analysis is performed at data from the tokamak COMPASS. It is a D-shaped tokamak with specular metallic vessel and possibility of the H-mode plasma. Data from fast visible light camera were used for tomographic reconstruction with background reflections subtraction to study plasma boundary. In this article, we show that despite highly specular tokamak wall, it is possible to obtain a realistic reconstruction. The developed algorithm shows robust results despite of systematic errors in the optical measurements and calibration. The motivation is to obtain an independent estimate of the plasma boundary shape.

  5. 3D-printed haptic "reverse" models for preoperative planning in soft tissue reconstruction: a case report.

    PubMed

    Chae, Michael P; Lin, Frank; Spychal, Robert T; Hunter-Smith, David J; Rozen, Warren Matthew

    2015-02-01

    In reconstructive surgery, preoperative planning is essential for optimal functional and aesthetic outcome. Creating a three-dimensional (3D) model from two-dimensional (2D) imaging data by rapid prototyping has been used in industrial design for decades but has only recently been introduced for medical application. 3D printing is one such technique that is fast, convenient, and relatively affordable. In this report, we present a case in which a reproducible method for producing a 3D-printed "reverse model" representing a skin wound defect was used for flap design and harvesting. This comprised a 82-year-old man with an exposed ankle prosthesis after serial soft tissue debridements for wound infection. Soft tissue coverage and dead-space filling were planned with a composite radial forearm free flap (RFFF). Computed tomographic angiography (CTA) of the donor site (left forearm), recipient site (right ankle), and the left ankle was performed. 2D data from the CTA was 3D-reconstructed using computer software, with a 3D image of the left ankle used as a "control." A 3D model was created by superimposing the left and right ankle images, to create a "reverse image" of the defect, and printed using a 3D printer. The RFFF was thus planned and executed effectively, without complication. To our knowledge, this is the first report of a mechanism of calculating a soft tissue wound defect and producing a 3D model that may be useful for surgical planning. 3D printing and particularly "reverse" modeling may be versatile options in reconstructive planning, and have the potential for broad application.

  6. Objective and subjective quality assessment of geometry compression of reconstructed 3D humans in a 3D virtual room

    NASA Astrophysics Data System (ADS)

    Mekuria, Rufael; Cesar, Pablo; Doumanis, Ioannis; Frisiello, Antonella

    2015-09-01

    Compression of 3D object based video is relevant for 3D Immersive applications. Nevertheless, the perceptual aspects of the degradation introduced by codecs for meshes and point clouds are not well understood. In this paper we evaluate the subjective and objective degradations introduced by such codecs in a state of art 3D immersive virtual room. In the 3D immersive virtual room, users are captured with multiple cameras, and their surfaces are reconstructed as photorealistic colored/textured 3D meshes or point clouds. To test the perceptual effect of compression and transmission, we render degraded versions with different frame rates in different contexts (near/far) in the scene. A quantitative subjective study with 16 users shows that negligible distortion of decoded surfaces compared to the original reconstructions can be achieved in the 3D virtual room. In addition, a qualitative task based analysis in a full prototype field trial shows increased presence, emotion, user and state recognition of the reconstructed 3D Human representation compared to animated computer avatars.

  7. On 3D reconstruction of bubbles in volcanic ash particles

    NASA Astrophysics Data System (ADS)

    Proussevitch, A.; Sahagian, D.; Mulukutla, G.; Kiely, C.

    2007-12-01

    Bubbles in volcanic ash particles are primarily represented by the remnants of films and plateau borders from disrupting foam. Without preservation of complete bubbles, measuring bubble size distributions a challenging task, but one for which we have taken a novel approach. Concavities in ash particles retain a record of bubble sizes in the curvature of their concave surfaces that resulted from bubble fragmentation and quenching during energetic magma eruptions. We have used two methods to measure bubble fragment curvature on the basis of 3D reconstruction of ash particle surfaces. One is based on High Resolution X-Ray Tomography (HRXRT) and the second one is based on stereo images from tilting Scattered Electron Microscopy (SEM). Both methods allow the creation of Digital Elevation Model (DEM) datasets of the ash particle surfaces which in turn are used to identify and measure vertical cross-sectional profiles of the individual bubble fragments ("craters"). Function fit analysis for circular or elliptical functions are applied to each bubble cross sectional profile in two orthogonal directions to reconstruct sizes of the original, complete bubbles. The method allows measurement of submicron (SEM; XUM), micron or larger (HRXRT) bubbles in ash particles. The bubble size distributions so obtained can provide valuable insights regarding magma dynamics and vesiculation that lead to explosive eruptions, as well as the processes of fragmentation in eruption columns. There are no previous systematic information/databases of vesiculation metrics for explosive silicic eruptions, but this new method can be used to produce these and thus provide better insights into prehistoric eruption styles for volcanic hazard assessment.

  8. Multiframe image point matching and 3-d surface reconstruction.

    PubMed

    Tsai, R Y

    1983-02-01

    This paper presents two new methods, the Joint Moment Method (JMM) and the Window Variance Method (WVM), for image matching and 3-D object surface reconstruction using multiple perspective views. The viewing positions and orientations for these perspective views are known a priori, as is usually the case for such applications as robotics and industrial vision as well as close range photogrammetry. Like the conventional two-frame correlation method, the JMM and WVM require finding the extrema of 1-D curves, which are proved to theoretically approach a delta function exponentially as the number of frames increases for the JMM and are much sharper than the two-frame correlation function for both the JMM and the WVM, even when the image point to be matched cannot be easily distinguished from some of the other points. The theoretical findings have been supported by simulations. It is also proved that JMM and WVM are not sensitive to certain radiometric effects. If the same window size is used, the computational complexity for the proposed methods is about n - 1 times that for the two-frame method where n is the number of frames. Simulation results show that the JMM and WVM require smaller windows than the two-frame correlation method with better accuracy, and therefore may even be more computationally feasible than the latter since the computational complexity increases quadratically as a function of the window size.

  9. A maximum entropy reconstruction technique for tomographic particle image velocimetry

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

  10. Evaluation of a multicore-optimized implementation for tomographic reconstruction.

    PubMed

    Agulleiro, Jose-Ignacio; Fernández, José Jesús

    2012-01-01

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

  11. Possibilities and limitations of the ART-Sample algorithm for reconstruction of 3D temperature fields and the influence of opaque obstacles

    PubMed Central

    Li, Yuanyang; Herman, Cila

    2013-01-01

    The need for the measurement of complex, unsteady, three-dimensional (3D) temperature distributions arises in a variety of engineering applications, and tomographic techniques are applied to accomplish this goal. Holographic interferometry (HI), one of the optical methods used for visualizing temperature fields, combined with tomographic reconstruction techniques requires multi-directional interferometric data to recover the 3D information. However, the presence of opaque obstacles (such as solid objects in the flow field and heaters) in the measurement volume, prevents the probing light beams from traversing the entire measurement volume. As a consequence, information on the average value of the field variable will be lost in regions located in the shade of the obstacle. The capability of the ART-Sample tomographic reconstruction method to recover 3D temperature distributions both in unobstructed temperature fields and in the presence of opaque obstacles is discussed in this paper. A computer code for tomographic reconstruction of 3D temperature fields from 2D projections was developed. In the paper, the reconstruction accuracy is discussed quantitatively both without and with obstacles in the measurement volume for a set of phantom functions mimicking realistic temperature distributions. The reconstruction performance is optimized while minimizing the number of irradiation directions (experimental hardware requirements) and computational effort. For the smooth temperature field both with and without obstacles, the reconstructions produced by this algorithm are good, both visually and using quantitative criteria. The results suggest that the location and the size of the obstacle and the number of viewing directions will affect the reconstruction of the temperature field. When the best performance parameters of the ART-Sample algorithm identified in this paper are used to reconstruct the 3D temperature field, the 3D reconstructions with and without obstacle are

  12. 3D reconstruction of the final PHILAE landing site: Abydos

    NASA Astrophysics Data System (ADS)

    Capanna, Claire; Jorda, Laurent; Lamy, Philippe; Gesquière, Gilles; Delmas, Cédric; Durand, Joëlle; Gaudon, Philippe; Jurado, Eric

    2015-11-01

    The Abydos region is the region of the final landing site of the PHILAE lander. The landing site has been potentially identified on images of this region acquired by the OSIRIS imaging system aboard the orbiter before (Oct 22, 2014) and after (Dec 6-13, 2014) the landing of PHILAE (Lamy et al., in prep.). Assuming that this identification is correct, we reconstructed the topography of Abydos in 3D using a method called ``multiresolution photoclinometry by deformation'' (MPCD, Capanna et al., The Visual Computer, 29(6-8): 825-835, 2013). The method works in two steps: (a) a DTM of this region is extracted from the global MPCD shape model, (b) the resulting triangular mesh is progressively deformed at increasing spatial resolution in order to match a set of 14 images of Abydos at pixel resolutions between 1 and 8 m. The method used to perform the image matching is the L-BFGS-b non-linear optimization (Morales et al., ACM Trans. Math. Softw., 38(1): 1-4, 2011).In spite of the very unfavourable illumination conditions, we achieve a vertical accuracy of about 3 m, while the horizontal sampling is 0.5 m. The accuracy is limited by high incidence angles on the images (about 60 deg on average) combined with a complex topography including numerous cliffs and a few overhangs. We also check the compatibility of the local DTM with the images obtained by the CIVA-P instrument aboard PHILAE. If the Lamy et al. identification is correct, our DTM shows that PHILAE landed in a cavity at the bottom of a small cliff of 8 m height.

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  14. Advanced system for 3D dental anatomy reconstruction and 3D tooth movement simulation during orthodontic treatment

    NASA Astrophysics Data System (ADS)

    Monserrat, Carlos; Alcaniz-Raya, Mariano L.; Juan, M. Carmen; Grau Colomer, Vincente; Albalat, Salvador E.

    1997-05-01

    This paper describes a new method for 3D orthodontics treatment simulation developed for an orthodontics planning system (MAGALLANES). We develop an original system for 3D capturing and reconstruction of dental anatomy that avoid use of dental casts in orthodontic treatments. Two original techniques are presented, one direct in which data are acquired directly form patient's mouth by mean of low cost 3D digitizers, and one mixed in which data are obtained by 3D digitizing of hydrocollids molds. FOr this purpose we have designed and manufactured an optimized optical measuring system based on laser structured light. We apply these 3D dental models to simulate 3D movement of teeth, including rotations, during orthodontic treatment. The proposed algorithms enable to quantify the effect of orthodontic appliance on tooth movement. The developed techniques has been integrated in a system named MAGALLANES. This original system present several tools for 3D simulation and planning of orthodontic treatments. The prototype system has been tested in several orthodontic clinic with very good results.

  15. DIII-D Equilibrium Reconstructions with New 3D Magnetic Probes

    NASA Astrophysics Data System (ADS)

    Lao, Lang; Strait, E. J.; Ferraro, N. M.; Ferron, J. R.; King, J. D.; Lee, X.; Meneghini, O.; Turnbull, A. D.; Huang, Y.; Qian, J. G.; Wingen, A.

    2015-11-01

    DIII-D equilibrium reconstructions with the recently installed new 3D magnetic diagnostic are presented. In addition to providing information to allow more accurate 2D reconstructions, the new 3D probes also provide useful information to guide computation of 3D perturbed equilibria. A new more comprehensive magnetic compensation has been implemented. Algorithms are being developed to allow EFIT to reconstruct 3D perturbed equilibria making use of the new 3D probes and plasma responses from 3D MHD codes such as GATO and M3D-C1. To improve the computation efficiency, all inactive probes in one of the toroidal planes in EFIT have been replaced with new probes from other planes. Other 3D efforts include testing of 3D reconstructions using V3FIT and a new 3D variational moment equilibrium code VMOM3D. Other EFIT developments include a GPU EFIT version and new safety factor and MSE-LS constraints. The accuracy and limitation of the new probes for 3D reconstructions will be discussed. Supported by US DOE under DE-FC02-04ER54698 and DE-FG02-95ER54309.

  16. Model-Based Tomographic Reconstruction of Objects Containing Known Components

    PubMed Central

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

    2015-01-01

    The likelihood of finding manufactured components (surgical tools, implants, etc.) within a tomographic field-of-view has been steadily increasing. One reason is the aging population and proliferation of prosthetic devices, such that more people undergoing diagnostic imaging have existing implants, particularly hip and knee implants. Another reason is that use of intraoperative imaging (e.g., cone-beam CT) for surgical guidance is increasing, wherein surgical tools and devices such as screws and plates are placed within or near to the target anatomy. When these components contain metal, the reconstructed volumes are likely to contain severe artifacts that adversely affect the image quality in tissues both near and far from the component. Because physical models of such components exist, there is a unique opportunity to integrate this knowledge into the reconstruction algorithm to reduce these artifacts. We present a model-based penalized-likelihood estimation approach that explicitly incorporates known information about component geometry and composition. The approach uses an alternating maximization method that jointly estimates the anatomy and the position and pose of each of the known components. We demonstrate that the proposed method can produce nearly artifact-free images even near the boundary of a metal implant in simulated vertebral pedicle screw reconstructions and even under conditions of substantial photon starvation. The simultaneous estimation of device pose also provides quantitative information on device placement that could be valuable to quality assurance and verification of treatment delivery. PMID:22614574

  17. Integration of real-time 3D capture, reconstruction, and light-field display

    NASA Astrophysics Data System (ADS)

    Zhang, Zhaoxing; Geng, Zheng; Li, Tuotuo; Pei, Renjing; Liu, Yongchun; Zhang, Xiao

    2015-03-01

    Effective integration of 3D acquisition, reconstruction (modeling) and display technologies into a seamless systems provides augmented experience of visualizing and analyzing real objects and scenes with realistic 3D sensation. Applications can be found in medical imaging, gaming, virtual or augmented reality and hybrid simulations. Although 3D acquisition, reconstruction, and display technologies have gained significant momentum in recent years, there seems a lack of attention on synergistically combining these components into a "end-to-end" 3D visualization system. We designed, built and tested an integrated 3D visualization system that is able to capture in real-time 3D light-field images, perform 3D reconstruction to build 3D model of the objects, and display the 3D model on a large autostereoscopic screen. In this article, we will present our system architecture and component designs, hardware/software implementations, and experimental results. We will elaborate on our recent progress on sparse camera array light-field 3D acquisition, real-time dense 3D reconstruction, and autostereoscopic multi-view 3D display. A prototype is finally presented with test results to illustrate the effectiveness of our proposed integrated 3D visualization system.

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

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

  19. 3D reconstruction of SEM images by use of optical photogrammetry software.

    PubMed

    Eulitz, Mona; Reiss, Gebhard

    2015-08-01

    Reconstruction of the three-dimensional (3D) surface of an object to be examined is widely used for structure analysis in science and many biological questions require information about their true 3D structure. For Scanning Electron Microscopy (SEM) there has been no efficient non-destructive solution for reconstruction of the surface morphology to date. The well-known method of recording stereo pair images generates a 3D stereoscope reconstruction of a section, but not of the complete sample surface. We present a simple and non-destructive method of 3D surface reconstruction from SEM samples based on the principles of optical close range photogrammetry. In optical close range photogrammetry a series of overlapping photos is used to generate a 3D model of the surface of an object. We adapted this method to the special SEM requirements. Instead of moving a detector around the object, the object itself was rotated. A series of overlapping photos was stitched and converted into a 3D model using the software commonly used for optical photogrammetry. A rabbit kidney glomerulus was used to demonstrate the workflow of this adaption. The reconstruction produced a realistic and high-resolution 3D mesh model of the glomerular surface. The study showed that SEM micrographs are suitable for 3D reconstruction by optical photogrammetry. This new approach is a simple and useful method of 3D surface reconstruction and suitable for various applications in research and teaching.

  20. Platform Technologies for Directly Reconstructing 3D Living Biomaterials.

    PubMed

    Jayasinghe, Suwan N; Auguste, Jensen; Scotton, Chris J

    2015-12-16

    Bio-electrospraying and cell electrospinning is explored for reconstructing living biomaterials for regenerative biology and medicine. The investigations carried out in this study demonstrate these approaches as platform biotechnologies for tissue reconstruction for repair, replacement, and rejuvenation of damaged and/or ageing tissues and/or organs.

  1. Tomographic reconstruction of indoor spatial temperature distributions using room impulse responses

    NASA Astrophysics Data System (ADS)

    Bleisteiner, M.; Barth, M.; Raabe, A.

    2016-03-01

    Temperature can be estimated by acoustic travel time measurements along known sound paths. By using a multitude of known sound paths in combination with a tomographic reconstruction technique a spatial and temporal resolution of the temperature field can be achieved. Based on it, this article focuses on an experimental method in order to determine the spatially differentiated development of room temperature with only one loudspeaker and one microphone. The theory of geometrical room acoustics is being used to identify sound paths under consideration of reflections. The travel time along a specific sound path is derived from the room impulse response. Temporal variances in room impulse response can be attributed primarily to a change in air temperature and airflow. It is shown that in the absence of airflow a 3D acoustic monitoring of the room temperature can be realized with a fairly limited use of hardware.

  2. Local motion-compensated method for high-quality 3D coronary artery reconstruction

    PubMed Central

    Liu, Bo; Bai, Xiangzhi; Zhou, Fugen

    2016-01-01

    The 3D reconstruction of coronary artery from X-ray angiograms rotationally acquired on C-arm has great clinical value. While cardiac-gated reconstruction has shown promising results, it suffers from the problem of residual motion. This work proposed a new local motion-compensated reconstruction method to handle this issue. An initial image was firstly reconstructed using a regularized iterative reconstruction method. Then a 3D/2D registration method was proposed to estimate the residual vessel motion. Finally, the residual motion was compensated in the final reconstruction using the extended iterative reconstruction method. Through quantitative evaluation, it was found that high-quality 3D reconstruction could be obtained and the result was comparable to state-of-the-art method. PMID:28018741

  3. Local motion-compensated method for high-quality 3D coronary artery reconstruction.

    PubMed

    Liu, Bo; Bai, Xiangzhi; Zhou, Fugen

    2016-12-01

    The 3D reconstruction of coronary artery from X-ray angiograms rotationally acquired on C-arm has great clinical value. While cardiac-gated reconstruction has shown promising results, it suffers from the problem of residual motion. This work proposed a new local motion-compensated reconstruction method to handle this issue. An initial image was firstly reconstructed using a regularized iterative reconstruction method. Then a 3D/2D registration method was proposed to estimate the residual vessel motion. Finally, the residual motion was compensated in the final reconstruction using the extended iterative reconstruction method. Through quantitative evaluation, it was found that high-quality 3D reconstruction could be obtained and the result was comparable to state-of-the-art method.

  4. The European-Alpine collision during the last 45Myrs - constraints obtained from comparing 3-D numerical subduction models and tomographic observations

    NASA Astrophysics Data System (ADS)

    Morra, G.; Regenauer-Lieb, K.; Kissling, E.; Lippitsch, R.

    2003-04-01

    We analyze the interaction of Adriatic and the European Plates driven self-consistently by slab pull in order to seperate out the roles of (1) intrinsic dynamics of the slab driven Adriatic microplate system, (2) interaction with the subducting European plate, (3) the pushing African plate and (4) the feedback of slab induced flow within the mantle. The simulation is based on a new three-dimensional solid-fluid solver that we developed for plate tectonics reconstruction. The method embeds a Lagrangian Finite Element model of the lithosphere into a creeping medium (Stokeslet Method see poster) representing the mantle. Density inhomogeneities within the subducting plate are inserted to obtain realistic reconstructions of tomographically observed slab lengths in both the Central Mediterranean and European-Alpine subduction systems. In a first step we analyse the system in the absence of the African convergence. With this asssumption the model is only driven by gravity and thus gives an insight into the internal dynamics of the Central-European microplate evolution. In a second step we add the African convergence as a large scale distributed force. Using this method the mechanical origin of rotation of the Adriatic microplate in the vise of the African-European convergence can be analysed and its impact on the collision in the Alps derived. While our solution space is a first set, the aim of the analysis is to obtain constraints of the history of Adriatic-European collision using the new solver as a toolbox. The method has the potential to act as a filter between geological observation, tomographic data and mechanical constraints within the framework of a dynamic 3-D plate tectonic evolution.

  5. Tomographic reconstruction using 4 views and tunable diode laser

    NASA Astrophysics Data System (ADS)

    Osborn Oliver, M.; T. M., Muruganandam

    2016-11-01

    Called the 'Reduced Back Projection' technique(or RBP), this new method is an improvement on existing tomographic reconstruction techniques in the field of laser diagnostics on a combustor exhaust. The highlight of this technique is the use of only FOUR views to create a planar reconstruction from path averaged data which is obtained from water absorption spectroscopy in the IR region near 1373nm. Water sensitive wavelengths are generated by using a Tunable Diode laser working in the IR region. For the purpose of this paper, work is done on a plane in the exhaust of a burner perpendicular to the flame direction. The geometry of the burner decides the distribution of water molecules in the interrogation plane. This technique is based on the back projection method but has been extensively modified and improved to work with just four views instead of the hundred or so views used in medical tomography. Simulations have been run to check the working of the new technique and compared with other current methods in tomography (SART, back projection, etc..). Preliminary experimentation over a simple two burner geometry has been performed. In both simulation and experiment, the RBP technique has yielded better results than existing methods by virtue of the new method being able to capture features where the other methods have failed. Thus, RBP can be applied to situations where resources, time and spatial constraints exist.

  6. Correction for acoustic attenuation effects in optoacoustic tomographic reconstructions

    NASA Astrophysics Data System (ADS)

    Deán-Ben, X. Luís; Razansky, Daniel; Ntziachristos, Vasilis

    2011-07-01

    The feasibility of correcting for the effects of acoustic attenuation in optoacoustic tomographic reconstructions obtained with model-based inversion is shown in this work. Acoustic attenuation is a physical phenomenon that takes place inevitably in actual acoustic media and becomes significant at high ultrasonic frequencies. The frequency dependence of acoustic attenuation and the associated dispersion lead to reduction of amplitude and broadening of the optoacoustic signals, which in turn cause, respectively, quantification errors and loss of resolution in the reconstructed images. In this work we imaged an agar phantom with embedded microparticles in three different scenarios, namely with the signals acquired with no attenuation, with the signals collected by placing an attenuating sample in between the phantom and the ultrasonic transducer and with the signals corrected for the effects of acoustic attenuation. The results obtained show that the quantification inaccuracies and the loss of resolution of the images can be partially corrected at the expense of introducing noise at high spatial frequencies due to the amplification of the high frequency components of the noise in the signals.

  7. High Resolution 3-D Tomographic Imaging by Wavelength and Polarization Diversity.

    DTIC Science & Technology

    1983-07-05

    case of lensless Fourier transform hologram discussed in [42]). This is so because not all projections of a shallow cap are extended in area and...unprecedented resolutions. The TDR technique results in a recording arrangement that yields what can be regarded as a 3-D lensless Fourier transform hologram...Electron Microscopy by Reduction to Two Dimensional Holographic Implementation", Trans. Amer. Crystal. Assoc., Vol. 12, pp. 27-41, 1976. 17. H.H

  8. Photogrammetry for rapid prototyping: development of noncontact 3D reconstruction technologies

    NASA Astrophysics Data System (ADS)

    Knyaz, Vladimir A.

    2002-04-01

    An important stage of rapid prototyping technology is generating computer 3D model of an object to be reproduced. Wide variety of techniques for 3D model generation exists beginning with manual 3D models generation and finishing with full-automated reverse engineering system. The progress in CCD sensors and computers provides the background for integration of photogrammetry as an accurate 3D data source with CAD/CAM. The paper presents the results of developing photogrammetric methods for non-contact spatial coordinates measurements and generation of computer 3D model of real objects. The technology is based on object convergent images processing for calculating its 3D coordinates and surface reconstruction. The hardware used for spatial coordinates measurements is based on PC as central processing unit and video camera as image acquisition device. The original software for Windows 9X realizes the complete technology of 3D reconstruction for rapid input of geometry data in CAD/CAM systems. Technical characteristics of developed systems are given along with the results of applying for various tasks of 3D reconstruction. The paper describes the techniques used for non-contact measurements and the methods providing metric characteristics of reconstructed 3D model. Also the results of system application for 3D reconstruction of complex industrial objects are presented.

  9. Automated reconstruction of 3D scenes from sequences of images

    NASA Astrophysics Data System (ADS)

    Pollefeys, M.; Koch, R.; Vergauwen, M.; Van Gool, L.

    Modelling of 3D objects from image sequences is a challenging problem and has been an important research topic in the areas of photogrammetry and computer vision for many years. In this paper, a system is presented which automatically extracts a textured 3D surface model from a sequence of images of a scene. The system can deal with unknown camera settings. In addition, the parameters of this camera are allowed to change during acquisition (e.g., by zooming or focusing). No prior knowledge about the scene is necessary to build the 3D models. Therefore, this system offers a high degree of flexibility. The system is based on state-of-the-art algorithms recently developed in computer vision. The 3D modelling task is decomposed into a number of successive steps. Gradually, more knowledge of the scene and the camera setup is retrieved. At this point, the obtained accuracy is not yet at the level required for most metrology applications, but the visual quality is very convincing. This system has been applied to a number of applications in archaeology. The Roman site of Sagalassos (southwest Turkey) was used as a test case to illustrate the potential of this new approach.

  10. The New Approach to Sport Medicine: 3-D Reconstruction

    ERIC Educational Resources Information Center

    Ince, Alparslan

    2015-01-01

    The aim of this study is to present a new approach to sport medicine. Comparative analysis of the Vertebrae Lumbales was done in sedentary group and Muay Thai athletes. It was done by acquiring three dimensional (3-D) data and models through photogrammetric methods from the Multi-detector Computerized Tomography (MDCT) images of the Vertebrae…

  11. Computerized 3-D reconstruction of complicated anatomical structure

    NASA Astrophysics Data System (ADS)

    Andreasen, Arne; Drewes, Asbjorn M.; Assentoft, Joergen E.

    1992-06-01

    In the study of the rabbit hippocampal region, images of 430 serial sections were aligned by a `parameter-shift' algorithm. The resulting 3-D matrix represents a fixed and stained but `whole' rabbit brain. From this virtual object the slice procedure, displacement, and re- alignment could be computer simulated and the artifacts associated with these procedures estimated.

  12. Robust 3D reconstruction system for human jaw modeling

    NASA Astrophysics Data System (ADS)

    Yamany, Sameh M.; Farag, Aly A.; Tazman, David; Farman, Allan G.

    1999-03-01

    This paper presents a model-based vision system for dentistry that will replace traditional approaches used in diagnosis, treatment planning and surgical simulation. Dentistry requires accurate 3D representation of the teeth and jaws for many diagnostic and treatment purposes. For example orthodontic treatment involves the application of force systems to teeth over time to correct malocclusion. In order to evaluate tooth movement progress, the orthodontists monitors this movement by means of visual inspection, intraoral measurements, fabrication of plastic models, photographs and radiographs, a process which is both costly and time consuming. In this paper an integrate system has been developed to record the patient's occlusion using computer vision. Data is acquired with an intraoral video camera. A modified shape from shading (SFS) technique, using perspective projection and camera calibration, is used to extract accurate 3D information from a sequence of 2D images of the jaw. A new technique for 3D data registration, using a Grid Closest Point transform and genetic algorithms, is used to register the SFS output. Triangulization is then performed, and a solid 3D model is obtained via a rapid prototype machine.

  13. Online reconstruction of 3D magnetic particle imaging data

    NASA Astrophysics Data System (ADS)

    Knopp, T.; Hofmann, M.

    2016-06-01

    Magnetic particle imaging is a quantitative functional imaging technique that allows imaging of the spatial distribution of super-paramagnetic iron oxide particles at high temporal resolution. The raw data acquisition can be performed at frame rates of more than 40 volumes s-1. However, to date image reconstruction is performed in an offline step and thus no direct feedback is available during the experiment. Considering potential interventional applications such direct feedback would be mandatory. In this work, an online reconstruction framework is implemented that allows direct visualization of the particle distribution on the screen of the acquisition computer with a latency of about 2 s. The reconstruction process is adaptive and performs block-averaging in order to optimize the signal quality for a given amount of reconstruction time.

  14. High-resolution reconstruction for 3D SPECT

    NASA Astrophysics Data System (ADS)

    Li, Tianfang; Wen, Junhai; Lu, Hongbing; Li, Xiang; Liang, Zhengrong

    2003-05-01

    In this work, we have developed a new method for SPECT (single photon emission computed tomography) image reconstruction, which has shown the potential to provide higher resolution results than any other conventional methods using the same projection data. Unlike the conventional FBP- (filtered backprojection) and EM- (expectation maximization) type algorithms, we utilize as much system response information as we can during the reconstruction process. This information can be pre-measured during the calibration process and stored in the computer. By selecting different sampling schemes for the point response measurement, different system kernel matrices are obtained. Reconstruction utilizing these kernels generates a set of reconstructed images of the same source. Based on these reconstructed images and their corresponding sampling schemes, we are able to achieve a high resolution final image that best represents the object. Because a uniform attenuation, resolution variation and some other effects are included during the formation of the system kernel matrices, the reconstruction from the acquired projection data also compensates for all these effects correctly.

  15. Research in Image Understanding as Applied to 3-D Microwave Tomographic Imaging with Near Optical Resolution.

    DTIC Science & Technology

    1987-03-01

    Inverse Scattering", Presented at the First Dennis Gabor Memorial Symposium, Technion City, Haifa, Israel, March, 1980. 3. "Radar Imaging" California Inst...Wiley & Sons, New York, 1983 [14] Gabor T. Herman, Image Reconstruction from Projections, Academic Press, New York, 1980 [15] T. H. Chu, N. H. Farhat

  16. Performance analysis of different surface reconstruction algorithms for 3D reconstruction of outdoor objects from their digital images.

    PubMed

    Maiti, Abhik; Chakravarty, Debashish

    2016-01-01

    3D reconstruction of geo-objects from their digital images is a time-efficient and convenient way of studying the structural features of the object being modelled. This paper presents a 3D reconstruction methodology which can be used to generate photo-realistic 3D watertight surface of different irregular shaped objects, from digital image sequences of the objects. The 3D reconstruction approach described here is robust, simplistic and can be readily used in reconstructing watertight 3D surface of any object from its digital image sequence. Here, digital images of different objects are used to build sparse, followed by dense 3D point clouds of the objects. These image-obtained point clouds are then used for generation of photo-realistic 3D surfaces, using different surface reconstruction algorithms such as Poisson reconstruction and Ball-pivoting algorithm. Different control parameters of these algorithms are identified, which affect the quality and computation time of the reconstructed 3D surface. The effects of these control parameters in generation of 3D surface from point clouds of different density are studied. It is shown that the reconstructed surface quality of Poisson reconstruction depends on Samples per node (SN) significantly, greater SN values resulting in better quality surfaces. Also, the quality of the 3D surface generated using Ball-Pivoting algorithm is found to be highly depend upon Clustering radius and Angle threshold values. The results obtained from this study give the readers of the article a valuable insight into the effects of different control parameters on determining the reconstructed surface quality.

  17. Variational approach to reconstruct surface from sparse and nonparallel contours in freehand 3D ultrasound imaging

    NASA Astrophysics Data System (ADS)

    Deng, Shuangcheng; Jiang, Lipei; Cao, Yingyu; Zhang, Junwen; Zheng, Haiyang

    2012-01-01

    The 3D reconstruction for freehand 3D ultrasound is a challenging issue because the recorded B-scans are not only sparse, but also non-parallel (actually they may intersect each other). Conventional volume reconstruction methods can't reconstruct sparse data efficiently while not introducing geometrical artifacts, and conventional surface reconstruction methods can't reconstruct surfaces from contours that are arbitrarily oriented in 3D space. We developed a new surface reconstruction method for freehand 3D ultrasound. It is based on variational implicit function which is presented by Greg Turk for shape transformation. In the new method, we first constructed on- & off-surface constraints from the segmented contours of all recorded B-scans, then used a variational interpolation technique to get a single implicit function in 3D. Finally, the implicit function was evaluated to extract the zero-valued surface as reconstruction result. Two experiment was conducted to assess our variational surface reconstruction method, and the experiment results have shown that the new method is capable of reconstructing surface smoothly from sparse contours which can be arbitrarily oriented in 3D space.

  18. Full-wave Moment Tensor and Tomographic Inversions Based on 3D Strain Green Tensor

    DTIC Science & Technology

    2010-01-31

    G. Jahnke, Wave propagation in 3D spherical sections: effects of subduction zones , Phys. Earth Planet. Inter., 132, 219-234, 2002. Komastitsch, D...is at scales smaller than the Fresnel zone . For example, a 1-Hz P/Pn wave recorded by a receiver ~1000 km from the source has a Fresnel zone width...approach, Eos Trans. AGU, 89(53), Fall Meet. Suppl., abstract T11E-06 Invited, 2008b. Sigloch, K., N. McQuarrie, G. Nolet, Two-stage subduction

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

    PubMed

    Agulleiro, Jose-Ignacio; Fernandez, Jose-Jesus

    2015-06-01

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

  20. 3D reconstruction of tropospheric cirrus clouds by stereovision system

    NASA Astrophysics Data System (ADS)

    Nadjib Kouahla, Mohamed; Moreels, Guy; Seridi, Hamid

    2016-07-01

    A stereo imaging method is applied to measure the altitude of cirrus clouds and provide a 3D map of the altitude of the layer centroid. They are located in the high troposphere and, sometimes in the lower stratosphere, between 6 and 10 km high. Two simultaneous images of the same scene are taken with Canon cameras (400D) in two sites distant of 37 Km. Each image processed in order to invert the perspective effect and provide a satellite-type view of the layer. Pairs of matched points that correspond to a physical emissive point in the common area are identified in calculating a correlation coefficient (ZNCC: Zero mean Normalized Cross-correlation or ZSSD: as Zero mean Sum of Squared Differences). This method is suitable for obtaining 3D representations in the case of low-contrast objects. An observational campaign was conducted in June 2014 in France. The images were taken simultaneously at Marnay (47°17'31.5" N, 5°44'58.8" E; altitude 275 m) 25 km northwest of Besancon and in Mont poupet (46°58'31.5" N, 5°52'22.7" E; altitude 600 m) southwest of Besancon at 43 km. 3D maps of the Natural cirrus clouds and artificial like "aircraft trails" are retrieved. They are compared with pseudo-relief intensity maps of the same region. The mean altitude of the cirrus barycenter is located at 8.5 ± 1km on June 11.

  1. 3-D Reconstruction From 2-D Radiographic Images and Its Application to Clinical Veterinary Medicine

    NASA Astrophysics Data System (ADS)

    Hamamoto, Kazuhiko; Sato, Motoyoshi

    3D imaging technique is very important and indispensable in diagnosis. The main stream of the technique is one in which 3D image is reconstructed from a set of slice images, such as X-ray CT and MRI. However, these systems require large space and high costs. On the other hand, a low cost and small size 3D imaging system is needed in clinical veterinary medicine, for example, in the case of diagnosis in X-ray car or pasture area. We propose a novel 3D imaging technique using 2-D X-ray radiographic images. This system can be realized by cheaper system than X-ray CT and enables to get 3D image in X-ray car or portable X-ray equipment. In this paper, a 3D visualization technique from 2-D radiographic images is proposed and several reconstructions are shown. These reconstructions are evaluated by veterinarians.

  2. Algebraic filter approach for fast approximation of nonlinear tomographic reconstruction methods

    NASA Astrophysics Data System (ADS)

    Plantagie, Linda; Batenburg, Kees Joost

    2015-01-01

    We present a computational approach for fast approximation of nonlinear tomographic reconstruction methods by filtered backprojection (FBP) methods. Algebraic reconstruction algorithms are the methods of choice in a wide range of tomographic applications, yet they require significant computation time, restricting their usefulness. We build upon recent work on the approximation of linear algebraic reconstruction methods and extend the approach to the approximation of nonlinear reconstruction methods which are common in practice. We demonstrate that if a blueprint image is available that is sufficiently similar to the scanned object, our approach can compute reconstructions that approximate iterative nonlinear methods, yet have the same speed as FBP.

  3. 3-D reconstruction of neurons from multichannel confocal laser scanning image series.

    PubMed

    Wouterlood, Floris G

    2005-08-01

    A confocal laser scanning microscope (CLSM) collects information from a thin, focal plane and ignores out-of-focus information. The operator configures separate channels (laser, filters, detector settings) for each fluorochrome used in a particular experiment. Then, 3-D reconstructions are made from Z-series of confocal images: one series per channel. Channel signal separation is extremely important and measures to avoid bleaching are vital. Post-acquisition deconvolution of the image series is then performed to increase resolution. In the 3-D reconstruction program described in this unit, reconstructions can be inspected in real time from any viewing angle. By altering viewing angles and by switching channels off and on, the spatial relationship of 3-D-reconstructed structures with respect to structures seen in other channels can be studied. Since each brand of CLSM, computer program, and 3-D reconstruction package has its own proprietary set of procedures, a general approach is provided wherever possible.

  4. [Upper airway's 3D analysis of patients with obstructive sleep apnea using tomographic cone beam].

    PubMed

    Bruwier, A; Poirrier, A L; Limme, M; Poirrier, R

    2014-12-01

    The progress of medical imaging over the last decades has led to a better understanding of the upper airway structure in sleep-disordered patients. The Obstructive Sleep Apnea Syndrome (OSA) is attributed to a functional narrowing of the upper airway, particularly of the oropharynx, during sleep. This narrowing is multifactorial. We have shown that in 60% cases, the maxilla (nasal pyramid) seems too narrow. A mandible retroposition may also play a dominant role in 30% of the cases. Both scenarios can be combined. Cone Beam Computed Tomography (CBCT) is a new medical imaging technique that permits to visualize the upper airway with less ionizing radiation than the conventional scanner. To date, only five authors have performed an upper airway's 3D analysis of sleep apnea patients with cone beam. A better understanding of the affected segment of the upper airway should help refine treatment options.

  5. Optic flow aided navigation and 3D scene reconstruction

    NASA Astrophysics Data System (ADS)

    Rollason, Malcolm

    2013-10-01

    An important enabler for low cost airborne systems is the ability to exploit low cost inertial instruments. An Inertial Navigation System (INS) can provide a navigation solution, when GPS is denied, by integrating measurements from inertial sensors. However, the gyrometer and accelerometer biases of low cost inertial sensors cause compound errors in the integrated navigation solution. This paper describes experiments to establish whether (and to what extent) the navigation solution can be aided by fusing measurements from an on-board video camera with measurements from the inertial sensors. The primary aim of the work was to establish whether optic flow aided navigation is beneficial even when the 3D structure within the observed scene is unknown. A further aim was to investigate whether an INS can help to infer 3D scene content from video. Experiments with both real and synthetic data have been conducted. Real data was collected using an AR Parrot quadrotor. Empirical results illustrate that optic flow provides a useful aid to navigation even when the 3D structure of the observed scene is not known. With optic flow aiding of the INS, the computed trajectory is consistent with the true camera motion, whereas the unaided INS yields a rapidly increasing position error (the data represents ~40 seconds, after which the unaided INS is ~50 metres in error and has passed through the ground). The results of the Monte Carlo simulation concur with the empirical result. Position errors, which grow as a quadratic function of time when unaided, are substantially checked by the availability of optic flow measurements.

  6. 3D model tools for architecture and archaeology reconstruction

    NASA Astrophysics Data System (ADS)

    Vlad, Ioan; Herban, Ioan Sorin; Stoian, Mircea; Vilceanu, Clara-Beatrice

    2016-06-01

    The main objective of architectural and patrimonial survey is to provide a precise documentation of the status quo of the surveyed objects (monuments, buildings, archaeological object and sites) for preservation and protection, for scientific studies and restoration purposes, for the presentation to the general public. Cultural heritage documentation includes an interdisciplinary approach having as purpose an overall understanding of the object itself and an integration of the information which characterize it. The accuracy and the precision of the model are directly influenced by the quality of the measurements realized on field and by the quality of the software. The software is in the process of continuous development, which brings many improvements. On the other side, compared to aerial photogrammetry, close range photogrammetry and particularly architectural photogrammetry is not limited to vertical photographs with special cameras. The methodology of terrestrial photogrammetry has changed significantly and various photographic acquisitions are widely in use. In this context, the present paper brings forward a comparative study of TLS (Terrestrial Laser Scanner) and digital photogrammetry for 3D modeling. The authors take into account the accuracy of the 3D models obtained, the overall costs involved for each technology and method and the 4th dimension - time. The paper proves its applicability as photogrammetric technologies are nowadays used at a large scale for obtaining the 3D model of cultural heritage objects, efficacious in their assessment and monitoring, thus contributing to historic conservation. Its importance also lies in highlighting the advantages and disadvantages of each method used - very important issue for both the industrial and scientific segment when facing decisions such as in which technology to invest more research and funds.

  7. 3-D seismic tomographic modelling of the crustal structure of northwestern Svalbard based on deep seismic soundings

    NASA Astrophysics Data System (ADS)

    Czuba, Wojciech

    2016-11-01

    Wide angle refraction and reflection measurements were carried out in the passive continental margin zone of the northwestern Svalbard during several expeditions in 1978-1999. Data from a set of 2-D archival and modern seismic profiles recorded in-line and off-line, and from an additional permanent seismic station, were altogether used for seismic modelling of the crustal structure of the study area. Seismic arrivals (airgun and chemical explosive sources) were recorded by land (onshore) seismic stations, ocean bottom seismometers (OBS), and ocean bottom hydrophone stations (OBH). Good quality refracted and reflected P waves have provided an excellent data base for a seismic modelling. Chemical explosive sources were recorded even up to 300 km distances. The 3-D tomographic inversion method was applied. The results are comparable to the earlier 2-D modelling. Additional off-line information allowed to develop a 3-D image of the crustal structure. The continental crust thins to the west and north. A minimum depth of about 6 km to the Moho interface was determined east of the Molloy Deep and in the Knipovich Ridge. The Moho discontinuity deepens down to about 30 km below the continental crust of Spitsbergen.

  8. 3-D seismic tomographic modelling of the crustal structure of northwestern Svalbard based on deep seismic soundings

    NASA Astrophysics Data System (ADS)

    Czuba, Wojciech

    2017-01-01

    Wide angle refraction and reflection measurements were carried out in the passive continental margin zone of the northwestern Svalbard during several expeditions in 1978-1999. Data from a set of 2-D archival and modern seismic profiles recorded in-line and off-line, and from an additional permanent seismic station, were altogether used for seismic modelling of the crustal structure of the study area. Seismic arrivals (airgun and chemical explosive sources) were recorded by land (onshore) seismic stations, ocean bottom seismometers (OBS), and ocean bottom hydrophone stations (OBH). Good quality refracted and reflected P waves have provided an excellent data base for a seismic modelling. Chemical explosive sources were recorded even up to 300 km distances. The 3-D tomographic inversion method was applied. The results are comparable to the earlier 2-D modelling. Additional off-line information allowed to develop a 3-D image of the crustal structure. The continental crust thins to the west and north. A minimum depth of about 6 km to the Moho interface was determined east of the Molloy Deep and in the Knipovich Ridge. The Moho discontinuity deepens down to about 30 km below the continental crust of Spitsbergen.

  9. Impact of Cn2 profile on tomographic reconstruction performance: application to E-ELT wide field AO systems

    NASA Astrophysics Data System (ADS)

    Costille, A.; Fusco, T.

    2012-07-01

    New techniques of Adaptive Optics (AO), generically called Wide Field AO, have been developed in the frame of the design study for new instruments for Extremely Large Telescopes (ELI). Concepts such as Multi-Conjugate AO are based on a tomographic reconstruction of the turbulent volume followed by a projection onto DM(s) in order to ensure a good correction in a large Field of View. These systems require a 3D phase reconstruction and a statistical representation of the turbulent volume through the knowledge of the Cn2 profile, which has a strong impact on performance. We focus our study on the analysis of the impact of the structure and the parameters, which define the Cn2 profile, on the performance of a given tomographic system for an ELI. In this article, we perform simulation to emphasize the terms which are directly linked to the knowledge of the true input Cn2 profile, which simulates the input turbulent perturbations, and to the Cn2 profile which is used as a model in the reconstruction process. We determine and discuss the level of the accuracy needed on the Cn2 profile to limit the tomographic error term and to ensure a good performance. We show that a good sampling of the input turbulence is required to ensure performance of the system.

  10. 3D reconstruction software comparison for short sequences

    NASA Astrophysics Data System (ADS)

    Strupczewski, Adam; Czupryński, BłaŻej

    2014-11-01

    Large scale multiview reconstruction is recently a very popular area of research. There are many open source tools that can be downloaded and run on a personal computer. However, there are few, if any, comparisons between all the available software in terms of accuracy on small datasets that a single user can create. The typical datasets for testing of the software are archeological sites or cities, comprising thousands of images. This paper presents a comparison of currently available open source multiview reconstruction software for small datasets. It also compares the open source solutions with a simple structure from motion pipeline developed by the authors from scratch with the use of OpenCV and Eigen libraries.

  11. New method to analyze internal disruptions with tomographic reconstructions

    NASA Astrophysics Data System (ADS)

    Tanzi, C. P.; de Blank, H. J.

    1997-03-01

    Sawtooth crashes have been investigated on the Rijnhuizen Tokamak Project (RTP) [N. J. Lopes Cardozo et al., Proceedings of the 14th International Conference on Plasma Physics and Controlled Nuclear Fusion Research, Würzburg, 1992 (International Atomic Energy Agency, Vienna, 1993), Vol. 1, p. 271]. Internal disruptions in tokamak plasmas often exhibit an m=1 poloidal mode structure prior to the collapse which can be clearly identified by means of multicamera soft x-ray diagnostics. In this paper tomographic reconstructions of such m=1 modes are analyzed with a new method, based on magnetohydrodynamic (MHD) invariants computed from the two-dimensional emissivity profiles, which quantifies the amount of profile flattening not only after the crash but also during the precursor oscillations. The results are interpreted by comparing them with two models which simulate the measurements of the m=1 redistribution of soft x-ray emissivity prior to the sawtooth crash. One model is based on the magnetic reconnection model of Kadomtsev. The other involves ideal MHD motion only. In cases where differences in magnetic topology between the two models cannot be seen in the tomograms, the analysis of profile flattening has an advantage. The analysis shows that in RTP the clearly observed m=1 displacement of some sawteeth requires the presence of convective ideal MHD motion, whereas other precursors are consistent with magnetic reconnection of up to 75% of the magnetic flux within the q=1 surface. The possibility of ideal interchange combined with enhanced cross-field transport is not excluded.

  12. Assessing 3D tunnel position in ACL reconstruction using a novel single image 3D-2D registration

    NASA Astrophysics Data System (ADS)

    Kang, X.; Yau, W. P.; Otake, Y.; Cheung, P. Y. S.; Hu, Y.; Taylor, R. H.

    2012-02-01

    The routinely used procedure for evaluating tunnel positions following anterior cruciate ligament (ACL) reconstructions based on standard X-ray images is known to pose difficulties in terms of obtaining accurate measures, especially in providing three-dimensional tunnel positions. This is largely due to the variability in individual knee joint pose relative to X-ray plates. Accurate results were reported using postoperative CT. However, its extensive usage in clinical routine is hampered by its major requirement of having CT scans of individual patients, which is not available for most ACL reconstructions. These difficulties are addressed through the proposed method, which aligns a knee model to X-ray images using our novel single-image 3D-2D registration method and then estimates the 3D tunnel position. In the proposed method, the alignment is achieved by using a novel contour-based 3D-2D registration method wherein image contours are treated as a set of oriented points. However, instead of using some form of orientation weighting function and multiplying it with a distance function, we formulate the 3D-2D registration as a probability density estimation using a mixture of von Mises-Fisher-Gaussian (vMFG) distributions and solve it through an expectation maximization (EM) algorithm. Compared with the ground-truth established from postoperative CT, our registration method in an experiment using a plastic phantom showed accurate results with errors of (-0.43°+/-1.19°, 0.45°+/-2.17°, 0.23°+/-1.05°) and (0.03+/-0.55, -0.03+/-0.54, -2.73+/-1.64) mm. As for the entry point of the ACL tunnel, one of the key measurements, it was obtained with high accuracy of 0.53+/-0.30 mm distance errors.

  13. Image reconstruction for a Positron Emission Tomograph optimized for breast cancer imaging

    SciTech Connect

    Virador, Patrick R.G.

    2000-04-01

    The author performs image reconstruction for a novel Positron Emission Tomography camera that is optimized for breast cancer imaging. This work addresses for the first time, the problem of fully-3D, tomographic reconstruction using a septa-less, stationary, (i.e. no rotation or linear motion), and rectangular camera whose Field of View (FOV) encompasses the entire volume enclosed by detector modules capable of measuring Depth of Interaction (DOI) information. The camera is rectangular in shape in order to accommodate breasts of varying sizes while allowing for soft compression of the breast during the scan. This non-standard geometry of the camera exacerbates two problems: (a) radial elongation due to crystal penetration and (b) reconstructing images from irregularly sampled data. Packing considerations also give rise to regions in projection space that are not sampled which lead to missing information. The author presents new Fourier Methods based image reconstruction algorithms that incorporate DOI information and accommodate the irregular sampling of the camera in a consistent manner by defining lines of responses (LORs) between the measured interaction points instead of rebinning the events into predefined crystal face LORs which is the only other method to handle DOI information proposed thus far. The new procedures maximize the use of the increased sampling provided by the DOI while minimizing interpolation in the data. The new algorithms use fixed-width evenly spaced radial bins in order to take advantage of the speed of the Fast Fourier Transform (FFT), which necessitates the use of irregular angular sampling in order to minimize the number of unnormalizable Zero-Efficiency Bins (ZEBs). In order to address the persisting ZEBs and the issue of missing information originating from packing considerations, the algorithms (a) perform nearest neighbor smoothing in 2D in the radial bins (b) employ a semi-iterative procedure in order to estimate the unsampled data

  14. 3D reconstruction with two webcams and a laser line projector

    NASA Astrophysics Data System (ADS)

    Li, Dongdong; Hui, Bingwei; Qiu, Shaohua; Wen, Gongjian

    2014-09-01

    Three-dimensional (3D) reconstruction is one of the most attractive research topics in photogrammetry and computer vision. Nowadays 3D reconstruction with simple and consumable equipment plays an important role. In this paper, a 3D reconstruction desktop system is built based on binocular stereo vision using a laser scanner. The hardware requirements are a simple commercial hand-held laser line projector and two common webcams for image acquisition. Generally, 3D reconstruction based on passive triangulation methods requires point correspondences among various viewpoints. The development of matching algorithms remains a challenging task in computer vision. In our proposal, with the help of a laser line projector, stereo correspondences are established robustly from epipolar geometry and the laser shadow on the scanned object. To establish correspondences more conveniently, epipolar rectification is employed using Bouguet's method after stereo calibration with a printed chessboard. 3D coordinates of the observed points are worked out with rayray triangulation and reconstruction outliers are removed with the planarity constraint of the laser plane. Dense 3D point clouds are derived from multiple scans under different orientations. Each point cloud is derived by sweeping the laser plane across the object requiring 3D reconstruction. The Iterative Closest Point algorithm is employed to register the derived point clouds. Rigid body transformation between neighboring scans is obtained to get the complete 3D point cloud. Finally polygon meshes are reconstructed from the derived point cloud and color images are used in texture mapping to get a lifelike 3D model. Experiments show that our reconstruction method is simple and efficient.

  15. Registration of Real-Time 3-D Ultrasound to Tomographic Images of the Abdominal Aorta.

    PubMed

    Brekken, Reidar; Iversen, Daniel Høyer; Tangen, Geir Arne; Dahl, Torbjørn

    2016-08-01

    The purpose of this study was to develop an image-based method for registration of real-time 3-D ultrasound to computed tomography (CT) of the abdominal aorta, targeting future use in ultrasound-guided endovascular intervention. We proposed a method in which a surface model of the aortic wall was segmented from CT, and the approximate initial location of this model relative to the ultrasound volume was manually indicated. The model was iteratively transformed to automatically optimize correspondence to the ultrasound data. Feasibility was studied using data from a silicon phantom and in vivo data from a volunteer with previously acquired CT. Through visual evaluation, the ultrasound and CT data were seen to correspond well after registration. Both aortic lumen and branching arteries were well aligned. The processing was done offline, and the registration took approximately 0.2 s per ultrasound volume. The results encourage further patient studies to investigate accuracy, robustness and clinical value of the approach.

  16. Shack-Hartmann tomographic wavefront reconstruction using LGS: analysis of spot elongation and fratricide effect

    NASA Astrophysics Data System (ADS)

    Robert, Clelia; Conan, Jean-Marc; Gratadour, Damien; Petit, Cyril; Fusco, Thierry

    Noise effects induced by elongation have to be considered globally in a multi-channel tomographic reconstruction analysis. Such an analysis allows a fine estimation of performance and to compare launching options. We developed a modal LGS tomographic code based on pseudo-analytical matrix formalism. This modal analysis is computing and memory intensive. Therefore we limit the simulation to downscaled cases with diameters ranging from D = 4 to 21 m. We also limit the number of turbulent layers to a few equivalent layers. Including spot elongation and Rayleigh fratricide effect, when considering a global tomographic reconstruction, edge launching gives lightly better performance and limits the risk of possible underestimation of fratricide scatter.

  17. Robust Reconstruction and Generalized Dual Hahn Moments Invariants Extraction for 3D Images

    NASA Astrophysics Data System (ADS)

    Mesbah, Abderrahim; Zouhri, Amal; El Mallahi, Mostafa; Zenkouar, Khalid; Qjidaa, Hassan

    2017-03-01

    In this paper, we introduce a new set of 3D weighed dual Hahn moments which are orthogonal on a non-uniform lattice and their polynomials are numerically stable to scale, consequent, producing a set of weighted orthonormal polynomials. The dual Hahn is the general case of Tchebichef and Krawtchouk, and the orthogonality of dual Hahn moments eliminates the numerical approximations. The computational aspects and symmetry property of 3D weighed dual Hahn moments are discussed in details. To solve their inability to invariability of large 3D images, which cause to overflow issues, a generalized version of these moments noted 3D generalized weighed dual Hahn moment invariants are presented where whose as linear combination of regular geometric moments. For 3D pattern recognition, a generalized expression of 3D weighted dual Hahn moment invariants, under translation, scaling and rotation transformations, have been proposed where a new set of 3D-GWDHMIs have been provided. In experimental studies, the local and global capability of free and noisy 3D image reconstruction of the 3D-WDHMs has been compared with other orthogonal moments such as 3D Tchebichef and 3D Krawtchouk moments using Princeton Shape Benchmark database. On pattern recognition using the 3D-GWDHMIs like 3D object descriptors, the experimental results confirm that the proposed algorithm is more robust than other orthogonal moments for pattern classification of 3D images with and without noise.

  18. Indoor space 3D visual reconstruction using mobile cart with laser scanner and cameras

    NASA Astrophysics Data System (ADS)

    Gashongore, Prince Dukundane; Kawasue, Kikuhito; Yoshida, Kumiko; Aoki, Ryota

    2017-02-01

    Indoor space 3D visual reconstruction has many applications and, once done accurately, it enables people to conduct different indoor activities in an efficient manner. For example, an effective and efficient emergency rescue response can be accomplished in a fire disaster situation by using 3D visual information of a destroyed building. Therefore, an accurate Indoor Space 3D visual reconstruction system which can be operated in any given environment without GPS has been developed using a Human-Operated mobile cart equipped with a laser scanner, CCD camera, omnidirectional camera and a computer. By using the system, accurate indoor 3D Visual Data is reconstructed automatically. The obtained 3D data can be used for rescue operations, guiding blind or partially sighted persons and so forth.

  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

    2013-03-22

    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.

  20. Time-resolved diffusion tomographic 2D and 3D imaging in highly scattering turbid media

    NASA Technical Reports Server (NTRS)

    Alfano, Robert R. (Inventor); Cai, Wei (Inventor); Liu, Feng (Inventor); Lax, Melvin (Inventor); Das, Bidyut B. (Inventor)

    1999-01-01

    A method for imaging objects in highly scattering turbid media. According to one embodiment of the invention, the method involves using a plurality of intersecting source/detectors sets and time-resolving equipment to generate a plurality of time-resolved intensity curves for the diffusive component of light emergent from the medium. For each of the curves, the intensities at a plurality of times are then inputted into the following inverse reconstruction algorithm to form an image of the medium: ##EQU1## wherein W is a matrix relating output at source and detector positions r.sub.s and r.sub.d, at time t, to position r, .LAMBDA. is a regularization matrix, chosen for convenience to be diagonal, but selected in a way related to the ratio of the noise, to fluctuations in the absorption (or diffusion) X.sub.j that we are trying to determine: .LAMBDA..sub.ij =.lambda..sub.j .delta..sub.ij with .lambda..sub.j =/<.DELTA.Xj.DELTA.Xj> Y is the data collected at the detectors, and X.sup.k is the kth iterate toward the desired absoption information. An algorithm, which combines a two dimensional (2D) matrix inversion with a one-dimensional (1D) Fourier transform inversion is used to obtain images of three dimensional hidden objects in turbid scattering media.

  1. Time-resolved diffusion tomographic 2D and 3D imaging in highly scattering turbid media

    NASA Technical Reports Server (NTRS)

    Alfano, Robert R. (Inventor); Cai, Wei (Inventor); Gayen, Swapan K. (Inventor)

    2000-01-01

    A method for imaging objects in highly scattering turbid media. According to one embodiment of the invention, the method involves using a plurality of intersecting source/detectors sets and time-resolving equipment to generate a plurality of time-resolved intensity curves for the diffusive component of light emergent from the medium. For each of the curves, the intensities at a plurality of times are then inputted into the following inverse reconstruction algorithm to form an image of the medium: wherein W is a matrix relating output at source and detector positions r.sub.s and r.sub.d, at time t, to position r, .LAMBDA. is a regularization matrix, chosen for convenience to be diagonal, but selected in a way related to the ratio of the noise, to fluctuations in the absorption (or diffusion) X.sub.j that we are trying to determine: .LAMBDA..sub.ij =.lambda..sub.j .delta..sub.ij with .lambda..sub.j =/<.DELTA.Xj.DELTA.Xj> Y is the data collected at the detectors, and X.sup.k is the kth iterate toward the desired absorption information. An algorithm, which combines a two dimensional (2D) matrix inversion with a one-dimensional (1D) Fourier transform inversion is used to obtain images of three dimensional hidden objects in turbid scattering media.

  2. 3D reconstruction of the hemocyanin subunit dimer from the chiton Acanthochiton fascicularis.

    PubMed

    Harris, J Robin; Meissner, Ulrich; Gebauer, Wolfgang; Markl, Jürgen

    2004-01-01

    Procedures are presented for the purification of the subunit dimer from Acanthochiton fasicularis hemocyanin. Electron microscopy of negatively stained specimens revealed a uniform population of macromolecules possessing the characteristic "boat shape". A 3D reconstruction from this EM data generated a approximately 3 nm resolution model that correlates well with earlier data of the purported subunit dimer, extracted from the 3D reconstruction of the didecamer of Haliotis tuberculata hemocyanin type 1.

  3. Reconstruction of 3d Digital Image of Weepingforsythia Pollen

    NASA Astrophysics Data System (ADS)

    Liu, Dongwu; Chen, Zhiwei; Xu, Hongzhi; Liu, Wenqi; Wang, Lina

    Confocal microscopy, which is a major advance upon normal light microscopy, has been used in a number of scientific fields. By confocal microscopy techniques, cells and tissues can be visualized deeply, and three-dimensional images created. Compared with conventional microscopes, confocal microscope improves the resolution of images by eliminating out-of-focus light. Moreover, confocal microscope has a higher level of sensitivity due to highly sensitive light detectors and the ability to accumulate images captured over time. In present studies, a series of Weeping Forsythia pollen digital images (35 images in total) were acquired with confocal microscope, and the three-dimensional digital image of the pollen reconstructed with confocal microscope. Our results indicate that it's a very easy job to analysis threedimensional digital image of the pollen with confocal microscope and the probe Acridine orange (AO).

  4. [Progress in application of 3D bioprinting in cartilage regeneration and reconstruction for tissue engineering].

    PubMed

    Liao, Junlin; Wang, Shaohua; Chen, Jia; Xie, Hongju; Zhou, Jianda

    2017-02-28

    Three-dimensional (3D) bioprinting provides an advanced technology for tissue engineering and regenerative medicine because of its ability to produce the models or organs with higher precision and more suitable for human body. It has been successfully used to produce a variety of cartilage scaffold materials. In addition, 3D bioprinter can directly to print tissue and organs with live chondrocytes. In conclusion, 3D bioprinting may have broad prospect for cartilage regeneration and reconstruction in tissue engineering.

  5. [Spatio-temporal image correlation (STIC) and tomographic ultrasound imaging (TUI)--combined clinical implementation in 3D/4D fetal echocardiography].

    PubMed

    Markov, D

    2010-01-01

    Two new forms of volume data image processing by three (3D) and four (4D) dimensional ultrasound named Spatio-Temporal Image Correlation (STIC) and Tomographic Ultrasound Imaging (TUI) are presented. The advantages and disadvantages of the combined clinical implementation of both modalities in fetal echocardiography are discussed.

  6. FIJI Macro 3D ART VeSElecT: 3D Automated Reconstruction Tool for Vesicle Structures of Electron Tomograms

    PubMed Central

    Kaltdorf, Kristin Verena; Schulze, Katja; Helmprobst, Frederik; Kollmannsberger, Philip; Stigloher, Christian

    2017-01-01

    Automatic image reconstruction is critical to cope with steadily increasing data from advanced microscopy. We describe here the Fiji macro 3D ART VeSElecT which we developed to study synaptic vesicles in electron tomograms. We apply this tool to quantify vesicle properties (i) in embryonic Danio rerio 4 and 8 days past fertilization (dpf) and (ii) to compare Caenorhabditis elegans N2 neuromuscular junctions (NMJ) wild-type and its septin mutant (unc-59(e261)). We demonstrate development-specific and mutant-specific changes in synaptic vesicle pools in both models. We confirm the functionality of our macro by applying our 3D ART VeSElecT on zebrafish NMJ showing smaller vesicles in 8 dpf embryos then 4 dpf, which was validated by manual reconstruction of the vesicle pool. Furthermore, we analyze the impact of C. elegans septin mutant unc-59(e261) on vesicle pool formation and vesicle size. Automated vesicle registration and characterization was implemented in Fiji as two macros (registration and measurement). This flexible arrangement allows in particular reducing false positives by an optional manual revision step. Preprocessing and contrast enhancement work on image-stacks of 1nm/pixel in x and y direction. Semi-automated cell selection was integrated. 3D ART VeSElecT removes interfering components, detects vesicles by 3D segmentation and calculates vesicle volume and diameter (spherical approximation, inner/outer diameter). Results are collected in color using the RoiManager plugin including the possibility of manual removal of non-matching confounder vesicles. Detailed evaluation considered performance (detected vesicles) and specificity (true vesicles) as well as precision and recall. We furthermore show gain in segmentation and morphological filtering compared to learning based methods and a large time gain compared to manual segmentation. 3D ART VeSElecT shows small error rates and its speed gain can be up to 68 times faster in comparison to manual annotation

  7. Automatic Texture Reconstruction of 3d City Model from Oblique Images

    NASA Astrophysics Data System (ADS)

    Kang, Junhua; Deng, Fei; Li, Xinwei; Wan, Fang

    2016-06-01

    In recent years, the photorealistic 3D city models are increasingly important in various geospatial applications related to virtual city tourism, 3D GIS, urban planning, real-estate management. Besides the acquisition of high-precision 3D geometric data, texture reconstruction is also a crucial step for generating high-quality and visually realistic 3D models. However, most of the texture reconstruction approaches are probably leading to texture fragmentation and memory inefficiency. In this paper, we introduce an automatic framework of texture reconstruction to generate textures from oblique images for photorealistic visualization. Our approach include three major steps as follows: mesh parameterization, texture atlas generation and texture blending. Firstly, mesh parameterization procedure referring to mesh segmentation and mesh unfolding is performed to reduce geometric distortion in the process of mapping 2D texture to 3D model. Secondly, in the texture atlas generation step, the texture of each segmented region in texture domain is reconstructed from all visible images with exterior orientation and interior orientation parameters. Thirdly, to avoid color discontinuities at boundaries between texture regions, the final texture map is generated by blending texture maps from several corresponding images. We evaluated our texture reconstruction framework on a dataset of a city. The resulting mesh model can get textured by created texture without resampling. Experiment results show that our method can effectively mitigate the occurrence of texture fragmentation. It is demonstrated that the proposed framework is effective and useful for automatic texture reconstruction of 3D city model.

  8. 3D surface reconstruction based on image stitching from gastric endoscopic video sequence

    NASA Astrophysics Data System (ADS)

    Duan, Mengyao; Xu, Rong; Ohya, Jun

    2013-09-01

    This paper proposes a method for reconstructing 3D detailed structures of internal organs such as gastric wall from endoscopic video sequences. The proposed method consists of the four major steps: Feature-point-based 3D reconstruction, 3D point cloud stitching, dense point cloud creation and Poisson surface reconstruction. Before the first step, we partition one video sequence into groups, where each group consists of two successive frames (image pairs), and each pair in each group contains one overlapping part, which is used as a stitching region. Fist, the 3D point cloud of each group is reconstructed by utilizing structure from motion (SFM). Secondly, a scheme based on SIFT features registers and stitches the obtained 3D point clouds, by estimating the transformation matrix of the overlapping part between different groups with high accuracy and efficiency. Thirdly, we select the most robust SIFT feature points as the seed points, and then obtain the dense point cloud from sparse point cloud via a depth testing method presented by Furukawa. Finally, by utilizing Poisson surface reconstruction, polygonal patches for the internal organs are obtained. Experimental results demonstrate that the proposed method achieves a high accuracy and efficiency for 3D reconstruction of gastric surface from an endoscopic video sequence.

  9. Optimum conditions for high-quality 3D reconstruction in confocal scanning microscopy

    NASA Astrophysics Data System (ADS)

    Kim, Taehoon; Kim, Taejoong; Lee, SeungWoo; Gweon, Dae-Gab; Seo, Jungwoo

    2006-02-01

    Confocal Scanning Microscopy (CSM) is very useful to reconstruct 3D image of Bio-cells and the objects that have specification shape in higher axial and lateral resolution and widely used as measurement instrument. A 3D reconstruction is used to visualize confocal images and consists of following processes. The First process is to get 3D data by collecting a series of images at regular focus intervals (Optical Sectioning). The Second process is to fit a curve to a series of 3D data points each pixel. The Third process is to search height information that has maximum value from curve-fitting. However, because of various systematic errors (NOISE) occurred when collecting the information of images through Optical Sectioning and large peak deviation occurred from curve-fitting error, high quality 3D reconstruction is not expected. Also, it takes much time to 3d Reconstruction by using many 3D data in order to acquire high quality and much cost to improve signal-to-noise (SNR) using a higher power laser. So, we are going to define SNR, peak deviation and the order of curve-fitting as important factors and simulate the relation between the factors in order to find a optimum condition for high quality 3D reconstruction in Confoal Scanning Microscopy. If we use optimum condition obtained by this simulation, using a suitable SNR and the suitable number of data and the suitable n-th order curve-fitting, small peak deviation is expected and then, 3D reconstruction of little better quality is expected. Also, it is expected to save.

  10. New method to analyze internal disruptions with tomographic reconstructions

    SciTech Connect

    Tanzi, C.P.; de Blank, H.J.

    1997-03-01

    Sawtooth crashes have been investigated on the Rijnhuizen Tokamak Project (RTP) [N. J. Lopes Cardozo {ital et al.}, {ital Proceedings of the 14th International Conference on Plasma Physics and Controlled Nuclear Fusion Research}, W{umlt u}rzburg, 1992 (International Atomic Energy Agency, Vienna, 1993), Vol. 1, p. 271]. Internal disruptions in tokamak plasmas often exhibit an m=1 poloidal mode structure prior to the collapse which can be clearly identified by means of multicamera soft x-ray diagnostics. In this paper tomographic reconstructions of such m=1 modes are analyzed with a new method, based on magnetohydrodynamic (MHD) invariants computed from the two-dimensional emissivity profiles, which quantifies the amount of profile flattening not only after the crash but also during the precursor oscillations. The results are interpreted by comparing them with two models which simulate the measurements of the m=1 redistribution of soft x-ray emissivity prior to the sawtooth crash. One model is based on the magnetic reconnection model of Kadomtsev. The other involves ideal MHD motion only. In cases where differences in magnetic topology between the two models cannot be seen in the tomograms, the analysis of profile flattening has an advantage. The analysis shows that in RTP the clearly observed m=1 displacement of some sawteeth requires the presence of convective ideal MHD motion, whereas other precursors are consistent with magnetic reconnection of up to 75{percent} of the magnetic flux within the q=1 surface. The possibility of ideal interchange combined with enhanced cross-field transport is not excluded. {copyright} {ital 1997 American Institute of Physics.}

  11. Three-dimensional reconstruction of flame temperature and emissivity distribution using optical tomographic and two-colour pyrometric techniques

    NASA Astrophysics Data System (ADS)

    Moinul Hossain, Md; Lu, Gang; Sun, Duo; Yan, Yong

    2013-07-01

    This paper presents an experimental investigation, visualization and validation in the three-dimensional (3D) reconstruction of flame temperature and emissivity distributions by using optical tomographic and two-colour pyrometric techniques. A multi-camera digital imaging system comprising eight optical imaging fibres and two RGB charged-couple device (CCD) cameras are used to acquire two-dimensional (2D) images of the flame simultaneously from eight equiangular directions. A combined logical filtered back-projection (LFBP) and simultaneous iterative reconstruction and algebraic reconstruction technique (SART) algorithm is utilized to reconstruct the grey-level intensity of the flame for the two primary colour (red and green) images. The temperature distribution of the flame is then determined from the ratio of the reconstructed grey-level intensities and the emissivity is estimated from the ratio of the grey level of a primary colour image to that of a blackbody source at the same temperature. The temperature measurement of the system was calibrated using a blackbody furnace as a standard temperature source. Experimental work was undertaken to validate the flame temperature obtained by the imaging system against that obtained using high-precision thermocouples. The difference between the two measurements is found no greater than ±9%. Experimental results obtained on a laboratory-scale propane fired combustion test rig demonstrate that the imaging system and applied technical approach perform well in the reconstruction of the 3D temperature and emissivity distributions of the sooty flame.

  12. 3D Reconstruction of a Rotating Erupting Prominence

    NASA Technical Reports Server (NTRS)

    Thompson, W. T.; Kliem, B.; Torok, T.

    2011-01-01

    A bright prominence associated with a coronal mass ejection (CME) was seen erupting from the Sun on 9 April 2008. This prominence was tracked by both the Solar Terrestrial Relations Observatory (STEREO) EUVI and COR1 telescopes, and was seen to rotate about the line of sight as it erupted; therefore, the event has been nicknamed the "Cartwheel CME." The threads of the prominence in the core of the CME quite clearly indicate the structure of a weakly to moderately twisted flux rope throughout the field of view, up to heliocentric heights of 4 solar radii. Although the STEREO separation was 48 deg, it was possible to match some sharp features in the later part of the eruption as seen in the 304 Angstrom line in EUVI and in the H alpha-sensitive bandpass of COR1 by both STEREO Ahead and Behind. These features could then be traced out in three dimensional space, and reprojected into a view in which the eruption is directed towards the observer. The reconstructed view shows that the alignment of the prominence to the vertical axis rotates as it rises up to a leading-edge height of approximately equals 2.5 solar radii, and then remains approximately constant. The alignment at 2.5 solar radii differs by about 115 deg. from the original filament orientation inferred from H alpha and EUV data, and the height profile of the rotation, obtained here for the first time, shows that two thirds of the total rotation is reached within approximately equals 0.5 solar radii above the photosphere. These features are well reproduced by numerical simulations of an unstable moderately twisted flux rope embedded in external flux with a relatively strong shear field component.

  13. 3D Reconstruction of a Rotating Erupting Prominence

    NASA Technical Reports Server (NTRS)

    Thompson, W. T.; Kliem, B.; Toeroek, T.

    2011-01-01

    A bright prominence associated with a coronal mass ejection (CME) was seen erupting from the Sun on 9 April 2008. This prominence was tracked by both the Solar Terrestrial Relations Observatory (STEREO) EUVI and COR1 telescopes, and was seen to rotate about the line of sight a it erupted; therefore, the event has been nicknamed the "Cartwheel CME." The threads of the prominence in the core of the CME quite clearly indicate the structure of a weakly to moderately twisted flux rope throughout the field of view, up to heliocentric heights of 4 solar radii. Although the STEREO separation was 48 deg, it was possible to match some sharp features in the later part of the eruption as seen in the 304 A line in EUVI and in the H-alpha-sensitive bandpass of COR I by both STEREO Ahead and Behind. These features could then be traced out in three-dimensional space, and reprojected into a view in which the eruption is directed toward the observer. The reconstructed view shows that the alignment of the prominence to the vertical axis rotates as it rises up to a leading-edge height of approximately equal to 2.5 solar radii, and then remains approximately constant. The alignment at 2.5 solar radii differs by about 115 deg from the original filament orientation inferred from H-alpha and EUV data, and the height profile of the rotation, obtained here for the first time, shows that two thirds of the total rotation are reached within approximately equal to 0.5 solar radii above the photosphere. These features are well reproduced by numerical simulations of an unstable moderately twisted flux rope embedded in external flux with a relatively strong shear field component.

  14. Virtual surgical planning and 3D printing in repeat calvarial vault reconstruction for craniosynostosis: technical note.

    PubMed

    LoPresti, Melissa; Daniels, Bradley; Buchanan, Edward P; Monson, Laura; Lam, Sandi

    2017-02-03

    Repeat surgery for restenosis after initial nonsyndromic craniosynostosis intervention is sometimes needed. Calvarial vault reconstruction through a healed surgical bed adds a level of intraoperative complexity and may benefit from preoperative and intraoperative definitions of biometric and aesthetic norms. Computer-assisted design and manufacturing using 3D imaging allows the precise formulation of operative plans in anticipation of surgical intervention. 3D printing turns virtual plans into anatomical replicas, templates, or customized implants by using a variety of materials. The authors present a technical note illustrating the use of this technology: a repeat calvarial vault reconstruction that was planned and executed using computer-assisted design and 3D printed intraoperative guides.

  15. Reconstruction of quadratic curves in 3D using two or more perspective views: simulation studies

    NASA Astrophysics Data System (ADS)

    Kumar, Sanjeev; Sukavanam, N.; Balasubramanian, R.

    2006-01-01

    The shapes of many natural and man-made objects have planar and curvilinear surfaces. The images of such curves usually do not have sufficient distinctive features to apply conventional feature-based reconstruction algorithms. In this paper, we describe a method of reconstruction of a quadratic curve in 3-D space as an intersection of two cones containing the respective projected curve images. The correspondence between this pair of projections of the curve is assumed to be established in this work. Using least-square curve fitting, the parameters of a curve in 2-D space are found. From this we are reconstructing the 3-D quadratic curve. Relevant mathematical formulations and analytical solutions for obtaining the equation of reconstructed curve are given. The result of the described reconstruction methodology are studied by simulation studies. This reconstruction methodology is applicable to LBW decision in cricket, path of the missile, Robotic Vision, path lanning etc.

  16. A fast 3D reconstruction system with a low-cost camera accessory

    NASA Astrophysics Data System (ADS)

    Zhang, Yiwei; Gibson, Graham M.; Hay, Rebecca; Bowman, Richard W.; Padgett, Miles J.; Edgar, Matthew P.

    2015-06-01

    Photometric stereo is a three dimensional (3D) imaging technique that uses multiple 2D images, obtained from a fixed camera perspective, with different illumination directions. Compared to other 3D imaging methods such as geometry modeling and 3D-scanning, it comes with a number of advantages, such as having a simple and efficient reconstruction routine. In this work, we describe a low-cost accessory to a commercial digital single-lens reflex (DSLR) camera system allowing fast reconstruction of 3D objects using photometric stereo. The accessory consists of four white LED lights fixed to the lens of a commercial DSLR camera and a USB programmable controller board to sequentially control the illumination. 3D images are derived for different objects with varying geometric complexity and results are presented, showing a typical height error of <3 mm for a 50 mm sized object.

  17. Imaging Techniques for Dense 3D reconstruction of Swimming Aquatic Life using Multi-view Stereo

    NASA Astrophysics Data System (ADS)

    Daily, David; Kiser, Jillian; McQueen, Sarah

    2016-11-01

    Understanding the movement characteristics of how various species of fish swim is an important step to uncovering how they propel themselves through the water. Previous methods have focused on profile capture methods or sparse 3D manual feature point tracking. This research uses an array of 30 cameras to automatically track hundreds of points on a fish as they swim in 3D using multi-view stereo. Blacktip sharks, sting rays, puffer fish, turtles and more were imaged in collaboration with the National Aquarium in Baltimore, Maryland using the multi-view stereo technique. The processes for data collection, camera synchronization, feature point extraction, 3D reconstruction, 3D alignment, biological considerations, and lessons learned will be presented. Preliminary results of the 3D reconstructions will be shown and future research into mathematically characterizing various bio-locomotive maneuvers will be discussed.

  18. A fast 3D reconstruction system with a low-cost camera accessory

    PubMed Central

    Zhang, Yiwei; Gibson, Graham M.; Hay, Rebecca; Bowman, Richard W.; Padgett, Miles J.; Edgar, Matthew P.

    2015-01-01

    Photometric stereo is a three dimensional (3D) imaging technique that uses multiple 2D images, obtained from a fixed camera perspective, with different illumination directions. Compared to other 3D imaging methods such as geometry modeling and 3D-scanning, it comes with a number of advantages, such as having a simple and efficient reconstruction routine. In this work, we describe a low-cost accessory to a commercial digital single-lens reflex (DSLR) camera system allowing fast reconstruction of 3D objects using photometric stereo. The accessory consists of four white LED lights fixed to the lens of a commercial DSLR camera and a USB programmable controller board to sequentially control the illumination. 3D images are derived for different objects with varying geometric complexity and results are presented, showing a typical height error of <3 mm for a 50 mm sized object. PMID:26057407

  19. 3-D reconstruction of neurons from multichannel confocal laser scanning image series.

    PubMed

    Wouterlood, Floris G

    2014-04-10

    A confocal laser scanning microscope (CLSM) collects information from a thin, focal plane and ignores out-of-focus information. Scanning of a specimen, with stepwise axial (Z-) movement of the stage in between each scan, produces Z-series of confocal images of a tissue volume, which then can be used to 3-D reconstruct structures of interest. The operator first configures separate channels (e.g., laser, filters, and detector settings) for each applied fluorochrome and then acquires Z-series of confocal images: one series per channel. Channel signal separation is extremely important. Measures to avoid bleaching are vital. Post-acquisition deconvolution of the image series is often performed to increase resolution before 3-D reconstruction takes place. In the 3-D reconstruction programs described in this unit, reconstructions can be inspected in real time from any viewing angle. By altering viewing angles and by switching channels off and on, the spatial relationships of 3-D-reconstructed structures with respect to structures visualized in other channels can be studied. Since each brand of CLSM, computer program, and 3-D reconstruction package has its own proprietary set of procedures, a general approach is provided in this protocol wherever possible.

  20. Fourier-based reconstruction for fully 3-D PET: optimization of interpolation parameters.

    PubMed

    Matej, Samuel; Kazantsev, Ivan G

    2006-07-01

    Fourier-based approaches for three-dimensional (3-D) reconstruction are based on the relationship between the 3-D Fourier transform (FT) of the volume and the two-dimensional (2-D) FT of a parallel-ray projection of the volume. The critical step in the Fourier-based methods is the estimation of the samples of the 3-D transform of the image from the samples of the 2-D transforms of the projections on the planes through the origin of Fourier space, and vice versa for forward-projection (reprojection). The Fourier-based approaches have the potential for very fast reconstruction, but their straightforward implementation might lead to unsatisfactory results if careful attention is not paid to interpolation and weighting functions. In our previous work, we have investigated optimal interpolation parameters for the Fourier-based forward and back-projectors for iterative image reconstruction. The optimized interpolation kernels were shown to provide excellent quality comparable to the ideal sinc interpolator. This work presents an optimization of interpolation parameters of the 3-D direct Fourier method with Fourier reprojection (3D-FRP) for fully 3-D positron emission tomography (PET) data with incomplete oblique projections. The reprojection step is needed for the estimation (from an initial image) of the missing portions of the oblique data. In the 3D-FRP implementation, we use the gridding interpolation strategy, combined with proper weighting approaches in the transform and image domains. We have found that while the 3-D reprojection step requires similar optimal interpolation parameters as found in our previous studies on Fourier-based iterative approaches, the optimal interpolation parameters for the main 3D-FRP reconstruction stage are quite different. Our experimental results confirm that for the optimal interpolation parameters a very good image accuracy can be achieved even without any extra spectral oversampling, which is a common practice to decrease errors

  1. Cervical vertebrae maturation index estimates on cone beam CT: 3D reconstructions vs sagittal sections

    PubMed Central

    Bonfim, Marco A E; Costa, André L F; Ximenez, Michel E L; Cotrim-Ferreira, Flávio A; Ferreira-Santos, Rívea I

    2016-01-01

    Objectives: The aim of this study was to evaluate the performance of CBCT three-dimensional (3D) reconstructions and sagittal sections for estimates of cervical vertebrae maturation index (CVMI). Methods: The sample consisted of 72 CBCT examinations from patients aged 8–16 years (45 females and 27 males) selected from the archives of two private clinics. Two calibrated observers (kappa scores: ≥0.901) interpreted the CBCT settings twice. Intra- and interobserver agreement for both imaging exhibition modes was analyzed by kappa statistics, which was also used to analyze the agreement between 3D reconstructions and sagittal sections. Correlations between cervical vertebrae maturation estimates and chronological age, as well as between the assessments by 3D reconstructions and sagittal sections, were analyzed using gamma Goodman–Kruskal coefficients (α = 0.05). Results: The kappa scores evidenced almost perfect agreement between the first and second assessments of the cervical vertebrae by 3D reconstructions (0.933–0.983) and sagittal sections (0.983–1.000). Similarly, the agreement between 3D reconstructions and sagittal sections was almost perfect (kappa index: 0.983). In most divergent cases, the difference between 3D reconstructions and sagittal sections was one stage of CVMI. Strongly positive correlations (>0.8, p < 0.001) were found not only between chronological age and CVMI but also between the estimates by 3D reconstructions and sagittal sections (p < 0.001). Conclusions: Although CBCT imaging must not be used exclusively for this purpose, it may be suitable for skeletal maturity assessments. PMID:26509559

  2. Parallel OSEM Reconstruction Algorithm for Fully 3-D SPECT on a Beowulf Cluster.

    PubMed

    Rong, Zhou; Tianyu, Ma; Yongjie, Jin

    2005-01-01

    In order to improve the computation speed of ordered subset expectation maximization (OSEM) algorithm for fully 3-D single photon emission computed tomography (SPECT) reconstruction, an experimental beowulf-type cluster was built and several parallel reconstruction schemes were described. We implemented a single-program-multiple-data (SPMD) parallel 3-D OSEM reconstruction algorithm based on message passing interface (MPI) and tested it with combinations of different number of calculating processors and different size of voxel grid in reconstruction (64×64×64 and 128×128×128). Performance of parallelization was evaluated in terms of the speedup factor and parallel efficiency. This parallel implementation methodology is expected to be helpful to make fully 3-D OSEM algorithms more feasible in clinical SPECT studies.

  3. A novel method for the 3-D reconstruction of scoliotic ribs from frontal and lateral radiographs.

    PubMed

    Seoud, Lama; Cheriet, Farida; Labelle, Hubert; Dansereau, Jean

    2011-05-01

    Among the external manifestations of scoliosis, the rib hump, which is associated with the ribs' deformities and rotations, constitutes the most disturbing aspect of the scoliotic deformity for patients. A personalized 3-D model of the rib cage is important for a better evaluation of the deformity, and hence, a better treatment planning. A novel method for the 3-D reconstruction of the rib cage, based only on two standard radiographs, is proposed in this paper. For each rib, two points are extrapolated from the reconstructed spine, and three points are reconstructed by stereo radiography. The reconstruction is then refined using a surface approximation. The method was evaluated using clinical data of 13 patients with scoliosis. A comparison was conducted between the reconstructions obtained with the proposed method and those obtained by using a previous reconstruction method based on two frontal radiographs. A first comparison criterion was the distances between the reconstructed ribs and the surface topography of the trunk, considered as the reference modality. The correlation between ribs axial rotation and back surface rotation was also evaluated. The proposed method successfully reconstructed the ribs of the 6th-12th thoracic levels. The evaluation results showed that the 3-D configuration of the new rib reconstructions is more consistent with the surface topography and provides more accurate measurements of ribs axial rotation.

  4. High-resolution 3-D P-wave tomographic imaging of the shallow magmatic system of Erebus volcano, Antarctica

    NASA Astrophysics Data System (ADS)

    Zandomeneghi, D.; Aster, R. C.; Barclay, A. H.; Chaput, J. A.; Kyle, P. R.

    2011-12-01

    Erebus volcano (Ross Island), the most active volcano in Antarctica, is characterized by a persistent phonolitic lava lake at its summit and a wide range of seismic signals associated with its underlying long-lived magmatic system. The magmatic structure in a 3 by 3 km area around the summit has been imaged using high-quality data from a seismic tomographic experiment carried out during the 2008-2009 austral field season (Zandomeneghi et al., 2010). An array of 78 short period, 14 broadband, and 4 permanent Mount Erebus Volcano Observatory seismic stations and a program of 12 shots were used to model the velocity structure in the uppermost kilometer over the volcano conduit. P-wave travel times were inverted for the 3-D velocity structure using the shortest-time ray tracing (50-m grid spacing) and LSQR inversion (100-m node spacing) of a tomography code (Toomey et al., 1994) that allows for the inclusion of topography. Regularization is controlled by damping and smoothing weights and smoothing lengths, and addresses complications that are inherent in a strongly heterogeneous medium featuring rough topography and a dense parameterization and distribution of receivers/sources. The tomography reveals a composite distribution of very high and low P-wave velocity anomalies (i.e., exceeding 20% in some regions), indicating a complex sub-lava-lake magmatic geometry immediately beneath the summit region and in surrounding areas, as well as the presence of significant high velocity shallow regions. The strongest and broadest low velocity zone is located W-NW of the crater rim, indicating the presence of an off-axis shallow magma body. This feature spatially corresponds to the inferred centroid source of VLP signals associated with Strombolian eruptions and lava lake refill (Aster et al., 2008). Other resolved structures correlate with the Side Crater and with lineaments of ice cave thermal anomalies extending NE and SW of the rim. High velocities in the summit area possibly

  5. Review of three-dimensional (3D) surface imaging for oncoplastic, reconstructive and aesthetic breast surgery.

    PubMed

    O'Connell, Rachel L; Stevens, Roger J G; Harris, Paul A; Rusby, Jennifer E

    2015-08-01

    Three-dimensional surface imaging (3D-SI) is being marketed as a tool in aesthetic breast surgery. It has recently also been studied in the objective evaluation of cosmetic outcome of oncological procedures. The aim of this review is to summarise the use of 3D-SI in oncoplastic, reconstructive and aesthetic breast surgery. An extensive literature review was undertaken to identify published studies. Two reviewers independently screened all abstracts and selected relevant articles using specific inclusion criteria. Seventy two articles relating to 3D-SI for breast surgery were identified. These covered endpoints such as image acquisition, calculations and data obtainable, comparison of 3D and 2D imaging and clinical research applications of 3D-SI. The literature provides a favourable view of 3D-SI. However, evidence of its superiority over current methods of clinical decision making, surgical planning, communication and evaluation of outcome is required before it can be accepted into mainstream practice.

  6. IVUSAngio tool: a publicly available software for fast and accurate 3D reconstruction of coronary arteries.

    PubMed

    Doulaverakis, Charalampos; Tsampoulatidis, Ioannis; Antoniadis, Antonios P; Chatzizisis, Yiannis S; Giannopoulos, Andreas; Kompatsiaris, Ioannis; Giannoglou, George D

    2013-11-01

    There is an ongoing research and clinical interest in the development of reliable and easily accessible software for the 3D reconstruction of coronary arteries. In this work, we present the architecture and validation of IVUSAngio Tool, an application which performs fast and accurate 3D reconstruction of the coronary arteries by using intravascular ultrasound (IVUS) and biplane angiography data. The 3D reconstruction is based on the fusion of the detected arterial boundaries in IVUS images with the 3D IVUS catheter path derived from the biplane angiography. The IVUSAngio Tool suite integrates all the intermediate processing and computational steps and provides a user-friendly interface. It also offers additional functionality, such as automatic selection of the end-diastolic IVUS images, semi-automatic and automatic IVUS segmentation, vascular morphometric measurements, graphical visualization of the 3D model and export in a format compatible with other computer-aided design applications. Our software was applied and validated in 31 human coronary arteries yielding quite promising results. Collectively, the use of IVUSAngio Tool significantly reduces the total processing time for 3D coronary reconstruction. IVUSAngio Tool is distributed as free software, publicly available to download and use.

  7. Discovering hotspots in functional genomic data superposed on 3D chromatin configuration reconstructions

    PubMed Central

    Capurso, Daniel; Bengtsson, Henrik; Segal, Mark R.

    2016-01-01

    The spatial organization of the genome influences cellular function, notably gene regulation. Recent studies have assessed the three-dimensional (3D) co-localization of functional annotations (e.g. centromeres, long terminal repeats) using 3D genome reconstructions from Hi-C (genome-wide chromosome conformation capture) data; however, corresponding assessments for continuous functional genomic data (e.g. chromatin immunoprecipitation-sequencing (ChIP-seq) peak height) are lacking. Here, we demonstrate that applying bump hunting via the patient rule induction method (PRIM) to ChIP-seq data superposed on a Saccharomyces cerevisiae 3D genome reconstruction can discover ‘functional 3D hotspots’, regions in 3-space for which the mean ChIP-seq peak height is significantly elevated. For the transcription factor Swi6, the top hotspot by P-value contains MSB2 and ERG11 – known Swi6 target genes on different chromosomes. We verify this finding in a number of ways. First, this top hotspot is relatively stable under PRIM across parameter settings. Second, this hotspot is among the top hotspots by mean outcome identified by an alternative algorithm, k-Nearest Neighbor (k-NN) regression. Third, the distance between MSB2 and ERG11 is smaller than expected (by resampling) in two other 3D reconstructions generated via different normalization and reconstruction algorithms. This analytic approach can discover functional 3D hotspots and potentially reveal novel regulatory interactions. PMID:26869583

  8. Impact of Level of Details in the 3d Reconstruction of Trees for Microclimate Modeling

    NASA Astrophysics Data System (ADS)

    Bournez, E.; Landes, T.; Saudreau, M.; Kastendeuch, P.; Najjar, G.

    2016-06-01

    In the 21st century, urban areas undergo specific climatic conditions like urban heat islands which frequency and intensity increase over the years. Towards the understanding and the monitoring of these conditions, vegetation effects on urban climate are studied. It appears that a natural phenomenon, the evapotranspiration of trees, generates a cooling effect in urban environment. In this work, a 3D microclimate model is used to quantify the evapotranspiration of trees in relation with their architecture, their physiology and the climate. These three characteristics are determined with field measurements and data processing. Based on point clouds acquired with terrestrial laser scanner (TLS), the 3D reconstruction of the tree wood architecture is performed. Then the 3D reconstruction of leaves is carried out from the 3D skeleton of vegetative shoots and allometric statistics. With the aim of extending the simulation on several trees simultaneously, it is necessary to apply the 3D reconstruction process on each tree individually. However, as well for the acquisition as for the processing, the 3D reconstruction approach is time consuming. Mobile laser scanners could provide point clouds in a faster way than static TLS, but this implies a lower point density. Also the processing time could be shortened, but under the assumption that a coarser 3D model is sufficient for the simulation. In this context, the criterion of level of details and accuracy of the tree 3D reconstructed model must be studied. In this paper first tests to assess their impact on the determination of the evapotranspiration are presented.

  9. Automated Reconstruction Algorithm for Identification of 3D Architectures of Cribriform Ductal Carcinoma In Situ

    PubMed Central

    Norton, Kerri-Ann; Namazi, Sameera; Barnard, Nicola; Fujibayashi, Mariko; Bhanot, Gyan; Ganesan, Shridar; Iyatomi, Hitoshi; Ogawa, Koichi; Shinbrot, Troy

    2012-01-01

    Ductal carcinoma in situ (DCIS) is a pre-invasive carcinoma of the breast that exhibits several distinct morphologies but the link between morphology and patient outcome is not clear. We hypothesize that different mechanisms of growth may still result in similar 2D morphologies, which may look different in 3D. To elucidate the connection between growth and 3D morphology, we reconstruct the 3D architecture of cribriform DCIS from resected patient material. We produce a fully automated algorithm that aligns, segments, and reconstructs 3D architectures from microscopy images of 2D serial sections from human specimens. The alignment algorithm is based on normalized cross correlation, the segmentation algorithm uses histogram equilization, Otsu's thresholding, and morphology techniques to segment the duct and cribra. The reconstruction method combines these images in 3D. We show that two distinct 3D architectures are indeed found in samples whose 2D histological sections are similarly identified as cribriform DCIS. These differences in architecture support the hypothesis that luminal spaces may form due to different mechanisms, either isolated cell death or merging fronds, leading to the different architectures. We find that out of 15 samples, 6 were found to have ‘bubble-like’ cribra, 6 were found to have ‘tube-like’ criba and 3 were ‘unknown.’ We propose that the 3D architectures found, ‘bubbles’ and ‘tubes’, account for some of the heterogeneity of the disease and may be prognostic indicators of different patient outcomes. PMID:22970156

  10. 3D Building Modeling and Reconstruction using Photometric Satellite and Aerial Imageries

    NASA Astrophysics Data System (ADS)

    Izadi, Mohammad

    In this thesis, the problem of three dimensional (3D) reconstruction of building models using photometric satellite and aerial images is investigated. Here, two systems are pre-sented: 1) 3D building reconstruction using a nadir single-view image, and 2) 3D building reconstruction using slant multiple-view aerial images. The first system detects building rooftops in orthogonal aerial/satellite images using a hierarchical segmentation algorithm and a shadow verification approach. The heights of detected buildings are then estimated using a fuzzy rule-based method, which measures the height of a building by comparing its predicted shadow region with the actual shadow evidence in the image. This system finally generated a KML (Keyhole Markup Language) file as the output, that contains 3D models of detected buildings. The second system uses the geolocation information of a scene containing a building of interest and uploads all slant-view images that contain this scene from an input image dataset. These images are then searched automatically to choose image pairs with different views of the scene (north, east, south and west) based on the geolocation and auxiliary data accompanying the input data (metadata that describes the acquisition parameters at the capture time). The camera parameters corresponding to these images are refined using a novel point matching algorithm. Next, the system independently reconstructs 3D flat surfaces that are visible in each view using an iterative algorithm. 3D surfaces generated for all views are combined, and redundant surfaces are removed to create a complete set of 3D surfaces. Finally, the combined 3D surfaces are connected together to generate a more complete 3D model. For the experimental results, both presented systems are evaluated quantitatively and qualitatively and different aspects of the two systems including accuracy, stability, and execution time are discussed.

  11. 3D reconstruction method from biplanar radiography using non-stereocorresponding points and elastic deformable meshes.

    PubMed

    Mitton, D; Landry, C; Véron, S; Skalli, W; Lavaste, F; De Guise, J A

    2000-03-01

    Standard 3D reconstruction of bones using stereoradiography is limited by the number of anatomical landmarks visible in more than one projection. The proposed technique enables the 3D reconstruction of additional landmarks that can be identified in only one of the radiographs. The principle of this method is the deformation of an elastic object that respects stereocorresponding and non-stereocorresponding observations available in different projections. This technique is based on the principle that any non-stereocorresponding point belongs to a line joining the X-ray source and the projection of the point in one view. The aim is to determine the 3D position of these points on their line of projection when submitted to geometrical and topological constraints. This technique is used to obtain the 3D geometry of 18 cadaveric upper cervical vertebrae. The reconstructed geometry obtained is compared with direct measurements using a magnetic digitiser. The order of precision determined with the point-to-surface distance between the reconstruction obtained with that technique and reference measurements is about 1 mm, depending on the vertebrae studied. Comparison results indicate that the obtained reconstruction is close to the actual vertebral geometry. This method can therefore be proposed to obtain the 3D geometry of vertebrae.

  12. Effects of point configuration on the accuracy in 3D reconstruction from biplane images

    SciTech Connect

    Dmochowski, Jacek; Hoffmann, Kenneth R.; Singh, Vikas; Xu Jinhui; Nazareth, Daryl P.

    2005-09-15

    Two or more angiograms are being used frequently in medical imaging to reconstruct locations in three-dimensional (3D) space, e.g., for reconstruction of 3D vascular trees, implanted electrodes, or patient positioning. A number of techniques have been proposed for this task. In this simulation study, we investigate the effect of the shape of the configuration of the points in 3D (the 'cloud' of points) on reconstruction errors for one of these techniques developed in our laboratory. Five types of configurations (a ball, an elongated ellipsoid (cigar), flattened ball (pancake), flattened cigar, and a flattened ball with a single distant point) are used in the evaluations. For each shape, 100 random configurations were generated, with point coordinates chosen from Gaussian distributions having a covariance matrix corresponding to the desired shape. The 3D data were projected into the image planes using a known imaging geometry. Gaussian distributed errors were introduced in the x and y coordinates of these projected points. Gaussian distributed errors were also introduced into the gantry information used to calculate the initial imaging geometry. The imaging geometries and 3D positions were iteratively refined using the enhanced-Metz-Fencil technique. The image data were also used to evaluate the feasible R-t solution volume. The 3D errors between the calculated and true positions were determined. The effects of the shape of the configuration, the number of points, the initial geometry error, and the input image error were evaluated. The results for the number of points, initial geometry error, and image error are in agreement with previously reported results, i.e., increasing the number of points and reducing initial geometry and/or image error, improves the accuracy of the reconstructed data. The shape of the 3D configuration of points also affects the error of reconstructed 3D configuration; specifically, errors decrease as the 'volume' of the 3D configuration

  13. An innovative strategy for the identification and 3D reconstruction of pancreatic cancer from CT images.

    PubMed

    Marconi, S; Pugliese, L; Del Chiaro, M; Pozzi Mucelli, R; Auricchio, F; Pietrabissa, A

    2016-09-01

    We propose an innovative tool for Pancreatic Ductal AdenoCarcinoma 3D reconstruction from Multi-Detector-Computed Tomography. The tumor mass is discriminated from health tissue, and the resulting segmentation labels are rendered preserving information on different hypodensity levels. The final 3D virtual model includes also pancreas and main peri-pancreatic vessels, and it is suitable for 3D printing. We performed a preliminary evaluation of the tool effectiveness presenting ten cases of Pancreatic Ductal AdenoCarcinoma processed with the tool to an expert radiologist who can correct the result of the discrimination. In seven of ten cases, the 3D reconstruction is accepted without any modification, while in three cases, only 1.88, 5.13, and 5.70 %, respectively, of the segmentation labels are modified, preliminary proving the high effectiveness of the tool.

  14. A 3D terrain reconstruction method of stereo vision based quadruped robot navigation system

    NASA Astrophysics Data System (ADS)

    Ge, Zhuo; Zhu, Ying; Liang, Guanhao

    2017-01-01

    To provide 3D environment information for the quadruped robot autonomous navigation system during walking through rough terrain, based on the stereo vision, a novel 3D terrain reconstruction method is presented. In order to solve the problem that images collected by stereo sensors have large regions with similar grayscale and the problem that image matching is poor at real-time performance, watershed algorithm and fuzzy c-means clustering algorithm are combined for contour extraction. Aiming at the problem of error matching, duel constraint with region matching and pixel matching is established for matching optimization. Using the stereo matching edge pixel pairs, the 3D coordinate algorithm is estimated according to the binocular stereo vision imaging model. Experimental results show that the proposed method can yield high stereo matching ratio and reconstruct 3D scene quickly and efficiently.

  15. A photogrammetry-based system for 3D surface reconstruction of prosthetics and orthotics.

    PubMed

    Li, Guang-kun; Gao, Fan; Wang, Zhi-gang

    2011-01-01

    The objective of this study is to develop an innovative close range digital photogrammetry (CRDP) system using the commercial digital SLR cameras to measure and reconstruct the 3D surface of prosthetics and orthotics. This paper describes the instrumentation, techniques and preliminary results of the proposed system. The technique works by taking pictures of the object from multiple view angles. The series of pictures were post-processed via feature point extraction, point match and 3D surface reconstruction. In comparison with the traditional method such as laser scanning, the major advantages of our instrument include the lower cost, compact and easy-to-use hardware, satisfactory measurement accuracy, and significantly less measurement time. Besides its potential applications in prosthetics and orthotics surface measurement, the simple setup and its ease of use will make it suitable for various 3D surface reconstructions.

  16. A Laser Line Auto-Scanning System for Underwater 3D Reconstruction.

    PubMed

    Chi, Shukai; Xie, Zexiao; Chen, Wenzhu

    2016-09-20

    In this study, a laser line auto-scanning system was designed to perform underwater close-range 3D reconstructions with high accuracy and resolution. The system changes the laser plane direction with a galvanometer to perform automatic scanning and obtain continuous laser strips for underwater 3D reconstruction. The system parameters were calibrated with the homography constraints between the target plane and image plane. A cost function was defined to optimize the galvanometer's rotating axis equation. Compensation was carried out for the refraction of the incident and emitted light at the interface. The accuracy and the spatial measurement capability of the system were tested and analyzed with standard balls under laboratory underwater conditions, and the 3D surface reconstruction for a sealing cover of an underwater instrument was proved to be satisfactory.

  17. 3D Reconstruction of the Retinal Arterial Tree Using Subject-Specific Fundus Images

    NASA Astrophysics Data System (ADS)

    Liu, D.; Wood, N. B.; Xu, X. Y.; Witt, N.; Hughes, A. D.; Samcg, Thom

    Systemic diseases, such as hypertension and diabetes, are associated with changes in the retinal microvasculature. Although a number of studies have been performed on the quantitative assessment of the geometrical patterns of the retinal vasculature, previous work has been confined to 2 dimensional (2D) analyses. In this paper, we present an approach to obtain a 3D reconstruction of the retinal arteries from a pair of 2D retinal images acquired in vivo. A simple essential matrix based self-calibration approach was employed for the "fundus camera-eye" system. Vessel segmentation was performed using a semi-automatic approach and correspondence between points from different images was calculated. The results of 3D reconstruction show the centreline of retinal vessels and their 3D curvature clearly. Three-dimensional reconstruction of the retinal vessels is feasible and may be useful in future studies of the retinal vasculature in disease.

  18. A Laser Line Auto-Scanning System for Underwater 3D Reconstruction

    PubMed Central

    Chi, Shukai; Xie, Zexiao; Chen, Wenzhu

    2016-01-01

    In this study, a laser line auto-scanning system was designed to perform underwater close-range 3D reconstructions with high accuracy and resolution. The system changes the laser plane direction with a galvanometer to perform automatic scanning and obtain continuous laser strips for underwater 3D reconstruction. The system parameters were calibrated with the homography constraints between the target plane and image plane. A cost function was defined to optimize the galvanometer’s rotating axis equation. Compensation was carried out for the refraction of the incident and emitted light at the interface. The accuracy and the spatial measurement capability of the system were tested and analyzed with standard balls under laboratory underwater conditions, and the 3D surface reconstruction for a sealing cover of an underwater instrument was proved to be satisfactory. PMID:27657074

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

    SciTech Connect

    Mueller, Kerstin; Schwemmer, Chris; Hornegger, Joachim; Zheng Yefeng; Wang Yang; Lauritsch, Guenter; Rohkohl, Christopher; Maier, Andreas K.; Schultz, Carl; Fahrig, Rebecca

    2013-03-15

    Purpose: For interventional cardiac procedures, anatomical and functional information about the cardiac chambers is of major interest. With the technology of angiographic C-arm systems it is possible to reconstruct intraprocedural three-dimensional (3D) images from 2D rotational angiographic projection data (C-arm CT). However, 3D reconstruction of a dynamic object is a fundamental problem in C-arm CT reconstruction. The 2D projections are acquired over a scan time of several seconds, thus the projection data show different states of the heart. A standard FDK reconstruction algorithm would use all acquired data for a filtered backprojection and result in a motion-blurred image. In this approach, a motion compensated reconstruction algorithm requiring knowledge of the 3D heart motion is used. The motion is estimated from a previously presented 3D dynamic surface model. This dynamic surface model results in a sparse motion vector field (MVF) defined at control points. In order to perform a motion compensated reconstruction, a dense motion vector field is required. The dense MVF is generated by interpolation of the sparse MVF. Therefore, the influence of different motion interpolation methods on the reconstructed image quality is evaluated. Methods: Four different interpolation methods, thin-plate splines (TPS), Shepard's method, a smoothed weighting function, and a simple averaging, were evaluated. The reconstruction quality was measured on phantom data, a porcine model as well as on in vivo clinical data sets. As a quality index, the 2D overlap of the forward projected motion compensated reconstructed ventricle and the segmented 2D ventricle blood pool was quantitatively measured with the Dice similarity coefficient and the mean deviation between extracted ventricle contours. For the phantom data set, the normalized root mean square error (nRMSE) and the universal quality index (UQI) were also evaluated in 3D image space. Results: The quantitative evaluation of all

  20. Multi time-step wavefront reconstruction for tomographic adaptive-optics systems.

    PubMed

    Ono, Yoshito H; Akiyama, Masayuki; Oya, Shin; Lardiére, Olivier; Andersen, David R; Correia, Carlos; Jackson, Kate; Bradley, Colin

    2016-04-01

    In tomographic adaptive-optics (AO) systems, errors due to tomographic wavefront reconstruction limit the performance and angular size of the scientific field of view (FoV), where AO correction is effective. We propose a multi time-step tomographic wavefront reconstruction method to reduce the tomographic error by using measurements from both the current and previous time steps simultaneously. We further outline the method to feed the reconstructor with both wind speed and direction of each turbulence layer. An end-to-end numerical simulation, assuming a multi-object AO (MOAO) system on a 30 m aperture telescope, shows that the multi time-step reconstruction increases the Strehl ratio (SR) over a scientific FoV of 10 arc min in diameter by a factor of 1.5-1.8 when compared to the classical tomographic reconstructor, depending on the guide star asterism and with perfect knowledge of wind speeds and directions. We also evaluate the multi time-step reconstruction method and the wind estimation method on the RAVEN demonstrator under laboratory setting conditions. The wind speeds and directions at multiple atmospheric layers are measured successfully in the laboratory experiment by our wind estimation method with errors below 2  ms-1. With these wind estimates, the multi time-step reconstructor increases the SR value by a factor of 1.2-1.5, which is consistent with a prediction from the end-to-end numerical simulation.

  1. GPU-Based 3D Cone-Beam CT Image Reconstruction for Large Data Volume

    PubMed Central

    Zhao, Xing; Hu, Jing-jing; Zhang, Peng

    2009-01-01

    Currently, 3D cone-beam CT image reconstruction speed is still a severe limitation for clinical application. The computational power of modern graphics processing units (GPUs) has been harnessed to provide impressive acceleration of 3D volume image reconstruction. For extra large data volume exceeding the physical graphic memory of GPU, a straightforward compromise is to divide data volume into blocks. Different from the conventional Octree partition method, a new partition scheme is proposed in this paper. This method divides both projection data and reconstructed image volume into subsets according to geometric symmetries in circular cone-beam projection layout, and a fast reconstruction for large data volume can be implemented by packing the subsets of projection data into the RGBA channels of GPU, performing the reconstruction chunk by chunk and combining the individual results in the end. The method is evaluated by reconstructing 3D images from computer-simulation data and real micro-CT data. Our results indicate that the GPU implementation can maintain original precision and speed up the reconstruction process by 110–120 times for circular cone-beam scan, as compared to traditional CPU implementation. PMID:19730744

  2. SU-E-J-128: 3D Surface Reconstruction of a Patient Using Epipolar Geometry

    SciTech Connect

    Kotoku, J; Nakabayashi, S; Kumagai, S; Ishibashi, T; Kobayashi, T; Haga, A; Saotome, N; Arai, N

    2014-06-01

    Purpose: To obtain a 3D surface data of a patient in a non-invasive way can substantially reduce the effort for the registration of patient in radiation therapy. To achieve this goal, we introduced the multiple view stereo technique, which is known to be used in a 'photo tourism' on the internet. Methods: 70 Images were taken with a digital single-lens reflex camera from different angles and positions. The camera positions and angles were inferred later in the reconstruction step. A sparse 3D reconstruction model was locating by SIFT features, which is robust for rotation and shift variance, in each image. We then found a set of correspondences between pairs of images by computing the fundamental matrix using the eight-point algorithm with RANSAC. After the pair matching, we optimized the parameter including camera positions to minimize the reprojection error by use of bundle adjustment technique (non-linear optimization). As a final step, we performed dense reconstruction and associate a color with each point using the library of PMVS. Results: Surface data were reconstructed well by visual inspection. The human skin is reconstructed well, althogh the reconstruction was time-consuming for direct use in daily clinical practice. Conclusion: 3D reconstruction using multi view stereo geometry is a promising tool for reducing the effort of patient setup. This work was supported by JSPS KAKENHI(25861128)

  3. MO-C-18A-01: Advances in Model-Based 3D Image Reconstruction

    SciTech Connect

    Chen, G; Pan, X; Stayman, J; Samei, E

    2014-06-15

    Recent years have seen the emergence of CT image reconstruction techniques that exploit physical models of the imaging system, photon statistics, and even the patient to achieve improved 3D image quality and/or reduction of radiation dose. With numerous advantages in comparison to conventional 3D filtered backprojection, such techniques bring a variety of challenges as well, including: a demanding computational load associated with sophisticated forward models and iterative optimization methods; nonlinearity and nonstationarity in image quality characteristics; a complex dependency on multiple free parameters; and the need to understand how best to incorporate prior information (including patient-specific prior images) within the reconstruction process. The advantages, however, are even greater – for example: improved image quality; reduced dose; robustness to noise and artifacts; task-specific reconstruction protocols; suitability to novel CT imaging platforms and noncircular orbits; and incorporation of known characteristics of the imager and patient that are conventionally discarded. This symposium features experts in 3D image reconstruction, image quality assessment, and the translation of such methods to emerging clinical applications. Dr. Chen will address novel methods for the incorporation of prior information in 3D and 4D CT reconstruction techniques. Dr. Pan will show recent advances in optimization-based reconstruction that enable potential reduction of dose and sampling requirements. Dr. Stayman will describe a “task-based imaging” approach that leverages models of the imaging system and patient in combination with a specification of the imaging task to optimize both the acquisition and reconstruction process. Dr. Samei will describe the development of methods for image quality assessment in such nonlinear reconstruction techniques and the use of these methods to characterize and optimize image quality and dose in a spectrum of clinical

  4. Alignment, segmentation and 3-D reconstruction of serial sections based on automated algorithm

    NASA Astrophysics Data System (ADS)

    Bian, Weiguo; Tang, Shaojie; Xu, Qiong; Lian, Qin; Wang, Jin; Li, Dichen

    2012-12-01

    A well-defined three-dimensional (3-D) reconstruction of bone-cartilage transitional structures is crucial for the osteochondral restoration. This paper presents an accurate, computationally efficient and fully-automated algorithm for the alignment and segmentation of two-dimensional (2-D) serial to construct the 3-D model of bone-cartilage transitional structures. Entire system includes the following five components: (1) image harvest, (2) image registration, (3) image segmentation, (4) 3-D reconstruction and visualization, and (5) evaluation. A computer program was developed in the environment of Matlab for the automatic alignment and segmentation of serial sections. Automatic alignment algorithm based on the position's cross-correlation of the anatomical characteristic feature points of two sequential sections. A method combining an automatic segmentation and an image threshold processing was applied to capture the regions and structures of interest. SEM micrograph and 3-D model reconstructed directly in digital microscope were used to evaluate the reliability and accuracy of this strategy. The morphology of 3-D model constructed by serial sections is consistent with the results of SEM micrograph and 3-D model of digital microscope.

  5. Real-time 3D reconstruction for collision avoidance in interventional environments.

    PubMed

    Ladikos, Alexander; Benhimane, Selim; Navab, Nassir

    2008-01-01

    With the increased presence of automated devices such as C-arms and medical robots and the introduction of a multitude of surgical tools, navigation systems and patient monitoring devices, collision avoidance has become an issue of practical value in interventional environments. In this paper, we present a real-time 3D reconstruction system for interventional environments which aims at predicting collisions by building a 3D representation of all the objects in the room. The 3D reconstruction is used to determine whether other objects are in the working volume of the device and to alert the medical staff before a collision occurs. In the case of C-arms, this allows faster rotational and angular movement which could for instance be used in 3D angiography to obtain a better reconstruction of contrasted vessels. The system also prevents staff to unknowingly enter the working volume of a device. This is of relevance in complex environments with many devices. The recovered 3D representation also opens the path to many new applications utilizing this data such as workflow analysis, 3D video generation or interventional room planning. To validate our claims, we performed several experiments with a real C-arm that show the validity of the approach. This system is currently being transferred to an interventional room in our university hospital.

  6. New techniques of determining focus position in gamma knife operation using 3D image reconstruction

    NASA Astrophysics Data System (ADS)

    Xiong, Yingen; Wang, Dezong; Zhou, Quan

    1994-09-01

    In this paper, new techniques of determining the focus of a disease position in a gamma knife operation are presented. In these techniques, the transparent 3D color image of the human body organ is reconstructed using a new three-dimensional reconstruction method, and then the position, the area, and the volume of focus of a disease such as cancer or a tumor are calculated. They are used in the gamma knife operation. The CT pictures are input into a digital image processing system. The useful information is extracted and the original data are obtained. Then the transparent 3D color image is reconstructed using these original data. By using this transparent 3D color image, the positions of the human body organ and the focus of a disease are determined in a coordinate system. While the 3D image is reconstructed, the area and the volume of human body organ and focus of a disease can be calculated at the same time. It is expressed through actual application that the positions of human body organ and focus of a disease can be determined exactly by using the transparent 3D color image. It is very useful in gamma knife operation or other surgical operation. The techniques presented in this paper have great application value.

  7. On the use of orientation filters for 3D reconstruction in event-driven stereo vision

    PubMed Central

    Camuñas-Mesa, Luis A.; Serrano-Gotarredona, Teresa; Ieng, Sio H.; Benosman, Ryad B.; Linares-Barranco, Bernabe

    2014-01-01

    The recently developed Dynamic Vision Sensors (DVS) sense visual information asynchronously and code it into trains of events with sub-micro second temporal resolution. This high temporal precision makes the output of these sensors especially suited for dynamic 3D visual reconstruction, by matching corresponding events generated by two different sensors in a stereo setup. This paper explores the use of Gabor filters to extract information about the orientation of the object edges that produce the events, therefore increasing the number of constraints applied to the matching algorithm. This strategy provides more reliably matched pairs of events, improving the final 3D reconstruction. PMID:24744694

  8. 3D reconstruction on CBCT in the cystic pathology of the jaws

    NASA Astrophysics Data System (ADS)

    Chioran, Doina; Nicoarǎ, Adrian; Roşu, Şerban; Cǎrligeriu, Virgil; Ianeş, Emilia

    2013-10-01

    The paper presents the image acquisition of Cone Beam Computer Tomography scans of human facial bones and their processing in order to obtain a 3D reconstruction model of the skull. The reconstructed model provides useful data to the physician in situations of maxillary cystic pathology but more important is the data about the relationship of the maxillary cyst with the surrounding anatomical elements. Using the B-splines a 3D volume model of the human facial bones can be achieved. This model can be exported in any CAD system, resulting a virtual model witch can be used in FEM analysis.

  9. On the use of orientation filters for 3D reconstruction in event-driven stereo vision.

    PubMed

    Camuñas-Mesa, Luis A; Serrano-Gotarredona, Teresa; Ieng, Sio H; Benosman, Ryad B; Linares-Barranco, Bernabe

    2014-01-01

    The recently developed Dynamic Vision Sensors (DVS) sense visual information asynchronously and code it into trains of events with sub-micro second temporal resolution. This high temporal precision makes the output of these sensors especially suited for dynamic 3D visual reconstruction, by matching corresponding events generated by two different sensors in a stereo setup. This paper explores the use of Gabor filters to extract information about the orientation of the object edges that produce the events, therefore increasing the number of constraints applied to the matching algorithm. This strategy provides more reliably matched pairs of events, improving the final 3D reconstruction.

  10. A new 3D reconstruction method of small solar system bodies

    NASA Astrophysics Data System (ADS)

    Capanna, C.; Jorda, L.; Lamy, P.; Gesquiere, G.

    2011-10-01

    The 3D reconstruction of small solar system bodies consitutes an essential step toward understanding and interpreting their physical and geological properties. We propose a new reconstruction method by photoclinometry based on the minimization of the chisquare difference between observed and synthetic images by deformation of a 3D triangular mesh. This method has been tested on images of the two asteroids (2867) Steins and (21) Lutetia observed during ESA's ROSETTA mission, and it will be applied to elaborate digital terrain models from images of the asteroid (4) Vesta, the target of NASA's DAWN spacecraft.

  11. Grammar-based Automatic 3D Model Reconstruction from Terrestrial Laser Scanning Data

    NASA Astrophysics Data System (ADS)

    Yu, Q.; Helmholz, P.; Belton, D.; West, G.

    2014-04-01

    The automatic reconstruction of 3D buildings has been an important research topic during the last years. In this paper, a novel method is proposed to automatically reconstruct the 3D building models from segmented data based on pre-defined formal grammar and rules. Such segmented data can be extracted e.g. from terrestrial or mobile laser scanning devices. Two steps are considered in detail. The first step is to transform the segmented data into 3D shapes, for instance using the DXF (Drawing Exchange Format) format which is a CAD data file format used for data interchange between AutoCAD and other program. Second, we develop a formal grammar to describe the building model structure and integrate the pre-defined grammars into the reconstruction process. Depending on the different segmented data, the selected grammar and rules are applied to drive the reconstruction process in an automatic manner. Compared with other existing approaches, our proposed method allows the model reconstruction directly from 3D shapes and takes the whole building into account.

  12. 3D reconstruction of cortical microtubules using multi-angle total internal reflection fluorescence microscopy

    NASA Astrophysics Data System (ADS)

    Jin, Luhong; Xiu, Peng; Zhou, Xiaoxu; Fan, Jiannan; Kuang, Cuifang; Liu, Xu; Xu, Yingke

    2017-01-01

    Total internal reflection fluorescence microscopy (TIRFM) has been widely used in biomedical research to visualize cellular processes near the cell surface. In this study, a novel multi-angle ring-illuminated TIRFM system, equipped with two galvo mirrors that are on conjugate plan of a 4f optical system was developed. Multi-angle TIRFM generates images with different penetration depths through the controlled variation of the incident angle of illuminating laser. We presented a method to perform three-dimensional (3-D) reconstruction of microtubules from multi-angle TIRFM images. The performance of our method was validated in simulated microtubules with variable signal-to-noise ratios (SNR) and the axial resolution and accuracy of reconstruction were evaluated in selecting different numbers of illumination angles or in different SNR conditions. In U373 cells, we reconstructed the 3-D localization of microtubules near the cell surface with high resolution using over a hundred different illumination angles. Theoretically, the presented TIRFM setup and 3-D reconstruction method can achieve 40 nm axial resolution in experimental conditions where SNR is as low as 2, with 35 different illumination angles. Moreover, our system and reconstruction method have the potential to be used in live cells to track membrane dynamics in 3-D.

  13. 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...

  14. TOMOGRAPHIC RECONSTRUCTION OF DIFFUSION PROPAGATORS FROM DW-MRI USING OPTIMAL SAMPLING LATTICES

    PubMed Central

    Ye, Wenxing; Entezari, Alireza; Vemuri, Baba C.

    2010-01-01

    This paper exploits the power of optimal sampling lattices in tomography based reconstruction of the diffusion propagator in diffusion weighted magnetic resonance imaging (DWMRI). Optimal sampling leads to increased accuracy of the tomographic reconstruction approach introduced by Pickalov and Basser [1]. Alternatively, the optimal sampling geometry allows for further reducing the number of samples while maintaining the accuracy of reconstruction of the diffusion propagator. The optimality of the proposed sampling geometry comes from the information theoretic advantages of sphere packing lattices in sampling multidimensional signals. These advantages are in addition to those accrued from the use of the tomographic principle used here for reconstruction. We present comparative results of reconstructions of the diffusion propagator using the Cartesian and the optimal sampling geometry for synthetic and real data sets. PMID:20596298

  15. Demonstration of digital hologram recording and 3D-scenes reconstruction in real-time

    NASA Astrophysics Data System (ADS)

    Cheremkhin, Pavel A.; Evtikhiev, Nikolay N.; Krasnov, Vitaly V.; Kulakov, Mikhail N.; Kurbatova, Ekaterina A.; Molodtsov, Dmitriy Y.; Rodin, Vladislav G.

    2016-04-01

    Digital holography is technique that allows to reconstruct information about 2D-objects and 3D-scenes. This is achieved by registration of interference pattern formed by two beams: object and reference ones. Pattern registered by the digital camera is processed. This allows to obtain amplitude and phase of the object beam. Reconstruction of shape of the 2D objects and 3D-scenes can be obtained numerically (using computer) and optically (using spatial light modulators - SLMs). In this work camera Megaplus II ES11000 was used for digital holograms recording. The camera has 4008 × 2672 pixels with sizes of 9 μm × 9 μm. For hologram recording, 50 mW frequency-doubled Nd:YAG laser with wavelength 532 nm was used. Liquid crystal on silicon SLM HoloEye PLUTO VIS was used for optical reconstruction of digital holograms. SLM has 1920 × 1080 pixels with sizes of 8 μm × 8 μm. At objects reconstruction 10 mW He-Ne laser with wavelength 632.8 nm was used. Setups for digital holograms recording and their optical reconstruction with the SLM were combined as follows. MegaPlus Central Control Software allows to display registered frames by the camera with a little delay on the computer monitor. The SLM can work as additional monitor. In result displayed frames can be shown on the SLM display in near real-time. Thus recording and reconstruction of the 3D-scenes was obtained in real-time. Preliminary, resolution of displayed frames was chosen equaled to the SLM one. Quantity of the pixels was limited by the SLM resolution. Frame rate was limited by the camera one. This holographic video setup was applied without additional program implementations that would increase time delays between hologram recording and object reconstruction. The setup was demonstrated for reconstruction of 3D-scenes.

  16. Using flow information to support 3D vessel reconstruction from rotational angiography

    SciTech Connect

    Waechter, Irina; Bredno, Joerg; Weese, Juergen; Barratt, Dean C.; Hawkes, David J.

    2008-07-15

    For the assessment of cerebrovascular diseases, it is beneficial to obtain three-dimensional (3D) morphologic and hemodynamic information about the vessel system. Rotational angiography is routinely used to image the 3D vascular geometry and we have shown previously that rotational subtraction angiography has the potential to also give quantitative information about blood flow. Flow information can be determined when the angiographic sequence shows inflow and possibly outflow of contrast agent. However, a standard volume reconstruction assumes that the vessel tree is uniformly filled with contrast agent during the whole acquisition. If this is not the case, the reconstruction exhibits artifacts. Here, we show how flow information can be used to support the reconstruction of the 3D vessel centerline and radii in this case. Our method uses the fast marching algorithm to determine the order in which voxels are analyzed. For every voxel, the rotational time intensity curve (R-TIC) is determined from the image intensities at the projection points of the current voxel. Next, the bolus arrival time of the contrast agent at the voxel is estimated from the R-TIC. Then, a measure of the intensity and duration of the enhancement is determined, from which a speed value is calculated that steers the propagation of the fast marching algorithm. The results of the fast marching algorithm are used to determine the 3D centerline by backtracking. The 3D radius is reconstructed from 2D radius estimates on the projection images. The proposed method was tested on computer simulated rotational angiography sequences with systematically varied x-ray acquisition, blood flow, and contrast agent injection parameters and on datasets from an experimental setup using an anthropomorphic cerebrovascular phantom. For the computer simulation, the mean absolute error of the 3D centerline and 3D radius estimation was 0.42 and 0.25 mm, respectively. For the experimental datasets, the mean absolute

  17. Using flow information to support 3D vessel reconstruction from rotational angiography.

    PubMed

    Waechter, Irina; Bredno, Joerg; Weese, Juergen; Barratt, Dean C; Hawkes, David J

    2008-07-01

    For the assessment of cerebrovascular diseases, it is beneficial to obtain three-dimensional (3D) morphologic and hemodynamic information about the vessel system. Rotational angiography is routinely used to image the 3D vascular geometry and we have shown previously that rotational subtraction angiography has the potential to also give quantitative information about blood flow. Flow information can be determined when the angiographic sequence shows inflow and possibly outflow of contrast agent. However, a standard volume reconstruction assumes that the vessel tree is uniformly filled with contrast agent during the whole acquisition. If this is not the case, the reconstruction exhibits artifacts. Here, we show how flow information can be used to support the reconstruction of the 3D vessel centerline and radii in this case. Our method uses the fast marching algorithm to determine the order in which voxels are analyzed. For every voxel, the rotational time intensity curve (R-TIC) is determined from the image intensities at the projection points of the current voxel. Next, the bolus arrival time of the contrast agent at the voxel is estimated from the R-TIC. Then, a measure of the intensity and duration of the enhancement is determined, from which a speed value is calculated that steers the propagation of the fast marching algorithm. The results of the fast marching algorithm are used to determine the 3D centerline by backtracking. The 3D radius is reconstructed from 2D radius estimates on the projection images. The proposed method was tested on computer simulated rotational angiography sequences with systematically varied x-ray acquisition, blood flow, and contrast agent injection parameters and on datasets from an experimental setup using an anthropomorphic cerebrovascular phantom. For the computer simulation, the mean absolute error of the 3D centerline and 3D radius estimation was 0.42 and 0.25 mm, respectively. For the experimental datasets, the mean absolute

  18. Accident or homicide--virtual crime scene reconstruction using 3D methods.

    PubMed

    Buck, Ursula; Naether, Silvio; Räss, Beat; Jackowski, Christian; Thali, Michael J

    2013-02-10

    The analysis and reconstruction of forensically relevant events, such as traffic accidents, criminal assaults and homicides are based on external and internal morphological findings of the injured or deceased person. For this approach high-tech methods are gaining increasing importance in forensic investigations. The non-contact optical 3D digitising system GOM ATOS is applied as a suitable tool for whole body surface and wound documentation and analysis in order to identify injury-causing instruments and to reconstruct the course of event. In addition to the surface documentation, cross-sectional imaging methods deliver medical internal findings of the body. These 3D data are fused into a whole body model of the deceased. Additional to the findings of the bodies, the injury inflicting instruments and incident scene is documented in 3D. The 3D data of the incident scene, generated by 3D laser scanning and photogrammetry, is also included into the reconstruction. Two cases illustrate the methods. In the fist case a man was shot in his bedroom and the main question was, if the offender shot the man intentionally or accidentally, as he declared. In the second case a woman was hit by a car, driving backwards into a garage. It was unclear if the driver drove backwards once or twice, which would indicate that he willingly injured and killed the woman. With this work, we demonstrate how 3D documentation, data merging and animation enable to answer reconstructive questions regarding the dynamic development of patterned injuries, and how this leads to a real data based reconstruction of the course of event.

  19. 3D Reconstruction from X-ray Fluoroscopy for Clinical Veterinary Medicine using Differential Volume Rendering

    NASA Astrophysics Data System (ADS)

    Khongsomboon, Khamphong; Hamamoto, Kazuhiko; Kondo, Shozo

    3D reconstruction from ordinary X-ray equipment which is not CT or MRI is required in clinical veterinary medicine. Authors have already proposed a 3D reconstruction technique from X-ray photograph to present bone structure. Although the reconstruction is useful for veterinary medicine, the thechnique has two problems. One is about exposure of X-ray and the other is about data acquisition process. An x-ray equipment which is not special one but can solve the problems is X-ray fluoroscopy. Therefore, in this paper, we propose a method for 3D-reconstruction from X-ray fluoroscopy for clinical veterinary medicine. Fluoroscopy is usually used to observe a movement of organ or to identify a position of organ for surgery by weak X-ray intensity. Since fluoroscopy can output a observed result as movie, the previous two problems which are caused by use of X-ray photograph can be solved. However, a new problem arises due to weak X-ray intensity. Although fluoroscopy can present information of not only bone structure but soft tissues, the contrast is very low and it is very difficult to recognize some soft tissues. It is very useful to be able to observe not only bone structure but soft tissues clearly by ordinary X-ray equipment in the field of clinical veterinary medicine. To solve this problem, this paper proposes a new method to determine opacity in volume rendering process. The opacity is determined according to 3D differential coefficient of 3D reconstruction. This differential volume rendering can present a 3D structure image of multiple organs volumetrically and clearly for clinical veterinary medicine. This paper shows results of simulation and experimental investigation of small dog and evaluation by veterinarians.

  20. 3D surface reconstruction of apples from 2D NIR images

    NASA Astrophysics Data System (ADS)

    Zhu, Bin; Jiang, Lu; Cheng, Xuemei; Tao, Yang

    2005-11-01

    Machine vision methods are widely used in apple defect detection and quality grading applications. Currently, 2D near-infrared (NIR) imaging of apples is often used to detect apple defects because the image intensity of defects is different from normal apple parts. However, a drawback of this method is that the apple calyx also exhibits similar image intensity to the apple defects. Since an apple calyx often appears in the NIR image, the false alarm rate is high with the 2D NIR imaging method. In this paper, a 2D NIR imaging method is extended to a 3D reconstruction so that the apple calyx can be differentiated from apple defects according to their different 3D depth information. The Lambertian model is used to evaluate the reflectance map of the apple surface, and then Pentland's Shape-From-Shading (SFS) method is applied to reconstruct the 3D surface information of the apple based on Fast Fourier Transform (FFT). Pentland's method is directly derived from human perception properties, making it close to the way human eyes recover 3D information from a 2D scene. In addition, the FFT reduces the computation time significantly. The reconstructed 3D apple surface maps are shown in the results, and different depths of apple calyx and defects are obtained correctly.

  1. A Hierarchical Building Segmentation in Digital Surface Models for 3D Reconstruction

    PubMed Central

    Yan, Yiming; Gao, Fengjiao; Deng, Shupei; Su, Nan

    2017-01-01

    In this study, a hierarchical method for segmenting buildings in a digital surface model (DSM), which is used in a novel framework for 3D reconstruction, is proposed. Most 3D reconstructions of buildings are model-based. However, the limitations of these methods are overreliance on completeness of the offline-constructed models of buildings, and the completeness is not easily guaranteed since in modern cities buildings can be of a variety of types. Therefore, a model-free framework using high precision DSM and texture-images buildings was introduced. There are two key problems with this framework. The first one is how to accurately extract the buildings from the DSM. Most segmentation methods are limited by either the terrain factors or the difficult choice of parameter-settings. A level-set method are employed to roughly find the building regions in the DSM, and then a recently proposed ‘occlusions of random textures model’ are used to enhance the local segmentation of the buildings. The second problem is how to generate the facades of buildings. Synergizing with the corresponding texture-images, we propose a roof-contour guided interpolation of building facades. The 3D reconstruction results achieved by airborne-like images and satellites are compared. Experiments show that the segmentation method has good performance, and 3D reconstruction is easily performed by our framework, and better visualization results can be obtained by airborne-like images, which can be further replaced by UAV images. PMID:28125018

  2. Toward 3D Reconstruction of Outdoor Scenes Using an MMW Radar and a Monocular Vision Sensor

    PubMed Central

    El Natour, Ghina; Ait-Aider, Omar; Rouveure, Raphael; Berry, François; Faure, Patrice

    2015-01-01

    In this paper, we introduce a geometric method for 3D reconstruction of the exterior environment using a panoramic microwave radar and a camera. We rely on the complementarity of these two sensors considering the robustness to the environmental conditions and depth detection ability of the radar, on the one hand, and the high spatial resolution of a vision sensor, on the other. Firstly, geometric modeling of each sensor and of the entire system is presented. Secondly, we address the global calibration problem, which consists of finding the exact transformation between the sensors’ coordinate systems. Two implementation methods are proposed and compared, based on the optimization of a non-linear criterion obtained from a set of radar-to-image target correspondences. Unlike existing methods, no special configuration of the 3D points is required for calibration. This makes the methods flexible and easy to use by a non-expert operator. Finally, we present a very simple, yet robust 3D reconstruction method based on the sensors’ geometry. This method enables one to reconstruct observed features in 3D using one acquisition (static sensor), which is not always met in the state of the art for outdoor scene reconstruction. The proposed methods have been validated with synthetic and real data. PMID:26473874

  3. Toward 3D reconstruction of outdoor scenes using an MMW radar and a monocular vision sensor.

    PubMed

    Natour, Ghina El; Ait-Aider, Omar; Rouveure, Raphael; Berry, François; Faure, Patrice

    2015-10-14

    In this paper, we introduce a geometric method for 3D reconstruction of the exterior environment using a panoramic microwave radar and a camera. We rely on the complementarity of these two sensors considering the robustness to the environmental conditions and depth detection ability of the radar, on the one hand, and the high spatial resolution of a vision sensor, on the other. Firstly, geometric modeling of each sensor and of the entire system is presented. Secondly, we address the global calibration problem, which consists of finding the exact transformation between the sensors' coordinate systems. Two implementation methods are proposed and compared, based on the optimization of a non-linear criterion obtained from a set of radar-to-image target correspondences. Unlike existing methods, no special configuration of the 3D points is required for calibration. This makes the methods flexible and easy to use by a non-expert operator. Finally, we present a very simple, yet robust 3D reconstruction method based on the sensors' geometry. This method enables one to reconstruct observed features in 3D using one acquisition (static sensor), which is not always met in the state of the art for outdoor scene reconstruction. The proposed methods have been validated with synthetic and real data.

  4. Some Methods of Applied Numerical Analysis to 3d Facial Reconstruction Software

    NASA Astrophysics Data System (ADS)

    Roşu, Şerban; Ianeş, Emilia; Roşu, Doina

    2010-09-01

    This paper deals with the collective work performed by medical doctors from the University Of Medicine and Pharmacy Timisoara and engineers from the Politechnical Institute Timisoara in the effort to create the first Romanian 3d reconstruction software based on CT or MRI scans and to test the created software in clinical practice.

  5. A Novel Image Compression Algorithm for High Resolution 3D Reconstruction

    NASA Astrophysics Data System (ADS)

    Siddeq, M. M.; Rodrigues, M. A.

    2014-06-01

    This research presents a novel algorithm to compress high-resolution images for accurate structured light 3D reconstruction. Structured light images contain a pattern of light and shadows projected on the surface of the object, which are captured by the sensor at very high resolutions. Our algorithm is concerned with compressing such images to a high degree with minimum loss without adversely affecting 3D reconstruction. The Compression Algorithm starts with a single level discrete wavelet transform (DWT) for decomposing an image into four sub-bands. The sub-band LL is transformed by DCT yielding a DC-matrix and an AC-matrix. The Minimize-Matrix-Size Algorithm is used to compress the AC-matrix while a DWT is applied again to the DC-matrix resulting in LL2, HL2, LH2 and HH2 sub-bands. The LL2 sub-band is transformed by DCT, while the Minimize-Matrix-Size Algorithm is applied to the other sub-bands. The proposed algorithm has been tested with images of different sizes within a 3D reconstruction scenario. The algorithm is demonstrated to be more effective than JPEG2000 and JPEG concerning higher compression rates with equivalent perceived quality and the ability to more accurately reconstruct the 3D models.

  6. 2D Feature Recognition And 3d Reconstruction In Solar Euv Images

    NASA Astrophysics Data System (ADS)

    Aschwanden, Markus J.

    2005-05-01

    EUV images show the solar corona in a typical temperature range of T >rsim 1 MK, which encompasses the most common coronal structures: loops, filaments, and other magnetic structures in active regions, the quiet Sun, and coronal holes. Quantitative analysis increasingly demands automated 2D feature recognition and 3D reconstruction, in order to localize, track, and monitor the evolution of such coronal structures. We discuss numerical tools that “fingerprint” curvi-linear 1D features (e.g., loops and filaments). We discuss existing finger-printing algorithms, such as the brightness-gradient method, the oriented-connectivity method, stereoscopic methods, time-differencing, and space time feature recognition. We discuss improved 2D feature recognition and 3D reconstruction techniques that make use of additional a priori constraints, using guidance from magnetic field extrapolations, curvature radii constraints, and acceleration and velocity constraints in time-dependent image sequences. Applications of these algorithms aid the analysis of SOHO/EIT, TRACE, and STEREO/SECCHI data, such as disentangling, 3D reconstruction, and hydrodynamic modeling of coronal loops, postflare loops, filaments, prominences, and 3D reconstruction of the coronal magnetic field in general.

  7. Identification of superficial defects in reconstructed 3D objects using phase-shifting fringe projection

    NASA Astrophysics Data System (ADS)

    Madrigal, Carlos A.; Restrepo, Alejandro; Branch, John W.

    2016-09-01

    3D reconstruction of small objects is used in applications of surface analysis, forensic analysis and tissue reconstruction in medicine. In this paper, we propose a strategy for the 3D reconstruction of small objects and the identification of some superficial defects. We applied a technique of projection of structured light patterns, specifically sinusoidal fringes and an algorithm of phase unwrapping. A CMOS camera was used to capture images and a DLP digital light projector for synchronous projection of the sinusoidal pattern onto the objects. We implemented a technique based on a 2D flat pattern as calibration process, so the intrinsic and extrinsic parameters of the camera and the DLP were defined. Experimental tests were performed in samples of artificial teeth, coal particles, welding defects and surfaces tested with Vickers indentation. Areas less than 5cm were studied. The objects were reconstructed in 3D with densities of about one million points per sample. In addition, the steps of 3D description, identification of primitive, training and classification were implemented to recognize defects, such as: holes, cracks, roughness textures and bumps. We found that pattern recognition strategies are useful, when quality supervision of surfaces has enough quantities of points to evaluate the defective region, because the identification of defects in small objects is a demanding activity of the visual inspection.

  8. Fuzzy zoning for feature matching technique in 3D reconstruction of nasal endoscopic images.

    PubMed

    Rattanalappaiboon, Surapong; Bhongmakapat, Thongchai; Ritthipravat, Panrasee

    2015-12-01

    3D reconstruction from nasal endoscopic images greatly supports an otolaryngologist in examining nasal passages, mucosa, polyps, sinuses, and nasopharyx. In general, structure from motion is a popular technique. It consists of four main steps; (1) camera calibration, (2) feature extraction, (3) feature matching, and (4) 3D reconstruction. Scale Invariant Feature Transform (SIFT) algorithm is normally used for both feature extraction and feature matching. However, SIFT algorithm relatively consumes computational time particularly in the feature matching process because each feature in an image of interest is compared with all features in the subsequent image in order to find the best matched pair. A fuzzy zoning approach is developed for confining feature matching area. Matching between two corresponding features from different images can be efficiently performed. With this approach, it can greatly reduce the matching time. The proposed technique is tested with endoscopic images created from phantoms and compared with the original SIFT technique in terms of the matching time and average errors of the reconstructed models. Finally, original SIFT and the proposed fuzzy-based technique are applied to 3D model reconstruction of real nasal cavity based on images taken from a rigid nasal endoscope. The results showed that the fuzzy-based approach was significantly faster than traditional SIFT technique and provided similar quality of the 3D models. It could be used for creating a nasal cavity taken by a rigid nasal endoscope.

  9. 3D image reconstruction algorithms for cryo-electron-microscopy images of virus particles

    NASA Astrophysics Data System (ADS)

    Doerschuk, Peter C.; Johnson, John E.

    2000-11-01

    A statistical model for the object and the complete image formation process in cryo electron microscopy of viruses is presented. Using this model, maximum likelihood reconstructions of the 3D structure of viruses are computed using the expectation maximization algorithm and an example based on Cowpea mosaic virus is provided.

  10. Multi-planar velocimetry for 3D reconstruction of the flow

    NASA Astrophysics Data System (ADS)

    Falahatpisheh, Ahmad; Pedrizzetti, Gianni; Kheradvar, Arash

    2012-11-01

    Several extensions of PIV have been proposed for measurements of 3D fields which are restricted for full-volume quantification. We have introduced a fundamentally different solution for experimentally characterizing the incompressible and time-periodic flows in 3D, such as those found in the cardiovascular system. 2D velocity data, acquired by 2C-PIV in multiple planes, is reconstructed to a 3D velocity field taking advantage of the incompressibility of the flow. Using 2D samples instead of scanning the entire 3D domain leads to higher temporal/spatial resolutions since each slice is acquired in a 2D fashion. Hence, there is the possibility of extension to other (medical) imaging modalities that cannot employ advanced 3D optical techniques. 2C-velocimetry on two perpendicular stacks is used for 3D interpolation. The interpolated velocity field is then corrected to satisfy the incompressibility constraint by adding an irrotational velocity field that projects the velocity into a divergence-free vector field space. The method has been validated by exemplary flows having both compact and non-compact structures and different levels of noise. The results show improvements in the reliability of the reconstructed vector field. Application to cardiac flow is also verified.

  11. Streaming video-based 3D reconstruction method compatible with existing monoscopic and stereoscopic endoscopy systems

    NASA Astrophysics Data System (ADS)

    Bouma, Henri; van der Mark, Wannes; Eendebak, Pieter T.; Landsmeer, Sander H.; van Eekeren, Adam W. M.; ter Haar, Frank B.; Wieringa, F. Pieter; van Basten, Jean-Paul

    2012-06-01

    Compared to open surgery, minimal invasive surgery offers reduced trauma and faster recovery. However, lack of direct view limits space perception. Stereo-endoscopy improves depth perception, but is still restricted to the direct endoscopic field-of-view. We describe a novel technology that reconstructs 3D-panoramas from endoscopic video streams providing a much wider cumulative overview. The method is compatible with any endoscope. We demonstrate that it is possible to generate photorealistic 3D-environments from mono- and stereoscopic endoscopy. The resulting 3D-reconstructions can be directly applied in simulators and e-learning. Extended to real-time processing, the method looks promising for telesurgery or other remote vision-guided tasks.

  12. 3D Surface Reconstruction of Plant Seeds by Volume Carving: Performance and Accuracies

    PubMed Central

    Roussel, Johanna; Geiger, Felix; Fischbach, Andreas; Jahnke, Siegfried; Scharr, Hanno

    2016-01-01

    We describe a method for 3D reconstruction of plant seed surfaces, focusing on small seeds with diameters as small as 200 μm. The method considers robotized systems allowing single seed handling in order to rotate a single seed in front of a camera. Even though such systems feature high position repeatability, at sub-millimeter object scales, camera pose variations have to be compensated. We do this by robustly estimating the tool center point from each acquired image. 3D reconstruction can then be performed by a simple shape-from-silhouette approach. In experiments we investigate runtimes, theoretically achievable accuracy, experimentally achieved accuracy, and show as a proof of principle that the proposed method is well sufficient for 3D seed phenotyping purposes. PMID:27375628

  13. A robust automated method to detect stent struts in 3D intravascular optical coherence tomographic image sequences

    NASA Astrophysics Data System (ADS)

    Wang, A.; Eggermont, J.; Dekker, N.; Garcia-Garcia, H. M.; Pawar, R.; Reiber, J. H. C.; Dijkstra, J.

    2012-03-01

    Intravascular optical coherence tomography (IVOCT) provides very high resolution cross-sectional image sequences of vessels. It has been rapidly accepted for stent implantation and its follow up evaluation. Given the large amount of stent struts in a single image sequence, only automated detection methods are feasible. In this paper, we present an automated stent strut detection technique which requires neither lumen nor vessel wall segmentation. To detect strut-pixel candidates, both global intensity histograms and local intensity profiles of the raw polar images are used. Gaussian smoothing is applied followed by specified Prewitt compass filters to detect the trailing shadow of each strut. The shadow edge positions assist the strut-pixel candidates clustering. In the end, a 3D guide wire filter is applied to remove the guide wire from the detection results. For validation, two experts marked 6738 struts in 1021 frames in 10 IVOCT image sequences from a one-year follow up study. The struts were labeled as malapposed, apposed or covered together with the image quality (high, medium, low). The inter-observer agreement was 96%. The algorithm was validated for different combinations of strut status and image quality. Compared to the manual results, 93% of the struts were correctly detected by the new method. For each combination, the lowest accuracy was 88%, which shows the robustness towards different situations. The presented method can detect struts automatically regardless of the strut status or the image quality, which can be used for quantitative measurement, 3D reconstruction and visualization of the implanted stents.

  14. Implicit Regularization for Reconstructing 3D Building Rooftop Models Using Airborne LiDAR Data

    PubMed Central

    Jung, Jaewook; Jwa, Yoonseok; Sohn, Gunho

    2017-01-01

    With rapid urbanization, highly accurate and semantically rich virtualization of building assets in 3D become more critical for supporting various applications, including urban planning, emergency response and location-based services. Many research efforts have been conducted to automatically reconstruct building models at city-scale from remotely sensed data. However, developing a fully-automated photogrammetric computer vision system enabling the massive generation of highly accurate building models still remains a challenging task. One the most challenging task for 3D building model reconstruction is to regularize the noises introduced in the boundary of building object retrieved from a raw data with lack of knowledge on its true shape. This paper proposes a data-driven modeling approach to reconstruct 3D rooftop models at city-scale from airborne laser scanning (ALS) data. The focus of the proposed method is to implicitly derive the shape regularity of 3D building rooftops from given noisy information of building boundary in a progressive manner. This study covers a full chain of 3D building modeling from low level processing to realistic 3D building rooftop modeling. In the element clustering step, building-labeled point clouds are clustered into homogeneous groups by applying height similarity and plane similarity. Based on segmented clusters, linear modeling cues including outer boundaries, intersection lines, and step lines are extracted. Topology elements among the modeling cues are recovered by the Binary Space Partitioning (BSP) technique. The regularity of the building rooftop model is achieved by an implicit regularization process in the framework of Minimum Description Length (MDL) combined with Hypothesize and Test (HAT). The parameters governing the MDL optimization are automatically estimated based on Min-Max optimization and Entropy-based weighting method. The performance of the proposed method is tested over the International Society for

  15. A Skeleton-Based 3D Shape Reconstruction of Free-Form Objects with Stereo Vision

    NASA Astrophysics Data System (ADS)

    Saini, Deepika; Kumar, Sanjeev

    2015-12-01

    In this paper, an efficient approach is proposed for recovering the 3D shape of a free-form object from its arbitrary pair of stereo images. In particular, the reconstruction problem is treated as the reconstruction of the skeleton and the external boundary of the object. The reconstructed skeleton is termed as the line-like representation or curve-skeleton of the 3D object. The proposed solution for object reconstruction is based on this evolved curve-skeleton. It is used as a seed for recovering shape of the 3D object, and the extracted boundary is used for terminating the growing process of the object. NURBS-skeleton is used to extract the skeleton of both views. Affine invariant property of the convex hulls is used to establish the correspondence between the skeletons and boundaries in the stereo images. In the growing process, a distance field is defined for each skeleton point as the smallest distance from that point to the boundary of the object. A sphere centered at a skeleton point of radius equal to the minimum distance to the boundary is tangential to the boundary. Filling in the spheres centered at each skeleton point reconstructs the object. Several results are presented in order to check the applicability and validity of the proposed algorithm.

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

    PubMed

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

    2005-09-01

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

  17. Non-convexly constrained image reconstruction from nonlinear tomographic X-ray measurements

    PubMed Central

    Blumensath, Thomas; Boardman, Richard

    2015-01-01

    The use of polychromatic X-ray sources in tomographic X-ray measurements leads to nonlinear X-ray transmission effects. As these nonlinearities are not normally taken into account in tomographic reconstruction, artefacts occur, which can be particularly severe when imaging objects with multiple materials of widely varying X-ray attenuation properties. In these settings, reconstruction algorithms based on a nonlinear X-ray transmission model become valuable. We here study the use of one such model and develop algorithms that impose additional non-convex constraints on the reconstruction. This allows us to reconstruct volumetric data even when limited measurements are available. We propose a nonlinear conjugate gradient iterative hard thresholding algorithm and show how many prior modelling assumptions can be imposed using a range of non-convex constraints. PMID:25939619

  18. Internet2-based 3D PET image reconstruction using a PC cluster

    NASA Astrophysics Data System (ADS)

    Shattuck, D. W.; Rapela, J.; Asma, E.; Chatzioannou, A.; Qi, J.; Leahy, R. M.

    2002-08-01

    We describe an approach to fast iterative reconstruction from fully three-dimensional (3D) PET data using a network of PentiumIII PCs configured as a Beowulf cluster. To facilitate the use of this system, we have developed a browser-based interface using Java. The system compresses PET data on the user's machine, sends these data over a network, and instructs the PC cluster to reconstruct the image. The cluster implements a parallelized version of our preconditioned conjugate gradient method for fully 3D MAP image reconstruction. We report on the speed-up factors using the Beowulf approach and the impacts of communication latencies in the local cluster network and the network connection between the user's machine and our PC cluster.

  19. Internet2-based 3D PET image reconstruction using a PC cluster.

    PubMed

    Shattuck, D W; Rapela, J; Asma, E; Chatzioannou, A; Qi, J; Leahy, R M

    2002-08-07

    We describe an approach to fast iterative reconstruction from fully three-dimensional (3D) PET data using a network of PentiumIII PCs configured as a Beowulf cluster. To facilitate the use of this system, we have developed a browser-based interface using Java. The system compresses PET data on the user's machine, sends these data over a network, and instructs the PC cluster to reconstruct the image. The cluster implements a parallelized version of our preconditioned conjugate gradient method for fully 3D MAP image reconstruction. We report on the speed-up factors using the Beowulf approach and the impacts of communication latencies in the local cluster network and the network connection between the user's machine and our PC cluster.

  20. Tensor-based Dictionary Learning for Dynamic Tomographic Reconstruction

    PubMed Central

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

    2015-01-01

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

  1. Tensor-based dictionary learning for dynamic tomographic reconstruction

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  2. Validation of Spherically Symmetric Inversion by Use of a Tomographically Reconstructed Three-Dimensional Electron Density of the Solar Corona

    NASA Technical Reports Server (NTRS)

    Wang, Tongjiang; Davila, Joseph M.

    2014-01-01

    Determining the coronal electron density by the inversion of white-light polarized brightness (pB) measurements by coronagraphs is a classic problem in solar physics. An inversion technique based on the spherically symmetric geometry (spherically symmetric inversion, SSI) was developed in the 1950s and has been widely applied to interpret various observations. However, to date there is no study of the uncertainty estimation of this method. We here present the detailed assessment of this method using a three-dimensional (3D) electron density in the corona from 1.5 to 4 solar radius as a model, which is reconstructed by a tomography method from STEREO/COR1 observations during the solar minimum in February 2008 (Carrington Rotation, CR 2066).We first show in theory and observation that the spherically symmetric polynomial approximation (SSPA) method and the Van de Hulst inversion technique are equivalent. Then we assess the SSPA method using synthesized pB images from the 3D density model, and find that the SSPA density values are close to the model inputs for the streamer core near the plane of the sky (POS) with differences generally smaller than about a factor of two; the former has the lower peak but extends more in both longitudinal and latitudinal directions than the latter. We estimate that the SSPA method may resolve the coronal density structure near the POS with angular resolution in longitude of about 50 deg. Our results confirm the suggestion that the SSI method is applicable to the solar minimum streamer (belt), as stated in some previous studies. In addition, we demonstrate that the SSPA method can be used to reconstruct the 3D coronal density, roughly in agreement with the reconstruction by tomography for a period of low solar activity (CR 2066). We suggest that the SSI method is complementary to the 3D tomographic technique in some cases, given that the development of the latter is still an ongoing research effort.

  3. Orbital Wall Reconstruction with Two-Piece Puzzle 3D Printed Implants: Technical Note

    PubMed Central

    Mommaerts, Maurice Y.; Büttner, Michael; Vercruysse, Herman; Wauters, Lauri; Beerens, Maikel

    2015-01-01

    The purpose of this article is to describe a technique for secondary reconstruction of traumatic orbital wall defects using titanium implants that act as three-dimensional (3D) puzzle pieces. We present three cases of large defect reconstruction using implants produced by Xilloc Medical B.V. (Maastricht, the Netherlands) with a 3D printer manufactured by LayerWise (3D Systems; Heverlee, Belgium), and designed using the biomedical engineering software programs ProPlan and 3-Matic (Materialise, Heverlee, Belgium). The smaller size of the implants allowed sequential implantation for the reconstruction of extensive two-wall defects via a limited transconjunctival incision. The precise fit of the implants with regard to the surrounding ledges and each other was confirmed by intraoperative 3D imaging (Mobile C-arm Systems B.V. Pulsera, Philips Medical Systems, Eindhoven, the Netherlands). The patients showed near-complete restoration of orbital volume and ocular motility. However, challenges remain, including traumatic fat atrophy and fibrosis. PMID:26889349

  4. Sensor Fusion of Cameras and a Laser for City-Scale 3D Reconstruction

    PubMed Central

    Bok, Yunsu; Choi, Dong-Geol; Kweon, In So

    2014-01-01

    This paper presents a sensor fusion system of cameras and a 2D laser sensor for large-scale 3D reconstruction. The proposed system is designed to capture data on a fast-moving ground vehicle. The system consists of six cameras and one 2D laser sensor, and they are synchronized by a hardware trigger. Reconstruction of 3D structures is done by estimating frame-by-frame motion and accumulating vertical laser scans, as in previous works. However, our approach does not assume near 2D motion, but estimates free motion (including absolute scale) in 3D space using both laser data and image features. In order to avoid the degeneration associated with typical three-point algorithms, we present a new algorithm that selects 3D points from two frames captured by multiple cameras. The problem of error accumulation is solved by loop closing, not by GPS. The experimental results show that the estimated path is successfully overlaid on the satellite images, such that the reconstruction result is very accurate. PMID:25375758

  5. 3D reconstruction of the coronary tree from two X-ray angiographic views

    NASA Astrophysics Data System (ADS)

    Sang, Nong; Peng, Weixue; Li, Heng; Zhang, Zhen; Zhang, Tianxu

    2006-03-01

    In this paper, we develop a method for the reconstruction of 3D coronary artery based on two perspective projections acquired on a standard single plane angiographic system in the same systole. Our reconstruction is based on the model of generalized cylinders, which are generated by sweeping a two-dimensional cross section along an axis in three-dimensional space. We restrict the cross section to be circular and always perpendicular to the tangent of the axis. Firstly, the vascular centerlines of the X-ray angiography images on both projections are semiautomatically extracted by multiscale vessel tracking using Gabor filters, and the radius of the coronary are also acquired simultaneously. Secondly, the relative geometry of the two projections is determined by the gantry information and 2D matching is realized through the epipolar geometry and the consistency of the vessels. Thirdly, we determine the three-dimensional (3D) coordinates of the identified object points from the image coordinates of the matched points and the calculated imaging system geometry. Finally, we link the consequent cross sections which are processed according to the radius and the direction information to obtain the 3D structure of the artery. The proposed 3D reconstruction method is validated on real data and is shown to perform robustly and accurately in the presence of noise.

  6. Real-Time Large Scale 3d Reconstruction by Fusing Kinect and Imu Data

    NASA Astrophysics Data System (ADS)

    Huai, J.; Zhang, Y.; Yilmaz, A.

    2015-08-01

    Kinect-style RGB-D cameras have been used to build large scale dense 3D maps for indoor environments. These maps can serve many purposes such as robot navigation, and augmented reality. However, to generate dense 3D maps of large scale environments is still very challenging. In this paper, we present a mapping system for 3D reconstruction that fuses measurements from a Kinect and an inertial measurement unit (IMU) to estimate motion. Our major achievements include: (i) Large scale consistent 3D reconstruction is realized by volume shifting and loop closure; (ii) The coarse-to-fine iterative closest point (ICP) algorithm, the SIFT odometry, and IMU odometry are combined to robustly and precisely estimate pose. In particular, ICP runs routinely to track the Kinect motion. If ICP fails in planar areas, the SIFT odometry provides incremental motion estimate. If both ICP and the SIFT odometry fail, e.g., upon abrupt motion or inadequate features, the incremental motion is estimated by the IMU. Additionally, the IMU also observes the roll and pitch angles which can reduce long-term drift of the sensor assembly. In experiments on a consumer laptop, our system estimates motion at 8Hz on average while integrating color images to the local map and saving volumes of meshes concurrently. Moreover, it is immune to tracking failures, and has smaller drift than the state-of-the-art systems in large scale reconstruction.

  7. 3D image reconstruction for PET by multi-slice rebinning and axial filtering

    SciTech Connect

    Lewitt, R.M. |; Muehllehner, G.; Karp, J.S.

    1991-12-01

    Two different approaches are used at present to reconstruct from 3D coincidence data in PET. We refer to these approaches as the single-slice rebinning approach and the fully-3D approach. The single-slice rebinning approach involves geometrical approximations, but it requires the least possible amount of computation. Fully-3D reconstruction algorithms, both iterative and non-iterative, do not make such approximations, but require much more computation. Multi-slice rebinning with axial filtering is a new approach which attempts to achieve the geometrical accuracy of the fully-3D approach with the simplicity and modest amount of computation of the single-slice rebinning approach. The first step (multi-slice rebinning) involves rebinning of coincidence lines into a stack of 2D sinograms, where multiple sinograms are incremented for each oblique coincidence line. This operation is followed by an axial filtering operation, either before or after slice-by-slice reconstruction, to reduce the blurring in the axial direction. Tests with simulated and experimental data indicate that the new method has better geometrical accuracy than single-slice rebinning, at the cost of only a modest increase in computation. 11 refs.

  8. External force back-projective composition and globally deformable optimization for 3-D coronary artery reconstruction.

    PubMed

    Yang, Jian; Cong, Weijian; Chen, Yang; Fan, Jingfan; Liu, Yue; Wang, Yongtian

    2014-02-21

    The clinical value of the 3D reconstruction of a coronary artery is important for the diagnosis and intervention of cardiovascular diseases. This work proposes a method based on a deformable model for reconstructing coronary arteries from two monoplane angiographic images acquired from different angles. First, an external force back-projective composition model is developed to determine the external force, for which the force distributions in different views are back-projected to the 3D space and composited in the same coordinate system based on the perspective projection principle of x-ray imaging. The elasticity and bending forces are composited as an internal force to maintain the smoothness of the deformable curve. Second, the deformable curve evolves rapidly toward the true vascular centerlines in 3D space and angiographic images under the combination of internal and external forces. Third, densely matched correspondence among vessel centerlines is constructed using a curve alignment method. The bundle adjustment method is then utilized for the global optimization of the projection parameters and the 3D structures. The proposed method is validated on phantom data and routine angiographic images with consideration for space and re-projection image errors. Experimental results demonstrate the effectiveness and robustness of the proposed method for the reconstruction of coronary arteries from two monoplane angiographic images. The proposed method can achieve a mean space error of 0.564 mm and a mean re-projection error of 0.349 mm.

  9. Virtual 3D bladder reconstruction for augmented medical records from white light cystoscopy (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Lurie, Kristen L.; Zlatev, Dimitar V.; Angst, Roland; Liao, Joseph C.; Ellerbee, Audrey K.

    2016-02-01

    Bladder cancer has a high recurrence rate that necessitates lifelong surveillance to detect mucosal lesions. Examination with white light cystoscopy (WLC), the standard of care, is inherently subjective and data storage limited to clinical notes, diagrams, and still images. A visual history of the bladder wall can enhance clinical and surgical management. To address this clinical need, we developed a tool to transform in vivo WLC videos into virtual 3-dimensional (3D) bladder models using advanced computer vision techniques. WLC videos from rigid cystoscopies (1280 x 720 pixels) were recorded at 30 Hz followed by immediate camera calibration to control for image distortions. Video data were fed into an automated structure-from-motion algorithm that generated a 3D point cloud followed by a 3D mesh to approximate the bladder surface. The highest quality cystoscopic images were projected onto the approximated bladder surface to generate a virtual 3D bladder reconstruction. In intraoperative WLC videos from 36 patients undergoing transurethral resection of suspected bladder tumors, optimal reconstruction was achieved from frames depicting well-focused vasculature, when the bladder was maintained at constant volume with minimal debris, and when regions of the bladder wall were imaged multiple times. A significant innovation of this work is the ability to perform the reconstruction using video from a clinical procedure collected with standard equipment, thereby facilitating rapid clinical translation, application to other forms of endoscopy and new opportunities for longitudinal studies of cancer recurrence.

  10. Interactive Retro-Deformation of Terrain for Reconstructing 3D Fault Displacements.

    PubMed

    Westerteiger, R; Compton, T; Bernadin, T; Cowgill, E; Gwinner, K; Hamann, B; Gerndt, A; Hagen, H

    2012-12-01

    Planetary topography is the result of complex interactions between geological processes, of which faulting is a prominent component. Surface-rupturing earthquakes cut and move landforms which develop across active faults, producing characteristic surface displacements across the fault. Geometric models of faults and their associated surface displacements are commonly applied to reconstruct these offsets to enable interpretation of the observed topography. However, current 2D techniques are limited in their capability to convey both the three-dimensional kinematics of faulting and the incremental sequence of events required by a given reconstruction. Here we present a real-time system for interactive retro-deformation of faulted topography to enable reconstruction of fault displacement within a high-resolution (sub 1m/pixel) 3D terrain visualization. We employ geometry shaders on the GPU to intersect the surface mesh with fault-segments interactively specified by the user and transform the resulting surface blocks in realtime according to a kinematic model of fault motion. Our method facilitates a human-in-the-loop approach to reconstruction of fault displacements by providing instant visual feedback while exploring the parameter space. Thus, scientists can evaluate the validity of traditional point-to-point reconstructions by visually examining a smooth interpolation of the displacement in 3D. We show the efficacy of our approach by using it to reconstruct segments of the San Andreas fault, California as well as a graben structure in the Noctis Labyrinthus region on Mars.

  11. A toolbox for ab initio 3-D reconstructions in single-particle electron microscopy.

    PubMed

    Voss, Neil R; Lyumkis, Dmitry; Cheng, Anchi; Lau, Pick-Wei; Mulder, Anke; Lander, Gabriel C; Brignole, Edward J; Fellmann, Denis; Irving, Christopher; Jacovetty, Erica L; Leung, Albert; Pulokas, James; Quispe, Joel D; Winkler, Hanspeter; Yoshioka, Craig; Carragher, Bridget; Potter, Clinton S

    2010-03-01

    Structure determination of a novel macromolecular complex via single-particle electron microscopy depends upon overcoming the challenge of establishing a reliable 3-D reconstruction using only 2-D images. There are a variety of strategies that deal with this issue, but not all of them are readily accessible and straightforward to use. We have developed a "toolbox" of ab initio reconstruction techniques that provide several options for calculating 3-D volumes in an easily managed and tightly controlled work-flow that adheres to standard conventions and formats. This toolbox is designed to streamline the reconstruction process by removing the necessity for bookkeeping, while facilitating transparent data transfer between different software packages. It currently includes procedures for calculating ab initio reconstructions via random or orthogonal tilt geometry, tomograms, and common lines, all of which have been tested using the 50S ribosomal subunit. Our goal is that the accessibility of multiple independent reconstruction algorithms via this toolbox will improve the ease with which models can be generated, and provide a means of evaluating the confidence and reliability of the final reconstructed map.

  12. a Method of 3d Measurement and Reconstruction for Cultural Relics in Museums

    NASA Astrophysics Data System (ADS)

    Zheng, S.; Zhou, Y.; Huang, R.; Zhou, L.; Xu, X.; Wang, C.

    2012-07-01

    Three-dimensional measurement and reconstruction during conservation and restoration of cultural relics have become an essential part of a modem museum regular work. Although many kinds of methods including laser scanning, computer vision and close-range photogrammetry have been put forward, but problems still exist, such as contradiction between cost and good result, time and fine effect. Aimed at these problems, this paper proposed a structure-light based method for 3D measurement and reconstruction of cultural relics in museums. Firstly, based on structure-light principle, digitalization hardware has been built and with its help, dense point cloud of cultural relics' surface can be easily acquired. To produce accurate 3D geometry model from point cloud data, multi processing algorithms have been developed and corresponding software has been implemented whose functions include blunder detection and removal, point cloud alignment and merge, 3D mesh construction and simplification. Finally, high-resolution images are captured and the alignment of these images and 3D geometry model is conducted and realistic, accurate 3D model is constructed. Based on such method, a complete system including hardware and software are built. Multi-kinds of cultural relics have been used to test this method and results prove its own feature such as high efficiency, high accuracy, easy operation and so on.

  13. 3D Reconstruction of Static Human Body with a Digital Camera

    NASA Astrophysics Data System (ADS)

    Remondino, Fabio

    2003-01-01

    Nowadays the interest in 3D reconstruction and modeling of real humans is one of the most challenging problems and a topic of great interest. The human models are used for movies, video games or ergonomics applications and they are usually created with 3D scanner devices. In this paper a new method to reconstruct the shape of a static human is presented. Our approach is based on photogrammetric techniques and uses a sequence of images acquired around a standing person with a digital still video camera or with a camcorder. First the images are calibrated and orientated using a bundle adjustment. After the establishment of a stable adjusted image block, an image matching process is performed between consecutive triplets of images. Finally the 3D coordinates of the matched points are computed with a mean accuracy of ca 2 mm by forward ray intersection. The obtained point cloud can then be triangulated to generate a surface model of the body or a virtual human model can be fitted to the recovered 3D data. Results of the 3D human point cloud with pixel color information are presented.

  14. Equilibrium Reconstructions with V3FIT and Current Evolution Modeling for 3-D Stellarator Plasmas

    NASA Astrophysics Data System (ADS)

    Schmitt, J. C.; Cianciosa, M.; Geiger, J.; Lazerson, S.

    2016-10-01

    V3FIT is a powerful equilibrium reconstruction tool for magnetic confinement fusion experiments which are inherently 3-D in nature (i.e. stellarators) or have 3-D components (tokamaks with 3-D shaping, reversed field pinches with helical states, etc). Here, we present details of the diagnostic modeling, constraints and the user interface for reconstructions of W7-X plasmas. For typical discharges during the OP1.1 run campaign of W7-X, the net toroidal current and current density profile do not reach steady-state. When modeling the current evolution in 3-D plasmas, both poloidal and toroidal currents are linked with both poloidal and toroidal fluxes. In contrast, in toroidally axisymmetric plasmas, the poloidal flux is linked only with the toroidal current and the toroidal current is linked only with the poloidal flux. Compared to an equivalently-sized axisymmetric configuration, the current diffusion in 3-D plasmas is enhanced, leading to a faster relaxation of the current profile to its steady-state. Implications for the time-evolution of the current and rotational transform profiles in stellarator plasmas are discussed. This work is supported by DoE Grant DE-SC00014529.

  15. 3D-Printing Technologies for Craniofacial Rehabilitation, Reconstruction, and Regeneration.

    PubMed

    Nyberg, Ethan L; Farris, Ashley L; Hung, Ben P; Dias, Miguel; Garcia, Juan R; Dorafshar, Amir H; Grayson, Warren L

    2017-01-01

    The treatment of craniofacial defects can present many challenges due to the variety of tissue-specific requirements and the complexity of anatomical structures in that region. 3D-printing technologies provide clinicians, engineers and scientists with the ability to create patient-specific solutions for craniofacial defects. Currently, there are three key strategies that utilize these technologies to restore both appearance and function to patients: rehabilitation, reconstruction and regeneration. In rehabilitation, 3D-printing can be used to create prostheses to replace or cover damaged tissues. Reconstruction, through plastic surgery, can also leverage 3D-printing technologies to create custom cutting guides, fixation devices, practice models and implanted medical devices to improve patient outcomes. Regeneration of tissue attempts to replace defects with biological materials. 3D-printing can be used to create either scaffolds or living, cellular constructs to signal tissue-forming cells to regenerate defect regions. By integrating these three approaches, 3D-printing technologies afford the opportunity to develop personalized treatment plans and design-driven manufacturing solutions to improve aesthetic and functional outcomes for patients with craniofacial defects.

  16. Supervised recursive segmentation of volumetric CT images for 3D reconstruction of lung and vessel tree.

    PubMed

    Li, Xuanping; Wang, Xue; Dai, Yixiang; Zhang, Pengbo

    2015-12-01

    Three dimensional reconstruction of lung and vessel tree has great significance to 3D observation and quantitative analysis for lung diseases. This paper presents non-sheltered 3D models of lung and vessel tree based on a supervised semi-3D lung tissues segmentation method. A recursive strategy based on geometric active contour is proposed instead of the "coarse-to-fine" framework in existing literature to extract lung tissues from the volumetric CT slices. In this model, the segmentation of the current slice is supervised by the result of the previous one slice due to the slight changes between adjacent slice of lung tissues. Through this mechanism, lung tissues in all the slices are segmented fast and accurately. The serious problems of left and right lungs fusion, caused by partial volume effects, and segmentation of pleural nodules can be settled meanwhile during the semi-3D process. The proposed scheme is evaluated by fifteen scans, from eight healthy participants and seven participants suffering from early-stage lung tumors. The results validate the good performance of the proposed method compared with the "coarse-to-fine" framework. The segmented datasets are utilized to reconstruct the non-sheltered 3D models of lung and vessel tree.

  17. Plane-based optimization for 3D object reconstruction from single line drawings.

    PubMed

    Liu, Jianzhuang; Cao, Liangliang; Li, Zhenguo; Tang, Xiaoou

    2008-02-01

    In previous optimization-based methods of 3D planar-faced object reconstruction from single 2D line drawings, the missing depths of the vertices of a line drawing (and other parameters in some methods) are used as the variables of the objective functions. A 3D object with planar faces is derived by finding values for these variables that minimize the objective functions. These methods work well for simple objects with a small number N of variables. As N grows, however, it is very difficult for them to find expected objects. This is because with the nonlinear objective functions in a space of large dimension N, the search for optimal solutions can easily get trapped into local minima. In this paper, we use the parameters of the planes that pass through the planar faces of an object as the variables of the objective function. This leads to a set of linear constraints on the planes of the object, resulting in a much lower dimensional nullspace where optimization is easier to achieve. We prove that the dimension of this nullspace is exactly equal to the minimum number of vertex depths which define the 3D object. Since a practical line drawing is usually not an exact projection of a 3D object, we expand the nullspace to a larger space based on the singular value decomposition of the projection matrix of the line drawing. In this space, robust 3D reconstruction can be achieved. Compared with two most related methods, our method not only can reconstruct more complex 3D objects from 2D line drawings, but also is computationally more efficient.

  18. A Bayesian approach for suppression of limited angular sampling artifacts in single particle 3D reconstruction.

    PubMed

    Moriya, Toshio; Acar, Erman; Cheng, R Holland; Ruotsalainen, Ulla

    2015-09-01

    In the single particle reconstruction, the initial 3D structure often suffers from the limited angular sampling artifact. Selecting 2D class averages of particle images generally improves the accuracy and efficiency of the reference-free 3D angle estimation, but causes an insufficient angular sampling to fill the information of the target object in the 3D frequency space. Similarly, the initial 3D structure by the random-conical tilt reconstruction has the well-known "missing cone" artifact. Here, we attempted to solve the limited angular sampling problem by sequentially applying maximum a posteriori estimate with expectation maximization algorithm (sMAP-EM). Using both simulated and experimental cryo-electron microscope images, the sMAP-EM was compared to the direct Fourier method on the basis of reconstruction error and resolution. To establish selection criteria of the final regularization weight for the sMAP-EM, the effects of noise level and sampling sparseness on the reconstructions were examined with evenly distributed sampling simulations. The frequency information filled in the missing cone of the conical tilt sampling simulations was assessed by developing new quantitative measurements. All the results of visual and numerical evaluations showed the sMAP-EM performed better than the direct Fourier method, regardless of the sampling method, noise level, and sampling sparseness. Furthermore, the frequency domain analysis demonstrated that the sMAP-EM can fill the meaningful information in the unmeasured angular space without detailed a priori knowledge of the objects. The current research demonstrated that the sMAP-EM has a high potential to facilitate the determination of 3D protein structures at near atomic-resolution.

  19. Minimizing camera-eye optical aberrations during the 3D reconstruction of retinal structures

    NASA Astrophysics Data System (ADS)

    Aldana-Iuit, Javier; Martinez-Perez, M. Elena; Espinosa-Romero, Arturo; Diaz-Uribe, Rufino

    2010-05-01

    3D reconstruction of blood vessels is a powerful visualization tool for physicians, since it allows them to refer to qualitative representation of their subject of study. In this paper we propose a 3D reconstruction method of retinal vessels from fundus images. The reconstruction method propose herein uses images of the same retinal structure in epipolar geometry. Images are preprocessed by RISA system for segmenting blood vessels and obtaining feature points for correspondences. The correspondence points process is solved using correlation. The LMedS analysis and Graph Transformation Matching algorithm are used for outliers suppression. Camera projection matrices are computed with the normalized eight point algorithm. Finally, we retrieve 3D position of the retinal tree points by linear triangulation. In order to increase the power of visualization, 3D tree skeletons are represented by surfaces via generalized cylinders whose radius correspond to morphological measurements obtained by RISA. In this paper the complete calibration process including the fundus camera and the optical properties of the eye, the so called camera-eye system is proposed. On one hand, the internal parameters of the fundus camera are obtained by classical algorithms using a reference pattern. On the other hand, we minimize the undesirable efects of the aberrations induced by the eyeball optical system assuming that contact enlarging lens corrects astigmatism, spherical and coma aberrations are reduced changing the aperture size and eye refractive errors are suppressed adjusting camera focus during image acquisition. Evaluation of two self-calibration proposals and results of 3D blood vessel surface reconstruction are presented.

  20. Automatic system for 3D reconstruction of the chick eye based on digital photographs.

    PubMed

    Wong, Alexander; Genest, Reno; Chandrashekar, Naveen; Choh, Vivian; Irving, Elizabeth L

    2012-01-01

    The geometry of anatomical specimens is very complex and accurate 3D reconstruction is important for morphological studies, finite element analysis (FEA) and rapid prototyping. Although magnetic resonance imaging, computed tomography and laser scanners can be used for reconstructing biological structures, the cost of the equipment is fairly high and specialised technicians are required to operate the equipment, making such approaches limiting in terms of accessibility. In this paper, a novel automatic system for 3D surface reconstruction of the chick eye from digital photographs of a serially sectioned specimen is presented as a potential cost-effective and practical alternative. The system is designed to allow for automatic detection of the external surface of the chick eye. Automatic alignment of the photographs is performed using a combination of coloured markers and an algorithm based on complex phase order likelihood that is robust to noise and illumination variations. Automatic segmentation of the external boundaries of the eye from the aligned photographs is performed using a novel level-set segmentation approach based on a complex phase order energy functional. The extracted boundaries are sampled to construct a 3D point cloud, and a combination of Delaunay triangulation and subdivision surfaces is employed to construct the final triangular mesh. Experimental results using digital photographs of the chick eye show that the proposed system is capable of producing accurate 3D reconstructions of the external surface of the eye. The 3D model geometry is similar to a real chick eye and could be used for morphological studies and FEA.

  1. Reconstruction of 3-D cloud geometry using a scanning cloud radar

    NASA Astrophysics Data System (ADS)

    Ewald, F.; Winkler, C.; Zinner, T.

    2014-11-01

    Clouds are one of the main reasons of uncertainties in the forecasts of weather and climate. In part, this is due to limitations of remote sensing of cloud microphysics. Present approaches often use passive spectral measurements for the remote sensing of cloud microphysical parameters. Large uncertainties are introduced by three dimensional (3-D) radiative transfer effects and cloud inhomogeneities. Such effects are largely caused by unknown orientation of cloud sides or by shadowed areas on the cloud. Passive ground based remote sensing of cloud properties at high spatial resolution could be improved crucially with this kind of additional knowledge of cloud geometry. To this end, a method for the accurate reconstruction of 3-D cloud geometry from cloud radar measurements is developed in this work. Using a radar simulator and simulated passive measurements of static LES model clouds, the effects of different radar scan resolutions and varying interpolation methods are evaluated. In reality a trade-off between scan resolution and scan duration has to be found as clouds are changing quickly. A reasonable choice is a scan resolution of 1 to 2°. The most suitable interpolation procedure identified is the barycentric interpolation method. The 3-D reconstruction method is demonstrated using radar scans of convective cloud cases with the Munich miraMACS, a 35 GHz scanning cloud radar. As a successful proof of concept, camera imagery collected at the radar location is reproduced for the observed cloud cases via 3-D volume reconstruction and 3-D radiative transfer simulation. Data sets provided by the presented reconstruction method will aid passive spectral ground-based measurements of cloud sides to retrieve microphysical parameters.

  2. Intuitive terrain reconstruction using height observation-based ground segmentation and 3D object boundary estimation.

    PubMed

    Song, Wei; Cho, Kyungeun; Um, Kyhyun; Won, Chee Sun; Sim, Sungdae

    2012-12-12

    Mobile robot operators must make rapid decisions based on information about the robot's surrounding environment. This means that terrain modeling and photorealistic visualization are required for the remote operation of mobile robots. We have produced a voxel map and textured mesh from the 2D and 3D datasets collected by a robot's array of sensors, but some upper parts of objects are beyond the sensors' measurements and these parts are missing in the terrain reconstruction result. This result is an incomplete terrain model. To solve this problem, we present a new ground segmentation method to detect non-ground data in the reconstructed voxel map. Our method uses height histograms to estimate the ground height range, and a Gibbs-Markov random field model to refine the segmentation results. To reconstruct a complete terrain model of the 3D environment, we develop a 3D boundary estimation method for non-ground objects. We apply a boundary detection technique to the 2D image, before estimating and refining the actual height values of the non-ground vertices in the reconstructed textured mesh. Our proposed methods were tested in an outdoor environment in which trees and buildings were not completely sensed. Our results show that the time required for ground segmentation is faster than that for data sensing, which is necessary for a real-time approach. In addition, those parts of objects that were not sensed are accurately recovered to retrieve their real-world appearances.

  3. Intuitive Terrain Reconstruction Using Height Observation-Based Ground Segmentation and 3D Object Boundary Estimation

    PubMed Central

    Song, Wei; Cho, Kyungeun; Um, Kyhyun; Won, Chee Sun; Sim, Sungdae

    2012-01-01

    Mobile robot operators must make rapid decisions based on information about the robot’s surrounding environment. This means that terrain modeling and photorealistic visualization are required for the remote operation of mobile robots. We have produced a voxel map and textured mesh from the 2D and 3D datasets collected by a robot’s array of sensors, but some upper parts of objects are beyond the sensors’ measurements and these parts are missing in the terrain reconstruction result. This result is an incomplete terrain model. To solve this problem, we present a new ground segmentation method to detect non-ground data in the reconstructed voxel map. Our method uses height histograms to estimate the ground height range, and a Gibbs-Markov random field model to refine the segmentation results. To reconstruct a complete terrain model of the 3D environment, we develop a 3D boundary estimation method for non-ground objects. We apply a boundary detection technique to the 2D image, before estimating and refining the actual height values of the non-ground vertices in the reconstructed textured mesh. Our proposed methods were tested in an outdoor environment in which trees and buildings were not completely sensed. Our results show that the time required for ground segmentation is faster than that for data sensing, which is necessary for a real-time approach. In addition, those parts of objects that were not sensed are accurately recovered to retrieve their real-world appearances. PMID:23235454

  4. Deep Learning Segmentation of Optical Microscopy Images Improves 3D Neuron Reconstruction.

    PubMed

    Li, Rongjian; Zeng, Tao; Peng, Hanchuan; Ji, Shuiwang

    2017-03-08

    Digital reconstruction, or tracing, of 3-dimensional (3D) neuron structure from microscopy images is a critical step toward reversing engineering the wiring and anatomy of a brain. Despite a number of prior attempts, this task remains very challenging, especially when images are contaminated by noises or have discontinued segments of neurite patterns. An approach for addressing such problems is to identify the locations of neuronal voxels using image segmentation methods prior to applying tracing or reconstruction techniques. This preprocessing step is expected to remove noises in the data, thereby leading to improved reconstruction results. In this work, we proposed to use 3D Convolutional neural networks (CNNs) for segmenting the neuronal microscopy images. Specifically, we designed a novel CNN architecture that takes volumetric images as the inputs and their voxel-wise segmentation maps as the outputs. The developed architecture allows us to train and predict using large microscopy images in an end-to-end manner. We evaluated the performance of our model on a variety of challenging 3D microscopy images from different organisms. Results showed that the proposed methods improved the tracing performance significantly when combined with different reconstruction algorithms.

  5. DIRECT DETECTION OF THE HELICAL MAGNETIC FIELD GEOMETRY FROM 3D RECONSTRUCTION OF PROMINENCE KNOT TRAJECTORIES

    SciTech Connect

    Zapiór, Maciej; Martinez-Gómez, David

    2016-02-01

    Based on the data collected by the Vacuum Tower Telescope located in the Teide Observatory in the Canary Islands, we analyzed the three-dimensional (3D) motion of so-called knots in a solar prominence of 2014 June 9. Trajectories of seven knots were reconstructed, giving information of the 3D geometry of the magnetic field. Helical motion was detected. From the equipartition principle, we estimated the lower limit of the magnetic field in the prominence to ≈1–3 G and from the Ampère’s law the lower limit of the electric current to ≈1.2 × 10{sup 9} A.

  6. Rapid 3D video/laser sensing and digital archiving with immediate on-scene feedback for 3D crime scene/mass disaster data collection and reconstruction

    NASA Astrophysics Data System (ADS)

    Altschuler, Bruce R.; Oliver, William R.; Altschuler, Martin D.

    1996-02-01

    We describe a system for rapid and convenient video data acquisition and 3-D numerical coordinate data calculation able to provide precise 3-D topographical maps and 3-D archival data sufficient to reconstruct a 3-D virtual reality display of a crime scene or mass disaster area. Under a joint U.S. army/U.S. Air Force project with collateral U.S. Navy support, to create a 3-D surgical robotic inspection device -- a mobile, multi-sensor robotic surgical assistant to aid the surgeon in diagnosis, continual surveillance of patient condition, and robotic surgical telemedicine of combat casualties -- the technology is being perfected for remote, non-destructive, quantitative 3-D mapping of objects of varied sizes. This technology is being advanced with hyper-speed parallel video technology and compact, very fast laser electro-optics, such that the acquisition of 3-D surface map data will shortly be acquired within the time frame of conventional 2-D video. With simple field-capable calibration, and mobile or portable platforms, the crime scene investigator could set up and survey the entire crime scene, or portions of it at high resolution, with almost the simplicity and speed of video or still photography. The survey apparatus would record relative position, location, and instantly archive thousands of artifacts at the site with 3-D data points capable of creating unbiased virtual reality reconstructions, or actual physical replicas, for the investigators, prosecutors, and jury.

  7. A Method for 3D Histopathology Reconstruction Supporting Mouse Microvasculature Analysis

    PubMed Central

    Xu, Yiwen; Pickering, J. Geoffrey; Nong, Zengxuan; Gibson, Eli; Arpino, John-Michael; Yin, Hao; Ward, Aaron D.

    2015-01-01

    Structural abnormalities of the microvasculature can impair perfusion and function. Conventional histology provides good spatial resolution with which to evaluate the microvascular structure but affords no 3-dimensional information; this limitation could lead to misinterpretations of the complex microvessel network in health and disease. The objective of this study was to develop and evaluate an accurate, fully automated 3D histology reconstruction method to visualize the arterioles and venules within the mouse hind-limb. Sections of the tibialis anterior muscle from C57BL/J6 mice (both normal and subjected to femoral artery excision) were reconstructed using pairwise rigid and affine registrations of 5 µm-thick, paraffin-embedded serial sections digitized at 0.25 µm/pixel. Low-resolution intensity-based rigid registration was used to initialize the nucleus landmark-based registration, and conventional high-resolution intensity-based registration method. The affine nucleus landmark-based registration was developed in this work and was compared to the conventional affine high-resolution intensity-based registration method. Target registration errors were measured between adjacent tissue sections (pairwise error), as well as with respect to a 3D reference reconstruction (accumulated error, to capture propagation of error through the stack of sections). Accumulated error measures were lower (p<0.01) for the nucleus landmark technique and superior vasculature continuity was observed. These findings indicate that registration based on automatic extraction and correspondence of small, homologous landmarks may support accurate 3D histology reconstruction. This technique avoids the otherwise problematic “banana-into-cylinder” effect observed using conventional methods that optimize the pairwise alignment of salient structures, forcing them to be section-orthogonal. This approach will provide a valuable tool for high-accuracy 3D histology tissue reconstructions for

  8. Fast tomographic reconstruction from limited data using artificial neural networks.

    PubMed

    Pelt, Daniël Maria; Batenburg, Kees Joost

    2013-12-01

    Image reconstruction from a small number of projections is a challenging problem in tomography. Advanced algorithms that incorporate prior knowledge can sometimes produce accurate reconstructions, but they typically require long computation times. Furthermore, the required prior knowledge can be very specific, limiting the type of images that can be reconstructed. Here, we present a reconstruction method that automatically learns prior knowledge using an artificial neural network. We show that this method can be viewed as a combination of filtered backprojection steps, and, therefore, has a relatively low computational cost. Results for two different cases show that the new method is able to use the learned information to produce high quality reconstructions in a short time, even when presented with a small number of projections.

  9. Digital 3D reconstructions using histological serial sections of lung tissue including the alveolar capillary network.

    PubMed

    Grothausmann, Roman; Knudsen, Lars; Ochs, Matthias; Mühlfeld, Christian

    2017-02-01

    Grothausmann R, Knudsen L, Ochs M, Mühlfeld C. Digital 3D reconstructions using histological serial sections of lung tissue including the alveolar capillary network. Am J Physiol Lung Cell Mol Physiol 312: L243-L257, 2017. First published December 2, 2016; doi:10.1152/ajplung.00326.2016-The alveolar capillary network (ACN) provides an enormously large surface area that is necessary for pulmonary gas exchange. Changes of the ACN during normal or pathological development or in pulmonary diseases are of great functional impact and warrant further analysis. Due to the complexity of the three-dimensional (3D) architecture of the ACN, 2D approaches are limited in providing a comprehensive impression of the characteristics of the normal ACN or the nature of its alterations. Stereological methods offer a quantitative way to assess the ACN in 3D in terms of capillary volume, surface area, or number but lack a 3D visualization to interpret the data. Hence, the necessity to visualize the ACN in 3D and to correlate this with data from the same set of data arises. Such an approach requires a large sample volume combined with a high resolution. Here, we present a technically simple and cost-efficient approach to create 3D representations of lung tissue ranging from bronchioles over alveolar ducts and alveoli up to the ACN from more than 1 mm sample extent to a resolution of less than 1 μm. The method is based on automated image acquisition of serially sectioned epoxy resin-embedded lung tissue fixed by vascular perfusion and subsequent automated digital reconstruction and analysis of the 3D data. This efficient method may help to better understand mechanisms of vascular development and pathology of the lung.

  10. GlaRe, a GIS tool to reconstruct the 3D surface of palaeoglaciers

    NASA Astrophysics Data System (ADS)

    Pellitero, Ramón; Rea, Brice R.; Spagnolo, Matteo; Bakke, Jostein; Ivy-Ochs, Susan; Frew, Craig R.; Hughes, Philip; Ribolini, Adriano; Lukas, Sven; Renssen, Hans

    2016-09-01

    Glacier reconstructions are widely used in palaeoclimatic studies and this paper presents a new semi-automated method for generating glacier reconstructions: GlaRe, is a toolbox coded in Python and operating in ArcGIS. This toolbox provides tools to generate the ice thickness from the bed topography along a palaeoglacier flowline applying the standard flow law for ice, and generates the 3D surface of the palaeoglacier using multiple interpolation methods. The toolbox performance has been evaluated using two extant glaciers, an icefield and a cirque/valley glacier from which the subglacial topography is known, using the basic reconstruction routine in GlaRe. Results in terms of ice surface, ice extent and equilibrium line altitude show excellent agreement that confirms the robustness of this procedure in the reconstruction of palaeoglaciers from glacial landforms such as frontal moraines.

  11. High-Performance 3D Compressive Sensing MRI Reconstruction Using Many-Core Architectures

    PubMed Central

    Kim, Daehyun; Trzasko, Joshua; Smelyanskiy, Mikhail; Haider, Clifton; Dubey, Pradeep; Manduca, Armando

    2011-01-01

    Compressive sensing (CS) describes how sparse signals can be accurately reconstructed from many fewer samples than required by the Nyquist criterion. Since MRI scan duration is proportional to the number of acquired samples, CS has been gaining significant attention in MRI. However, the computationally intensive nature of CS reconstructions has precluded their use in routine clinical practice. In this work, we investigate how different throughput-oriented architectures can benefit one CS algorithm and what levels of acceleration are feasible on different modern platforms. We demonstrate that a CUDA-based code running on an NVIDIA Tesla C2050 GPU can reconstruct a 256 × 160 × 80 volume from an 8-channel acquisition in 19 seconds, which is in itself a significant improvement over the state of the art. We then show that Intel's Knights Ferry can perform the same 3D MRI reconstruction in only 12 seconds, bringing CS methods even closer to clinical viability. PMID:21922017

  12. Fast 3D spine reconstruction of postoperative patients using a multilevel statistical model.

    PubMed

    Lecron, Fabian; Boisvert, Jonathan; Mahmoudi, Saïd; Labelle, Hubert; Benjelloun, Mohammed

    2012-01-01

    Severe cases of spinal deformities such as scoliosis are usually treated by a surgery where instrumentation (hooks, screws and rods) is installed to the spine to correct deformities. Even if the purpose is to obtain a normal spine curve, the result is often straighter than normal. In this paper, we propose a fast statistical reconstruction algorithm based on a general model which can deal with such instrumented spines. To this end, we present the concept of multilevel statistical model where the data are decomposed into a within-group and a between-group component. The reconstruction procedure is formulated as a second-order cone program which can be solved very fast (few tenths of a second). Reconstruction errors were evaluated on real patient data and results showed that multilevel modeling allows better 3D reconstruction than classical models.

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

    SciTech Connect

    Huang, J. S.; Wei, L. F.; Oh, C. H.

    2011-03-15

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

  14. CAVAREV—an open platform for evaluating 3D and 4D cardiac vasculature reconstruction

    NASA Astrophysics Data System (ADS)

    Rohkohl, Christopher; Lauritsch, Günter; Keil, Andreas; Hornegger, Joachim

    2010-05-01

    The 3D reconstruction of cardiac vasculature, e.g. the coronary arteries, using C-arm CT (rotational angiography) is an active and challenging field of research. There are numerous publications on different reconstruction techniques. However, there is still a lack of comparability of achieved results for several reasons: foremost, datasets used in publications are not open to public and thus experiments are not reproducible by other researchers. Further, the results highly depend on the vasculature motion, i.e. cardiac and breathing motion patterns which are also not comparable across publications. We aim to close this gap by providing an open platform, called Cavarev (CArdiac VAsculature Reconstruction EValuation). It features two simulated dynamic projection datasets based on the 4D XCAT phantom with contrasted coronary arteries which was derived from patient data. In the first dataset, the vasculature undergoes a continuous periodic motion. The second dataset contains aperiodic heart motion by including additional breathing motion. The geometry calibration and acquisition protocol were obtained from a real-world C-arm system. For qualitative evaluation of the reconstruction results, the correlation of the morphology is used. Two segmentation-based quality measures are introduced which allow us to assess the 3D and 4D reconstruction quality. They are based on the spatial overlap of the vasculature reconstruction with the ground truth. The measures enable a comprehensive analysis and comparison of reconstruction results independent from the utilized reconstruction algorithm. An online platform (www.cavarev.com) is provided where the datasets can be downloaded, researchers can manage and publish algorithm results and download a reference C++ and Matlab implementation.

  15. Image-based reconstruction of 3D myocardial infarct geometry for patient specific applications

    NASA Astrophysics Data System (ADS)

    Ukwatta, Eranga; Rajchl, Martin; White, James; Pashakhanloo, Farhad; Herzka, Daniel A.; McVeigh, Elliot; Lardo, Albert C.; Trayanova, Natalia; Vadakkumpadan, Fijoy

    2015-03-01

    Accurate reconstruction of the three-dimensional (3D) geometry of a myocardial infarct from two-dimensional (2D) multi-slice image sequences has important applications in the clinical evaluation and treatment of patients with ischemic cardiomyopathy. However, this reconstruction is challenging because the resolution of common clinical scans used to acquire infarct structure, such as short-axis, late-gadolinium enhanced cardiac magnetic resonance (LGE-CMR) images, is low, especially in the out-of-plane direction. In this study, we propose a novel technique to reconstruct the 3D infarct geometry from low resolution clinical images. Our methodology is based on a function called logarithm of odds (LogOdds), which allows the broader class of linear combinations in the LogOdds vector space as opposed to being limited to only a convex combination in the binary label space. To assess the efficacy of the method, we used high-resolution LGE-CMR images of 36 human hearts in vivo, and 3 canine hearts ex vivo. The infarct was manually segmented in each slice of the acquired images, and the manually segmented data were downsampled to clinical resolution. The developed method was then applied to the downsampled image slices, and the resulting reconstructions were compared with the manually segmented data. Several existing reconstruction techniques were also implemented, and compared with the proposed method. The results show that the LogOdds method significantly outperforms all the other tested methods in terms of region overlap.

  16. Image-based 3D reconstruction and virtual environmental walk-through

    NASA Astrophysics Data System (ADS)

    Sun, Jifeng; Fang, Lixiong; Luo, Ying

    2001-09-01

    We present a 3D reconstruction method, which combines geometry-based modeling, image-based modeling and rendering techniques. The first component is an interactive geometry modeling method which recovery of the basic geometry of the photographed scene. The second component is model-based stereo algorithm. We discus the image processing problems and algorithms of walking through in virtual space, then designs and implement a high performance multi-thread wandering algorithm. The applications range from architectural planning and archaeological reconstruction to virtual environments and cinematic special effects.

  17. Characterizing heterogeneity among virus particles by stochastic 3D signal reconstruction

    NASA Astrophysics Data System (ADS)

    Xu, Nan; Gong, Yunye; Wang, Qiu; Zheng, Yili; Doerschuk, Peter C.

    2015-09-01

    In single-particle cryo electron microscopy, many electron microscope images each of a single instance of a biological particle such as a virus or a ribosome are measured and the 3-D electron scattering intensity of the particle is reconstructed by computation. Because each instance of the particle is imaged separately, it should be possible to characterize the heterogeneity of the different instances of the particle as well as a nominal reconstruction of the particle. In this paper, such an algorithm is described and demonstrated on the bacteriophage Hong Kong 97. The algorithm is a statistical maximum likelihood estimator computed by an expectation maximization algorithm implemented in Matlab software.

  18. Reconstruction of high resolution MLC leaf positions using a low resolution detector for accurate 3D dose reconstruction in IMRT

    NASA Astrophysics Data System (ADS)

    Visser, R.; Godart, J.; Wauben, D. J. L.; Langendijk, J. A.; van't Veld, A. A.; Korevaar, E. W.

    2016-12-01

    In pre-treatment dose verification, low resolution detector systems are unable to identify shifts of individual leafs of high resolution multi leaf collimator (MLC) systems from detected changes in the dose deposition. The goal of this study was to introduce an alternative approach (the shutter technique) combined with a previous described iterative reconstruction method to accurately reconstruct high resolution MLC leaf positions based on low resolution measurements. For the shutter technique, two additional radiotherapy treatment plans (RT-plans) were generated in addition to the original RT-plan; one with even MLC leafs closed for reconstructing uneven leaf positions and one with uneven MLC leafs closed for reconstructing even leaf positions. Reconstructed leaf positions were then implemented in the original RT-plan for 3D dose reconstruction. The shutter technique was evaluated for a 6 MV Elekta SLi linac with 5 mm MLC leafs (Agility™) in combination with the MatriXX Evolution detector with detector spacing of 7.62 mm. Dose reconstruction was performed with the COMPASS system (v2.0). The measurement setup allowed one row of ionization chambers to be affected by two adjacent leaf pairs. Measurements were obtained for various field sizes with MLC leaf position errors ranging from 1.0 mm to 10.0 mm. Furthermore, one clinical head and neck IMRT treatment beam with MLC introduced leaf position errors of 5.0 mm was evaluated to illustrate the impact of the shutter technique on 3D dose reconstruction. Without the shutter technique, MLC leaf position reconstruction showed reconstruction errors up to 6.0 mm. Introduction of the shutter technique allowed MLC leaf position reconstruction for the majority of leafs with sub-millimeter accuracy resulting in a reduction of dose reconstruction errors. The shutter technique in combination with the iterative reconstruction method allows high resolution MLC leaf position reconstruction using low resolution

  19. 3D image reconstruction on x-ray micro-computed tomography

    NASA Astrophysics Data System (ADS)

    Louk, Andreas C.

    2015-03-01

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

  20. A case of pulmonary artery intimal sarcoma diagnosed with multislice CT scan with 3D reconstruction.

    PubMed

    Choi, Eui-Young; Yoon, Young-Won; Kwon, Hyuck Moon; Kim, Dongsoo; Park, Byung-Eun; Hong, Yoo-Sun; Koo, Ja-Seung; Kim, Tae-Hoon; Kim, Hyun-Seung

    2004-06-30

    Pulmonary artery intimal sarcoma is a rare highly lethal disease, with additional retrograde extension to pulmonic valve and right ventricle being an extremely rare condition. It is frequently mistaken for pulmonary thromboembolism. We report a case of 64-year-old woman with progressive dyspnea initially suspected and treated for pulmonary thromboembolism. Her helical chest CT scan with 3 dimensional (3D) reconstruction combined with echocardiography revealed a compacting main pulmonary artery mass extending to the right ventricular outflow tract and the right pulmonary artery. After excision of the mass, the patient's condition improved dramatically, and the pathologic findings revealed pulmonary intimal sarcoma. This report emphasizes that helical chest CT with 3D reconstruction can be an important tool to differentiate the characteristics of pulmonary artery lesions, such as intimal sarcoma and thromboembolism.

  1. Hollow Cone Electron Imaging for Single Particle 3D Reconstruction of Proteins

    PubMed Central

    Tsai, Chun-Ying; Chang, Yuan-Chih; Lobato, Ivan; Van Dyck, Dirk; Chen, Fu-Rong

    2016-01-01

    The main bottlenecks for high-resolution biological imaging in electron microscopy are radiation sensitivity and low contrast. The phase contrast at low spatial frequencies can be enhanced by using a large defocus but this strongly reduces the resolution. Recently, phase plates have been developed to enhance the contrast at small defocus but electrical charging remains a problem. Single particle cryo-electron microscopy is mostly used to minimize the radiation damage and to enhance the resolution of the 3D reconstructions but it requires averaging images of a massive number of individual particles. Here we present a new route to achieve the same goals by hollow cone dark field imaging using thermal diffuse scattered electrons giving about a 4 times contrast increase as compared to bright field imaging. We demonstrate the 3D reconstruction of a stained GroEL particle can yield about 13.5 Å resolution but using a strongly reduced number of images. PMID:27292544

  2. Hollow Cone Electron Imaging for Single Particle 3D Reconstruction of Proteins.

    PubMed

    Tsai, Chun-Ying; Chang, Yuan-Chih; Lobato, Ivan; Van Dyck, Dirk; Chen, Fu-Rong

    2016-06-13

    The main bottlenecks for high-resolution biological imaging in electron microscopy are radiation sensitivity and low contrast. The phase contrast at low spatial frequencies can be enhanced by using a large defocus but this strongly reduces the resolution. Recently, phase plates have been developed to enhance the contrast at small defocus but electrical charging remains a problem. Single particle cryo-electron microscopy is mostly used to minimize the radiation damage and to enhance the resolution of the 3D reconstructions but it requires averaging images of a massive number of individual particles. Here we present a new route to achieve the same goals by hollow cone dark field imaging using thermal diffuse scattered electrons giving about a 4 times contrast increase as compared to bright field imaging. We demonstrate the 3D reconstruction of a stained GroEL particle can yield about 13.5 Å resolution but using a strongly reduced number of images.

  3. Hollow Cone Electron Imaging for Single Particle 3D Reconstruction of Proteins

    NASA Astrophysics Data System (ADS)

    Tsai, Chun-Ying; Chang, Yuan-Chih; Lobato, Ivan; van Dyck, Dirk; Chen, Fu-Rong

    2016-06-01

    The main bottlenecks for high-resolution biological imaging in electron microscopy are radiation sensitivity and low contrast. The phase contrast at low spatial frequencies can be enhanced by using a large defocus but this strongly reduces the resolution. Recently, phase plates have been developed to enhance the contrast at small defocus but electrical charging remains a problem. Single particle cryo-electron microscopy is mostly used to minimize the radiation damage and to enhance the resolution of the 3D reconstructions but it requires averaging images of a massive number of individual particles. Here we present a new route to achieve the same goals by hollow cone dark field imaging using thermal diffuse scattered electrons giving about a 4 times contrast increase as compared to bright field imaging. We demonstrate the 3D reconstruction of a stained GroEL particle can yield about 13.5 Å resolution but using a strongly reduced number of images.

  4. Full-aspect 3D target reconstruction of interferometric circular SAR

    NASA Astrophysics Data System (ADS)

    Lin, Yun; Bao, Qian; Hou, Liying; Yu, Lingjuan; Hong, Wen

    2016-10-01

    Circular SAR has several attractive features, such as full-aspect observation, high resolution, and 3D target reconstruction capability, thus it has important potential in fine feature description of typical targets. However, the 3D reconstruction capability relies on the scattering persistence of the target. For target with a highly directive scattering property, the resolution in the direction perpendicular to the instantaneous slant plane is very low compared to the range and azimuth resolutions, and the 3D structure of target can hardly be obtained. In this paper, an Interferometric Circular SAR (InCSAR) method is proposed to reconstruct the full-aspect 3D structure of typical targets. InCSAR uses two sensors with a small incident angle difference to collect data in a circular trajectory. The method proposed in this paper calculates the interferometric phase difference (IPD) of the image pair at equally spaced height slices, and mask the original image with an IPD threshold. The main principle is that when a scatterer is imaged at a wrong height, the image pair has an offset, which results in a nonzero IPD, and only when the scatterer is correctly imaged at its true height, the IPD is near zero. The IPD threshold is used to retain scatterers that is correctly imaged at the right height, and meanwhile eliminate scatterers that is imaged at a wrong height, thus the 3D target structure can be retrieved. The proposed method is validated by real data processing, both the data collected in the microwave chamber and the GOTCHA airborne data.

  5. On the 3-D reconstruction of Coronal Mass Ejections using coronagraph data

    NASA Astrophysics Data System (ADS)

    Mierla, M.; Inhester, B.; Antunes, A.; Boursier, Y.; Byrne, J. P.; Colaninno, R.; Davila, J.; de Koning, C. A.; Gallagher, P. T.; Gissot, S.; Howard, R. A.; Howard, T. A.; Kramar, M.; Lamy, P.; Liewer, P. C.; Maloney, S.; Marqué, C.; McAteer, R. T. J.; Moran, T.; Rodriguez, L.; Srivastava, N.; St. Cyr, O. C.; Stenborg, G.; Temmer, M.; Thernisien, A.; Vourlidas, A.; West, M. J.; Wood, B. E.; Zhukov, A. N.

    2010-01-01

    Coronal Mass ejections (CMEs) are enormous eruptions of magnetized plasma expelled from the Sun into the interplanetary space, over the course of hours to days. They can create major disturbances in the interplanetary medium and trigger severe magnetic storms when they collide with the Earth's magnetosphere. It is important to know their real speed, propagation direction and 3-D configuration in order to accurately predict their arrival time at the Earth. Using data from the SECCHI coronagraphs onboard the STEREO mission, which was launched in October 2006, we can infer the propagation direction and the 3-D structure of such events. In this review, we first describe different techniques that were used to model the 3-D configuration of CMEs in the coronagraph field of view (up to 15 R⊙). Then, we apply these techniques to different CMEs observed by various coronagraphs. A comparison of results obtained from the application of different reconstruction algorithms is presented and discussed.

  6. Reconstruction of a 3D stereotactic brain atlas and its contour-to-contour elastic deformation

    NASA Astrophysics Data System (ADS)

    Kimura, Masahiko; Otsuki, Taisuke

    1993-06-01

    We describe a refined method for estimating the 3-D geometry of cerebral structures of a patient's brain from magnetic resonance (MR) images by adapting a 3-D atlas to the images. The 3-D atlas represents the figures of anatomical subdivisions of deep cerebral structures as series of contours reconstructed from a stereotactic printed atlas. The method correlates corresponding points and curve segments that are recognizable in both the atlas and the image, by elastically deforming the atlas two-dimensionally, while maintaining the point-to-point and contour-to-contour correspondence, until equilibrium is reached. We have used the method experimentally for a patient with Parkinson's disease, and successfully estimated the substructures of the thalamus to be treated.

  7. Interdisciplinary Data Fusion for Diachronic 3d Reconstruction of Historic Sites

    NASA Astrophysics Data System (ADS)

    Micoli, L. L.; Gonizzi Barsanti, S.; Guidi, G.

    2017-02-01

    In recent decades, 3D reconstruction has progressively become a tool to show archaeological and architectural monuments in their current state, presumed past aspect and to predict their future evolution. The 3D representations trough time can be useful in order to study and preserve the memory of Cultural Heritage and to plan maintenance and promotion of the historical sites. This paper represent a case study, at architectonic and urbanistic scale, based on methodological approach for CH time-varying representations proposed by JPI-CH European Project called Cultural Heritage Through Time (CHT2). The work is focused on the area of Milan Roman circus, relatively to which was conducted both a thorough philological research based on several sources and a 3D survey campaign of still accessible remains, aiming at obtaining the monumental representation of the area in 3 different ages.

  8. Transmission of hologram data and 3D image reconstruction using white LED light

    NASA Astrophysics Data System (ADS)

    Sato, Koki; Tozuka, Masataka; Takano, Kunihiko; Ohki, Makoto

    2012-03-01

    Transmission of hologram is very important to realizing the holographic 3D TV. Transmission of Computer Generated Hologram(CGH) data using SSTV wire-less method was tried before and one frame with 76.8k bit data transmitted by 2kbbs was reported1-2). In this research we consider about more high speed transmission and more high resolution hologram data transmission and reconstruction using white LED.

  9. 3D reconstruction from a monocular vision system for unmanned ground vehicles

    NASA Astrophysics Data System (ADS)

    Tompkins, R. Cortland; Diskin, Yakov; Youssef, Menatoallah M.; Asari, Vijayan K.

    2011-11-01

    In this paper we present a 3D reconstruction technique designed to support an autonomously navigated unmanned system. The algorithm and methods presented focus on the 3D reconstruction of a scene, with color and distance information, using only a single moving camera. In this way, the system may provide positional self-awareness for navigation within a known, GPS-denied area. It can also be used to construct a new model of unknown areas. Existing 3D reconstruction methods for GPS-denied areas often rely on expensive inertial measurement units to establish camera location and orientation. The algorithm proposed---after the preprocessing tasks of stabilization and video enhancement---performs Speeded-Up Robust Feature extraction, in which we locate unique stable points within every frame. Additional features are extracted using an optical flow method, with the resultant points fused and pruned based on several quality metrics. Each unique point is then tracked through the video sequence and assigned a disparity value used to compute the depth for each feature within the scene. The algorithm also assigns each feature point a horizontal and vertical coordinate using the camera's field of views specifications. From this, a resultant point cloud consists of thousands of feature points plotted from a particular camera position and direction, generated from pairs of sequential frames. The proposed method can use the yaw, pitch and roll information calculated from visual cues within the image data to accurately compute location and orientation. This positioning information enables the reconstruction of a robust 3D model particularly suitable for autonomous navigation and mapping tasks.

  10. Custom-made, 3D, intraoperative surgical guides for nasal reconstruction.

    PubMed

    Sultan, Babar; Byrne, Patrick J

    2011-11-01

    This article presents the use of an intraoperative surgical guide created by 3D laser surface scanning and rapid prototyping. The authors present outcomes of 3 patients in whom the nasal surgical guide was used intraoperatively for reconstruction of full-thickness, complex nasal defects. This effort highlights the multidisciplinary approach involving a surgeon and anaplastologist integrated with the latest technology to provide patients with the best possible outcomes.

  11. Tomographic reconstruction of damage images in hollow cylinders using Lamb waves.

    PubMed

    Hu, Bin; Hu, Ning; Li, Leilei; Li, Weiguo; Tang, Shan; Li, Yuan; Peng, Xianghe; Homma, Atsushi; Liu, Yaolu; Wu, Liangke; Ning, Huiming

    2014-09-01

    Lamb wave tomography (LWT) is a potential and efficient technique for non-destructive tomographic reconstruction of damage images in structural components or materials. A two-stage inverse algorithm proposed by the authors for quickly reconstructing the damage images was applied to hollow cylinders. An aluminum hollow cylinder with an internal surface pit and a Carbon Fiber Reinforced Plastic (CFRP) laminated hollow cylinder with an artificial internal surface damage were used to validate the proposed method. The results show that the present method is capable of successfully reconstructing the images of the above damages in a larger inspection area with much less experimental data compared to some conventional ultrasonic tomography techniques.

  12. A general few-projection method for tomographic reconstruction of samples consisting of several distinct materials

    SciTech Connect

    Myers, Glenn R.; Thomas, C. David L.; Clement, John G.; Paganin, David M.; Gureyev, Timur E.

    2010-01-11

    We present a method for tomographic reconstruction of objects containing several distinct materials, which is capable of accurately reconstructing a sample from vastly fewer angular projections than required by conventional algorithms. The algorithm is more general than many previous discrete tomography methods, as: (i) a priori knowledge of the exact number of materials is not required; (ii) the linear attenuation coefficient of each constituent material may assume a small range of a priori unknown values. We present reconstructions from an experimental x-ray computed tomography scan of cortical bone acquired at the SPring-8 synchrotron.

  13. A general few-projection method for tomographic reconstruction of samples consisting of several distinct materials

    NASA Astrophysics Data System (ADS)

    Myers, Glenn R.; Thomas, C. David L.; Paganin, David M.; Gureyev, Timur E.; Clement, John G.

    2010-01-01

    We present a method for tomographic reconstruction of objects containing several distinct materials, which is capable of accurately reconstructing a sample from vastly fewer angular projections than required by conventional algorithms. The algorithm is more general than many previous discrete tomography methods, as: (i) a priori knowledge of the exact number of materials is not required; (ii) the linear attenuation coefficient of each constituent material may assume a small range of a priori unknown values. We present reconstructions from an experimental x-ray computed tomography scan of cortical bone acquired at the SPring-8 synchrotron.

  14. 3D reconstruction of a carotid bifurcation from 2D transversal ultrasound images.

    PubMed

    Yeom, Eunseop; Nam, Kweon-Ho; Jin, Changzhu; Paeng, Dong-Guk; Lee, Sang-Joon

    2014-12-01

    Visualizing and analyzing the morphological structure of carotid bifurcations are important for understanding the etiology of carotid atherosclerosis, which is a major cause of stroke and transient ischemic attack. For delineation of vasculatures in the carotid artery, ultrasound examinations have been widely employed because of a noninvasive procedure without ionizing radiation. However, conventional 2D ultrasound imaging has technical limitations in observing the complicated 3D shapes and asymmetric vasodilation of bifurcations. This study aims to propose image-processing techniques for better 3D reconstruction of a carotid bifurcation in a rat by using 2D cross-sectional ultrasound images. A high-resolution ultrasound imaging system with a probe centered at 40MHz was employed to obtain 2D transversal images. The lumen boundaries in each transverse ultrasound image were detected by using three different techniques; an ellipse-fitting, a correlation mapping to visualize the decorrelation of blood flow, and the ellipse-fitting on the correlation map. When the results are compared, the third technique provides relatively good boundary extraction. The incomplete boundaries of arterial lumen caused by acoustic artifacts are somewhat resolved by adopting the correlation mapping and the distortion in the boundary detection near the bifurcation apex was largely reduced by using the ellipse-fitting technique. The 3D lumen geometry of a carotid artery was obtained by volumetric rendering of several 2D slices. For the 3D vasodilatation of the carotid bifurcation, lumen geometries at the contraction and expansion states were simultaneously depicted at various view angles. The present 3D reconstruction methods would be useful for efficient extraction and construction of the 3D lumen geometries of carotid bifurcations from 2D ultrasound images.

  15. Sensor fusion of cameras and a laser for city-scale 3D reconstruction.

    PubMed

    Bok, Yunsu; Choi, Dong-Geol; Kweon, In So

    2014-11-04

    This paper presents a sensor fusion system of cameras and a 2D laser sensorfor large-scale 3D reconstruction. The proposed system is designed to capture data on afast-moving ground vehicle. The system consists of six cameras and one 2D laser sensor,and they are synchronized by a hardware trigger. Reconstruction of 3D structures is doneby estimating frame-by-frame motion and accumulating vertical laser scans, as in previousworks. However, our approach does not assume near 2D motion, but estimates free motion(including absolute scale) in 3D space using both laser data and image features. In orderto avoid the degeneration associated with typical three-point algorithms, we present a newalgorithm that selects 3D points from two frames captured by multiple cameras. The problemof error accumulation is solved by loop closing, not by GPS. The experimental resultsshow that the estimated path is successfully overlaid on the satellite images, such that thereconstruction result is very accurate.

  16. Comparison Between Two Generic 3d Building Reconstruction Approaches - Point Cloud Based VS. Image Processing Based

    NASA Astrophysics Data System (ADS)

    Dahlke, D.; Linkiewicz, M.

    2016-06-01

    This paper compares two generic approaches for the reconstruction of buildings. Synthesized and real oblique and vertical aerial imagery is transformed on the one hand into a dense photogrammetric 3D point cloud and on the other hand into photogrammetric 2.5D surface models depicting a scene from different cardinal directions. One approach evaluates the 3D point cloud statistically in order to extract the hull of structures, while the other approach makes use of salient line segments in 2.5D surface models, so that the hull of 3D structures can be recovered. With orders of magnitudes more analyzed 3D points, the point cloud based approach is an order of magnitude more accurate for the synthetic dataset compared to the lower dimensioned, but therefor orders of magnitude faster, image processing based approach. For real world data the difference in accuracy between both approaches is not significant anymore. In both cases the reconstructed polyhedra supply information about their inherent semantic and can be used for subsequent and more differentiated semantic annotations through exploitation of texture information.

  17. 3D TEM reconstruction and segmentation process of laminar bio-nanocomposites

    SciTech Connect

    Iturrondobeitia, M. Okariz, A.; Fernandez-Martinez, R.; Jimbert, P.; Guraya, T.; Ibarretxe, J.

    2015-03-30

    The microstructure of laminar bio-nanocomposites (Poly (lactic acid)(PLA)/clay) depends on the amount of clay platelet opening after integration with the polymer matrix and determines the final properties of the material. Transmission electron microscopy (TEM) technique is the only one that can provide a direct observation of the layer dispersion and the degree of exfoliation. However, the orientation of the clay platelets, which affects the final properties, is practically immeasurable from a single 2D TEM image. This issue can be overcome using transmission electron tomography (ET), a technique that allows the complete 3D characterization of the structure, including the measurement of the orientation of clay platelets, their morphology and their 3D distribution. ET involves a 3D reconstruction of the study volume and a subsequent segmentation of the study object. Currently, accurate segmentation is performed manually, which is inefficient and tedious. The aim of this work is to propose an objective/automated segmentation methodology process of a 3D TEM tomography reconstruction. In this method the segmentation threshold is optimized by minimizing the variation of the dimensions of the segmented objects and matching the segmented V{sub clay} (%) and the actual one. The method is first validated using a fictitious set of objects, and then applied on a nanocomposite.

  18. Quality Analysis on 3d Buidling Models Reconstructed from Uav Imagery

    NASA Astrophysics Data System (ADS)

    Jarzabek-Rychard, M.; Karpina, M.

    2016-06-01

    Recent developments in UAV technology and structure from motion techniques have effected that UAVs are becoming standard platforms for 3D data collection. Because of their flexibility and ability to reach inaccessible urban parts, drones appear as optimal solution for urban applications. Building reconstruction from the data collected with UAV has the important potential to reduce labour cost for fast update of already reconstructed 3D cities. However, especially for updating of existing scenes derived from different sensors (e.g. airborne laser scanning), a proper quality assessment is necessary. The objective of this paper is thus to evaluate the potential of UAV imagery as an information source for automatic 3D building modeling at LOD2. The investigation process is conducted threefold: (1) comparing generated SfM point cloud to ALS data; (2) computing internal consistency measures of the reconstruction process; (3) analysing the deviation of Check Points identified on building roofs and measured with a tacheometer. In order to gain deep insight in the modeling performance, various quality indicators are computed and analysed. The assessment performed according to the ground truth shows that the building models acquired with UAV-photogrammetry have the accuracy of less than 18 cm for the plannimetric position and about 15 cm for the height component.

  19. 3D volume reconstruction of a mouse brain histological sections using warp filtering

    SciTech Connect

    Ju, Tao; Warren, Joe; Carson, James P.; Bello, Musodiq; Kakadiaris, Ioannis; Chiu, Wah; Thaller, Christina; Eichele, Gregor

    2006-09-30

    Sectioning tissues for optical microscopy often introduces upon the resulting sections distortions that make 3D reconstruction difficult. Here we present an automatic method for producing a smooth 3D volume from distorted 2D sections in the absence of any undistorted references. The method is based on pairwise elastic image warps between successive tissue sections, which can be computed by 2D image registration. Using a Gaussian filter, an average warp is computed for each section from the pairwise warps in a group of its neighboring sections. The average warps deform each section to match its neighboring sections, thus creating a smooth volume where corresponding features on successive sections lie close to each other. The proposed method can be used with any existing 2D image registration method for 3D reconstruction. In particular, we present a novel image warping algorithm based on dynamic programming that extends Dynamic Time Warping in 1D speech recognition to compute pairwise warps between high-resolution 2D images. The warping algorithm efficiently computes a restricted class of 2D local deformations that are characteristic between successive tissue sections. Finally, a validation framework is proposed and applied to evaluate the quality of reconstruction using both real sections and a synthetic volume.

  20. 3D volume reconstruction of a mouse brain from histological sections using warp filtering.

    PubMed

    Ju, Tao; Warren, Joe; Carson, James; Bello, Musodiq; Kakadiaris, Ioannis; Chiu, Wah; Thaller, Christina; Eichele, Gregor

    2006-09-30

    Sectioning tissues for optical microscopy often introduces upon the resulting sections distortions that make 3D reconstruction difficult. Here we present an automatic method for producing a smooth 3D volume from distorted 2D sections in the absence of any undistorted references. The method is based on pairwise elastic image warps between successive tissue sections, which can be computed by 2D image registration. Using a Gaussian filter, an average warp is computed for each section from the pairwise warps in a group of its neighboring sections. The average warps deform each section to match its neighboring sections, thus creating a smooth volume where corresponding features on successive sections lie close to each other. The proposed method can be used with any existing 2D image registration method for 3D reconstruction. In particular, we present a novel image warping algorithm based on dynamic programming that extends Dynamic Time Warping in 1D speech recognition to compute pairwise warps between high-resolution 2D images. The warping algorithm efficiently computes a restricted class of 2D local deformations that are characteristic between successive tissue sections. Finally, a validation framework is proposed and applied to evaluate the quality of reconstruction using both real sections and a synthetic volume.

  1. Comparison of 3D Reconstructive Technologies Used for Morphometric Research and the Translation of Knowledge Using a Decision Matrix

    ERIC Educational Resources Information Center

    Martin, Charys M.; Roach, Victoria A.; Nguyen, Ngan; Rice, Charles L.; Wilson, Timothy D.

    2013-01-01

    The use of three-dimensional (3D) models for education, pre-operative assessment, presurgical planning, and measurement have become more prevalent. With the increase in prevalence of 3D models there has also been an increase in 3D reconstructive software programs that are used to create these models. These software programs differ in…

  2. A novel 3D template for mandible and maxilla reconstruction: Rapid prototyping using stereolithography

    PubMed Central

    Kumta, Samir; Kumta, Monica; Jain, Leena; Purohit, Shrirang; Ummul, Rani

    2015-01-01

    Introduction: Replication of the exact three-dimensional (3D) structure of the maxilla and mandible is now a priority whilst attempting reconstruction of these bones to attain a complete functional and aesthetic rehabilitation. We hereby present the process of rapid prototyping using stereolithography to produce templates for modelling bone grafts and implants for maxilla/mandible reconstructions, its applications in tumour/trauma, and outcomes for primary and secondary reconstruction. Materials and Methods: Stereolithographic template-assisted reconstruction was used on 11 patients for the reconstruction of the mandible/maxilla primarily following tumour excision and secondarily for the realignment of post-traumatic malunited fractures or deformity corrections. Data obtained from the computed tomography (CT) scans with 1-mm resolution were converted into a computer-aided design (CAD) using the CT Digital Imaging and Communications in Medicine (DICOM) data. Once a CAD model was constructed, it was converted into a stereolithographic format and then processed by the rapid prototyping technology to produce the physical anatomical model using a resin. This resin model replicates the native mandible, which can be thus used off table as a guide for modelling the bone grafts. Discussion: This conversion of two-dimensional (2D) data from CT scan into 3D models is a very precise guide to shaping the bone grafts. Further, this CAD can reconstruct the defective half of the mandible using the mirror image principle, and the normal anatomical model can be created to aid secondary reconstructions. Conclusion: This novel approach allows a precise translation of the treatment plan directly to the surgical field. It is also an important teaching tool for implant moulding and fixation, and helps in patient counselling. PMID:26933279

  3. Rapid reconstruction of 3D neuronal morphology from light microscopy images with augmented rayburst sampling.

    PubMed

    Ming, Xing; Li, Anan; Wu, Jingpeng; Yan, Cheng; Ding, Wenxiang; Gong, Hui; Zeng, Shaoqun; Liu, Qian

    2013-01-01

    Digital reconstruction of three-dimensional (3D) neuronal morphology from light microscopy images provides a powerful technique for analysis of neural circuits. It is time-consuming to manually perform this process. Thus, efficient computer-assisted approaches are preferable. In this paper, we present an innovative method for the tracing and reconstruction of 3D neuronal morphology from light microscopy images. The method uses a prediction and refinement strategy that is based on exploration of local neuron structural features. We extended the rayburst sampling algorithm to a marching fashion, which starts from a single or a few seed points and marches recursively forward along neurite branches to trace and reconstruct the whole tree-like structure. A local radius-related but size-independent hemispherical sampling was used to predict the neurite centerline and detect branches. Iterative rayburst sampling was performed in the orthogonal plane, to refine the centerline location and to estimate the local radius. We implemented the method in a cooperative 3D interactive visualization-assisted system named flNeuronTool. The source code in C++ and the binaries are freely available at http://sourceforge.net/projects/flneurontool/. We validated and evaluated the proposed method using synthetic data and real datasets from the Digital Reconstruction of Axonal and Dendritic Morphology (DIADEM) challenge. Then, flNeuronTool was applied to mouse brain images acquired with the Micro-Optical Sectioning Tomography (MOST) system, to reconstruct single neurons and local neural circuits. The results showed that the system achieves a reasonable balance between fast speed and acceptable accuracy, which is promising for interactive applications in neuronal image analysis.

  4. A Geodynamic Grand Challenge: Time-Reversed Mantle Convection Reconstructions From Tomographic Images of Present-Day Mantle Structure

    NASA Astrophysics Data System (ADS)

    Glisovic, P.; Forte, A. M.; Moucha, R.

    2009-12-01

    One of the most complex challenges in current geodynamics research is the reconstruction of the past evolution of 3-D mantle temperature structure from seismic tomographic images of present-day lateral heterogeneity in the mantle. Early efforts to address this problem have been based on backward advection approximations based on the assumption that mantle convection is a very-high Rayleigh number process (e.g. Forte & Mitrovica 1997; Steinberger & O'Connell 1997). Over the past decade further progress has been achieved and new techniques have been proposed, such as the 4-D variational (Bunge et al. 2003) and quasi-reversible (Ismail-Zadeh et al. 2007) approaches. An enduring challenge is the construction of time-reversed mantle convection simulations that yield maximum consistency with a wide suite of surface geodynamic constraints on mantle rheology and 3-D structure inferred from seismic tomography. Resolving this outstanding problem is of crucial importance, because a successful reconstruction of the time-dependent, 3-D mantle convective structure in the geological past provides unique insights into the origin and evolution of a number of fundamental surface processes that include topography changes, eustatic sea level variations, state of stress in the lithosphere, and Earth rotation variations. A key concern in these reconstructions is quantifying the inherent uncertainties and the implications for surface geodynamic observables. We will explore these issues and compare the efficacy of different backward convection techniques using a new mantle convection model based on recent joint seismic-geodynamic tomography inversions (Simmons et al., GJI, 2009).

  5. Fast alternating projection methods for constrained tomographic reconstruction.

    PubMed

    Liu, Li; Han, Yongxin; Jin, Mingwu

    2017-01-01

    The alternating projection algorithms are easy to implement and effective for large-scale complex optimization problems, such as constrained reconstruction of X-ray computed tomography (CT). A typical method is to use projection onto convex sets (POCS) for data fidelity, nonnegative constraints combined with total variation (TV) minimization (so called TV-POCS) for sparse-view CT reconstruction. However, this type of method relies on empirically selected parameters for satisfactory reconstruction and is generally slow and lack of convergence analysis. In this work, we use a convex feasibility set approach to address the problems associated with TV-POCS and propose a framework using full sequential alternating projections or POCS (FS-POCS) to find the solution in the intersection of convex constraints of bounded TV function, bounded data fidelity error and non-negativity. The rationale behind FS-POCS is that the mathematically optimal solution of the constrained objective function may not be the physically optimal solution. The breakdown of constrained reconstruction into an intersection of several feasible sets can lead to faster convergence and better quantification of reconstruction parameters in a physical meaningful way than that in an empirical way of trial-and-error. In addition, for large-scale optimization problems, first order methods are usually used. Not only is the condition for convergence of gradient-based methods derived, but also a primal-dual hybrid gradient (PDHG) method is used for fast convergence of bounded TV. The newly proposed FS-POCS is evaluated and compared with TV-POCS and another convex feasibility projection method (CPTV) using both digital phantom and pseudo-real CT data to show its superior performance on reconstruction speed, image quality and quantification.

  6. Fast, automatic, and accurate catheter reconstruction in HDR brachytherapy using an electromagnetic 3D tracking system

    SciTech Connect

    Poulin, Eric; Racine, Emmanuel; Beaulieu, Luc; Binnekamp, Dirk

    2015-03-15

    Purpose: In high dose rate brachytherapy (HDR-B), current catheter reconstruction protocols are relatively slow and error prone. The purpose of this technical note is to evaluate the accuracy and the robustness of an electromagnetic (EM) tracking system for automated and real-time catheter reconstruction. Methods: For this preclinical study, a total of ten catheters were inserted in gelatin phantoms with different trajectories. Catheters were reconstructed using a 18G biopsy needle, used as an EM stylet and equipped with a miniaturized sensor, and the second generation Aurora{sup ®} Planar Field Generator from Northern Digital Inc. The Aurora EM system provides position and orientation value with precisions of 0.7 mm and 0.2°, respectively. Phantoms were also scanned using a μCT (GE Healthcare) and Philips Big Bore clinical computed tomography (CT) system with a spatial resolution of 89 μm and 2 mm, respectively. Reconstructions using the EM stylet were compared to μCT and CT. To assess the robustness of the EM reconstruction, five catheters were reconstructed twice and compared. Results: Reconstruction time for one catheter was 10 s, leading to a total reconstruction time inferior to 3 min for a typical 17-catheter implant. When compared to the μCT, the mean EM tip identification error was 0.69 ± 0.29 mm while the CT error was 1.08 ± 0.67 mm. The mean 3D distance error was found to be 0.66 ± 0.33 mm and 1.08 ± 0.72 mm for the EM and CT, respectively. EM 3D catheter trajectories were found to be more accurate. A maximum difference of less than 0.6 mm was found between successive EM reconstructions. Conclusions: The EM reconstruction was found to be more accurate and precise than the conventional methods used for catheter reconstruction in HDR-B. This approach can be applied to any type of catheters and applicators.

  7. Rapidly converging multigrid reconstruction of cone-beam tomographic data

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  8. Application of 3D photo-reconstruction in soil erosion studies

    NASA Astrophysics Data System (ADS)

    Castillo, Carlos; James, Michael; Pérez, Rafael; Gómez, Jose Alfonso

    2014-05-01

    3D photo-reconstruction (3D-PR) has been applied successfully to obtain elevation models using uncalibrated and nonmetric cameras for a range of geoscience applications (e.g. James and Robson, 2012), including gully erosion assessment (Castillo et al., 2012). However, its application in soil erosion studies is currently at the outset. The aim of this work is to compare 3D-PR with conventional techniques that have been employed traditionally for different purposes in soil erosion studies. In this preliminary work, we tested three applications that involve volume calculations: estimation of soil bulk density (BD), quantification of soil erosion at road banks (RB) and sedimentation rates behind check dams (CD). For each analysis, a PR field survey was carried out simultaneously with a conventional method (volume of water was used for BD, and total station surveys for RB and CD). For the 3D-PR technique, the accuracy as a function of the number of pictures taken was evaluated. In this study we explore the difference in the volume estimates between 3D-PR and conventional techniques as well as the time requirements for each method in order to compare their performance and optimal field of application.

  9. Tomographic Reconstruction of Mercury's Exosphere from MESSENGER Flyby Data

    NASA Technical Reports Server (NTRS)

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

    2011-01-01

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

  10. Using videogrammetry and 3D image reconstruction to identify crime suspects

    NASA Astrophysics Data System (ADS)

    Klasen, Lena M.; Fahlander, Olov

    1997-02-01

    The anthropometry and movements are unique for every individual human being. We identify persons we know by recognizing the way the look and move. By quantifying these measures and using image processing methods this method can serve as a tool in the work of the police as a complement to the ability of the human eye. The idea is to use virtual 3-D parameterized models of the human body to measure the anthropometry and movements of a crime suspect. The Swedish National Laboratory of Forensic Science in cooperation with SAAB Military Aircraft have developed methods for measuring the lengths of persons from video sequences. However, there is so much unused information in a digital image sequence from a crime scene. The main approach for this paper is to give an overview of the current research project at Linkoping University, Image Coding Group where methods to measure anthropometrical data and movements by using virtual 3-D parameterized models of the person in the crime scene are being developed. The length of an individual might vary up to plus or minus 10 cm depending on whether the person is in upright position or not. When measuring during the best available conditions, the length still varies within plus or minus 1 cm. Using a full 3-D model provides a rich set of anthropometric measures describing the person in the crime scene. Once having obtained such a model the movements can be quantified as well. The results depend strongly on the accuracy of the 3-D model and the strategy of having such an accurate 3-D model is to make one estimate per image frame by using 3-D scene reconstruction, and an averaged 3-D model as the final result from which the anthropometry and movements are calculated.

  11. Measurement Matrix Optimization and Mismatch Problem Compensation for DLSLA 3-D SAR Cross-Track Reconstruction

    PubMed Central

    Bao, Qian; Jiang, Chenglong; Lin, Yun; Tan, Weixian; Wang, Zhirui; Hong, Wen

    2016-01-01

    With a short linear array configured in the cross-track direction, downward looking sparse linear array three-dimensional synthetic aperture radar (DLSLA 3-D SAR) can obtain the 3-D image of an imaging scene. To improve the cross-track resolution, sparse recovery methods have been investigated in recent years. In the compressive sensing (CS) framework, the reconstruction performance depends on the property of measurement matrix. This paper concerns the technique to optimize the measurement matrix and deal with the mismatch problem of measurement matrix caused by the off-grid scatterers. In the model of cross-track reconstruction, the measurement matrix is mainly affected by the configuration of antenna phase centers (APC), thus, two mutual coherence based criteria are proposed to optimize the configuration of APCs. On the other hand, to compensate the mismatch problem of the measurement matrix, the sparse Bayesian inference based method is introduced into the cross-track reconstruction by jointly estimate the scatterers and the off-grid error. Experiments demonstrate the performance of the proposed APCs’ configuration schemes and the proposed cross-track reconstruction method. PMID:27556471

  12. Measurement Matrix Optimization and Mismatch Problem Compensation for DLSLA 3-D SAR Cross-Track Reconstruction.

    PubMed

    Bao, Qian; Jiang, Chenglong; Lin, Yun; Tan, Weixian; Wang, Zhirui; Hong, Wen

    2016-08-22

    With a short linear array configured in the cross-track direction, downward looking sparse linear array three-dimensional synthetic aperture radar (DLSLA 3-D SAR) can obtain the 3-D image of an imaging scene. To improve the cross-track resolution, sparse recovery methods have been investigated in recent years. In the compressive sensing (CS) framework, the reconstruction performance depends on the property of measurement matrix. This paper concerns the technique to optimize the measurement matrix and deal with the mismatch problem of measurement matrix caused by the off-grid scatterers. In the model of cross-track reconstruction, the measurement matrix is mainly affected by the configuration of antenna phase centers (APC), thus, two mutual coherence based criteria are proposed to optimize the configuration of APCs. On the other hand, to compensate the mismatch problem of the measurement matrix, the sparse Bayesian inference based method is introduced into the cross-track reconstruction by jointly estimate the scatterers and the off-grid error. Experiments demonstrate the performance of the proposed APCs' configuration schemes and the proposed cross-track reconstruction method.

  13. 3D nanostructure reconstruction based on the SEM imaging principle, and applications.

    PubMed

    Zhu, Fu-Yun; Wang, Qi-Qi; Zhang, Xiao-Sheng; Hu, Wei; Zhao, Xin; Zhang, Hai-Xia

    2014-05-09

    This paper addresses a novel 3D reconstruction method for nanostructures based on the scanning electron microscopy (SEM) imaging principle. In this method, the shape from shading (SFS) technique is employed, to analyze the gray-scale information of a single top-view SEM image which contains all the visible surface information, and finally to reconstruct the 3D surface morphology. It offers not only unobstructed observation from various angles but also the exact physical dimensions of nanostructures. A convenient and commercially available tool (NanoViewer) is developed based on this method for nanostructure analysis and characterization of properties. The reconstruction result coincides well with the SEM nanostructure image and is verified in different ways. With the extracted structure information, subsequent research of the nanostructure can be carried out, such as roughness analysis, optimizing properties by structure improvement and performance simulation with a reconstruction model. Efficient, practical and non-destructive, the method will become a powerful tool for nanostructure surface observation and characterization.

  14. Model-based adaptive 3D sonar reconstruction in reverberating environments.

    PubMed

    Saucan, Augustin-Alexandru; Sintes, Christophe; Chonavel, Thierry; Caillec, Jean-Marc Le

    2015-10-01

    In this paper, we propose a novel model-based approach for 3D underwater scene reconstruction, i.e., bathymetry, for side scan sonar arrays in complex and highly reverberating environments like shallow water areas. The presence of multipath echoes and volume reverberation generates false depth estimates. To improve the resulting bathymetry, this paper proposes and develops an adaptive filter, based on several original geometrical models. This multimodel approach makes it possible to track and separate the direction of arrival trajectories of multiple echoes impinging the array. Echo tracking is perceived as a model-based processing stage, incorporating prior information on the temporal evolution of echoes in order to reject cluttered observations generated by interfering echoes. The results of the proposed filter on simulated and real sonar data showcase the clutter-free and regularized bathymetric reconstruction. Model validation is carried out with goodness of fit tests, and demonstrates the importance of model-based processing for bathymetry reconstruction.

  15. Test of 3D CT reconstructions by EM + TV algorithm from undersampled data

    SciTech Connect

    Evseev, Ivan; Ahmann, Francielle; Silva, Hamilton P. da

    2013-05-06

    Computerized tomography (CT) plays an important role in medical imaging for diagnosis and therapy. However, CT imaging is connected with ionization radiation exposure of patients. Therefore, the dose reduction is an essential issue in CT. In 2011, the Expectation Maximization and Total Variation Based Model for CT Reconstruction (EM+TV) was proposed. This method can reconstruct a better image using less CT projections in comparison with the usual filtered back projection (FBP) technique. Thus, it could significantly reduce the overall dose of radiation in CT. This work reports the results of an independent numerical simulation for cone beam CT geometry with alternative virtual phantoms. As in the original report, the 3D CT images of 128 Multiplication-Sign 128 Multiplication-Sign 128 virtual phantoms were reconstructed. It was not possible to implement phantoms with lager dimensions because of the slowness of code execution even by the CORE i7 CPU.

  16. Tomographic image reconstruction via estimation of sparse unidirectional gradients.

    PubMed

    Polak, Adam G; Mroczka, Janusz; Wysoczański, Dariusz

    2017-02-01

    Since computed tomography (CT) was developed over 35 years ago, new mathematical ideas and computational algorithms have been continuingly elaborated to improve the quality of reconstructed images. In recent years, a considerable effort can be noticed to apply the sparse solution of underdetermined system theory to the reconstruction of CT images from undersampled data. Its significance stems from the possibility of obtaining good quality CT images from low dose projections. Among diverse approaches, total variation (TV) minimizing 2D gradients of an image, seems to be the most popular method. In this paper, a new method for CT image reconstruction via sparse gradients estimation (SGE), is proposed. It consists in estimating 1D gradients specified in four directions using the iterative reweighting algorithm. To investigate its properties and to compare it with TV and other related methods, numerical simulations were performed according to the Monte Carlo scheme, using the Shepp-Logan and more realistic brain phantoms scanned at 9-60 directions in the range from 0 to 179°, with measurement data disturbed by additive Gaussians noise characterized by the relative level of 0.1%, 0.2%, 0.5%, 1%, 2% and 5%. The accuracy of image reconstruction was assessed in terms of the relative root-mean-square (RMS) error. The results show that the proposed SGE algorithm has returned more accurate images than TV for the cases fulfilling the sparsity conditions. Particularly, it preserves sharp edges of regions representing different tissues or organs and yields images of much better quality reconstructed from a small number of projections disturbed by relatively low measurement noise.

  17. 3D reconstruction of digitized histological sections for vasculature quantification in the mouse hind limb

    NASA Astrophysics Data System (ADS)

    Xu, Yiwen; Pickering, J. Geoffrey; Nong, Zengxuan; Gibson, Eli; Ward, Aaron D.

    2014-03-01

    In contrast to imaging modalities such as magnetic resonance imaging and micro computed tomography, digital histology reveals multiple stained tissue features at high resolution (0.25μm/pixel). However, the two-dimensional (2D) nature of histology challenges three-dimensional (3D) quantification and visualization of the different tissue components, cellular structures, and subcellular elements. This limitation is particularly relevant to the vasculature, which has a complex and variable structure within tissues. The objective of this study was to perform a fully automated 3D reconstruction of histology tissue in the mouse hind limb preserving the accurate systemic orientation of the tissues, stained with hematoxylin and immunostained for smooth muscle α actin. We performed a 3D reconstruction using pairwise rigid registrations of 5μm thick, paraffin-embedded serial sections, digitized at 0.25μm/pixel. Each registration was performed using the iterative closest points algorithm on blood vessel landmarks. Landmarks were vessel centroids, determined according to a signed distance map of each pixel to a decision boundary in hue-saturation-value color space; this decision boundary was determined based on manual annotation of a separate training set. Cell nuclei were then automatically extracted and corresponded to refine the vessel landmark registration. Homologous nucleus landmark pairs appearing on not more than two adjacent slides were chosen to avoid registrations which force curved or non-sectionorthogonal structures to be straight and section-orthogonal. The median accumulated target registration errors ± interquartile ranges for the vessel landmark registration, and the nucleus landmark refinement were 43.4+/-42.8μm and 2.9+/-1.7μm, respectively (p<0.0001). Fully automatic and accurate 3D rigid reconstruction of mouse hind limb histology imaging is feasible based on extracted vasculature and nuclei.

  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. Feature-constrained surface reconstruction approach for point cloud data acquired with 3D laser scanner

    NASA Astrophysics Data System (ADS)

    Wang, Yongbo; Sheng, Yehua; Lu, Guonian; Tian, Peng; Zhang, Kai

    2008-04-01

    Surface reconstruction is an important task in the field of 3d-GIS, computer aided design and computer graphics (CAD & CG), virtual simulation and so on. Based on available incremental surface reconstruction methods, a feature-constrained surface reconstruction approach for point cloud is presented. Firstly features are extracted from point cloud under the rules of curvature extremes and minimum spanning tree. By projecting local sample points to the fitted tangent planes and using extracted features to guide and constrain the process of local triangulation and surface propagation, topological relationship among sample points can be achieved. For the constructed models, a process named consistent normal adjustment and regularization is adopted to adjust normal of each face so that the correct surface model is achieved. Experiments show that the presented approach inherits the convenient implementation and high efficiency of traditional incremental surface reconstruction method, meanwhile, it avoids improper propagation of normal across sharp edges, which means the applicability of incremental surface reconstruction is greatly improved. Above all, appropriate k-neighborhood can help to recognize un-sufficient sampled areas and boundary parts, the presented approach can be used to reconstruct both open and close surfaces without additional interference.

  20. Comparative validation of single-shot optical techniques for laparoscopic 3-D surface reconstruction.

    PubMed

    Maier-Hein, L; Groch, A; Bartoli, A; Bodenstedt, S; Boissonnat, G; Chang, P-L; Clancy, N T; Elson, D S; Haase, S; Heim, E; Hornegger, J; Jannin, P; Kenngott, H; Kilgus, T; Müller-Stich, B; Oladokun, D; Röhl, S; Dos Santos, T R; Schlemmer, H-P; Seitel, A; Speidel, S; Wagner, M; Stoyanov, D

    2014-10-01

    Intra-operative imaging techniques for obtaining the shape and morphology of soft-tissue surfaces in vivo are a key enabling technology for advanced surgical systems. Different optical techniques for 3-D surface reconstruction in laparoscopy have been proposed, however, so far no quantitative and comparative validation has been performed. Furthermore, robustness of the methods to clinically important factors like smoke or bleeding has not yet been assessed. To address these issues, we have formed a joint international initiative with the aim of validating different state-of-the-art passive and active reconstruction methods in a comparative manner. In this comprehensive in vitro study, we investigated reconstruction accuracy using different organs with various shape and texture and also tested reconstruction robustness with respect to a number of factors like the pose of the endoscope as well as the amount of blood or smoke present in the scene. The study suggests complementary advantages of the different techniques with respect to accuracy, robustness, point density, hardware complexity and computation time. While reconstruction accuracy under ideal conditions was generally high, robustness is a remaining issue to be addressed. Future work should include sensor fusion and in vivo validation studies in a specific clinical context. To trigger further research in surface reconstruction, stereoscopic data of the study will be made publically available at www.open-CAS.com upon publication of the paper.

  1. Multiview and light-field reconstruction algorithms for 360° multiple-projector-type 3D display.

    PubMed

    Zhong, Qing; Peng, Yifan; Li, Haifeng; Su, Chen; Shen, Weidong; Liu, Xu

    2013-07-01

    Both multiview and light-field reconstructions are proposed for a multiple-projector 3D display system. To compare the performance of the reconstruction algorithms in the same system, an optimized multiview reconstruction algorithm with sub-view-zones (SVZs) is proposed. The algorithm divided the conventional view zones in multiview display into several SVZs and allocates more view images. The optimized reconstruction algorithm unifies the conventional multiview reconstruction and light-field reconstruction algorithms, which can indicate the difference in performance when multiview reconstruction is changed to light-field reconstruction. A prototype consisting of 60 projectors with an arc diffuser as its screen is constructed to verify the algorithms. Comparison of different configurations of SVZs shows that light-field reconstruction provides large-scale 3D images with the smoothest motion parallax; thus it may provide better overall performance for large-scale 360° display than multiview reconstruction.

  2. HADES-CCG, a new tomographic reconstruction tool

    SciTech Connect

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

    2000-09-07

    We have developed a new tomography code, HADES-CCG. This code uses HADES, a radiographic simulation code, to perform forward- and back-projection and is coupled to a Constrained Conjugate Gradient (CCG) optimizer. An iterative solution to the reconstruction problem is found which is optimal, given the detector noise model, a source model and the appropriate attenuation cross-sections. By explicitly including experimental effects in forward- and back-projection, these effects are not folded back into the object model.

  3. Tomographic fluorescence reconstruction by a spectral projected gradient pursuit method

    NASA Astrophysics Data System (ADS)

    Ye, Jinzuo; An, Yu; Mao, Yamin; Jiang, Shixin; Yang, Xin; Chi, Chongwei; Tian, Jie

    2015-03-01

    In vivo fluorescence molecular imaging (FMI) has played an increasingly important role in biomedical research of preclinical area. Fluorescence molecular tomography (FMT) further upgrades the two-dimensional FMI optical information to three-dimensional fluorescent source distribution, which can greatly facilitate applications in related studies. However, FMT presents a challenging inverse problem which is quite ill-posed and ill-conditioned. Continuous efforts to develop more practical and efficient methods for FMT reconstruction are still needed. In this paper, a method based on spectral projected gradient pursuit (SPGP) has been proposed for FMT reconstruction. The proposed method was based on the directional pursuit framework. A mathematical strategy named the nonmonotone line search was associated with the SPGP method, which guaranteed the global convergence. In addition, the Barzilai-Borwein step length was utilized to build the new step length of the SPGP method, which was able to speed up the convergence of this gradient method. To evaluate the performance of the proposed method, several heterogeneous simulation experiments including multisource cases as well as comparative analyses have been conducted. The results demonstrated that, the proposed method was able to achieve satisfactory source localizations with a bias less than 1 mm; the computational efficiency of the method was one order of magnitude faster than the contrast method; and the fluorescence reconstructed by the proposed method had a higher contrast to the background than the contrast method. All the results demonstrated the potential for practical FMT applications with the proposed method.

  4. Tomographic shadowgraphy for three-dimensional reconstruction of instantaneous spray distributions

    NASA Astrophysics Data System (ADS)

    Klinner, Joachim; Willert, Christian

    2012-08-01

    Tomographic shadowgraphy is an image-based optical technique capable of reconstructing the three dimensional instantaneous spray distributions within a given volume. The method is based on a multiple view imaging setup with inline illumination provided by current-pulsed LEDs, which results in droplet shadows being projected onto multiple sensor planes. Each camera records image pairs with short inter-framing times that allow the trajectories of the individual droplets to be estimated using conventional three-dimensional particle tracking approaches. The observed volume is calibrated with a traversed micro-target. A comparison is made between several photogrammetric and polynomial least-square camera calibration techniques regarding their accuracy in deep volume calibration at magnifications close to unity. A calibration method based on volume calibration from multiple planar homographies at equally spaced z-planes was found to produce the most reliable calibration. The combination of back-projected images at each voxel plane efficiently reproduces the droplet positions in three-dimensional space by line-of-sight (LOS) intensity reconstruction. Further improvement of the reconstruction can be achieved by iterative tomographic reconstruction, namely simultaneous multiplicative algebraic reconstruction technique (SMART). The quality of spray reconstruction is investigated using experimental data from multiple view shadowgraphs of hollow cone and flat fan water sprays. The investigations are further substantiated with simulations using synthetic data.

  5. a Line-Based 3d Roof Model Reconstruction Algorithm: Tin-Merging and Reshaping (tmr)

    NASA Astrophysics Data System (ADS)

    Rau, J.-Y.

    2012-07-01

    Three-dimensional building model is one of the major components of a cyber-city and is vital for the realization of 3D GIS applications. In the last decade, the airborne laser scanning (ALS) data is widely used for 3D building model reconstruction and object extraction. Instead, based on 3D roof structural lines, this paper presents a novel algorithm for automatic roof models reconstruction. A line-based roof model reconstruction algorithm, called TIN-Merging and Reshaping (TMR), is proposed. The roof structural line, such as edges, eaves and ridges, can be measured manually from aerial stereo-pair, derived by feature line matching or inferred from ALS data. The originality of the TMR algorithm for 3D roof modelling is to perform geometric analysis and topology reconstruction among those unstructured lines and then reshapes the roof-type using elevation information from the 3D structural lines. For topology reconstruction, a line constrained Delaunay Triangulation algorithm is adopted where the input structural lines act as constraint and their vertex act as input points. Thus, the constructed TINs will not across the structural lines. Later at the stage of Merging, the shared edge between two TINs will be check if the original structural line exists. If not, those two TINs will be merged into a polygon. Iterative checking and merging of any two neighboured TINs/Polygons will result in roof polygons on the horizontal plane. Finally, at the Reshaping stage any two structural lines with fixed height will be used to adjust a planar function for the whole roof polygon. In case ALS data exist, the Reshaping stage can be simplified by adjusting the point cloud within the roof polygon. The proposed scheme reduces the complexity of 3D roof modelling and makes the modelling process easier. Five test datasets provided by ISPRS WG III/4 located at downtown Toronto, Canada and Vaihingen, Germany are used for experiment. The test sites cover high rise buildings and residential

  6. Single-View 3D Scene Reconstruction and Parsing by Attribute Grammar.

    PubMed

    Liu, Xiaobai; Zhao, Yibiao; Zhu, Song-Chun

    2017-03-29

    In this paper, we present an attribute grammar for solving two coupled tasks: i) parsing an 2D image into semantic regions; and ii) recovering the 3D scene structures of all regions. The proposed grammar consists of a set of production rules, each describing a kind of spatial relation between planar surfaces in 3D scenes. These production rules are used to decompose an input image into a hierarchical parse graph representation where each graph node indicates a planar surface or a composite surface. Different from other stochastic image grammars, the proposed grammar augments each graph node with a set of attribute variables to depict scene-level global geometry, e.g. camera focal length, or local geometry, e.g., surface normal, contact lines between surfaces. These geometric attributes impose constraints between a node and its off-springs in the parse graph. Under a probabilistic framework, we develop a Markov Chain Monte Carlo method to construct a parse graph that optimizes the 2D image recognition and 3D scene reconstruction purposes simultaneously. We evaluated our method on both public benchmarks and newly collected datasets. Experiments demonstrate that the proposed method is capable of achieving state-of-the-art scene reconstruction of a single image.

  7. Fine-Scale Population Estimation by 3D Reconstruction of Urban Residential Buildings

    PubMed Central

    Wang, Shixin; Tian, Ye; Zhou, Yi; Liu, Wenliang; Lin, Chenxi

    2016-01-01

    Fine-scale population estimation is essential in emergency response and epidemiological applications as well as urban planning and management. However, representing populations in heterogeneous urban regions with a finer resolution is a challenge. This study aims to obtain fine-scale population distribution based on 3D reconstruction of urban residential buildings with morphological operations using optical high-resolution (HR) images from the Chinese No. 3 Resources Satellite (ZY-3). Specifically, the research area was first divided into three categories when dasymetric mapping was taken into consideration. The results demonstrate that the morphological building index (MBI) yielded better results than built-up presence index (PanTex) in building detection, and the morphological shadow index (MSI) outperformed color invariant indices (CIIT) in shadow extraction and height retrieval. Building extraction and height retrieval were then combined to reconstruct 3D models and to estimate population. Final results show that this approach is effective in fine-scale population estimation, with a mean relative error of 16.46% and an overall Relative Total Absolute Error (RATE) of 0.158. This study gives significant insights into fine-scale population estimation in complicated urban landscapes, when detailed 3D information of buildings is unavailable. PMID:27775670

  8. Reconstruction of 3D VMEC equilibria with helical cores in DIII-D

    NASA Astrophysics Data System (ADS)

    Wingen, A.; Wilcox, R. S.; Cianciosa, M. R.; Seal, S. K.; Unterberg, E. A.; Hirshman, S. P.; Piovesan, P.; Turco, F.

    2016-10-01

    A helical core is a feature accessible by high performance hybrid discharges. It becomes dominant, if the 3/2 tearing mode, typically dominating hybrid discharges, is suppressed. It has been experimentally verified in ASDEX-U, and recently in DIII-D. The VMEC/V3FIT codes allow for 3D reconstruction, which is shown here for the first time in a tokamak. The reconstructed helical core equilibrium can be used to numerically study the properties of an experimentally observed helical core. The helical core is a saturated internal kink, excited by 3D perturbation fields and driven primarily by the pressure gradient near q = 1. It is bifurcated from an axisymmetric state by 3D fields. It flattens the q-profile in the core, potentially stabilizing sawteeth. It contributes to flux pumping, which broadens the current density profile. This analysis will help to determine possible benefits or disadvantages for the high beta hybrid scenario. Supported by US DOE under DE-AC05-00OR227251, DE-FG02-04ER547612, DE-FC02-04ER546983 and DE-AC02-09CH114663.

  9. Active illumination based 3D surface reconstruction and registration for image guided medialization laryngoplasty

    NASA Astrophysics Data System (ADS)

    Jin, Ge; Lee, Sang-Joon; Hahn, James K.; Bielamowicz, Steven; Mittal, Rajat; Walsh, Raymond

    2007-03-01

    The medialization laryngoplasty is a surgical procedure to improve the voice function of the patient with vocal fold paresis and paralysis. An image guided system for the medialization laryngoplasty will help the surgeons to accurately place the implant and thus reduce the failure rates of the surgery. One of the fundamental challenges in image guided system is to accurately register the preoperative radiological data to the intraoperative anatomical structure of the patient. In this paper, we present a combined surface and fiducial based registration method to register the preoperative 3D CT data to the intraoperative surface of larynx. To accurately model the exposed surface area, a structured light based stereo vision technique is used for the surface reconstruction. We combined the gray code pattern and multi-line shifting to generate the intraoperative surface of the larynx. To register the point clouds from the intraoperative stage to the preoperative 3D CT data, a shape priori based ICP method is proposed to quickly register the two surfaces. The proposed approach is capable of tracking the fiducial markers and reconstructing the surface of larynx with no damage to the anatomical structure. We used off-the-shelf digital cameras, LCD projector and rapid 3D prototyper to develop our experimental system. The final RMS error in the registration is less than 1mm.

  10. Bias Field Inconsistency Correction of Motion-Scattered Multislice MRI for Improved 3D Image Reconstruction

    PubMed Central

    Kim, Kio; Habas, Piotr A.; Rajagopalan, Vidya; Scott, Julia A.; Corbett-Detig, James M.; Rousseau, Francois; Barkovich, A. James; Glenn, Orit A.; Studholme, Colin

    2012-01-01

    A common solution to clinical MR imaging in the presence of large anatomical motion is to use fast multi-slice 2D studies to reduce slice acquisition time and provide clinically usable slice data. Recently, techniques have been developed which retrospectively correct large scale 3D motion between individual slices allowing the formation of a geometrically correct 3D volume from the multiple slice stacks. One challenge, however, in the final reconstruction process is the possibility of varying intensity bias in the slice data, typically due to the motion of the anatomy relative to imaging coils. As a result, slices which cover the same region of anatomy at different times may exhibit different sensitivity. This bias field inconsistency can induce artifacts in the final 3D reconstruction that can impact both clinical interpretation of key tissue boundaries and the automated analysis of the data. Here we describe a framework to estimate and correct the bias field inconsistency in each slice collectively across all motion corrupted image slices. Experiments using synthetic and clinical data show that the proposed method reduces intensity variability in tissues and improves the distinction between key tissue types. PMID:21511561

  11. Bias field inconsistency correction of motion-scattered multislice MRI for improved 3D image reconstruction.

    PubMed

    Kim, Kio; Habas, Piotr A; Rajagopalan, Vidya; Scott, Julia A; Corbett-Detig, James M; Rousseau, Francois; Barkovich, A James; Glenn, Orit A; Studholme, Colin

    2011-09-01

    A common solution to clinical MR imaging in the presence of large anatomical motion is to use fast multislice 2D studies to reduce slice acquisition time and provide clinically usable slice data. Recently, techniques have been developed which retrospectively correct large scale 3D motion between individual slices allowing the formation of a geometrically correct 3D volume from the multiple slice stacks. One challenge, however, in the final reconstruction process is the possibility of varying intensity bias in the slice data, typically due to the motion of the anatomy relative to imaging coils. As a result, slices which cover the same region of anatomy at different times may exhibit different sensitivity. This bias field inconsistency can induce artifacts in the final 3D reconstruction that can impact both clinical interpretation of key tissue boundaries and the automated analysis of the data. Here we describe a framework to estimate and correct the bias field inconsistency in each slice collectively across all motion corrupted image slices. Experiments using synthetic and clinical data show that the proposed method reduces intensity variability in tissues and improves the distinction between key tissue types.

  12. Reconstruction of 3D tree stem models from low-cost terrestrial laser scanner data

    NASA Astrophysics Data System (ADS)

    Kelbe, Dave; Romanczyk, Paul; van Aardt, Jan; Cawse-Nicholson, Kerry

    2013-05-01

    With the development of increasingly advanced airborne sensing systems, there is a growing need to support sensor system design, modeling, and product-algorithm development with explicit 3D structural ground truth commensurate to the scale of acquisition. Terrestrial laser scanning is one such technique which could provide this structural information. Commercial instrumentation to suit this purpose has existed for some time now, but cost can be a prohibitive barrier for some applications. As such we recently developed a unique laser scanning system from readily-available components, supporting low cost, highly portable, and rapid measurement of below-canopy 3D forest structure. Tools were developed to automatically reconstruct tree stem models as an initial step towards virtual forest scene generation. The objective of this paper is to assess the potential of this hardware/algorithm suite to reconstruct 3D stem information for a single scan of a New England hardwood forest site. Detailed tree stem structure (e.g., taper, sweep, and lean) is recovered for trees of varying diameter, species, and range from the sensor. Absolute stem diameter retrieval accuracy is 12.5%, with a 4.5% overestimation bias likely due to the LiDAR beam divergence.

  13. 3D reconstruction from images taken with a coaxial camera rig

    NASA Astrophysics Data System (ADS)

    Kirby, Richard; Whitaker, Ross

    2016-09-01

    A coaxial camera rig consists of a pair of cameras which acquire images along the same optical axis but at different distances from the scene using different focal length optics. The coaxial geometry permits the acquisition of image pairs through a substantially smaller opening than would be required by a traditional binocular stereo camera rig. This is advantageous in applications where physical space is limited, such as in an endoscope. 3D images acquired through an endoscope are desirable, but the lack of physical space for a traditional stereo baseline is problematic. While image acquisition along a common optical axis has been known for many years; 3D reconstruction from such image pairs has not been possible in the center region due to the very small disparity between corresponding points. This characteristic of coaxial image pairs has been called the unrecoverable point problem. We introduce a novel method to overcome the unrecoverable point problem in coaxial camera rigs, using a variational methods optimization algorithm to map pairs of optical flow fields from different focal length cameras in a coaxial camera rig. Our method uses the ratio of the optical flow fields for 3D reconstruction. This results in accurate image pair alignment and produces accurate dense depth maps. We test our method on synthetic optical flow fields and on real images. We demonstrate our method's accuracy by evaluating against a ground-truth. Accuracy is comparable to a traditional binocular stereo camera rig, but without the traditional stereo baseline and with substantially smaller occlusions.

  14. 3D Sorghum Reconstructions from Depth Images Identify QTL Regulating Shoot Architecture1[OPEN

    PubMed Central

    2016-01-01

    Dissecting the genetic basis of complex traits is aided by frequent and nondestructive measurements. Advances in range imaging technologies enable the rapid acquisition of three-dimensional (3D) data from an imaged scene. A depth camera was used to acquire images of sorghum (Sorghum bicolor), an important grain, forage, and bioenergy crop, at multiple developmental time points from a greenhouse-grown recombinant inbred line population. A semiautomated software pipeline was developed and used to generate segmented, 3D plant reconstructions from the images. Automated measurements made from 3D plant reconstructions identified quantitative trait loci for standard measures of shoot architecture, such as shoot height, leaf angle, and leaf length, and for novel composite traits, such as shoot compactness. The phenotypic variability associated with some of the quantitative trait loci displayed differences in temporal prevalence; for example, alleles closely linked with the sorghum Dwarf3 gene, an auxin transporter and pleiotropic regulator of both leaf inclination angle and shoot height, influence leaf angle prior to an effect on shoot height. Furthermore, variability in composite phenotypes that measure overall shoot architecture, such as shoot compactness, is regulated by loci underlying component phenotypes like leaf angle. As such, depth imaging is an economical and rapid method to acquire shoot architecture phenotypes in agriculturally important plants like sorghum to study the genetic basis of complex traits. PMID:27528244

  15. Detectability limitations with 3-D point reconstruction algorithms using digital radiography

    SciTech Connect

    Lindgren, Erik

    2015-03-31

    The estimated impact of pores in clusters on component fatigue will be highly conservative when based on 2-D rather than 3-D pore positions. To 3-D position and size defects using digital radiography and 3-D point reconstruction algorithms in general require a lower inspection time and in some cases work better with planar geometries than X-ray computed tomography. However, the increase in prior assumptions about the object and the defects will increase the intrinsic uncertainty in the resulting nondestructive evaluation output. In this paper this uncertainty arising when detecting pore defect clusters with point reconstruction algorithms is quantified using simulations. The simulation model is compared to and mapped to experimental data. The main issue with the uncertainty is the possible masking (detectability zero) of smaller defects around some other slightly larger defect. In addition, the uncertainty is explored in connection to the expected effects on the component fatigue life and for different amount of prior object-defect assumptions made.

  16. Improved tomographic reconstruction of large-scale real-world data by filter optimization.

    PubMed

    Pelt, Daniël M; De Andrade, Vincent

    2017-01-01

    In advanced tomographic experiments, large detector sizes and large numbers of acquired datasets can make it difficult to process the data in a reasonable time. At the same time, the acquired projections are often limited in some way, for example having a low number of projections or a low signal-to-noise ratio. Direct analytical reconstruction methods are able to produce reconstructions in very little time, even for large-scale data, but the quality of these reconstructions can be insufficient for further analysis in cases with limited data. Iterative reconstruction methods typically produce more accurate reconstructions, but take significantly more time to compute, which limits their usefulness in practice. In this paper, we present the application of the SIRT-FBP method to large-scale real-world tomographic data. The SIRT-FBP method is able to accurately approximate the simultaneous iterative reconstruction technique (SIRT) method by the computationally efficient filtered backprojection (FBP) method, using precomputed experiment-specific filters. We specifically focus on the many implementation details that are important for application on large-scale real-world data, and give solutions to common problems that occur with experimental data. We show that SIRT-FBP filters can be computed in reasonable time, even for large problem sizes, and that precomputed filters can be reused for future experiments. Reconstruction results are given for three different experiments, and are compared with results of popular existing methods. The results show that the SIRT-FBP method is able to accurately approximate iterative reconstructions of experimental data. Furthermore, they show that, in practice, the SIRT-FBP method can produce more accurate reconstructions than standard direct analytical reconstructions with popular filters, without increasing the required computation time.

  17. 3D surface reconstruction and visualization of the Drosophila wing imaginal disc at cellular resolution

    NASA Astrophysics Data System (ADS)

    Bai, Linge; Widmann, Thomas; Jülicher, Frank; Dahmann, Christian; Breen, David

    2013-01-01

    Quantifying and visualizing the shape of developing biological tissues provide information about the morphogenetic processes in multicellular organisms. The size and shape of biological tissues depend on the number, size, shape, and arrangement of the constituting cells. To better understand the mechanisms that guide tissues into their final shape, it is important to investigate the cellular arrangement within tissues. Here we present a data processing pipeline to generate 3D volumetric surface models of epithelial tissues, as well as geometric descriptions of the tissues' apical cell cross-sections. The data processing pipeline includes image acquisition, editing, processing and analysis, 2D cell mesh generation, 3D contourbased surface reconstruction, cell mesh projection, followed by geometric calculations and color-based visualization of morphological parameters. In their first utilization we have applied these procedures to construct a 3D volumetric surface model at cellular resolution of the wing imaginal disc of Drosophila melanogaster. The ultimate goal of the reported effort is to produce tools for the creation of detailed 3D geometric models of the individual cells in epithelial tissues. To date, 3D volumetric surface models of the whole wing imaginal disc have been created, and the apicolateral cell boundaries have been identified, allowing for the calculation and visualization of cell parameters, e.g. apical cross-sectional area of cells. The calculation and visualization of morphological parameters show position-dependent patterns of cell shape in the wing imaginal disc. Our procedures should offer a general data processing pipeline for the construction of 3D volumetric surface models of a wide variety of epithelial tissues.

  18. Computer-aided planning and reconstruction of cranial 3D implants.

    PubMed

    Gall, Markus; Xing Li; Xiaojun Chen; Schmalstieg, Dieter; Egger, Jan

    2016-08-01

    In this contribution, a prototype for semiautomatic computer-aided planning and reconstruction of cranial 3D Implants is presented. The software prototype guides the user through the workflow, beginning with loading and mirroring the patient's head to obtain an initial curvature of the cranial implant. However, naïve mirroring is not sufficient for an implant, because human heads are in general too asymmetric. Thus, the user can perform Laplacian smoothing, followed by Delaunay triangulation, for generating an aesthetic looking and well-fitting implant. Finally, our software prototype allows to save the designed 3D model of the implant as a STL-file for 3D printing. The 3D printed implant can be used for further pre-interventional planning or even as the final implant for the patient. In summary, our findings show that a customized MeVisLab prototype can be an alternative to complex commercial planning software, which may not be available in a clinic.

  19. Acceleration of EM-Based 3D CT Reconstruction Using FPGA.

    PubMed

    Choi, Young-Kyu; Cong, Jason

    2016-06-01

    Reducing radiation doses is one of the key concerns in computed tomography (CT) based 3D reconstruction. Although iterative methods such as the expectation maximization (EM) algorithm can be used to address this issue, applying this algorithm to practice is difficult due to the long execution time. Our goal is to decrease this long execution time to an order of a few minutes, so that low-dose 3D reconstruction can be performed even in time-critical events. In this paper we introduce a novel parallel scheme that takes advantage of numerous block RAMs on field-programmable gate arrays (FPGAs). Also, an external memory bandwidth reduction strategy is presented to reuse both the sinogram and the voxel intensity. Moreover, a customized processing engine based on the FPGA is presented to increase overall throughput while reducing the logic consumption. Finally, a hardware and software flow is proposed to quickly construct a design for various CT machines. The complete reconstruction system is implemented on an FPGA-based server-class node. Experiments on actual patient data show that a 26.9 × speedup can be achieved over a 16-thread multicore CPU implementation.

  20. Automated Atom-By-Atom Three-Dimensional (3D) Reconstruction of Field Ion Microscopy Data.

    PubMed

    Dagan, Michal; Gault, Baptiste; Smith, George D W; Bagot, Paul A J; Moody, Michael P

    2017-03-20

    An automated procedure has been developed for the reconstruction of field ion microscopy (FIM) data that maintains its atomistic nature. FIM characterizes individual atoms on the specimen's surface, evolving subject to field evaporation, in a series of two-dimensional (2D) images. Its unique spatial resolution enables direct imaging of crystal defects as small as single vacancies. To fully exploit FIM's potential, automated analysis tools are required. The reconstruction algorithm developed here relies on minimal assumptions and is sensitive to atomic coordinates of all imaged atoms. It tracks the atoms across a sequence of images, allocating each to its respective crystallographic plane. The result is a highly accurate 3D lattice-resolved reconstruction. The procedure is applied to over 2000 tungsten atoms, including ion-implanted planes. The approach is further adapted to analyze carbides in a steel matrix, demonstrating its applicability to a range of materials. A vast amount of information is collected during the experiment that can underpin advanced analyses such as automated detection of "out of sequence" events, subangstrom surface displacements and defects effects on neighboring atoms. These analyses have the potential to reveal new insights into the field evaporation process and contribute to improving accuracy and scope of 3D FIM and atom probe characterization.

  1. Compressed sensing reconstruction for whole-heart imaging with 3D radial trajectories: a graphics processing unit implementation.

    PubMed

    Nam, Seunghoon; Akçakaya, Mehmet; Basha, Tamer; Stehning, Christian; Manning, Warren J; Tarokh, Vahid; Nezafat, Reza

    2013-01-01

    A disadvantage of three-dimensional (3D) isotropic acquisition in whole-heart coronary MRI is the prolonged data acquisition time. Isotropic 3D radial trajectories allow undersampling of k-space data in all three spatial dimensions, enabling accelerated acquisition of the volumetric data. Compressed sensing (CS) reconstruction can provide further acceleration in the acquisition by removing the incoherent artifacts due to undersampling and improving the image quality. However, the heavy computational overhead of the CS reconstruction has been a limiting factor for its application. In this article, a parallelized implementation of an iterative CS reconstruction method for 3D radial acquisitions using a commercial graphics processing unit is presented. The execution time of the graphics processing unit-implemented CS reconstruction was compared with that of the C++ implementation, and the efficacy of the undersampled 3D radial acquisition with CS reconstruction was investigated in both phantom and whole-heart coronary data sets. Subsequently, the efficacy of CS in suppressing streaking artifacts in 3D whole-heart coronary MRI with 3D radial imaging and its convergence properties were studied. The CS reconstruction provides improved image quality (in terms of vessel sharpness and suppression of noise-like artifacts) compared with the conventional 3D gridding algorithm, and the graphics processing unit implementation greatly reduces the execution time of CS reconstruction yielding 34-54 times speed-up compared with C++ implementation.

  2. Single particle cryo-electron microscopy and 3-D reconstruction of viruses.

    PubMed

    Guo, Fei; Jiang, Wen

    2014-01-01

    With fast progresses in instrumentation, image processing algorithms, and computational resources, single particle electron cryo-microscopy (cryo-EM) 3-D reconstruction of icosahedral viruses has now reached near-atomic resolutions (3-4 Å). With comparable resolutions and more predictable outcomes, cryo-EM is now considered a preferred method over X-ray crystallography for determination of atomic structure of icosahedral viruses. At near-atomic resolutions, all-atom models or backbone models can be reliably built that allow residue level understanding of viral assembly and conformational changes among different stages of viral life cycle. With the developments of asymmetric reconstruction, it is now possible to visualize the complete structure of a complex virus with not only its icosahedral shell but also its multiple non-icosahedral structural features. In this chapter, we will describe single particle cryo-EM experimental and computational procedures for both near-atomic resolution reconstruction of icosahedral viruses and asymmetric reconstruction of viruses with both icosahedral and non-icosahedral structure components. Procedures for rigorous validation of the reconstructions and resolution evaluations using truly independent de novo initial models and refinements are also introduced.

  3. Single Particle Cryo-electron Microscopy and 3-D Reconstruction of Viruses

    PubMed Central

    Guo, Fei; Jiang, Wen

    2014-01-01

    With fast progresses in instrumentation, image processing algorithms, and computational resources, single particle electron cryo-microscopy (cryo-EM) 3-D reconstruction of icosahedral viruses has now reached near-atomic resolutions (3–4 Å). With comparable resolutions and more predictable outcomes, cryo-EM is now considered a preferred method over X-ray crystallography for determination of atomic structure of icosahedral viruses. At near-atomic resolutions, all-atom models or backbone models can be reliably built that allow residue level understanding of viral assembly and conformational changes among different stages of viral life cycle. With the developments of asymmetric reconstruction, it is now possible to visualize the complete structure of a complex virus with not only its icosahedral shell but also its multiple non-icosahedral structural features. In this chapter, we will describe single particle cryo-EM experimental and computational procedures for both near-atomic resolution reconstruction of icosahedral viruses and asymmetric reconstruction of viruses with both icosahedral and non-icosahedral structure components. Procedures for rigorous validation of the reconstructions and resolution evaluations using truly independent de novo initial models and refinements are also introduced. PMID:24357374

  4. 3D Equilibrium Reconstruction with Internal Measurements on Madison Symmetric Torus

    NASA Astrophysics Data System (ADS)

    Koliner, J. J.; Chapman, B. E.; Sarff, J. S.; Anderson, J. K.; Munaretto, S.; Capecchi, W.; Lin, L.; Hanson, J. D.; Cianciosa, M. R.

    2014-10-01

    Plasmas in the MST reversed field pinch (RFP) bifurcate to a helical equilibrium, forming a single helical axis (SHAx) at high plasma current (Ip ~ 500 kA) and low density (ne ~ 0.5 - 1019 m-3) . In order to understand the physics of confinement and self-organization in SHAx, 3D equilibrium reconstruction is needed. The V3FIT equilibrium reconstruction code is applied using measurements from the 11-chord interferometer-polarimeter, 22-point Thomson scattering system, 4-camera soft x-ray probes, and magnetics. Equilibria have been generated using a fixed plasma boundary with no external currents. Model signals fit well to observed signals, χ2 ~ 1, and the zero crossing of line-averaged neBz from Faraday rotation is matched by the model. External magnetics are shown to be an inadequate equilibrium constraint with the VMEC model, due to possible shear in the poloidal phase of the helical structure, as well as strong contribution to the edge magnetic field from currents in the conducting shell. To address this shortcoming, a filament current model has been created to simulate the conducting shell with many external currents for a free plasma boundary. Axisymmetric equilibria have been reconstructed using the filament model and compared to solutions obtained with the MSTFIT axisymmetric equilibrium reconstruction code. The filament model has been extended to allow reconstruction of helical equilibria. Supported by DoE.

  5. 3D reconstruction in laparoscopy with close-range photometric stereo.

    PubMed

    Collins, Toby; Bartoli, Adrien

    2012-01-01

    In this paper we present the first solution to 3D reconstruction in monocular laparoscopy using methods based on Photometric Stereo (PS). Our main contributions are to provide the new theory and practical solutions to successfully apply PS in close-range imaging conditions. We are specifically motivated by a solution with minimal hardware modification to existing laparoscopes. In fact the only physical modification we make is to adjust the colour of the laparoscope's illumination via three colour filters placed at its tip. Once calibrated, our approach can compute 3D from a single image, does not require correspondence estimation, and computes absolute depth densely. We demonstrate the potential of our approach with ground truth ex-vivo and in-vivo experimentation.

  6. Imaging and 3D reconstruction of cerebrovascular structures in embryonic zebrafish.

    PubMed

    Ethell, Douglas W; Cameron, D Joshua

    2014-04-22

    Zebrafish are a powerful tool to study developmental biology and pathology in vivo. The small size and relative transparency of zebrafish embryos make them particularly useful for the visual examination of processes such as heart and vascular development. In several recent studies transgenic zebrafish that express EGFP in vascular endothelial cells were used to image and analyze complex vascular networks in the brain and retina, using confocal microscopy. Descriptions are provided to prepare, treat and image zebrafish embryos that express enhanced green fluorescent protein (EGFP), and then generate comprehensive 3D renderings of the cerebrovascular system. Protocols include the treatment of embryos, confocal imaging, and fixation protocols that preserve EGFP fluorescence. Further, useful tips on obtaining high-quality images of cerebrovascular structures, such as removal the eye without damaging nearby neural tissue are provided. Potential pitfalls with confocal imaging are discussed, along with the steps necessary to generate 3D reconstructions from confocal image stacks using freely available open source software.

  7. First 3D reconstruction of the rhizocephalan root system using MicroCT

    NASA Astrophysics Data System (ADS)

    Noever, Christoph; Keiler, Jonas; Glenner, Henrik

    2016-07-01

    Parasitic barnacles (Cirripedia: Rhizocephala) are highly specialized parasites of crustaceans. Instead of an alimentary tract for feeding they utilize a system of roots, which infiltrates the body of their hosts to absorb nutrients. Using X-ray micro computer tomography (MicroCT) and computer-aided 3D-reconstruction, we document the spatial organization of this root system, the interna, inside the intact host and also demonstrate its use for morphological examinations of the parasites reproductive part, the externa. This is the first 3D visualization of the unique root system of the Rhizocephala in situ, showing how it is related to the inner organs of the host. We investigated the interna from different parasitic barnacles of the family Peltogastridae, which are parasitic on anomuran crustaceans. Rhizocephalan parasites of pagurid hermit crabs and lithodid crabs were analysed in this study.

  8. A new ionospheric tomographic algorithm — constrained multiplicative algebraic reconstruction technique (CMART)

    NASA Astrophysics Data System (ADS)

    Wen, Debao; Liu, Sanzhi

    2010-08-01

    For the limitation of the conventional multiplicative algebraic reconstruction technique (MART), a constrained MART (CMART) is proposed in this paper. In the new tomographic algorithm, a popular two-dimensional multi-point finite difference approximation of the second order Laplacian operator is used to smooth the electron density field. The feasibility and superiority of the new method are demonstrated by using the numerical simulation experiment. Finally, the CMART is used to reconstruct the regional electron density field by using the actual GNSS data under geomagnetic quiet and disturbed days. The available ionosonde data from Beijing station further validates the superiority of the new method.

  9. Grammar-Supported 3d Indoor Reconstruction from Point Clouds for As-Built Bim

    NASA Astrophysics Data System (ADS)

    Becker, S.; Peter, M.; Fritsch, D.

    2015-03-01

    The paper presents a grammar-based approach for the robust automatic reconstruction of 3D interiors from raw point clouds. The core of the approach is a 3D indoor grammar which is an extension of our previously published grammar concept for the modeling of 2D floor plans. The grammar allows for the modeling of buildings whose horizontal, continuous floors are traversed by hallways providing access to the rooms as it is the case for most office buildings or public buildings like schools, hospitals or hotels. The grammar is designed in such way that it can be embedded in an iterative automatic learning process providing a seamless transition from LOD3 to LOD4 building models. Starting from an initial low-level grammar, automatically derived from the window representations of an available LOD3 building model, hypotheses about indoor geometries can be generated. The hypothesized indoor geometries are checked against observation data - here 3D point clouds - collected in the interior of the building. The verified and accepted geometries form the basis for an automatic update of the initial grammar. By this, the knowledge content of the initial grammar is enriched, leading to a grammar with increased quality. This higher-level grammar can then be applied to predict realistic geometries to building parts where only sparse observation data are available. Thus, our approach allows for the robust generation of complete 3D indoor models whose quality can be improved continuously as soon as new observation data are fed into the grammar-based reconstruction process. The feasibility of our approach is demonstrated based on a real-world example.

  10. 3D Scene Reconstruction Using Omnidirectional Vision and LiDAR: A Hybrid Approach

    PubMed Central

    Vlaminck, Michiel; Luong, Hiep; Goeman, Werner; Philips, Wilfried

    2016-01-01

    In this paper, we propose a novel approach to obtain accurate 3D reconstructions of large-scale environments by means of a mobile acquisition platform. The system incorporates a Velodyne LiDAR scanner, as well as a Point Grey Ladybug panoramic camera system. It was designed with genericity in mind, and hence, it does not make any assumption about the scene or about the sensor set-up. The main novelty of this work is that the proposed LiDAR mapping approach deals explicitly with the inhomogeneous density of point clouds produced by LiDAR scanners. To this end, we keep track of a global 3D map of the environment, which is continuously improved and refined by means of a surface reconstruction technique. Moreover, we perform surface analysis on consecutive generated point clouds in order to assure a perfect alignment with the global 3D map. In order to cope with drift, the system incorporates loop closure by determining the pose error and propagating it back in the pose graph. Our algorithm was exhaustively tested on data captured at a conference building, a university campus and an industrial site of a chemical company. Experiments demonstrate that it is capable of generating highly accurate 3D maps in very challenging environments. We can state that the average distance of corresponding point pairs between the ground truth and estimated point cloud approximates one centimeter for an area covering approximately 4000 m2. To prove the genericity of the system, it was tested on the well-known Kitti vision benchmark. The results show that our approach competes with state of the art methods without making any additional assumptions. PMID:27854315

  11. 3D Scene Reconstruction Using Omnidirectional Vision and LiDAR: A Hybrid Approach.

    PubMed

    Vlaminck, Michiel; Luong, Hiep; Goeman, Werner; Philips, Wilfried

    2016-11-16

    In this paper, we propose a novel approach to obtain accurate 3D reconstructions of large-scale environments by means of a mobile acquisition platform. The system incorporates a Velodyne LiDAR scanner, as well as a Point Grey Ladybug panoramic camera system. It was designed with genericity in mind, and hence, it does not make any assumption about the scene or about the sensor set-up. The main novelty of this work is that the proposed LiDAR mapping approach deals explicitly with the inhomogeneous density of point clouds produced by LiDAR scanners. To this end, we keep track of a global 3D map of the environment, which is continuously improved and refined by means of a surface reconstruction technique. Moreover, we perform surface analysis on consecutive generated point clouds in order to assure a perfect alignment with the global 3D map. In order to cope with drift, the system incorporates loop closure by determining the pose error and propagating it back in the pose graph. Our algorithm was exhaustively tested on data captured at a conference building, a university campus and an industrial site of a chemical company. Experiments demonstrate that it is capable of generating highly accurate 3D maps in very challenging environments. We can state that the average distance of corresponding point pairs between the ground truth and estimated point cloud approximates one centimeter for an area covering approximately 4000 m 2 . To prove the genericity of the system, it was tested on the well-known Kitti vision benchmark. The results show that our approach competes with state of the art methods without making any additional assumptions.

  12. Canine neuroanatomy: Development of a 3D reconstruction and interactive application for undergraduate veterinary education

    PubMed Central

    Raffan, Hazel; Guevar, Julien; Poyade, Matthieu; Rea, Paul M.

    2017-01-01

    Current methods used to communicate and present the complex arrangement of vasculature related to the brain and spinal cord is limited in undergraduate veterinary neuroanatomy training. Traditionally it is taught with 2-dimensional (2D) diagrams, photographs and medical imaging scans which show a fixed viewpoint. 2D representations of 3-dimensional (3D) objects however lead to loss of spatial information, which can present problems when translating this to the patient. Computer-assisted learning packages with interactive 3D anatomical models have become established in medical training, yet equivalent resources are scarce in veterinary education. For this reason, we set out to develop a workflow methodology creating an interactive model depicting the vasculature of the canine brain that could be used in undergraduate education. Using MR images of a dog and several commonly available software programs, we set out to show how combining image editing, segmentation and surface generation, 3D modeling and texturing can result in the creation of a fully interactive application for veterinary training. In addition to clearly identifying a workflow methodology for the creation of this dataset, we have also demonstrated how an interactive tutorial and self-assessment tool can be incorporated into this. In conclusion, we present a workflow which has been successful in developing a 3D reconstruction of the canine brain and associated vasculature through segmentation, surface generation and post-processing of readily available medical imaging data. The reconstructed model was implemented into an interactive application for veterinary education that has been designed to target the problems associated with learning neuroanatomy, primarily the inability to visualise complex spatial arrangements from 2D resources. The lack of similar resources in this field suggests this workflow is original within a veterinary context. There is great potential to explore this method, and introduce

  13. Robust affine-invariant feature points matching for 3D surface reconstruction of complex landslide scenes

    NASA Astrophysics Data System (ADS)

    Stumpf, André; Malet, Jean-Philippe; Allemand, Pascal; Skupinski, Grzegorz; Deseilligny, Marc-Pierrot

    2013-04-01

    Multi-view stereo surface reconstruction from dense terrestrial photographs is being increasingly applied for geoscience applications such as quantitative geomorphology, and a number of different software solution and processing streamlines have been suggested. For image matching, camera self-calibration and bundle block adjustment, most approaches make use of scale-invariant feature transform (SIFT) to identify homologous points in multiple images. SIFT-like point matching is robust to apparent translation, rotation, and scaling of objects in multiple viewing geometries but the number of correctly identified matching points typically declines drastically with increasing angles between the viewpoints. For the application of multi-view stereo of complex landslide scenes, the viewing geometry is often constrained by the local topography and barriers such as rocks and vegetation occluding the target. Under such conditions it is not uncommon to encounter view angle differences of > 30% that hinder the image matching and eventually prohibit the joint estimation of the camera parameters from all views. Recently an affine invariant extension of the SIFT detector (ASIFT) has been demonstrated to provide more robust matches when large view-angle differences become an issue. In this study the ASIFT detector was adopted to detect homologous points in terrestrial photographs preceding 3D reconstruction of different parts (main scarp, toe) of the Super-Sauze landslide (Southern French Alps). 3D surface models for different time periods and different parts of the landslide were derived using the multi-view stereo framework implemented in MicMac (©IGN). The obtained 3D models were compared with reconstructions using the traditional SIFT detectors as well as alternative structure-from-motion implementations. An estimate of the absolute accuracy of the photogrammetric models was obtained through co-registration and comparison with high-resolution terrestrial LiDAR scans.

  14. Visualization and 3D Reconstruction of Flame Cells of Taenia solium (Cestoda)

    PubMed Central

    Valverde-Islas, Laura E.; Arrangoiz, Esteban; Vega, Elio; Robert, Lilia; Villanueva, Rafael; Reynoso-Ducoing, Olivia; Willms, Kaethe; Zepeda-Rodríguez, Armando; Fortoul, Teresa I.; Ambrosio, Javier R.

    2011-01-01

    Background Flame cells are the terminal cells of protonephridial systems, which are part of the excretory systems of invertebrates. Although the knowledge of their biological role is incomplete, there is a consensus that these cells perform excretion/secretion activities. It has been suggested that the flame cells participate in the maintenance of the osmotic environment that the cestodes require to live inside their hosts. In live Platyhelminthes, by light microscopy, the cells appear beating their flames rapidly and, at the ultrastructural, the cells have a large body enclosing a tuft of cilia. Few studies have been performed to define the localization of the cytoskeletal proteins of these cells, and it is unclear how these proteins are involved in cell function. Methodology/Principal Findings Parasites of two different developmental stages of T. solium were used: cysticerci recovered from naturally infected pigs and intestinal adults obtained from immunosuppressed and experimentally infected golden hamsters. Hamsters were fed viable cysticerci to recover adult parasites after one month of infection. In the present studies focusing on flame cells of cysticerci tissues was performed. Using several methods such as video, confocal and electron microscopy, in addition to computational analysis for reconstruction and modeling, we have provided a 3D visual rendition of the cytoskeletal architecture of Taenia solium flame cells. Conclusions/Significance We consider that visual representations of cells open a new way for understanding the role of these cells in the excretory systems of Platyhelminths. After reconstruction, the observation of high resolution 3D images allowed for virtual observation of the interior composition of cells. A combination of microscopic images, computational reconstructions and 3D modeling of cells appears to be useful for inferring the cellular dynamics of the flame cell cytoskeleton. PMID:21412407

  15. Local and Non-local Regularization Techniques in Emission (PET/SPECT) Tomographic Image Reconstruction Methods.

    PubMed

    Ahmad, Munir; Shahzad, Tasawar; Masood, Khalid; Rashid, Khalid; Tanveer, Muhammad; Iqbal, Rabail; Hussain, Nasir; Shahid, Abubakar; Fazal-E-Aleem

    2016-06-01

    Emission tomographic image reconstruction is an ill-posed problem due to limited and noisy data and various image-degrading effects affecting the data and leads to noisy reconstructions. Explicit regularization, through iterative reconstruction methods, is considered better to compensate for reconstruction-based noise. Local smoothing and edge-preserving regularization methods can reduce reconstruction-based noise. However, these methods produce overly smoothed images or blocky artefacts in the final image because they can only exploit local image properties. Recently, non-local regularization techniques have been introduced, to overcome these problems, by incorporating geometrical global continuity and connectivity present in the objective image. These techniques can overcome drawbacks of local regularization methods; however, they also have certain limitations, such as choice of the regularization function, neighbourhood size or calibration of several empirical parameters involved. This work compares different local and non-local regularization techniques used in emission tomographic imaging in general and emission computed tomography in specific for improved quality of the resultant images.

  16. Portable and accurate 3D scanner for breast implant design and reconstructive plastic surgery

    NASA Astrophysics Data System (ADS)

    Rigotti, Camilla; Borghese, Nunzio A.; Ferrari, Stefano; Baroni, Guido; Ferrigno, Giancarlo

    1998-06-01

    In order to evaluate the proper breast implant, the surgeon relies on a standard set of measurements manually taken on the subject. This approach does not allow to obtain an accurate reconstruction of the breast shape and asymmetries can easily arise after surgery. The purpose of this work is to present a method which can help the surgeon in the choice of the shape and dimensions of a prosthesis allowing for a perfect symmetry between the prosthesis and the controlateral breast and can be used as a 3D visual feedback in plastic surgery.

  17. Nonintrusive 3D reconstruction of human bone models to simulate their bio-mechanical response

    NASA Astrophysics Data System (ADS)

    Alexander, Tsouknidas; Antonis, Lontos; Savvas, Savvakis; Nikolaos, Michailidis

    2012-06-01

    3D finite element models representing functional parts of the human skeletal system, have been repeatedly introduced over the last years, to simulate biomechanical response of anatomical characteristics or investigate surgical treatment. The reconstruction of geometrically accurate FEM models, poses a significant challenge for engineers and physicians, as recent advances in tissue engineering dictate highly customized implants, while facilitating the production of alloplast materials that are employed to restore, replace or supplement the function of human tissue. The premises of every accurate reconstruction method, is to encapture the precise geometrical characteristics of the examined tissue and thus the selection of a sufficient imaging technique is of the up-most importance. This paper reviews existing and potential applications related to the current state-of-the-art of medical imaging and simulation techniques. The procedures are examined by introducing their concepts; strengths and limitations, while the authors also present part of their recent activities in these areas. [Figure not available: see fulltext.

  18. Two reconstruction procedures for a 3D phaseless inverse scattering problem for the generalized Helmholtz equation

    NASA Astrophysics Data System (ADS)

    Klibanov, Michael V.; Romanov, Vladimir G.

    2016-01-01

    The 3D inverse scattering problem of the reconstruction of the unknown dielectric permittivity in the generalized Helmholtz equation is considered. Applications are in imaging of nanostructures and biological cells. The main difference with the conventional inverse scattering problems is that only the modulus of the scattering wave field is measured. The phase is not measured. The initializing wave field is the incident plane wave. On the other hand, in the previous recent works of the authors about the ‘phaseless topic’ the case of the point source was considered (Klibanov and Romanov 2015 J. Inverse Ill-Posed Problem 23 415-28 J. Inverse Ill-Posed Problem 23 187-93). Two reconstruction procedures are developed.

  19. An adaptive learning approach for 3-D surface reconstruction from point clouds.

    PubMed

    Junior, Agostinho de Medeiros Brito; Neto, Adrião Duarte Dória; de Melo, Jorge Dantas; Goncalves, Luiz Marcos Garcia

    2008-06-01

    In this paper, we propose a multiresolution approach for surface reconstruction from clouds of unorganized points representing an object surface in 3-D space. The proposed method uses a set of mesh operators and simple rules for selective mesh refinement, with a strategy based on Kohonen's self-organizing map (SOM). Basically, a self-adaptive scheme is used for iteratively moving vertices of an initial simple mesh in the direction of the set of points, ideally the object boundary. Successive refinement and motion of vertices are applied leading to a more detailed surface, in a multiresolution, iterative scheme. Reconstruction was experimented on with several point sets, including different shapes and sizes. Results show generated meshes very close to object final shapes. We include measures of performance and discuss robustness.

  20. 2-D And 3-D Reconstructions Of The Olfactory System Of The Rat

    NASA Astrophysics Data System (ADS)

    Reisner, Alex H.; Bell, G. A.; Bucholtz, C. A.; Rosenfeld, Dov; Tsui, K. K.

    1989-04-01

    The olfactory system of the rat is a useful model for the study of mammalian sensory systems. However, the anatomy of the nasal epithelium, where the cells responsible for detecting odors are located, is extremely complex. Therefore, we have focused our attention on the development of two- and three-dimensional automated imaging methods. The presentation of pure odorants to the experimental animal together with the injection of [14M-deoxyglucose has been combined with autoradiography of frozen sectioned material. Several approaches have been used to obtain optimal alignments of the digitized images of the sections so as to be able to generate appropriate 2-D and 3-D reconstructions. Such reconstructions allow visualization of the ethmo-turbinal bones (turbinates) and the associated soft tissue and appear to be useful in analyzing and highlighting differential metabolic activity.

  1. Effects of camera location on the reconstruction of 3D flare trajectory with two cameras

    NASA Astrophysics Data System (ADS)

    Özsaraç, Seçkin; Yeşilkaya, Muhammed

    2015-05-01

    Flares are used as valuable electronic warfare assets for the battle against infrared guided missiles. The trajectory of the flare is one of the most important factors that determine the effectiveness of the counter measure. Reconstruction of the three dimensional (3D) position of a point, which is seen by multiple cameras, is a common problem. Camera placement, camera calibration, corresponding pixel determination in between the images of different cameras and also the triangulation algorithm affect the performance of 3D position estimation. In this paper, we specifically investigate the effects of camera placement on the flare trajectory estimation performance by simulations. Firstly, 3D trajectory of a flare and also the aircraft, which dispenses the flare, are generated with simple motion models. Then, we place two virtual ideal pinhole camera models on different locations. Assuming the cameras are tracking the aircraft perfectly, the view vectors of the cameras are computed. Afterwards, using the view vector of each camera and also the 3D position of the flare, image plane coordinates of the flare on both cameras are computed using the field of view (FOV) values. To increase the fidelity of the simulation, we have used two sources of error. One is used to model the uncertainties in the determination of the camera view vectors, i.e. the orientations of the cameras are measured noisy. Second noise source is used to model the imperfections of the corresponding pixel determination of the flare in between the two cameras. Finally, 3D position of the flare is estimated using the corresponding pixel indices, view vector and also the FOV of the cameras by triangulation. All the processes mentioned so far are repeated for different relative camera placements so that the optimum estimation error performance is found for the given aircraft and are trajectories.

  2. Adapted morphing model for 3D volume reconstruction applied to abdominal CT images

    NASA Astrophysics Data System (ADS)

    Fadeev, Aleksey; Eltonsy, Nevine; Tourassi, Georgia; Martin, Robert; Elmaghraby, Adel

    2005-04-01

    The purpose of this study was to develop a 3D volume reconstruction model for volume rendering and apply this model to abdominal CT data. The model development includes two steps: (1) interpolation of given data for a complete 3D model, and (2) visualization. First, CT slices are interpolated using a special morphing algorithm. The main idea of this algorithm is to take a region from one CT slice and locate its most probable correspondence in the adjacent CT slice. The algorithm determines the transformation function of the region in between two adjacent CT slices and interpolates the data accordingly. The most probable correspondence of a region is obtained using correlation analysis between the given region and regions of the adjacent CT slice. By applying this technique recursively, taking progressively smaller subregions within a region, a high quality and accuracy interpolation is obtained. The main advantages of this morphing algorithm are 1) its applicability not only to parallel planes like CT slices but also to general configurations of planes in 3D space, and 2) its fully automated nature as it does not require control points to be specified by a user compared to most morphing techniques. Subsequently, to visualize data, a specialized volume rendering card (TeraRecon VolumePro 1000) was used. To represent data in 3D space, special software was developed to convert interpolated CT slices to 3D objects compatible with the VolumePro card. Visual comparison between the proposed model and linear interpolation clearly demonstrates the superiority of the proposed model.

  3. Error analysis of tomographic reconstructions in the absence of projection data.

    PubMed

    Shakya, Snehlata; Munshi, Prabhat

    2015-06-13

    Error estimates for tomographic reconstructions (using Fourier transform-based algorithm) are available for cases where projection data are available. These data are used for reconstructions with different filter functions and the reliability of these reconstructions can be checked as per guidelines of those error estimates. There are cases where projection data are large (in gigabytes or terabytes) so storage of these data becomes an issue. It leads to storing of only the reconstructed images. Error estimation in such cases is presented here. Second-level projection data are calculated from the given reconstructed images ('first-level' images). These 'second-level' data are now used to generate 'second-level' reconstructed images. Different filter functions are employed to check the fidelity of these 'second-level' images. This inference is extended to first-level images in view of the characteristics of the convolution operator. This approach is validated with experimental data obtained by the X-ray micro-CT scanner installed at IIT Kanpur. Five specimens (of same material) have been scanned. Data are available in this case thus we have performed a comparative error estimate analysis for the 'first-level' reconstructions (data obtained from CT machine) and second-level reconstructions (data generated from first-level reconstructions). We observe that both approaches show similar outcome. It indicates that error estimates can also be applied to images when data are not available.

  4. Single-view 3D reconstruction of correlated gamma-neutron sources

    DOE PAGES

    Monterial, Mateusz; Marleau, Peter; Pozzi, Sara A.

    2017-01-05

    We describe a new method of 3D image reconstruction of neutron sources that emit correlated gammas (e.g. Cf- 252, Am-Be). This category includes a vast majority of neutron sources important in nuclear threat search, safeguards and non-proliferation. Rather than requiring multiple views of the source this technique relies on the source’s intrinsic property of coincidence gamma and neutron emission. As a result only a single-view measurement of the source is required to perform the 3D reconstruction. In principle, any scatter camera sensitive to gammas and neutrons with adequate timing and interaction location resolution can perform this reconstruction. Using a neutronmore » double scatter technique, we can calculate a conical surface of possible source locations. By including the time to a correlated gamma we further constrain the source location in three-dimensions by solving for the source-to-detector distance along the surface of said cone. As a proof of concept we applied these reconstruction techniques on measurements taken with the the Mobile Imager of Neutrons for Emergency Responders (MINER). Two Cf-252 sources measured at 50 and 60 cm from the center of the detector were resolved in their varying depth with average radial distance relative resolution of 26%. To demonstrate the technique’s potential with an optimized system we simulated the measurement in MCNPX-PoliMi assuming timing resolution of 200 ps (from 2 ns in the current system) and source interaction location resolution of 5 mm (from 3 cm). Furthermore, these simulated improvements in scatter camera performance resulted in radial distance relative resolution decreasing to an average of 11%.« less

  5. Image reconstruction for 3D light microscopy with a regularized linear method incorporating a smoothness prior

    NASA Astrophysics Data System (ADS)

    Preza, Chrysanthe; Miller, Michael I.; Conchello, Jose-Angel

    1993-07-01

    We have shown that the linear least-squares (LLS) estimate of the intensities of a 3-D object obtained from a set of optical sections is unstable due to the inversion of small and zero-valued eigenvalues of the point-spread function (PSF) operator. The LLS solution was regularized by constraining it to lie in a subspace spanned by the eigenvectors corresponding to a selected number of the largest eigenvalues. In this paper we extend the regularized LLS solution to a maximum a posteriori (MAP) solution induced by a prior formed from a 'Good's like' smoothness penalty. This approach also yields a regularized linear estimator which reduces noise as well as edge artifacts in the reconstruction. The advantage of the linear MAP (LMAP) estimate over the current regularized LLS (RLLS) is its ability to regularize the inverse problem by smoothly penalizing components in the image associated with small eigenvalues. Computer simulations were performed using a theoretical PSF and a simple phantom to compare the two regularization techniques. It is shown that the reconstructions using the smoothness prior, give superior variance and bias results compared to the RLLS reconstructions. Encouraging reconstructions obtained with the LMAP method from real microscopical images of a 10 micrometers fluorescent bead, and a four-cell Volvox embryo are shown.

  6. 3D Equilibrium Reconstruction with Improved Magnetic Diagnostics on the Compact Toroidal Hybrid

    NASA Astrophysics Data System (ADS)

    Ma, Xinxing; Hanson, James D.; Hartwell, Gregory J.; Knowlton, Stephen F.; Maurer, David A.

    2013-10-01

    Equilibrium reconstructions using the three-dimensional V3FIT code [ 1 ] have been performed for low density (low β) current carrying plasmas on the Compact Toroidal Hybrid (CTH), a torsatron in which the magnetic configuration can be strongly modified by an ohmically-driven plasma current. These reconstructions use 50 external magnetic diagnostic measurements, including segmented and full Rogowski coils, saddle loops, poloidal and radial magnetic pickup coils. Time dependent 3D reconstructions document the evolution of the plasma cross section and current profile, with calculated value of βθ much less than the plasma internal inductance, li. Reconstructions typically show the plasma to move outward in major radius and become less elongated in poloidal cross section with increasing plasma current. In plasmas with low vacuum transform (ιvac ~ 0 . 04), the plasma current profile peaks with li above 0 . 84 when the total transform is 1 / 2 , which typically leads disruption. With values of ιvac >= 0 . 1 , li remains low (~ 0 . 7), and the discharges no longer disrupt. This work is supported by the USDoE under grant DE-FG02-00ER54610.

  7. Implementation of a close range photogrammetric system for 3D reconstruction of a scoliotic torso

    NASA Astrophysics Data System (ADS)

    Detchev, Ivan Denislavov

    Scoliosis is a deformity of the human spine most commonly encountered with children. After being detected, periodic examinations via x-rays are traditionally used to measure its progression. However, due to the increased risk of cancer, a non-invasive and radiation-free scoliosis detection and progression monitoring methodology is needed. Quantifying the scoliotic deformity through the torso surface is a valid alternative, because of its high correlation with the internal spine curvature. This work proposes a low-cost multi-camera photogrammetric system for semi-automated 3D reconstruction of a torso surface with sub-millimetre level accuracy. The thesis describes the system design and calibration for optimal accuracy. It also covers the methodology behind the reconstruction and registration procedures. The experimental results include the complete reconstruction of a scoliotic torso mannequin. The final accuracy is evaluated through the goodness of fit between the reconstructed surface and a more accurate set of points measured by a coordinate measuring machine.

  8. Tomographic Reconstruction of Flows in DIII-D

    NASA Astrophysics Data System (ADS)

    Meyer, William; Allen, Steve; Howard, John

    2015-11-01

    The DIII-D flow diagnostic produces video of interference images with horizontal fringes that contain spatial emissivity, flow, and temperature information from the lower divertor. Frames are demodulated and compared against a reference interference image to produce phase and contrast images which are the emissivity weighted flow and temperature integrated along the line-of-site, respectively. Inversion of the flow (phase) images require knowledge of the scalar product of the parallel flow vector, from the equilibrium calculations, and each camera pixel line-of-site. Four response matrices are pre-calculated: the emissivity line integral and the line integral of the scalar product of the lines-of-site with the orthogonal unit vectors of parallel flow. Equilibrium data determines the relative weight of the component matrices used in the final flow matrix. Early reconstructions have shown flow reversal during forward and reverse toroidal field plasmas. Ongoing work is to extract temperature information from the contrast images. Prepared by LLNL under Contract DE-AC52-07NA27344. This material is based upon work supported by the U.S. DOE, Office of Science, Fusion Energy Sciences.

  9. Micro-CT images reconstruction and 3D visualization for small animal studying

    NASA Astrophysics Data System (ADS)

    Gong, Hui; Liu, Qian; Zhong, Aijun; Ju, Shan; Fang, Quan; Fang, Zheng

    2005-01-01

    A small-animal x-ray micro computed tomography (micro-CT) system has been constructed to screen laboratory small animals and organs. The micro-CT system consists of dual fiber-optic taper-coupled CCD detectors with a field-of-view of 25x50 mm2, a microfocus x-ray source, a rotational subject holder. For accurate localization of rotation center, coincidence between the axis of rotation and centre of image was studied by calibration with a polymethylmethacrylate cylinder. Feldkamp"s filtered back-projection cone-beam algorithm is adopted for three-dimensional reconstruction on account of the effective corn-beam angle is 5.67° of the micro-CT system. 200x1024x1024 matrix data of micro-CT is obtained with the magnification of 1.77 and pixel size of 31x31μm2. In our reconstruction software, output image size of micro-CT slices data, magnification factor and rotation sample degree can be modified in the condition of different computational efficiency and reconstruction region. The reconstructed image matrix data is processed and visualization by Visualization Toolkit (VTK). Data parallelism of VTK is performed in surface rendering of reconstructed data in order to improve computing speed. Computing time of processing a 512x512x512 matrix datasets is about 1/20 compared with serial program when 30 CPU is used. The voxel size is 54x54x108 μm3. The reconstruction and 3-D visualization images of laboratory rat ear are presented.

  10. The Return of the Siegesburg - 3D-RECONSTRUCTION of a Disappeared and Forgotten Monument

    NASA Astrophysics Data System (ADS)

    Deggim, S.; Kersten, T. P.; Lindstaedt, M.; Hinrichsen, N.

    2017-02-01

    Many Cultural Heritage (CH) monuments are destroyed in the past and they are often lost forever. If there is no contemporary metric documentation of the historic objects available, the monument and the information about this monument could be disappeared and forgotten forever. The Siegesburg (also known as Segeberg castle) located on the "Kalkberg" (Chalk Mountain) in Bad Segeberg in Northern Germany, is a typical example for such a monument, which was destroyed by Swedish troops at the end of the Thirty Years' War in 1644. This important monument was only documented by a few historic isometric maps, but the castle and even the later castle ruin were totally destructed and demolished over the last centuries and disappeared forever. Furthermore, this significant memorial is even forgotten in many people's mind. This contribution describes the physical and virtual return of the Siegesburg by 3D reconstruction using historic sources. The laboratory for Photogrammetry & Laser Scanning of the HafenCity University Hamburg conducted this project in co-operation with the museum Alt-Segeberger Bürgerhaus (Old-Segeberg town house). The process of the 3D reconstruction and visualisation of both the Kalkberg and the castle is presented in this paper.

  11. Reconstruction and Visualization of Coordinated 3D Cell Migration Based on Optical Flow.

    PubMed

    Kappe, Christopher P; Schütz, Lucas; Gunther, Stefan; Hufnagel, Lars; Lemke, Steffen; Leitte, Heike

    2016-01-01

    Animal development is marked by the repeated reorganization of cells and cell populations, which ultimately determine form and shape of the growing organism. One of the central questions in developmental biology is to understand precisely how cells reorganize, as well as how and to what extent this reorganization is coordinated. While modern microscopes can record video data for every cell during animal development in 3D+t, analyzing these videos remains a major challenge: reconstruction of comprehensive cell tracks turned out to be very demanding especially with decreasing data quality and increasing cell densities. In this paper, we present an analysis pipeline for coordinated cellular motions in developing embryos based on the optical flow of a series of 3D images. We use numerical integration to reconstruct cellular long-term motions in the optical flow of the video, we take care of data validation, and we derive a LIC-based, dense flow visualization for the resulting pathlines. This approach allows us to handle low video quality such as noisy data or poorly separated cells, and it allows the biologists to get a comprehensive understanding of their data by capturing dynamic growth processes in stills. We validate our methods using three videos of growing fruit fly embryos.

  12. A 3D endoscopy reconstruction as a saliency map for analysis of polyp shapes

    NASA Astrophysics Data System (ADS)

    Ruano, Josue; Martínez, Fabio; Gómez, Martín.; Romero, Eduardo

    2015-01-01

    A first diagnosis of colorectal cancer is performed by examination of polyp shape and appearance during an endoscopy routine procedure. However, the video-endoscopy is highly noisy because exacerbated physiological conditions like increased motility or secretion may limit the visual analysis of lesions. In this work a 3D reconstruction of the digestive tract is proposed, facilitating the polyp shape evaluation by highlighting its surface geometry and allowing an analysis from different perspectives. The method starts by a spatio-temporal map, constructed to group the different regions of the tract by their similar dynamic patterns during the sequence. Then, such map was convolved with a second derivative of a Gaussian kernel that emulates the camera distortion and allows to highlight the polyp surface. The position initialization in each frame of the kernel was computed from expert manual delineation and propagated along the sequence based on. Results show reliable reconstructions, with a salient 3D polyp structure that can then be better observed.

  13. A Gauss-Seidel Iteration Scheme for Reference-Free 3-D Histological Image Reconstruction

    PubMed Central

    Daum, Volker; Steidl, Stefan; Maier, Andreas; Köstler, Harald; Hornegger, Joachim

    2015-01-01

    Three-dimensional (3-D) reconstruction of histological slice sequences offers great benefits in the investigation of different morphologies. It features very high-resolution which is still unmatched by in-vivo 3-D imaging modalities, and tissue staining further enhances visibility and contrast. One important step during reconstruction is the reversal of slice deformations introduced during histological slice preparation, a process also called image unwarping. Most methods use an external reference, or rely on conservative stopping criteria during the unwarping optimization to prevent straightening of naturally curved morphology. Our approach shows that the problem of unwarping is based on the superposition of low-frequency anatomy and high-frequency errors. We present an iterative scheme that transfers the ideas of the Gauss-Seidel method to image stacks to separate the anatomy from the deformation. In particular, the scheme is universally applicable without restriction to a specific unwarping method, and uses no external reference. The deformation artifacts are effectively reduced in the resulting histology volumes, while the natural curvature of the anatomy is preserved. The validity of our method is shown on synthetic data, simulated histology data using a CT data set and real histology data. In the case of the simulated histology where the ground truth was known, the mean Target Registration Error (TRE) between the unwarped and original volume could be reduced to less than 1 pixel on average after 6 iterations of our proposed method. PMID:25312918

  14. A Gauss-Seidel iteration scheme for reference-free 3-D histological image reconstruction.

    PubMed

    Gaffling, Simone; Daum, Volker; Steidl, Stefan; Maier, Andreas; Kostler, Harald; Hornegger, Joachim

    2015-02-01

    Three-dimensional (3-D) reconstruction of histological slice sequences offers great benefits in the investigation of different morphologies. It features very high-resolution which is still unmatched by in vivo 3-D imaging modalities, and tissue staining further enhances visibility and contrast. One important step during reconstruction is the reversal of slice deformations introduced during histological slice preparation, a process also called image unwarping. Most methods use an external reference, or rely on conservative stopping criteria during the unwarping optimization to prevent straightening of naturally curved morphology. Our approach shows that the problem of unwarping is based on the superposition of low-frequency anatomy and high-frequency errors. We present an iterative scheme that transfers the ideas of the Gauss-Seidel method to image stacks to separate the anatomy from the deformation. In particular, the scheme is universally applicable without restriction to a specific unwarping method, and uses no external reference. The deformation artifacts are effectively reduced in the resulting histology volumes, while the natural curvature of the anatomy is preserved. The validity of our method is shown on synthetic data, simulated histology data using a CT data set and real histology data. In the case of the simulated histology where the ground truth was known, the mean Target Registration Error (TRE) between the unwarped and original volume could be reduced to less than 1 pixel on average after six iterations of our proposed method.

  15. Skeletal camera network embedded structure-from-motion for 3D scene reconstruction from UAV images

    NASA Astrophysics Data System (ADS)

    Xu, Zhihua; Wu, Lixin; Gerke, Markus; Wang, Ran; Yang, Huachao

    2016-11-01

    Structure-from-Motion (SfM) techniques have been widely used for 3D scene reconstruction from multi-view images. However, due to the large computational costs of SfM methods there is a major challenge in processing highly overlapping images, e.g. images from unmanned aerial vehicles (UAV). This paper embeds a novel skeletal camera network (SCN) into SfM to enable efficient 3D scene reconstruction from a large set of UAV images. First, the flight control data are used within a weighted graph to construct a topologically connected camera network (TCN) to determine the spatial connections between UAV images. Second, the TCN is refined using a novel hierarchical degree bounded maximum spanning tree to generate a SCN, which contains a subset of edges from the TCN and ensures that each image is involved in at least a 3-view configuration. Third, the SCN is embedded into the SfM to produce a novel SCN-SfM method, which allows performing tie-point matching only for the actually connected image pairs. The proposed method was applied in three experiments with images from two fixed-wing UAVs and an octocopter UAV, respectively. In addition, the SCN-SfM method was compared to three other methods for image connectivity determination. The comparison shows a significant reduction in the number of matched images if our method is used, which leads to less computational costs. At the same time the achieved scene completeness and geometric accuracy are comparable.

  16. Stratification approach for 3-D euclidean reconstruction of nonrigid objects from uncalibrated image sequences.

    PubMed

    Wang, Guanghui; Wu, Q M Jonathan

    2008-02-01

    This paper addresses the problem of 3-D reconstruction of nonrigid objects from uncalibrated image sequences. Under the assumption of affine camera and that the nonrigid object is composed of a rigid part and a deformation part, we propose a stratification approach to recover the structure of nonrigid objects by first reconstructing the structure in affine space and then upgrading it to the Euclidean space. The novelty and main features of the method lies in several aspects. First, we propose a deformation weight constraint to the problem and prove the invariability between the recovered structure and shape bases under this constraint. The constraint was not observed by previous studies. Second, we propose a constrained power factorization algorithm to recover the deformation structure in affine space. The algorithm overcomes some limitations of a previous singular-value-decomposition-based method. It can even work with missing data in the tracking matrix. Third, we propose to separate the rigid features from the deformation ones in 3-D affine space, which makes the detection more accurate and robust. The stratification matrix is estimated from the rigid features, which may relax the influence of large tracking errors in the deformation part. Extensive experiments on synthetic data and real sequences validate the proposed method and show improvements over existing solutions.

  17. The Effect of Underwater Imagery Radiometry on 3d Reconstruction and Orthoimagery

    NASA Astrophysics Data System (ADS)

    Agrafiotis, P.; Drakonakis, G. I.; Georgopoulos, A.; Skarlatos, D.

    2017-02-01

    The work presented in this paper investigates the effect of the radiometry of the underwater imagery on automating the 3D reconstruction and the produced orthoimagery. Main aim is to investigate whether pre-processing of the underwater imagery improves the 3D reconstruction using automated SfM - MVS software or not. Since the processing of images either separately or in batch is a time-consuming procedure, it is critical to determine the necessity of implementing colour correction and enhancement before the SfM - MVS procedure or directly to the final orthoimage when the orthoimagery is the deliverable. Two different test sites were used to capture imagery ensuring different environmental conditions, depth and complexity. Three different image correction methods are applied: A very simple automated method using Adobe Photoshop, a developed colour correction algorithm using the CLAHE (Zuiderveld, 1994) method and an implementation of the algorithm described in Bianco et al., (2015). The produced point clouds using the initial and the corrected imagery are then being compared and evaluated.

  18. Application of 3D reconstruction for surgical treatment of hepatic alveolar echinococcosis

    PubMed Central

    He, Yi-Biao; Bai, Lei; Aji, Tuerganaili; Jiang, Yi; Zhao, Jin-Ming; Zhang, Jin-Hui; Shao, Ying-Mei; Liu, Wen-Ya; Wen, Hao

    2015-01-01

    AIM: To evaluate the reliability and accuracy of three-dimensional (3D) reconstruction for liver resection in patients with hepatic alveolar echinococcosis (HAE). METHODS: One-hundred and six consecutive patients with HAE underwent hepatectomy at our hospital between May 2011 and January 2015. Fifty-nine patients underwent preoperative 3D reconstruction and “virtual” 3D liver resection before surgery (Group A). Another 47 patients used conventional imaging methods for preoperative assessment (Group B). Outcomes of hepatectomy were compared between the two groups. RESULTS: There was no significant difference in preoperative data between the two groups. Compared with patients in Group B, those in Group A had a significantly shorter operation time (227.1 ± 51.4 vs 304.6 ± 88.1 min; P < 0.05), less intraoperative blood loss (308.1 ± 135.4 vs 458.1 ± 175.4 mL; P < 0.05), and lower requirement for intraoperative blood transfusion (186.4 ± 169.6 vs 289.4 ± 199.2 mL; P < 0.05). Estimated resection liver volumes in both groups had good correlation with actual graft weight (Group A: r = 0.978; Group B: r = 0.960). There was a significant higher serum level of albumin in Group A (26.3 ± 5.9 vs 22.6 ± 4.3 g/L, P < 0.05). Other postoperative laboratory parameters (serum levels of aminotransferase and bilirubin; prothrombin time) and duration of postoperative hospital stay were similar. Sixteen complications occurred in Group A and 19 in Group B. All patients were followed for 3-46 (mean, 17.3) mo. There was no recurrence of lesions in Group A, but two recurrences in Group B. There were three deaths: two from cerebrovascular accident, and one from car accident. CONCLUSION: 3D reconstruction provides comprehensive and precise anatomical information for the liver. It also improves the chance of success and reduces the risk of hepatectomy in HAE. PMID:26401085

  19. Development and Implementation of a Web-Enabled 3D Consultation Tool for Breast Augmentation Surgery Based on 3D-Image Reconstruction of 2D Pictures

    PubMed Central

    Garcia, Jaime; Olariu, Radu; Dindoyal, Irving; Le Huu, Serge

    2012-01-01

    Background Producing a rich, personalized Web-based consultation tool for plastic surgeons and patients is challenging. Objective (1) To develop a computer tool that allows individual reconstruction and simulation of 3-dimensional (3D) soft tissue from ordinary digital photos of breasts, (2) to implement a Web-based, worldwide-accessible preoperative surgical planning platform for plastic surgeons, and (3) to validate this tool through a quality control analysis by comparing 3D laser scans of the patients with the 3D reconstructions with this tool from original 2-dimensional (2D) pictures of the same patients. Methods The proposed system uses well-established 2D digital photos for reconstruction into a 3D torso, which is then available to the user for interactive planning. The simulation is performed on dedicated servers, accessible via Internet. It allows the surgeon, together with the patient, to previsualize the impact of the proposed breast augmentation directly during the consultation before a surgery is decided upon. We retrospectively conduced a quality control assessment of available anonymized pre- and postoperative 2D digital photographs of patients undergoing breast augmentation procedures. The method presented above was used to reconstruct 3D pictures from 2D digital pictures. We used a laser scanner capable of generating a highly accurate surface model of the patient’s anatomy to acquire ground truth data. The quality of the computed 3D reconstructions was compared with the ground truth data used to perform both qualitative and quantitative evaluations. Results We evaluated the system on 11 clinical cases for surface reconstructions and 4 clinical cases of postoperative simulations, using laser surface scan technologies showing a mean reconstruction error between 2 and 4 mm and a maximum outlier error of 16 mm. Qualitative and quantitative analyses from plastic surgeons demonstrate the potential of these new emerging technologies. Conclusions We

  20. Automatic feature detection for 3D surface reconstruction from HDTV endoscopic videos

    NASA Astrophysics Data System (ADS)

    Groch, Anja; Baumhauer, Matthias; Meinzer, Hans-Peter; Maier-Hein, Lena

    2010-02-01

    A growing number of applications in the field of computer-assisted laparoscopic interventions depend on accurate and fast 3D surface acquisition. The most commonly applied methods for 3D reconstruction of organ surfaces from 2D endoscopic images involve establishment of correspondences in image pairs to allow for computation of 3D point coordinates via triangulation. The popular feature-based approach for correspondence search applies a feature descriptor to compute high-dimensional feature vectors describing the characteristics of selected image points. Correspondences are established between image points with similar feature vectors. In a previous study, the performance of a large set of state-of-the art descriptors for the use in minimally invasive surgery was assessed. However, standard Phase Alternating Line (PAL) endoscopic images were utilized for this purpose. In this paper, we apply some of the best performing feature descriptors to in-vivo PAL endoscopic images as well as to High Definition Television (HDTV) endoscopic images of the same scene and show that the quality of the correspondences can be increased significantly when using high resolution images.

  1. 3D endobronchial ultrasound reconstruction and analysis for multimodal image-guided bronchoscopy

    NASA Astrophysics Data System (ADS)

    Zang, Xiaonan; Bascom, Rebecca; Gilbert, Christopher R.; Toth, Jennifer W.; Higgins, William E.

    2014-03-01

    State-of-the-art image-guided intervention (IGI) systems for lung-cancer management draw upon high-resolution three-dimensional multi-detector computed-tomography (MDCT) images and bronchoscopic video. An MDCT scan provides a high-resolution three-dimensional (3D) image of the chest that is used for preoperative procedure planning, while bronchoscopy gives live intraoperative video of the endobronchial airway tree structure. However, because neither source provides live extraluminal information on suspect nodules or lymph nodes, endobronchial ultrasound (EBUS) is often introduced during a procedure. Unfortunately, existing IGI systems provide no direct synergistic linkage between the MDCT/video data and EBUS data. Hence, EBUS proves difficult to use and can lead to inaccurate interpretations. To address this drawback, we present a prototype of a multimodal IGI system that brings together the various image sources. The system enables 3D reconstruction and visualization of structures depicted in the 2D EBUS video stream. It also provides a set of graphical tools that link the EBUS data directly to the 3D MDCT and bronchoscopic video. Results using phantom and human data indicate that the new system could potentially enable smooth natural incorporation of EBUS into the system-level work flow of bronchoscopy.

  2. A new combined prior based reconstruction method for compressed sensing in 3D ultrasound imaging

    NASA Astrophysics Data System (ADS)

    Uddin, Muhammad S.; Islam, Rafiqul; Tahtali, Murat; Lambert, Andrew J.; Pickering, Mark R.

    2015-03-01

    Ultrasound (US) imaging is one of the most popular medical imaging modalities, with 3D US imaging gaining popularity recently due to its considerable advantages over 2D US imaging. However, as it is limited by long acquisition times and the huge amount of data processing it requires, methods for reducing these factors have attracted considerable research interest. Compressed sensing (CS) is one of the best candidates for accelerating the acquisition rate and reducing the data processing time without degrading image quality. However, CS is prone to introduce noise-like artefacts due to random under-sampling. To address this issue, we propose a combined prior-based reconstruction method for 3D US imaging. A Laplacian mixture model (LMM) constraint in the wavelet domain is combined with a total variation (TV) constraint to create a new regularization regularization prior. An experimental evaluation conducted to validate our method using synthetic 3D US images shows that it performs better than other approaches in terms of both qualitative and quantitative measures.

  3. Automatic Reconstruction of 3D Building Models from Terrestrial Laser Scanner Data

    NASA Astrophysics Data System (ADS)

    El Meouche, R.; Rezoug, M.; Hijazi, I.; Maes, D.

    2013-11-01

    With modern 3D laser scanners we can acquire a large amount of 3D data in only a few minutes. This technology results in a growing number of applications ranging from the digitalization of historical artifacts to facial authentication. The modeling process demands a lot of time and work (Tim Volodine, 2007). In comparison with the other two stages, the acquisition and the registration, the degree of automation of the modeling stage is almost zero. In this paper, we propose a new surface reconstruction technique for buildings to process the data obtained by a 3D laser scanner. These data are called a point cloud which is a collection of points sampled from the surface of a 3D object. Such a point cloud can consist of millions of points. In order to work more efficiently, we worked with simplified models which contain less points and so less details than a point cloud obtained in situ. The goal of this study was to facilitate the modeling process of a building starting from 3D laser scanner data. In order to do this, we wrote two scripts for Rhinoceros 5.0 based on intelligent algorithms. The first script finds the exterior outline of a building. With a minimum of human interaction, there is a thin box drawn around the surface of a wall. This box is able to rotate 360° around an axis in a corner of the wall in search for the points of other walls. In this way we can eliminate noise points. These are unwanted or irrelevant points. If there is an angled roof, the box can also turn around the edge of the wall and the roof. With the different positions of the box we can calculate the exterior outline. The second script draws the interior outline in a surface of a building. By interior outline we mean the outline of the openings like windows or doors. This script is based on the distances between the points and vector characteristics. Two consecutive points with a relative big distance will form the outline of an opening. Once those points are found, the interior outline

  4. A comparative study of the effects of using normalized patches for penalized likelihood tomographic reconstruction

    NASA Astrophysics Data System (ADS)

    Ren, Xue; Lee, Soo-Jin

    2016-03-01

    Patch-based regularization methods, which have proven useful not only for image denoising, but also for tomographic reconstruction, penalize image roughness based on the intensity differences between two nearby patches. However, when two patches are not considered to be similar in the general sense of similarity but still have similar features in a scaled domain after normalizing the two patches, the difference between the two patches in the scaled domain is smaller than the intensity difference measured in the standard method. Standard patch-based methods tend to ignore such similarities due to the large intensity differences between the two patches. In this work, for patch-based penalized likelihood tomographic reconstruction, we propose a new approach to the similarity measure using the normalized patch differences as well as the intensity-based patch differences. A normalized patch difference is obtained by normalizing and scaling the intensity-based patch difference. To selectively take advantage of the standard patch (SP) and normalized patch (NP), we use switching schemes that can select either SP or NP based on the gradient of a reconstructed image. In this case the SP is selected for restoring large-scaled piecewise-smooth regions, while the NP is selected for preserving the contrast of fine details. The numerical experiments using software phantom demonstrate that our proposed methods not only improve overall reconstruction accuracy in terms of the percentage error, but also reveal better recovery of fine details in terms of the contrast recovery coefficient.

  5. In-air versus underwater comparison of 3D reconstruction accuracy using action sport cameras.

    PubMed

    Bernardina, Gustavo R D; Cerveri, Pietro; Barros, Ricardo M L; Marins, João C B; Silvatti, Amanda P

    2017-01-25

    Action sport cameras (ASC) have achieved a large consensus for recreational purposes due to ongoing cost decrease, image resolution and frame rate increase, along with plug-and-play usability. Consequently, they have been recently considered for sport gesture studies and quantitative athletic performance evaluation. In this paper, we evaluated the potential of two ASCs (GoPro Hero3+) for in-air (laboratory) and underwater (swimming pool) three-dimensional (3D) motion analysis as a function of different camera setups involving the acquisition frequency, image resolution and field of view. This is motivated by the fact that in swimming, movement cycles are characterized by underwater and in-air phases what imposes the technical challenge of having a split volume configuration: an underwater measurement volume observed by underwater cameras and an in-air measurement volume observed by in-air cameras. The reconstruction of whole swimming cycles requires thus merging of simultaneous measurements acquired in both volumes. Characterizing and optimizing the instrumental errors of such a configuration makes mandatory the assessment of the instrumental errors of both volumes. In order to calibrate the camera stereo pair, black spherical markers placed on two calibration tools, used both in-air and underwater, and a two-step nonlinear optimization were exploited. The 3D reconstruction accuracy of testing markers and the repeatability of the estimated camera parameters accounted for system performance. For both environments, statistical tests were focused on the comparison of the different camera configurations. Then, each camera configuration was compared across the two environments. In all assessed resolutions, and in both environments, the reconstruction error (true distance between the two testing markers) was less than 3mm and the error related to the working volume diagonal was in the range of 1:2000 (3×1.3×1.5m(3)) to 1:7000 (4.5×2.2×1.5m(3)) in agreement with the

  6. 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.

  7. SALSA3D: A Tomographic Model of Compressional Wave Slowness in the Earth’s Mantle for Improved Travel-Time Prediction and Travel-Time Prediction Uncertainty

    SciTech Connect

    Ballard, Sanford; Hipp, James R.; Begnaud, Michael L.; Young, Christopher J.; Encarnacao, Andre V.; Chael, Eric P.; Phillips, W. Scott

    2016-10-11

    The task of monitoring the Earth for nuclear explosions relies heavily on seismic data to detect, locate, and characterize suspected nuclear tests. In this study, motivated by the need to locate suspected explosions as accurately and precisely as possible, we developed a tomographic model of the compressional wave slowness in the Earth’s mantle with primary focus on the accuracy and precision of travel-time predictions for P and Pn ray paths through the model. Path-dependent travel-time prediction uncertainties are obtained by computing the full 3D model covariance matrix and then integrating slowness variance and covariance along ray paths from source to receiver. Path-dependent travel-time prediction uncertainties reflect the amount of seismic data that was used in tomography with very low values for paths represented by abundant data in the tomographic data set and very high values for paths through portions of the model that were poorly sampled by the tomography data set. The pattern of travel-time prediction uncertainty is a direct result of the off-diagonal terms of the model covariance matrix and underscores the importance of incorporating the full model covariance matrix in the determination of travel-time prediction uncertainty. In addition, the computed pattern of uncertainty differs significantly from that of 1D distance-dependent travel-time uncertainties computed using traditional methods, which are only appropriate for use with travel times computed through 1D velocity models.

  8. SALSA3D: A Tomographic Model of Compressional Wave Slowness in the Earth’s Mantle for Improved Travel-Time Prediction and Travel-Time Prediction Uncertainty

    DOE PAGES

    Ballard, Sanford; Hipp, James R.; Begnaud, Michael L.; ...

    2016-10-11

    The task of monitoring the Earth for nuclear explosions relies heavily on seismic data to detect, locate, and characterize suspected nuclear tests. In this study, motivated by the need to locate suspected explosions as accurately and precisely as possible, we developed a tomographic model of the compressional wave slowness in the Earth’s mantle with primary focus on the accuracy and precision of travel-time predictions for P and Pn ray paths through the model. Path-dependent travel-time prediction uncertainties are obtained by computing the full 3D model covariance matrix and then integrating slowness variance and covariance along ray paths from source tomore » receiver. Path-dependent travel-time prediction uncertainties reflect the amount of seismic data that was used in tomography with very low values for paths represented by abundant data in the tomographic data set and very high values for paths through portions of the model that were poorly sampled by the tomography data set. The pattern of travel-time prediction uncertainty is a direct result of the off-diagonal terms of the model covariance matrix and underscores the importance of incorporating the full model covariance matrix in the determination of travel-time prediction uncertainty. In addition, the computed pattern of uncertainty differs significantly from that of 1D distance-dependent travel-time uncertainties computed using traditional methods, which are only appropriate for use with travel times computed through 1D velocity models.« less

  9. Confocal laser scanning microscopy and 3-D reconstructions of neuronal structures in human brain cortex.

    PubMed

    Belichenko, P V; Dahlström, A

    1995-09-01

    Human brain material was studied with Lucifer yellow (LY) microinjections, indirect Texas red immunofluorescence, and confocal laser scanning microscopy (CLSM). The scanned images were transferred to a Silicon Graphics (SG) IRIS computer equipped with software for reconstructing the 3-D architecture of cells. By employing dual channel CLSM (Bio-Rad MRC 600), LY-injected cells and Texas red immunofluorescence could be studied simultaneously. Autopsy material with 2- to 48-h postmortem delays (6 control and 2 Rett's syndrome cases) as well as biopsy material (14 cases with therapy-resistant partial epilepsy--TRPE--undergoing neurosurgery) were used. In each specimen, 100-200 pyramidal and nonpyramidal neurons were visualized by LY microinjection. Single neurons were imaged and 2-D reconstructions of each neuron were made using z-projections of serial optical images; 3-D reconstructions and rotations were computed using the SG workstation, with VoxelView software from Vital Images (UK), and stored in a "neuronal library" on laser or magnetic optical disks. In Ret's syndrome cases and in patients with TRPE various abnormalities in the dendritic geometry of pyramidal and nonpyramidal cells have been found. The combination of LY injections with immunofluorescence allows the investigation of transmitter-related substances around the LY-injected cells. Using antibodies to synaptic vesicle proteins, presynaptic elements docking onto individual spines have been demonstrated. This approach may contribute to the understanding of different neurological and psychiatric disorders and may be useful in the Mapping of the Human Brain project. It may also be integrated with functional imaging by PET scan and with the human genome project.

  10. Roles of equalization in radar imaging: modeling for superesolution in 3D reconstruction

    NASA Astrophysics Data System (ADS)

    Merched, Ricardo

    2012-12-01

    In radar imaging, resolution is generally dictated by its corresponding system point spread function, the response to a point source as a result of an external excitation. This notion of resolution turns out to be rather questionable, as the interpretation of echoes received from a range of continuous targets according to a linear model allows one to cast the imaging problem as a communication system that maps the target reflectivity function onto measurements, which in turn suggests that by virtue of sampling and equalization, one can achieve unlimited spatial resolution. This article reviews the fundamental problem inherent to pulse compression in a multistatic multi-input-multi-output (MIMO) scenario, from a communications viewpoint, in both focused and un-focused scenarios. We generalize the notion of 1D range compression and replace it by a more general 4D pulse compression. The process of focusing and scanning over a 3D object can be interpreted as a MIMO 4D convolution between a reflectivity tensor and a space-varying system, which naturally induces a 4D MIMO channel convolution model. This implies that several well-established block and linear equalization methods can be easily extended to a 3D scenario with the purpose of achieving exact reconstruction of a given reflectivity volume. That is, assuming that no multiple scattering occurs, resolution is only limited in range by the sampling device in the unfocused case, while unlimited in case of focusing at multiple depths. Exact reconstruction under a zero-forcing or least-squares criterion depends solely on the amount of diversity induced by sampling in both space (via scanning rate) and time (via sampling rate), which further allows for a tradeoff between range and cross-range resolution. For instance, the fastest scanning rate is achieved by steering non overlapping beams, in which case portions of the object can be reconstructed independently from each other.

  11. 3D reconstruction and spatial auralization of the "Painted Dolmen" of Antelas

    NASA Astrophysics Data System (ADS)

    Dias, Paulo; Campos, Guilherme; Santos, Vítor; Casaleiro, Ricardo; Seco, Ricardo; Sousa Santos, Beatriz

    2008-02-01

    This paper presents preliminary results on the development of a 3D audiovisual model of the Anta Pintada (painted dolmen) of Antelas, a Neolithic chamber tomb located in Oliveira de Frades and listed as Portuguese national monument. The final aim of the project is to create a highly accurate Virtual Reality (VR) model of this unique archaeological site, capable of providing not only visual but also acoustic immersion based on its actual geometry and physical properties. The project started in May 2006 with in situ data acquisition. The 3D geometry of the chamber was captured using a Laser Range Finder. In order to combine the different scans into a complete 3D visual model, reconstruction software based on the Iterative Closest Point (ICP) algorithm was developed using the Visualization Toolkit (VTK). This software computes the boundaries of the room on a 3D uniform grid and populates its interior with "free-space nodes", through an iterative algorithm operating like a torchlight illuminating a dark room. The envelope of the resulting set of "free-space nodes" is used to generate a 3D iso-surface approximating the interior shape of the chamber. Each polygon of this surface is then assigned the acoustic absorption coefficient of the corresponding boundary material. A 3D audiovisual model operating in real-time was developed for a VR Environment comprising head-mounted display (HMD) I-glasses SVGAPro, an orientation sensor (tracker) InterTrax 2 with 3 Degrees Of Freedom (3DOF) and stereo headphones. The auralisation software is based on a geometric model. This constitutes a first approach, since geometric acoustics have well-known limitations in rooms with irregular surfaces. The immediate advantage lies in their inherent computational efficiency, which allows real-time operation. The program computes the early reflections forming the initial part of the chamber's impulse response (IR), which carry the most significant cues for source localisation. These early

  12. Single-Particle Cryo-EM and 3D Reconstruction of Hybrid Nanoparticles with Electron-Dense Components.

    PubMed

    Yu, Guimei; Yan, Rui; Zhang, Chuan; Mao, Chengde; Jiang, Wen

    2015-10-01

    Single-particle cryo-electron microscopy (cryo-EM), accompanied with 3D reconstruction, is a broadly applicable tool for the structural characterization of macromolecules and nanoparticles. Recently, the cryo-EM field has pushed the limits of this technique to higher resolutions and samples of smaller molecular mass, however, some samples still present hurdles to this technique. Hybrid particles with electron-dense components, which have been studied using single-particle cryo-EM yet with limited success in 3D reconstruction due to the interference caused by electron-dense elements, constitute one group of such challenging samples. To process such hybrid particles, a masking method is developed in this work to adaptively remove pixels arising from electron-dense portions in individual projection images while maintaining maximal biomass signals for subsequent 2D alignment, 3D reconstruction, and iterative refinements. As demonstrated by the success in 3D reconstruction of an octahedron DNA/gold hybrid particle, which has been previously published without a 3D reconstruction, the devised strategy that combines adaptive masking and standard single-particle 3D reconstruction approach has overcome the hurdle of electron-dense elements interference, and is generally applicable to cryo-EM structural characterization of most, if not all, hybrid nanomaterials with electron-dense components.

  13. Exceptionally Preserved Cambrian Trilobite Digestive System Revealed in 3D by Synchrotron-Radiation X-Ray Tomographic Microscopy

    PubMed Central

    Eriksson, Mats E.; Terfelt, Fredrik

    2012-01-01

    The Cambrian ‘Orsten’ fauna comprises exceptionally preserved and phosphatised microscopic arthropods. The external morphology of these fossils is well known, but their internal soft-tissue anatomy has remained virtually unknown. Here, we report the first non-biomineralised tissues from a juvenile polymerid trilobite, represented by digestive structures, glands, and connective strands harboured in a hypostome from the Swedish ‘Orsten’ fauna. Synchrotron-radiation X-ray tomographic microscopy enabled three-dimensional internal recordings at sub-micrometre resolution. The specimen provides the first unambiguous evidence for a J-shaped anterior gut and the presence of a crop with a constricted alimentary tract in the Trilobita. Moreover, the gut is Y-shaped in cross section, probably due to a collapsed lumen of that shape, another feature which has not previously been observed in trilobites. The combination of anatomical features suggests that the trilobite hypostome is functionally analogous to the labrum of euarthropods and that it was a sophisticated element closely integrated with the digestive system. This study also briefly addresses the preservational bias of the ‘Orsten’ fauna, particularly the near-absence of polymerid trilobites, and the taphonomy of the soft-tissue-harbouring hypostome. PMID:22558180

  14. Exceptionally preserved Cambrian trilobite digestive system revealed in 3D by synchrotron-radiation X-ray tomographic microscopy.

    PubMed

    Eriksson, Mats E; Terfelt, Fredrik

    2012-01-01

    The Cambrian 'Orsten' fauna comprises exceptionally preserved and phosphatised microscopic arthropods. The external morphology of these fossils is well known, but their internal soft-tissue anatomy has remained virtually unknown. Here, we report the first non-biomineralised tissues from a juvenile polymerid trilobite, represented by digestive structures, glands, and connective strands harboured in a hypostome from the Swedish 'Orsten' fauna. Synchrotron-radiation X-ray tomographic microscopy enabled three-dimensional internal recordings at sub-micrometre resolution. The specimen provides the first unambiguous evidence for a J-shaped anterior gut and the presence of a crop with a constricted alimentary tract in the Trilobita. Moreover, the gut is Y-shaped in cross section, probably due to a collapsed lumen of that shape, another feature which has not previously been observed in trilobites. The combination of anatomical features suggests that the trilobite hypostome is functionally analogous to the labrum of euarthropods and that it was a sophisticated element closely integrated with the digestive system. This study also briefly addresses the preservational bias of the 'Orsten' fauna, particularly the near-absence of polymerid trilobites, and the taphonomy of the soft-tissue-harbouring hypostome.

  15. 3D-ANTLERS: Virtual Reconstruction and Three-Dimensional Measurement

    NASA Astrophysics Data System (ADS)

    Barba, S.; Fiorillo, F.; De Feo, E.

    2013-02-01

    The main objective of this paper is to establish a procedural method for measuring and cataloguing antlers through the use of laser scanner and of a 3D reconstruction of complex modeling. The deer's antlers have been used as a test and subjected to capture and measurement. For this purpose multiple data sources techniques have been studied and compared, (also considering low-cost sensors) estimating the accuracy and its errors in order to demonstrate the validity of the process. A further development is the comparison of results with applications of digital photogrammetry, considering also cloud computing software. The study has began with an introduction to sensors, addressing the underlying characteristics of the technology available, the scope and the limits of these applications. We have focused particularly on the "structured light", as the acquisition will be completed through three-dimensional scanners: DAVID and the ARTEC MH. The first is a low-cost sensor, a basic webcam and a linear laser pointer, red coloured, that leads to acquisition of three-dimensional strips. The other one is a hand scanner; even in this case we will explain how to represent a 3D model, with a pipeline that provides data export from the "proprietary" to a "reverse engineering" software. Typically, these are the common steps to the two approaches that have been performed in WRAP format: point sampling, manual and global registration, repair normals, surface editing and texture projection. In fact, after a first and common data processing was done with the use of a software supplied with the equipment, the proto-models thus obtained were treated in Geomagic Studio, which was also chosen to allow the homogenization and standardization of data in order to make a more objective comparison. It is commonplace to observe that the editing of the digital mock-up obtained with the DAVID - which had not yet been upgraded to the 3.5 release at the time of this study - is substantially different

  16. Putting 3D modelling and 3D printing into practice: virtual surgery and preoperative planning to reconstruct complex post-traumatic skeletal deformities and defects

    PubMed Central

    Tetsworth, Kevin; Block, Steve; Glatt, Vaida

    2017-01-01

    3D printing technology has revolutionized and gradually transformed manufacturing across a broad spectrum of industries, including healthcare. Nowhere is this more apparent than in orthopaedics with many surgeons already incorporating aspects of 3D modelling and virtual procedures into their routine clinical practice. As a more extreme application, patient-specific 3D printed titanium truss cages represent a novel approach for managing the challenge of segmental bone defects. This review illustrates the potential indications of this innovative technique using 3D printed titanium truss cages in conjunction with the Masquelet technique. These implants are custom designed during a virtual surgical planning session with the combined input of an orthopaedic surgeon, an orthopaedic engineering professional and a biomedical design engineer. The ability to 3D model an identical replica of the original intact bone in a virtual procedure is of vital importance when attempting to precisely reconstruct normal anatomy during the actual procedure. Additionally, other important factors must be considered during the planning procedure, such as the three-dimensional configuration of the implant. Meticulous design is necessary to allow for successful implantation through the planned surgical exposure, while being aware of the constraints imposed by local anatomy and prior implants. This review will attempt to synthesize the current state of the art as well as discuss our personal experience using this promising technique. It will address implant design considerations including the mechanical, anatomical and functional aspects unique to each case. PMID:28220752

  17. Putting 3D modelling and 3D printing into practice: virtual surgery and preoperative planning to reconstruct complex post-traumatic skeletal deformities and defects.

    PubMed

    Tetsworth, Kevin; Block, Steve; Glatt, Vaida

    2017-01-01

    3D printing technology has revolutionized and gradually transformed manufacturing across a broad spectrum of industries, including healthcare. Nowhere is this more apparent than in orthopaedics with many surgeons already incorporating aspects of 3D modelling and virtual procedures into their routine clinical practice. As a more extreme application, patient-specific 3D printed titanium truss cages represent a novel approach for managing the challenge of segmental bone defects. This review illustrates the potential indications of this innovative technique using 3D printed titanium truss cages in conjunction with the Masquelet technique. These implants are custom designed during a virtual surgical planning session with the combined input of an orthopaedic surgeon, an orthopaedic engineering professional and a biomedical design engineer. The ability to 3D model an identical replica of the original intact bone in a virtual procedure is of vital importance when attempting to precisely reconstruct normal anatomy during the actual procedure. Additionally, other important factors must be considered during the planning procedure, such as the three-dimensional configuration of the implant. Meticulous design is necessary to allow for successful implantation through the planned surgical exposure, while being aware of the constraints imposed by local anatomy and prior implants. This review will attempt to synthesize the current state of the art as well as discuss our personal experience using this promising technique. It will address implant design considerations including the mechanical, anatomical and functional aspects unique to each case.

  18. X-ray imaging and 3D reconstruction of in-flight exploding foil initiator flyers

    NASA Astrophysics Data System (ADS)

    Willey, T. M.; Champley, K.; Hodgin, R.; Lauderbach, L.; Bagge-Hansen, M.; May, C.; Sanchez, N.; Jensen, B. J.; Iverson, A.; van Buuren, T.

    2016-06-01

    Exploding foil initiators (EFIs), also known as slapper initiators or detonators, offer clear safety and timing advantages over other means of initiating detonation in high explosives. This work outlines a new capability for imaging and reconstructing three-dimensional images of operating EFIs. Flyer size and intended velocity were chosen based on parameters of the imaging system. The EFI metal plasma and plastic flyer traveling at 2.5 km/s were imaged with short ˜80 ps pulses spaced 153.4 ns apart. A four-camera system acquired 4 images from successive x-ray pulses from each shot. The first frame was prior to bridge burst, the 2nd images the flyer about 0.16 mm above the surface but edges of the foil and/or flyer are still attached to the substrate. The 3rd frame captures the flyer in flight, while the 4th shows a completely detached flyer in a position that is typically beyond where slappers strike initiating explosives. Multiple acquisitions at different incident angles and advanced computed tomography reconstruction algorithms were used to produce a 3-dimensional image of the flyer at 0.16 and 0.53 mm above the surface. Both the x-ray images and the 3D reconstruction show a strong anisotropy in the shape of the flyer and underlying foil parallel vs. perpendicular to the initiating current and electrical contacts. These results provide detailed flyer morphology during the operation of the EFI.

  19. Rapid 3D dynamic arterial spin labeling with a sparse model-based image reconstruction.

    PubMed

    Zhao, Li; Fielden, Samuel W; Feng, Xue; Wintermark, Max; Mugler, John P; Meyer, Craig H

    2015-11-01

    Dynamic arterial spin labeling (ASL) MRI measures the perfusion bolus at multiple observation times and yields accurate estimates of cerebral blood flow in the presence of variations in arterial transit time. ASL has intrinsically low signal-to-noise ratio (SNR) and is sensitive to motion, so that extensive signal averaging is typically required, leading to long scan times for dynamic ASL. The goal of this study was to develop an accelerated dynamic ASL method with improved SNR and robustness to motion using a model-based image reconstruction that exploits the inherent sparsity of dynamic ASL data. The first component of this method is a single-shot 3D turbo spin echo spiral pulse sequence accelerated using a combination of parallel imaging and compressed sensing. This pulse sequence was then incorporated into a dynamic pseudo continuous ASL acquisition acquired at multiple observation times, and the resulting images were jointly reconstructed enforcing a model of potential perfusion time courses. Performance of the technique was verified using a numerical phantom and it was validated on normal volunteers on a 3-Tesla scanner. In simulation, a spatial sparsity constraint improved SNR and reduced estimation errors. Combined with a model-based sparsity constraint, the proposed method further improved SNR, reduced estimation error and suppressed motion artifacts. Experimentally, the proposed method resulted in significant improvements, with scan times as short as 20s per time point. These results suggest that the model-based image reconstruction enables rapid dynamic ASL with improved accuracy and robustness.

  20. Accurate 3D reconstruction by a new PDS-OSEM algorithm for HRRT

    NASA Astrophysics Data System (ADS)

    Chen, Tai-Been; Horng-Shing Lu, Henry; Kim, Hang-Keun; Son, Young-Don; Cho, Zang-Hee

    2014-03-01

    State-of-the-art high resolution research tomography (HRRT) provides high resolution PET images with full 3D human brain scanning. But, a short time frame in dynamic study causes many problems related to the low counts in the acquired data. The PDS-OSEM algorithm was proposed to reconstruct the HRRT image with a high signal-to-noise ratio that provides accurate information for dynamic data. The new algorithm was evaluated by simulated image, empirical phantoms, and real human brain data. Meanwhile, the time activity curve was adopted to validate a reconstructed performance of dynamic data between PDS-OSEM and OP-OSEM algorithms. According to simulated and empirical studies, the PDS-OSEM algorithm reconstructs images with higher quality, higher accuracy, less noise, and less average sum of square error than those of OP-OSEM. The presented algorithm is useful to provide quality images under the condition of low count rates in dynamic studies with a short scan time.

  1. 3D reconstruction and standardization of the rat vibrissal cortex for precise registration of single neuron morphology.

    PubMed

    Egger, Robert; Narayanan, Rajeevan T; Helmstaedter, Moritz; de Kock, Christiaan P J; Oberlaender, Marcel

    2012-01-01

    The three-dimensional (3D) structure of neural circuits is commonly studied by reconstructing individual or small groups of neurons in separate preparations. Investigation of structural organization principles or quantification of dendritic and axonal innervation thus requires integration of many reconstructed morphologies into a common reference frame. Here we present a standardized 3D model of the rat vibrissal cortex and introduce an automated registration tool that allows for precise placement of single neuron reconstructions. We (1) developed an automated image processing pipeline to reconstruct 3D anatomical landmarks, i.e., the barrels in Layer 4, the pia and white matter surfaces and the blood vessel pattern from high-resolution images, (2) quantified these landmarks in 12 different rats, (3) generated an average 3D model of the vibrissal cortex and (4) used rigid transformations and stepwise linear scaling to register 94 neuron morphologies, reconstructed from in vivo stainings, to the standardized cortex model. We find that anatomical landmarks vary substantially across the vibrissal cortex within an individual rat. In contrast, the 3D layout of the entire vibrissal cortex remains remarkably preserved across animals. This allows for precise registration of individual neuron reconstructions with approximately 30 µm accuracy. Our approach could be used to reconstruct and standardize other anatomically defined brain areas and may ultimately lead to a precise digital reference atlas of the rat brain.

  2. The Performance Evaluation of Multi-Image 3d Reconstruction Software with Different Sensors

    NASA Astrophysics Data System (ADS)

    Mousavi, V.; Khosravi, M.; Ahmadi, M.; Noori, N.; Naveh, A. Hosseini; Varshosaz, M.

    2015-12-01

    Today, multi-image 3D reconstruction is an active research field and generating three dimensional model of the objects is one the most discussed issues in Photogrammetry and Computer Vision that can be accomplished using range-based or image-based methods. Very accurate and dense point clouds generated by range-based methods such as structured light systems and laser scanners has introduced them as reliable tools in the industry. Image-based 3D digitization methodologies offer the option of reconstructing an object by a set of unordered images that depict it from different viewpoints. As their hardware requirements are narrowed down to a digital camera and a computer system, they compose an attractive 3D digitization approach, consequently, although range-based methods are generally very accurate, image-based methods are low-cost and can be easily used by non-professional users. One of the factors affecting the accuracy of the obtained model in image-based methods is the software and algorithm used to generate three dimensional model. These algorithms are provided in the form of commercial software, open source and web-based services. Another important factor in the accuracy of the obtained model is the type of sensor used. Due to availability of mobile sensors to the public, popularity of professional sensors and the advent of stereo sensors, a comparison of these three sensors plays an effective role in evaluating and finding the optimized method to generate three-dimensional models. Lots of research has been accomplished to identify a suitable software and algorithm to achieve an accurate and complete model, however little attention is paid to the type of sensors used and its effects on the quality of the final model. The purpose of this paper is deliberation and the introduction of an appropriate combination of a sensor and software to provide a complete model with the highest accuracy. To do this, different software, used in previous studies, were compared and

  3. Inlining 3d Reconstruction, Multi-Source Texture Mapping and Semantic Analysis Using Oblique Aerial Imagery

    NASA Astrophysics Data System (ADS)

    Frommholz, D.; Linkiewicz, M.; Poznanska, A. M.

    2016-06-01

    This paper proposes an in-line method for the simplified reconstruction of city buildings from nadir and oblique aerial images that at the same time are being used for multi-source texture mapping with minimal resampling. Further, the resulting unrectified texture atlases are analyzed for façade elements like windows to be reintegrated into the original 3D models. Tests on real-world data of Heligoland/ Germany comprising more than 800 buildings exposed a median positional deviation of 0.31 m at the façades compared to the cadastral map, a correctness of 67% for the detected windows and good visual quality when being rendered with GPU-based perspective correction. As part of the process building reconstruction takes the oriented input images and transforms them into dense point clouds by semi-global matching (SGM). The point sets undergo local RANSAC-based regression and topology analysis to detect adjacent planar surfaces and determine their semantics. Based on this information the roof, wall and ground surfaces found get intersected and limited in their extension to form a closed 3D building hull. For texture mapping the hull polygons are projected into each possible input bitmap to find suitable color sources regarding the coverage and resolution. Occlusions are detected by ray-casting a full-scale digital surface model (DSM) of the scene and stored in pixel-precise visibility maps. These maps are used to derive overlap statistics and radiometric adjustment coefficients to be applied when the visible image parts for each building polygon are being copied into a compact texture atlas without resampling whenever possible. The atlas bitmap is passed to a commercial object-based image analysis (OBIA) tool running a custom rule set to identify windows on the contained façade patches. Following multi-resolution segmentation and classification based on brightness and contrast differences potential window objects are evaluated against geometric constraints and

  4. 3D shape reconstruction of specular surfaces by using phase measuring deflectometry

    NASA Astrophysics Data System (ADS)

    Zhou, Tian; Chen, Kun; Wei, Haoyun; Li, Yan

    2016-10-01

    The existing estimation methods for recovering height information from surface gradient are mainly divided into Modal and Zonal te