3D fast reconstruction in positron emission tomography
The issue of long reconstruction times in positron emission tomography (PET) has been addressed from several points of view, resulting in an affordable dedicated system capable of handling routine 3D reconstructions in a few minutes per frame : on the hardware side using fast processors and a parallel architecture, and on the software side, using efficient implementation of computationally less intensive algorithms
Surface reconstruction of 3D objects in computerized tomography
This paper deals with the problem of surface reconstruction of 3D objects from their boundaries in a family of slice images in computerized tomography (CT). Its mathematical formulation is first given, in which it is considered as a problem of functional minimization. Next, the corresponding Euler partial differential equation is derived and it is then solved by the finite difference method. Numerical solution can be found by using the iterative method
Dose fractionation theorem in 3-D reconstruction (tomography)
Glaeser, R.M. [Lawrence Berkeley National Lab., CA (United States)
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.
3D image reconstruction of fiber systems using electron tomography
Over the past several years, electron microscopists and materials researchers have shown increased interest in electron tomography (reconstruction of three-dimensional information from a tilt series of bright field images obtained in a transmission electron microscope (TEM)). In this research, electron tomography has been used to reconstruct a three-dimensional image for fiber structures from secondary electron images in a scanning electron microscope (SEM). The implementation of this technique is used to examine the structure of fiber system before and after deformation. A test sample of steel wool was tilted around a single axis from −10° to 60° by one-degree steps with images taken at every degree; three-dimensional images were reconstructed for the specimen of fine steel fibers. This method is capable of reconstructing the three-dimensional morphology of this type of lineal structure, and to obtain features such as tortuosity, contact points, and linear density that are of importance in defining the mechanical properties of these materials. - Highlights: • The electron tomography technique has been adapted to the SEM for analysis of linear structures. • Images are obtained by secondary electron imaging through a given depth of field, making them analogous to projected images. • Quantitative descriptions of the microstructure can be obtained including tortuosity and contact points per volume
3D parameter reconstruction in hyperspectral diffuse optical tomography
Saibaba, Arvind K.; Krishnamurthy, Nishanth; Anderson, Pamela G.; Kainerstorfer, Jana M.; Sassaroli, Angelo; Miller, Eric L.; Fantini, Sergio; Kilmer, Misha E.
2015-03-01
The imaging of shape perturbation and chromophore concentration using Diffuse Optical Tomography (DOT) data can be mathematically described as an ill-posed and non-linear inverse problem. The reconstruction algorithm for hyperspectral data using a linearized Born model is prohibitively expensive, both in terms of computation and memory. We model the shape of the perturbation using parametric level-set approach (PaLS). We discuss novel computational strategies for reducing the computational cost based on a Krylov subspace approach for parameteric linear systems and a compression strategy for the parameter-to-observation map. We will demonstrate the validity of our approach by comparison with experiments.
Advanced 3D-reconstruction of biological specimen monitored by non-invasive optical tomography
Imaging of intricate and delicate subcellular structures along with reliable 3D-reconstruction of cells and tissues may be achieved on the basis of confocal laser scanning microscopy (optical tomography) provided that certain criteria such as proper loading of fluorescent dyes, image acquisition under defined electro-optical conditions, suitable image pre- and postprocessing, etc., are taken into account prior to volume- or surface-rendering for 3D-visualization. (author)
The accuracy of Single Photon Emission Computed Tomography (SPECT) images is degraded by physical effects, namely photon attenuation, Compton scatter and spatially varying collimator response. The 3D nature of these effects is usually neglected by the methods used to correct for these effects. To deal with the 3D nature of the problem, a 3D projector modeling the spread of photons in 3D can be used in iterative tomographic reconstruction. The 3D projector can be estimated analytically with some approximations, or using precise Monte Carlo simulations. This latter approach has not been applied to fully 3D reconstruction yet due to impractical storage and computation time. The goal of this paper was to determine the gain to be expected from fully 3D Monte Carlo (F3DMC) modeling of the projector in iterative reconstruction, compared to conventional 2D and 3D reconstruction methods. As a proof-of-concept, two small datasets were considered. The projections of the two phantoms were simulated using the Monte Carlo simulation code GATE, as well as the corresponding projector, by taking into account all physical effects (attenuation, scatter, camera point spread function) affecting the imaging process. F3DMC was implemented by using this 3D projector in a maximum likelihood expectation maximization (MLEM) iterative reconstruction. To assess the value of F3DMC, data were reconstructed using 4 methods: filtered backprojection (FBP), MLEM without attenuation correction (MLEM), MLEM with attenuation correction, Jaszczak scatter correction and 3D correction for depth-dependent spatial resolution using an analytical model (MLEMC) and F3DMC. Our results suggest that F3DMC improves mainly imaging sensitivity and signal-to-noise ratio (SNR): sensitivity is multiplied by about 103 and SNR is increased by 20 to 70% compared to MLEMC. Computation of a more robust projector and application of the method on more realistic datasets are currently under investigation. (authors)
In vivo bioluminescence tomography based on multi-view projection and 3D surface reconstruction
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.
X-ray propagation-based phase-contrast imaging is an attractive phase-sensitive imaging technique that has found applications in many research fields. Here, we report the investigations of a method which can quantitatively reconstruct in 3D the refractive index decrement of a quasi-homogeneous object using single-distance phase-contrast tomography data. The method extends the Born-type approximation phase-retrieval algorithm, which is based on the phase-attenuation duality (ε = δ/β, with constant ε) and suitable for homogeneous objects, to tomography and we study its application to quasi-homogeneous objects. The noise performance and the phase-attenuation duality influences of the method are also investigated. In simulation, the method allows us to quantitatively reconstruct the 3D refractive index decrement for quasi-homogeneous and weakly absorbing samples and it performs well in the practical noise situation. Furthermore, it shows a substantial contrast increase and successfully distinguishes different materials in a quasi-homogeneous and weakly absorbing sample from experimental data, even with inappropriate ε value. (paper)
2D and 3D reconstructions in acousto-electric tomography
Kuchment, Peter
2011-04-18
We propose and test stable algorithms for the reconstruction of the internal conductivity of a biological object using acousto-electric measurements. Namely, the conventional impedance tomography scheme is supplemented by scanning the object with acoustic waves that slightly perturb the conductivity and cause the change in the electric potential measured on the boundary of the object. These perturbations of the potential are then used as the data for the reconstruction of the conductivity. The present method does not rely on \\'perfectly focused\\' acoustic beams. Instead, more realistic propagating spherical fronts are utilized, and then the measurements that would correspond to perfect focusing are synthesized. In other words, we use synthetic focusing. Numerical experiments with simulated data show that our techniques produce high-quality images, both in 2D and 3D, and that they remain accurate in the presence of high-level noise in the data. Local uniqueness and stability for the problem also hold. © 2011 IOP Publishing Ltd.
GPS tomography. Validation of reconstructed 3-D humidity fields with radiosonde profiles
Shangguan, M.; Bender, M.; Ramatschi, M.; Dick, G.; Wickert, J. [Helmholtz Centre Potsdam, German Research Centre for Geosciences (GFZ), Potsdam (Germany); Raabe, A. [Leipzig Institute for Meteorology (LIM), Leipzig (Germany); Galas, R. [Technische Univ. Berlin (Germany). Dept. for Geodesy and Geoinformation Sciences
2013-11-01
Water vapor plays an important role in meteorological applications; GeoForschungsZentrum (GFZ) therefore developed a tomographic system to derive 3-D distributions of the tropospheric water vapor above Germany using GPS data from about 300 ground stations. Input data for the tomographic reconstructions are generated by the Earth Parameter and Orbit determination System (EPOS) software of the GFZ, which provides zenith total delay (ZTD), integrated water vapor (IWV) and slant total delay (STD) data operationally with a temporal resolution of 2.5 min (STD) and 15 min (ZTD, IWV). The water vapor distribution in the atmosphere is derived by tomographic reconstruction techniques. The quality of the solution is dependent on many factors such as the spatial coverage of the atmosphere with slant paths, the spatial distribution of their intersections and the accuracy of the input observations. Independent observations are required to validate the tomographic reconstructions and to get precise information on the accuracy of the derived 3-D water vapor fields. To determine the quality of the GPS tomography, more than 8000 vertical water vapor profiles at 13 German radiosonde stations were used for the comparison. The radiosondes were launched twice a day (at 00:00 UTC and 12:00 UTC) in 2007. In this paper, parameters of the entire profiles such as the wet refractivity, and the zenith wet delay have been compared. Before the validation the temporal and spatial distribution of the slant paths, serving as a basis for tomographic reconstruction, as well as their angular distribution were studied. The mean wet refractivity differences between tomography and radiosonde data for all points vary from -1.3 to 0.3, and the root mean square is within the range of 6.5-9. About 32% of 6803 profiles match well, 23% match badly and 45% are difficult to classify as they match only in parts.
GPS tomography: validation of reconstructed 3-D humidity fields with radiosonde profiles
M. Shangguan
2013-09-01
Full Text Available Water vapor plays an important role in meteorological applications; GeoForschungsZentrum (GFZ therefore developed a tomographic system to derive 3-D distributions of the tropospheric water vapor above Germany using GPS data from about 300 ground stations. Input data for the tomographic reconstructions are generated by the Earth Parameter and Orbit determination System (EPOS software of the GFZ, which provides zenith total delay (ZTD, integrated water vapor (IWV and slant total delay (STD data operationally with a temporal resolution of 2.5 min (STD and 15 min (ZTD, IWV. The water vapor distribution in the atmosphere is derived by tomographic reconstruction techniques. The quality of the solution is dependent on many factors such as the spatial coverage of the atmosphere with slant paths, the spatial distribution of their intersections and the accuracy of the input observations. Independent observations are required to validate the tomographic reconstructions and to get precise information on the accuracy of the derived 3-D water vapor fields. To determine the quality of the GPS tomography, more than 8000 vertical water vapor profiles at 13 German radiosonde stations were used for the comparison. The radiosondes were launched twice a day (at 00:00 UTC and 12:00 UTC in 2007. In this paper, parameters of the entire profiles such as the wet refractivity, and the zenith wet delay have been compared. Before the validation the temporal and spatial distribution of the slant paths, serving as a basis for tomographic reconstruction, as well as their angular distribution were studied. The mean wet refractivity differences between tomography and radiosonde data for all points vary from −1.3 to 0.3, and the root mean square is within the range of 6.5–9. About 32% of 6803 profiles match well, 23% match badly and 45% are difficult to classify as they match only in parts.
Analysis of bite marks in foodstuffs by computer tomography (cone beam CT)--3D reconstruction.
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
Bilski, B. J.; Jozwicka, A.; Kujawinska, M.
2007-09-01
Constant development of microelements' technology requires a creation of new instruments to determine their basic physical parameters in 3D. The most efficient non-destructive method providing 3D information is tomography. In this paper we present Digital Holographic Tomography (DHT), in which input data is provided by means of Di-git- al Holography (DH). The main advantage of DH is the capability to capture several projections with a single hologram [1]. However, these projections have uneven angular distribution and their number is significantly limited. Therefore - Algebraic Reconstruction Technique (ART), where a few phase projections may be sufficient for proper 3D phase reconstruction, is implemented. The error analysis of the method and its additional limitations due to shape and dimensions of investigated object are presented. Finally, the results of ART application to DHT method are also presented on data reconstructed from numerically generated hologram of a multimode fibre.
The successful combination of electron beam precession and bright field electron tomography for 3D reconstruction is reported. Beam precession is demonstrated to be a powerful technique to reduce the contrast artifacts due to diffraction and curvature in thin foils. Taking advantage of these benefits, Precession assisted electron tomography has been applied to reconstruct the morphology of Sn precipitates embedded in an Al matrix, from a tilt series acquired in a range from +49o to -61o at intervals of 2o and with a precession angle of 0.6o in bright field mode. The combination of electron tomography and beam precession in conventional TEM mode is proposed as an alternative procedure to obtain 3D reconstructions of nano-objects without a scanning system or a high angle annular dark field detector. -- Highlights: → Electron beam precession reduces spurious diffraction contrast in bright field mode. → Bend contour related contrast depends on precession angle. → Electron beam precession is combined with bright field electron tomography. → Precession assisted BF tomography allowed 3D reconstruction of a Sn precipitate.
Fast iterative image reconstruction methods for fully 3D multispectral bioluminescence tomography
We investigate fast iterative image reconstruction methods for fully 3D multispectral bioluminescence tomography for applications in small animal imaging. Our forward model uses a diffusion approximation for optically inhomogeneous tissue, which we solve using a finite element method (FEM). We examine two approaches to incorporating the forward model into the solution of the inverse problem. In a conventional direct calculation approach one computes the full forward model by repeated solution of the FEM problem, once for each potential source location. We describe an alternative on-the-fly approach where one does not explicitly solve for the full forward model. Instead, the solution to the forward problem is included implicitly in the formulation of the inverse problem, and the FEM problem is solved at each iteration for the current image estimate. We evaluate the convergence speeds of several representative iterative algorithms. We compare the computation cost of those two approaches, concluding that the on-the-fly approach can lead to substantial reductions in total cost when combined with a rapidly converging iterative algorithm
The accuracy of Single-Photon Emission Computed Tomography images is degraded by physical effects, namely photon attenuation, Compton scatter and spatially varying collimator response. The 3D nature of these effects is usually neglected by the methods used to correct for these effects. To deal with the 3D nature of the problem, a 3D projector modeling the spread of photons in 3D can be used in iterative tomographic reconstruction. The 3D projector can be estimated analytically with some approximations, or using precise Monte Carlo simulations. This latter approach has not been applied to fully 3D reconstruction yet due to impractical storage and computation time. The goal of this paper was to determine the gain to be expected from fully 3D Monte Carlo (F3DMC) modeling of the projector in iterative reconstruction, compared to conventional 2D and 3D reconstruction methods. As a proof-of-concept, two small datasets were considered. The projections of the two phantoms were simulated using the Monte Carlo simulation code GATE, as well as the corresponding projector, by taking into account all physical effects (attenuation, scatter, camera point spread function) affecting the imaging process. F3DMC was implemented by using this 3D projector in a maximum likelihood expectation maximization (MLEM) iterative reconstruction. To assess the value of F3DMC, data were reconstructed using four methods: filtered backprojection, MLEM without attenuation correction (MLEM), MLEM with attenuation correction, Jaszczak scatter correction and 3D correction for depth-dependent spatial resolution using an analytical model (MLEMC) and F3DMC. Our results suggest that F3DMC improves mainly imaging sensitivity and signal-to-noise ratio (SNR): sensitivity is multiplied by about 103 and SNR is increased by 20-70% compared to MLEMC. Computation of a more robust projector and application of the method on more realistic datasets are currently under investigation
A fully three-dimensional (3D) one-step late (OSL), maximum a posteriori (MAP) reconstruction algorithm based on the median root prior (MRP) was implemented and evaluated for the reconstruction of 3D positron emission tomography (PET) studies. The algorithm uses the ordered subsets (OS) scheme for convergence acceleration and data update during iterations. The algorithm was implemented using the software package developed within the EU project PARAPET (www.brunel.ac.uk/ masrppet). The MRP algorithm was evaluated using experimental phantom and real 3D PET brain studies. Various experimental set-ups in terms of activity distribution and counting statistics were considered. The performance of the algorithm was assessed by calculating figures of merit such as: contrast, coefficient of variation, activity ratio between two regions and full width at half of maximum for resolution measurements. The performance of MRP was compared with that of 3D ordered subsets-expectation maximisation (OSEM) and 3D re-projection (3DRP) algorithms. In all the experimental situations considered, MRP showed: (1) convergence to a stable solution, (2) effectiveness in noise reduction, particularly for low statistics data, (3) good preservation of spatial details. Compared with the OSEM and 3DRP algorithms, MRP provides comparable or better results depending on the parameters used for the reconstruction of the images. (orig.)
3D reconstruction for partial data electrical impedance tomography using a sparsity prior
Garde, Henrik; Knudsen, Kim
In electrical impedance tomography the electrical conductivity inside a physical body is computed from electro-static boundary measurements. The focus of this paper is to extend recent results for the 2D problem to 3D: prior information about the sparsity and spatial distribution of the...
Mory, Cyril, E-mail: cyril.mory@philips.com [Université de Lyon, CREATIS, CNRS UMR5220, Inserm U1044, INSA-Lyon, Université Lyon 1, F-69621 Villeurbanne Cedex (France); Philips Research Medisys, 33 rue de Verdun, 92156 Suresnes (France); Auvray, Vincent; Zhang, Bo [Philips Research Medisys, 33 rue de Verdun, 92156 Suresnes (France); Grass, Michael; Schäfer, Dirk [Philips Research, Röntgenstrasse 24–26, D-22335 Hamburg (Germany); Chen, S. James; Carroll, John D. [Department of Medicine, Division of Cardiology, University of Colorado Denver, 12605 East 16th Avenue, Aurora, Colorado 80045 (United States); Rit, Simon [Université de Lyon, CREATIS, CNRS UMR5220, Inserm U1044, INSA-Lyon, Université Lyon 1 (France); Centre Léon Bérard, 28 rue Laënnec, F-69373 Lyon (France); Peyrin, Françoise [Université de Lyon, CREATIS, CNRS UMR5220, Inserm U1044, INSA-Lyon, Université Lyon 1, F-69621 Villeurbanne Cedex (France); X-ray Imaging Group, European Synchrotron, Radiation Facility, BP 220, F-38043 Grenoble Cedex (France); Douek, Philippe; Boussel, Loïc [Université de Lyon, CREATIS, CNRS UMR5220, Inserm U1044, INSA-Lyon, Université Lyon 1 (France); Hospices Civils de Lyon, 28 Avenue du Doyen Jean Lépine, 69500 Bron (France)
2014-02-15
Purpose: Reconstruction of the beating heart in 3D + time in the catheter laboratory using only the available C-arm system would improve diagnosis, guidance, device sizing, and outcome control for intracardiac interventions, e.g., electrophysiology, valvular disease treatment, structural or congenital heart disease. To obtain such a reconstruction, the patient's electrocardiogram (ECG) must be recorded during the acquisition and used in the reconstruction. In this paper, the authors present a 4D reconstruction method aiming to reconstruct the heart from a single sweep 10 s acquisition. Methods: The authors introduce the 4D RecOnstructiOn using Spatial and TEmporal Regularization (short 4D ROOSTER) method, which reconstructs all cardiac phases at once, as a 3D + time volume. The algorithm alternates between a reconstruction step based on conjugate gradient and four regularization steps: enforcing positivity, averaging along time outside a motion mask that contains the heart and vessels, 3D spatial total variation minimization, and 1D temporal total variation minimization. Results: 4D ROOSTER recovers the different temporal representations of a moving Shepp and Logan phantom, and outperforms both ECG-gated simultaneous algebraic reconstruction technique and prior image constrained compressed sensing on a clinical case. It generates 3D + time reconstructions with sharp edges which can be used, for example, to estimate the patient's left ventricular ejection fraction. Conclusions: 4D ROOSTER can be applied for human cardiac C-arm CT, and potentially in other dynamic tomography areas. It can easily be adapted to other problems as regularization is decoupled from projection and back projection.
3D Reconstruction of the Glycocalyx Structure in Mammalian Capillaries using Electron Tomography
Arkill, Kp; Neal, Cr; Mantell, Jm;
2012-01-01
Visualising the molecular strands making up the glycocalyx in the lumen of small blood vessels has proved to be difficult using conventional transmission electron microscopy techniques. Images obtained from tissue stained in a variety of ways have revealed a regularity in the organisation of the...... success (e.g. freeze fracture). A new approach is therefore needed. Here we demonstrate the effectiveness of using the relatively novel electron microscopy technique of 3D electron tomography ontwo differently stained preparations to reveal details of the architecture of the glycocalyx just above the...
Bhowmik, Tanmoy; Liu, Hanli; Ye, Zhou; Oraintara, Soontorn
2016-03-01
Diffuse optical tomography (DOT) is a relatively low cost and portable imaging modality for reconstruction of optical properties in a highly scattering medium, such as human tissue. The inverse problem in DOT is highly ill-posed, making reconstruction of high-quality image a critical challenge. Because of the nature of sparsity in DOT, sparsity regularization has been utilized to achieve high-quality DOT reconstruction. However, conventional approaches using sparse optimization are computationally expensive and have no selection criteria to optimize the regularization parameter. In this paper, a novel algorithm, Dimensionality Reduction based Optimization for DOT (DRO-DOT), is proposed. It reduces the dimensionality of the inverse DOT problem by reducing the number of unknowns in two steps and thereby makes the overall process fast. First, it constructs a low resolution voxel basis based on the sensing-matrix properties to find an image support. Second, it reconstructs the sparse image inside this support. To compensate for the reduced sensitivity with increasing depth, depth compensation is incorporated in DRO-DOT. An efficient method to optimally select the regularization parameter is proposed for obtaining a high-quality DOT image. DRO-DOT is also able to reconstruct high-resolution images even with a limited number of optodes in a spatially limited imaging set-up.
Full text: SPECT involves acquiring a set of projection images using one or more rotating gamma cameras. The projections are then reconstructed to create transverse slices. Patient motion during the scan can introduce inconsistencies into the data leading to artifacts. There remains a need for robust and effective motion correction. One approach uses the (corrupt) data itself to derive the patient position at each projection angle. Corrected data is periodically incorporated into a 3-D reconstruction. Fundamental aspects of the algorithm mechanics, particularly performance in the presence of Poisson noise, have been examined. Brain SPECT studies were simulated using a digital version of the Huffman brain phantom. Projection datasets with Poisson noise imposed, generated for different positions of the phantom, were combined and reconstructed to produce motion-corrupted reconstructions. To examine the behaviour of the cost function as the object position was changed, the corrupted re-construction was forward projected and the mean square difference (MSD) between the resulting re-projections and corresponding original projections was calculated. The ability to detect mis-positioned projections for different degrees of freedom, the importance of using dual-head camera geometry, and the effect of smoothing the original projections prior to the MSD calculation were assessed. Re-projection of the corrupt reconstruction was able to correctly identify mis-positioned projection data. The degree of movement as defined by MSD was more easily identified for translations than for rotations. Noise resulted in an increasing bias that made it difficult to distinguish the minimum MSD, particularly for z-axis rotations. This was improved by median filtering of projections. Right-angled dual-head geometry is necessary to provide stability to the algorithm and to better identify motion in all 6 degrees of freedom. These findings will assist the optimisation of a fully automated motion
Huerta, N. J.; Murphy, M. A.; Natarajan, V.; Weber, G.; Hamann, B.; Sumner, D. Y.
2005-12-01
Three-dimensional visualization of intricate microbial structures in rocks is essential to understand the growth of ancient microbial communities. We have imaged and reconstructed the three-dimensional morphology of 2.5-2.6 billion year old intricate microbialites preserved in carbonate using both serial sectioning and neutron computed tomography (NCT). Reconstruction techniques vary with data type and sample preservation. NCT is a non-destructive technique for imaging organic-containing samples with sufficiently high hydrogen concentrations. The resolution of reconstruction is finer than 500 microns. We reconstructed microbialites preserved as organic inclusions in calcite using NCT. Reconstructions are interpreted using volume rendering, segmentation, and an interactive Matlab/visualization environment. Visualizations demonstrate the intricacy of the structures. Noise currently limits automatic growth surface extraction, but growth of structures can be qualitatively evaluated. One of the largest obstacles to date is efficient manipulation of large data sets. Our current visualization approach always renders the supplied data set at full resolution, which requires down-sampling of datasets larger than 256 pixels3 (acquired volume data consists of up to 2048 pixels3) to isolate regions of interest and extract important features. We are exploring the use of multi-resolution techniques that store a dataset at different levels of detail and chose an appropriate resolution during user-interaction. Such an approach will allow us to visualize raw data at full resolution. Serial sectioning and scanning successive horizons provides reconstructions of samples lacking sufficient hydrogen for NCT. This technique destroys the sample and has a lower resolution than NCT. However, intricate networks of microbial laminae surrounded by cement-filled voids can be characterized using this technique. After microbial surfaces are manually interpreted on slices, the images lack noise
Time-Resolved Diffuse Optical Tomography (TR-DOT) is a new non-invasive imaging technique increasingly used in the clinical and preclinical fields. It yields optical absorption and scattering maps of the explored organs, and related physiological parameters. Time-Resolved Fluorescence Diffuse Optical Tomography (TR-FDOT) is based on the detection of fluorescence photons. It provides spatio-temporal maps of fluorescent probe concentrations and life times, and allows access to metabolic and molecular imaging which is important for diagnosis and therapeutic monitoring, particularly in oncology. The main goal of this thesis was to reconstruct 3D TR-DOT/TR-FDOT images of small animals using time-resolved optical technology. Data were acquired using optical fibers fixed around the animal without contact with its surface. The work was achieved in four steps: 1)- Setting up an imaging device to record the 3D coordinates of an animal's surface; 2)- Modeling the no-contact approach to solve the forward problem; 3)- Processing of the measured signals taking into account the impulse response of the device; 4)- Implementation of a new image reconstruction method based on a selection of carefully chosen points. As a result, good-quality 3D optical images were obtained owing to reduced cross-talk between absorption and scattering. Moreover, the computation time was cut down, compared to full-time methods using whole temporal profiles. (author)
3D Reconstruction Technique for Tomographic PIV
姜楠; 包全; 杨绍琼
2015-01-01
Tomographic particle image velocimetry(Tomo-PIV) is a state-of-the-art experimental technique based on a method of optical tomography to achieve the three-dimensional(3D) reconstruction for three-dimensional three-component(3D-3C) flow velocity measurements. 3D reconstruction for Tomo-PIV is carried out herein. Meanwhile, a 3D simplified tomographic reconstruction model reduced from a 3D volume light inten-sity field with 2D projection images into a 2D Tomo-slice plane with 1D projecting lines, i.e., simplifying this 3D reconstruction into a problem of 2D Tomo-slice plane reconstruction, is applied thereafter. Two kinds of the most well-known algebraic reconstruction techniques, algebraic reconstruction technique(ART) and multiple algebraic reconstruction technique(MART), are compared as well. The principles of the two reconstruction algorithms are discussed in detail, which has been performed by a series of simulation images, yielding the corresponding recon-struction images that show different features between the ART and MART algorithm, and then their advantages and disadvantages are discussed. Further discussions are made for the standard particle image reconstruction when the background noise of the pre-initial particle image has been removed. Results show that the particle image recon-struction has been greatly improved. The MART algorithm is much better than the ART. Furthermore, the computa-tional analyses of two parameters(the particle density and the number of cameras), are performed to study their effects on the reconstruction. Lastly, the 3D volume particle field is reconstructed by using the improved algorithm based on the simplified 3D tomographic reconstruction model, which proves that the algorithm simplification is feasible and it can be applied to the reconstruction of 3D volume particle field in a Tomo-PIV system.
In order to improve quality of 3D X-ray tomography reconstruction for Non Destructive Testing (NDT), we investigate in this paper hierarchical Bayesian methods. In NDT, useful prior information on the volume like the limited number of materials or the presence of homogeneous area can be included in the iterative reconstruction algorithms. In hierarchical Bayesian methods, not only the volume is estimated thanks to the prior model of the volume but also the hyper parameters of this prior. This additional complexity in the reconstruction methods when applied to large volumes (from 5123 to 81923 voxels) results in an increasing computational cost. To reduce it, the hierarchical Bayesian methods investigated in this paper lead to an algorithm acceleration by Variational Bayesian Approximation (VBA) [1] and hardware acceleration thanks to projection and back-projection operators paralleled on many core processors like GPU [2]. In this paper, we will consider a Student-t prior on the gradient of the image implemented in a hierarchical way [3, 4, 1]. Operators H (forward or projection) and Ht (adjoint or back-projection) implanted in multi-GPU [2] have been used in this study. Different methods will be evalued on synthetic volume 'Shepp and Logan' in terms of quality and time of reconstruction. We used several simple regularizations of order 1 and order 2. Other prior models also exists [5]. Sometimes for a discrete image, we can do the segmentation and reconstruction at the same time, then the reconstruction can be done with less projections
Zhao, Yue; Zhu, Dianwen; Baikejiang, Reheman; Li, Changqing
2015-11-10
This work introduces a fast, low-cost, robust method based on fringe pattern and phase shifting to obtain three-dimensional (3D) mouse surface geometry for fluorescence molecular tomography (FMT) imaging. We used two pico projector/webcam pairs to project and capture fringe patterns from different views. We first calibrated the pico projectors and the webcams to obtain their system parameters. Each pico projector/webcam pair had its own coordinate system. We used a cylindrical calibration bar to calculate the transformation matrix between these two coordinate systems. After that, the pico projectors projected nine fringe patterns with a phase-shifting step of 2π/9 onto the surface of a mouse-shaped phantom. The deformed fringe patterns were captured by the corresponding webcam respectively, and then were used to construct two phase maps, which were further converted to two 3D surfaces composed of scattered points. The two 3D point clouds were further merged into one with the transformation matrix. The surface extraction process took less than 30 seconds. Finally, we applied the Digiwarp method to warp a standard Digimouse into the measured surface. The proposed method can reconstruct the surface of a mouse-sized object with an accuracy of 0.5 mm, which we believe is sufficient to obtain a finite element mesh for FMT imaging. We performed an FMT experiment using a mouse-shaped phantom with one embedded fluorescence capillary target. With the warped finite element mesh, we successfully reconstructed the target, which validated our surface extraction approach. PMID:26560789
3D Ion Temperature Reconstruction
Tanabe, Hiroshi; You, Setthivoine; Balandin, Alexander; Inomoto, Michiaki; Ono, Yasushi
2009-11-01
The TS-4 experiment at the University of Tokyo collides two spheromaks to form a single high-beta compact toroid. Magnetic reconnection during the merging process heats and accelerates the plasma in toroidal and poloidal directions. The reconnection region has a complex 3D topology determined by the pitch of the spheromak magnetic fields at the merging plane. A pair of multichord passive spectroscopic diagnostics have been established to measure the ion temperature and velocity in the reconnection volume. One setup measures spectral lines across a poloidal plane, retrieving velocity and temperature from Abel inversion. The other, novel setup records spectral lines across another section of the plasma and reconstructs velocity and temperature from 3D vector and 2D scalar tomography techniques. The magnetic field linking both measurement planes is determined from in situ magnetic probe arrays. The ion temperature is then estimated within the volume between the two measurement planes and at the reconnection region. The measurement is followed over several repeatable discharges to follow the heating and acceleration process during the merging reconnection.
Automated tracing of filaments in 3D electron tomography reconstructions using Sculptor and Situs.
Rusu, Mirabela; Starosolski, Zbigniew; Wahle, Manuel; Rigort, Alexander; Wriggers, Willy
2012-05-01
The molecular graphics program Sculptor and the command-line suite Situs are software packages for the integration of biophysical data across spatial resolution scales. Herein, we provide an overview of recently developed tools relevant to cryo-electron tomography (cryo-ET), with an emphasis on functionality supported by Situs 2.7.1 and Sculptor 2.1.1. We describe a work flow for automatically segmenting filaments in cryo-ET maps including denoising, local normalization, feature detection, and tracing. Tomograms of cellular actin networks exhibit both cross-linked and bundled filament densities. Such filamentous regions in cryo-ET data sets can then be segmented using a stochastic template-based search, VolTrac. The approach combines a genetic algorithm and a bidirectional expansion with a tabu search strategy to localize and characterize filamentous regions. The automated filament segmentation by VolTrac compares well to a manual one performed by expert users, and it allows an efficient and reproducible analysis of large data sets. The software is free, open source, and can be used on Linux, Macintosh or Windows computers. PMID:22433493
Virtual 3-D Facial Reconstruction
Martin Paul Evison
2000-06-01
Full Text Available Facial reconstructions in archaeology allow empathy with people who lived in the past and enjoy considerable popularity with the public. It is a common misconception that facial reconstruction will produce an exact likeness; a resemblance is the best that can be hoped for. Research at Sheffield University is aimed at the development of a computer system for facial reconstruction that will be accurate, rapid, repeatable, accessible and flexible. This research is described and prototypical 3-D facial reconstructions are presented. Interpolation models simulating obesity, ageing and ethnic affiliation are also described. Some strengths and weaknesses in the models, and their potential for application in archaeology are discussed.
3D reconstruction of tensors and vectors
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.
Borowska-Solonynko, Aleksandra; Solonynko, Bohdan
2015-02-01
Forensic pathologists are often called upon to determine the mechanism and severity of injuries in living individuals. Such expert testimony is often based solely on hand-written clinical notes. The victims' injuries may also be visualized via three-dimensional (3D) reconstruction of computed tomography (CT) images. This method has certain benefits but is not free from limitations. This paper presents two case reports. The first case is that of a female who was brought to the hospital with a knife thrust into her body. The prosecutor's questions focused on the wound channel. The information obtained from the patient's medical records was very general with many contradictory statements. A re-evaluation of the available CT scan data and a subsequent 3D reconstruction helped determine the exact course of the wound channel. The other case was that of a young male, hospitalized based on CT evidence of bilateral rib fractions, who claimed to have been assaulted by police officers. Court expert witnesses were already in possession of a 3D reconstruction showing symmetrical fractures of the patient's lower ribs with bone fragment displacement. An expert witness in radiology definitively excluded the presence of any actual fractures, and explained their apparent visibility in the three-dimensionally reconstructed image as a motion artifact. These two cases suggest that a professionally conducted 3D CT reconstruction is a very useful tool in providing expert testimony on injuries in living victims. However, the deceptive simplicity of conducting such a reconstruction may encourage inexperienced individuals to undertake it, and thus lead to erroneous conclusions. PMID:25623187
Mike Reichelt
Full Text Available Varicella-zoster virus (VZV is a human alphaherpesvirus that causes varicella (chickenpox and herpes zoster (shingles. Like all herpesviruses, the VZV DNA genome is replicated in the nucleus and packaged into nucleocapsids that must egress across the nuclear membrane for incorporation into virus particles in the cytoplasm. Our recent work showed that VZV nucleocapsids are sequestered in nuclear cages formed from promyelocytic leukemia protein (PML in vitro and in human dorsal root ganglia and skin xenografts in vivo. We sought a method to determine the three-dimensional (3D distribution of nucleocapsids in the nuclei of herpesvirus-infected cells as well as the 3D shape, volume and ultrastructure of these unique PML subnuclear domains. Here we report the development of a novel 3D imaging and reconstruction strategy that we term Serial Section Array-Scanning Electron Microscopy (SSA-SEM and its application to the analysis of VZV-infected cells and these nuclear PML cages. We show that SSA-SEM permits large volume imaging and 3D reconstruction at a resolution sufficient to localize, count and distinguish different types of VZV nucleocapsids and to visualize complete PML cages. This method allowed a quantitative determination of how many nucleocapsids can be sequestered within individual PML cages (sequestration capacity, what proportion of nucleocapsids are entrapped in single nuclei (sequestration efficiency and revealed the ultrastructural detail of the PML cages. More than 98% of all nucleocapsids in reconstructed nuclear volumes were contained in PML cages and single PML cages sequestered up to 2,780 nucleocapsids, which were shown by electron tomography to be embedded and cross-linked by an filamentous electron-dense meshwork within these unique subnuclear domains. This SSA-SEM analysis extends our recent characterization of PML cages and provides a proof of concept for this new strategy to investigate events during virion assembly at the
3D Reconstruction of NMR Images
Peter Izak; Milan Smetana; Libor Hargas; Miroslav Hrianka; Pavol Spanik
2007-01-01
This paper introduces experiment of 3D reconstruction NMR images scanned from magnetic resonance device. There are described methods which can be used for 3D reconstruction magnetic resonance images in biomedical application. The main idea is based on marching cubes algorithm. For this task was chosen sophistication method by program Vision Assistant, which is a part of program LabVIEW.
Landis, W. J.; Hodgens, K. J.; McKee, M. D.; Nanci, A.; Song, M. J.; Kiyonaga, S.; Arena, J.; McEwen, B.
1992-01-01
To gain insight into the structure and possible function of extracellular vesicles in certain calcifying vertebrate tissues, normally mineralizing leg tendons from the domestic turkey, Meleagris gallopavo, have been studied in two separate investigations, one concerning the electron microscopic immunolocalization of the 66 kDa phosphoprotein, osteopontin, and the other detailing the organization and distribution of mineral crystals associated with the vesicles as determined by high voltage microscopic tomography and 3-D graphic image reconstruction. Immunolabeling shows that osteopontin is related to extracellular vesicles of the tendon in the sense that its initial presence appears coincident with the development of mineral associated with the vesicle loci. By high voltage electron microscopy and 3-D imaging techniques, mineral crystals are found to consist of small irregularly shaped particles somewhat randomly oriented throughout individual vesicles sites. Their appearance is different from that found for the mineral observed within calcifying tendon collagen, and their 3-D disposition is not regularly ordered. Possible spatial and temporal relationships of vesicles, osteopontin, mineral, and collagen are being examined further by these approaches.
Forensic 3D Scene Reconstruction
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.
Forensic 3D Scene Reconstruction
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
Michálek, Jan
2015-01-01
Roč. 21, č. 6 (2015), s. 1602-1615. ISSN 1431-9276 R&D Projects: GA MŠk(CZ) LH13028; GA ČR(CZ) GA13-12412S Institutional support: RVO:67985823 Keywords : optical projection tomography * microscopy * artifacts * total variation * data mismatch Subject RIV: EA - Cell Biology Impact factor: 1.877, year: 2014
3D Reconstruction of NMR Images
Peter Izak
2007-01-01
Full Text Available This paper introduces experiment of 3D reconstruction NMR images scanned from magnetic resonance device. There are described methods which can be used for 3D reconstruction magnetic resonance images in biomedical application. The main idea is based on marching cubes algorithm. For this task was chosen sophistication method by program Vision Assistant, which is a part of program LabVIEW.
Ordered subsets convex algorithm for 3D terahertz transmission tomography
Recur, Benoît; Balacey, Hugo; Bou Sleiman, Joyce; Perraud, Jean-Baptiste; Guillet, Jean-Paul; Kingston, Andrew; Mounaix, Patrick
2014-01-01
International audience We investigate in this paper a new reconstruction method in order to perform 3D Terahertz (THz) tomography using a continuous wave acquisition setup in transmission mode. This method is based on the Maximum Likelihood for TRansmission tomography (ML-TR) first developed for X-ray imaging. We optimize the Ordered Subsets Convex (OSC) implementation of the ML-TR by including the Gaussian propagation model of THz waves and take into account the intensity distributions of...
Neural Network Based 3D Surface Reconstruction
Vincy Joseph
2009-11-01
Full Text Available This paper proposes a novel neural-network-based adaptive hybrid-reflectance three-dimensional (3-D surface reconstruction model. The neural network combines the diffuse and specular components into a hybrid model. The proposed model considers the characteristics of each point and the variant albedo to prevent the reconstructed surface from being distorted. The neural network inputs are the pixel values of the two-dimensional images to be reconstructed. The normal vectors of the surface can then be obtained from the output of the neural network after supervised learning, where the illuminant direction does not have to be known in advance. Finally, the obtained normal vectors can be applied to integration method when reconstructing 3-D objects. Facial images were used for training in the proposed approach
3D Reconstruction in Magnetic Resonance Imaging
Mikulka, J.; Bartušek, Karel
Cambridge : The Electromagnetics Academy, 2010, s. 1043-1046. ISBN 978-1-934142-14-1. [PIERS 2010 Cambridge. Cambridge (US), 05.07.2010-08.07.2010] R&D Projects: GA ČR GA102/09/0314 Institutional research plan: CEZ:AV0Z20650511 Keywords : 3D reconstruction * magnetic resonance imaging Subject RIV: JA - Electronics ; Optoelectronics, Electrical Engineering
APPLICATION OF 3D MODELING IN 3D PRINTING FOR THE LOWER JAW RECONSTRUCTION
Yu. Yu. Dikov
2015-01-01
Full Text Available Aim of study: improvement of functional and aesthetic results of microsurgery reconstructions of the lower jaw due to the use of the methodology of 3D modeling and 3D printing. Application of this methodology has been demonstrated on the example of treatment of 4 patients with locally distributed tumors of the mouth cavity, who underwent excision of the tumor with simultaneous reconstruction of the lower jaw with revascularized fibular graft.Before, one patient has already undergo segmental resection of the lower jaw with the defect replacement with the avascular ileac graft and a reconstruction plate. Then, a relapse of the disease and lysis of the graft has developed with him. Modeling of the graft according to the shape of the lower jaw was performed by making osteotomies of the bone part of the graft using three-dimensional virtual models created by computed tomography data. Then these 3D models were printed with a 3D printer of plastic with the scale of 1:1 with the fused deposition modeling (FDM technology and were used during the surgery in the course of modeling of the graft. Sterilizing of the plastic model was performed in the formalin chamber.This methodology allowed more specific reconstruction of the resected fragment of the lower jaw and get better functional and aesthetic results and prepare patients to further dental rehabilitation. Advantages of this methodology are the possibility of simultaneous performance of stages of reconstruction and resection and shortening of the time of surgery.
3-D flame temperature field reconstruction with multiobjective neural network
Xiong Wan(万雄); Yiqing Gao(高益庆); Yuanmei Wang(汪元美)
2003-01-01
A novel 3-D temperature field reconstruction method is proposed in this paper, which is based on multi-wavelength thermometry and Hopfield neural network computed tomography. A mathematical modelof multi-wavelength thermometry is founded, and a neural network algorithm based on multiobjectiveoptimization is developed. Through computer simulation and comparison with the algebraic reconstructiontechnique (ART) and the filter back-projection algorithm (FBP), the reconstruction result of the newmethod is discussed in detail. The study shows that the new method always gives the best reconstructionresults. At last, temperature distribution of a section of four peaks candle flame is reconstructed with thisnovel method.
3D imaging of nanomaterials by discrete tomography
The field of discrete tomography focuses on the reconstruction of samples that consist of only a few different materials. Ideally, a three-dimensional (3D) reconstruction of such a sample should contain only one grey level for each of the compositions in the sample. By exploiting this property in the reconstruction algorithm, either the quality of the reconstruction can be improved significantly, or the number of required projection images can be reduced. The discrete reconstruction typically contains fewer artifacts and does not have to be segmented, as it already contains one grey level for each composition. Recently, a new algorithm, called discrete algebraic reconstruction technique (DART), has been proposed that can be used effectively on experimental electron tomography datasets. In this paper, we propose discrete tomography as a general reconstruction method for electron tomography in materials science. We describe the basic principles of DART and show that it can be applied successfully to three different types of samples, consisting of embedded ErSi2 nanocrystals, a carbon nanotube grown from a catalyst particle and a single gold nanoparticle, respectively.
Fully 3D GPU PET reconstruction
Fully 3D iterative tomographic image reconstruction is computationally very demanding. Graphics Processing Unit (GPU) has been proposed for many years as potential accelerators in complex scientific problems, but it has not been used until the recent advances in the programmability of GPUs that the best available reconstruction codes have started to be implemented to be run on GPUs. This work presents a GPU-based fully 3D PET iterative reconstruction software. This new code may reconstruct sinogram data from several commercially available PET scanners. The most important and time-consuming parts of the code, the forward and backward projection operations, are based on an accurate model of the scanner obtained with the Monte Carlo code PeneloPET and they have been massively parallelized on the GPU. For the PET scanners considered, the GPU-based code is more than 70 times faster than a similar code running on a single core of a fast CPU, obtaining in both cases the same images. The code has been designed to be easily adapted to reconstruct sinograms from any other PET scanner, including scanner prototypes.
Fully 3D GPU PET reconstruction
Herraiz, J.L., E-mail: joaquin@nuclear.fis.ucm.es [Grupo de Fisica Nuclear, Departmento Fisica Atomica, Molecular y Nuclear, Universidad Complutense de Madrid (Spain); Espana, S. [Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA (United States); Cal-Gonzalez, J. [Grupo de Fisica Nuclear, Departmento Fisica Atomica, Molecular y Nuclear, Universidad Complutense de Madrid (Spain); Vaquero, J.J. [Departmento de Bioingenieria e Ingenieria Espacial, Universidad Carlos III, Madrid (Spain); Desco, M. [Departmento de Bioingenieria e Ingenieria Espacial, Universidad Carlos III, Madrid (Spain); Unidad de Medicina y Cirugia Experimental, Hospital General Universitario Gregorio Maranon, Madrid (Spain); Udias, J.M. [Grupo de Fisica Nuclear, Departmento Fisica Atomica, Molecular y Nuclear, Universidad Complutense de Madrid (Spain)
2011-08-21
Fully 3D iterative tomographic image reconstruction is computationally very demanding. Graphics Processing Unit (GPU) has been proposed for many years as potential accelerators in complex scientific problems, but it has not been used until the recent advances in the programmability of GPUs that the best available reconstruction codes have started to be implemented to be run on GPUs. This work presents a GPU-based fully 3D PET iterative reconstruction software. This new code may reconstruct sinogram data from several commercially available PET scanners. The most important and time-consuming parts of the code, the forward and backward projection operations, are based on an accurate model of the scanner obtained with the Monte Carlo code PeneloPET and they have been massively parallelized on the GPU. For the PET scanners considered, the GPU-based code is more than 70 times faster than a similar code running on a single core of a fast CPU, obtaining in both cases the same images. The code has been designed to be easily adapted to reconstruct sinograms from any other PET scanner, including scanner prototypes.
3-D Reconstruction From Satellite Images
Denver, Troelz
1999-01-01
The aim of this project has been to implement a software system, that is able to create a 3-D reconstruction from two or more 2-D photographic images made from different positions. The height is determined from the disparity difference of the images. The general purpose of the system is mapping of......, where various methods have been tested in order to optimize the performance. The match results are used in the reconstruction part to establish a 3-D digital representation and finally, different presentation forms are discussed....... treated individually. A detailed treatment of various lens distortions is required, in order to correct for these problems. This subject is included in the acquisition part. In the calibration part, the perspective distortion is removed from the images. Most attention has been paid to the matching problem...
Analysis of the of bones through 3D computerized tomography
This work shows the analysis of the internal structure of the bones samples through 3D micro tomography technique (3D-μTC). The comprehension of the bone structure is particularly important when related to osteoporosis diagnosis because this implies in a deterioration of the trabecular bone architecture, which increases the fragility and the possibility to have bone fractures. Two bone samples (human calcaneous and Wistar rat femur) were used, and the method was a radiographic system in real time with an X Ray microfocus tube. The quantifications parameters are based on stereological principles and they are five: a bone volume fraction, trabecular number, the ratio between surface and bone volume, the trabecular thickness and the trabecular separation. The quantifications were done with a program developed especially for this purpose in Nuclear Instrumentation Laboratory - COPPE/UFRJ. This program uses as input the 3D reconstructions images and generates a table with the quantifications. The results of the human calcaneous quantifications are presented in tables 1 and 2, and the 3D reconstructions are illustrated in Figure 5. The Figure 6 illustrate the 2D reconstructed image and the Figure 7 the 3D visualization respectively of the Wistar femur sample. The obtained results show that the 3D-μTC is a powerful technique that can be used to analyze bone microstructures. (author)
Software for 3D diagnostic image reconstruction and analysis
Recent advances in computer technologies have opened new frontiers in medical diagnostics. Interesting possibilities are the use of three-dimensional (3D) imaging and the combination of images from different modalities. Software prepared in our laboratories devoted to 3D image reconstruction and analysis from computed tomography and ultrasonography is presented. In developing our software it was assumed that it should be applicable in standard medical practice, i.e. it should work effectively with a PC. An additional feature is the possibility of combining 3D images from different modalities. The reconstruction and data processing can be conducted using a standard PC, so low investment costs result in the introduction of advanced and useful diagnostic possibilities. The program was tested on a PC using DICOM data from computed tomography and TIFF files obtained from a 3D ultrasound system. The results of the anthropomorphic phantom and patient data were taken into consideration. A new approach was used to achieve spatial correlation of two independently obtained 3D images. The method relies on the use of four pairs of markers within the regions under consideration. The user selects the markers manually and the computer calculates the transformations necessary for coupling the images. The main software feature is the possibility of 3D image reconstruction from a series of two-dimensional (2D) images. The reconstructed 3D image can be: (1) viewed with the most popular methods of 3D image viewing, (2) filtered and processed to improve image quality, (3) analyzed quantitatively (geometrical measurements), and (4) coupled with another, independently acquired 3D image. The reconstructed and processed 3D image can be stored at every stage of image processing. The overall software performance was good considering the relatively low costs of the hardware used and the huge data sets processed. The program can be freely used and tested (source code and program available at
Quantitative nanoscale analysis in 3D using electron tomography
State-of-the-art electron tomography has been established as a powerful tool to image complex structures with nanometer resolution in 3D. Especially STEM tomography is used extensively in materials science in such diverse areas as catalysis, semiconductor materials, and polymer composites mainly providing qualitative information on morphology, shape and distribution of materials. However, for an increasing number of studies quantitative information, e.g. surface area, fractal dimensions, particle distribution or porosity are needed. A quantitative analysis is typically performed after segmenting the tomographic data, which is one of the main sources of error for the quantification. In addition to noise, systematic errors due to the missing wedge and due to artifacts from the reconstruction algorithm itself are responsible for these segmentation errors and improved algorithms are needed. This presentation will provide an overview of the possibilities and limitations of quantitative nanoscale analysis by electron tomography. Using catalysts and nano composites as applications examples, intensities and intensity variations observed for the 3D volume reconstructed by WBP and SIRT will be quantitatively compared to alternative reconstruction algorithms; implications for quantification of electron (or X-ray) tomographic data will be discussed and illustrated for quantification of particle size distributions, particle correlations, surface area, and fractal dimensions in 3D.
3D reconstruction methods of coronal structures by radio observations
Aschwanden, Markus J.; Bastian, T. S.; White, Stephen M.
1992-11-01
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.
3D diffraction tomography for visualization of contrast media
Pai, Vinay M.; Stein, Ashley; Kozlowski, Megan; George, Ashvin; Kopace, Rael; Bennett, Eric; Auxier, Julie A.; Wen, Han
2011-03-01
In x-ray CT, the ability to selectively isolate a contrast agent signal from the surrounding soft tissue and bone can greatly enhance contrast visibility and enable quantification of contrast concentration. We present here a 3D diffraction tomography implementation for selectively retaining volumetric diffraction signal from contrast agent particles that are within a banded size range while suppressing the background signal from soft tissue and bone. For this purpose, we developed a CT implementation of a single-shot x-ray diffraction imaging technique utilizing gratings. This technique yields both diffraction and absorption images from a single grating-modulated projection image through analysis in the spatial frequency domain. A solution of iron oxide nano-particles, having very different x-ray diffraction properties from tissue, was injected into ex vivo chicken wing and in vivo rat specimens respectively and imaged in a 3D diffraction CT setup. Following parallel beam reconstruction, it is noted that while the soft tissue, bone and contrast media are observed in the absorption volume reconstruction, only the contrast media is observed in the diffraction volume reconstruction. This 3D diffraction tomographic reconstruction permits the visualization and quantification of the contrast agent isolated from the soft tissue and bone background.
3D SPIRAL COMPUTED TOMOGRAPHY FOR THE DIAGNOSIS OF AN ABDOMINAL TUMOUR
R.C. Tiutiuca; Iuliana Eva
2006-01-01
Patients with digestive illnesses requires a full exploration, cases where imagistic assets support (echographic examination, radiological data, computed tomography, magnetic resonance) are very usefully. Computed tomography, in this process, has a special value. The results from axial images are sustained by the informations supplied from three-dimensional reconstruction processes (3D reconstruction) with relevant importance in establishment of diagnosis and therapeutic plan.
Photogrammetric 3D reconstruction using mobile imaging
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.
Although time consuming, Monte-Carlo simulations remain an efficient tool enabling to assess correction methods for degrading physical effects in medical imaging. We have optimized and validated a reconstruction method baptized F3DMC (Fully 3D Monte Carlo) in which the physical effects degrading the image formation process were modelled using Monte-Carlo methods and integrated within the system matrix. We used the Monte-Carlo simulation toolbox GATE. We validated GATE in SPECT by modelling the gamma-camera (Philips AXIS) used in clinical routine. Techniques of threshold, filtering by a principal component analysis and targeted reconstruction (functional regions, hybrid regions) were used in order to improve the precision of the system matrix and to reduce the number of simulated photons as well as the time consumption required. The EGEE Grid infrastructures were used to deploy the GATE simulations in order to reduce their computation time. Results obtained with F3DMC were compared with the reconstruction methods (FBP, ML-EM, MLEMC) for a simulated phantom and with the OSEM-C method for the real phantom. Results have shown that the F3DMC method and its variants improve the restoration of activity ratios and the signal to noise ratio. By the use of the grid EGEE, a significant speed-up factor of about 300 was obtained. These results should be confirmed by performing studies on complex phantoms and patients and open the door to a unified reconstruction method, which could be used in SPECT and also in PET. (author)
3D/3D registration of coronary CTA and biplane XA reconstructions for improved image guidance
Dibildox, Gerardo, E-mail: g.dibildox@erasmusmc.nl; Baka, Nora; Walsum, Theo van [Biomedical Imaging Group Rotterdam, Departments of Radiology and Medical Informatics, Erasmus Medical Center, 3015 GE Rotterdam (Netherlands); Punt, Mark; Aben, Jean-Paul [Pie Medical Imaging, 6227 AJ Maastricht (Netherlands); Schultz, Carl [Department of Cardiology, Erasmus Medical Center, 3015 GE Rotterdam (Netherlands); Niessen, Wiro [Quantitative Imaging Group, Faculty of Applied Sciences, Delft University of Technology, 2628 CJ Delft, The Netherlands and Biomedical Imaging Group Rotterdam, Departments of Radiology and Medical Informatics, Erasmus Medical Center, 3015 GE Rotterdam (Netherlands)
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.
3D visualization using pulsed and CW digital holographic tomography techniques (Invited Paper)
G. Nehmetallah; P. P. Banerjee; D. Ferree; R. Kephart; S. Praharaj
2011-01-01
We outline the use of digital holographic tomography to determine the three-dimensional (3D) shapes of falling and static objects, such as lenslets and water droplets. Reconstruction of digitally recorded inline holograms is performed using multiplicative and Radon transform techniques to reveal the exact 3D shapes of the objects.%We outline the use of digital holographic tomography to determine the three-dimensional (3D) shapes of falling and static objects,such as lenslets and water droplets.Reconstruction of digitally recorded inline holograms is performed using multiplicative and Radon transform techniques to reveal the exact 3D shapes of the objects.
Probe Trajectory Interpolation for 3D Reconstruction of Freehand Ultrasound
Coupé, Pierrick; Hellier, Pierre; Morandi, Xavier; Barillot, Christian
2007-01-01
Three-dimensional (3D) Freehand ultrasound uses the acquisition of non parallel B-scans localized in 3D by a tracking system (optic, mechanical or magnetic). Using the positions of the irregularly spaced B-scans, a regular 3D lattice volume can be reconstructed, to which conventional 3D computer vision algorithms (registration and segmentation) can be applied. This paper presents a new 3D reconstruction method which explicitly accounts for the probe trajectory. Experiments were conducted on p...
Digital Reconstruction of 3D Polydisperse Dry Foam
Chieco, A.; Feitosa, K.; Roth, A. E.; Korda, P. T.; Durian, D. J.
2012-02-01
Dry foam is a disordered packing of bubbles that distort into familiar polyhedral shapes. We have implemented a method that uses optical axial tomography to reconstruct the internal structure of a dry foam in three dimensions. The technique consists of taking a series of photographs of the dry foam against a uniformly illuminated background at successive angles. By summing the projections we create images of the foam cross section. Image analysis of the cross sections allows us to locate Plateau borders and vertices. The vertices are then connected according to Plateau's rules to reconstruct the internal structure of the foam. Using this technique we are able to visualize a large number of bubbles of real 3D foams and obtain statistics of faces and edges.
Animal testing using 3D microwave tomography system for breast cancer detection.
Lee, Jong Moon; Son, Sung Ho; Kim, Hyuk Je; Kim, Bo Ra; Choi, Heyng Do; Jeon, Soon Ik
2014-01-01
The three dimensional microwave tomography (3D MT) system of the Electronics and Telecommunications Research Institute (ETRI) comprises an antenna array, transmitting receiving module, switch matrix module and a signal processing component. This system also includes a patient interface bed as well as a 3D reconstruction algorithm. Here, we perform a comparative analysis of image reconstruction results using the assembled system and MRI results, which is used to image the breasts of dogs. Microwave imaging reconstruction results (at 1,500 MHz) obtained using the ETRI 3D MT system are presented. The system provides computationally reliable diagnosis results from the reconstructed MT Image. PMID:25160233
3D ultrasound computer tomography: update from a clinical study
Hopp, T.; Zapf, M.; Kretzek, E.; Henrich, J.; Tukalo, A.; Gemmeke, H.; Kaiser, C.; Knaudt, J.; Ruiter, N. V.
2016-04-01
Ultrasound Computer Tomography (USCT) is a promising new imaging method for breast cancer diagnosis. We developed a 3D USCT system and tested it in a pilot study with encouraging results: 3D USCT was able to depict two carcinomas, which were present in contrast enhanced MRI volumes serving as ground truth. To overcome severe differences in the breast shape, an image registration was applied. We analyzed the correlation between average sound speed in the breast and the breast density estimated from segmented MRIs and found a positive correlation with R=0.70. Based on the results of the pilot study we now carry out a successive clinical study with 200 patients. For this we integrated our reconstruction methods and image post-processing into a comprehensive workflow. It includes a dedicated DICOM viewer for interactive assessment of fused USCT images. A new preview mode now allows intuitive and faster patient positioning. We updated the USCT system to decrease the data acquisition time by approximately factor two and to increase the penetration depth of the breast into the USCT aperture by 1 cm. Furthermore the compute-intensive reflectivity reconstruction was considerably accelerated, now allowing a sub-millimeter volume reconstruction in approximately 16 minutes. The updates made it possible to successfully image first patients in our ongoing clinical study.
Fully Automatic 3D Reconstruction of Histological Images
Bagci, Ulas; Bai, Li
2009-01-01
In this paper, we propose a computational framework for 3D volume reconstruction from 2D histological slices using registration algorithms in feature space. To improve the quality of reconstructed 3D volume, first, intensity variations in images are corrected by an intensity standardization process which maps image intensity scale to a standard scale where similar intensities correspond to similar tissues. Second, a subvolume approach is proposed for 3D reconstruction by dividing standardized...
Applicability of 3D-CT facial reconstruction for forensic individual identification
Rocha Sara dos Santos; Ramos Dalton Luiz de Paula; Cavalcanti Marcelo de Gusmão Paraíso
2003-01-01
Computed tomography (CT) is used in several clinical dentistry applications even by axial slices and two and three-dimensional reconstructed images (2D-CT and 3D-CT). The purpose of the current study is to assess the precision of linear measurements made in 3D-CT using craniometric patterns for individual identification in Forensic Dentistry. Five cadaver heads were submitted to a spiral computed tomography using axial slices, and 3D-CT reconstructions were obtained by volume rendering techni...
3D Surface Reconstruction and Automatic Camera Calibration
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.
3D Reconstruction in Spiral Multislice CT Scans
M. Ghafouri
2005-08-01
Full Text Available Introduction & Background: The rapid development of spiral (helical computed tomography (CT has resulted in exciting new applications for CT. One of these applications, three-dimensional (3D CT with volume ren-dering, is now a major area of clinical and academic interest. One of the greatest advantages of spiral CT with 3D volume rendering is that it provides all the necessary information in a single radiologic study (and there-fore at the lowest possible price in cases that previously required two or more studies. Three-dimensional vol-ume rendering generates clinically accurate and immediately available images from the full CT data set with-out extensive editing. It allows the radiologist and clinician to address specific questions concerning patient care by interactively exploring different aspects of the data set. Three-dimensional images integrate a series of axial CT sections into a form that is often easier to interpret than the sections themselves and can be made to appear similar to other more familiar images such as catheter angiograms. The data are organized into a 3D matrix of volume elements (voxels. The screen of the computer monitor is a 2D-surface composed of discrete picture elements (pixels. Presenting what is stored in memory (ie, floating within the monitor on a 2D-screen is a challenge, but it is the very problem that 3D reconstruc-tion software has creatively solved. Voxel selection is usually accomplished by projecting lines (rays through the data set that correspond to the pixel matrix of the desired 2D image. Differences in the images produced with various 3D rendering techniques are the result of variations in how voxels are selected and weighted. In this article, I compare 3D volume rendering of spiral CT data with other rendering techniques (shaded surface display, maximum intensity projection and present a brief history of 3D volume rendering and discuss the im-plementation of this promising technology in terms of
3D Reconstruction by Kinect Sensor:A Brief Review
LI Shi-rui; TAO Ke-lu; WANG Si-yuan; LI Hai-yang; CAO Wei-guo; LI Hua
2014-01-01
While Kinect was originally designed as a motion sensing input device of the gaming console Microsoft Xbox 360 for gaming purposes, it’s easy-to-use, low-cost, reliability, speed of the depth measurement and relatively high quality of depth measurement make it can be used for 3D reconstruction. It could make 3D scanning technology more accessible to everyday users and turn 3D reconstruction models into much widely used asset for many applications. In this paper, we focus on Kinect 3D reconstruction.
Glasses for 3D ultrasound computer tomography: phase compensation
Zapf, M.; Hopp, T.; Ruiter, N. V.
2016-03-01
Ultrasound Computer Tomography (USCT), developed at KIT, is a promising new imaging system for breast cancer diagnosis, and was successfully tested in a pilot study. The 3D USCT II prototype consists of several hundreds of ultrasound (US) transducers on a semi-ellipsoidal aperture. Spherical waves are sequentially emitted by individual transducers and received in parallel by many transducers. Reflectivity volumes are reconstructed by synthetic aperture focusing (SAFT). However, straight forward SAFT imaging leads to blurred images due to system imperfections. We present an extension of a previously proposed approach to enhance the images. This approach includes additional a priori information and system characteristics. Now spatial phase compensation was included. The approach was evaluated with a simulation and clinical data sets. An increase in the image quality was observed and quantitatively measured by SNR and other metrics.
Assessing the Value of 3D Reconstruction in Building Construction
Murthy, Uma; Boardman, David; Garg, Chirag
2012-01-01
3-dimensional (3D) reconstruction is an emerging field in image processing and computer vision that aims to create 3D visualizations/ models of objects/ scenes from image sets. However, its commercial applications and benefits are yet to be fully explored. In this paper, we describe ongoing work towards assessing the value of 3D reconstruction in the building construction domain. We present preliminary results from a user study, where our objective is to understand the use of visual informati...
Lima, I.; Lopes, R.T. [Coordenacao dos Programas de Pos-Graduacao de Engenharia (COPPE), Rio de Janeiro, RJ (Brazil). Lab. de Instrumentacao Nuclear; Oliveira, L.F. [Universidade do Estado do Rio de Janeiro (UERJ), RJ (Brazil). Inst. de Fisica. Dept. de Fisica Aplicada e Termodinamica; Alves, J.M. [Universidade de Sao Paulo (USP), Sao Carlos, SP (Brazil). Escola de Engenharia
2009-03-15
This work shows the analysis of the internal structure of the bones samples through 3D micro tomography technique (3D-{mu}TC). The comprehension of the bone structure is particularly important when related to osteoporosis diagnosis because this implies in a deterioration of the trabecular bone architecture, which increases the fragility and the possibility to have bone fractures. Two bone samples (human calcaneous and Wistar rat femur) were used, and the method was a radiographic system in real time with an X Ray microfocus tube. The quantifications parameters are based on stereological principles and they are five: a bone volume fraction, trabecular number, the ratio between surface and bone volume, the trabecular thickness and the trabecular separation. The quantifications were done with a program developed especially for this purpose in Nuclear Instrumentation Laboratory - COPPE/UFRJ. This program uses as input the 3D reconstructions images and generates a table with the quantifications. The results of the human calcaneous quantifications are presented in tables 1 and 2, and the 3D reconstructions are illustrated in Figure 5. The Figure 6 illustrate the 2D reconstructed image and the Figure 7 the 3D visualization respectively of the Wistar femur sample. The obtained results show that the 3D-{mu}TC is a powerful technique that can be used to analyze bone microstructures. (author)
Reconstruction of 3-D Temperature Field in Holographic Interferometry
无
2001-01-01
The tomography technique is commonly used for the reconstruction of holographic interferometry. However, the current reconstruction method doesn't consider the measurement errors which are non-avoidable in the measurement and will degrade the reconstruction quality. The factors affecting the reconstruction quality are analyzed and the distribution law of the reconstruction error with experimental errors is discussed. Finally, a method to improve the reconstruction quality—the Kalman filter method is presented.
Fast fully 3-D image reconstruction in PET using planograms.
Brasse, D; Kinahan, P E; Clackdoyle, R; Defrise, M; Comtat, C; Townsend, D W
2004-04-01
We present a method of performing fast and accurate three-dimensional (3-D) backprojection using only Fourier transform operations for line-integral data acquired by planar detector arrays in positron emission tomography. This approach is a 3-D extension of the two-dimensional (2-D) linogram technique of Edholm. By using a special choice of parameters to index a line of response (LOR) for a pair of planar detectors, rather than the conventional parameters used to index a LOR for a circular tomograph, all the LORs passing through a point in the field of view (FOV) lie on a 2-D plane in the four-dimensional (4-D) data space. Thus, backprojection of all the LORs passing through a point in the FOV corresponds to integration of a 2-D plane through the 4-D "planogram." The key step is that the integration along a set of parallel 2-D planes through the planogram, that is, backprojection of a plane of points, can be replaced by a 2-D section through the origin of the 4-D Fourier transform of the data. Backprojection can be performed as a sequence of Fourier transform operations, for faster implementation. In addition, we derive the central-section theorem for planogram format data, and also derive a reconstruction filter for both backprojection-filtering and filtered-backprojection reconstruction algorithms. With software-based Fourier transform calculations we provide preliminary comparisons of planogram backprojection to standard 3-D backprojection and demonstrate a reduction in computation time by a factor of approximately 15. PMID:15084067
3D Equilibrium Reconstructions in DIII-D
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.
El Bitar, Ziad [Ecole Doctorale des Sciences Fondamentales, Universite Blaise Pascal, U.F.R de Recherches Scientifiques et Techniques, 34, avenue Carnot - BP 185, 63006 Clermont-Ferrand Cedex (France); Laboratoire de Physique Corpusculaire, CNRS/IN2P3, 63177 Aubiere (France)
2006-12-15
Although time consuming, Monte-Carlo simulations remain an efficient tool enabling to assess correction methods for degrading physical effects in medical imaging. We have optimized and validated a reconstruction method baptized F3DMC (Fully 3D Monte Carlo) in which the physical effects degrading the image formation process were modelled using Monte-Carlo methods and integrated within the system matrix. We used the Monte-Carlo simulation toolbox GATE. We validated GATE in SPECT by modelling the gamma-camera (Philips AXIS) used in clinical routine. Techniques of threshold, filtering by a principal component analysis and targeted reconstruction (functional regions, hybrid regions) were used in order to improve the precision of the system matrix and to reduce the number of simulated photons as well as the time consumption required. The EGEE Grid infrastructures were used to deploy the GATE simulations in order to reduce their computation time. Results obtained with F3DMC were compared with the reconstruction methods (FBP, ML-EM, MLEMC) for a simulated phantom and with the OSEM-C method for the real phantom. Results have shown that the F3DMC method and its variants improve the restoration of activity ratios and the signal to noise ratio. By the use of the grid EGEE, a significant speed-up factor of about 300 was obtained. These results should be confirmed by performing studies on complex phantoms and patients and open the door to a unified reconstruction method, which could be used in SPECT and also in PET. (author)
3D Building Reconstruction Using Dense Photogrammetric Point Cloud
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.
Fully Automatic 3D Reconstruction of Histological Images
Bagci, Ulas
2009-01-01
In this paper, we propose a computational framework for 3D volume reconstruction from 2D histological slices using registration algorithms in feature space. To improve the quality of reconstructed 3D volume, first, intensity variations in images are corrected by an intensity standardization process which maps image intensity scale to a standard scale where similar intensities correspond to similar tissues. Second, a subvolume approach is proposed for 3D reconstruction by dividing standardized slices into groups. Third, in order to improve the quality of the reconstruction process, an automatic best reference slice selection algorithm is developed based on an iterative assessment of image entropy and mean square error of the registration process. Finally, we demonstrate that the choice of the reference slice has a significant impact on registration quality and subsequent 3D reconstruction.
Three-Dimensional Optical Coherence Tomography (3D OCT) Project
National Aeronautics and Space Administration — Applied Science Innovations, Inc. proposes to develop a new tool of 3D optical coherence tomography (OCT) for cellular level imaging at video frame rates and...
Three-Dimensional Optical Coherence Tomography (3D OCT) Project
National Aeronautics and Space Administration — Applied Science Innovations, Inc. proposes a new tool of 3D optical coherence tomography (OCT) for cellular level imaging at video frame rates and dramatically...
3D Reconstruction in Magnetic Resonance Imaging
Mikulka, J.; Bartušek, Karel
2010-01-01
Roč. 6, č. 7 (2010), s. 617-620. ISSN 1931-7360 R&D Projects: GA ČR GA102/09/0314 Institutional research plan: CEZ:AV0Z20650511 Keywords : reconstruction methods * magnetic resonance imaging Subject RIV: JA - Electronics ; Optoelectronics, Electrical Engineering
Array antenna diagnostics with the 3D reconstruction algorithm
Cappellin, Cecilia; Meincke, Peter; Pivnenko, Sergey; Jørgensen, Erik
The 3D reconstruction algorithm is applied to a slotted waveguide array measured at the DTU-ESA Spherical Near-Field Antenna Test Facility. One slot of the array is covered by conductive tape and an error is present in the array excitation. Results show the accuracy obtainable by the 3D reconstru......The 3D reconstruction algorithm is applied to a slotted waveguide array measured at the DTU-ESA Spherical Near-Field Antenna Test Facility. One slot of the array is covered by conductive tape and an error is present in the array excitation. Results show the accuracy obtainable by the 3D...
A 3D Model Reconstruction Method Using Slice Images
LI Hong-an; KANG Bao-sheng
2013-01-01
Aiming at achieving the high accuracy 3D model from slice images, a new model reconstruction method using slice im-ages is proposed. Wanting to extract the outermost contours from slice images, the method of the improved GVF-Snake model with optimized force field and ray method is employed. And then, the 3D model is reconstructed by contour connection using the im-proved shortest diagonal method and judgment function of contour fracture. The results show that the accuracy of reconstruction 3D model is improved.
Interior Reconstruction Using the 3d Hough Transform
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.
Application of CT 3D reconstruction in diagnosing atlantoaxial subluxation
段少银; 林清池; 庞瑞麟
2004-01-01
Objective:To evaluate and compare the diagnostic value in atlantoaxial subluxation by CT three-dimensional (3D) reconstruction.Methods:3D reconstruction fimdings of 41 patients with atlantoaxiai subluxation were retrospectively analyzed, and comparisons were made among images of transverse section, multiplanar reformorting (MPR), surface shade display (SSD), maximum intensity project (MIP), and volume rendering (VR). Results:Of 41 patients with atlantoaxial subluxation, 31 belonged to rotary dislocation, 5 antedislocation, and 5 hind dislocation. All the cases showed the dislocated joint panel of atlantoaxial articulation.Fifteen cases showed deviation of the odontoid process and 8 cases widened distance between the dens and anterior arch of the atlas. The dislocated joint panel of atlantoaxial articulation was more clearly seen with SSD-3D imaging than any other methods. Conclusions:Atlantoaxial subluxation can well be diagnosed by CT 3D reconstruction, in which SSD-3D imaging is optimal.
Stereo Based 3D Face Reconstruction
Falešník, Milan
2013-01-01
Tato práce se zabývá vytvořením programu pro rekonstrukc trojrozměrného modelu lidské tváře za pomocí dvojice kamer. Pro řešení využívá výpočtu hloubkové mapy a následný převod do trojrozměrného prostoru. Využívá Viola-Jones detektor pro detekci tváře. Využívá knihovny OpenCV a také částečně PCL. This thesis presents a system for reconstruction of three-dimensional model of human face by using pair of cameras. To solve this problem, depth map calculation is used and then the depth map is t...
Vector spherical harmonics application to 3-D tomography problem
Balandin, A. L.
2007-04-01
A method of series expansion with the aid of vector spherical harmonics intended for inverting line integrated data is proposed to investigate 3-D vector fields in the spherical plasmas. A set of numerical computations demonstrating the 3-D reconstruction of the model vector fields has been performed to assess the inversion method proposed.
A new algorithm for 3D reconstruction from support functions
Gardner, Richard; Kiderlen, Markus
2009-01-01
We introduce a new algorithm for reconstructing an unknown shape from a finite number of noisy measurements of its support function. The algorithm, based on a least squares procedure, is very easy to program in standard software such as Matlab and allows, for the first time, good 3D reconstructions...
Filtering of measurement noise with the 3D reconstruction algorithm
Cappellin, Cecilia; Pivnenko, Sergey
2014-01-01
Two different antenna models are set up in GRASP and CHAMP, and noise is added to the radiated field. The noisy field is then given as input to the 3D reconstruction of DIATOOL and the SWE coefficients and the far-field radiated by the reconstructed currents are compared with the noise-free resul...
Reconstruction of High Resolution 3D Objects from Incomplete Images and 3D Information
Alexander Pacheco
2014-05-01
Full Text Available To this day, digital object reconstruction is a quite complex area that requires many techniques and novel approaches, in which high-resolution 3D objects present one of the biggest challenges. There are mainly two different methods that can be used to reconstruct high resolution objects and images: passive methods and active methods. This methods depend on the type of information available as input for modeling 3D objects. The passive methods use information contained in the images and the active methods make use of controlled light sources, such as lasers. The reconstruction of 3D objects is quite complex and there is no unique solution- The use of specific methodologies for the reconstruction of certain objects it’s also very common, such as human faces, molecular structures, etc. This paper proposes a novel hybrid methodology, composed by 10 phases that combine active and passive methods, using images and a laser in order to supplement the missing information and obtain better results in the 3D object reconstruction. Finally, the proposed methodology proved its efficiency in two complex topological complex objects.
Camera Calibration by Registration Stereo Reconstruction to 3D Model
Klečka, J.
2015-01-01
Paper aims at unusual way to camera calibration. The main idea is that by registration of uncalibrated stereo reconstruction to 3D model of the same scene is eliminated ambiguity of the reconstruction. The reason for this is that exact metric scene reconstruction from image pair can be understate as information equivalent to calibration of the source camera pair. Described principles were verified by experiment on real data and results are presented at the end of the paper.
Usefulness of reconstructed 3D-CT for magerl technique
It is obviously important to determine safe screwing in transarticular atlanto-axial fixation by the Magerl technique by evaluating the morphological features of the screw passing route. In the present study, we investigated the availability of reconstructed 3D-CT to prevent vertebral artery injury in this technique. Thirty patients underwent reconstructed 3D-CT prior to the operation to determine whether safe screw fixation by the Magerl technique, imaging coronal, and sagittal reconstruction CT were possible. As a result, safe screwing was found to be impossible in four cases, of which two therefore underwent Brooks's method and the other two cases O-C2 fusion. Twenty-six cases who were compatible with Magerl's method had no neuro-vascular complications. We concluded that reconstructed 3D-CT is useful for determining safe screw fixation by the Magerl technique. (author)
Light field display and 3D image reconstruction
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.
[3D Super-resolution Reconstruction and Visualization of Pulmonary Nodules from CT Image].
Wang, Bing; Fan, Xing; Yang, Ying; Tian, Xuedong; Gu, Lixu
2015-08-01
The aim of this study was to propose an algorithm for three-dimensional projection onto convex sets (3D POCS) to achieve super resolution reconstruction of 3D lung computer tomography (CT) images, and to introduce multi-resolution mixed display mode to make 3D visualization of pulmonary nodules. Firstly, we built the low resolution 3D images which have spatial displacement in sub pixel level between each other and generate the reference image. Then, we mapped the low resolution images into the high resolution reference image using 3D motion estimation and revised the reference image based on the consistency constraint convex sets to reconstruct the 3D high resolution images iteratively. Finally, we displayed the different resolution images simultaneously. We then estimated the performance of provided method on 5 image sets and compared them with those of 3 interpolation reconstruction methods. The experiments showed that the performance of 3D POCS algorithm was better than that of 3 interpolation reconstruction methods in two aspects, i.e., subjective and objective aspects, and mixed display mode is suitable to the 3D visualization of high resolution of pulmonary nodules. PMID:26710449
3D Reconstruction in Spiral Multislice CT Scans
M. Ghafouri
2005-01-01
Introduction & Background: The rapid development of spiral (helical) computed tomography (CT) has resulted in exciting new applications for CT. One of these applications, three-dimensional (3D) CT with volume ren-dering, is now a major area of clinical and academic interest. One of the greatest advantages of spiral CT with 3D volume rendering is that it provides all the necessary information in a single radiologic study (and there-fore at the lowest possible price) in cases that previousl...
Improving automated 3D reconstruction methods via vision metrology
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.
3D electron tomography of biological photonic crystals
Butz, Benjamin; Winter, Benjamin; Vieweg, Benito; Knoke, Isabel; Spallek, Stefanie; Spiecker, Erdmann [CENEM, Universitaet Erlangen-Nuernberg (Germany); Schroeder-Turk, Gerd; Mecke, Klaus [Theoretische Physik I, Universitaet Erlangen-Nuernberg (Germany)
2011-07-01
Photonic crystals, i.e. periodical nanostructures of materials with different dielectric constants, are highly interesting for applications in optics, optoelectronics, and sensing. By tailoring the geometrical parameters radically different and improved optical properties (e.g., optical band-gap structure, extreme refractive indices, or high anisotropy) can be achieved. Naturally occurring photonic crystals, like butterfly scales, exoskeletons of insects (chitin), or seashells (nacre), can serve as model systems for understanding the relationship between structure and optical properties. Butterfly scales are studied by TEM using a FEI Titan{sup 3} 80-300 instrument. An optimized FIB technique or ultramicrotome sectioning were used to prepare the sensitive specimens with desired thickness. Since the periodical structures have dimensions on the sub-{mu}m scale, HAADF-STEM tomography was employed for obtaining extended tilt series under conditions of atomic-number sensitive imaging. Since the solid crystal consists of chemically homogeneous chitin while the pores are unfilled, the distinct contrast in the images can easily be interpreted in terms of the local projected mass density allowing to reconstruct the chitin distribution within the optical unit cell of the scales with high 3D resolution.
3D electron tomography of biological photonic crystals
Photonic crystals, i.e. periodical nanostructures of materials with different dielectric constants, are highly interesting for applications in optics, optoelectronics, and sensing. By tailoring the geometrical parameters radically different and improved optical properties (e.g., optical band-gap structure, extreme refractive indices, or high anisotropy) can be achieved. Naturally occurring photonic crystals, like butterfly scales, exoskeletons of insects (chitin), or seashells (nacre), can serve as model systems for understanding the relationship between structure and optical properties. Butterfly scales are studied by TEM using a FEI Titan3 80-300 instrument. An optimized FIB technique or ultramicrotome sectioning were used to prepare the sensitive specimens with desired thickness. Since the periodical structures have dimensions on the sub-μm scale, HAADF-STEM tomography was employed for obtaining extended tilt series under conditions of atomic-number sensitive imaging. Since the solid crystal consists of chemically homogeneous chitin while the pores are unfilled, the distinct contrast in the images can easily be interpreted in terms of the local projected mass density allowing to reconstruct the chitin distribution within the optical unit cell of the scales with high 3D resolution.
Rapidly 3D Texture Reconstruction Based on Oblique Photography
ZHANG Chunsen
2015-07-01
Full Text Available This paper proposes a city texture fast reconstruction method based on aerial tilt image for reconstruction of three-dimensional city model. Based on the photogrammetry and computer vision theory and using the city building digital surface model obtained by prior treatment, through collinear equation calculation geometric projection of object and image space, to obtain the three-dimensional information and texture information of the structure and through certain the optimal algorithm selecting the optimal texture on the surface of the object, realize automatic extraction of the building side texture and occlusion handling of the dense building texture. The real image texture reconstruction results show that: the method to the 3D city model texture reconstruction has the characteristics of high degree of automation, vivid effect and low cost and provides a means of effective implementation for rapid and widespread real texture rapid reconstruction of city 3D model.
Building with Drones: Accurate 3D Facade Reconstruction using MAVs
Daftry, Shreyansh; Hoppe, Christof; Bischof, Horst
2015-01-01
Automatic reconstruction of 3D models from images using multi-view Structure-from-Motion methods has been one of the most fruitful outcomes of computer vision. These advances combined with the growing popularity of Micro Aerial Vehicles as an autonomous imaging platform, have made 3D vision tools ubiquitous for large number of Architecture, Engineering and Construction applications among audiences, mostly unskilled in computer vision. However, to obtain high-resolution and accurate reconstruc...
3D reconstruction based on spatial vanishing information
Yuan Shu; Zheng Tan
2005-01-01
An approach for the three-dimensional (3D) reconstruction of architectural scenes from two un-calibrated images is described in this paper. From two views of one architectural structure, three pairs of corresponding vanishing points of three major mutual orthogonal directions can be extracted. The simple but powerful constraints of parallelism and orthogonal lines in architectural scenes can be used to calibrate the cameras and to recover the 3D information of the structure. This approach is applied to the real images of architectural scenes, and a 3D model of a building in virtual reality modelling language (VRML) format is presented which illustrates the method with successful performance.
3D surface reconstruction multi-scale hierarchical approaches
Bellocchio, Francesco; Ferrari, Stefano; Piuri, Vincenzo
2012-01-01
3D Surface Reconstruction: Multi-Scale Hierarchical Approaches presents methods to model 3D objects in an incremental way so as to capture more finer details at each step. The configuration of the model parameters, the rationale and solutions are described and discussed in detail so the reader has a strong understanding of the methodology. Modeling starts from data captured by 3D digitizers and makes the process even more clear and engaging. Innovative approaches, based on two popular machine learning paradigms, namely Radial Basis Functions and the Support Vector Machines, are also introduced
Improvement of geometrical measurements from 3D-SEM reconstructions
Carli, Lorenzo; De Chiffre, Leonardo; Horsewell, Andy;
2009-01-01
external diameter of 0.26mm. A series of measurements were performed to determine the accuracy of 3D reconstructions obtained using stereo-photogrammetry methods, finding a procedure to determine the optimum number of rotations of the object for an acceptable measuring uncertainty. It was determined that...
Automated 3D reconstruction of interiors with multiple scan views
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/.
3D multifocus astigmatism and compressed sensing (3D MACS) based superresolution reconstruction.
Huang, Jiaqing; Sun, Mingzhai; Gumpper, Kristyn; Chi, Yuejie; Ma, Jianjie
2015-03-01
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 ℓ 1-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
3D Observation of GEMS by Electron Tomography
Matsuno, Junya; Miyake, Akira; Tsuchiyama, Akira; Nakamura-Messenger, Keiko; Messenger, Scott
2014-01-01
Amorphous silicates in chondritic porous interplanetary dust particles (CP-IDPs) coming from comets are dominated by glass with embedded metal and sulfides (GEMS). GEMS grains are submicron-sized rounded objects (typically 100-500) nm in diameter) with anaometer-sized (10-50 nm) Fe-Ni metal and sulfide grains embedded in an amorphous silicate matrix. Several formation processes for GEMS grains have been proposed so far, but these models are still being debated [2-5]. Bradley et al. proposed that GEMS grains are interstellar silicate dust that survived various metamorphism or alteration processes in the protoplanetary disk and that they are amorphiation products of crystalline silicates in the interstellar medium by sputter-deposition of cosmic ray irradiation, similar to space weathering [2,4]. This consideration is based on the observation of nano-sized crystals (approximately 10 nm) called relict grains in GEMS grains and their shapes are pseudomorphs to the host GEMS grains. On the other hand, Keller and Messenger proposed that most GEMS formed in the protoplanetary disk as condensates from high temperature gas [3,5]. This model is based on the fact that most GEMS grains have solar isotopic compositions and have extremely heterogeneous and non-solar elemental compositions. Keller and Messenger (2011) also reported that amorphous silicates in GEMS grains are surrounded by sulfide grains, which formed as sulfidization of metallic iron grains located on the GEMS surface. The previous studies were performed with 2D observation by using transmission electron microscopy (TEM) or scanning TEM (STEM). In order to understand the structure of GEMS grains described above more clearly, we observed 3D structure of GEMS grains by electron tomography using a TEM/STEM (JEM-2100F, JEOL) at Kyoto University. Electron tomography gives not only 3D structures but also gives higher spatial resolution (approximately a few nm) than that in conventional 2D image, which is restricted by
Is 3D true non linear traveltime tomography reasonable ?
Herrero, A.; Virieux, J.
2003-04-01
The data sets requiring 3D analysis tools in the context of seismic exploration (both onshore and offshore experiments) or natural seismicity (micro seismicity surveys or post event measurements) are more and more numerous. Classical linearized tomographies and also earthquake localisation codes need an accurate 3D background velocity model. However, if the medium is complex and a priori information not available, a 1D analysis is not able to provide an adequate background velocity image. Moreover, the design of the acquisition layouts is often intrinsically 3D and renders difficult even 2D approaches, especially in natural seismicity cases. Thus, the solution relies on the use of a 3D true non linear approach, which allows to explore the model space and to identify an optimal velocity image. The problem becomes then practical and its feasibility depends on the available computing resources (memory and time). In this presentation, we show that facing a 3D traveltime tomography problem with an extensive non-linear approach combining fast travel time estimators based on level set methods and optimisation techniques such as multiscale strategy is feasible. Moreover, because management of inhomogeneous inversion parameters is more friendly in a non linear approach, we describe how to perform a jointly non-linear inversion for the seismic velocities and the sources locations.
3D reconstruction of multiple stained histology images
Yi Song
2013-01-01
Full Text Available Context: Three dimensional (3D tissue reconstructions from the histology images with different stains allows the spatial alignment of structural and functional elements highlighted by different stains for quantitative study of many physiological and pathological phenomena. This has significant potential to improve the understanding of the growth patterns and the spatial arrangement of diseased cells, and enhance the study of biomechanical behavior of the tissue structures towards better treatments (e.g. tissue-engineering applications. Methods: This paper evaluates three strategies for 3D reconstruction from sets of two dimensional (2D histological sections with different stains, by combining methods of 2D multi-stain registration and 3D volumetric reconstruction from same stain sections. Setting and Design: The different strategies have been evaluated on two liver specimens (80 sections in total stained with Hematoxylin and Eosin (H and E, Sirius Red, and Cytokeratin (CK 7. Results and Conclusion: A strategy of using multi-stain registration to align images of a second stain to a volume reconstructed by same-stain registration results in the lowest overall error, although an interlaced image registration approach may be more robust to poor section quality.
3D reconstruction, a new challenge in industrial radiography
In a NDT context, industrial radiography enables the detection of defects through their projection on a film. EDF has studied the benefit that may be brought in terms of localisation and orientation of the defects by the mean of 3D reconstruction using a very limited number of radiographs. The reconstruction issue consists of solving an integral equation of the first kind ; in a noisy context, the reconstruction belongs to the so-called ill-posed class of problem. Appropriate solutions may only be found with the help of regularization technique, by the introduction of a priori knowledge concerning the unknown solution and also by the use of a statistical modelization of the physical process which produces radiographs. Another approach simplifies the problem and reconstructs the skeleton of a defect only. All these methods coming from applied mathematical sciences enable a more precise diagnosis in non-destructive testing of thick inhomogeneous material. (authors). 4 refs., 4 figs
Using the 2-D data provided by CT-Tomography and MRI-tomography of oral and maxillofacial diseases (cyst, benign tumor, primary tumor and regional lymphnodes of malignant tumor), 3-D images were reconstructed and spatial analysis was attempted. We report the general concepts. The hardware used consisted of the Hewlett-Packard HP-9000/300, which utilizes a 16-bit CPU. A digitizer was used to construct 3-D images from serial CT-tomography and MRI-tomography images. Output was displayed on a color monitor and photographs. The 3 cases on which we used this technique included a 19-year-old male with plunging ranula, a 50-year-old male with maxillary pleomorphic adenoma, and a 58-year-old male with squamous cell carcinoma of the maxillary sinus (T3N3M0). As 3-D reconstruction can be done in any arbitrary direction or cross section, it is possible to spatially determine the position of the disease inside the body, its progression, and its relationship with adjacent organs. Through image analysis, it is possible to better understand the volume and surface area of the disease. 3-D image reconstruction is an effective tool in the determination of diagnosis, therapeutic guidelines, and surgical indications, as well as effectiveness of treatment. (author)
Reconstruction of 3D morphology of polyhedral nanoparticles
The three-dimensional (3D) faceting morphology of ceria nanoparticles is analysed using transmission electron microscopy (TEM)-based computed tomography on the nanometre scale. A novel tomography mode of electron energy loss spectroscopic imaging using a single energy window for inelastically scattered electrons is introduced and found to be reliable and fast for freestanding nanoparticles. To compare the new tomographic method with other methods, we provide the first comprehensive application of three complementary TEM-based imaging techniques, including bright field TEM and annular dark field specific TEM (STEM). Traditional bright-field TEM tomography is found to be applicable, in spite of obvious artefacts, for crystalline particles of constant composition. However, the safest interpretation is achieved by a combined recording of bright field and spectroscopic images
Twenty-fold acceleration of 3D projection reconstruction MPI
Konkle, Justin J.; Goodwill, Patrick W.; Saritas, Emine Ulku; Zheng, Bo; Lu, Kuan; Conolly, Steven M.
2013-01-01
We experimentally demonstrate a 20-fold improvement in acquisition time in projection reconstruction (PR) magnetic particle imaging (MPI) relative to the state-of-the-art PR MPI imaging results. We achieve this acceleration in our imaging system by introducing an additional Helmholtz electromagnet pair, which creates a slow shift (focus) field. Because of magnetostimulation limits in humans, we show that scan time with three-dimensional (3D) PR MPI is theoretically within the same order of ma...
Automatic Reconstruction of Personalized Avatars from 3D Face Scans
Zollhoefer, Michael; Martinek, Michael; Greiner, Guenther; Stamminger, Marc; Suessmuth, Jochen
2011-01-01
Abstract We present a simple algorithm for computing a high quality personalized avatar from a single color image and the corresponding depth map which have been captured by Microsoft's Kinect sensor. Due to the low market price of our hardware setup, 3D face scanning becomes feasible for home use. The proposed algorithm combines the advantages of robust non-rigid registration and fitting of a morphable face model. We obtain a high quality reconstruction of the facial geometry and ...
3DSEM++: Adaptive and intelligent 3D SEM surface reconstruction.
Tafti, Ahmad P; Holz, Jessica D; Baghaie, Ahmadreza; Owen, Heather A; He, Max M; Yu, Zeyun
2016-08-01
Structural analysis of microscopic objects is a longstanding topic in several scientific disciplines, such as biological, mechanical, and materials sciences. The scanning electron microscope (SEM), as a promising imaging equipment has been around for decades to determine the surface properties (e.g., compositions or geometries) of specimens by achieving increased magnification, contrast, and resolution greater than one nanometer. Whereas SEM micrographs still remain two-dimensional (2D), many research and educational questions truly require knowledge and facts about their three-dimensional (3D) structures. 3D surface reconstruction from SEM images leads to remarkable understanding of microscopic surfaces, allowing informative and qualitative visualization of the samples being investigated. In this contribution, we integrate several computational technologies including machine learning, contrario methodology, and epipolar geometry to design and develop a novel and efficient method called 3DSEM++ for multi-view 3D SEM surface reconstruction in an adaptive and intelligent fashion. The experiments which have been performed on real and synthetic data assert the approach is able to reach a significant precision to both SEM extrinsic calibration and its 3D surface modeling. PMID:27200484
An automated 3D reconstruction method of UAV images
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.
Projective 3D-reconstruction of Uncalibrated Endoscopic Images
P. Faltin
2010-01-01
Full Text Available The most common medical diagnostic method for urinary bladder cancer is cystoscopy. This inspection of the bladder is performed by a rigid endoscope, which is usually guided close to the bladder wall. This causes a very limited field of view; difficulty of navigation is aggravated by the usage of angled endoscopes. These factors cause difficulties in orientation and visual control. To overcome this problem, the paper presents a method for extracting 3D information from uncalibrated endoscopic image sequences and for reconstructing the scene content. The method uses the SURF-algorithm to extract features from the images and relates the images by advanced matching. To stabilize the matching, the epipolar geometry is extracted for each image pair using a modified RANSAC-algorithm. Afterwards these matched point pairs are used to generate point triplets over three images and to describe the trifocal geometry. The 3D scene points are determined by applying triangulation to the matched image points. Thus, these points are used to generate a projective 3D reconstruction of the scene, and provide the first step for further metric reconstructions.
3D X-ray microscopy: image formation, tomography and instrumentation
Selin, Mårten
2016-01-01
Tomography in soft X-ray microscopy is an emerging technique for obtaining quantitative 3D structural information about cells. One of its strengths, compared with other techniques, is that it can image intact cells in their near-native state at a few 10 nm’s resolution, without staining. However, the methods for reconstructing 3D-data rely on algorithms that assume projection data, which the images are generally not due to the imaging systems’ limited depth of focus. To bring out the full pot...
Applicability of 3D-CT facial reconstruction for forensic individual identification
Rocha Sara dos Santos
2003-01-01
Full Text Available Computed tomography (CT is used in several clinical dentistry applications even by axial slices and two and three-dimensional reconstructed images (2D-CT and 3D-CT. The purpose of the current study is to assess the precision of linear measurements made in 3D-CT using craniometric patterns for individual identification in Forensic Dentistry. Five cadaver heads were submitted to a spiral computed tomography using axial slices, and 3D-CT reconstructions were obtained by volume rendering technique with computer graphics tools. Ten (10 craniometric measurements were determined in 3D-CT images by two examiners independently, twice each, and the standard error of intra- and inter-examiner measurements was assessed. The results demonstrated a low standard error of those measurements, from 0.85% to 3.09%. In conclusion, the linear measurements obtained in osseous and soft tissue structures were considered to be precise in 3D-CT with high imaging quality and resolution.
Applicability of 3D-CT facial reconstruction for forensic individual identification
Computed tomography (CT) is used in several clinical dentistry applications even by axial slices and two and three-dimensional reconstructed images (2D-CT and 3D-CT). The purpose of the current study is to assess the precision of linear measurements made in 3D-CT using cranio metric patterns for individual identification in Forensic Dentistry. Five cadaver heads were submitted to a spiral computed tomography using axial slices, and 3D-CT reconstructions were obtained by volume rendering technique with computer graphics tools. Ten (10) cranio metric measurements were determined in 3D-CT images by two examiners independently, twice each, and the standard error of intra- and inter-examiner measurements was assessed. The results demonstrated a low standard error of those measurements, from 0.85% to 3.09%. In conclusion, the linear measurements obtained in osseous and soft tissue structures were considered to be precise in 3D-CT with high imaging quality and resolution. (author)
Applicability of 3D-CT facial reconstruction for forensic individual identification
Rocha, Sara dos Santos [Sao Paulo Univ., SP (Brazil). Odontologia Forense; Ramos, Dalton Luiz de Paula [Sao Paulo Univ., SP (Brazil). Dept. of Odontologia Social; Cavalcanti, Marcelo de Gusmao Paraiso [Sao Paulo Univ., SP (Brazil). Dept. de Radiologia
2003-03-01
Computed tomography (CT) is used in several clinical dentistry applications even by axial slices and two and three-dimensional reconstructed images (2D-CT and 3D-CT). The purpose of the current study is to assess the precision of linear measurements made in 3D-CT using cranio metric patterns for individual identification in Forensic Dentistry. Five cadaver heads were submitted to a spiral computed tomography using axial slices, and 3D-CT reconstructions were obtained by volume rendering technique with computer graphics tools. Ten (10) cranio metric measurements were determined in 3D-CT images by two examiners independently, twice each, and the standard error of intra- and inter-examiner measurements was assessed. The results demonstrated a low standard error of those measurements, from 0.85% to 3.09%. In conclusion, the linear measurements obtained in osseous and soft tissue structures were considered to be precise in 3D-CT with high imaging quality and resolution. (author)
Large Scale 3D Image Reconstruction in Optical Interferometry
Schutz, Antony; Mary, David; Thiébaut, Eric; Soulez, Ferréol
2015-01-01
Astronomical optical interferometers (OI) sample the Fourier transform of the intensity distribution of a source at the observation wavelength. Because of rapid atmospheric perturbations, the phases of the complex Fourier samples (visibilities) cannot be directly exploited , and instead linear relationships between the phases are used (phase closures and differential phases). Consequently, specific image reconstruction methods have been devised in the last few decades. Modern polychromatic OI instruments are now paving the way to multiwavelength imaging. This paper presents the derivation of a spatio-spectral ("3D") image reconstruction algorithm called PAINTER (Polychromatic opticAl INTErferometric Reconstruction software). The algorithm is able to solve large scale problems. It relies on an iterative process, which alternates estimation of polychromatic images and of complex visibilities. The complex visibilities are not only estimated from squared moduli and closure phases, but also from differential phase...
3D Reconstruction of Coronary Artery Vascular Smooth Muscle Cells.
Tong Luo
Full Text Available 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.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±14.9 μm, 4.6±0.6 μm and 6.2±1.8 μm (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°.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.
3D temperature field reconstruction using ultrasound sensing system
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.
Nam, Sang Hwa; Park, Jong Yeon; Lee, Young Jun; Kim, Kun Il; Kim, Byung Soo; Wang, Soo Guen [Pusan National University, Busan (Korea, Republic of); Sol, Chang Hyo [Hong-In Total Imaing Diagnostic Clinic, Pusan (Korea, Republic of)
1994-01-15
CT or MRT is performed in preoperative staging of laryngeal cancer. These methods are used in assessment of the deep tissues and cartilage of the larynx, but cannot compete with laryngoscopy in the evaluation of the laryngeal surface. The purpose of this study is to evaluate feasibility and clinical value of the 3-D reconstruction of the mucosal surface in laryngeal cancer. Twenty two patients with laryngeal cancer proved by means of surgical exploration (pathologic) or clinical examinations including laryngoscope, imaging studies and biopsy underwent preoperative staging with computed tomography(CT) and three dimensional(3D) CT reconstruction. The TNM classification of the American Joint Committee on Cancer was used to compare the imaging findings with pathologic or clinical staging. When the extension of primary tumor(T staging) was evaluated, the findings at only transaxial CT and those at pathologic or clinical examination were concordant in 8 of 14 cases(57.1%) of supraglottic tumor, and 3 of 6 cases(50%) of glottic tumor. The overall accuracy of CT with additional 3D-reconstruction was 85.7% for assessment of supraglottic tumor, and 66.6% for glottic tumor. 3D CT reconstruction after transaxial CT may improve outcome in preoperative staging of laryngeal cancer and has a potential value in guiding management decisions.
CT or MRT is performed in preoperative staging of laryngeal cancer. These methods are used in assessment of the deep tissues and cartilage of the larynx, but cannot compete with laryngoscopy in the evaluation of the laryngeal surface. The purpose of this study is to evaluate feasibility and clinical value of the 3-D reconstruction of the mucosal surface in laryngeal cancer. Twenty two patients with laryngeal cancer proved by means of surgical exploration (pathologic) or clinical examinations including laryngoscope, imaging studies and biopsy underwent preoperative staging with computed tomography(CT) and three dimensional(3D) CT reconstruction. The TNM classification of the American Joint Committee on Cancer was used to compare the imaging findings with pathologic or clinical staging. When the extension of primary tumor(T staging) was evaluated, the findings at only transaxial CT and those at pathologic or clinical examination were concordant in 8 of 14 cases(57.1%) of supraglottic tumor, and 3 of 6 cases(50%) of glottic tumor. The overall accuracy of CT with additional 3D-reconstruction was 85.7% for assessment of supraglottic tumor, and 66.6% for glottic tumor. 3D CT reconstruction after transaxial CT may improve outcome in preoperative staging of laryngeal cancer and has a potential value in guiding management decisions
3D artefact for concurrent scale calibration in Computed Tomography
Stolfi, Alessandro; De Chiffre, Leonardo
2016-01-01
A novel artefact for calibration of the scale in 3D X-ray Computed Tomography (CT) is presented. The artefact comprises a carbon fibre tubular structure on which a number of reference ruby spheres are glued. The artefact is positioned and scanned together with the workpiece inside the CT scanner...... providing a reference system for measurement. The artefact allows a considerable reduction of time by compressing the full process of calibration, scanning, measurement, and re-calibration, into a single process. The method allows a considerable reduction of the amount of data generated from CT scanning. A...
3D Cone Beam Volumetric Tomography Dedicated to Maxillofacial Radiology
Masoud Varshosaz
2009-01-01
"nThe 3D cone beam volume/computed tomography (CBVT/CBCT) has been designed for imaging the hard tissues of the maxillofacial region, although it has been used in some era of medical imaging for many years. CBVT is capable of providing a sub-millimeter resolution with the short scanning time of mostly less than 20 seconds and radiation dosages reportedly up to 15 times lower than those of spiral CT scans. In less than a decade, CBVT has revolutionized oral and maxillofacial ra...
One-step reconstruction of assembled 3D holographic scenes
Velez Zea, Alejandro; Barrera-Ramírez, John Fredy; Torroba, Roberto
2015-12-01
We present a new experimental approach for reconstructing in one step 3D scenes otherwise not feasible in a single snapshot from standard off-axis digital hologram architecture, due to a lack of illuminating resources or a limited setup size. Consequently, whenever a scene could not be wholly illuminated or the size of the scene surpasses the available setup disposition, this protocol can be implemented to solve these issues. We need neither to alter the original setup in every step nor to cover the whole scene by the illuminating source, thus saving resources. With this technique we multiplex the processed holograms of actual diffuse objects composing a scene using a two-beam off-axis holographic setup in a Fresnel approach. By registering individually the holograms of several objects and applying a spatial filtering technique, the filtered Fresnel holograms can then be added to produce a compound hologram. The simultaneous reconstruction of all objects is performed in one step using the same recovering procedure employed for single holograms. Using this technique, we were able to reconstruct, for the first time to our knowledge, a scene by multiplexing off-axis holograms of the 3D objects without cross talk. This technique is important for quantitative visualization of optically packaged multiple images and is useful for a wide range of applications. We present experimental results to support the method.
3D reconstruction of porous electrodes and microstructure modelling
Joos, Jochen; Rueger, Bernd; Weber, Andre; Ivers-Tiffee, Ellen [Karlsruher Institute fuer Technologie (KIT), Karlsruhe (DE). Inst. fuer Werkstoffe der Elektrotechnik (IWE); Carraro, Thomas [Heidelberg Univ. (Germany). Inst. fuer Angewandte Mathematik
2010-07-01
The performance of a solid oxide fuel cell (SOFC) is limited by electrode polarisation processes, depending both on material composition and microstructure characteristics. To understand and improve electrode performance, a detailed knowledge of the electrode microstructure is essential. Recent developments in 3D image reconstruction combined with Focused Ion Beam (FIB) and Scanning Electron Microscopy (SEM) techniques proved a way to achieve highly detailed microstructural data. From this data the determination of valuable microstructural parameters is possible. The microstructure is commonly described by parameters as volume/porosity fraction, tortuosity of pores/materal (or: tortuosity of electronic and ionic transport in 2-phase materials), three-phase boundary length (electronic conducting electrodes) or electrode surface area (mixed conducting electrodes). Based on these parameters and with the help of adequate models, the electrode performance can be estimated. It is obvious that the accurateness of the model prediction depends on the quality of the parameters. Different groups reported first trials in the reconstruction of SOFC electrodes by FIB/SEM methods. They all used the reconstruction to calculate microstructural parameters. But nevertheless a lot of questions remain, primarily questions concerning the accuracy of the reconstruction or the minimum size of the volume that has to be reconstructed to obtain meaningful results. In this contribution, a ZEISS 1540XB CrossBeam {sup registered} was used to provide over 700 consecutive images of a porous LSCF (La{sub 0.58}Sr{sub 0.4}CO{sub 0.2.}Fe{sub 0.8}O{sub 3-{delta}})-cathode. The calculation of the key microstructural parameters (i) volume/porosity fraction (ii) electrode surface area and (iii) tortuosity of pores and material from 3D FIB/SEM-data will be presented. Additionally the influence of the reconstruction-volume on the calculated parameters will be discussed. Also the presented technique is
3D Human cartilage surface characterization by optical coherence tomography
Brill, Nicolai; Riedel, Jörn; Schmitt, Robert; Tingart, Markus; Truhn, Daniel; Pufe, Thomas; Jahr, Holger; Nebelung, Sven
2015-10-01
Early diagnosis and treatment of cartilage degeneration is of high clinical interest. Loss of surface integrity is considered one of the earliest and most reliable signs of degeneration, but cannot currently be evaluated objectively. Optical Coherence Tomography (OCT) is an arthroscopically available light-based non-destructive real-time imaging technology that allows imaging at micrometre resolutions to millimetre depths. As OCT-based surface evaluation standards remain to be defined, the present study investigated the diagnostic potential of 3D surface profile parameters in the comprehensive evaluation of cartilage degeneration. To this end, 45 cartilage samples of different degenerative grades were obtained from total knee replacements (2 males, 10 females; mean age 63.8 years), cut to standard size and imaged using a spectral-domain OCT device (Thorlabs, Germany). 3D OCT datasets of 8 × 8, 4 × 4 and 1 × 1 mm (width × length) were obtained and pre-processed (image adjustments, morphological filtering). Subsequent automated surface identification algorithms were used to obtain the 3D primary profiles, which were then filtered and processed using established algorithms employing ISO standards. The 3D surface profile thus obtained was used to calculate a set of 21 3D surface profile parameters, i.e. height (e.g. Sa), functional (e.g. Sk), hybrid (e.g. Sdq) and segmentation-related parameters (e.g. Spd). Samples underwent reference histological assessment according to the Degenerative Joint Disease classification. Statistical analyses included calculation of Spearman’s rho and assessment of inter-group differences using the Kruskal Wallis test. Overall, the majority of 3D surface profile parameters revealed significant degeneration-dependent differences and correlations with the exception of severe end-stage degeneration and were of distinct diagnostic value in the assessment of surface integrity. None of the 3D
Pragmatic fully 3D image reconstruction for the MiCES mouse imaging PET scanner
We present a pragmatic approach to image reconstruction for data from the micro crystal elements system (MiCES) fully 3D mouse imaging positron emission tomography (PET) scanner under construction at the University of Washington. Our approach is modelled on fully 3D image reconstruction used in clinical PET scanners, which is based on Fourier rebinning (FORE) followed by 2D iterative image reconstruction using ordered-subsets expectation-maximization (OSEM). The use of iterative methods allows modelling of physical effects (e.g., statistical noise, detector blurring, attenuation, etc), while FORE accelerates the reconstruction process by reducing the fully 3D data to a stacked set of independent 2D sinograms. Previous investigations have indicated that non-stationary detector point-spread response effects, which are typically ignored for clinical imaging, significantly impact image quality for the MiCES scanner geometry. To model the effect of non-stationary detector blurring (DB) in the FORE+OSEM(DB) algorithm, we have added a factorized system matrix to the ASPIRE reconstruction library. Initial results indicate that the proposed approach produces an improvement in resolution without an undue increase in noise and without a significant increase in the computational burden. The impact on task performance, however, remains to be evaluated
3D TEM reconstruction and segmentation process of laminar bio-nanocomposites
Iturrondobeitia, M., E-mail: maider.iturrondobeitia@ehu.es; Okariz, A.; Fernandez-Martinez, R.; Jimbert, P.; Guraya, T.; Ibarretxe, J. [eMERG, University of the Basque Country, Rafael Moreno Pitxitxi street 2 and 3, 48013, Bilbao (Spain)
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.
Computerized 3-D reconstruction of two "double teeth".
Lyroudia, K; Mikrogeorgis, G; Nikopoulos, N; Samakovitis, G; Molyvdas, I; Pitas, I
1997-10-01
"Double teeth" is a root malformation in the dentition and the purpose of this study was to reconstruct three-dimensionally the external and internal morphology of two "double teeth". The first set of "double teeth" was formed by the conjunction of a mandibular molar and a premolar, and the second by a conjunction of a maxillary molar and a supernumerary tooth. The process of 3-D reconstruction included serial cross-sectioning, photographs of the sections, digitization of the photographs, extraction of the boundaries of interest for each section, surface representation using triangulation and, finally, surface rendering using photorealistic effects. The resulting three-dimensional representations of the two teeth helped us visualize their external and internal anatomy. The results showed: a) in the first case, fusion of the radical and coronal dentin, as well as fusion of the pulp chambers; and b) in the second case, fusion only of the radical dentin and the pulp chambers. PMID:9550051
Towards automated electron holographic tomography for 3D mapping of electrostatic potentials
Electron-holographic tomography (EHT), that is, the combination of off-axis electron holography with electron tomography, was successfully applied for the quantitative 3D mapping of electrostatic potentials at the nanoscale. Here we present the first software package (THOMAS) for semi-automated acquisition of holographic tilt series, a prerequisite for efficient data collection. Using THOMAS, the acquisition time for a holographic tilt series, consisting of object and reference holograms, is reduced by a factor of five on average, compared to the previous, completely manual approaches. Moreover, the existing software packages for retrieving amplitude and phase information from electron holograms have been extended, now including a one-step procedure for holographic tilt series reconstruction. Furthermore, a modified SIRT algorithm (WSIRT) was implemented for the quantitative 3D reconstruction of the electrostatic potential from the aligned phase tilt series. Finally, the application of EHT to a polystyrene latex sphere test-specimen and a pn-doped Ge 'needle'-shaped specimen are presented, illustrating the quantitative character of EHT. For both specimens the mean inner potential (MIP) values were accurately determined from the reconstructed 3D potential. For the Ge specimen, additionally the 'built-in' voltage across the pn junction of 0.5 V was obtained.
3D particle tracking velocimetry using dynamic discrete tomography for plasma physics applications
Moseev, Dmitry; Alpers, Andreas; Gritzmann, Peter;
2013-01-01
3D particle tracking velocimetry (PTV) is a diagnostic technique which is widely used for studying flows, combustion, and plasmas. Current tomographic particle tracking methods are based on the multiplicative algebraic reconstruction technique and used for reconstructing the distribution of multi......-pixel sized particles as greylevel images. Reconstructions obtained by these methods do not necessarily match the experimental data. We propose a new algorithm which can be used for tracking dust particles in tokamaks and stellarators, as well as in low-temperature and complex plasmas. The dynamic discrete...... tomography algorithm is efficient for data from two projection directions and exact. The non-uniqueness can be detected and tracked individually. The algorithm performance is proportional to N3 on average where N is the number of particles in the reconstruction. There is a room for further improvement of the...
4D image reconstruction for emission tomography
An overview of the theory of 4D image reconstruction for emission tomography is given along with a review of the current state of the art, covering both positron emission tomography and single photon emission computed tomography (SPECT). By viewing 4D image reconstruction as a matter of either linear or non-linear parameter estimation for a set of spatiotemporal functions chosen to approximately represent the radiotracer distribution, the areas of so-called ‘fully 4D’ image reconstruction and ‘direct kinetic parameter estimation’ are unified within a common framework. Many choices of linear and non-linear parameterization of these functions are considered (including the important case where the parameters have direct biological meaning), along with a review of the algorithms which are able to estimate these often non-linear parameters from emission tomography data. The other crucial components to image reconstruction (the objective function, the system model and the raw data format) are also covered, but in less detail due to the relatively straightforward extension from their corresponding components in conventional 3D image reconstruction. The key unifying concept is that maximum likelihood or maximum a posteriori (MAP) estimation of either linear or non-linear model parameters can be achieved in image space after carrying out a conventional expectation maximization (EM) update of the dynamic image series, using a Kullback-Leibler distance metric (comparing the modeled image values with the EM image values), to optimize the desired parameters. For MAP, an image-space penalty for regularization purposes is required. The benefits of 4D and direct reconstruction reported in the literature are reviewed, and furthermore demonstrated with simple simulation examples. It is clear that the future of reconstructing dynamic or functional emission tomography images, which often exhibit high levels of spatially correlated noise, should ideally exploit these 4D
Optimized 3D Street Scene Reconstruction from Driving Recorder Images
Yongjun Zhang
2015-07-01
Full Text Available The paper presents an automatic region detection based method to reconstruct street scenes from driving recorder images. The driving recorder in this paper is a dashboard camera that collects images while the motor vehicle is moving. An enormous number of moving vehicles are included in the collected data because the typical recorders are often mounted in the front of moving vehicles and face the forward direction, which can make matching points on vehicles and guardrails unreliable. Believing that utilizing these image data can reduce street scene reconstruction and updating costs because of their low price, wide use, and extensive shooting coverage, we therefore proposed a new method, which is called the Mask automatic detecting method, to improve the structure results from the motion reconstruction. Note that we define vehicle and guardrail regions as “mask” in this paper since the features on them should be masked out to avoid poor matches. After removing the feature points in our new method, the camera poses and sparse 3D points that are reconstructed with the remaining matches. Our contrast experiments with the typical pipeline of structure from motion (SfM reconstruction methods, such as Photosynth and VisualSFM, demonstrated that the Mask decreased the root-mean-square error (RMSE of the pairwise matching results, which led to more accurate recovering results from the camera-relative poses. Removing features from the Mask also increased the accuracy of point clouds by nearly 30%–40% and corrected the problems of the typical methods on repeatedly reconstructing several buildings when there was only one target building.
3D Coronal Density Reconstruction and Retrieving the Magnetic Field Structure during Solar Minimum
Kramar, M; Mikić, Z; Davila, J
2014-01-01
Measurement of the coronal magnetic field is a crucial ingredient in understanding the nature of solar coronal phenomena at all scales. We employed STEREO/COR1 data obtained during a deep minimum of solar activity in February 2008 (Carrington rotation CR 2066) to retrieve and analyze the three-dimensional (3D) coronal electron density in the range of heights from 1.5 to 4 Rsun using a tomography method. With this, we qualitatively deduced structures of the coronal magnetic field. The 3D electron density analysis is complemented by the 3D STEREO/EUVI emissivity in the 195 A band obtained by tomography for the same CR. A global 3D MHD model of the solar corona was used to relate the reconstructed 3D density and emissivity to open/closed magnetic field structures. We show that the density maximum locations can serve as an indicator of current sheet position, while the locations of the density gradient maximum can be a reliable indicator of coronal hole boundaries. We find that the magnetic field configuration du...
3D Reconstruction of virtual colon structures from colonoscopy images.
Hong, DongHo; Tavanapong, Wallapak; Wong, Johnny; Oh, JungHwan; de Groen, Piet C
2014-01-01
This paper presents the first fully automated reconstruction technique of 3D virtual colon segments from individual colonoscopy images. It is the basis of new software applications that may offer great benefits for improving quality of care for colonoscopy patients. For example, a 3D map of the areas inspected and uninspected during colonoscopy can be shown on request of the endoscopist during the procedure. The endoscopist may revisit the suggested uninspected areas to reduce the chance of missing polyps that reside in these areas. The percentage of the colon surface seen by the endoscopist can be used as a coarse objective indicator of the quality of the procedure. The derived virtual colon models can be stored for post-procedure training of new endoscopists to teach navigation techniques that result in a higher level of procedure quality. Our technique does not require a prior CT scan of the colon or any global positioning device. Our experiments on endoscopy images of an Olympus synthetic colon model reveal encouraging results with small average reconstruction errors (4.1 mm for the fold depths and 12.1 mm for the fold circumferences). PMID:24225230
Digital 3D facial reconstruction of George Washington
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.
Fast vision-based catheter 3D reconstruction
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.
3D Reconstruction of Irregular Buildings and Buddha Statues
Zhang, K.; Li, M.-j.
2014-04-01
Three-dimensional laser scanning could acquire object's surface data quickly and accurately. However, the post-processing of point cloud is not perfect and could be improved. Based on the study of 3D laser scanning technology, this paper describes the details of solutions to modelling irregular ancient buildings and Buddha statues in Jinshan Temple, which aiming at data acquisition, modelling and texture mapping, etc. In order to modelling irregular ancient buildings effectively, the structure of each building is extracted manually by point cloud and the textures are mapped by the software of 3ds Max. The methods clearly combine 3D laser scanning technology with traditional modelling methods, and greatly improves the efficiency and accuracy of the ancient buildings restored. On the other hand, the main idea of modelling statues is regarded as modelling objects in reverse engineering. The digital model of statues obtained is not just vivid, but also accurate in the field of surveying and mapping. On this basis, a 3D scene of Jinshan Temple is reconstructed, which proves the validity of the solutions.
Accuracy assessment of 3D bone reconstructions using CT: an intro comparison.
Lalone, Emily A; Willing, Ryan T; Shannon, Hannah L; King, Graham J W; Johnson, James A
2015-08-01
Computed tomography provides high contrast imaging of the joint anatomy and is used routinely to reconstruct 3D models of the osseous and cartilage geometry (CT arthrography) for use in the design of orthopedic implants, for computer assisted surgeries and computational dynamic and structural analysis. The objective of this study was to assess the accuracy of bone and cartilage surface model reconstructions by comparing reconstructed geometries with bone digitizations obtained using an optical tracking system. Bone surface digitizations obtained in this study determined the ground truth measure for the underlying geometry. We evaluated the use of a commercially available reconstruction technique using clinical CT scanning protocols using the elbow joint as an example of a surface with complex geometry. To assess the accuracies of the reconstructed models (8 fresh frozen cadaveric specimens) against the ground truth bony digitization-as defined by this study-proximity mapping was used to calculate residual error. The overall mean error was less than 0.4 mm in the cortical region and 0.3 mm in the subchondral region of the bone. Similarly creating 3D cartilage surface models from CT scans using air contrast had a mean error of less than 0.3 mm. Results from this study indicate that clinical CT scanning protocols and commonly used and commercially available reconstruction algorithms can create models which accurately represent the true geometry. PMID:26037323
3D RECONSTRUCTION FROM MULTI-VIEW MEDICAL X-RAY IMAGES – REVIEW AND EVALUATION OF EXISTING METHODS
S. Hosseinian
2015-12-01
Full Text Available The 3D concept is extremely important in clinical studies of human body. Accurate 3D models of bony structures are currently required in clinical routine for diagnosis, patient follow-up, surgical planning, computer assisted surgery and biomechanical applications. However, 3D conventional medical imaging techniques such as computed tomography (CT scan and magnetic resonance imaging (MRI have serious limitations such as using in non-weight-bearing positions, costs and high radiation dose(for CT. Therefore, 3D reconstruction methods from biplanar X-ray images have been taken into consideration as reliable alternative methods in order to achieve accurate 3D models with low dose radiation in weight-bearing positions. Different methods have been offered for 3D reconstruction from X-ray images using photogrammetry which should be assessed. In this paper, after demonstrating the principles of 3D reconstruction from X-ray images, different existing methods of 3D reconstruction of bony structures from radiographs are classified and evaluated with various metrics and their advantages and disadvantages are mentioned. Finally, a comparison has been done on the presented methods with respect to several metrics such as accuracy, reconstruction time and their applications. With regards to the research, each method has several advantages and disadvantages which should be considered for a specific application.
Block matching 3D random noise filtering for absorption optical projection tomography
Fumene Feruglio, P; Vinegoni, C; Weissleder, R [Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, 185 Cambridge Street, Boston, MA 02114 (United States); Gros, J [Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston MA 02115 (United States); Sbarbati, A, E-mail: cvinegoni@mgh.harvard.ed [Department of Morphological and Biomedical Sciences, University of Verona, Strada Le Grazie 8, 37134 Verona (Italy)
2010-09-21
Absorption and emission optical projection tomography (OPT), alternatively referred to as optical computed tomography (optical-CT) and optical-emission computed tomography (optical-ECT), are recently developed three-dimensional imaging techniques with value for developmental biology and ex vivo gene expression studies. The techniques' principles are similar to the ones used for x-ray computed tomography and are based on the approximation of negligible light scattering in optically cleared samples. The optical clearing is achieved by a chemical procedure which aims at substituting the cellular fluids within the sample with a cell membranes' index matching solution. Once cleared the sample presents very low scattering and is then illuminated with a light collimated beam whose intensity is captured in transillumination mode by a CCD camera. Different projection images of the sample are subsequently obtained over a 360{sup 0} full rotation, and a standard backprojection algorithm can be used in a similar fashion as for x-ray tomography in order to obtain absorption maps. Because not all biological samples present significant absorption contrast, it is not always possible to obtain projections with a good signal-to-noise ratio, a condition necessary to achieve high-quality tomographic reconstructions. Such is the case for example, for early stage's embryos. In this work we demonstrate how, through the use of a random noise removal algorithm, the image quality of the reconstructions can be considerably improved even when the noise is strongly present in the acquired projections. Specifically, we implemented a block matching 3D (BM3D) filter applying it separately on each acquired transillumination projection before performing a complete three-dimensional tomographical reconstruction. To test the efficiency of the adopted filtering scheme, a phantom and a real biological sample were processed. In both cases, the BM3D filter led to a signal-to-noise ratio
de Boer, B. A.; Soufan, A. T.; Hagoort, J.; Mohun, T. J.; van den Hoff, M. J. B.; Hasman, A.; Voorbraak, F. P. J. M.; Moorman, A. F. M.; Ruijter, J.M.
2011-01-01
Interpretation of the results of anatomical and embryological studies relies heavily on proper visualization of complex morphogenetic processes and patterns of gene expression in a three-dimensional (3D) context. However, reconstruction of complete 3D datasets is time consuming and often researchers study only a few sections. To help in understanding the resulting 2D data we developed a program (TRACTS) that places such arbitrary histological sections into a high-resolution 3D model of the de...
B.A. de Boer; A.T. Soufan; J. Hagoort; T.J. Mohun; M.J.B. van den Hoff; A. Hasman; F.P.J.M. Voorbraak; A.F.M. Moorman; J.M. Ruijter
2011-01-01
Interpretation of the results of anatomical and embryological studies relies heavily on proper visualization of complex morphogenetic processes and patterns of gene expression in a three-dimensional (3D) context. However, reconstruction of complete 3D datasets is time consuming and often researchers
3-D waveform tomography sensitivity kernels for anisotropic media
Djebbi, R.
2014-01-01
The complications in anisotropic multi-parameter inversion lie in the trade-off between the different anisotropy parameters. We compute the tomographic waveform sensitivity kernels for a VTI acoustic medium perturbation as a tool to investigate this ambiguity between the different parameters. We use dynamic ray tracing to efficiently handle the expensive computational cost for 3-D anisotropic models. Ray tracing provides also the ray direction information necessary for conditioning the sensitivity kernels to handle anisotropy. The NMO velocity and η parameter kernels showed a maximum sensitivity for diving waves which results in a relevant choice of those parameters in wave equation tomography. The δ parameter kernel showed zero sensitivity; therefore it can serve as a secondary parameter to fit the amplitude in the acoustic anisotropic inversion. Considering the limited penetration depth of diving waves, migration velocity analysis based kernels are introduced to fix the depth ambiguity with reflections and compute sensitivity maps in the deeper parts of the model.
New solutions and applications of 3D computer tomography image processing
Effenberger, Ira; Kroll, Julia; Verl, Alexander
2008-02-01
As nowadays the industry aims at fast and high quality product development and manufacturing processes a modern and efficient quality inspection is essential. Compared to conventional measurement technologies, industrial computer tomography (CT) is a non-destructive technology for 3D-image data acquisition which helps to overcome their disadvantages by offering the possibility to scan complex parts with all outer and inner geometric features. In this paper new and optimized methods for 3D image processing, including innovative ways of surface reconstruction and automatic geometric feature detection of complex components, are presented, especially our work of developing smart online data processing and data handling methods, with an integrated intelligent online mesh reduction. Hereby the processing of huge and high resolution data sets is guaranteed. Besides, new approaches for surface reconstruction and segmentation based on statistical methods are demonstrated. On the extracted 3D point cloud or surface triangulation automated and precise algorithms for geometric inspection are deployed. All algorithms are applied to different real data sets generated by computer tomography in order to demonstrate the capabilities of the new tools. Since CT is an emerging technology for non-destructive testing and inspection more and more industrial application fields will use and profit from this new technology.
Test of 3D CT reconstructions by EM + TV algorithm from undersampled data
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 128×128×128 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.
Test of 3D CT reconstructions by EM + TV algorithm from undersampled data
Evseev, Ivan; Ahmann, Francielle; Silva, Hamilton P. da [Universidade Tecnologica Federal do Parana - UTFPR/FB, 85601-970, Caixa Postal 135, Francisco Beltrao - PR (Brazil); Schelin, Hugo R. [Universidade Tecnologica Federal do Parana-UTFPR/FB,85601-970,Caixa Postal 135,Francisco Beltrao-PR (Brazil) and Faculdades Pequeno Principe-FPP, Av. Iguacu, 333, Rebou (Brazil); Yevseyeva, Olga [Universidade Federal de Santa Catarina - UFSC/ARA, 88900-000, Rua Pedro Joao Pereira, 150, Ararangua - SC (Brazil); Klock, Margio C. L. [Universidade Federal do Parana - UFPR Litoral, 80230-901, Rua Jaguaraiva 512, Caioba, Matinhos - PR (Brazil)
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.
Sara dos Santos Rocha; Dalton Luiz de Paula Ramos; Marcelo Gusmão Paraíso Cavalcanti
2003-01-01
Computed tomography (CT) is used in several clinical dentistry applications even by axial slices and two and three-dimensional reconstructed images (2D-CT and 3D-CT). The purpose of the current study is to assess the precision of linear measurements made in 3D-CT using craniometric patterns for individual identification in Forensic Dentistry. Five cadaver heads were submitted to a spiral computed tomography using axial slices, and 3D-CT reconstructions were obtained by volume rendering techni...
The new CORIMP CME catalog & 3D reconstructions
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.
Inclusion of high resolution MODIS maps on a 3D tropospheric water vapor GPS tomography model
Benevides, Pedro; Catalao, Joao; Nico, Giovanni; Miranda, Pedro M. A.
2015-10-01
Observing the water vapor distribution on the troposphere remains a challenge for the weather forecast. Radiosondes provide precise water vapor profiles of the troposphere, but lack geographical and temporal coverage, while satellite meteorological maps have good spatial resolution but even poorer temporal resolution. GPS has proved its capacity to measure the integrated water vapor in all weather conditions with high temporal sampling frequency. However these measurements lack a vertical water vapor discretization. Reconstruction of the slant path GPS observation to the satellite allows oblique water vapor measurements. Implementation of a 3D grid of voxels along the troposphere over an area where GPS stations are available enables the observation ray tracing. A relation between the water vapor density and the distanced traveled inside the voxels is established, defining GPS tomography. An inverse problem formulation is needed to obtain a water vapor solution. The combination of precipitable water vapor (PWV) maps obtained from MODIS satellite data with the GPS tomography is performed in this work. The MODIS PWV maps can have 1 or 5 km pixel resolution, being obtained 2 times per day in the same location at most. The inclusion of MODIS PWV maps provides an enhanced horizontal resolution for the tomographic solution and benefits the stability of the inversion problem. A 3D tomographic grid was adjusted over a regional area covering Lisbon, Portugal, where a GNSS network of 9 receivers is available. Radiosonde measurements in the area are used to evaluate the 3D water vapor tomography maps.
Neurofunctional systems. 3D reconstructions with correlated neuroimaging
This book introduces, for the first time, computer-generated images of the neurofunctional systems of the human brain. These images are more accurate than drawings. The main views presented are of the medial lemniscus system, auditory system, visual system, basal ganglia, corticospinal system, and the limbic system. The arteries and sulci of the cerebral hemispheres are also illustrated by computer. These images provide a three-dimensional orientation of the intracranial space and help, for example, to assess vascular functional disturbance of the brain. Clinicians will find these images valuable for the spatial interpretation of magnetic resonance (MR), computed tomography (CT), and positron emission tomography (PET) images since many neurofunctional systems cannot be visualized as isolated structures in neuroimaging. Computer-assisted surface reconstructions of the neurofunctional systems and the cerebral arteries serve as a basis for constructing these computer-generated images. The surface reconstructions are anatomically realistic having been created from brain sections with minimal deformations. The method of computer graphics, known as ray tracing, produces digital images form these reconstructions. The computer-generated methods are explained. The computer-generated images are accompanied by illustrations and texts on neuroanatomy and clinical practice. The neurofunctional systems of the human brain are also shown in sections so that the reader can mentally reconstruct the neurofunctional systems, thus facilitating the transformation of information into textbooks and atlantes of MR and CT imaging. The aim of this book is acquaint the reader with the three-dimensional aspects of the neurofunctional systems and the cerebral arteries of the human brain using methods of computer graphics. Computer scientists and those interested in this technique are provided with basic neuroanatomic and neurofunctional information. Physicians will have a clearer understanding
New X-Ray Tomography Method Based on the 3D Radon Transform Compatible with Anisotropic Sources
Vassholz, M.; Koberstein-Schwarz, B.; Ruhlandt, A.; Krenkel, M.; Salditt, T.
2016-02-01
In this work, we propose a novel computed tomography (CT) approach for three-dimensional (3D) object reconstruction, based on a generalized tomographic geometry with two-dimensional angular sampling (two angular degrees of freedom). The reconstruction is based on the 3D radon transform and is compatible with anisotropic beam conditions. This allows isotropic 3D imaging with a source, which can be extended along one direction for increased flux, while high resolution is achieved by a small source size only in the orthogonal direction. This novel scheme for analytical CT is demonstrated by numerical simulations and proof-of-concept experiments. In this way high resolution and coherence along a single direction determines the reconstruction quality of the entire 3D data set, opening up, for example, new opportunities to achieve nanoscale resolution and/or phase contrast with low brilliance sources such as laboratory x-ray or neutron sources.
Gene Electrotransfer in 3D Reconstructed Human Dermal Tissue.
Madi, Moinecha; Rols, Marie-Pierre; Gibot, Laure
2016-01-01
Gene electrotransfer into the skin is of particular interest for the development of medical applications including DNA vaccination, cancer treatment, wound healing or treatment of local skin disorders. However, such clinical applications are currently limited due to poor understanding of the mechanisms governing DNA electrotransfer within human tissue. Nowadays, most studies are carried out in rodent models but rodent skin varies from human skin in terms of cell composition and architecture. We used a tissue-engineering approach to study gene electrotransfer mechanisms in a human tissue context. Primary human dermal fibroblasts were cultured according to the self-assembly method to produce 3D reconstructed human dermal tissue. In this study, we showed that cells of the reconstructed cutaneous tissue were efficiently electropermeabilized by applying millisecond electric pulses, without affecting their viability. A reporter gene was successfully electrotransferred into this human tissue and gene expression was detected for up to 48h. Interestingly, the transfected cells were solely located on the upper surface of the tissue, where they were in close contact with plasmid DNA solution. Furthermore, we report evidences that electrotransfection success depends on plasmid mobility within tissue- rich in collagens, but not on cell proliferation status. In conclusion, in addition to proposing a reliable alternative to animal experiments, tissue engineering produces valid biological tool for the in vitro study of gene electrotransfer mechanisms in human tissue. PMID:27029947
3D virtual reconstruction of the Pleistocene cheetah skull from the Tangshan, Nanjing, China
DONG Wei; HOU Xinwen; LIU Jinyi; FANG Yingsan; JIN Changzhu; ZHU Qizhi
2007-01-01
The development of computer tomography and image processing has made it possible to establish virtual 3D reconstruction and non-invasive dissection of fossil specimens. We used these methods to reconstruct a virtual 3D skull of a Pleistocene cheetah skull from the Tuozi cave, Tangshan, Nanjing, and virtually dissected it for anatomic studies, and measured the volumes of different parts of the endocranium. The endocranium of the cheetah skull has showed that its frontal sinus is beehive-like, the frontal lobe of cerebra is relatively large but the temporal lobe is relatively small, its cerebral sulcus and gyrus are more complicated than those of the domestic cat, similar to those of the domestic dog, but simpler than those of giant panda, pig, cattle and horse. The technology of virtual 3D reconstruction and non-invasive dissection of fossil specimens can extend the morphological study from the exterior to the interior, and it can also help to study fragile specimens and virtually backup rare and precious specimens.
A fast rebinning algorithm for 3D positron emission tomography using John's equation
Defrise, Michel; Liu, Xuan
1999-08-01
Volume imaging in positron emission tomography (PET) requires the inversion of the three-dimensional (3D) x-ray transform. The usual solution to this problem is based on 3D filtered-backprojection (FBP), but is slow. Alternative methods have been proposed which factor the 3D data into independent 2D data sets corresponding to the 2D Radon transforms of a stack of parallel slices. Each slice is then reconstructed using 2D FBP. These so-called rebinning methods are numerically efficient but are approximate. In this paper a new exact rebinning method is derived by exploiting the fact that the 3D x-ray transform of a function is the solution to the second-order partial differential equation first studied by John. The method is proposed for two sampling schemes, one corresponding to a pair of infinite plane detectors and another one corresponding to a cylindrical multi-ring PET scanner. The new FORE-J algorithm has been implemented for this latter geometry and was compared with the approximate Fourier rebinning algorithm FORE and with another exact rebinning algorithm, FOREX. Results with simulated data demonstrate a significant improvement in accuracy compared to FORE, while the reconstruction time is doubled. Compared to FOREX, the FORE-J algorithm is slightly less accurate but more than three times faster.
Advanced reconstruction algorithms for electron tomography: From comparison to combination
Goris, B. [EMAT, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp (Belgium); Roelandts, T. [Vision Lab, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk (Belgium); Batenburg, K.J. [Vision Lab, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk (Belgium); Centrum Wiskunde and Informatica, Science Park 123, NL-1098XG Amsterdam (Netherlands); Heidari Mezerji, H. [EMAT, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp (Belgium); Bals, S., E-mail: sara.bals@ua.ac.be [EMAT, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp (Belgium)
2013-04-15
In this work, the simultaneous iterative reconstruction technique (SIRT), the total variation minimization (TVM) reconstruction technique and the discrete algebraic reconstruction technique (DART) for electron tomography are compared and the advantages and disadvantages are discussed. Furthermore, we describe how the result of a three dimensional (3D) reconstruction based on TVM can provide objective information that is needed as the input for a DART reconstruction. This approach results in a tomographic reconstruction of which the segmentation is carried out in an objective manner. - Highlights: ► A comparative study between different reconstruction algorithms for tomography is performed. ► Reconstruction algorithms that uses prior knowledge about the specimen have a superior result. ► One reconstruction algorithm can provide the prior knowledge for a second algorithm.
3-D Reconstruction of Medical Image Using Wavelet Transform and Snake Model
Jinyong Cheng
2009-12-01
Full Text Available Medical image segmentation is an important step in 3-D reconstruction, and 3-D reconstruction from medical images is an important application of computer graphics and biomedicine image processing. An improved image segmentation method which is suitable for 3-D reconstruction is presented in this paper. A 3-D reconstruction algorithm is used to reconstruct the 3-D model from medical images. Rough edge is obtained by multi-scale wavelet transform at first. With the rough edge, improved gradient vector flow snake model is used and the object contour in the image is found. In the experiments, we reconstruct 3-D models of kidney, liver and brain putamen. The performances of the experiments indicate that the new algorithm can produce accurate 3-D reconstruction.
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.
Diachronic 3d Reconstruction for Lost Cultural Heritage
Guidi, G.; Russo, M.
2011-09-01
Cultural Heritage artifacts can often be underestimated for their hidden presence in the landscape. Such problem is particularly large in countries like Italy, where the massive amount of "famous" artifacts tends to neglect other presences unless properly exposed, or when the remains are dramatically damaged leaving very few interpretation clues to the visitor. In such cases a virtual presentation of the Cultural Heritage site can be of great help, specially for explaining the evolution of its status, giving sometimes sense to few spare stones. The definition of these digital representations deal with two crucial aspects: on the one hand the possibility of 3D surveying the relics in order to have an accurate geometrical image of the current status of the artifact; on the other hand the presence of historical sources both in form of written text or images, that once properly matched with the current geometrical data, may help to recreate digitally a set of 3D models representing visually the various historical phases (diachronic model), up to the current one. The core of this article is the definition of an integrated methodology that starts from an high-resolution digital survey of the remains of an ancient building and develops a coherent virtual reconstruction from different historical sources, suggesting a scalable method suitable to be re-used for generating a 4D (geometry + time) model of the artifact. This approach has been experimented on the "Basilica di San Giovanni in Conca" in Milan, a very significant example for its complex historic evolution that combines evident historic values with an invisible presence inside the city.
DIACHRONIC 3D RECONSTRUCTION FOR LOST CULTURAL HERITAGE
G. Guidi
2012-09-01
Full Text Available Cultural Heritage artifacts can often be underestimated for their hidden presence in the landscape. Such problem is particularly large in countries like Italy, where the massive amount of "famous" artifacts tends to neglect other presences unless properly exposed, or when the remains are dramatically damaged leaving very few interpretation clues to the visitor. In such cases a virtual presentation of the Cultural Heritage site can be of great help, specially for explaining the evolution of its status, giving sometimes sense to few spare stones. The definition of these digital representations deal with two crucial aspects: on the one hand the possibility of 3D surveying the relics in order to have an accurate geometrical image of the current status of the artifact; on the other hand the presence of historical sources both in form of written text or images, that once properly matched with the current geometrical data, may help to recreate digitally a set of 3D models representing visually the various historical phases (diachronic model, up to the current one. The core of this article is the definition of an integrated methodology that starts from an high-resolution digital survey of the remains of an ancient building and develops a coherent virtual reconstruction from different historical sources, suggesting a scalable method suitable to be re-used for generating a 4D (geometry + time model of the artifact. This approach has been experimented on the "Basilica di San Giovanni in Conca" in Milan, a very significant example for its complex historic evolution that combines evident historic values with an invisible presence inside the city.
Samir Kumta
2015-01-01
Full Text Available 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.
Lazaro, D
2003-10-01
Monte Carlo simulations are currently considered in nuclear medical imaging as a powerful tool to design and optimize detection systems, and also to assess reconstruction algorithms and correction methods for degrading physical effects. Among the many simulators available, none of them is considered as a standard in nuclear medical imaging: this fact has motivated the development of a new generic Monte Carlo simulation platform (GATE), based on GEANT4 and dedicated to SPECT/PET (single photo emission computed tomography / positron emission tomography) applications. We participated during this thesis to the development of the GATE platform within an international collaboration. GATE was validated in SPECT by modeling two gamma cameras characterized by a different geometry, one dedicated to small animal imaging and the other used in a clinical context (Philips AXIS), and by comparing the results obtained with GATE simulations with experimental data. The simulation results reproduce accurately the measured performances of both gamma cameras. The GATE platform was then used to develop a new 3-dimensional reconstruction method: F3DMC (fully 3-dimension Monte-Carlo) which consists in computing with Monte Carlo simulation the transition matrix used in an iterative reconstruction algorithm (in this case, ML-EM), including within the transition matrix the main physical effects degrading the image formation process. The results obtained with the F3DMC method were compared to the results obtained with three other more conventional methods (FBP, MLEM, MLEMC) for different phantoms. The results of this study show that F3DMC allows to improve the reconstruction efficiency, the spatial resolution and the signal to noise ratio with a satisfactory quantification of the images. These results should be confirmed by performing clinical experiments and open the door to a unified reconstruction method, which could be applied in SPECT but also in PET. (author)
Reconstruction tomography from incomplete projections
In some instances, reconstruction radionuclide tomography must be carried out from projections that do not include projection values for all portions of the object to be reconstructed. This may occur, for example, when the field of view of the detector is limited, or when an opaque foreign body is present within the object. The effects of such incomplete projections upon reconstructions of computer-simulated phantoms were studied, using iterative and convolution methods. Several methods for reducing the resulting artifacts and inaccuracies are discussed
Matysik P.
2015-12-01
Full Text Available In this paper the possibility of using X-ray computed tomography (CT in quantitative metallographic studies of homogeneous and composite materials is presented. Samples of spheroidal cast iron, Fe-Ti powder mixture compact and epoxy composite reinforced with glass fibers, were subjected to comparative structural tests. Volume fractions of each of the phase structure components were determined by conventional methods with the use of a scanning electron microscopy (SEM and X-ray diffraction (XRD quantitative analysis methods. These results were compared with those obtained by the method of spatial analysis of the reconstructed CT image. Based on the comparative analysis, taking into account the selectivity of data verification methods and the accuracy of the obtained results, the authors conclude that the method of computed tomography is suitable for quantitative analysis of several types of structural materials.
3D Cone Beam Volumetric Tomography Dedicated to Maxillofacial Radiology
Masoud Varshosaz
2009-01-01
Full Text Available "nThe 3D cone beam volume/computed tomography (CBVT/CBCT has been designed for imaging the hard tissues of the maxillofacial region, although it has been used in some era of medical imaging for many years. CBVT is capable of providing a sub-millimeter resolution with the short scanning time of mostly less than 20 seconds and radiation dosages reportedly up to 15 times lower than those of spiral CT scans. In less than a decade, CBVT has revolutionized oral and maxillofacial radiology and is known as the “Standard of Care”. Although development was initially directed towards multiplanar viewing for dental implant and orthodontic treatment planning, secondary applications in other areas continue to expand such as maxillo-facial trauma, temporomandibular joint disorders, sinuse pathosis and upper airway evaluation. The intent of this presentation is to provide an overview of CBVT technology, advantages and disadvantages compared to the other modalities such as 2D images and medical CT and examples of justified cases in the oral & maxillofacial region.
FIT3D Toolbox : multiple view geometry and 3D reconstruction for MATLAB
Esteban, I.; Dijk, J.; Groen, F.
2010-01-01
FIT3D is a Toolbox built for Matlab that aims at unifying and distributing a set of tools that will allow the researcher to obtain a complete 3D model from a set of calibrated images. In this paper we motivate and present the structure of the toolbox in a tutorial and example based approach. Given i
A LabVIEW based user-friendly nano-CT image alignment and 3D reconstruction platform
Wang, Shenghao; Wang, Zhili; Gao, Kun; Wu, Zhao; Zhu, Peiping; Wu, Ziyu
2014-01-01
X-ray nanometer computed tomography (nano-CT) offers applications and opportunities in many scientific researches and industrial areas. Here we present a user-friendly and fast LabVIEW based package running, after acquisition of the raw projection images, a procedure to obtain the inner structure of the sample under analysis. At first, a reliable image alignment procedure fixes possible misalignments among image series due to mechanical errors, thermal expansion and other external contributions, then a novel fast parallel beam 3D reconstruction performs the tomographic reconstruction. The remarkable improved reconstruction after the image calibration confirms the fundamental role of the image alignment procedure. It minimizes blurring and additional streaking artifacts present in a reconstructed slice that cause loss of information and faked structures in the observed material. The nano-CT image alignment and 3D reconstruction LabVIEW package significantly reducing the data process, makes faster and easier th...
A Method for Interactive 3D Reconstruction of Piecewise Planar Objects from Single Images
Sturm, Peter; Maybank, Steve
1999-01-01
We present an approach for 3D reconstruction of objects from a single image. Obviously, constraints on the 3D structure are needed to perform this task. Our approach is based on user-provided coplanarity, perpendicularity and parallelism constraints. These are used to calibrate the image and perform 3D reconstruction. The method is described in detail and results are provided.
Wolf, Daniel; Lubk, Axel; Prete, Paola; Lovergine, Nico; Lichte, Hannes
2016-09-01
Off-axis electron holography (EH) is a powerful method for mapping projected electric potentials, such as built-in potentials in semiconductor devices, in two dimensions (2D) at nanometer resolution. However, not well-defined thickness profiles, surface effects, and composition changes of the sample under investigation complicate the interpretation of the projected potentials. Here, we demonstrate how these problems can be overcome by combining EH with tomographic techniques, that is, electron holographic tomography (EHT), reconstructing electric potentials in 3D. We present EHT reconstructions of an n-type MOSFET including its dopant-related built-in potentials inside the device, as well as of a GaAs/AlGaAs core-multishell nanowire containing a 5 nm thick quantum well tube.
Maxillary sinus 3D segmentation and reconstruction from cone beam CT data sets
Purpose: Segmentation of the maxillary sinuses for three-dimensional (3D) reconstruction, visualization and volumetry is sought using an automated algorithm applied to cone beam computed tomographic (CBCT) data sets. Materials and methods: Cone beam computed tomography (CBCT) data sets of three subjects aged 9, 17, and 27 were used in 3D segmentation and reconstruction. The maxillary sinuses were obtained by propagation from one start point in the right sinus and one start point in the left sinus to the whole regions of both sinuses. The procedure was based on voxel intensity distributions and common anatomic structures, specifically each middle meatus of the nasal cavity. A program was written in C++ and VTK languages to demonstrate the surface topological shapes of the maxillary sinuses. Results: The developed segmentation algorithm separated maxillary sinuses successfully permitting accurate comparisons. It was robust and efficient. 3D morphological features of the maxillary sinuses were observed from three human subjects. Conclusions: Automated segmentation of maxillary sinuses from CBCT data sets is feasible using the proposed method. This tool might be useful for visualization, pathological diagnosis, and treatment planning of maxillary sinus disorders. (orig.)
Reconstructing 3-D skin surface motion for the DIET breast cancer screening system.
Botterill, Tom; Lotz, Thomas; Kashif, Amer; Chase, J Geoffrey
2014-05-01
Digital image-based elasto-tomography (DIET) is a prototype system for breast cancer screening. A breast is imaged while being vibrated, and the observed surface motion is used to infer the internal stiffness of the breast, hence identifying tumors. This paper describes a computer vision system for accurately measuring 3-D surface motion. A model-based segmentation is used to identify the profile of the breast in each image, and the 3-D surface is reconstructed by fitting a model to the profiles. The surface motion is measured using a modern optical flow implementation customized to the application, then trajectories of points on the 3-D surface are given by fusing the optical flow with the reconstructed surfaces. On data from human trials, the system is shown to exceed the performance of an earlier marker-based system at tracking skin surface motion. We demonstrate that the system can detect a 10 mm tumor in a silicone phantom breast. PMID:24770915
MicroPET is a low-cost, high-resolution positron emission tomography (PET) scanner designed for imaging small animals. MicroPET operates exclusively without septa, acquiring fully three-dimensional (3-D) data sets. The performance of the projection-reprojection (3DRP), variable axial rebinning (VARB), single slice rebinning (SSRB), and Fourier rebinning (FORE) methods for reconstruction of microPET data were evaluated. The algorithms were compared with respect to resolution, noise variance, and reconstruction time. Results suggested that the 3DRP algorithm gives the best combination of resolution and noise performance in 9 min of reconstruction time on a Sun UltraSparc I workstation. The FORE algorithm provided the most acceptable accelerated method of reconstruction, giving similar resolution performance with a 10%--20% degradation in noise variance in under 2 min. Significant degradation in the axial resolution was measured with the VARB and SSRB methods, offsetting the decrease in reconstruction time achieved with those methods. In-plane angular mashing of the 3-D data before reconstruct ion led to a 50% reduction in reconstruction time but also introduced unacceptable tangential blurring artifacts. This thorough evaluation of analytical 3-D reconstruction techniques allowed for optimal selection of a reconstruction method for the diverse range of microPET applications
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® 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
Poulin, Eric; Racine, Emmanuel; Beaulieu, Luc, E-mail: Luc.Beaulieu@phy.ulaval.ca [Département de physique, de génie physique et d’optique et Centre de recherche sur le cancer de l’Université Laval, Université Laval, Québec, Québec G1V 0A6, Canada and Département de radio-oncologie et Axe Oncologie du Centre de recherche du CHU de Québec, CHU de Québec, 11 Côte du Palais, Québec, Québec G1R 2J6 (Canada); Binnekamp, Dirk [Integrated Clinical Solutions and Marketing, Philips Healthcare, Veenpluis 4-6, Best 5680 DA (Netherlands)
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.
Acceleration of EM-Based 3D CT Reconstruction Using FPGA.
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. PMID:26462240
Three-dimensional surface reconstruction for industrial computed tomography
Modern high resolution medical computed tomography (CT) scanners can produce geometrically accurate sectional images of many types of industrial objects. Computer software has been developed to convert serial CT scans into a 3-D surface form, suitable for display on the scanner itself. This software, originally developed for imaging the skull, has been adapted for application to industrial CT scanning, where serial CT scans through an object of interest may be reconstructed to demonstrate spatial relationships in three dimensions that cannot be easily understood using the original slices. The methods of 3-D reconstruction and solid modeling are reviewed, and reconstruction in three dimensions from CT scans through familiar objects is demonstrated
Contribution of 3-D electrical resistivity tomography for landmines detection
M. Metwaly
2008-12-01
Full Text Available Landmines are a type of inexpensive weapons widely used in the pre-conflicted areas in many countries worldwide. The two main types are the metallic and non-metallic (mostly plastic landmines. They are most commonly investigated by magnetic, ground penetrating radar (GPR, and metal detector (MD techniques. These geophysical techniques however have significant limitations in resolving the non-metallic landmines and wherever the host materials are conductive. In this work, the 3-D electric resistivity tomography (ERT technique is evaluated as an alternative and/or confirmation detection system for both landmine types, which are buried in different soil conditions and at different depths. This can be achieved using the capacitive resistivity imaging system, which does not need direct contact with the ground surface. Synthetic models for each case have been introduced using metallic and non-metallic bodies buried in wet and dry environments. The inversion results using the L_{1} norm least-squares optimization method tend to produce robust blocky models of the landmine body. The dipole axial and the dipole equatorial arrays tend to have the most favorable geometry by applying dynamic capacitive electrode and they show significant signal strength for data sets with up to 5% noise. Increasing the burial depth relative to the electrode spacing as well as the noise percentage in the resistivity data is crucial in resolving the landmines at different environments. The landmine with dimension and burial depth of one electrode separation unit is over estimated while the spatial resolutions decrease as the burial depth and noise percentage increase.
3-D reconstruction for mass lesions in the head and neck
3-D reconstructions in the head and neck were carried out on 21 normals and 11 patients with space-occupying lesions, both before and after the administration of Gd-DTPA. The 3-D reconstructions were obtained by the 'ray-tracing' method. For the 3-D reconstructions, portions of the skull surface image were removed to permit views of the deeper tissues. The 3-D reconstructions included an hypoglossus neurinoma, a glomus tumour, two carcinomas of the maxillary antra, three naso-pharyngeal carcinomas, a parotid adenoma, an oro-pharyngeal haemangioma and two lesions in the neck. The 3-D reconstructions provided a better understanding of the morphology than was obtained from the two-dimensional images. 3-D reconstructions of lesions in the head and neck will become a valuable diagnostic method for demonstrating space-occupying lesions, particularly with regard to surgical planning. (orig.)
AUTOMATIC TEXTURE RECONSTRUCTION OF 3D CITY MODEL FROM OBLIQUE IMAGES
Kang, Junhua; Deng, Fei; LI, XINWEI; WAN, FANG
2016-01-01
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....
Direct fourier methods in 3D-reconstruction from cone-beam data
The problem of 3D-reconstruction is encountered in both medical and industrial applications of X-ray tomography. A method able to utilize a complete set of projections complying with Tuys condition was proposed by Grangeat. His method is mathematically exact and consists of two distinct phases. In phase 1 cone-beam projection data are used to produce the derivative of the radon transform. In phase 2, after interpolation, the radon transform data are used to reconstruct the three-dimensional object function. To a large extent our method is an extension of the Grangeat method. Our aim is to reduce the computational complexity, i.e. to produce a faster method. The most taxing procedure during phase 1 is computation of line-integrals in the detector plane. By applying the direct Fourier method in reverse for this computation, we reduce the complexity of phase 1 from O(N4) to O(N3logN). Phase 2 can be performed either as a straight 3D-reconstruction or as a sequence of two 2D-reconstructions in vertical and horizontal planes, respectively. Direct Fourier methods can be applied for the 2D- and for the 3D-reconstruction, which reduces the complexity of phase 2 from O(N4) to O(N3logN) as well. In both cases, linogram techniques are applied. For 3D-reconstruction the inversion formula contains the second derivative filter instead of the well-known ramp-filter employed in the 2D-case. The derivative filter is more well-behaved than the 2D ramp-filter. This implies that less zeropadding is necessary which brings about a further reduction of the computational efforts. The method has been verified by experiments on simulated data. The image quality is satisfactory and independent of cone-beam angles. For a 5123 volume we estimate that our method is ten times faster than Grangeats method
Performance Evaluating of some Methods in 3D Depth Reconstruction from a Single Image
Wen, Wei
2009-01-01
We studied the problem of 3D reconstruction from a single image. The 3D reconstruction is one of the basic problems in Computer Vision. The 3D reconstruction is usually achieved by using two or multiple images of a scene. However recent researches in Computer Vision field have enabled us to recover the 3D information even from only one single image. The methods used in such reconstructions are based on depth information, projection geometry, image content, human psychology and so on. Each met...
Fast implementations of 3D PET reconstruction using vector and parallel programming techniques
Computationally intensive techniques that offer potential clinical use have arisen in nuclear medicine. Examples include iterative reconstruction, 3D PET data acquisition and reconstruction, and 3D image volume manipulation including image registration. One obstacle in achieving clinical acceptance of these techniques is the computational time required. This study focuses on methods to reduce the computation time for 3D PET reconstruction through the use of fast computer hardware, vector and parallel programming techniques, and algorithm optimization. The strengths and weaknesses of i860 microprocessor based workstation accelerator boards are investigated in implementations of 3D PET reconstruction
Full 3D Microwave Tomography enhanced GPR surveys: a case study
Catapano, Ilaria; Soldovieri, Francesco; Affinito, Antonio; Hugenschmidt, Johannes
2014-05-01
Ground Penetrating Radar (GPR) systems are well assessed non-invasive diagnostic tools capable of providing high resolution images of the inner structure of the probed spatial region. Owing to this capability, GPR systems are nowadays more and more considered in the frame of civil engineering surveys since they may give information on constructive details as well as on the aging and risk factors affecting the healthiness of an infrastructure. In this frame, accurate, reliable and easily interpretable images of the probed scenarios are mandatory in order to support the management of maintenance works and assure the safety of structures. Such a requirement motivates the use of different and sophisticated data processing approaches in order to compare more than one image of the same scene, thus improving the reliability and objectiveness of the GPR survey results. Among GPR data processing procedures, Microwave Tomography approaches based on the Born approximation face the imaging as the solution of a linear inverse problem, which is solved by using the Truncated Singular Value Decomposition as a regularized inversion scheme [1]. So far, an approach exploiting a 2D scalar model of the scattering phenomenon have been adopted to process GPR data gathered along a single scan. In this case, 3D images are obtained by interpolating 2D reconstructions (this is referred commonly as pseudo 3D imaging). Such an imaging approach have provided valuable results in several real cases dealing with not only surveys for civil engineering but also archeological prospection, subservice monitoring, security surveys and so on [1-4]. These encouraging results have motivated the development of a full 3D Microwave Tomography approach capable of accounting for the vectorial nature of the wave propagation. The reconstruction capabilities of this novel approach have been assessed mainly against experimental data collected in laboratory controlled conditions. The obtained results corroborate
Image quality in positron emission tomography (PET) can be assessed with physical parameters, as spatial resolution and signal-to-noise ratio, or using psychophysical approaches, which include the observer performance and the considered task (ROC analysis). For PET in oncology, such a task is the detection of hot lesions. The aim of the present study was to assess the lesion detection performance due to adequate modeling of the scanner and the measurement process in the image reconstruction process. We compared the standard OSEM software of the manufacturer with a sophisticated fully 3D iterative reconstruction technique (USC MAP). A rectangular phantom with 6 oblique line sources in a homogeneous background (2.6 kBq/ml 18F) was imaged dynamically with an ECAT EXACT HR+ scanner in 3D mode. Reconstructed activity contrasts varied between 15 and 0, as the line sources were filled with 11C (3.2 MBq/ml). Measured attenuation and standard randoms, dead time, and scatter corrections of the manufacturer were employed. For the ROC analysis, a software tool presented a cut-out of the phantom (15x15 pixels) to two observers. These cut-outs were rated (5 classes) and the area Az under the ROC curve was determined as a measure of detection performance. The improvement for Az with USC MAP compared to the OSEM reconstructions ranged between 0.02 and 0.23 for signal-to-noise ratios of the background between 2.8 and 3.1 and lesion contrast between 2.1 and 4.2. This study demonstrates that adequate modeling of the measurement process in the reconstruction algorithm improves the detection of small hot lesions markedly
DIII-D Equilibrium Reconstructions with New 3D Magnetic Probes
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.
Automatic Reconstruction of Spacecraft 3D Shape from Imagery
Poelman, C.; Radtke, R.; Voorhees, H.
We describe a system that computes the three-dimensional (3D) shape of a spacecraft from a sequence of uncalibrated, two-dimensional images. While the mathematics of multi-view geometry is well understood, building a system that accurately recovers 3D shape from real imagery remains an art. A novel aspect of our approach is the combination of algorithms from computer vision, photogrammetry, and computer graphics. We demonstrate our system by computing spacecraft models from imagery taken by the Air Force Research Laboratory's XSS-10 satellite and DARPA's Orbital Express satellite. Using feature tie points (each identified in two or more images), we compute the relative motion of each frame and the 3D location of each feature using iterative linear factorization followed by non-linear bundle adjustment. The "point cloud" that results from this traditional shape-from-motion approach is typically too sparse to generate a detailed 3D model. Therefore, we use the computed motion solution as input to a volumetric silhouette-carving algorithm, which constructs a solid 3D model based on viewpoint consistency with the image frames. The resulting voxel model is then converted to a facet-based surface representation and is texture-mapped, yielding realistic images from arbitrary viewpoints. We also illustrate other applications of the algorithm, including 3D mensuration and stereoscopic 3D movie generation.
3D multifocus astigmatism and compressed sensing (3D MACS) based superresolution reconstruction
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) localiza...
Integration of real-time 3D capture, reconstruction, and light-field display
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.
Electron tomography based on a total variation minimization reconstruction technique
Goris, B., E-mail: bart.goris@ua.ac.be [EMAT, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp (Belgium); Van den Broek, W. [EMAT, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp (Belgium); Batenburg, K.J. [Centrum Wiskunde and Informatica, Science Park 123, NL-1098XG Amsterdam (Netherlands); Vision Lab, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk (Belgium); Heidari Mezerji, H.; Bals, S. [EMAT, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp (Belgium)
2012-02-15
The 3D reconstruction of a tilt series for electron tomography is mostly carried out using the weighted backprojection (WBP) algorithm or using one of the iterative algorithms such as the simultaneous iterative reconstruction technique (SIRT). However, it is known that these reconstruction algorithms cannot compensate for the missing wedge. Here, we apply a new reconstruction algorithm for electron tomography, which is based on compressive sensing. This is a field in image processing specialized in finding a sparse solution or a solution with a sparse gradient to a set of ill-posed linear equations. Therefore, it can be applied to electron tomography where the reconstructed objects often have a sparse gradient at the nanoscale. Using a combination of different simulated and experimental datasets, it is shown that missing wedge artefacts are reduced in the final reconstruction. Moreover, it seems that the reconstructed datasets have a higher fidelity and are easier to segment in comparison to reconstructions obtained by more conventional iterative algorithms. -- Highlights: Black-Right-Pointing-Pointer A reconstruction algorithm for electron tomography is investigated based on total variation minimization. Black-Right-Pointing-Pointer Missing wedge artefacts are reduced by this algorithm. Black-Right-Pointing-Pointer The reconstruction is easier to segment. Black-Right-Pointing-Pointer More reliable quantitative information can be obtained.
Coronary computed tomography angiography (coronary CTA) is a powerful non-invasive imaging method to evaluate coronary artery disease. Nowadays, coronary CTA estimated effective radiation dose can be dramatically reduced using state-of-the-art scanners, such as 320-row detector CT (320-CT), without changing coronary CTA diagnostic accuracy. To optimize and further reduce the radiation dose, new iterative reconstruction algorithms were released recently by several CT manufacturers, and now they are used routinely in coronary CTA. This paper presents our first experience using coronary CTA with 320-CT and the Adaptive Iterative Dose Reduction 3D (AIDR-3D). In addition, we describe the current indications for coronary CTA in our practice as well as the acquisition standard protocols and protocols related to CT application for radiation dose reduction. In conclusion, coronary CTA radiation dose can be dramatically reduced following the 'as low as reasonable achievable' principle by combination of exam indication and well-documented technics for radiation dose reduction, such as beta blockers, low-kV, and also the newest iterative dose reduction software as AIDR-3D. (author)
Regional application of multi-layer artificial neural networks in 3-D ionosphere tomography
Ghaffari Razin, Mir Reza; Voosoghi, Behzad
2016-08-01
Tomography is a very cost-effective method to study physical properties of the ionosphere. In this paper, residual minimization training neural network (RMTNN) is used in voxel-based tomography to reconstruct of 3-D ionosphere electron density with high spatial resolution. For numerical experiments, observations collected at 37 GPS stations from Iranian permanent GPS network (IPGN) are used. A smoothed TEC approach was used for absolute STEC recovery. To improve the vertical resolution, empirical orthogonal functions (EOFs) obtained from international reference ionosphere 2012 (IRI-2012) used as object function in training neural network. Ionosonde observations is used for validate reliability of the proposed method. Minimum relative error for RMTNN is 1.64% and maximum relative error is 15.61%. Also root mean square error (RMSE) of 0.17 × 1011 (electrons/m3) is computed for RMTNN which is less than RMSE of IRI2012. The results show that RMTNN has higher accuracy and compiles speed than other ionosphere reconstruction methods.
3D optical phase reconstruction within PMMA samples using a spectral OCT system
Briones-R., Manuel d. J.; De La Torre-Ibarra, Manuel H.; Mendoza Santoyo, Fernando
2015-08-01
The optical coherence tomography (OCT) technique has proved to be a useful method in biomedical areas such as ophthalmology, dentistry, dermatology, among many others. In all these applications the main target is to reconstruct the internal structure of the samples from which the physician's expertise may recognize and diagnose the existence of a disease. Nowadays OCT has been applied one step further and is used to study the mechanics of some particular type of materials, where the resulting information involves more than just their internal structure and the measurement of parameters such as displacements, stress and strain. Here we report on a spectral OCT system used to image the internal 3D microstructure and displacement maps from a PMMA (Poly-methyl-methacrylate) sample, subjected to a deformation by a controlled three point bending and tilting. The internal mechanical response of the polymer is shown as consecutive 2D images.
3D neutron computed tomography. Requirements and applications
Other than X-rays, neutrons can penetrate most metals easily while delivering a high contrast for many light-weight elements. Especially their high sensitivity for hydrogen makes them a valuable tool for the detection of organic materials like lubricants, plastics or sealants within metal housings. Neutron radiography and tomography complement the application of X-ray for the inspection of complex and critical components like in automotive and aerospace applications. An overview about the technical and mathematical differences between neutron and X-ray tomography is given and the imperfections and limitations of a neutron setup are shown. Several examples of technical neutron computed tomography are given. (author)
3D Maize Plant Reconstruction Based on Georeferenced Overlapping LiDAR Point Clouds
Miguel Garrido; Dimitris S. Paraforos; David Reiser; Manuel Vázquez Arellano; Griepentrog, Hans W; Constantino Valero
2015-01-01
3D crop reconstruction with a high temporal resolution and by the use of non-destructive measuring technologies can support the automation of plant phenotyping processes. Thereby, the availability of such 3D data can give valuable information about the plant development and the interaction of the plant genotype with the environment. This article presents a new methodology for georeferenced 3D reconstruction of maize plant structure. For this purpose a total station, an IMU, and several 2D LiD...
Image Reconstruction from 2D stack of MRI/CT to 3D using Shapelets
Arathi T
2014-12-01
Full Text Available Image reconstruction is an active research field, due to the increasing need for geometric 3D models in movie industry, games, virtual environments and in medical fields. 3D image reconstruction aims to arrive at the 3D model of an object, from its 2D images taken at different viewing angles. Medical images are multimodal, which includes MRI, CT scan image, PET and SPECT images. Of these, MRI and CT scan images of an organ when taken, is available as a stack of 2D images, taken at different angles. This 2D stack of images is used to get a 3D view of the organ of interest, to aid doctors in easier diagnosis. Existing 3D reconstruction techniques are voxel based techniques, which tries to reconstruct the 3D view based on the intensity value stored at each voxel location. These techniques don’t make use of the shape/depth information available in the 2D image stack. In this work, a 3D reconstruction technique for MRI/CT 2D image stack, based on Shapelets has been proposed. Here, the shape/depth information available in each 2D image in the image stack is manipulated to get a 3D reconstruction, which gives a more accurate 3D view of the organ of interest. Experimental results exhibit the efficiency of this proposed technique.
3-D Virtual and Physical Reconstruction of Bendego Iron
Belmonte, S. L. R.; Zucolotto, M. E.; Fontes, R. C.; dos Santos, J. R. L.
2012-09-01
The use of 3D laser scanning to meteoritic to preserve the original shape of the meteorites before cutting and the facility of saved the datas in STL format (stereolithography) to print three-dimensional physical models and generate a digital replica.
Online reconstruction of 3D magnetic particle imaging data
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.
Online reconstruction of 3D magnetic particle imaging data.
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. PMID:27182668
Reconstruction of Building Facades in 3D for Remote Inspection Using a Multicopter
Ottemo, Torjus Sveier
2014-01-01
This thesis' focus is on how computer vision can be used to reconstruct building facades in 3D based on images taken by an unmanned aerial vehicle for the purpose of inspection. It explores and presents different algorithms needed for 3D reconstruction of facades and how this can be used to improve facade inspection both in terms of user friendliness for the operator and increased efficiency. The thesis resulted in a reconstruction application with an interactive graphical user interface...
3-D Reconstruction From 2-D Radiographic Images and Its Application to Clinical Veterinary Medicine
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.
Autonomous Planetary 3-D Reconstruction From Satellite Images
Denver, Troelz
1999-01-01
A common task for many deep space missions is autonomous generation of 3-D representations of planetary surfaces onboard unmanned spacecrafts. The basic problem for this class of missions is, that the closed loop time is far too long. The closed loop time is defined as the time from when a human...... of seconds to a few minutes, the closed loop time effectively precludes active human control.The only way to circumvent this problem is to build an artificial feature extractor operating autonomously onboard the spacecraft.Different artificial feature extractors are presented and their efficiency...... is discussed.Based on such features, 3-D representations may be compiled from two or more 2-D satellite images. The main purposes of such a mapping system are extraction of landing sites, objects of scientific interest and general planetary surveying. All data processing is performed autonomously onboard...
3D reconstruction of worn parts for flexible remanufacture based on robotic arc welding
Yin Ziqiang; Zhang Guangjun; Gao Hongming; Wu Lin
2010-01-01
3D reconstruction of worn parts is the foundation for remanufacturing system based on robotic arc welding,because it can provide 3D geometric information for robot task plan.In this investigation,a nocwl 3D reconstruction system based on linear structured light vision sensing is developed,This system hardware consists of a MTC368-CB CCD camera,a MLH-645laser projector and a DH-CG300 image grabbing card.This system software is developed to control the image data capture.In order to reconstruct the 3D geometric information from the captured image,a two steps rapid calibration algorithm is proposed.The 3D reconstruction experiment shows a satisfactory result.
Single view-based 3D face reconstruction robust to self-occlusion
Lee, Youn Joo; Lee, Sung Joo; Park, Kang Ryoung; Jo, Jaeik; Kim, Jaihie
2012-12-01
State-of-the-art 3D morphable model (3DMM) is used widely for 3D face reconstruction based on a single image. However, this method has a high computational cost, and hence, a simplified 3D morphable model (S3DMM) was proposed as an alternative. Unlike the original 3DMM, S3DMM uses only a sparse 3D facial shape, and therefore, it incurs a lower computational cost. However, this method is vulnerable to self-occlusion due to head rotation. Therefore, we propose a solution to the self-occlusion problem in S3DMM-based 3D face reconstruction. This research is novel compared with previous works, in the following three respects. First, self-occlusion of the input face is detected automatically by estimating the head pose using a cylindrical head model. Second, a 3D model fitting scheme is designed based on selected visible facial feature points, which facilitates 3D face reconstruction without any effect from self-occlusion. Third, the reconstruction performance is enhanced by using the estimated pose as the initial pose parameter during the 3D model fitting process. The experimental results showed that the self-occlusion detection had high accuracy and our proposed method delivered a noticeable improvement in the 3D face reconstruction performance compared with previous methods.
3D planning in the reconstruction of maxillofacial defects
Schepers, Rutger Hendrik
2016-01-01
Resection of a tumor in the upper- or lower jaw often results in a large defect, because with the tumor resection also an adjacent part of the jaw is resected. The most favorable treatment for large defects is the combination of a bony free vascularized graft to reconstruct the defect with implants to retain prosthetic constructions. The Free vascularized Fibula Flap (FFF) is a versatile flap that commonly is used to reconstruct such bony and soft tissue defects. It is shown that oral rehabil...
Analytic 3D image reconstruction using all detected events
We present the results of testing a previously presented algorithm for three-dimensional image reconstruction that uses all gamma-ray coincidence events detected by a PET volume-imaging scanner. By using two iterations of an analytic filter-backprojection method, the algorithm is not constrained by the requirement of a spatially invariant detector point spread function, which limits normal analytic techniques. Removing this constraint allows the incorporation of all detected events, regardless of orientation, which improves the statistical quality of the final reconstructed image
Wang Wenli; Hawkins, William; Gagnon, Daniel [Philips Medical Systems, Inc., 595 Miner Road, Cleveland, OH 44143-2175 (United States)
2004-06-07
A single photon emission computed tomography (SPECT) rotating slat collimator with strip detector acquires distance-weighted plane integral data, along with the attenuation factor and distance-dependent detector response. In order to image a 3D object, the slat collimator device has first to spin around its axis and then rotate around the object to produce 3D projection measurements. Compared to the slice-by-slice 2D reconstruction for the parallel-hole collimator and line integral data, a more complex 3D reconstruction is needed for the slat collimator and plane integral data. In this paper, we propose a 3D RBI-EM reconstruction algorithm with spherically-symmetric basis function, also called 'blobs', for the slat collimator. It has a closed and spherically symmetric analytical expression for the 3D Radon transform, which makes it easier to compute the plane integral than the voxel. It is completely localized in the spatial domain and nearly band-limited in the frequency domain. Its size and shape can be controlled by several parameters to have desired reconstructed image quality. A mathematical lesion phantom study has demonstrated that the blob reconstruction can achieve better contrast-noise trade-offs than the voxel reconstruction without greatly degrading the image resolution. A real lesion phantom study further confirmed this and showed that a slat collimator with CZT detector has better image quality than the conventional parallel-hole collimator with NaI detector. The improvement might be due to both the slat collimation and the better energy resolution of the CZT detector.
Wang, Wenli; Hawkins, William; Gagnon, Daniel
2004-06-01
A single photon emission computed tomography (SPECT) rotating slat collimator with strip detector acquires distance-weighted plane integral data, along with the attenuation factor and distance-dependent detector response. In order to image a 3D object, the slat collimator device has first to spin around its axis and then rotate around the object to produce 3D projection measurements. Compared to the slice-by-slice 2D reconstruction for the parallel-hole collimator and line integral data, a more complex 3D reconstruction is needed for the slat collimator and plane integral data. In this paper, we propose a 3D RBI-EM reconstruction algorithm with spherically-symmetric basis function, also called 'blobs', for the slat collimator. It has a closed and spherically symmetric analytical expression for the 3D Radon transform, which makes it easier to compute the plane integral than the voxel. It is completely localized in the spatial domain and nearly band-limited in the frequency domain. Its size and shape can be controlled by several parameters to have desired reconstructed image quality. A mathematical lesion phantom study has demonstrated that the blob reconstruction can achieve better contrast-noise trade-offs than the voxel reconstruction without greatly degrading the image resolution. A real lesion phantom study further confirmed this and showed that a slat collimator with CZT detector has better image quality than the conventional parallel-hole collimator with NaI detector. The improvement might be due to both the slat collimation and the better energy resolution of the CZT detector.
A single photon emission computed tomography (SPECT) rotating slat collimator with strip detector acquires distance-weighted plane integral data, along with the attenuation factor and distance-dependent detector response. In order to image a 3D object, the slat collimator device has first to spin around its axis and then rotate around the object to produce 3D projection measurements. Compared to the slice-by-slice 2D reconstruction for the parallel-hole collimator and line integral data, a more complex 3D reconstruction is needed for the slat collimator and plane integral data. In this paper, we propose a 3D RBI-EM reconstruction algorithm with spherically-symmetric basis function, also called 'blobs', for the slat collimator. It has a closed and spherically symmetric analytical expression for the 3D Radon transform, which makes it easier to compute the plane integral than the voxel. It is completely localized in the spatial domain and nearly band-limited in the frequency domain. Its size and shape can be controlled by several parameters to have desired reconstructed image quality. A mathematical lesion phantom study has demonstrated that the blob reconstruction can achieve better contrast-noise trade-offs than the voxel reconstruction without greatly degrading the image resolution. A real lesion phantom study further confirmed this and showed that a slat collimator with CZT detector has better image quality than the conventional parallel-hole collimator with NaI detector. The improvement might be due to both the slat collimation and the better energy resolution of the CZT detector
Method for 3D fibre reconstruction on a microrobotic platform.
Hirvonen, J; Myllys, M; Kallio, P
2016-07-01
Automated handling of a natural fibrous object requires a method for acquiring the three-dimensional geometry of the object, because its dimensions cannot be known beforehand. This paper presents a method for calculating the three-dimensional reconstruction of a paper fibre on a microrobotic platform that contains two microscope cameras. The method is based on detecting curvature changes in the fibre centreline, and using them as the corresponding points between the different views of the images. We test the developed method with four fibre samples and compare the results with the references measured with an X-ray microtomography device. We rotate the samples through 16 different orientations on the platform and calculate the three-dimensional reconstruction to test the repeatability of the algorithm and its sensitivity to the orientation of the sample. We also test the noise sensitivity of the algorithm, and record the mismatch rate of the correspondences provided. We use the iterative closest point algorithm to align the measured three-dimensional reconstructions with the references. The average point-to-point distances between the reconstructed fibre centrelines and the references are 20-30 μm, and the mismatch rate is low. Given the manipulation tolerance, this shows that the method is well suited to automated fibre grasping. This has also been demonstrated with actual grasping experiments. PMID:26695385
Reconstruction of 3D models of cast sculptures using close-range photogrammetry
Ž. Santoši
2015-10-01
Full Text Available This paper presents the possibilities of application of close-range photogrammetry, based on the Structure-from- Motion (SfM approach, in 3D model’s reconstruction of bronze cast sculptures. Special attention was dedicated to the analysis of image processing strategy, and its impact on the 3D model reconstruction quality. For the purpose of analysis a bust of Nikola Tesla, placed in front of the Faculty of Technical Sciences University of Novi Sad was used. Experimental results indicate that the strategy employing multi-group photo processing provides substantial reductions in processing time while providing satisfactory results in 3D reconstruction.
Effects of point configuration on the accuracy in 3D reconstruction from biplane images
Dmochowski, Jacek; Hoffmann, Kenneth R.; Singh, Vikas; Xu, Jinhui; Nazareth, Daryl P.
2005-01-01
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 type...
3D model tools for architecture and archaeology reconstruction
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.
3D Image Reconstruction from Compton camera data
Kuchment, Peter
2016-01-01
In this paper, we address analytically and numerically the inversion of the integral transform (\\emph{cone} or \\emph{Compton} transform) that maps a function on $\\mathbb{R}^3$ to its integrals over conical surfaces. It arises in a variety of imaging techniques, e.g. in astronomy, optical imaging, and homeland security imaging, especially when the so called Compton cameras are involved. Several inversion formulas are developed and implemented numerically in $3D$ (the much simpler $2D$ case was considered in a previous publication).
Quantitative Reconstructions of 3D Chemical Nanostructures in Nanowires.
Rueda-Fonseca, P; Robin, E; Bellet-Amalric, E; Lopez-Haro, M; Den Hertog, M; Genuist, Y; André, R; Artioli, A; Tatarenko, S; Ferrand, D; Cibert, J
2016-03-01
Energy dispersive X-ray spectrometry is used to extract a quantitative 3D composition profile of heterostructured nanowires. The analysis of hypermaps recorded along a limited number of projections, with a preliminary calibration of the signal associated with each element, is compared to the intensity profiles calculated for a model structure with successive shells of circular, elliptic, or faceted cross sections. This discrete tomographic technique is applied to II-VI nanowires grown by molecular beam epitaxy, incorporating ZnTe and CdTe and their alloys with Mn and Mg, with typical size down to a few nanometers and Mn or Mg content as low as 10%. PMID:26837636
Track reconstruction by GPU in 3D particle tracking detectors
Bozza, Cristiano, E-mail: kryss@sa.infn.it [Department of Physics of the University of Salerno and INFN Gruppo Collegato di Salerno, via Giovanni Paolo II 132, Fisciano, SA 84084 (Italy); De Sio, Chiara [Department of Physics of the University of Salerno and INFN Gruppo Collegato di Salerno, via Giovanni Paolo II 132, Fisciano, SA 84084 (Italy); Kose, Umut [CERN, Geneva (Switzerland); Stellacci, Simona Maria [Department of Physics of the University of Salerno and INFN Gruppo Collegato di Salerno, via Giovanni Paolo II 132, Fisciano, SA 84084 (Italy)
2015-09-11
3D detectors for high-energy physics have always needed large computing power. Its availability has sometimes determined the statistics and performance of experiments. The increasing specific computing power of GPUs in recent years offers new opportunities for this field of application that should not be missed. The paper shows a novel algorithm that supports, as a by-product of speed, wider angular acceptance with respect to established techniques based on CPUs. While the algorithm has been developed in the environment of nuclear emulsions, it has been conceived from the very beginning as a tool for general tracking in 3D detectors. The overall logic can apply to many operational contexts in which tracking occurs in high combinatorial background. The performances of the algorithm are evaluated from different points of view, describing the details of the computing technique that are common to tracking problems and discussing measurements and data from a test-beam exposure. Computing speed has been evaluated on a broad variety of hardware, investigating an approximated scaling formula.
Track reconstruction by GPU in 3D particle tracking detectors
3D detectors for high-energy physics have always needed large computing power. Its availability has sometimes determined the statistics and performance of experiments. The increasing specific computing power of GPUs in recent years offers new opportunities for this field of application that should not be missed. The paper shows a novel algorithm that supports, as a by-product of speed, wider angular acceptance with respect to established techniques based on CPUs. While the algorithm has been developed in the environment of nuclear emulsions, it has been conceived from the very beginning as a tool for general tracking in 3D detectors. The overall logic can apply to many operational contexts in which tracking occurs in high combinatorial background. The performances of the algorithm are evaluated from different points of view, describing the details of the computing technique that are common to tracking problems and discussing measurements and data from a test-beam exposure. Computing speed has been evaluated on a broad variety of hardware, investigating an approximated scaling formula
3D reconstruction software comparison for short sequences
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.
Assessing 3D tunnel position in ACL reconstruction using a novel single image 3D-2D registration
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.
Wearable 3-D Photoacoustic Tomography for Functional Brain Imaging in Behaving Rats
Tang, Jianbo; Jason E. Coleman; DAI, XIANJIN; Jiang, Huabei
2016-01-01
Understanding the relationship between brain function and behavior remains a major challenge in neuroscience. Photoacoustic tomography (PAT) is an emerging technique that allows for noninvasive in vivo brain imaging at micrometer-millisecond spatiotemporal resolution. In this article, a novel, miniaturized 3D wearable PAT (3D-wPAT) technique is described for brain imaging in behaving rats. 3D-wPAT has three layers of fully functional acoustic transducer arrays. Phantom imaging experiments rev...
Experimental Investigation of Material Flows Within FSWs Using 3D Tomography
Charles R. Tolle; Timothy A. White; Karen S. Miller; Denis E. Clark; Herschel B. Smartt
2008-06-01
There exists significant prior work using tracers or pre-placed hardened markers within friction stir welding (FSWing) to experimentally explore material flow within the FSW process. Our experiments replaced markers with a thin sheet of copper foil placed between the 6061 aluminum lap and butt joints that were then welded. The absorption characteristics of x-rays for copper and aluminum are significantly different allowing for non-destructive evaluation (NDE) methods such as x-ray computed tomography (CT) to be used to demonstrate the material movement within the weldment on a much larger scale than previously shown. 3D CT reconstruction of the copper components of the weldment allows for a unique view into the final turbulent state of the welding process as process parameters are varied. The x-ray CT data of a section of the weld region was collected using a cone-beam x-ray imaging system developed at the INL. Six-hundred projections were collected over 360-degrees using a 160-kVp Bremsstrahlung x-ray generator (25-micrometer focal spot) and amorphoussilicon x-ray detector. The region of the object that was imaged was about 3cm tall and 1.5cm x 1cm in cross section, and was imaged at a magnification of about 3.6x. The data were reconstructed on a 0.5x0.5x0.5 mm3 voxel grid. After reconstruction, the aluminum and copper could be easily discriminated using a gray level threshold allowing visualization of the copper components. Fractal analysis of the tomographic reconstructed material topology is investigated as a means to quantify macro level material flow based on process parameters. The results of multi-pass FSWs show increased refinement of the copper trace material. Implications of these techniques for quantifying process flow are discussed.
Manifold Constrained Transfer of Facial Geometric Knowledge for 3D Caricature Reconstruction
Jun-Fa Liu; Wen-Jing He; Tao Chen; Yi-Qiang Chen
2013-01-01
3D caricatures are important attractive elements of the interface in virtual environment such as online game.However,very limited 3D caricatures exist in the real world.Meanwhile,creating 3D caricatures manually is rather costly,and even professional skills are needed.This paper proposes a novel and effective manifold transfer algorithm to reconstruct 3D caricatures according to their original 2D caricatures.We first manually create a small dataset with only 100 3D caricature models and use them to initialize the whole 3D dataset.After that,manifold transfer algorithm is carried out to refine the dataset.The algorithm comprises of two steps.The first is to perform manifold alignment between 2D and 3D caricatures to get a "standard" manifold map； the second is to reconstruct all the 3D caricatures based on the manifold map.The proposed approach utilizes and transfers knowledge of 2D caricatures to the target 3D caricatures well.Comparative experiments show that the approach reconstructs 3D caricatures more effectively and the results conform more to the styles of the original 2D caricatures than the Principal Components Analysis (PCA) based method.
Auto-masked 2D/3D image registration and its validation with clinical cone-beam computed tomography
Image-guided alignment procedures in radiotherapy aim at minimizing discrepancies between the planned and the real patient setup. For that purpose, we developed a 2D/3D approach which rigidly registers a computed tomography (CT) with two x-rays by maximizing the agreement in pixel intensity between the x-rays and the corresponding reconstructed radiographs from the CT. Moreover, the algorithm selects regions of interest (masks) in the x-rays based on 3D segmentations from the pre-planning stage. For validation, orthogonal x-ray pairs from different viewing directions of 80 pelvic cone-beam CT (CBCT) raw data sets were used. The 2D/3D results were compared to corresponding standard 3D/3D CBCT-to-CT alignments. Outcome over 8400 2D/3D experiments showed that parametric errors in root mean square were <0.18° (rotations) and <0.73 mm (translations), respectively, using rank correlation as intensity metric. This corresponds to a mean target registration error, related to the voxels of the lesser pelvis, of <2 mm in 94.1% of the cases. From the results we conclude that 2D/3D registration based on sequentially acquired orthogonal x-rays of the pelvis is a viable alternative to CBCT-based approaches if rigid alignment on bony anatomy is sufficient, no volumetric intra-interventional data set is required and the expected error range fits the individual treatment prescription. (paper)
Assist feature printability prediction by 3-D resist profile reconstruction
Zheng, Xin; Huang, Jensheng; Chin, Fook; Kazarian, Aram; Kuo, Chun-Chieh
2012-06-01
properties may then be used to optimize the printability vs. efficacy of an SRAF either prior to or during an Optical Proximity Correction (OPC) run. The process models that are used during OPC have never been able to reliably predict which SRAFs will print. This appears to be due to the fact that OPC process models are generally created using data that does not include printed subresolution patterns. An enhancement to compact modeling capability to predict Assist Features (AF) printability is developed and discussed. A hypsometric map representing 3-D resist profile was built by applying a first principle approximation to estimate the "energy loss" from the resist top to bottom. Such a 3-D resist profile is an extrapolation of a well calibrated traditional OPC model without any additional information. Assist features are detected at either top of resist (dark field) or bottom of resist (bright field). Such detection can be done by just extracting top or bottom resist models from our 3-D resist model. There is no measurement of assist features needed when we build AF but it can be included if interested but focusing on resist calibration to account for both exposure dosage and focus change sensitivities. This approach significantly increases resist model's capability for predicting printed SRAF accuracy. And we don't need to calibrate an SRAF model in addition to the OPC model. Without increase in computation time, this compact model can draw assist feature contour with real placement and size at any vertical plane. The result is compared and validated with 3-D rigorous modeling as well as SEM images. Since this method does not change any form of compact modeling, it can be integrated into current MBAF solutions without any additional work.
Digital Holographic Capture and Optoelectronic Reconstruction for 3D Displays
Damien P. Kelly
2010-01-01
Full Text Available The application of digital holography as a viable solution to 3D capture and display technology is examined. A review of the current state of the field is presented in which some of the major challenges involved in a digital holographic solution are highlighted. These challenges include (i the removal of the DC and conjugate image terms, which are features of the holographic recording process, (ii the reduction of speckle noise, a characteristic of a coherent imaging process, (iii increasing the angular range of perspective of digital holograms (iv and replaying captured and/or processed digital holograms using spatial light modulators. Each of these challenges are examined theoretically and several solutions are put forward. Experimental results are presented that demonstrate the validity of the theoretical solutions.
Positron Emission Tomography with Three-Dimensional Reconstruction
The development of two different low-cost scanners for positron emission tomography (PET) based on 3D acquisition are presented. The first scanner consists of two rotating scintillation cameras, and produces quantitative images, which have shown to be clinically useful. The second one is a system with two opposed sets of detectors, based on the limited angle tomography principle, dedicated for mammographic studies. The development of low-cost PET scanners can increase the clinical impact of PET, which is an expensive modality, only available at a few centres world-wide and mainly used as a research tool. A 3D reconstruction method was developed that utilizes all the available data. The size of the data-sets is considerably reduced, using the single-slice rebinning approximation. The 3D reconstruction is divided into 1D axial deconvolution and 2D transaxial reconstruction, which makes it relatively fast. This method was developed for the rotating scanner, but was also implemented for multi-ring scanners with and without inter plane septa. An iterative 3D reconstruction method was developed for the limited angle scanner, based on the new concept of 'mobile pixels', which reduces the finite pixel errors and leads to an improved signal to noise ratio. 100 refs
Wang, Cuihuan; Kim, Leonard; Barnard, Nicola; Khan, Atif; Pierce, Mark C.
2016-02-01
Our long term goal is to develop a high-resolution imaging method for comprehensive assessment of tissue removed during lumpectomy procedures. By identifying regions of high-grade disease within the excised specimen, we aim to develop patient-specific post-operative radiation treatment regimens. We have assembled a benchtop spectral-domain optical coherence tomography (SD-OCT) system with 1320 nm center wavelength. Automated beam scanning enables "sub-volumes" spanning 5 mm x 5 mm x 2 mm (500 A-lines x 500 B-scans x 2 mm in depth) to be collected in under 15 seconds. A motorized sample positioning stage enables multiple sub-volumes to be acquired across an entire tissue specimen. Sub-volumes are rendered from individual B-scans in 3D Slicer software and en face (XY) images are extracted at specific depths. These images are then tiled together using MosaicJ software to produce a large area en face view (up to 40 mm x 25 mm). After OCT imaging, specimens were sectioned and stained with HE, allowing comparison between OCT image features and disease markers on histopathology. This manuscript describes the technical aspects of image acquisition and reconstruction, and reports initial qualitative comparison between large area en face OCT images and HE stained tissue sections. Future goals include developing image reconstruction algorithms for mapping an entire sample, and registering OCT image volumes with clinical CT and MRI images for post-operative treatment planning.
Vallet, B.; Soheilian, B.; Brédif, M.
2014-08-01
The 3D reconstruction of similar 3D objects detected in 2D faces a major issue when it comes to grouping the 2D detections into clusters to be used to reconstruct the individual 3D objects. Simple clustering heuristics fail as soon as similar objects are close. This paper formulates a framework to use the geometric quality of the reconstruction as a hint to do a proper clustering. We present a methodology to solve the resulting combinatorial optimization problem with some simplifications and approximations in order to make it tractable. The proposed method is applied to the reconstruction of 3D traffic signs from their 2D detections to demonstrate its capacity to solve ambiguities.
Bayesian 3d velocity field reconstruction with VIRBIuS
Lavaux, G
2015-01-01
I describe a new Bayesian based algorithm to infer the full three dimensional velocity field from observed distances and spectroscopic galaxy catalogues. In addition to the velocity field itself, the algorithm reconstructs true distances, some cosmological parameters and specific non-linearities in the velocity field. The algorithm takes care of selection effects, miscalibration issues and can be easily extended to handle direct fitting of, e.g., the inverse Tully-Fisher relation. I first describe the algorithm in details alongside its performances. This algorithm is implemented in the VIRBIuS (VelocIty Reconstruction using Bayesian Inference Software) software package. I then test it on different mock distance catalogues with a varying complexity of observational issues. The model proved to give robust measurement of velocities for mock catalogues of 3,000 galaxies. I expect the core of the algorithm to scale to tens of thousands galaxies. It holds the promises of giving a better handle on future large and d...
Bayesian 3D velocity field reconstruction with VIRBIUS
Lavaux, Guilhem
2016-03-01
I describe a new Bayesian-based algorithm to infer the full three dimensional velocity field from observed distances and spectroscopic galaxy catalogues. In addition to the velocity field itself, the algorithm reconstructs true distances, some cosmological parameters and specific non-linearities in the velocity field. The algorithm takes care of selection effects, miscalibration issues and can be easily extended to handle direct fitting of e.g. the inverse Tully-Fisher relation. I first describe the algorithm in details alongside its performances. This algorithm is implemented in the VIRBIUS (VelocIty Reconstruction using Bayesian Inference Software) software package. I then test it on different mock distance catalogues with a varying complexity of observational issues. The model proved to give robust measurement of velocities for mock catalogues of 3000 galaxies. I expect the core of the algorithm to scale to tens of thousands galaxies. It holds the promises of giving a better handle on future large and deep distance surveys for which individual errors on distance would impede velocity field inference.
Chen, Jianlin; Wang, Linyuan; Yan, Bin; Zhang, Hanming; Cheng, Genyang
2015-01-01
Iterative reconstruction algorithms for computed tomography (CT) through total variation regularization based on piecewise constant assumption can produce accurate, robust, and stable results. Nonetheless, this approach is often subject to staircase artefacts and the loss of fine details. To overcome these shortcomings, we introduce a family of novel image regularization penalties called total generalized variation (TGV) for the effective production of high-quality images from incomplete or noisy projection data for 3D reconstruction. We propose a new, fast alternating direction minimization algorithm to solve CT image reconstruction problems through TGV regularization. Based on the theory of sparse-view image reconstruction and the framework of augmented Lagrange function method, the TGV regularization term has been introduced in the computed tomography and is transformed into three independent variables of the optimization problem by introducing auxiliary variables. This new algorithm applies a local linearization and proximity technique to make the FFT-based calculation of the analytical solutions in the frequency domain feasible, thereby significantly reducing the complexity of the algorithm. Experiments with various 3D datasets corresponding to incomplete projection data demonstrate the advantage of our proposed algorithm in terms of preserving fine details and overcoming the staircase effect. The computation cost also suggests that the proposed algorithm is applicable to and is effective for CBCT imaging. Theoretical and technical optimization should be investigated carefully in terms of both computation efficiency and high resolution of this algorithm in application-oriented research. PMID:26756406
GPU-Based 3D Cone-Beam CT Image Reconstruction for Large Data Volume
Xing Zhao; Jing-jing Hu; Peng Zhang
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...
Reconstructing 3D building models from laser scanning to calculate the heat demand
Neidhart, Hauke; Sester, Monika
2008-09-15
The objective of the project is to determine the heat demand of settlement areas using geospatial data, especially airborne laser scanning data. With airborne laser scanning it possible to record detailed 3D data for great areas. With this 3D data it is possible to reconstruct 3D building models. The geometry then can be used to derive information for the calculation of the heat demand
Identification and classification in le fort type fractures by using 2D and 3D computed tomography
CHEN We-jian; YANG Yun-jun; FANG Yi-ming; XU Fang-hong; ZHANG Lin; CAO Guo-quan
2006-01-01
Objective:To evaluate the usefulness of twodimensional (2D) and three-dimensional (3D) computed tomography (CT) in the identification and classification of Le Fort type fractures.Methods: Sixty-two patients with different types of Le Fort fractures underwent CT scanning and 3D-CT reconstruction. The data were analyzed by multiplanar reconstruction (MPR), surface shaded display (SSD) and volume rendering (VR) respectively.Results: The patients with Le Fort Ⅰ , Le Fort Ⅱfracture and Le Fort Ⅲ fracture accounted for 16.1%,14.5 % and 12.9 % respectively. The compound fractures were the most common type and accounted for 56.5 % ( n =35, 18 cases with Le Fort Ⅰ + Ⅱ fracture, 10 cases with Le Fort Ⅱ + Ⅲ fracture and 7 cases with Le Fort Ⅰ + Ⅱ + Ⅲfracture). Fifty-five cases coexisted with other fractures in maxillofacial region. 2D-CT could be used to define the tiny fractures and the deep-structure fractures more accurately compared with 3D-CT, but the real impression of Le Fort type fractures could not be correctly evaluated on 2D-CT.3D-CT could clearly demonstrate the whole shape of Le Fort type fractures and identify the classification of Le Fort fractures.Conclusions: 3D-CT is the best imaging method for the diagnosis of Le Fort type fractures and can provide valuable information of space relationship, especially for the design of treatment plan before operation.
3-D Adaptive Sparsity Based Image Compression With Applications to Optical Coherence Tomography.
Fang, Leyuan; Li, Shutao; Kang, Xudong; Izatt, Joseph A; Farsiu, Sina
2015-06-01
We present a novel general-purpose compression method for tomographic images, termed 3D adaptive sparse representation based compression (3D-ASRC). In this paper, we focus on applications of 3D-ASRC for the compression of ophthalmic 3D optical coherence tomography (OCT) images. The 3D-ASRC algorithm exploits correlations among adjacent OCT images to improve compression performance, yet is sensitive to preserving their differences. Due to the inherent denoising mechanism of the sparsity based 3D-ASRC, the quality of the compressed images are often better than the raw images they are based on. Experiments on clinical-grade retinal OCT images demonstrate the superiority of the proposed 3D-ASRC over other well-known compression methods. PMID:25561591
Automatic Texture Reconstruction of 3d City Model from Oblique Images
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.
Katsumura, Seiko; Sato, Keita; Ikawa, Tomoko; Yamamura, Keiko; Ando, Eriko; Shigeta, Yuko; Ogawa, Takumi
2016-01-01
Computed tomography (CT) scanning has recently been introduced into forensic medicine and dentistry. However, the presence of metal restorations in the dentition can adversely affect the quality of three-dimensional reconstruction from CT scans. In this study, we aimed to evaluate the reproducibility of a "high-precision, reconstructed 3D model" obtained from a conebeam CT scan of dentition, a method that might be particularly helpful in forensic medicine. We took conebeam CT and helical CT images of three dry skulls marked with 47 measuring points; reconstructed three-dimensional images; and measured the distances between the points in the 3D images with a computer-aided design/computer-aided manufacturing (CAD/CAM) marker. We found that in comparison with the helical CT, conebeam CT is capable of reproducing measurements closer to those obtained from the actual samples. In conclusion, our study indicated that the image-reproduction from a conebeam CT scan was more accurate than that from a helical CT scan. Furthermore, the "high-precision reconstructed 3D model" facilitates reliable visualization of full-sized oral and maxillofacial regions in both helical and conebeam CT scans. PMID:26832374
Image Reconstruction from 2D stack of MRI/CT to 3D using Shapelets
Arathi T; Latha Parameswaran
2014-01-01
Image reconstruction is an active research field, due to the increasing need for geometric 3D models in movie industry, games, virtual environments and in medical fields. 3D image reconstruction aims to arrive at the 3D model of an object, from its 2D images taken at different viewing angles. Medical images are multimodal, which includes MRI, CT scan image, PET and SPECT images. Of these, MRI and CT scan images of an organ when taken, is available as a stack of 2D images, taken at different a...
3D Reconstruction of a Rotating Erupting Prominence
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.
On reliability of 3D reconstructions of thermal plasma jet radiation by inverse Radon transform
Sekerešová, Zuzana; Hlína, Jan
2011-01-01
Roč. 56, č. 2 (2011), s. 171-183. ISSN 0001-7043 Institutional research plan: CEZ:AV0Z20570509 Keywords : thermal plasma jet * tomography * image reconstruction Subject RIV: BL - Plasma and Gas Discharge Physics
Application of generalized regression neural network on fast 3D reconstruction
Babakhani Asad; DU Zhi-jiang; SUN Li-ning; Kardan Reza; Mianji A. Fereidoun
2007-01-01
In robot-assisted surgery projects,researchers should be able to make fast 3 D reconstruction. Usually 2D images acquired with common diagnostic equipments such as UT, CT and MRI are not enough and complete for an accurate 3D reconstruction. There are some interpolation methods for approximating non value voxels which consume large execution time. A novel algorithm is introduced based on generalized regression neural network (GRNN) which can interpolate unknown voxles fast and reliable. The GRNN interpolation is used to produce new 2D images between each two succeeding ultrasonic images. It is shown that the composition of GRNN with image distance transformation can produce higher quality 3D shapes. The results of this method are compared with other interpolation methods practically. It shows this method can decrease overall time consumption on online 3D reconstruction.
Eric Hummel
Full Text Available The complex architecture of their structural elements and compartments is a hallmark of eukaryotic cells. The creation of high resolution models of whole cells has been limited by the relatively low resolution of conventional light microscopes and the requirement for ultrathin sections in transmission electron microscopy. We used soft x-ray tomography to study the 3D ultrastructural organization of whole cells of the unicellular green alga Chlamydomonas reinhardtii at unprecedented spatial resolution. Intact frozen hydrated cells were imaged using the natural x-ray absorption contrast of the sample without any staining. We applied different fiducial-based and fiducial-less alignment procedures for the 3D reconstructions. The reconstructed 3D volumes of the cells show features down to 30 nm in size. The whole cell tomograms reveal ultrastructural details such as nuclear envelope membranes, thylakoids, basal apparatus, and flagellar microtubule doublets. In addition, the x-ray tomograms provide quantitative data from the cell architecture. Therefore, nanoscale soft x-ray tomography is a new valuable tool for numerous qualitative and quantitative applications in plant cell biology.
Fully 3D PET image reconstruction with a 4D sinogram blurring kernel
Tohme, Michel S.; Qi, Jinyi [California Univ., Davis, CA (United States). Dept. of Biomedical Engineering; Zhou, Jian
2011-07-01
Accurately modeling PET system response is essential for high-resolution image reconstruction. Traditionally, sinogram blurring effects are modeled as a 2D blur in each sinogram plane. Such 2D blurring kernel is insufficient for fully 3D PET data, which has four dimensions. In this paper, we implement a fully 3D PET image reconstruction using a 4D sinogram blurring kernel estimated from point source scans and perform phantom experiments to evaluate the improvements in image quality over methods with existing 2D blurring kernels. The results show that the proposed reconstruction method can achieve better spatial resolution and contrast recovery than existing methods. (orig.)
Technology Corner: Virtual Crime Scene Reconstruction: The Basics of 3D Modeling
Nick Flor
2011-12-01
Full Text Available Digital crime scenes take place in the context of physical crime scenes. Virtual crime scene reconstruction is an activity where investigators create a 3-dimensional (3-D model of an actual crime scene for the purpose of determining the events that lead to the crime. While virtual crime scene reconstruction is currently used for analyzing physical scenes, it can also help investigators visualize and explore ways digital media could have been used to perpetrate a crime. In this technology corner we explore one of the technologies underlying virtual crime scene reconstruction: 3-D modeling.Â
3-D reconstruction of neurons from multichannel confocal laser scanning image series.
Wouterlood, Floris G
2014-01-01
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. PMID:24723320
A user-friendly nano-CT image alignment and 3D reconstruction platform based on LabVIEW
Wang, Sheng-Hao; Zhang, Kai; Wang, Zhi-Li; Gao, Kun; Wu, Zhao; Zhu, Pei-Ping; Wu, Zi-Yu
2015-01-01
X-ray computed tomography at the nanometer scale (nano-CT) offers a wide range of applications in scientific and industrial areas. Here we describe a reliable, user-friendly, and fast software package based on LabVIEW that may allow us to perform all procedures after the acquisition of raw projection images in order to obtain the inner structure of the investigated sample. A suitable image alignment process to address misalignment problems among image series due to mechanical manufacturing errors, thermal expansion, and other external factors has been considered, together with a novel fast parallel beam 3D reconstruction procedure that was developed ad hoc to perform the tomographic reconstruction. We have obtained remarkably improved reconstruction results at the Beijing Synchrotron Radiation Facility after the image calibration, the fundamental role of this image alignment procedure was confirmed, which minimizes the unwanted blurs and additional streaking artifacts that are always present in reconstructed slices. Moreover, this nano-CT image alignment and its associated 3D reconstruction procedure are fully based on LabVIEW routines, significantly reducing the data post-processing cycle, thus making the activity of the users faster and easier during experimental runs.
Samir Kumta; Monica Kumta; Leena Jain; Shrirang Purohit; Rani Ummul
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. Materi...
M. Capone
2015-02-01
benefits and the troubles. From a methodological point of view this is our workflow: - theoretical study about geometrical configuration of rib vault systems; - 3D model based on theoretical hypothesis about geometric definition of the vaults' form; - 3D model based on image matching 3D reconstruction methods; - comparison between 3D theoretical model and 3D model based on image matching;