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Ferretti, G. R., and A. Jankowski. "Tomodensitométrie volumique : reconstructions 2D et 3D." Revue des Maladies Respiratoires 27, no. 10 (December 2010): 1267–74. http://dx.doi.org/10.1016/j.rmr.2010.10.009.
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Powell, Leila C., Scott T. Kay, Arif Babul, and Andisheh Mahdavi. "Investigating the Relationship Between the Hot Gas and the Dark Matter Components of Galaxy Clusters." Proceedings of the International Astronomical Union 3, S244 (June 2007): 374–75. http://dx.doi.org/10.1017/s1743921307014342.
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AbstractVarious differences in galaxy cluster properties derived from X-ray and weak lensing observations have been highlighted in the literature. One such difference is the observation of mass concentrations in lensing maps which have no X-ray counterparts (e.g. Jee, White, Ford et al. 2005). We investigate this issue by identifying substructures in maps of projected total mass (analogous to weak lensing mass reconstructions) and maps of projected X-ray surface brightness for three simulated clusters. We then compare the 2D mass substructures with both 3D subhalo data and the 2D X-ray substructures. Here we present preliminary results from the first comparison, where we have assessed the impact of projecting the data on subhalo identification.
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Tang, Jinghua, Dianne W. Taylor, and Kenneth A. Taylor. "Cryo-EM 3D Reconstruction of Skeletal Muscle α-Actinin." Microscopy and Microanalysis 6, S2 (August 2000): 248–49. http://dx.doi.org/10.1017/s1431927600033730.
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α-Actinin is a member of the spectrin superfamily of actin crosslinking proteins. The molecule is an antiparallel homodimer with a polypeptide chain weight of 94-103 kDa. Each chain can be divided into three domains: the N-terminal 250 amino acids forms an actin binding domain, the central domain consisting of four spectrin-like, triple-helical repeats and the Cterminal which contains two EF hand motifs (Baron et al, 1987).Two models have been proposed for the alignment of the triple helical repeats in the α-actinin structure, an aligned model (Baron et al., 1987) and a staggered model (Taylor and Taylor, 1993). In order to resolve the controversy, we proceeded with the cryo-EM 3D reconstruction from 2D crystal grown on a positively charged lipid monolayer. From rabbit erector spinae aactinin, we obtain better ordered 2D crystals from which we have calculated a 3D reconstruction to ∼15 Å resolution.
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Narasimhadhan, A. V., and Kasi Rajgopal. "FDK-Type Algorithms with No Backprojection Weight for Circular and Helical Scan CT." International Journal of Biomedical Imaging 2012 (2012): 1–12. http://dx.doi.org/10.1155/2012/969432.
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We develop two Feldkamp-type reconstruction algorithms with no backprojection weight for circular and helical trajectory with planar detector geometry. Advances in solid-state electronic detector technologies lend importance to CT systems with the equispaced linear array, the planar (flat panel) detectors, and the corresponding algorithms. We derive two exact Hilbert filtered backprojection (FBP) reconstruction algorithms with no backprojection weight for 2D fan-beam equispace linear array detector geometry (complement of the equi-angular curved array detector). Based on these algorithms, the Feldkamp-type algorithms with no backprojection weight for 3D reconstruction are developed using the standard heuristic extension of the divergent beam FBP algorithm. The simulation results show that the axial intensity drop in the reconstructed image using the FDK algorithms with no backprojection weight with circular trajectory is similar to that obtained by using Hu's and T-FDK, algorithms. Further, we present efficient algorithms to reduce the axial intensity drop encountered in the standard FDK reconstructions in circular cone-beam CT. The proposed algorithms consist of mainly two steps: reconstruction of the object using FDK algorithm with no backprojection weight and estimation of the missing term. The efficient algorithms are compared with the FDK algorithm, Hu's algorithm, T-FDK, and Zhu et al.'s algorithm in terms of axial intensity drop and noise. Simulation shows that the efficient algorithms give similar performance in axial intensity drop as that of Zhu et al.'s algorithm while one of the efficient algorithms outperforms Zhu et al.'s algorithm in terms of computational complexity.
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Orthuber, E., and J. Avbelj. "3D BUILDING RECONSTRUCTION FROM LIDAR POINT CLOUDS BY ADAPTIVE DUAL CONTOURING." ISPRS Annals of Photogrammetry, Remote Sensing and Spatial Information Sciences II-3/W4 (March 11, 2015): 157–64. http://dx.doi.org/10.5194/isprsannals-ii-3-w4-157-2015.
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This paper presents a novel workflow for data-driven building reconstruction from Light Detection and Ranging (LiDAR) point clouds. The method comprises building extraction, a detailed roof segmentation using region growing with adaptive thresholds, segment boundary creation, and a structural 3D building reconstruction approach using adaptive 2.5D Dual Contouring. First, a 2D-grid is overlain on the segmented point cloud. Second, in each grid cell 3D vertices of the building model are estimated from the corresponding LiDAR points. Then, the number of 3D vertices is reduced in a quad-tree collapsing procedure, and the remaining vertices are connected according to their adjacency in the grid. Roof segments are represented by a Triangular Irregular Network (TIN) and are connected to each other by common vertices or - at height discrepancies - by vertical walls. Resulting 3D building models show a very high accuracy and level of detail, including roof superstructures such as dormers. The workflow is tested and evaluated for two data sets, using the evaluation method and test data of the “ISPRS Test Project on Urban Classification and 3D Building Reconstruction” (Rottensteiner et al., 2012). Results show that the proposed method is comparable with the state of the art approaches, and outperforms them regarding undersegmentation and completeness of the scene reconstruction.
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Saidi, Mohamed. "L’intérêt de la segmentation en 2D et la reconstruction en 3D d’un processus tumoral de la hanche." Morphologie 100, no. 330 (September 2016): 151. http://dx.doi.org/10.1016/j.morpho.2016.07.157.
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Baba, Assia, and Mohamed Saidi. "L’intérêt de la segmentation en 2D et la reconstruction en 3D dans les différentes pathologies médico-chirurgicales." Morphologie 102, no. 338 (September 2018): 163. http://dx.doi.org/10.1016/j.morpho.2018.07.061.
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Sorzano, C. O. S., J. Vargas, J. Otón, J. M. de la Rosa-Trevín, J. L. Vilas, M. Kazemi, R. Melero, et al. "A Survey of the Use of Iterative Reconstruction Algorithms in Electron Microscopy." BioMed Research International 2017 (2017): 1–17. http://dx.doi.org/10.1155/2017/6482567.
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One of the key steps in Electron Microscopy is the tomographic reconstruction of a three-dimensional (3D) map of the specimen being studied from a set of two-dimensional (2D) projections acquired at the microscope. This tomographic reconstruction may be performed with different reconstruction algorithms that can be grouped into several large families: direct Fourier inversion methods, back-projection methods, Radon methods, or iterative algorithms. In this review, we focus on the latter family of algorithms, explaining the mathematical rationale behind the different algorithms in this family as they have been introduced in the field of Electron Microscopy. We cover their use in Single Particle Analysis (SPA) as well as in Electron Tomography (ET).
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Naldi, Giovanni, Barbara Avuzzi, Simona Fantini, Mauro Carrara, Ester Orlandi, Elisa Massafra, and Stefano Tomatis. "A SEGMENTATION PROBLEM IN QUANTITATIVE ASSESSMENT OF ORGAN DISPOSITION IN RADIOTHERAPY." Image Analysis & Stereology 30, no. 3 (November 1, 2011): 179. http://dx.doi.org/10.5566/ias.v30.p179-186.
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Radiotherapeutic treatment of cancer is best conducted if the prescription dose is given to the tumor while surrounding normal tissues are maximally spared. With the aim to meet these requirements the complexity of radiotherapy techniques have steadily increased under a strong technological impulse, especially in the last decades. One problem involves the rate of the particular disposition of the structures of interest in a patient. Recently the authors (Tomatis et al., 2010; 2011) have proposed a computational approach in order to represent quantitatively the geometrical features of organs at risk, summarized in characteristics of distance, shape and orientation of such organs in respect to the target. A basic problem to solve before to compute the risk index, is the segmentation of the organs involved in the radiotherapy planning. Here we described a 3D segmentation method by using the clinical computed tomography (CT) data of the patients. Our algorithm is based on different steps, a preprocessing phase where a nonlinear diffusion filter is applied; a level set based method for extract 2D countours; a postprocessing reconstruction of 3D volume from 2D segmented slices. Some comparisons with manually traced segmentation by clinical experts are provided.
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Jovicevic, Jovan, and Alan Bewick. "A study of the initial stages of the electrochemical deposition of metals on foreign substrates: Lead and thallium on copper and silver surfaces: General discussion." Facta universitatis - series: Physics, Chemistry and Technology 3, no. 2 (2005): 183–203. http://dx.doi.org/10.2298/fupct0502183j.
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The basic applicability of the UPD theory of Gerischer et al. has been confirmed in the case of lead and thallium deposition on copper and silver single crystals, but it was shown also that this is only one of the important factors. It was established that the effect of substrate structure on the mechanism of the UPD monolayer formation plays an important role in the addition to the effect of electronegativity difference between the substrate and depositing atoms. An effect of changing the concentration of depositing metal and specifically adsorbing anion were found and attributed to the changes in the electronegativity of the substrate and underpotential layer as a result of changing the electrode potential. It was conclusively proven by the analysis of the peaked current-time transients obtained by potential step measurements and the very sharp voltammetry peaks, that first order 2D phase transformations are possible in UPD systems. It was also found that the L.S.V. peaks reflecting such processes must not be expected to be free from the influence of slow kinetics. It was established that the 2D crystalline metal-like phases with the closest-packed epitaxial structure exist as a stable, final product in UPD. Moreover, the possibility of higher order 2D transformations in UPD has been given strong support by the evidence of gradual monolayer density change with increasing driving force. Lead UPD on vitreous carbon was found to be the result of substrate reconstruction induced by the repeated deposition and dissolution leading to surface condition changes favoring deposition of the first layer. UPD monolayers on copper and silver surfaces always preceded OPD and had a profound effect on its nucleation overpotential (making it very small indeed) or even changing its character from 3D into 2D (in the case of vitreous carbon substrate). It was also shown that lead and thallium OPD on copper and silver single crystals starts off by charge transfer controlled instantaneous 3D nucleation and subsequent growth of 3D centers. Finally, the results obtained in the experiments performed have shown that electrochemical techniques can prove very suitable in the study of 2D phase transformation kinetics and that their further employment in this field should prove particularly rewarding.
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Jessen, Kristian, Margot G. Gerritsen, and Bradley T. Mallison. "High-Resolution Prediction of Enhanced Condensate Recovery Processes." SPE Journal 13, no. 02 (June 1, 2008): 257–66. http://dx.doi.org/10.2118/99619-pa.
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Summary This paper investigates the accuracy of first- and high-order numerical methods in simulating enhanced condensate processes in 1D, 2D, and 3D. We compare the predictions of a standard single point upwind (SPU) scheme with a third-order accurate finite difference (FD) simulator based on a third-order essentially nonoscillatory (ENO) flux reconstruction with matching temporal accuracy. We include physical dispersion in the mathematical model of these multiphase, multicomponent systems. The comparisons demonstrate that SPU schemes may fail to predict the formation of the mobile liquid bank at the leading edge of the displacement unless an impractical number of gridblocks is used in the simulations. In contrast, the high-order FD simulator is demonstrated to accurately predict the liquid bank at much lower grid resolution, providing for a more efficient simulation approach. In 2D displacement calculations with gravity included, the CPU requirement of the SPU scheme was found to be more than 50 times larger than for the ENO scheme for a given level of accuracy. In 2D vertical cross-sections, the predicted component recovery is demonstrated to vary upward of 8% depending on the selected numerical scheme for a given grid resolution and dispersivity. In these settings, the SPU solutions converge to the ENO results upon significant grid refinement. In 3D displacement calculations, the magnitude of the predicted condensate bank is also found to be very different depending on the selected numerical scheme. Relative to the 2D displacement calculations, condensate banking and gravity segregation is observed to have less impact on the process performance prediction because of the permeability configuration in the 3D model used here, but it could have a high impact in different settings. We include an explicit representation of longitudinal and transverse dispersion in the porous medium to demonstrate the grid resolution required to resolve physical dispersion at a given simulation length scale, and to show that condensate banks can also form in more realistic dispersive systems. Grid-refinement studies in 1D and 2D demonstrate, again, that the ENO scheme outperforms the SPU scheme for a given Peclet (Pe) number. Converged solutions are obtained with the ENO scheme using a relatively small number of grid cells. In addition, we show the behavior of the two schemes for varying Peclet numbers on a fixed simulation grid. For this grid, the ENO scheme is shown to be sensitive to the Peclet number, signifying that physical dispersion is not overwhelmed by numerical diffusion. For the SPU scheme, however, the solutions are almost independent of the Peclet number, which indicates that numerical diffusion dominates. Introduction Significant portions of the current hydrocarbon reserves are found in gas-condensate-carrying formations. Production of hydrocarbons from these reserves is expected to increase upward of 100% by 2015 (Cambridge Energy Research Associates 2005). Primary production of these reserves will result in significant loss of the heavy ends because of liquid dropout once the reservoir pressure reaches the dew point pressure. Enhanced condensate recovery by gas cycling/injection schemes are often applied to extend the lifetime of condensate reservoirs. These processes are inherently compositional, as the component transfer between an immobile liquid phase and a mobile gas phase is the key mechanism for enhancing recovery. Numerical simulation of such processes is very challenging because the prediction of the local displacement efficiency and the global sweep can be very sensitive to numerical diffusion. Various authors have shown that numerical artifacts can alter the displacement characteristics and lead to significant underprediction of the local displacement efficiency (Stalkup et al. 1990; Lim et al. 1997; Johns et al. 2002; Jessen et al. 2004). In their numerical studies of gas injection in depleted condensate reservoirs, Høier and Whitson (2001) demonstrated that near-miscible gas injection may, in some cases, lead to the formation of a condensate bank at the leading edge of the displacement. In addition, for some injection settings, the liquid bank was shown to exceed the critical liquid saturation and hence become mobile. Their analysis was based on 1D displacement calculations. The work of Jessen and Orr (2004) demonstrated that the prediction of condensate banks that exceed the critical condensate saturation by numerical calculations requires a firm control of numerical diffusion. They used analytical solutions based on the method of characteristics (MOC) (Johns et al. 1993) as well as a high-resolution FD simulator developed by Mallison et al. (2005) to investigate the complex interplay of flow and phase behavior in enhanced condensate recovery processes in 1D. In this work, we extend this investigation of enhanced condensate recovery processes to 2D and 3D. We include gravity to study the impact of a mobile liquid bank on the overall efficiency of the enhanced condensate recovery (ECR) process. We investigate the grid resolutions needed for both numerical schemes to resolve the condensate banks, and the impact of numerical errors on the predicted recovery in the presence of gravity. We also study the importance of physical dispersion in ECR processes. In particular, we are interested in understanding the grid resolution that is required to resolve the physical dispersion terms by controlling the level of numerical diffusion. We note that physical dispersion/diffusion is required to obtain a converged solution in 2D and 3D for this type of displacement problem. In the following section, we introduce the mathematical model for multicomponent multiphase flow in porous media, including an explicit representation of dispersive terms. We then describe the implementation in our compositional simulator. Next, we discuss the condensate system investigated in this work and present simulation results for enhanced condensate recovery in 1D, 2D, and 3D. Finally, we draw conclusions from the presented material.
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Coenen, M., F. Rottensteiner, and C. Heipke. "PRECISE VEHICLE RECONSTRUCTION FOR AUTONOMOUS DRIVING APPLICATIONS." ISPRS Annals of Photogrammetry, Remote Sensing and Spatial Information Sciences IV-2/W5 (May 29, 2019): 21–28. http://dx.doi.org/10.5194/isprs-annals-iv-2-w5-21-2019.
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<p><strong>Abstract.</strong> Interactive motion planing and collaborative positioning will play a key role in future autonomous driving applications. For this purpose, the precise reconstruction and pose estimation of other traffic participants, especially of other vehicles, is a fundamental task and will be tackled in this paper based on street level stereo images obtained from a moving vehicle. We learn a shape prior, consisting of vehicle geometry and appearance features, and we fit a vehicle model to initially detected vehicles. This is achieved by minimising an energy function, jointly incorporating 3D and 2D information to infer the model’s optimal and precise pose parameters. For evaluation we use the object detection and orientation benchmark of the KITTI dataset (Geiger et al., 2012). We can show a significant benefit of each of the individual energy terms of the overall objective function. We achieve good results with up to 94.8% correct and precise pose estimations with an average absolute error smaller than 3&deg; for the orientation and 33&thinsp;cm for position.</p>
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Fadli, F., N. Kutty, Z. Wang, S. Zlatanova, L. Mahdjoubi, P. Boguslawski, and V. Zverovich. "EXTENDING INDOOR OPEN STREET MAPPING ENVIRONMENTS TO NAVIGABLE 3D CITYGML BUILDING MODELS: EMERGENCY RESPONSE ASSESSMENT." ISPRS - International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences XLII-4 (September 19, 2018): 161–68. http://dx.doi.org/10.5194/isprs-archives-xlii-4-161-2018.
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<p><strong>Abstract.</strong> Disaster scenarios in high-rise buildings such as the Address Downtown, Dubai or Grenfell Tower, London have showed ones again the importance of data information availability for emergency management in buildings. 3D visualization of indoor routing services using extensive and high quality geographic data sources is essential for spatial analysis in emergency responses. In order to facilitate emergency response simulations, a combination of geometrical, graphical and semantic information is essential. Successful and efficient emergency evacuation responses is facilitated by the availability of both digital static and dynamic information of the incident site. However, interruptions may be encountered with the availability of dynamic data, where static data developed using indoor navigation ontologies serve as an alternative to inform the first responders. Thus, it is necessary to obtain a firm, interactive and quasi-realistic virtual simulation of the building environments. Voxelized CityGML models imported into voxel based hazard simulation systems fits well into the simulation algorithm requirements (Groger et al., 2008; Moreno et.al, 2010). Therefore, the research investigates an alternative platform for generating CityGML spatial analysis models. LoD4 models are developed using Computer Aided Design (Auto CAD) 2D files, crowdsourced geo-data (OpenStreetMap) and open source tools. A combination of software packages is utilized for 3D reconstruction of building interiors. This process is achieved through a Java application developed by researchers at Heidelberg University. Conclusions drawn from the research validate the 3D CityGML model generation process as an international standard to effectively enhance the outcome of emergency evacuation simulations of high rise buildings.</p>
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Poreba, Martyna, and François Goulette. "Recalage rigide de relevé laser par mise en correspondance robuste basée sur des segments." Revue Française de Photogrammétrie et de Télédétection, no. 207 (September 24, 2014): 3–17. http://dx.doi.org/10.52638/rfpt.2014.208.
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Le recalage se révèle indispensable pour assembler des relevés laser devant servir à l'analyse, à la documentation et à la reconstruction tridimensionnelle d'environnements. Ce problème apparaît lorsqu'une zone d'intérêt est numérisée, au fil du temps, deux ou plusieurs fois, ou quand sa complexité nécessite un accroissement du nombre de stations de scanner laser fixes. Aussi, en raison de la variété des techniques disponibles d'acquisition, l'intégration multi-données devient une question importante puisqu'elle permet de mettre en cohérence des données contenant souvent une information complémentaire. La vaste majorité des algorithmes existants s'appuient sur les éléments ponctuels. C'est pourquoi les méthodes ICP basées-point demeurent actuellement les plus répandues. Cet article propose l'utilisation des segments sous forme d'intersections entre les plans principaux, pour un recalage rigide des nuages de points mobiles avec d'autres données, qu'elles soient 2D ou 3D. Ces primitives peuvent être aisément extraites, même dans les données laser hétérogènes de faible densité. Quelques méthodes de recalage basées-lignes ont été examinées afin de vérifier leur précision et robustesse au bruit. Les erreurs des paramètres estimés ainsi qu'un nouveau critère — distance modifiée de Hausdorff ont été employés pour les besoins d'une analyse quantitative. Au vu de ces éléments, une chaîne complète nommée RLMR-FMII 2 comprenant un recalage grossier suivi par un recalage fin est proposée pour calculer les paramètres de pose à partir de segments appariés.Étant donné que la mise en correspondance automatique d'entités linéaires est ardue et influence l'estimation des paramètres optimaux de transformation, une méthode d'appariement étudiant la similitude relative est avancée. Enfin, l'efficacité de cette méthode de recalage par mise en correspondance préalable des segments est évaluée et discutée.
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Fuller, James, Joseph Batchelor, Kevin Knockenhauer, Hans-Peter Biemann, and Robert Peters. "Cryo-EM Structure of BIVV001 Reveals Coagulation Factor VIII-Von Willebrand Factor D'D3 Interaction Mode." Blood 134, Supplement_1 (November 13, 2019): 94. http://dx.doi.org/10.1182/blood-2019-126645.
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Introduction Coagulation Factor VIII (FVIII) is a serine protease cofactor that directly interacts with coagulation factors IXa and X on activated platelets, and enhances FIXa activity toward FX by 105. von Willebrand Factor (VWF), via its D'D3 domains, interacts with FVIII and prevents premature deposition on phospholipids until activation by thrombin. Thrombin cleavage at Arg1689 of FVIII promotes VWF dissociation by disrupting the FVIII a3 high affinity interaction with the VWF D' domain. VWF extends the half-life of circulating FVIII from less than 3 hours to ~11 hours in humans. While crystal structures of FVIII and VWF D'D3 alone have been solved, the atomic details of a formed complex are unknown. We sought to determine the FVIII-VWF D'D3 complex structure by using BIVV001, our investigational new drug currently in clinical trials for the treatment of Hemophilia A. BIVV001 (rFVIIIFc-VWF-XTEN) is a novel fusion protein consisting of single chain B-domain deleted (BDD) human FVIII, the Fc domain of human immunoglobulin G1 (IgG1), the FVIII-binding D'D3 domain of human von Willebrand factor, and 2 XTEN polypeptide linkers. The Fc, VWF, and XTEN linker portions of the molecule are each designed to extend the half-life of FVIII. We anticipated that the tethering of FVIII to D'D3 through the Fc dimer in BIVV001 would stabilize the complex for structural studies. Given the large size of BIVV001, at 312 kDa, we thought it an ideal target for structure determination by single particle cryo-EM. Methods We collected a total of 3955 micrographs of BIVV001 embedded in vitreous ice at 81,000x magnification using a Titan Krios electron microscope equipped with a Gatan BioQuantum K3 energy filter and camera operating in super-resolution mode. Preferential particle orientation was a major challenge that was overcome through a variety of methods. Micrograph movies were motion-corrected and summed, and over 2 million candidate particle coordinates were extracted. Repeated rounds of reference-free 2D classification resulted in a set of 1.2 million particles that generated a reasonable ab initio/de novo 3D model. Initial full 3D refinements of this model produced a map at approximately 5 Å resolution, into which available crystal structures can be readily fit. Subsequent iterative 3D refinement and 3D classification resulted in a final map at high resolution, into which an atomic model was built. Results The structure of BIVV001 was solved by single particle cryo-EM. D' of VWF interacts with the front face of the C1 and A3 domains of FVIII, consistent with a lower resolution, negative stain EM map (Yee et al. 2015. Blood). Interface residues on FVIII identified in an HDX-MS dataset (Chiu et al. 2015. Blood.) largely correspond to this high affinity interaction. D' protrudes upward from the VWF D3 domain, which sits centrally located between the C1 and C2 domains of FVIII at a 45° tilt. By occupying this position, D3 likely sterically blocks the FVIII C domains from binding to membrane. The VWD3 module of the D3 domain contacts the base of the C1 domain, whereas C8-3 binds to the bottom of the C2 domain. The conserved Ca2+ site in VWD3 identified previously (Dong et al. 2019. Blood.) is in the interface with C1. This is consistent with Yee et al., where docking placed D3 below the C domains. In that study, a lack of density between FVIII and VWF D3 in the 3D reconstruction, due to flexibility, prevented the detailed analysis that is possible here. In this study, flexibility in this region is also apparent, as C2 is less well ordered than the rest of FVIII and VWF D3 is the least well-ordered portion of the resolved structure. The XTEN linkers are not visible in the final map and were not apparent in any 2D class averages. The Fc is absent in most 2D class averages, due to a lack of consistent positioning relative to FVIII. In the rare cases where the Fc is visible, it adopts a preferred position on the back side of FVIII below the A3 protrusion. Conclusions The structure of BIVV001 has been solved by cryo-electron microscopy to high resolution. Alignment with previous results and the averaging out of BIVV001 elaborations suggests the structure obtained here likely represents WT FVIII-D'D3. This structure demonstrates how VWF D'D3 prevents premature FVIII deposition on phospholipids. The structural basis of type 2N von Willebrand Disease mutations in D'D3 can be readily interpreted. Next steps include solving a FVIII-D'D3 dimer structure at high resolution. Disclosures Fuller: Sanofi: Employment. Batchelor:Sanofi: Employment. Knockenhauer:Sanofi: Employment. Biemann:Sanofi: Employment. Peters:Sanofi: Employment.
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Staderini, Edoardo, Marilisa De Luca, Ettore Candida, Maria Ida Rizzo, Oriana Rajabtork Zadeh, Daria Bucci, Mario Zama, Carlo Lajolo, Massimo Cordaro, and Patrizia Gallenzi. "Lay People Esthetic Evaluation of Primary Surgical Repair on Three-Dimensional Images of Cleft Lip and Palate Patients." Medicina 55, no. 9 (September 8, 2019): 576. http://dx.doi.org/10.3390/medicina55090576.
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Background and Objectives: Previous literature has disclosed that facial attractiveness affects the esthetic evaluation of nose and lip deformity on frontal and lateral photographs. However, it has never been debated if the removal of the external facial features on three-dimensional (3D) models (“cropped assessment bias”) could provide a considerable usefulness in the interpretation and comparison of the results. Additionally, it has been assumed on two-dimensional (2D) studies that esthetic assessment biases with respect to observer gender, and it is not acknowledged if and to the extent that “gender assessment bias” may be influenced by a three-dimensional layout. The aim of this study is to investigate if facial traits and observers’ gender may affect the esthetic ratings of unilateral cleft lip and palate (UCLP) patients after soft tissue reconstruction. Materials and Methods: Three-dimensional images of ten UCLP patients’ images were acquired before the intervention (T0), one-month (T1) and six-months (T2) postoperative. Geomagic® software (version 2014; 3D Systems, Rock Hill, SC, USA) was used to remove the external facial features of 3D surface models. Five-point scale developed by Asher-McDade et al. was used to rate both nasolabial attractiveness and impairment for full-face (FF) and cropped-face (CF) 3D images. Forty-three judges (21 males, 22 females) were enrolled for the esthetic evaluation. Intraclass correlation coefficient (ICC) was used to test intra- and inter-examiner reliability; a value of 0.7 was set as the minimum acceptable level of reliability. Results: When comparing the 2 sets of observations (FF and CF), the ICC ranged from 0.654 to 0.823. Concerning gender assessment bias, the ICC ranged from 0.438 to 0.686 and from 0.722 to 0.788 for males and females, respectively. Concerning inter-examiner reliability, ICC for questions 2–7 ranged from 0.448 to 0.644 and from 0.659 to 0.817 at T0 and T2, respectively. Conclusions: The removal of external facial features provides subtle differences on the esthetic assessment of UCLP patients. Moreover, based on our data, examiners’ gender differences may affect esthetic assessment of UCLP patients. Despite the subjectivity of esthetic judgments, a reliable, validated and reproducible scoring protocol should consider the influence of gender differences on 3D esthetic assessment of UCLP patients.
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Gao, Si, Fucai Zhang, A. I. Kirkland, Xiaoqing Pan, and Peng Wang. "Electron Ptychography: From 2D to 3D Reconstructions." Microscopy and Microanalysis 23, S1 (July 2017): 346–47. http://dx.doi.org/10.1017/s1431927617002410.
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Kuchment, Peter, and Leonid Kunyansky. "2D and 3D reconstructions in acousto-electric tomography." Inverse Problems 27, no. 5 (April 18, 2011): 055013. http://dx.doi.org/10.1088/0266-5611/27/5/055013.
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Dillavou, Ellen D., David G. Buck, Satish C. Muluk, and Michel S. Makaroun. "Two-Dimensional versus Three-Dimensional CT Scan for Aortic Measurement." Journal of Endovascular Therapy 10, no. 3 (June 2003): 531–38. http://dx.doi.org/10.1177/152660280301000319.
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Purpose: To examine if 3-dimensional (3D) reconstructions of computed tomographic (CT) data, by imaging perpendicular to blood flow, can improve aortic diameter measurement accuracy over axial (2D) CT. Methods: Two independent, blinded observers used electronic calipers to measure the minor axis and the line perpendicular to it on 40 2.5-mm 2D CT scans from 31 patients. A circular electronic tool was used to estimate diameters on 3D reconstructions from the same 40 scans. Measurements of the aortic neck were obtained 5 mm below the renal arteries and the widest slice of the aneurysm was used to measure sac diameter. Only the minor axis was measured at the iliac arteries immediately above the left (LI) and right (RI) iliac bifurcations. Datasets were compared with an intraclass correlation coefficient (ICC), Bland and Altman variation assessments, and absolute differences. Results: ICC between 2D and 3D scans demonstrated high correlation with 2D minor axis measurements (neck=0.9282, sac=0.8956, RI=0.8755, LI=0.7381). 3D to 2D major axis correlation was lower (neck=0.6388, sac=0.8995). Variation between 3D and 2D minor axis measurements was low (0.51-mm average variation from the mean for the minor axis and 1.30-mm variation for the major axis). Average absolute difference between 3D and 2D diameters was 1.01 mm (minor axis) versus 2.61 mm (major axis). Interobserver correlation was highest for sac measurements both in 2D minor axis (ICC=0.8990) and 3D (ICC=0.9518). Conclusions: Minor axis measurements on axial CT scan can substitute for diameters obtained from 3D reconstructions in most clinical situations.
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Protas, Bartosz, Bernd R. Noack, and Jan Östh. "Optimal nonlinear eddy viscosity in Galerkin models of turbulent flows." Journal of Fluid Mechanics 766 (February 4, 2015): 337–67. http://dx.doi.org/10.1017/jfm.2015.14.
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AbstractWe propose a variational approach to the identification of an optimal nonlinear eddy viscosity as a subscale turbulence representation for proper orthogonal decomposition (POD) models. The ansatz for the eddy viscosity is given in terms of an arbitrary function of the resolved fluctuation energy. This function is found as a minimizer of a cost functional measuring the difference between the target data coming from a resolved direct or large-eddy simulation of the flow and its reconstruction based on the POD model. The optimization is performed with a data-assimilation approach generalizing the 4D-VAR method. POD models with optimal eddy viscosities are presented for a 2D incompressible mixing layer at $\mathit{Re}=500$ (based on the initial vorticity thickness and the velocity of the high-speed stream) and a 3D Ahmed body wake at $\mathit{Re}=300\,000$ (based on the body height and the free-stream velocity). The variational optimization formulation elucidates a number of interesting physical insights concerning the eddy-viscosity ansatz used. The 20-dimensional model of the mixing-layer reveals a negative eddy-viscosity regime at low fluctuation levels which improves the transient times towards the attractor. The 100-dimensional wake model yields more accurate energy distributions as compared to the nonlinear modal eddy-viscosity benchmark proposed recently by Östh et al. (J. Fluid Mech., vol. 747, 2014, pp. 518–544). Our methodology can be applied to construct quite arbitrary closure relations and, more generally, constitutive relations optimizing statistical properties of a broad class of reduced-order models.
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Navaneet, K. L., Priyanka Mandikal, Mayank Agarwal, and R. Venkatesh Babu. "CAPNet: Continuous Approximation Projection for 3D Point Cloud Reconstruction Using 2D Supervision." Proceedings of the AAAI Conference on Artificial Intelligence 33 (July 17, 2019): 8819–26. http://dx.doi.org/10.1609/aaai.v33i01.33018819.
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Knowledge of 3D properties of objects is a necessity in order to build effective computer vision systems. However, lack of large scale 3D datasets can be a major constraint for datadriven approaches in learning such properties. We consider the task of single image 3D point cloud reconstruction, and aim to utilize multiple foreground masks as our supervisory data to alleviate the need for large scale 3D datasets. A novel differentiable projection module, called ‘CAPNet’, is introduced to obtain such 2D masks from a predicted 3D point cloud. The key idea is to model the projections as a continuous approximation of the points in the point cloud. To overcome the challenges of sparse projection maps, we propose a loss formulation termed ‘affinity loss’ to generate outlierfree reconstructions. We significantly outperform the existing projection based approaches on a large-scale synthetic dataset. We show the utility and generalizability of such a 2D supervised approach through experiments on a real-world dataset, where lack of 3D data can be a serious concern. To further enhance the reconstructions, we also propose a test stage optimization procedure to obtain reconstructions that display high correspondence with the observed input image.
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Orman, Gunes, Matthias W. Wagner, Daniel Seeburg, Carlos A. Zamora, Alexander Oshmyansky, Aylin Tekes, Andrea Poretti, George I. Jallo, Thierry A. G. M. Huisman, and Thangamadhan Bosemani. "Pediatric skull fracture diagnosis: should 3D CT reconstructions be added as routine imaging?" Journal of Neurosurgery: Pediatrics 16, no. 4 (October 2015): 426–31. http://dx.doi.org/10.3171/2015.3.peds1553.
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OBJECT The authors compared the efficacy of combining 2D+3D CT reconstructions with standard 2D CT images in the diagnosis of linear skull fractures in children with head trauma. METHODS This was a retrospective evaluation of consecutive head CT studies of children presenting with head trauma. Two experienced pediatric neuroradiologists in consensus created the standard of reference. Three readers independently evaluated the 2D CT images alone and then in combination with the 3D reconstructions for the diagnosis of linear skull fractures. Sensitivity and specificity in the diagnosis of linear skull fractures utilizing 2D and 2D+3D CT in combination were measured for children less than 2 years of age and for all children for analysis by the 3 readers. RESULTS Included in the study were 250 consecutive CT studies of 250 patients (167 boys and 83 girls). The mean age of the children was 7.82 years (range 4 days to 17.4 years). 2D+3D CT combined had a higher sensitivity and specificity (83.9% and 97.1%, respectively) compared with 2D alone (78.2% and 92.8%, respectively) with statistical significance for specificity (p < 0.05) in children less than 2 years of age. 2D+3D CT combined had a higher sensitivity and specificity (81.3% and 90.5%, respectively) compared with 2D alone (74.5% and 89.1%, respectively) with statistical significance for sensitivity (p < 0.05) in all children. CONCLUSIONS In this study, 2D+3D CT in combination showed increased sensitivity in the diagnosis of linear skull fractures in all children and increased specificity in children less than 2 years of age. In children less than 2 years of age, added confidence in the interpretation of fractures by distinguishing them from sutures may have a significant implication in the setting of nonaccidental trauma. Furthermore, 3D CT is available at no added cost, scan time, or radiation exposure, providing trainees and clinicians with limited experience an additional valuable tool for routine imaging of pediatric head trauma.
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Leonard, A., F. Lanusse, and J. L. Starck. "Weak lensing reconstructions in 2D and 3D: implications for cluster studies." Monthly Notices of the Royal Astronomical Society 449, no. 1 (March 20, 2015): 1146–57. http://dx.doi.org/10.1093/mnras/stv386.
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Jäderling, Fredrik, Tommy Nyberg, Michael Öberg, Stefan Carlsson, Mikael Skorpil, and Lennart Blomqvist. "Accuracy in local staging of prostate cancer by adding a three-dimensional T2-weighted sequence with radial reconstructions in magnetic resonance imaging." Acta Radiologica Open 7, no. 2 (February 2018): 205846011875460. http://dx.doi.org/10.1177/2058460118754607.
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Background The evidence supporting the use of magnetic resonance imaging (MRI) in prostate cancer detection has been established, but its accuracy in local staging is questioned. Purpose To investigate the additional value of multi-planar radial reconstructions of a three-dimensional (3D) T2-weighted (T2W) MRI sequence, intercepting the prostate capsule perpendicularly, for improving local staging of prostate cancer. Material and Methods Preoperative, bi-parametric prostate MRI examinations in 94 patients operated between June 2014 and January 2015 where retrospectively reviewed by two experienced abdominal radiologists. Each patient was presented in two separate sets including diffusion-weighted imaging, without and with the 3D T2W set that included radial reconstructions. Each set was read at least two months apart. Extraprostatic tumor extension (EPE) was assessed according to a 5-point grading scale. Sensitivity and specificity for EPE was calculated and presented as receiver operating characteristics (ROC) with area under the curve (AUC), using histology from whole-mount prostate specimen as gold standard. Inter-rater agreement was calculated for the two different reading modes using Cohen’s kappa. Results The AUC for detection of EPE for Readers 1 and 2 in the two-dimensional (2D) set was 0.70 and 0.68, respectively, and for the 2D + 3D set 0.62 and 0.65, respectively. Inter-rater agreement (Reader 1 vs. Reader 2) on EPE using Cohen’s kappa for the 2D and 2D + 3D set, respectively, was 0.42 and 0.17 (i.e. moderate and poor agreement, respectively). Conclusion The addition of 3D T2W MRI with radial reconstructions did not improve local staging in prostate cancer.
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Schell, Adam, John M. Rhee, John Holbrook, Eric Lenehan, and Kun Young Park. "Assessing Foraminal Stenosis in the Cervical Spine: A Comparison of Three-Dimensional Computed Tomographic Surface Reconstruction to Two-Dimensional Modalities." Global Spine Journal 7, no. 3 (April 11, 2017): 266–71. http://dx.doi.org/10.1177/2192568217699190.
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Study Design: Retrospective radiographic study. Objective: The optimal radiographic modality for assessing cervical foraminal stenosis is unclear. Determination on conventional axial cuts is made difficult due in part to the complex, oblique orientation of the cervical neuroforamen. The utility of 3-dimensonal (3D) computed tomography (CT) reconstruction in improving neuroforaminal assessment is not well understood. The objective of this study is to determine inter-rater variability in grading cervical foraminal stenosis using 3 different CT imaging modalities: 3D CT surface reconstructions (3DSR), 2D sagittal oblique multiplanar reformations (2D-SOMPR), and conventional 2D axial CT imaging. Methods: Pretreatment CT scans of 25 patients undergoing surgery for cervical spondylotic radiculopathy were analyzed at 2 levels: C5-C6 and C6-C7. Simple interrater agreement and kappa-Fleiss coefficients were calculated for each imaging modality and stenosis grade. Image reviewers (attending spine surgeon, attending neuroradiologist, spine fellow) interpreted each CT scan in 3 different formats: axial, 2D-SOMPR, and 3DSR. Four cervical foramina at 2 spinal levels were graded as normal (no stenosis), mild (≤25% stenosis), moderate (25%-50% stenosis), or severe (>50% stenosis). Results: Across all imaging modalities, interrater reliability was fair when grading foraminal stenosis (κ < 0.4). Agreement was lowest for the axial images (κ = 0.119) and highest for the 3D CT reconstructions (κ = 0.334). 2D-SOMPR images also led to improved interrater reliability when compared with axial images (κ = 0.255). Conclusion: Grading cervical foraminal stenosis using conventional axial CT imaging is difficult with low interrater reliability. CT modalities that provide a circumferential view of the cervical foramen, such as 2D-SOMPR and 3D CT reconstruction, had higher rates of interobserver reliability in grading foraminal stenosis than conventional axial cuts, with 3D having the highest. As these 3D reconstructions can be obtained at no additional cost or radiation exposure over a conventional CT scan, and because they can provide useful information in determining levels being considered for surgical decompression, we recommend they be utilized when evaluating cervical foramina.
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Seright, R. S., J. Liang, W. Brent Lindquist, and John H. Dunsmuir. "Characterizing Disproportionate Permeability Reduction Using Synchrotron X-Ray Computed Microtomography." SPE Reservoir Evaluation & Engineering 5, no. 05 (October 1, 2002): 355–64. http://dx.doi.org/10.2118/79717-pa.
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Summary X-ray computed microtomography was used to investigate why gels reduce permeability to water more than that to oil in strongly water-wet Berea sandstone and in an oil-wet porous polyethylene core. Although the two porous media had very different porosities (22% vs. 40%), the distributions of pore sizes and aspect ratios were similar. A Cr(III)-acetate-HPAM gel caused comparable oil and water permeability reductions in both porous media. In both cores, the gel reduced permeability to water by a factor 80 to 90 times more than that to oil. However, the distributions of water and oil saturations (vs. pore size) were substantially different before, during, and after gel placement. This paper examines the mechanism for the disproportionate permeability reduction in the two porous media. Introduction Many polymers and gels can reduce the permeability to water more than that to oil or gas.1–15 This property is critical to the success of water-shutoff treatments in production wells if hydrocarbon- productive zones cannot be protected during polymer or gelant placement.2,3 However, the magnitude of the effect has been unpredictable from one application to the next. Presumably, the effect would be more predictable and controllable if we understood why the phenomenon occurs. Although many mechanisms have been considered (see Table 1), the underlying cause of the disproportionate permeability reduction remains elusive. Previously, we used NMR imaging to observe disproportionate permeability reduction on a microscopic scale.16 Results from these experiments revealed that the imaging technique had many limitations that prevented us from obtaining reliable pore-level images. Most importantly, the spatial resolution was on the order of hundreds of micrometers, which was too low to clearly distinguish fluid pathways on the pore level. In this paper, we describe imaging experiments using high-resolution computed X-ray microtomography (XMT) to compare the oil and water pathways and fluid distributions before and after gel treatment. The current generation of synchrotron-based XMT scanners provides the ability to obtain 3D pore-level images of rock samples with a spatial resolution on the order of micrometers. 17–23 For this study, we used the ExxonMobil beamline X2-B at the Natl. Synchrotron Light Source.18 X2-B is a dedicated XMT imaging facility capable of producing continuous registered stacks of 2,048×2,048×1,024 14-bit 3D images of X-ray linear attenuation coefficients at energies tunable from 8 to 40 keV. The highly collimated synchrotron X-rays permit the reconstruction of a 3D image from 2D projections taken at uniformly spaced angles between 0 and 180°. X2-B converts the pattern X-rays transmitted by the specimen (projections) to a visible light image with a thin single crystal of CsI(Na). This image was magnified by an optical microscope objective onto a 1,024×1,024 charge coupled device (CCD). Using Fourier methods, the set of angular projections at each row of pixels in the CCD was used to reconstruct the crosssectional slice at that row. These slices were stacked to form the 3D image. In this work, a 5×microscope objective was used to provide a pixel size of 4.1 µm and a 4.1-mm field of view. Because part of the core was outside the imaged area, a profile extension method was used to supress edge artifacts. Several authors used XMT to characterize the microscopic structure of porous media.17,19,23 For a 15-darcy sandstone, Coles et al.19 found a mean tortuosity of 2.7, with a range from 1.5 to 4.5. Along a 2.2-mm-long section of this core, porosity varied only a few percent around the average value (26.4%). After oilflooding, this core was waterflooded to a water saturation of 25.1%. Interestingly, large variations in water saturation were observed along the 2.2-mm-long section, ranging from 12 to 39%. A 3D view showed the nonwetting phase (water, in this case) to exist as large ganglia (blobs of nonwetting phase that extend over multiple pores, often exhibiting a branched structure).19 Chatzis et al.24,25 suggested that rock heterogeneity can be responsible for saturation variations within a porous medium. Nonwetting phase saturations that are lower than expected can occur when clusters of small pores are dispersed in a matrix dominated by large pores. In contrast, nonwetting phase saturations that are higher than expected can occur when clusters of large pores are dispersed in a matrix dominated by small pores.24 However, significant saturation variations can occur even in homogeneous porous media, depending on the pore-body/pore-throat aspect ratio. For homogeneous 2D micromodels, Chatzis et al.24 reported piston-like displacements with very little trapping of the nonwetting phase when the aspect ratio was 2 or less. However, for aspect ratios around 3, large nonwetting phase clusters formed as the wetting phase formed fingers while displacing the nonwetting phase. At higher aspect ratios, the nonwetting phase tended to be trapped in individual pores rather than in large clusters of pores. The pore coordination number had a minor effect on nonwetting phase residual saturations.24 Using XMT data, Lindquist et al.23 extensively characterized pore- and throat-size distributions for Fontainebleau sandstones. As core porosity increased from 7.5 to 22%, they found that the average pore coordination number increased from 3.4 to 3.8; the average channel length decreased from 200 to 130 µm; the average throat area increased from 1,600 to 2,200 mum2; and the average pore volume remained fairly constant at approximately 0.0004 mm3. The aspect ratio (effective average pore radius/effective average throat radius) was greater than 2 in 65% of pores and greater than 3 in 40%. The aspect ratios tended to increase slightly as porosity decreased.
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Xiong, Zi Ming, Gang Wan, and Xue Feng Cao. "Automatic Alignment of 3D Point Clouds to Orthographic Images." Advanced Materials Research 591-593 (November 2012): 1265–68. http://dx.doi.org/10.4028/www.scientific.net/amr.591-593.1265.
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Recent progress in structure-from-motion (SfM) has led to robust techniques that can operate in extremely general conditions. However, a limitation of SfM is that the scene can only be recovered up to a similarity transformation. We address the problem of automatically aligning 3D point clouds from SfM reconstructions to orthographic images. We extract feature lines from 3D point clouds, and project the feature lines onto the ground plane to create a 2D feature lines. So we reduce this alignment problem to a 2D line to 2D line alignment(match), and a novel technique for the automatic feature lines matching is presented in this paper.
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Altahawi, Faysal, Jason Pierce, Mercan Aslan, Xiaojuan Li, Carl S. Winalski, and Naveen Subhas. "3D MRI of the Knee." Seminars in Musculoskeletal Radiology 25, no. 03 (June 2021): 455–67. http://dx.doi.org/10.1055/s-0041-1730400.
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AbstractThree-dimensional (3D) magnetic resonance imaging (MRI) of the knee is widely used in musculoskeletal (MSK) imaging. Currently, 3D sequences are most commonly used for morphological imaging. Isotropic 3D MRI provides higher out-of-plane resolution than standard two-dimensional (2D) MRI, leading to reduced partial volume averaging artifacts and allowing for multiplanar reconstructions in any plane with any thickness from a single high-resolution isotropic acquisition. Specifically, isotropic 3D fast spin-echo imaging, with options for tissue weighting similar to those used in multiplanar 2D FSE imaging, is of particular interest to MSK radiologists. New applications for 3D spatially encoded sequences are also increasingly available for clinical use. These applications offer advantages over standard 2D techniques for metal artifact reduction, quantitative cartilage imaging, nerve imaging, and bone shape analysis. Emerging fast imaging techniques can be used to overcome the long acquisition times that have limited the adoption of 3D imaging in clinical protocols.
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Zamora, Natalia, Jose M. Llamas, Rosa Cibrián, Jose L. Gandia, and Vanessa Paredes. "Cephalometric measurements from 3D reconstructed images compared with conventional 2D images." Angle Orthodontist 81, no. 5 (April 7, 2011): 856–64. http://dx.doi.org/10.2319/121210-717.1.
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Abstract Objective: To assess whether the values of different measurements taken on three-dimensional (3D) reconstructions from cone-beam computed tomography (CBCT) are comparable with those taken on two-dimensional (2D) images from conventional lateral cephalometric radiographs (LCRs) and to examine if there are differences between the different types of CBCT software when taking those measurements. Material and Methods: Eight patients were selected who had both an LRC and a CBCT. The 3D reconstructions of each patient in the CBCT were evaluated using two different software packages, NemoCeph 3D and InVivo5. An observer took 10 angular and 3 linear measurements on each of the three types of record on two different occasions. Results: Intraobserver reliability was high except for the mandibular plane and facial cone (from the LCR), the Na-Ans distance (using NemoCeph 3D), and facial cone and the Ans-Me distance (using InVivo5). No statistically significant differences were found for the angular and linear measurements between the LCRs and the CBCTs for any measurement, and the correlation levels were high for all measurements. Conclusion: No statistically significant differences were found between the angular and linear measurements taken with the LCR and those taken with the CBCT. Neither were there any statistically significant differences between the angular or linear measurements using the two CBCT software packages.
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Khan, AR, M. Cocker, JD Spence, M. Alturkustani, C. Currie, C. Cathie, L. Hammond, et al. "3D carotid reconstructions: imaging, pathology, algorithms and pipelines." Canadian Journal of Neurological Sciences / Journal Canadien des Sciences Neurologiques 42, S1 (May 2015): S37. http://dx.doi.org/10.1017/cjn.2015.170.
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Background: Whole-slide scanning of tissue sections spatially informed by imaging studies offers the opportunity to reconstruct specimens for co-registration to 3D imaging data. Digital image analysis algorithms can be designed to analyze and reconstruct such specimens via electronic “pipelines”. Methods: A goal of the Canadian Atherosclerosis Imaging Network (CAIN) is to improve the assessment of carotid atheromatous disease through studies that inform clinical imaging with gold-standard data (plaque pathology). To achieve this, sectioned atheromas are manually annotated and analyzed by electronic algorithm for pathological features of interest. Resulting images are then reassembled in 3D for registration to ultrasound, CT, PET-CT and MRI studies. Results: Carotid endarterectomy specimens were sub-serially sectioned, stained, digitized and annotated manually and by electronic algorithms. Resulting 2D images were successfully rendered, reassembled and analyzed in 3D using ex-vivo micro-CT as a spatial reference. Furthermore, histology quantification using colour deconvolution was found to be preferred over hue-saturation-intensity methods 94.7-100% of the time in a blinded multiple rater study. Conclusion: Automated “pipelines” greatly facilitate 3D reconstruction in comparison to traditional slice-by-slice methods. Transformations spatially guided by pre-existing imaging data is not only faster, but has superior objectivity and fidelity. With embedded annotations, 3D pathology maps become a rich, micron-level, permanent digital pathological database for correlative studies.
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Tulunoglu, Ozlem, Elcin Esenlik, Ayse Gulsen, and Ibrahim Tulunoglu. "A Comparison of Three-Dimensional and Two-Dimensional Cephalometric Evaluations of Children with Cleft Lip and Palate." European Journal of Dentistry 05, no. 04 (October 2011): 451–58. http://dx.doi.org/10.1055/s-0039-1698918.
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ABSTRACTObjectives: The aim of this retrospective study was to compare the consistency of orthodontic measurement performed on cephalometric films and 3D CT images of cleft lip and palate (CLP) patients. Methods: The study was conducted with 2D radiographs and 3D CT images of 9 boys and 6 girls aged 7-12 with CLP. 3D reconstructions were performed using MIMICS software. Results: Frontal analysis found statistical differences for all parameters except occlusal plane tilt (OcP-tilt) and McNamara analysis found statistical differences in 2D and 3D measurements for all parameters except ANS-Me and Co-Gn; Steiner analysis found statistical differences for all parameters except SND, SNB and Max1-SN. Intra-group variability in measurements was also very low for all parameters for both 2D and 3D images. Conclusions: Study results indicate significant differences between measurements taken from 2D and 3D images in patients with cleft lip and palate. (Eur J Dent 2011;5:451-458)
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Boccuzzi, F., M. Busso, L. Cardinale, and C. Fava. "Primary tracheo-bronchial amyloidosis studied with 64-slice MDCT (2D and 3D reconstructions)." Thorax 66, no. 10 (December 16, 2010): 929–30. http://dx.doi.org/10.1136/thx.2010.150557.
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Lescher, Stephanie, Sonja Gehrisch, Sigrun Klein, and Joachim Berkefeld. "Time-resolved 3D rotational angiography: display of detailed neurovascular anatomy in patients with intracranial vascular malformations." Journal of NeuroInterventional Surgery 9, no. 9 (August 4, 2016): 887–94. http://dx.doi.org/10.1136/neurintsurg-2016-012462.
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PurposeThe purpose of this pilot study was to demonstrate the applicability of time-resolved three-dimensional (3D) reconstructions from 3D digital subtraction angiography (DSA) rotational angiography (RA) datasets (four-dimensional (4D) DSA) to provide a more detailed display of the architecture of intracranial vascular malformations.MethodsThe experimental reconstruction software was applied to the existing 3D DSA datasets obtained with Siemens Artis zee biplane neuroangiography equipment. We included 27 patients with clinical indications for 3DRA for preinterventional or preoperative evaluation of intracranial dural arteriovenous fistulas (dAVFs, n=8) or arteriovenous malformations (AVMs, n=19). A modified DSA acquisition protocol covering an extended rotation angle of the C-arm of 260° during a scan time of 12 s was used. 4D volumes were displayed with up to 30 frames/s in a transparent volume rendering (VRT) mode and time-resolved multiplanar reconstructions (MPRs). Arterial feeders, fistulous points, or the shunt zone within the AVM nidus and venous drainage patterns as well as associated aneurysms were assessed after definition of a standardized evaluation procedure by consensus of two reviewers in comparison with 2D DSA and conventional 3D reconstructions.ResultsIn all cases calculation of 4D reconstructions were technically feasible and evaluable. In two cases image quality was slightly compromised by movement artifacts. Compared with standard DSA projection images and 3D reconstructions, 4D VRTs and MPRs were rated significantly superior to define a proper projection and display of the shunt zone. In 12 out of 27 cases 4D reconstructions showed details of the angioarchitecture at the fistulous point or the nidus better than the other modalities and came close to the quality of superselective angiography. The efficacy of 3D and 4D applications was equal in the detection of pre- and intranidal aneurysms. The course of long arterial feeders and draining veins was difficult to assess on VRTs and MPRs. Especially for dAVFs, 2D DSA was clearly superior in identifying meningeal feeders. For detecting smaller vessels and for distinction between angiographic phases, 2D DSA is still considered to be superior to 4D imaging. Venous drainage was slightly better displayed in 4D reconstructions.ConclusionsTime-resolved 3DRA with 4D VRTs and MPRs is technically feasible and provides a detailed display of the angioarchitecture at the fistulous point or the nidus. Visualization of all angiographic features demands additional post-processing. Further standardization of evaluation tools and studies with blinded independent reviewers are necessary before the new technique can replace conventional neuroangiographic approaches.
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Sandoval-Garcia, Carolina, Kevin Royalty, Pengfei Yang, David Niemann, Azam Ahmed, Beverly Aagaard-Kienitz, Mustafa K. Başkaya, Sebastian Schafer, and Charles Strother. "4D DSA a new technique for arteriovenous malformation evaluation: a feasibility study." Journal of NeuroInterventional Surgery 8, no. 3 (January 12, 2015): 300–304. http://dx.doi.org/10.1136/neurintsurg-2014-011534.
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BackgroundThe angioarchitectural features of an arteriovenous malformation (AVM) provide key information regarding natural history and treatment planning. Because of rapid filling and vascular overlap, two-dimensional (2D) and three-dimensional (3D) digital subtraction angiography (DSA) are often suboptimal for evaluation of these features. We have developed an algorithm that derives a series of fully time-resolved 3D DSA volumes (four-dimensional (4D) DSA) at up to 30 frames/s from a conventional 3D DSA. The temporal/spatial resolution of 4D reconstructions is significantly higher than that provided by current MR angiography and CT angiography techniques. 4D reconstruction allows viewing of an AVM from any angle at any time during its opacification. This feasibility study investigated the potential of 4D DSA to improve the ability to analyze angioarchitectural features compared with conventional 2D and 3D DSA.Methods2D, 3D, and 4D DSA reconstructions of angiographic studies of six AVMs were evaluated by three cerebrovascular neurosurgeons and one interventional neuroradiologist. These observers evaluated the ability of each modality to visualize the angioarchitectural features of the AVMs. They also compared the information provided using the combination of 2D and 3D DSA with that provided by a 4D DSA reconstruction.ResultsBy consensus, 4D DSA provided the best ability to visualize the internal features of the AVM including intranidal aneurysms, fistulae, venous obstructions, and sequence of filling and draining. 2D and 3D images in comparison were limited because of overlap of the vasculature.ConclusionsIn this small series, 4D DSA provided better ability to visualize the angioarchitecture of an AVM than conventional methods. Further experience is required to determine the ultimate utility of this technique.
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Le Floch-Prigent, P., and S. Verdeille. "Homarus gammarus : scanner sérié et reconstructions 3D d’un animal entier." Morphologie 102, no. 338 (September 2018): 188. http://dx.doi.org/10.1016/j.morpho.2018.07.033.
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Tsourlos, P. "INVERSION OF ELECTRICAL RESISTIVITY TOMOGRAPHY DATA DERIVING FROM 3D STRUCTURES." Bulletin of the Geological Society of Greece 36, no. 3 (January 1, 2004): 1289. http://dx.doi.org/10.12681/bgsg.16472.
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In this work the effectiveness of 2D and 3D algorithms for inverting Electrical Resistivity Tomography (ERT) data deriving from 3D structures is studied. Further, an analysis of data-collection strategies in the case of 3D structures is being carried out. Dense 2D measurements are nconsidered a practical tool for mapping 3D structures given the current limitations in ERT hardware. To perform the tests 2D and a 3D inversion programs are used. Both schemes use a forward model based on a 2.5D and 3D finite element scheme respectively. For both the 2D and 3D cases a fully non-linear inversion scheme based on a smoothness constrained algorithm is used. The Jacobian matrix is calculated using the adjoined equation technique. Comparisons are being carried out by means of synthetic examples for 3D models and dense 2D measurements with their axis parallel to the X (X-lines) and/or Y (Y lines) directions. For the case of 3D structures and 2D inversion tests results illustrate that both X-line, Y-line measurements are required to delineate the modeling body. However, when 3D inversion is considered either Xline or Y-line measurements are adequate to produce good quality reconstructions of the subsurface. Overall, results clearly illustrate the superiority of 3D over 2D inversion schemes in the case of 3D structures both in view of quality and logistics. Despite the increased computational time required by 3D inversion schemes, good quality results can be produced. Further, 2D inversion techniques require effectively a double amount of measurements to produce acceptable results. The ongoing advancement of fast computers renders the described approach of combining dense 2-D measurement with 3D inversion practical for routine data treatment.
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Fox, W. Christopher, Scott Wawrzyniak, and William F. Chandler. "Intraoperative acquisition of three-dimensional imaging for frameless stereotactic guidance during transsphenoidal pituitary surgery using the Arcadis Orbic System." Journal of Neurosurgery 108, no. 4 (April 2008): 746–50. http://dx.doi.org/10.3171/jns/2008/108/4/0746.
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Object Intraoperative fluoroscopy has long been used for anatomical localization in transsphenoidal pituitary surgery. More recently, frameless stereotaxy has been used to supplement 2D sagittal radiographs with 3D multiplanar reconstructions. Use of Arcadis Orbic allows both conventional fluoroscopic views and multiplanar reconstructions to be acquired intraoperatively without need for preoperative planning studies. The authors report their initial experience using Arcadis Orbic during transsphenoidal pituitary surgery. Methods To test the system, the authors placed a dehydrated human skull in a radiolucent head holder, and obtained standard 2D fluoroscopic images of the skull base and sella turcica. Arcadis Orbic was then used with frameless stereotaxy to register 3D multiplanar reconstructed images of skull base anatomy. The authors then used Arcadis Orbic in 26 transsphenoidal pituitary tumor resections and compared image quality, accuracy, and ease-of-use to standard techniques. Results Arcadis Orbic 2D fluoroscopic images matched or exceeded the quality of images acquired by standard C-arm machines. Arcadis Orbic multiplanar reconstructions provided excellent images of the skull base when compared with preoperative Stealth computed tomography (CT) studies. Intraoperative frameless stereotactic navigation using Arcadis Orbic was highly accurate and more reliable than registering preoperative CT images. Conclusions Arcadis Orbic provides excellent quality 2- and 3D images during transsphenoidal pituitary surgery, and intraoperative frameless navigation using these images is highly accurate. Arcadis Orbic is easy to use, even in patients with large body habitus, and image acquisition takes no longer than registration during a frameless stereotactic case. Based upon our preliminary experience, Arcadis Orbic precludes the need for preoperative CT studies in patients with pituitary lesions requiring frameless stereotactic navigation.
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Becker, Minerva, Pier-Olivier Duboé, Alexandra Platon, Romain Kohler, Jean-Pierre Tasu, Christoph D. Becker, and Pierre-Alexandre Poletti. "MDCT in the Assessment of Laryngeal Trauma: Value of 2D Multiplanar and 3D Reconstructions." American Journal of Roentgenology 201, no. 4 (October 2013): W639—W647. http://dx.doi.org/10.2214/ajr.12.9813.
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Yu, Honggang, Marios S. Pattichis, Carla Agurto, and M. Beth Goens. "A 3D Freehand Ultrasound System for Multi-view Reconstructions from Sparse 2D Scanning Planes." BioMedical Engineering OnLine 10, no. 1 (2011): 7. http://dx.doi.org/10.1186/1475-925x-10-7.
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Thévenin, F., R. Campagna, D. Richarme, A. Feydy, H. Guerini, A. Chevrot, and J. L. Drapé. "OA-WP-14 Fractures de l’acetabulum : radiographies, TDM et reconstructions 3D." Journal de Radiologie 89, no. 10 (October 2008): 1599. http://dx.doi.org/10.1016/s0221-0363(08)76992-0.
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Seizeur, R., R. Gérard, J. Marion, C. Lefèvre, M. Nonent, P. Forlodou, and B. Sénécail. "Étude anatomique et angioscanographique avec reconstructions 3D de l’arbre artériel pulmonaire." Morphologie 94, no. 306 (August 2010): 45–50. http://dx.doi.org/10.1016/j.morpho.2010.02.004.
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Salas, Desirée, Antoine Le Gall, Jean-Bernard Fiche, Alessandro Valeri, Yonggang Ke, Patrick Bron, Gaetan Bellot, and Marcelo Nollmann. "Angular reconstitution-based 3D reconstructions of nanomolecular structures from superresolution light-microscopy images." Proceedings of the National Academy of Sciences 114, no. 35 (August 15, 2017): 9273–78. http://dx.doi.org/10.1073/pnas.1704908114.
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Superresolution light microscopy allows the imaging of labeled supramolecular assemblies at a resolution surpassing the classical diffraction limit. A serious limitation of the superresolution approach is sample heterogeneity and the stochastic character of the labeling procedure. To increase the reproducibility and the resolution of the superresolution results, we apply multivariate statistical analysis methods and 3D reconstruction approaches originally developed for cryogenic electron microscopy of single particles. These methods allow for the reference-free 3D reconstruction of nanomolecular structures from two-dimensional superresolution projection images. Since these 2D projection images all show the structure in high-resolution directions of the optical microscope, the resulting 3D reconstructions have the best possible isotropic resolution in all directions.
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Ozkadif, S., E. Eken, MO Dayan, and K. Besoluk. "Determination of sex-related differences based on 3D reconstruction of the chinchilla (Chinchilla lanigera) vertebral column from MDCT scans." Veterinární Medicína 62, No. 4 (April 10, 2017): 204–10. http://dx.doi.org/10.17221/19/2015-vetmed.
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This study was undertaken to obtain and analyse, on the basis of sex, three-dimensional (3D) reconstructions obtained by a 3D computer program from two-dimensional (2D) vertebral column sections taken by multidetector computed tomography (MDCT) images, in the chinchilla. A total of 16 adult chinchillas (Chinchilla lanigera) of both sexes were used. The MDCT images were taken under general anaesthesia, and were then transferred to a personal computer on which 3D reconstructions were carried out using a 3D modelling program (Mimics 13.1). The volume, surface area and vertebral body length of each vertebra (except caudal region) forming the vertebral column were measured from the 3D models created. The ratios (in percentage) of the measurements of each vertebra (except the sacral ones) forming the vertebral column region (cervical part, thoracic part, lumbar part) were determined for statistical analysis. We detected significant differences (P < 0.05) between sexes in all vertebrae forming the vertebral column of the chinchilla with respect to volume, surface area and vertebral body length, except for C6 and L1. This study is the first to carry out 3D reconstructions of data obtained from CT images in the chinchilla and the obtained results contribute to a more detailed understanding of the anatomy of this species. Our strategy may also be useful for the design of experiments exploring the vertebral column in domestic mammals and humans.
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Leijsen, Reijer, Patrick Fuchs, Wyger Brink, Andrew Webb, and Rob Remis. "Developments in Electrical-Property Tomography Based on the Contrast-Source Inversion Method." Journal of Imaging 5, no. 2 (February 1, 2019): 25. http://dx.doi.org/10.3390/jimaging5020025.
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The main objective of electrical-property tomography (EPT) is to retrieve dielectric tissue parameters from B ^ 1 + data as measured by a magnetic-resonance (MR) scanner. This is a so-called hybrid inverse problem in which data are defined inside the reconstruction domain of interest. In this paper, we discuss recent and new developments in EPT based on the contrast-source inversion (CSI) method. After a short review of the basics of this method, two- and three-dimensional implementations of CSI–EPT are presented along with a very efficient variant of 2D CSI–EPT called first-order induced current EPT (foIC-EPT). Practical implementation issues that arise when applying the method to measured data are addressed as well, and the limitations of a two-dimensional approach are extensively discussed. Tissue-parameter reconstructions of an anatomically correct male head model illustrate the performance of two- and three-dimensional CSI–EPT. We show that 2D implementation only produces reliable reconstructions under very special circumstances, while accurate reconstructions can be obtained with 3D CSI–EPT.
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van Heteren, S., J. A. C. Meekes, M. A. J. Bakker, V. Gaffney, S. Fitch, B. R. Gearey, and B. F. Paap. "Reconstructing North Sea palaeolandscapes from 3D and high-density 2D seismic data: An overview." Netherlands Journal of Geosciences - Geologie en Mijnbouw 93, no. 1-2 (March 13, 2014): 31–42. http://dx.doi.org/10.1017/njg.2014.4.
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AbstractThe North Sea subsurface shows the marks of long-term tectonic subsidence. Much of it contains a thick record of glacial and interglacial deposits and landscapes, formed during multiple glacial cycles and the associated regressions and transgressions during the past two million years. At times of lower sea level than today, areas that are presently submerged were fertile lowlands more favourable for hunting and gathering than the surrounding upland. These drowned lowlands are not captured by traditional 1:250,000 geological maps of the North Sea subsurface because the underlying seismic and core data are commonly too widely spaced to achieve this. Palaeolandscape mapping requires identification of building blocks with spatial scales in the order of 1 km or less. As high-density 2D and high-quality 3D seismics are becoming available for an increasing part of the North Sea, glacial and interglacial palaeolandscapes can be reconstructed for more and more areas. An overview of published palaeolandscape reconstructions shows that shallow time slices through 3D data provide map views that are very suitable for the identification of landscape elements. For optimal results, each time slice needs to be validated and ground-truthed with 2D seismics and with descriptions and analyses of cores and borehole samples. Interpretations should be made by teams of geoscientists with a sufficiently broad range of expertise to recognise and classify even subtle or unfamiliar patterns and features. The resulting reconstructions will provide a context and an environmental setting for Palaeolithic, Mesolithic, and Neolithic societies and finds.
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Zhu, Linqi, Chong Zhang, Chaomo Zhang, Xueqing Zhou, Zhansong Zhang, Xin Nie, Weinan Liu, and Boyuan Zhu. "Challenges and Prospects of Digital Core-Reconstruction Research." Geofluids 2019 (May 20, 2019): 1–29. http://dx.doi.org/10.1155/2019/7814180.
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The simulation of various rock properties based on three-dimensional digital cores plays an increasingly important role in oil and gas exploration and development. The accuracy of 3D digital core reconstruction is important for determining rock properties. In this paper, existing 3D digital core-reconstruction methods are divided into two categories: 3D digital cores based on physical experiments and 3D digital core stochastic reconstructions based on two-dimensional (2D) slices. Additionally, 2D slice-based digital core stochastic reconstruction techniques are classified into four types: a stochastic reconstruction method based on 2D slice mathematical-feature statistical constraints, a stochastic reconstruction method based on statistical constraints that are related to 2D slice morphological characteristics, a physics process-based stochastic reconstruction method, and a hybrid stochastic reconstruction method. The progress related to these various stochastic reconstruction methods, the characteristics of constructed 3D digital cores, and the potential of these methods are analysed and discussed in detail. Finally, reasonable prospects are presented based on the current state of this research area. Currently, studies on digital core reconstruction, especially for the 3D digital core stochastic reconstruction method based on 2D slices, are still very rough, and much room for improvement remains. In particular, we emphasize the importance of evaluating functions, multiscale 3D digital cores, multicomponent 3D digital cores, and disciplinary intersection methods in the 3D construction of digital cores. These four directions should provide focus, alongside challenges, for this research area in the future. This review provides important insights into 3D digital core reconstruction.
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Kim, Taehyung, Dong-Hyun Kang, Shinyong Shim, Maesoon Im, Bo Kyoung Seo, Hyungmin Kim, and Byung Chul Lee. "Versatile Low-Cost Volumetric 3D Ultrasound Imaging Using Gimbal-Assisted Distance Sensors and an Inertial Measurement Unit." Sensors 20, no. 22 (November 19, 2020): 6613. http://dx.doi.org/10.3390/s20226613.
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This study aims at creating low-cost, three-dimensional (3D), freehand ultrasound image reconstructions from commercial two-dimensional (2D) probes. The low-cost system that can be attached to a commercial 2D ultrasound probe consists of commercial ultrasonic distance sensors, a gimbal, and an inertial measurement unit (IMU). To calibrate irregular movements of the probe during scanning, relative position data were collected from the ultrasonic sensors that were attached to a gimbal. The directional information was provided from the IMU. All the data and 2D ultrasound images were combined using a personal computer to reconstruct 3D ultrasound image. The relative position error of the proposed system was less than 0.5%. The overall shape of the cystic mass in the breast phantom was similar to those from 2D and sections of 3D ultrasound images. Additionally, the pressure and deformations of lesions could be obtained and compensated by contacting the probe to the surface of the soft tissue using the acquired position data. The proposed method did not require any initial marks or receivers for the reconstruction of a 3D ultrasound image using a 2D ultrasound probe. Even though our system is less than $500, a valuable volumetric ultrasound image could be provided to the users.
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Franzini-Armstrong, Clara. "Electron microscopy: from 2D to 3D images with special reference to muscle." European Journal of Translational Myology 25, no. 1 (January 12, 2015): 5. http://dx.doi.org/10.4081/ejtm.2015.4836.
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This is a brief and necessarily very sketchy presentation of the evolution in electron microscopy (EM) imaging that was driven by the necessity of extracting 3-D views from the essentially 2-D images produced by the electron beam. The lens design of standard transmission electron microscope has not been greatly altered since its inception. However, technical advances in specimen preparation, image collection and analysis gradually induced an astounding progression over a period of about 50 years. From the early images that redefined tissues, cell and cell organelles at the sub-micron level, to the current nano-resolution reconstructions of organelles and proteins the step is very large. The review is written by an investigator who has followed the field for many years, but often from the sidelines, and with great wonder. Her interest in muscle ultrastructure colors the writing. More specific detailed reviews are presented in this issue.
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Khoshdel, Vahab, Mohammad Asefi, Ahmed Ashraf, and Joe LoVetri. "Full 3D Microwave Breast Imaging Using a Deep-Learning Technique." Journal of Imaging 6, no. 8 (August 11, 2020): 80. http://dx.doi.org/10.3390/jimaging6080080.
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A deep learning technique to enhance 3D images of the complex-valued permittivity of the breast obtained via microwave imaging is investigated. The developed technique is an extension of one created to enhance 2D images. We employ a 3D Convolutional Neural Network, based on the U-Net architecture, that takes in 3D images obtained using the Contrast-Source Inversion (CSI) method and attempts to produce the true 3D image of the permittivity. The training set consists of 3D CSI images, along with the true numerical phantom images from which the microwave scattered field utilized to create the CSI reconstructions was synthetically generated. Each numerical phantom varies with respect to the size, number, and location of tumors within the fibroglandular region. The reconstructed permittivity images produced by the proposed 3D U-Net show that the network is not only able to remove the artifacts that are typical of CSI reconstructions, but it also enhances the detectability of the tumors. We test the trained U-Net with 3D images obtained from experimentally collected microwave data as well as with images obtained synthetically. Significantly, the results illustrate that although the network was trained using only images obtained from synthetic data, it performed well with images obtained from both synthetic and experimental data. Quantitative evaluations are reported using Receiver Operating Characteristics (ROC) curves for the tumor detectability and RMS error for the enhancement of the reconstructions.
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Zawy Alsofy, Samer, Makoto Nakamura, Ayman Suleiman, Ioanna Sakellaropoulou, Heinz Welzel Saravia, David Shalamberidze, Asem Salma, and Ralf Stroop. "Cerebral Anatomy Detection and Surgical Planning in Patients with Anterior Skull Base Meningiomas Using a Virtual Reality Technique." Journal of Clinical Medicine 10, no. 4 (February 10, 2021): 681. http://dx.doi.org/10.3390/jcm10040681.
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Anterior skull base meningiomas represent a wide cohort of tumors with different locations, extensions, configurations, and anatomical relationships. Diagnosis of these tumors and review of their therapies are inseparably connected with cranial imaging. We analyzed the influence of three-dimensional-virtual reality (3D-VR) reconstructions versus conventional computed tomography (CT) and magnetic resonance imaging (MRI) images (two-dimensional (2D) and screen 3D) on the identification of anatomical structures and on the surgical planning in patients with anterior skull base meningiomas. Medical files were retrospectively analyzed regarding patient- and disease-related data. Preoperative 2D-CT and 2D-MRI scans were retrospectively reconstructed to 3D-VR images and visualized via VR software to detect the characteristics of tumors. A questionnaire of experienced neurosurgeons evaluated the influence of the VR visualization technique on identification of tumor morphology and relevant anatomy and on surgical strategy. Thirty patients were included and 600 answer sheets were evaluated. The 3D-VR modality significantly influenced the detection of tumor-related anatomical structures (p = 0.002), recommended head positioning (p = 0.005), and surgical approach (p = 0.03). Therefore, the reconstruction of conventional preoperative 2D scans into 3D images and the spatial and anatomical presentation in VR models enabled greater understanding of anatomy and pathology, and thus influenced operation planning and strategy.