Science.gov

Sample records for 3d volumetric approach

  1. FELIX: a volumetric 3D laser display

    NASA Astrophysics Data System (ADS)

    Bahr, Detlef; Langhans, Knut; Gerken, Martin; Vogt, Carsten; Bezecny, Daniel; Homann, Dennis

    1996-03-01

    In this paper, an innovative approach of a true 3D image presentation in a space filling, volumetric laser display will be described. The introduced prototype system is based on a moving target screen that sweeps the display volume. Net result is the optical equivalent of a 3D array of image points illuminated to form a model of the object which occupies a physical space. Wireframe graphics are presented within the display volume which a group of people can walk around and examine simultaneously from nearly any orientation and without any visual aids. Further to the detailed vector scanning mode, a raster scanned system and a combination of both techniques are under development. The volumetric 3D laser display technology for true reproduction of spatial images can tremendously improve the viewers ability to interpret data and to reliably determine distance, shape and orientation. Possible applications for this development range from air traffic control, where moving blips of light represent individual aircrafts in a true to scale projected airspace of an airport, to various medical applications (e.g. electrocardiography, computer-tomography), to entertainment and education visualization as well as imaging in the field of engineering and Computer Aided Design.

  2. Volumetric 3D Display System with Static Screen

    NASA Technical Reports Server (NTRS)

    Geng, Jason

    2011-01-01

    Current display technology has relied on flat, 2D screens that cannot truly convey the third dimension of visual information: depth. In contrast to conventional visualization that is primarily based on 2D flat screens, the volumetric 3D display possesses a true 3D display volume, and places physically each 3D voxel in displayed 3D images at the true 3D (x,y,z) spatial position. Each voxel, analogous to a pixel in a 2D image, emits light from that position to form a real 3D image in the eyes of the viewers. Such true volumetric 3D display technology provides both physiological (accommodation, convergence, binocular disparity, and motion parallax) and psychological (image size, linear perspective, shading, brightness, etc.) depth cues to human visual systems to help in the perception of 3D objects. In a volumetric 3D display, viewers can watch the displayed 3D images from a completely 360 view without using any special eyewear. The volumetric 3D display techniques may lead to a quantum leap in information display technology and can dramatically change the ways humans interact with computers, which can lead to significant improvements in the efficiency of learning and knowledge management processes. Within a block of glass, a large amount of tiny dots of voxels are created by using a recently available machining technique called laser subsurface engraving (LSE). The LSE is able to produce tiny physical crack points (as small as 0.05 mm in diameter) at any (x,y,z) location within the cube of transparent material. The crack dots, when illuminated by a light source, scatter the light around and form visible voxels within the 3D volume. The locations of these tiny voxels are strategically determined such that each can be illuminated by a light ray from a high-resolution digital mirror device (DMD) light engine. The distribution of these voxels occupies the full display volume within the static 3D glass screen. This design eliminates any moving screen seen in previous

  3. Volumetric (3D) compressive sensing spectral domain optical coherence tomography

    PubMed Central

    Xu, Daguang; Huang, Yong; Kang, Jin U.

    2014-01-01

    In this work, we proposed a novel three-dimensional compressive sensing (CS) approach for spectral domain optical coherence tomography (SD OCT) volumetric image acquisition and reconstruction. Instead of taking a spectral volume whose size is the same as that of the volumetric image, our method uses a sub set of the original spectral volume that is under-sampled in all three dimensions, which reduces the amount of spectral measurements to less than 20% of that required by the Shan-non/Nyquist theory. The 3D image is recovered from the under-sampled spectral data dimension-by-dimension using the proposed three-step CS reconstruction strategy. Experimental results show that our method can significantly reduce the sampling rate required for a volumetric SD OCT image while preserving the image quality. PMID:25426320

  4. Volumetric image display for complex 3D data visualization

    NASA Astrophysics Data System (ADS)

    Tsao, Che-Chih; Chen, Jyh Shing

    2000-05-01

    A volumetric image display is a new display technology capable of displaying computer generated 3D images in a volumetric space. Many viewers can walk around the display and see the image from omni-directions simultaneously without wearing any glasses. The image is real and possesses all major elements in both physiological and psychological depth cues. Due to the volumetric nature of its image, the VID can provide the most natural human-machine interface in operations involving 3D data manipulation and 3D targets monitoring. The technology creates volumetric 3D images by projecting a series of profiling images distributed in the space form a volumetric image because of the after-image effect of human eyes. Exemplary applications in biomedical image visualization were tested on a prototype display, using different methods to display a data set from Ct-scans. The features of this display technology make it most suitable for applications that require quick understanding of the 3D relations, need frequent spatial interactions with the 3D images, or involve time-varying 3D data. It can also be useful for group discussion and decision making.

  5. Volumetric visualization of 3D data

    NASA Technical Reports Server (NTRS)

    Russell, Gregory; Miles, Richard

    1989-01-01

    In recent years, there has been a rapid growth in the ability to obtain detailed data on large complex structures in three dimensions. This development occurred first in the medical field, with CAT (computer aided tomography) scans and now magnetic resonance imaging, and in seismological exploration. With the advances in supercomputing and computational fluid dynamics, and in experimental techniques in fluid dynamics, there is now the ability to produce similar large data fields representing 3D structures and phenomena in these disciplines. These developments have produced a situation in which currently there is access to data which is too complex to be understood using the tools available for data reduction and presentation. Researchers in these areas are becoming limited by their ability to visualize and comprehend the 3D systems they are measuring and simulating.

  6. Volumetric 3D display using a DLP projection engine

    NASA Astrophysics Data System (ADS)

    Geng, Jason

    2012-03-01

    In this article, we describe a volumetric 3D display system based on the high speed DLPTM (Digital Light Processing) projection engine. Existing two-dimensional (2D) flat screen displays often lead to ambiguity and confusion in high-dimensional data/graphics presentation due to lack of true depth cues. Even with the help of powerful 3D rendering software, three-dimensional (3D) objects displayed on a 2D flat screen may still fail to provide spatial relationship or depth information correctly and effectively. Essentially, 2D displays have to rely upon capability of human brain to piece together a 3D representation from 2D images. Despite the impressive mental capability of human visual system, its visual perception is not reliable if certain depth cues are missing. In contrast, volumetric 3D display technologies to be discussed in this article are capable of displaying 3D volumetric images in true 3D space. Each "voxel" on a 3D image (analogous to a pixel in 2D image) locates physically at the spatial position where it is supposed to be, and emits light from that position toward omni-directions to form a real 3D image in 3D space. Such a volumetric 3D display provides both physiological depth cues and psychological depth cues to human visual system to truthfully perceive 3D objects. It yields a realistic spatial representation of 3D objects and simplifies our understanding to the complexity of 3D objects and spatial relationship among them.

  7. A low-resolution 3D holographic volumetric display

    NASA Astrophysics Data System (ADS)

    Khan, Javid; Underwood, Ian; Greenaway, Alan; Halonen, Mikko

    2010-05-01

    A simple low resolution volumetric display is presented, based on holographic volume-segments. The display system comprises a proprietary holographic screen, laser projector, associated optics plus a control unit. The holographic screen resembles a sheet of frosted glass about A4 in size (20x30cm). The holographic screen is rear-illuminated by the laser projector, which is in turn driven by the controller, to produce simple 3D images that appear outside the plane of the screen. A series of spatially multiplexed and interleaved interference patterns are pre-encoded across the surface of the holographic screen. Each illumination pattern is capable of reconstructing a single holographic volume-segment. Up to nine holograms are multiplexed on the holographic screen in a variety of configurations including a series of numeric and segmented digits. The demonstrator has good results under laboratory conditions with moving colour 3D images in front of or behind the holographic screen.

  8. Iterative Reconstruction of Volumetric Particle Distribution for 3D Velocimetry

    NASA Astrophysics Data System (ADS)

    Wieneke, Bernhard; Neal, Douglas

    2011-11-01

    A number of different volumetric flow measurement techniques exist for following the motion of illuminated particles. For experiments that have lower seeding densities, 3D-PTV uses recorded images from typically 3-4 cameras and then tracks the individual particles in space and time. This technique is effective in flows that have lower seeding densities. For flows that have a higher seeding density, tomographic PIV uses a tomographic reconstruction algorithm (e.g. MART) to reconstruct voxel intensities of the recorded volume followed by the cross-correlation of subvolumes to provide the instantaneous 3D vector fields on a regular grid. A new hybrid algorithm is presented which iteratively reconstructs the 3D-particle distribution directly using particles with certain imaging properties instead of voxels as base functions. It is shown with synthetic data that this method is capable of reconstructing densely seeded flows up to 0.05 particles per pixel (ppp) with the same or higher accuracy than 3D-PTV and tomographic PIV. Finally, this new method is validated using experimental data on a turbulent jet.

  9. Combining volumetric edge display and multiview display for expression of natural 3D images

    NASA Astrophysics Data System (ADS)

    Yasui, Ryota; Matsuda, Isamu; Kakeya, Hideki

    2006-02-01

    In the present paper the authors present a novel stereoscopic display method combining volumetric edge display technology and multiview display technology to realize presentation of natural 3D images where the viewers do not suffer from contradiction between binocular convergence and focal accommodation of the eyes, which causes eyestrain and sickness. We adopt volumetric display method only for edge drawing, while we adopt stereoscopic approach for flat areas of the image. Since focal accommodation of our eyes is affected only by the edge part of the image, natural focal accommodation can be induced if the edges of the 3D image are drawn on the proper depth. The conventional stereo-matching technique can give us robust depth values of the pixels which constitute noticeable edges. Also occlusion and gloss of the objects can be roughly expressed with the proposed method since we use stereoscopic approach for the flat area. We can attain a system where many users can view natural 3D objects at the consistent position and posture at the same time in this system. A simple optometric experiment using a refractometer suggests that the proposed method can give us 3-D images without contradiction between binocular convergence and focal accommodation.

  10. 3D X-ray tomography to evaluate volumetric objects

    NASA Astrophysics Data System (ADS)

    de Oliveira, Luís. F.; Lopes, Ricardo T.; de Jesus, Edgar F. O.; Braz, Delson

    2003-06-01

    The 3D-CT and stereological techniques are used concomitantly. The quantitative stereology yields measurements that reflects areas, volumes, lengths, rates and frequencies of the test body. Two others quantification, connectivity and anisotropy, can be used as well to complete the analysis. In this paper, it is presented the application of 3D-CT and the stereological quantification to analyze a special kind of test body: ceramic filters which have an internal structure similar to cancellous bone. The stereology is adapted to work with the 3D nature of the tomographic data. It is presented too the results of connectivity and anisotropy.

  11. A volumetric sensor for real-time 3D mapping and robot navigation

    NASA Astrophysics Data System (ADS)

    Fournier, Jonathan; Ricard, Benoit; Laurendeau, Denis

    2006-05-01

    The use of robots for (semi-) autonomous operations in complex terrains such as urban environments poses difficult mobility, mapping, and perception challenges. To be able to work efficiently, a robot should be provided with sensors and software such that it can perceive and analyze the world in 3D. Real-time 3D sensing and perception in this operational context are paramount. To address these challenges, DRDC Valcartier has developed over the past years a compact sensor that combines a wide baseline stereo camera and a laser scanner with a full 360 degree azimuth and 55 degree elevation field of view allowing the robot to view and manage overhang obstacles as well as obstacles at ground level. Sensing in 3D is common but to efficiently navigate and work in complex terrain, the robot should also perceive, decide and act in three dimensions. Therefore, 3D information should be preserved and exploited in all steps of the process. To achieve this, we use a multiresolution octree to store the acquired data, allowing mapping of large environments while keeping the representation compact and memory efficient. Ray tracing is used to build and update the 3D occupancy model. This model is used, via a temporary 2.5D map, for navigation, obstacle avoidance and efficient frontier-based exploration. This paper describes the volumetric sensor concept, describes its design features and presents an overview of the 3D software framework that allows 3D information persistency through all computation steps. Simulation and real-world experiments are presented at the end of the paper to demonstrate the key elements of our approach.

  12. 3-D Volumetric Evaluation of Human Mandibular Growth

    PubMed Central

    Reynolds, Mathew; Reynolds, Michael; Adeeb, Samer; El-Bialy, Tarek

    2011-01-01

    Bone growth is a complex process that is controlled by a multitude of mechanisms that are not fully understood.Most of the current methods employed to measure the growth of bones focus on either studying cadaveric bones from different individuals of different ages, or successive two-dimensional (2D) radiographs. Both techniques have their known limitations. The purpose of this study was to explore a technique for quantifying the three dimensional (3D) growth of an adolescent human mandible over the period of one year utilizing cone beam computed tomography (CBCT) scans taken for regular orthodontic records. Three -dimensional virtual models were created from the CBCT data using mainstream medical imaging software. A comparison between computer-generated surface meshes of successive 3-D virtual models illustrates the magnitude of relative mandible growth. The results of this work are in agreement with previously reported data from human cadaveric studies and implantable marker studies. The presented method provides a new relatively simple basis (utilizing commercially available software) to visualize and evaluate individualized 3D (mandibular) growth in vivo. PMID:22046201

  13. 3D texture analysis of solitary pulmonary nodules using co-occurrence matrix from volumetric lung CT images

    NASA Astrophysics Data System (ADS)

    Dhara, Ashis Kumar; Mukhopadhyay, Sudipta; Khandelwal, Niranjan

    2013-02-01

    In this paper we have investigated a new approach for texture features extraction using co-occurrence matrix from volumetric lung CT image. Traditionally texture analysis is performed in 2D and is suitable for images collected from 2D imaging modality. The use of 3D imaging modalities provide the scope of texture analysis from 3D object and 3D texture feature are more realistic to represent 3D object. In this work, Haralick's texture features are extended in 3D and computed from volumetric data considering 26 neighbors. The optimal texture features to characterize the internal structure of Solitary Pulmonary Nodules (SPN) are selected based on area under curve (AUC) values of ROC curve and p values from 2-tailed Student's t-test. The selected texture feature in 3D to represent SPN can be used in efficient Computer Aided Diagnostic (CAD) design plays an important role in fast and accurate lung cancer screening. The reduced number of input features to the CAD system will decrease the computational time and classification errors caused by irrelevant features. In the present work, SPN are classified from Ground Glass Nodule (GGN) using Artificial Neural Network (ANN) classifier considering top five 3D texture features and top five 2D texture features separately. The classification is performed on 92 SPN and 25 GGN from Imaging Database Resources Initiative (IDRI) public database and classification accuracy using 3D texture features and 2D texture features provide 97.17% and 89.1% respectively.

  14. The effect of volumetric (3D) tactile symbols within inclusive tactile maps.

    PubMed

    Gual, Jaume; Puyuelo, Marina; Lloveras, Joaquim

    2015-05-01

    Point, linear and areal elements, which are two-dimensional and of a graphic nature, are the morphological elements employed when designing tactile maps and symbols for visually impaired users. However, beyond the two-dimensional domain, there is a fourth group of elements - volumetric elements - which mapmakers do not take sufficiently into account when it comes to designing tactile maps and symbols. This study analyses the effect of including volumetric, or 3D, symbols within a tactile map. In order to do so, the researchers compared two tactile maps. One of them uses only two-dimensional elements and is produced using thermoforming, one of the most popular systems in this field, while the other includes volumetric symbols, thus highlighting the possibilities opened up by 3D printing, a new area of production. The results of the study show that including 3D symbols improves the efficiency and autonomous use of these products. PMID:25683526

  15. Average Cross-Sectional Area of DebriSat Fragments Using Volumetrically Constructed 3D Representations

    NASA Technical Reports Server (NTRS)

    Scruggs, T.; Moraguez, M.; Patankar, K.; Fitz-Coy, N.; Liou, J.-C.; Sorge, M.; Huynh, T.

    2016-01-01

    Debris fragments from the hypervelocity impact testing of DebriSat are being collected and characterized for use in updating existing satellite breakup models. One of the key parameters utilized in these models is the ballistic coefficient of the fragment which is directly related to its area-to-mass ratio. However, since the attitude of fragments varies during their orbital lifetime, it is customary to use the average cross-sectional area in the calculation of the area-to-mass ratio. The average cross-sectional area is defined as the average of the projected surface areas perpendicular to the direction of motion and has been shown to be equal to one-fourth of the total surface area of a convex object. Unfortunately, numerous fragments obtained from the DebriSat experiment show significant concavity (i.e., shadowing) and thus we have explored alternate methods for computing the average cross-sectional area of the fragments. An imaging system based on the volumetric reconstruction of a 3D object from multiple 2D photographs of the object was developed for use in determining the size characteristic (i.e., characteristics length) of the DebriSat fragments. For each fragment, the imaging system generates N number of images from varied azimuth and elevation angles and processes them using a space-carving algorithm to construct a 3D point cloud of the fragment. This paper describes two approaches for calculating the average cross-sectional area of debris fragments based on the 3D imager. Approach A utilizes the constructed 3D object to generate equally distributed cross-sectional area projections and then averages them to determine the average cross-sectional area. Approach B utilizes a weighted average of the area of the 2D photographs to directly compute the average cross-sectional area. A comparison of the accuracy and computational needs of each approach is described as well as preliminary results of an analysis to determine the "optimal" number of images needed for

  16. An interface for precise and comfortable 3D work with volumetric medical datasets.

    PubMed

    Serra, L; Hern, N; Guan, C G; Lee, E; Lee, Y H; Yeo, T T; Chan, C; Kockro, R A

    1999-01-01

    We have developed a 3D/2D paradigm of interaction that combines manipulation of precise 3D volumetric data with unambiguous widget interaction. Precise 3D interaction is ensured by a combination of resting the lower arms on an armrest and pivoting the hands around the wrist. Unambiguous 2D interaction is achieved by providing passive haptic feedback by means of a virtual control panel whose position coincides with the physical surfaces encasing the system. We have tested this interface with a neurosurgical planning application that has been clinically used for 17 skull-base cases at two local hospitals. PMID:10538381

  17. JP3D compressed-domain watermarking of volumetric medical data sets

    NASA Astrophysics Data System (ADS)

    Ouled Zaid, Azza; Makhloufi, Achraf; Olivier, Christian

    2010-01-01

    Increasing transmission of medical data across multiple user systems raises concerns for medical image watermarking. Additionaly, the use of volumetric images triggers the need for efficient compression techniques in picture archiving and communication systems (PACS), or telemedicine applications. This paper describes an hybrid data hiding/compression system, adapted to volumetric medical imaging. The central contribution is to integrate blind watermarking, based on turbo trellis-coded quantization (TCQ), to JP3D encoder. Results of our method applied to Magnetic Resonance (MR) and Computed Tomography (CT) medical images have shown that our watermarking scheme is robust to JP3D compression attacks and can provide relative high data embedding rate whereas keep a relative lower distortion.

  18. Morphological and Volumetric Assessment of Cerebral Ventricular System with 3D Slicer Software.

    PubMed

    Gonzalo Domínguez, Miguel; Hernández, Cristina; Ruisoto, Pablo; Juanes, Juan A; Prats, Alberto; Hernández, Tomás

    2016-06-01

    We present a technological process based on the 3D Slicer software for the three-dimensional study of the brain's ventricular system with teaching purposes. It values the morphology of this complex brain structure, as a whole and in any spatial position, being able to compare it with pathological studies, where its anatomy visibly changes. 3D Slicer was also used to obtain volumetric measurements in order to provide a more comprehensive and detail representation of the ventricular system. We assess the potential this software has for processing high resolution images, taken from Magnetic Resonance and generate the three-dimensional reconstruction of ventricular system. PMID:27147517

  19. An inverse hyper-spherical harmonics-based formulation for reconstructing 3D volumetric lung deformations

    NASA Astrophysics Data System (ADS)

    Santhanam, Anand P.; Min, Yugang; Mudur, Sudhir P.; Rastogi, Abhinav; Ruddy, Bari H.; Shah, Amish; Divo, Eduardo; Kassab, Alain; Rolland, Jannick P.; Kupelian, Patrick

    2010-07-01

    A method to estimate the deformation operator for the 3D volumetric lung dynamics of human subjects is described in this paper. For known values of air flow and volumetric displacement, the deformation operator and subsequently the elastic properties of the lung are estimated in terms of a Green's function. A Hyper-Spherical Harmonic (HSH) transformation is employed to compute the deformation operator. The hyper-spherical coordinate transformation method discussed in this paper facilitates accounting for the heterogeneity of the deformation operator using a finite number of frequency coefficients. Spirometry measurements are used to provide values for the airflow inside the lung. Using a 3D optical flow-based method, the 3D volumetric displacement of the left and right lungs, which represents the local anatomy and deformation of a human subject, was estimated from 4D-CT dataset. Results from an implementation of the method show the estimation of the deformation operator for the left and right lungs of a human subject with non-small cell lung cancer. Validation of the proposed method shows that we can estimate the Young's modulus of each voxel within a 2% error level.

  20. Parallel implementation of 3D FFT with volumetric decomposition schemes for efficient molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Jung, Jaewoon; Kobayashi, Chigusa; Imamura, Toshiyuki; Sugita, Yuji

    2016-03-01

    Three-dimensional Fast Fourier Transform (3D FFT) plays an important role in a wide variety of computer simulations and data analyses, including molecular dynamics (MD) simulations. In this study, we develop hybrid (MPI+OpenMP) parallelization schemes of 3D FFT based on two new volumetric decompositions, mainly for the particle mesh Ewald (PME) calculation in MD simulations. In one scheme, (1d_Alltoall), five all-to-all communications in one dimension are carried out, and in the other, (2d_Alltoall), one two-dimensional all-to-all communication is combined with two all-to-all communications in one dimension. 2d_Alltoall is similar to the conventional volumetric decomposition scheme. We performed benchmark tests of 3D FFT for the systems with different grid sizes using a large number of processors on the K computer in RIKEN AICS. The two schemes show comparable performances, and are better than existing 3D FFTs. The performances of 1d_Alltoall and 2d_Alltoall depend on the supercomputer network system and number of processors in each dimension. There is enough leeway for users to optimize performance for their conditions. In the PME method, short-range real-space interactions as well as long-range reciprocal-space interactions are calculated. Our volumetric decomposition schemes are particularly useful when used in conjunction with the recently developed midpoint cell method for short-range interactions, due to the same decompositions of real and reciprocal spaces. The 1d_Alltoall scheme of 3D FFT takes 4.7 ms to simulate one MD cycle for a virus system containing more than 1 million atoms using 32,768 cores on the K computer.

  1. Extending a teleradiology system by tools for 3D-visualization and volumetric analysis through a plug-in mechanism.

    PubMed

    Evers, H; Mayer, A; Engelmann, U; Schröter, A; Baur, U; Wolsiffer, K; Meinzer, H P

    1998-01-01

    This paper describes ongoing research concerning interactive volume visualization coupled with tools for volumetric analysis. To establish an easy to use application, the 3D-visualization has been embedded in a state of the art teleradiology system, where additional functionality is often desired beyond basic image transfer and management. Major clinical requirements for deriving spatial measures are covered by the tools, in order to realize extended diagnosis support and therapy planning. Introducing the general plug-in mechanism this work exemplarily describes the useful extension of an approved application. Interactive visualization was achieved by a hybrid approach taking advantage of both the precise volume visualization based on the Heidelberg Raytracing Model and the graphics acceleration of modern workstations. Several tools for volumetric analysis extend the 3D-viewing. They offer 3D-pointing devices to select locations in the data volume, measure anatomical structures or control segmentation processes. A haptic interface provides a realistic perception while navigating within the 3D-reconstruction. The work is closely related to research work in the field of heart, liver and head surgery. In cooperation with our medical partners the development of tools as presented proceed the integration of image analysis into clinical routine. PMID:10384617

  2. 3D imaging in volumetric scattering media using phase-space measurements.

    PubMed

    Liu, Hsiou-Yuan; Jonas, Eric; Tian, Lei; Zhong, Jingshan; Recht, Benjamin; Waller, Laura

    2015-06-01

    We demonstrate the use of phase-space imaging for 3D localization of multiple point sources inside scattering material. The effect of scattering is to spread angular (spatial frequency) information, which can be measured by phase space imaging. We derive a multi-slice forward model for homogenous volumetric scattering, then develop a reconstruction algorithm that exploits sparsity in order to further constrain the problem. By using 4D measurements for 3D reconstruction, the dimensionality mismatch provides significant robustness to multiple scattering, with either static or dynamic diffusers. Experimentally, our high-resolution 4D phase-space data is collected by a spectrogram setup, with results successfully recovering the 3D positions of multiple LEDs embedded in turbid scattering media. PMID:26072807

  3. Volumetric CT-based segmentation of NSCLC using 3D-Slicer

    PubMed Central

    Velazquez, Emmanuel Rios; Parmar, Chintan; Jermoumi, Mohammed; Mak, Raymond H.; van Baardwijk, Angela; Fennessy, Fiona M.; Lewis, John H.; De Ruysscher, Dirk; Kikinis, Ron; Lambin, Philippe; Aerts, Hugo J. W. L.

    2013-01-01

    Accurate volumetric assessment in non-small cell lung cancer (NSCLC) is critical for adequately informing treatments. In this study we assessed the clinical relevance of a semiautomatic computed tomography (CT)-based segmentation method using the competitive region-growing based algorithm, implemented in the free and public available 3D-Slicer software platform. We compared the 3D-Slicer segmented volumes by three independent observers, who segmented the primary tumour of 20 NSCLC patients twice, to manual slice-by-slice delineations of five physicians. Furthermore, we compared all tumour contours to the macroscopic diameter of the tumour in pathology, considered as the “gold standard”. The 3D-Slicer segmented volumes demonstrated high agreement (overlap fractions > 0.90), lower volume variability (p = 0.0003) and smaller uncertainty areas (p = 0.0002), compared to manual slice-by-slice delineations. Furthermore, 3D-Slicer segmentations showed a strong correlation to pathology (r = 0.89, 95%CI, 0.81–0.94). Our results show that semiautomatic 3D-Slicer segmentations can be used for accurate contouring and are more stable than manual delineations. Therefore, 3D-Slicer can be employed as a starting point for treatment decisions or for high-throughput data mining research, such as Radiomics, where manual delineating often represent a time-consuming bottleneck. PMID:24346241

  4. Volumetric CT-based segmentation of NSCLC using 3D-Slicer.

    PubMed

    Velazquez, Emmanuel Rios; Parmar, Chintan; Jermoumi, Mohammed; Mak, Raymond H; van Baardwijk, Angela; Fennessy, Fiona M; Lewis, John H; De Ruysscher, Dirk; Kikinis, Ron; Lambin, Philippe; Aerts, Hugo J W L

    2013-01-01

    Accurate volumetric assessment in non-small cell lung cancer (NSCLC) is critical for adequately informing treatments. In this study we assessed the clinical relevance of a semiautomatic computed tomography (CT)-based segmentation method using the competitive region-growing based algorithm, implemented in the free and public available 3D-Slicer software platform. We compared the 3D-Slicer segmented volumes by three independent observers, who segmented the primary tumour of 20 NSCLC patients twice, to manual slice-by-slice delineations of five physicians. Furthermore, we compared all tumour contours to the macroscopic diameter of the tumour in pathology, considered as the "gold standard". The 3D-Slicer segmented volumes demonstrated high agreement (overlap fractions > 0.90), lower volume variability (p = 0.0003) and smaller uncertainty areas (p = 0.0002), compared to manual slice-by-slice delineations. Furthermore, 3D-Slicer segmentations showed a strong correlation to pathology (r = 0.89, 95%CI, 0.81-0.94). Our results show that semiautomatic 3D-Slicer segmentations can be used for accurate contouring and are more stable than manual delineations. Therefore, 3D-Slicer can be employed as a starting point for treatment decisions or for high-throughput data mining research, such as Radiomics, where manual delineating often represent a time-consuming bottleneck. PMID:24346241

  5. 3D Volumetric Strain Modelling of Eruptions at Soufrière Hills Volcano Montserrat

    NASA Astrophysics Data System (ADS)

    Young, N. K.; Gottsmann, J.

    2015-12-01

    Volumetric strain data has captured a number of Vulcanian explosions at Soufrière Hills Volcano, Montserrat, which involve the uppermost part of the magmatic system. We previously used volumetric strain data from during one of these explosions to elucidate the geometry of the shallow plumbing system and crustal mechanics at Montserrat for mechanically plausible depressurisation amplitudes. Our results from both forward and inverse 2D models found that it was necessary to incorporate a mechanically weak shallow crust and mechanically compliant halo of material around the highest part of the SHV magmatic system i.e. the conduit, in order to implement geologically realistic conditions of depressurisation and rock strength. However, this model lacks complexity that cannot be implemented in a 2D environment. Here, in the first study of its kind, we use Finite Element Analysis of volumetric strain data in a 3D domain incorporating topography and mechanical complexities as imaged by seismic and gravimetric data. Our model implements topography from a DEM covering the island and surrounding bathymetry and include the mechanically stiff extinct volcanic cores of the Silver Hills and the Centre Hills. Here we present our preliminary findings from the 3D strain modelling and the effect of the extinct volcanic cores on strain partitioning on Montserrat.

  6. High-power, red-emitting DBR-TPL for possible 3d holographic or volumetric displays

    NASA Astrophysics Data System (ADS)

    Feise, D.; Fiebig, C.; Blume, G.; Pohl, J.; Eppich, B.; Paschke, K.

    2013-03-01

    To create holographic or volumetric displays, it is highly desirable to move from conventional imaging projection displays, where the light is filtered from a constant source towards flying spot, where the correct amount of light is generated for every pixel. The only light sources available for such an approach, which requires visible, high output power with a spatial resolution beyond conventional lamps, are lasers. When adding the market demands for high electro-optical conversion efficiency, direct electrical modulation capability, compactness, reliability and massproduction compliance, this leaves only semiconductor diode lasers. We present red-emitting tapered diode lasers (TPL) emitting a powerful, visible, nearly diffraction limited beam (M²1/e² < 1.5) and a single longitudinal mode, which are well suited for 3d holographic and volumetric imaging. The TPLs achieved an optical output power in excess of 500 mW in the wavelength range between 633 nm and 638 nm. The simultaneous inclusion of a distributed Bragg reflector (DBR) surface grating provides wavelength selectivity and hence a spectral purity with a width Δλ < 5 pm. These properties allow dense spectral multiplexing to achieve output powers of several watts, which would be required for 3d volumetric display applications.

  7. Evaluation of feature-based 3-d registration of probabilistic volumetric scenes

    NASA Astrophysics Data System (ADS)

    Restrepo, Maria I.; Ulusoy, Ali O.; Mundy, Joseph L.

    2014-12-01

    Automatic estimation of the world surfaces from aerial images has seen much attention and progress in recent years. Among current modeling technologies, probabilistic volumetric models (PVMs) have evolved as an alternative representation that can learn geometry and appearance in a dense and probabilistic manner. Recent progress, in terms of storage and speed, achieved in the area of volumetric modeling, opens the opportunity to develop new frameworks that make use of the PVM to pursue the ultimate goal of creating an entire map of the earth, where one can reason about the semantics and dynamics of the 3-d world. Aligning 3-d models collected at different time-instances constitutes an important step for successful fusion of large spatio-temporal information. This paper evaluates how effectively probabilistic volumetric models can be aligned using robust feature-matching techniques, while considering different scenarios that reflect the kind of variability observed across aerial video collections from different time instances. More precisely, this work investigates variability in terms of discretization, resolution and sampling density, errors in the camera orientation, and changes in illumination and geographic characteristics. All results are given for large-scale, outdoor sites. In order to facilitate the comparison of the registration performance of PVMs to that of other 3-d reconstruction techniques, the registration pipeline is also carried out using Patch-based Multi-View Stereo (PMVS) algorithm. Registration performance is similar for scenes that have favorable geometry and the appearance characteristics necessary for high quality reconstruction. In scenes containing trees, such as a park, or many buildings, such as a city center, registration performance is significantly more accurate when using the PVM.

  8. DSA volumetric 3D reconstructions of intracranial aneurysms: A pictorial essay

    PubMed Central

    Cieściński, Jakub; Serafin, Zbigniew; Strześniewski, Piotr; Lasek, Władysław; Beuth, Wojciech

    2012-01-01

    Summary A gold standard of cerebral vessel imaging remains the digital subtraction angiography (DSA) performed in three projections. However, in specific clinical cases, many additional projections are required, or a complete visualization of a lesion may even be impossible with 2D angiography. Three-dimensional (3D) reconstructions of rotational angiography were reported to improve the performance of DSA significantly. In this pictorial essay, specific applications of this technique are presented in the management of intracranial aneurysms, including: preoperative aneurysm evaluation, intraoperative imaging, and follow-up. Volumetric reconstructions of 3D DSA are a valuable tool for cerebral vessels imaging. They play a vital role in the assessment of intracranial aneurysms, especially in evaluation of the aneurysm neck and the aneurysm recanalization. PMID:22844309

  9. The Derivation of Fault Volumetric Properties from 3D Trace Maps Using Outcrop Constrained Discrete Fracture Network Models

    NASA Astrophysics Data System (ADS)

    Hodgetts, David; Seers, Thomas

    2015-04-01

    Fault systems are important structural elements within many petroleum reservoirs, acting as potential conduits, baffles or barriers to hydrocarbon migration. Large, seismic-scale faults often serve as reservoir bounding seals, forming structural traps which have proved to be prolific plays in many petroleum provinces. Though inconspicuous within most seismic datasets, smaller subsidiary faults, commonly within the damage zones of parent structures, may also play an important role. These smaller faults typically form narrow, tabular low permeability zones which serve to compartmentalize the reservoir, negatively impacting upon hydrocarbon recovery. Though considerable improvements have been made in the visualization field to reservoir-scale fault systems with the advent of 3D seismic surveys, the occlusion of smaller scale faults in such datasets is a source of significant uncertainty during prospect evaluation. The limited capacity of conventional subsurface datasets to probe the spatial distribution of these smaller scale faults has given rise to a large number of outcrop based studies, allowing their intensity, connectivity and size distributions to be explored in detail. Whilst these studies have yielded an improved theoretical understanding of the style and distribution of sub-seismic scale faults, the ability to transform observations from outcrop to quantities that are relatable to reservoir volumes remains elusive. These issues arise from the fact that outcrops essentially offer a pseudo-3D window into the rock volume, making the extrapolation of surficial fault properties such as areal density (fracture length per unit area: P21), to equivalent volumetric measures (i.e. fracture area per unit volume: P32) applicable to fracture modelling extremely challenging. Here, we demonstrate an approach which harnesses advances in the extraction of 3D trace maps from surface reconstructions using calibrated image sequences, in combination with a novel semi

  10. 3-D Technology Approaches for Biological Ecologies

    NASA Astrophysics Data System (ADS)

    Liu, Liyu; Austin, Robert; U. S-China Physical-Oncology Sciences Alliance (PS-OA) Team

    Constructing three dimensional (3-D) landscapes is an inevitable issue in deep study of biological ecologies, because in whatever scales in nature, all of the ecosystems are composed by complex 3-D environments and biological behaviors. Just imagine if a 3-D technology could help complex ecosystems be built easily and mimic in vivo microenvironment realistically with flexible environmental controls, it will be a fantastic and powerful thrust to assist researchers for explorations. For years, we have been utilizing and developing different technologies for constructing 3-D micro landscapes for biophysics studies in in vitro. Here, I will review our past efforts, including probing cancer cell invasiveness with 3-D silicon based Tepuis, constructing 3-D microenvironment for cell invasion and metastasis through polydimethylsiloxane (PDMS) soft lithography, as well as explorations of optimized stenting positions for coronary bifurcation disease with 3-D wax printing and the latest home designed 3-D bio-printer. Although 3-D technologies is currently considered not mature enough for arbitrary 3-D micro-ecological models with easy design and fabrication, I hope through my talk, the audiences will be able to sense its significance and predictable breakthroughs in the near future. This work was supported by the State Key Development Program for Basic Research of China (Grant No. 2013CB837200), the National Natural Science Foundation of China (Grant No. 11474345) and the Beijing Natural Science Foundation (Grant No. 7154221).

  11. Quantitative evaluation of 3D dosimetry for stereotactic volumetric-modulated arc delivery using COMPASS.

    PubMed

    Vikraman, Subramani; Manigandan, Durai; Karrthick, Karukkupalayam Palaniappan; Sambasivaselli, Raju; Senniandavar, Vellaingiri; Ramu, Mahendran; Rajesh, Thiyagarajan; Lutz, Muller; Muthukumaran, Manavalan; Karthikeyan, Nithyanantham; Tejinder, Kataria

    2015-01-01

    The purpose of this study was to evaluate quantitatively the patient-specific 3D dosimetry tool COMPASS with 2D array MatriXX detector for stereotactic volumetric-modulated arc delivery. Twenty-five patients CT images and RT structures from different sites (brain, head & neck, thorax, abdomen, and spine) were taken from CyberKnife Multiplan planning system for this study. All these patients underwent radical stereotactic treatment in CyberKnife. For each patient, linac based volumetric-modulated arc therapy (VMAT) stereotactic plans were generated in Monaco TPS v3.1 using Elekta Beam Modulator MLC. Dose prescription was in the range of 5-20 Gy per fraction. Target prescription and critical organ constraints were tried to match the delivered treatment plans. Each plan quality was analyzed using conformity index (CI), conformity number (CN), gradient Index (GI), target coverage (TC), and dose to 95% of volume (D95). Monaco Monte Carlo (MC)-calculated treatment plan delivery accuracy was quantitatively evaluated with COMPASS-calculated (CCA) dose and COMPASS indirectly measured (CME) dose based on dose-volume histogram metrics. In order to ascertain the potential of COMPASS 3D dosimetry for stereotactic plan delivery, 2D fluence verification was performed with MatriXX using MultiCube phantom. Routine quality assurance of absolute point dose verification was performed to check the overall delivery accuracy. Quantitative analyses of dose delivery verification were compared with pass and fail criteria of 3 mm and 3% distance to agreement and dose differences. Gamma passing rate was compared with 2D fluence verification from MatriXX with MultiCube. Comparison of COMPASS reconstructed dose from measured fluence and COMPASS computed dose has shown a very good agreement with TPS calculated dose. Each plan was evaluated based on dose volume parameters for target volumes such as dose at 95% of volume (D95) and average dose. For critical organs dose at 20% of volume (D20), dose

  12. Optimizing nonrigid registration performance between volumetric true 3D ultrasound images in image-guided neurosurgery

    NASA Astrophysics Data System (ADS)

    Ji, Songbai; Fan, Xiaoyao; Roberts, David W.; Hartov, Alex; Paulsen, Keith D.

    2011-03-01

    Compensating for brain shift as surgery progresses is important to ensure sufficient accuracy in patient-to-image registration in the operating room (OR) for reliable neuronavigation. Ultrasound has emerged as an important and practical imaging technique for brain shift compensation either by itself or through computational modeling that estimates whole-brain deformation. Using volumetric true 3D ultrasound (3DUS), it is possible to nonrigidly (e.g., based on B-splines) register two temporally different 3DUS images directly to generate feature displacement maps for data assimilation in the biomechanical model. Because of a large amount of data and number of degrees-of-freedom (DOFs) involved, however, a significant computational cost may be required that can adversely influence the clinical feasibility of the technique for efficiently generating model-updated MR (uMR) in the OR. This paper parametrically investigates three B-splines registration parameters and their influence on the computational cost and registration accuracy: number of grid nodes along each direction, floating image volume down-sampling rate, and number of iterations. A simulated rigid body displacement field was employed as a ground-truth against which the accuracy of displacements generated from the B-splines nonrigid registration was compared. A set of optimal parameters was then determined empirically that result in a registration computational cost of less than 1 min and a sub-millimetric accuracy in displacement measurement. These resulting parameters were further applied to a clinical surgery case to demonstrate their practical use. Our results indicate that the optimal set of parameters result in sufficient accuracy and computational efficiency in model computation, which is important for future application of the overall biomechanical modeling to generate uMR for image-guidance in the OR.

  13. Novel volumetric 3D display based on point light source optical reconstruction using multi focal lens array

    NASA Astrophysics Data System (ADS)

    Lee, Jin su; Lee, Mu young; Kim, Jun oh; Kim, Cheol joong; Won, Yong Hyub

    2015-03-01

    Generally, volumetric 3D display panel produce volume-filling three dimensional images. This paper discusses a volumetric 3D display based on periodical point light sources(PLSs) construction using a multi focal lens array(MFLA). The voxel of discrete 3D images is formed in the air via construction of point light source emitted by multi focal lens array. This system consists of a parallel beam, a spatial light modulator(SLM), a lens array, and a polarizing filter. The multi focal lens array is made with UV adhesive polymer droplet control using a dispersing machine. The MFLA consists of 20x20 circular lens array. Each lens aperture of the MFLA shows 300um on average. The polarizing filter is placed after the SLM and the MFLA to set in phase mostly mode. By the point spread function, the PLSs of the system are located by the focal length of each lens of the MFLA. It can also provide the moving parallax and relatively high resolution. However it has a limit of viewing angle and crosstalk by a property of each lens. In our experiment, we present the letter `C', `O', `DE' and ball's surface with the different depth location. It could be seen clearly that when CCD camera is moved to its position following as transverse axis of the display system. From our result, we expect that varifocal lens like EWOD and LC-lens can be applied for real time volumetric 3D display system.

  14. Oxygen- and Nitrogen-Enriched 3D Porous Carbon for Supercapacitors of High Volumetric Capacity.

    PubMed

    Li, Jia; Liu, Kang; Gao, Xiang; Yao, Bin; Huo, Kaifu; Cheng, Yongliang; Cheng, Xiaofeng; Chen, Dongchang; Wang, Bo; Sun, Wanmei; Ding, Dong; Liu, Meilin; Huang, Liang

    2015-11-11

    Efficient utilization and broader commercialization of alternative energies (e.g., solar, wind, and geothermal) hinges on the performance and cost of energy storage and conversion systems. For now and in the foreseeable future, the combination of rechargeable batteries and electrochemical capacitors remains the most promising option for many energy storage applications. Porous carbonaceous materials have been widely used as an electrode for batteries and supercapacitors. To date, however, the highest specific capacitance of an electrochemical double layer capacitor is only ∼200 F/g, although a wide variety of synthetic approaches have been explored in creating optimized porous structures. Here, we report our findings in the synthesis of porous carbon through a simple, one-step process: direct carbonization of kelp in an NH3 atmosphere at 700 °C. The resulting oxygen- and nitrogen-enriched carbon has a three-dimensional structure with specific surface area greater than 1000 m(2)/g. When evaluated as an electrode for electrochemical double layer capacitors, the porous carbon structure demonstrated excellent volumetric capacitance (>360 F/cm(3)) with excellent cycling stability. This simple approach to low-cost carbonaceous materials with unique architecture and functionality could be a promising alternative to fabrication of porous carbon structures for many practical applications, including batteries and fuel cells. PMID:26477268

  15. Intraoperative patient registration using volumetric true 3D ultrasound without fiducials

    PubMed Central

    Ji, Songbai; Roberts, David W.; Hartov, Alex; Paulsen, Keith D.

    2012-01-01

    Purpose: Accurate patient registration is crucial for effective image-guidance in open cranial surgery. Typically, it is accomplished by matching skin-affixed fiducials manually identified in the operating room (OR) with their counterparts in the preoperative images, which not only consumes OR time and personnel resources but also relies on the presence (and subsequent fixation) of the fiducials during the preoperative scans (until the procedure begins). In this study, the authors present a completely automatic, volumetric image-based patient registration technique that does not rely on fiducials by registering tracked (true) 3D ultrasound (3DUS) directly with preoperative magnetic resonance (MR) images. Methods: Multistart registrations between binary 3DUS and MR volumes were first executed to generate an initial starting point without incorporating prior information on the US transducer contact point location or orientation for subsequent registration between grayscale 3DUS and MR via maximization of either mutual information (MI) or correlation ratio (CR). Patient registration was then computed through concatenation of spatial transformations. Results: In ten (N = 10) patient cases, an average fiducial (marker) distance error (FDE) of 5.0 mm and 4.3 mm was achieved using MI or CR registration (FDE was smaller with CR vs MI in eight of ten cases), which are comparable to values reported for typical fiducial- or surface-based patient registrations. The translational and rotational capture ranges were found to be 24.0 mm and 27.0° for binary registrations (up to 32.8 mm and 36.4°), 12.2 mm and 25.6° for MI registrations (up to 18.3 mm and 34.4°), and 22.6 mm and 40.8° for CR registrations (up to 48.5 mm and 65.6°), respectively. The execution time to complete a patient registration was 12–15 min with parallel processing, which can be significantly reduced by confining the 3DUS transducer location to the center of craniotomy in MR before registration (an

  16. On Alternative Approaches to 3D Image Perception: Monoscopic 3D Techniques

    NASA Astrophysics Data System (ADS)

    Blundell, Barry G.

    2015-06-01

    In the eighteenth century, techniques that enabled a strong sense of 3D perception to be experienced without recourse to binocular disparities (arising from the spatial separation of the eyes) underpinned the first significant commercial sales of 3D viewing devices and associated content. However following the advent of stereoscopic techniques in the nineteenth century, 3D image depiction has become inextricably linked to binocular parallax and outside the vision science and arts communities relatively little attention has been directed towards earlier approaches. Here we introduce relevant concepts and terminology and consider a number of techniques and optical devices that enable 3D perception to be experienced on the basis of planar images rendered from a single vantage point. Subsequently we allude to possible mechanisms for non-binocular parallax based 3D perception. Particular attention is given to reviewing areas likely to be thought-provoking to those involved in 3D display development, spatial visualization, HCI, and other related areas of interdisciplinary research.

  17. Formation of 3D structures in a volumetric photocurable material via a holographic method

    NASA Astrophysics Data System (ADS)

    Vorzobova, N. D.; Bulgakova, V. G.; Veselov, V. O.

    2015-12-01

    The principle of forming 3D polymer structures is considered, based on the display of the 3D intensity distribution of radiation formed by a hologram in the bulk of a photocurable material. The conditions are determined for limiting the cure depth and reproducing the projected wavefront configuration.

  18. An evaluation of cine-mode 3D portal image dosimetry for Volumetric Modulated Arc Therapy

    NASA Astrophysics Data System (ADS)

    Ansbacher, W.; Swift, C.-L.; Greer, P. B.

    2010-11-01

    We investigated cine-mode portal imaging on a Varian Trilogy accelerator and found that the linearity and other dosimetric properties are sufficient for 3D dose reconstruction as used in patient-specific quality assurance for VMAT (RapidArc) treatments. We also evaluated the gantry angle label in the portal image file header as a surrogate for the true imaged angle. The precision is only just adequate for the 3D evaluation method chosen, as discrepancies of 2° were observed.

  19. Volumetric HIFU ablation under 3D guidance of rapid MRI thermometry.

    PubMed

    Köhler, Max O; Mougenot, Charles; Quesson, Bruno; Enholm, Julia; Le Bail, Brigitte; Laurent, Christophe; Moonen, Chrit T W; Ehnholm, Gösta J

    2009-08-01

    A volumetric sonication method is proposed that produces volume ablations by steering the focal point along a predetermined trajectory consisting of multiple concentric outward-moving circles. This method was tested in vivo on pig thigh muscle (32 ablations in nine animals). Trajectory diameters were 4, 12, and 16 mm with sonication duration depending on the trajectory size and ranging from 20 to 73 s. Despite the larger trajectories requiring more energy to reach necrosis within the desired volume, the ablated volume per unit applied energy increased with trajectory size, indicating improved treatment efficiency for larger trajectories. The higher amounts of energy required for the larger trajectories also increased the risk of off-focus heating, especially along the beam axis in the near field. To avoid related adverse effects, rapid volumetric multiplane MR thermometry was introduced for simultaneous monitoring of the temperature and thermal dose evolution along the beam axis and in the near field, as well as in the target region with a total coverage of six slices acquired every 3 s. An excellent correlation was observed between the thermal dose and both the nonperfused (R=0.929 for the diameter and R=0.964 for the length) and oedematous (R=0.913 for the diameter and R=0.939 for the length) volumes as seen in contrast-enhanced T1-weighted difference images and T2-weighted postsonication images, respectively. Histology confirmed the presence of a homogeneous necrosis inside the heated volumes. These results show that volumetric high-intensity focused ultrasound (HIFU) sonication allows for efficiently creating large thermal lesions while reducing treatment duration and also that the rapid multiplane MR thermometry improves the safety of the therapeutic procedure by monitoring temperature evolution both inside as well as outside the targeted volume. PMID:19746786

  20. Influence of georeference for saturated excess overland flow modelling using 3D volumetric soft geo-objects

    NASA Astrophysics Data System (ADS)

    Izham, Mohamad Yusoff; Muhamad Uznir, Ujang; Alias, Abdul Rahman; Ayob, Katimon; Wan Ruslan, Ismail

    2011-04-01

    Existing 2D data structures are often insufficient for analysing the dynamism of saturation excess overland flow (SEOF) within a basin. Moreover, all stream networks and soil surface structures in GIS must be preserved within appropriate projection plane fitting techniques known as georeferencing. Inclusion of 3D volumetric structure of the current soft geo-objects simulation model would offer a substantial effort towards representing 3D soft geo-objects of SEOF dynamically within a basin by visualising saturated flow and overland flow volume. This research attempts to visualise the influence of a georeference system towards the dynamism of overland flow coverage and total overland flow volume generated from the SEOF process using VSG data structure. The data structure is driven by Green-Ampt methods and the Topographic Wetness Index (TWI). VSGs are analysed by focusing on spatial object preservation techniques of the conformal-based Malaysian Rectified Skew Orthomorphic (MRSO) and the equidistant-based Cassini-Soldner projection plane under the existing geodetic Malaysian Revised Triangulation 1948 (MRT48) and the newly implemented Geocentric Datum for Malaysia (GDM2000) datum. The simulated result visualises deformation of SEOF coverage under different georeference systems via its projection planes, which delineate dissimilar computation of SEOF areas and overland flow volumes. The integration of Georeference, 3D GIS and the saturation excess mechanism provides unifying evidence towards successful landslide and flood disaster management through envisioning the streamflow generating process (mainly SEOF) in a 3D environment.

  1. Compression of medical volumetric datasets: physical and psychovisual performance comparison of the emerging JP3D standard and JPEG2000

    NASA Astrophysics Data System (ADS)

    Kimpe, T.; Bruylants, T.; Sneyders, Y.; Deklerck, R.; Schelkens, P.

    2007-03-01

    The size of medical data has increased significantly over the last few years. This poses severe problems for the rapid transmission of medical data across the hospital network resulting into longer access times of the images. Also longterm storage of data becomes more and more a problem. In an attempt to overcome the increasing data size often lossless or lossy compression algorithms are being used. This paper compares the existing JPEG2000 compression algorithm and the new emerging JP3D standard for compression of volumetric datasets. The main benefit of JP3D is that this algorithm truly is a 3D compression algorithm that exploits correlation not only within but also in between slices of a dataset. We evaluate both lossless and lossy modes of these algorithms. As a first step we perform an objective evaluation. Using RMSE and PSNR metrics we determine which compression algorithm performs best and this for multiple compression ratios and for several clinically relevant medical datasets. It is well known that RMSE and PSNR often do not correlate well with subjectively perceived image quality. Therefore we also perform a psycho visual analysis by means of a numerical observer. With this observer model we analyze how compression artifacts actually are perceived by a human observer. Results show superior performance of the new JP3D algorithm compared to the existing JPEG2000 algorithm.

  2. A 3-D SAR approach to IFSAR processing

    SciTech Connect

    DOERRY,ARMIN W.; BICKEL,DOUGLAS L.

    2000-03-01

    Interferometric SAR (IFSAR) can be shown to be a special case of 3-D SAR image formation. In fact, traditional IFSAR processing results in the equivalent of merely a super-resolved, under-sampled, 3-D SAR image. However, when approached as a 3-D SAR problem, a number of IFSAR properties and anomalies are easily explained. For example, IFSAR decorrelation with height is merely ordinary migration in 3-D SAR. Consequently, treating IFSAR as a 3-D SAR problem allows insight and development of proper motion compensation techniques and image formation operations to facilitate optimal height estimation. Furthermore, multiple antenna phase centers and baselines are easily incorporated into this formulation, providing essentially a sparse array in the elevation dimension. This paper shows the Polar Format image formation algorithm extended to 3 dimensions, and then proceeds to apply it to the IFSAR collection geometry. This suggests a more optimal reordering of the traditional IFSAR processing steps.

  3. Robust volumetric change detection using mutual information with 3D fractals

    NASA Astrophysics Data System (ADS)

    Rahmes, Mark; Akbari, Morris; Henning, Ronda; Pokorny, John

    2014-06-01

    We discuss a robust method for quantifying change of multi-temporal remote sensing point data in the presence of affine registration errors. Three dimensional image processing algorithms can be used to extract and model an electronic module, consisting of a self-contained assembly of electronic components and circuitry, using an ultrasound scanning sensor. Mutual information (MI) is an effective measure of change. We propose a multi-resolution 3D fractal algorithm which is a novel extension to MI or regional mutual information (RMI). Our method is called fractal mutual information (FMI). This extension efficiently takes neighborhood fractal patterns of corresponding voxels (3D pixels) into account. The goal of this system is to quantify the change in a module due to tampering and provide a method for quantitative and qualitative change detection and analysis.

  4. Nondestructive volumetric 3-D chemical mapping of nickel-sulfur compounds at the nanoscale

    SciTech Connect

    Harris W. M.; Chu Y.; Nelson, G.J.; Kiss, A.M.; Izzo Jr, J.R.; Liu, Y.; Liu, M.; Wang, S.; Chiu W.K.S.

    2012-04-04

    Nano-structures of nickel (Ni) and nickel subsulfide (Ni{sub 3}S{sub 2}) materials were studied and mapped in 3D with high-resolution x-ray nanotomography combined with full field XANES spectroscopy. This method for characterizing these phases in complex microstructures is an important new analytical imaging technique, applicable to a wide range of nanoscale and mesoscale electrochemical systems.

  5. Utility of 3D SPACE T2-weighted volumetric sequence in the localization of spinal dural arteriovenous fistula.

    PubMed

    Kannath, Santhosh Kumar; Alampath, Praveen; Enakshy Rajan, Jayadevan; Thomas, Bejoy; Sankara Sarma, P; Tirur Raman, Kapilamoorthy

    2016-07-01

    OBJECTIVE The aim of this study was to investigate the utility of a heavily T2-weighted volumetric MRI sequence (3D sampling perfection with application-optimized contrasts using different flip-angle evolutions [SPACE]) in the feeder localization of spinal dural arteriovenous fistula (SDAVF). METHODS Patients who were diagnosed with SDAVF and who had 3D SPACE source images available for review were identified from a retrospective review of medical records. A total of 16 patients were identified, and MR images were analyzed separately by 2 blinded observers. The accuracy of the observation and interobserver agreement were measured by Kendall's tau and kappa statistics. RESULTS The site of fistula was accurately predicted by Observers 1 and 2 in 81% and 88% of cases, respectively, which improved to 94% when the level was considered within 1 vertebral level. The observer agreement with gold-standard angiography and interobserver agreement were found to be highly significant (p < 0.0001). CONCLUSIONS The 3D SPACE MRI sequence is valuable in the precise detection of the site of SDAVF. It may help to tailor digital subtraction angiography and thereby reduce the radiation exposure, contrast load, and study time. PMID:26943253

  6. A 3D Approach to First Year English Education

    ERIC Educational Resources Information Center

    Zeegers, Margaret

    2013-01-01

    Purpose: The purpose of this paper is to explore the suggestive possibilities of an approach to undergraduate English teacher education that the author has called the 3D Approach--Develop professional knowledge, Display professional knowledge, Disseminate professional knowledge--in relation to a number of groups of first year pre-service teachers…

  7. Initialisation of 3D level set for hippocampus segmentation from volumetric brain MR images

    NASA Astrophysics Data System (ADS)

    Hajiesmaeili, Maryam; Dehmeshki, Jamshid; Bagheri Nakhjavanlo, Bashir; Ellis, Tim

    2014-04-01

    Shrinkage of the hippocampus is a primary biomarker for Alzheimer's disease and can be measured through accurate segmentation of brain MR images. The paper will describe the problem of initialisation of a 3D level set algorithm for hippocampus segmentation that must cope with the some challenging characteristics, such as small size, wide range of intensities, narrow width, and shape variation. In addition, MR images require bias correction, to account for additional inhomogeneity associated with the scanner technology. Due to these inhomogeneities, using a single initialisation seed region inside the hippocampus is prone to failure. Alternative initialisation strategies are explored, such as using multiple initialisations in different sections (such as the head, body and tail) of the hippocampus. The Dice metric is used to validate our segmentation results with respect to ground truth for a dataset of 25 MR images. Experimental results indicate significant improvement in segmentation performance using the multiple initialisations techniques, yielding more accurate segmentation results for the hippocampus.

  8. 3D volumetric modeling of grapevine biomass using Tripod LiDAR

    USGS Publications Warehouse

    Keightley, K.E.; Bawden, G.W.

    2010-01-01

    Tripod mounted laser scanning provides the means to generate high-resolution volumetric measures of vegetation structure and perennial woody tissue for the calculation of standing biomass in agronomic and natural ecosystems. Other than costly destructive harvest methods, no technique exists to rapidly and accurately measure above-ground perennial tissue for woody plants such as Vitis vinifera (common grape vine). Data collected from grapevine trunks and cordons were used to study the accuracy of wood volume derived from laser scanning as compared with volume derived from analog measurements. A set of 10 laser scan datasets were collected for each of 36 vines from which volume was calculated using combinations of two, three, four, six and 10 scans. Likewise, analog volume measurements were made by submerging the vine trunks and cordons in water and capturing the displaced water. A regression analysis examined the relationship between digital and non-digital techniques among the 36 vines and found that the standard error drops rapidly as additional scans are added to the volume calculation process and stabilizes at the four-view geometry with an average Pearson's product moment correlation coefficient of 0.93. Estimates of digital volumes are systematically greater than those of analog volumes and can be explained by the manner in which each technique interacts with the vine tissue. This laser scanning technique yields a highly linear relationship between vine volume and tissue mass revealing a new, rapid and non-destructive method to remotely measure standing biomass. This application shows promise for use in other ecosystems such as orchards and forests. ?? 2010 Elsevier B.V.

  9. Accuracy of 3D volumetric image registration based on CT, MR and PET/CT phantom experiments.

    PubMed

    Li, Guang; Xie, Huchen; Ning, Holly; Citrin, Deborah; Capala, Jacek; Maass-Moreno, Roberto; Guion, Peter; Arora, Barbara; Coleman, Norman; Camphausen, Kevin; Miller, Robert W

    2008-01-01

    Registration is critical for image-based treatment planning and image-guided treatment delivery. Although automatic registration is available, manual, visual-based image fusion using three orthogonal planar views (3P) is always employed clinically to verify and adjust an automatic registration result. However, the 3P fusion can be time consuming, observer dependent, as well as prone to errors, owing to the incomplete 3-dimensional (3D) volumetric image representations. It is also limited to single-pixel precision (the screen resolution). The 3D volumetric image registration (3DVIR) technique was developed to overcome these shortcomings. This technique introduces a 4th dimension in the registration criteria beyond the image volume, offering both visual and quantitative correlation of corresponding anatomic landmarks within the two registration images, facilitating a volumetric image alignment, and minimizing potential registration errors. The 3DVIR combines image classification in real-time to select and visualize a reliable anatomic landmark, rather than using all voxels for alignment. To determine the detection limit of the visual and quantitative 3DVIR criteria, slightly misaligned images were simulated and presented to eight clinical personnel for interpretation. Both of the criteria produce a detection limit of 0.1 mm and 0.1 degree. To determine the accuracy of the 3DVIR method, three imaging modalities (CT, MR and PET/CT) were used to acquire multiple phantom images with known spatial shifts. Lateral shifts were applied to these phantoms with displacement intervals of 5.0+/-0.1 mm. The accuracy of the 3DVIR technique was determined by comparing the image shifts determined through registration to the physical shifts made experimentally. The registration accuracy, together with precision, was found to be: 0.02+/-0.09 mm for CT/CT images, 0.03+/-0.07 mm for MR/MR images, and 0.03+/-0.35 mm for PET/CT images. This accuracy is consistent with the detection limit

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

    ERIC Educational Resources Information Center

    Ince, Alparslan

    2015-01-01

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

  11. Geospatial Modelling Approach for 3d Urban Densification Developments

    NASA Astrophysics Data System (ADS)

    Koziatek, O.; Dragićević, S.; Li, S.

    2016-06-01

    With growing populations, economic pressures, and the need for sustainable practices, many urban regions are rapidly densifying developments in the vertical built dimension with mid- and high-rise buildings. The location of these buildings can be projected based on key factors that are attractive to urban planners, developers, and potential buyers. Current research in this area includes various modelling approaches, such as cellular automata and agent-based modelling, but the results are mostly linked to raster grids as the smallest spatial units that operate in two spatial dimensions. Therefore, the objective of this research is to develop a geospatial model that operates on irregular spatial tessellations to model mid- and high-rise buildings in three spatial dimensions (3D). The proposed model is based on the integration of GIS, fuzzy multi-criteria evaluation (MCE), and 3D GIS-based procedural modelling. Part of the City of Surrey, within the Metro Vancouver Region, Canada, has been used to present the simulations of the generated 3D building objects. The proposed 3D modelling approach was developed using ESRI's CityEngine software and the Computer Generated Architecture (CGA) language.

  12. Volumetric LiDAR scanning of a wind turbine wake and comparison with a 3D analytical wake model

    NASA Astrophysics Data System (ADS)

    Carbajo Fuertes, Fernando; Porté-Agel, Fernando

    2016-04-01

    A correct estimation of the future power production is of capital importance whenever the feasibility of a future wind farm is being studied. This power estimation relies mostly on three aspects: (1) a reliable measurement of the wind resource in the area, (2) a well-established power curve of the future wind turbines and, (3) an accurate characterization of the wake effects; the latter being arguably the most challenging one due to the complexity of the phenomenon and the lack of extensive full-scale data sets that could be used to validate analytical or numerical models. The current project addresses the problem of obtaining a volumetric description of a full-scale wake of a 2MW wind turbine in terms of velocity deficit and turbulence intensity using three scanning wind LiDARs and two sonic anemometers. The characterization of the upstream flow conditions is done by one scanning LiDAR and two sonic anemometers, which have been used to calculate incoming vertical profiles of horizontal wind speed, wind direction and an approximation to turbulence intensity, as well as the thermal stability of the atmospheric boundary layer. The characterization of the wake is done by two scanning LiDARs working simultaneously and pointing downstream from the base of the wind turbine. The direct LiDAR measurements in terms of radial wind speed can be corrected using the upstream conditions in order to provide good estimations of the horizontal wind speed at any point downstream of the wind turbine. All this data combined allow for the volumetric reconstruction of the wake in terms of velocity deficit as well as turbulence intensity. Finally, the predictions of a 3D analytical model [1] are compared to the 3D LiDAR measurements of the wind turbine. The model is derived by applying the laws of conservation of mass and momentum and assuming a Gaussian distribution for the velocity deficit in the wake. This model has already been validated using high resolution wind-tunnel measurements

  13. Optimized Volumetric Modulated Arc Therapy Versus 3D-CRT for Early Stage Mediastinal Hodgkin Lymphoma Without Axillary Involvement: A Comparison of Second Cancers and Heart Disease Risk

    SciTech Connect

    Filippi, Andrea Riccardo; Ragona, Riccardo; Piva, Cristina; Scafa, Davide; Fiandra, Christian; Fusella, Marco; Giglioli, Francesca Romana; Lohr, Frank; Ricardi, Umberto

    2015-05-01

    Purpose: The purpose of this study was to evaluate the risks of second cancers and cardiovascular diseases associated with an optimized volumetric modulated arc therapy (VMAT) planning solution in a selected cohort of stage I/II Hodgkin lymphoma (HL) patients treated with either involved-node or involved-site radiation therapy in comparison with 3-dimensional conformal radiation therapy (3D-CRT). Methods and Materials: Thirty-eight patients (13 males and 25 females) were included. Disease extent was mediastinum alone (n=8, 21.1%); mediastinum plus unilateral neck (n=19, 50%); mediastinum plus bilateral neck (n=11, 29.9%). Prescription dose was 30 Gy in 2-Gy fractions. Only 5 patients had mediastinal bulky disease at diagnosis (13.1%). Anteroposterior 3D-CRT was compared with a multiarc optimized VMAT solution. Lung, breast, and thyroid cancer risks were estimated by calculating a lifetime attributable risk (LAR), with a LAR ratio (LAR{sub VMAT}-to-LAR{sub 3D-CRT}) as a comparative measure. Cardiac toxicity risks were estimated by calculating absolute excess risk (AER). Results: The LAR ratio favored 3D-CRT for lung cancer induction risk in mediastinal alone (P=.004) and mediastinal plus unilateral neck (P=.02) presentations. LAR ratio for breast cancer was lower for VMAT in mediastinal plus bilateral neck presentations (P=.02), without differences for other sites. For thyroid cancer, no significant differences were observed, regardless of anatomical presentation. A significantly lower AER of cardiac (P=.038) and valvular diseases (P<.0001) was observed for VMAT regardless of disease extent. Conclusions: In a cohort of patients with favorable characteristics in terms of disease extent at diagnosis (large prevalence of nonbulky presentations without axillary involvement), optimized VMAT reduced heart disease risk with comparable risks of thyroid and breast cancer, with an increase in lung cancer induction probability. The results are however strongly influenced by

  14. Towards a 3d Spatial Urban Energy Modelling Approach

    NASA Astrophysics Data System (ADS)

    Bahu, J.-M.; Koch, A.; Kremers, E.; Murshed, S. M.

    2013-09-01

    Today's needs to reduce the environmental impact of energy use impose dramatic changes for energy infrastructure and existing demand patterns (e.g. buildings) corresponding to their specific context. In addition, future energy systems are expected to integrate a considerable share of fluctuating power sources and equally a high share of distributed generation of electricity. Energy system models capable of describing such future systems and allowing the simulation of the impact of these developments thus require a spatial representation in order to reflect the local context and the boundary conditions. This paper describes two recent research approaches developed at EIFER in the fields of (a) geo-localised simulation of heat energy demand in cities based on 3D morphological data and (b) spatially explicit Agent-Based Models (ABM) for the simulation of smart grids. 3D city models were used to assess solar potential and heat energy demand of residential buildings which enable cities to target the building refurbishment potentials. Distributed energy systems require innovative modelling techniques where individual components are represented and can interact. With this approach, several smart grid demonstrators were simulated, where heterogeneous models are spatially represented. Coupling 3D geodata with energy system ABMs holds different advantages for both approaches. On one hand, energy system models can be enhanced with high resolution data from 3D city models and their semantic relations. Furthermore, they allow for spatial analysis and visualisation of the results, with emphasis on spatially and structurally correlations among the different layers (e.g. infrastructure, buildings, administrative zones) to provide an integrated approach. On the other hand, 3D models can benefit from more detailed system description of energy infrastructure, representing dynamic phenomena and high resolution models for energy use at component level. The proposed modelling strategies

  15. Right approach to 3D modeling using CAD tools

    NASA Astrophysics Data System (ADS)

    Baddam, Mounica Reddy

    The thesis provides a step-by-step methodology to enable an instructor dealing with CAD tools to optimally guide his/her students through an understandable 3D modeling approach which will not only enhance their knowledge about the tool's usage but also enable them to achieve their desired result in comparatively lesser time. In the known practical field, there is particularly very little information available to apply CAD skills to formal beginners' training sessions. Additionally, advent of new software in 3D domain cumulates updating into a more difficult task. Keeping up to the industry's advanced requirements emphasizes the importance of more skilled hands in the field of CAD development, rather than just prioritizing manufacturing in terms of complex software features. The thesis analyses different 3D modeling approaches specified to the varieties of CAD tools currently available in the market. Utilizing performance-time databases, learning curves have been generated to measure their performance time, feature count etc. Based on the results, improvement parameters have also been provided for (Asperl, 2005).

  16. Evolutionary approach to introduce 3D into the cockpit

    NASA Astrophysics Data System (ADS)

    Theunissen, Eric; Sachs, Gottfried; Dobler, Klaus

    1998-07-01

    Perspective flightpath displays and the depiction of 3-D terrain are regarded as a potential means to increase safety. Although the technology to generate such presentations in real-time is available, other issues which are required for a safe introduction must still be resolved. This paper focuses on some of the major obstacles which are still present. It discusses several objections against perspective flightpath displays and shows why most of them are no longer justified. The potential for an increase in safety is related to navigation, guidance, and control task requirements, and potential implementations, ranging in complexity, to satisfy these requirements are discussed. This classification allows a gradual transition from today's 2-D symbolic displays to future spatial displays. The paper proposes an approach which supports an evolutionary introduction of 3-D navigation displays into the cockpit.

  17. Silicon-Embedding Approaches to 3-D Toroidal Inductor Fabrication

    SciTech Connect

    Yu, XH; Kim, M; Herrault, F; Ji, CH; Kim, J; Allen, MG

    2013-06-01

    This paper presents complementary-metal-oxide-semiconductor-compatible silicon-embedding techniques for on-chip integration of microelectromechanical-system devices with 3-D complex structures. By taking advantage of the "dead volume" within the bulk of the silicon wafer, functional devices with large profile can be embedded into the substrate without consuming valuable die area on the wafer surface or increasing the packaging complexity. Furthermore, through-wafer interconnects can be implemented to connect the device to the circuitry on the wafer surface. The key challenge of embedding structures within the wafer volume is processing inside deep trenches. To achieve this goal in an area-efficient manner, straight-sidewall trenches are desired, adding additional difficulty to the embedding process. Two approaches to achieve this goal are presented in this paper, i.e., a lithography-based process and a shadow-mask-based process. The lithography-based process utilizes a spray-coating technique and proximity lithography in combination with thick epoxy processing and laminated dry-film lithography. The shadow-mask-based process employs a specially designed 3-D silicon shadow mask to enable simultaneous metal patterning on both the vertical sidewall and the bottom surface of the trench during deposition, eliminating multiple lithography steps and reducing the process time. Both techniques have been demonstrated through the embedding of the topologically complex 3-D toroidal inductors into the silicon substrate for power supply on-chip (PwrSoC) applications. Embedded 3-D inductors that possess 25 turns and a diameter of 6 mm in a silicon trench of 300-mu m depth achieve overall inductances of 45-60 nH, dc resistances of 290-400 m Omega, and quality factors of 16-17.5 at 40-70 MHz.

  18. 3D Volumetric Evaluation of Lipiodol Retention in HCC after Chemoembolization: A Quantitative Comparison between CBCT and MDCT

    PubMed Central

    Wang, Zhijun; Lin, MingDe; Lesage, David; Chen, Rongxin; Chapiro, Julius; Gu, Tara; Tacher, Vania; Duran, Rafael; Geschwind, Jean-François

    2014-01-01

    Rationale and Objectives To evaluate the capability of cone-beam computed tomography (CBCT) acquired immediately after transcatheter arterial chemoembolization (TACE) in determining Lipiodol retention quantitatively and volumetrically when compared to 1-day post-procedure unenhanced MDCT. Materials and methods From June to December, 2012, fifteen patients met the inclusion criteria of unresectable hepatocellular carcinoma (HCC) that was treated with conventional TACE (cTACE), and had intra-procedural CBCT and 1-day post-TACE MDCT. Four patients were excluded because the Lipiodol was diffuse throughout the entire liver or Lipiodol deposition was not clear on both CBCT and MDCT. Eleven patients with a total of 31 target lesions were included in the analysis. A quantitative and 3D software was used to assess complete, localized and diffuse lipiodol deposition. Tumor volume, Lipiodol volume in the tumor, % Lipiodol retention, and Lipiodol enhancement in Hounsfield Unit (HU) were calculated and compared between CBCT and MDCT using two-tailed student’s t-test and Bland-Altman plots. Results The mean value of tumor volume, Lipiodol deposited regions, calculated average % Lipiodol retention, and HU value of CBCT were not significantly different from those of MDCT (tumor volume: 9.37±11.35cm3 vs. 9.34±11.44cm3, P=0.991; Lipiodol volume: 7.84±9.34cm3 vs. 7.84±9.60 cm3, P=0.998; % Lipiodol retention: 89.3%±14.7% vs. 90.2% ± 14.9%, P=0.811; HU value: 307.7±160.1 HU vs. 257.2±120.0 HU, P=0.139). Bland-Altman plots showed only minimal difference and high agreement when comparing CBCT to MDCT. Conclusion CBCT has a similar capability, intraprocedurally, to assess Lipiodol deposition in 3D for patients with HCC treated with cTACE when compared to MDCT. PMID:24507426

  19. Size-based emphysema cluster analysis on low attenuation area in 3D volumetric CT: comparison with pulmonary functional test

    NASA Astrophysics Data System (ADS)

    Lee, Minho; Kim, Namkug; Lee, Sang Min; Seo, Joon Beom; Oh, Sang Young

    2015-03-01

    To quantify low attenuation area (LAA) of emphysematous regions according to cluster size in 3D volumetric CT data of chronic obstructive pulmonary disease (COPD) patients and to compare these indices with their pulmonary functional test (PFT). Sixty patients with COPD were scanned by a more than 16-multi detector row CT scanner (Siemens Sensation 16 and 64) within 0.75mm collimation. Based on these LAA masks, a length scale analysis to estimate each emphysema LAA's size was performed as follows. At first, Gaussian low pass filter from 30mm to 1mm kernel size with 1mm interval on the mask was performed from large to small size, iteratively. Centroid voxels resistant to the each filter were selected and dilated by the size of the kernel, which was regarded as the specific size emphysema mask. The slopes of area and number of size based LAA (slope of semi-log plot) were analyzed and compared with PFT. PFT parameters including DLco, FEV1, and FEV1/FVC were significantly (all p-value< 0.002) correlated with the slopes (r-values; -0.73, 0.54, 0.69, respectively) and EI (r-values; -0.84, -0.60, -0.68, respectively). In addition, the D independently contributed regression for FEV1 and FEV1/FVC (adjust R sq. of regression study: EI only, 0.70, 0.45; EI and D, 0.71, 0.51, respectively). By the size based LAA segmentation and analysis, we evaluated the Ds of area, number, and distribution of size based LAA, which would be independent factors for predictor of PFT parameters.

  20. Amygdala–hippocampal shape differences in schizophrenia: the application of 3D shape models to volumetric MR data

    PubMed Central

    Shenton, Martha E.; Gerig, Guido; McCarley, Robert W.; Székely, Gábor; Kikinis, Ron

    2010-01-01

    Evidence suggests that some structural brain abnormalities in schizophrenia are neurodevelopmental in origin. There is also growing evidence to suggest that shape deformations in brain structure may reflect abnormalities in neurodevelopment. While many magnetic resonance (MR) imaging studies have investigated brain area and volume measures in schizophrenia, fewer have focused on shape deformations. In this MR study we used a 3D shape representation technique, based on spherical harmonic functions, to analyze left and right amygdala-hippocampus shapes in each of 15 patients with schizophrenia and 15 healthy controls matched for age, gender, handedness and parental socioeconomic status. Left/right asymmetry was also measured for both shape and volume differences. Additionally, shape and volume measurements were combined in a composite analysis. There were no differences between groups in overall volume or shape. Left/right amygdala–hippocampal asymmetry, however, was significantly larger in patients than controls for both relative volume and shape. The local brain regions responsible for the left/right asymmetry differences in patients with schizophrenia were in the tail of the hippocampus (including both the inferior aspect adjacent to parahippocampal gyrus and the superior aspect adjacent to the lateral geniculate nucleus and more anteriorly to the cerebral peduncles) and in portions of the amygdala body (including the anterior–superior aspect adjacent to the basal nucleus). Also, in patients, increased volumetric asymmetry tended to be correlated with increased left/right shape asymmetry. Furthermore, a combined analysis of volume and shape asymmetry resulted in improved differentiation between groups. Classification function analyses correctly classified 70% of cases using volume, 73.3% using shape, and 87% using combined volume and shape measures. These findings suggest that shape provides important new information toward characterizing the pathophysiology

  1. Analysis of direct clinical consequences of MLC positional errors in volumetric-modulated arc therapy using 3D dosimetry system.

    PubMed

    Nithiyanantham, Karthikeyan; Mani, Ganesh K; Subramani, Vikraman; Mueller, Lutz; Palaniappan, Karrthick K; Kataria, Tejinder

    2015-01-01

    In advanced, intensity-modulated external radiotherapy facility, the multileaf collimator has a decisive role in the beam modulation by creating multiple segments or dynamically varying field shapes to deliver a uniform dose distribution to the target with maximum sparing of normal tissues. The position of each MLC leaf has become more critical for intensity-modulated delivery (step-and-shoot IMRT, dynamic IMRT, and VMAT) compared to 3D CRT, where it defines only field boundaries. We analyzed the impact of the MLC positional errors on the dose distribution for volumetric-modulated arc therapy, using a 3D dosimetry system. A total of 15 VMAT cases, five each for brain, head and neck, and prostate cases, were retrospectively selected for the study. All the plans were generated in Monaco 3.0.0v TPS (Elekta Corporation, Atlanta, GA) and delivered using Elekta Synergy linear accelerator. Systematic errors of +1, +0.5, +0.3, 0, -1, -0.5, -0.3 mm were introduced in the MLC bank of the linear accelerator and the impact on the dose distribution of VMAT delivery was measured using the COMPASS 3D dosim-etry system. All the plans were created using single modulated arcs and the dose calculation was performed using a Monte Carlo algorithm in a grid size of 3 mm. The clinical endpoints D95%, D50%, D2%, and Dmax,D20%, D50% were taken for the evaluation of the target and critical organs doses, respectively. A significant dosimetric effect was found for many cases even with 0.5 mm of MLC positional errors. The average change of dose D 95% to PTV for ± 1 mm, ± 0.5 mm, and ±0.3mm was 5.15%, 2.58%, and 0.96% for brain cases; 7.19%, 3.67%, and 1.56% for head and neck cases; and 8.39%, 4.5%, and 1.86% for prostate cases, respectively. The average deviation of dose Dmax was 5.4%, 2.8%, and 0.83% for brainstem in brain cases; 8.2%, 4.4%, and 1.9% for spinal cord in H&N; and 10.8%, 6.2%, and 2.1% for rectum in prostate cases, respectively. The average changes in dose followed a linear

  2. Objective 3D face recognition: Evolution, approaches and challenges.

    PubMed

    Smeets, Dirk; Claes, Peter; Vandermeulen, Dirk; Clement, John Gerald

    2010-09-10

    Face recognition is a natural human ability and a widely accepted identification and authentication method. In modern legal settings, a lot of credence is placed on identifications made by eyewitnesses. Consequently these are based on human perception which is often flawed and can lead to situations where identity is disputed. Therefore, there is a clear need to secure identifications in an objective way based on anthropometric measures. Anthropometry has existed for many years and has evolved with each advent of new technology and computing power. As a result of this, face recognition methodology has shifted from a purely 2D image-based approach to the use of 3D facial shape. However, one of the main challenges still remaining is the non-rigid structure of the face, which can change permanently over varying time-scales and briefly with facial expressions. The majority of face recognition methods have been developed by scientists with a very technical background such as biometry, pattern recognition and computer vision. This article strives to bridge the gap between these communities and the forensic science end-users. A concise review of face recognition using 3D shape is given. Methods using 3D shape applied to data embodying facial expressions are tabulated for reference. From this list a categorization of different strategies to deal with expressions is presented. The underlying concepts and practical issues relating to the application of each strategy are given, without going into technical details. The discussion clearly articulates the justification to establish archival, reference databases to compare and evaluate different strategies. PMID:20395086

  3. Registration of 3D spectral OCT volumes combining ICP with a graph-based approach

    NASA Astrophysics Data System (ADS)

    Niemeijer, Meindert; Lee, Kyungmoo; Garvin, Mona K.; Abràmoff, Michael D.; Sonka, Milan

    2012-02-01

    The introduction of spectral Optical Coherence Tomography (OCT) scanners has enabled acquisition of high resolution, 3D cross-sectional volumetric images of the retina. 3D-OCT is used to detect and manage eye diseases such as glaucoma and age-related macular degeneration. To follow-up patients over time, image registration is a vital tool to enable more precise, quantitative comparison of disease states. In this work we present a 3D registrationmethod based on a two-step approach. In the first step we register both scans in the XY domain using an Iterative Closest Point (ICP) based algorithm. This algorithm is applied to vessel segmentations obtained from the projection image of each scan. The distance minimized in the ICP algorithm includes measurements of the vessel orientation and vessel width to allow for a more robust match. In the second step, a graph-based method is applied to find the optimal translation along the depth axis of the individual A-scans in the volume to match both scans. The cost image used to construct the graph is based on the mean squared error (MSE) between matching A-scans in both images at different translations. We have applied this method to the registration of Optic Nerve Head (ONH) centered 3D-OCT scans of the same patient. First, 10 3D-OCT scans of 5 eyes with glaucoma imaged in vivo were registered for a qualitative evaluation of the algorithm performance. Then, 17 OCT data set pairs of 17 eyes with known deformation were used for quantitative assessment of the method's robustness.

  4. 3D imaging of soil pore network: two different approaches

    NASA Astrophysics Data System (ADS)

    Matrecano, M.; Di Matteo, B.; Mele, G.; Terribile, F.

    2009-04-01

    system but on less noisy images. SSAT system showed more flexibility in terms of sample size although both techniques allowed investigation on REVs (Representative Elementary Volumes) for most of macroscopic properties describing soil processes. Morover, undoubted advantages of not destructivity and ease sample preparation for the Skysan 1172 are balanced by lower overall costs for the SSAT and its potential of producing 3D representation of soil features different from the simple solid/porous phases. Both approaches allow to use exactly the same image analysis procedures on the reconstructed 3D images although require some specific pre-processing treatments.

  5. Development of a temporal multiplexed 3D beam-scanning Lissajous trajectory microscope for rapid multimodal volumetric imaging

    NASA Astrophysics Data System (ADS)

    Newman, Justin A.; Sullivan, Shane Z.; Dinh, Janny; Sarkar, Sreya; Simpson, Garth J.

    2016-03-01

    A beam-scanning microscope is described based on a temporally multiplexed Lissajous trajectory for achieving 1 kHz frame rate 3D imaging. The microscope utilizes two fast-scan resonant mirrors to direct the optical beam on a circuitous, Lissajous trajectory through the field of view. Acquisition of two simultaneous focal planes is achieved by implementation of an optical delay line, producing a second incident beam at a different focal plane relative to the initial incident beam. High frame rates are achieved by separating the full time-domain data into shorter sub-trajectories resulting in undersampling of the field of view. A model-based image reconstruction (MBIR) 3D in-painting algorithm is utilized for interpolating the missing data to recover full images. The MBIR algorithm uses a maximum a posteriori estimation with a generalized Gaussian Markov random field prior model for image interpolation. Because images are acquired using photomultiplier tubes or photodiodes, parallelization for multi-channel imaging is straightforward. Preliminary results obtained using a Lissajous trajectory beam-scanning approach coupled with temporal multiplexing by the implementation of an optical delay line demonstrate the ability to acquire 2 distinct focal planes simultaneously at frame rates >450 Hz for full 512 × 512 images. The use of multi-channel data acquisition cards allows for simultaneous multimodal image acquisition with perfect image registry between all imaging modalities. Also discussed here is the implementation of Lissajous trajectory beam-scanning on commercially available microscope hardware.

  6. An approach towards 3D sensitive AFM cantilevers

    NASA Astrophysics Data System (ADS)

    Koops, Richard; Fokkema, Vincent

    2014-04-01

    The atomic force microscope (AFM) tapping mode is a highly sensitive local probing technique that is very useful to study and measure surface properties down to the atomic scale. The tapping mode is mostly implemented using the resonance of the first bending mode of the cantilever and therefore provides sensitivity mainly along the direction of this oscillation. Driven by the semiconductor industry, there is an increasing need for accurate measurements of nanoscale structures for side wall characterization by AFM that requires additional sensitivity in the lateral direction. The conventional tapping mode has been augmented by various authors, for example by tilting the cantilever system (Cho et al 2011 Rev. Sci. Instrum. 82 023707) to access the sidewall or using a torsion mode (Dai et al 2011 Meas. Sci. Technol. 22 094009) of the cantilever to provide additional lateral sensitivity. These approaches however trade lateral sensitivity for vertical sensitivity or still lack sensitivity in the remaining lateral direction. We present an approach towards true 3D sensitivity for AFM cantilevers based on simultaneous excitation and optical detection of multiple cantilever resonance modes along three axes. Tuning the excitation of the cantilever to specific frequencies provides a mechanism to select only those cantilever modes that have the desired characteristics. Additionally, cantilever engineering has been used to design and create a substructure within the cantilever that has been optimized for specific resonance behavior around 4 MHz. In contrast to the conventional approach of using a piezo to actuate the cantilever modulation, we present results on photo-thermal excitation using an intensity modulated low-power laser source. By tightly focusing the excitation spot on the cantilever we were able to attain a deflection efficiency of 0.7 nm µW-1 for the first bending mode. The presented approach results in an efficient all optical excitation and deflection detection

  7. True-Depth: a new type of true 3D volumetric display system suitable for CAD, medical imaging, and air-traffic control

    NASA Astrophysics Data System (ADS)

    Dolgoff, Eugene

    1998-04-01

    Floating Images, Inc. is developing a new type of volumetric monitor capable of producing a high-density set of points in 3D space. Since the points of light actually exist in space, the resulting image can be viewed with continuous parallax, both vertically and horizontally, with no headache or eyestrain. These 'real' points in space are always viewed with a perfect match between accommodation and convergence. All scanned points appear to the viewer simultaneously, making this display especially suitable for CAD, medical imaging, air-traffic control, and various military applications. This system has the potential to display imagery so accurately that a ruler could be placed within the aerial image to provide precise measurement in any direction. A special virtual imaging arrangement allows the user to superimpose 3D images on a solid object, making the object look transparent. This is particularly useful for minimally invasive surgery in which the internal structure of a patient is visible to a surgeon in 3D. Surgical procedures can be carried out through the smallest possible hole while the surgeon watches the procedure from outside the body as if the patient were transparent. Unlike other attempts to produce volumetric imaging, this system uses no massive rotating screen or any screen at all, eliminating down time due to breakage and possible danger due to potential mechanical failure. Additionally, it is also capable of displaying very large images.

  8. A volumetric model-based 2D to 3D registration method for measuring kinematics of natural knees with single-plane fluoroscopy

    SciTech Connect

    Tsai, Tsung-Yuan; Lu, Tung-Wu; Chen, Chung-Ming; Kuo, Mei-Ying; Hsu, Horng-Chaung

    2010-03-15

    Purpose: Accurate measurement of the three-dimensional (3D) rigid body and surface kinematics of the natural human knee is essential for many clinical applications. Existing techniques are limited either in their accuracy or lack more realistic experimental evaluation of the measurement errors. The purposes of the study were to develop a volumetric model-based 2D to 3D registration method, called the weighted edge-matching score (WEMS) method, for measuring natural knee kinematics with single-plane fluoroscopy to determine experimentally the measurement errors and to compare its performance with that of pattern intensity (PI) and gradient difference (GD) methods. Methods: The WEMS method gives higher priority to matching of longer edges of the digitally reconstructed radiograph and fluoroscopic images. The measurement errors of the methods were evaluated based on a human cadaveric knee at 11 flexion positions. Results: The accuracy of the WEMS method was determined experimentally to be less than 0.77 mm for the in-plane translations, 3.06 mm for out-of-plane translation, and 1.13 deg. for all rotations, which is better than that of the PI and GD methods. Conclusions: A new volumetric model-based 2D to 3D registration method has been developed for measuring 3D in vivo kinematics of natural knee joints with single-plane fluoroscopy. With the equipment used in the current study, the accuracy of the WEMS method is considered acceptable for the measurement of the 3D kinematics of the natural knee in clinical applications.

  9. 3D real holographic image movies are projected into a volumetric display using dynamic digital micromirror device (DMD) holograms.

    NASA Astrophysics Data System (ADS)

    Huebschman, Michael L.; Hunt, Jeremy; Garner, Harold R.

    2006-04-01

    The Texas Instruments Digital Micromirror Device (DMD) is being used as the recording medium for display of pre-calculated digital holograms. The high intensity throughput of the reflected laser light from DMD holograms enables volumetric display of projected real images as well as virtual images. A single DMD and single laser projector system has been designed to reconstruct projected images in a 6''x 6''x 4.5'' volumetric display. The volumetric display is composed of twenty-four, 6''-square, PSCT liquid crystal plates which are each cycled on and off to reduce unnecessary scatter in the volume. The DMD is an XGA format array, 1024x768, with 13.6 micron pitch mirrors. This holographic projection system has been used in the assessment of hologram image resolution, maximum image size, optical focusing of the real image, image look-around, and physiological depth cues. Dynamic movement images are projected by transferring the appropriately sequenced holograms to the DMD at movie frame rates.

  10. Treatment of left sided breast cancer for a patient with funnel chest: Volumetric-modulated arc therapy vs. 3D-CRT and intensity-modulated radiotherapy

    SciTech Connect

    Haertl, Petra M.; Pohl, Fabian; Weidner, Karin; Groeger, Christian; Koelbl, Oliver; Dobler, Barbara

    2013-04-01

    This case study presents a rare case of left-sided breast cancer in a patient with funnel chest, which is a technical challenge for radiation therapy planning. To identify the best treatment technique for this case, 3 techniques were compared: conventional tangential fields (3D conformal radiotherapy [3D-CRT]), intensity-modulated radiotherapy (IMRT), and volumetric-modulated arc therapy (VMAT). The plans were created for a SynergyS® (Elekta, Ltd, Crawley, UK) linear accelerator with a BeamModulator™ head and 6-MV photons. The planning system was Oncentra Masterplan® v3.3 SP1 (Nucletron BV, Veenendal, Netherlands). Calculations were performed with collapsed cone algorithm. Dose prescription was 50.4 Gy to the average of the planning target volume (PTV). PTV coverage and homogeneity was comparable for all techniques. VMAT allowed reducing dose to the ipsilateral organs at risk (OAR) and the contralateral breast compared with IMRT and 3D-CRT: The volume of the left lung receiving 20 Gy was 19.3% for VMAT, 26.1% for IMRT, and 32.4% for 3D-CRT. In the heart, a D{sub 15%} of 9.7 Gy could be achieved with VMAT compared with 14 Gy for IMRT and 46 Gy for 3D-CRT. In the contralateral breast, D{sub 15%} was 6.4 Gy for VMAT, 8.8 Gy for IMRT, and 10.2 Gy for 3D-CRT. In the contralateral lung, however, the lowest dose was achieved with 3D-CRT with D{sub 10%} of 1.7 Gy for 3D-CRT, and 6.7 Gy for both IMRT and VMAT. The lowest number of monitor units (MU) per 1.8-Gy fraction was required by 3D-CRT (192 MU) followed by VMAT (518 MU) and IMRT (727 MU). Treatment time was similar for 3D-CRT (3 min) and VMAT (4 min) but substantially increased for IMRT (13 min). VMAT is considered the best treatment option for the presented case of a patient with funnel chest. It allows reducing dose in most OAR without compromising target coverage, keeping delivery time well below 5 minutes.

  11. An automatic approach for 3D registration of CT scans

    NASA Astrophysics Data System (ADS)

    Hu, Yang; Saber, Eli; Dianat, Sohail; Vantaram, Sreenath Rao; Abhyankar, Vishwas

    2012-03-01

    CT (Computed tomography) is a widely employed imaging modality in the medical field. Normally, a volume of CT scans is prescribed by a doctor when a specific region of the body (typically neck to groin) is suspected of being abnormal. The doctors are required to make professional diagnoses based upon the obtained datasets. In this paper, we propose an automatic registration algorithm that helps healthcare personnel to automatically align corresponding scans from 'Study' to 'Atlas'. The proposed algorithm is capable of aligning both 'Atlas' and 'Study' into the same resolution through 3D interpolation. After retrieving the scanned slice volume in the 'Study' and the corresponding volume in the original 'Atlas' dataset, a 3D cross correlation method is used to identify and register various body parts.

  12. Metrological verification of 3D scanners: a preliminary approach

    NASA Astrophysics Data System (ADS)

    Anchini, R.; Di Leo, G.; Liguori, C.; Paolillo, A.; Pietrosanto, A.; Strazzullo, G.

    2007-01-01

    The paper deals with the metrological characterization of 3D scanners, and proposes a procedure for their experimental verification in accord with the suggestions of the ISO GUM. The procedure is based on the application of a statistical method for the evaluation of the standard uncertainty to the results of a comparison with a Coordinate Measuring Machine (CMM). Finally the results of the experimental verification of a fringe pattern system are reported and discussed in detail.

  13. High-dose radiotherapy in inoperable nonsmall cell lung cancer: comparison of volumetric modulated arc therapy, dynamic IMRT and 3D conformal radiotherapy.

    PubMed

    Bree, Ingrid de; van Hinsberg, Mariëlle G E; van Veelen, Lieneke R

    2012-01-01

    Conformal 3D radiotherapy (3D-CRT) combined with chemotherapy for inoperable non-small cell lung cancer (NSCLC) to the preferable high dose is often not achievable because of dose-limiting organs. This reduces the probability of regional tumor control. Therefore, the surplus value of using intensity-modulated radiation therapy (IMRT) techniques, specifically volumetric modulated arc therapy (RapidArc [RA]) and dynamic IMRT (d-IMRT) has been investigated. RA and d-IMRT plans were compared with 3D-CRT treatment plans for 20 patients eligible for concurrent high-dose chemoradiotherapy, in whom a dose of 60 Gy was not achievable. Comparison of dose delivery in the target volume and organs at risk was carried out by evaluating 3D dose distributions and dose-volume histograms. Quality of the dose distribution was assessed using the inhomogeneity and conformity index. For most patients, a higher dose to the target volume can be delivered using RA or d-IMRT; in 15% of the patients a dose ≥60 Gy was possible. Both IMRT techniques result in a better conformity of the dose (p < 0.001). There are no significant differences in homogeneity of dose in the target volume. IMRT techniques for NSCLC patients allow higher dose to the target volume, thus improving regional tumor control. PMID:22459649

  14. SU-E-T-624: Quantitative Evaluation of 2D Versus 3D Dosimetry for Stereotactic Volumetric Modulated Arc Delivery Using COMPASS

    SciTech Connect

    Vikraman, S; Karrthick, K; Rajesh, T; Sambasivaselli, R; Senniandanvar, V; Kataria, T; Manigandan, D; Karthikeyan, N; Muthukumaran, M

    2014-06-15

    Purpose: The purpose of this study was to evaluate quantitatively 2D versus 3D dosimetry for stereotactic volumetric modulated arc delivery using COMPASS with 2D array. Methods: Twenty-five patients CT images and RT structures of different sites like brain, head and neck, thorax, abdomen and spine were taken from Multiplan planning system for this study. All these patients underwent radical stereotactic treatment in Cyberknife. For each patient, linac based VMAT stereotactic plans were generated in Monaco TPS v 3.1 using Elekta Beam Modulator MLC. Dose prescription was in the range of 5-20Gy/fraction.TPS calculated VMAT plan delivery accuracy was quantitatively evaluated with COMPASS measured dose and calculated dose based on DVH metrics. In order to ascertain the potential of COMPASS 3D dosimetry for stereotactic plan delivery, 2D fluence verification was performed with MatriXX using Multicube. Results: For each site, D{sub 9} {sub 5} was achieved with 100% of prescription dose with maximum 0.05SD. Conformity index (CI) was observed closer to 1.15 in all cases. Maximum deviation of 2.62 % was observed for D{sub 9} {sub 5} when compared TPS versus COMPASS measured. Considerable deviations were observed in head and neck cases compare to other sites. The maximum mean and standard deviation for D{sub 9} {sub 5}, average target dose and average gamma were -0.78±1.72, -1.10±1.373 and 0.39±0.086 respectively. Numbers of pixels passing 2D fluence verification were observed as a mean of 99.36% ±0.455 SD with 3% dose difference and 3mm DTA. For critical organs in head and neck cases, significant dose differences were observed in 3D dosimetry while the target doses were matched well within limit in both 2D and 3D dosimetry. Conclusion: The quantitative evaluations of 2D versus 3D dosimetry for stereotactic volumetric modulated plans showed the potential of highlighting the delivery errors. This study reveals that COMPASS 3D dosimetry is an effective tool for patient

  15. Volumetric modulated arc planning for lung stereotactic body radiotherapy using conventional and unflattened photon beams: a dosimetric comparison with 3D technique

    PubMed Central

    2011-01-01

    Purpose Frequently, three-dimensional (3D) conformal beams are used in lung cancer stereotactic body radiotherapy (SBRT). Recently, volumetric modulated arc therapy (VMAT) was introduced as a new treatment modality. VMAT techniques shorten delivery time, reducing the possibility of intrafraction target motion. However dose distributions can be quite different from standard 3D therapy. This study quantifies those differences, with focus on VMAT plans using unflattened photon beams. Methods A total of 15 lung cancer patients previously treated with 3D or VMAT SBRT were randomly selected. For each patient, non-coplanar 3D, coplanar and non-coplanar VMAT and flattening filter free VMAT (FFF-VMAT) plans were generated to meet the same objectives with 50 Gy covering 95% of the PTV. Two dynamic arcs were used in each VMAT plan. The couch was set at ± 5° to the 0° straight position for the two non-coplanar arcs. Pinnacle version 9.0 (Philips Radiation Oncology, Fitchburg WI) treatment planning system with VMAT capabilities was used. We analyzed the conformity index (CI), which is the ratio of the total volume receiving at least the prescription dose to the target volume receiving at least the prescription dose; the conformity number (CN) which is the ratio of the target coverage to CI; and the gradient index (GI) which is the ratio of the volume of 50% of the prescription isodose to the volume of the prescription isodose; as well as the V20, V5, and mean lung dose (MLD). Paired non-parametric analysis of variance tests with post-tests were performed to examine the statistical significance of the differences of the dosimetric indices. Results Dosimetric indices CI, CN and MLD all show statistically significant improvement for all studied VMAT techniques compared with 3D plans (p < 0.05). V5 and V20 show statistically significant improvement for the FFF-VMAT plans compared with 3D (p < 0.001). GI is improved for the FFF-VMAT and the non-coplanar VMAT plans (p < 0.01 and p

  16. A 3D Sensor Based on a Profilometrical Approach

    PubMed Central

    Pedraza-Ortega, Jesús Carlos; Gorrostieta-Hurtado, Efren; Delgado-Rosas, Manuel; Canchola-Magdaleno, Sandra L.; Ramos-Arreguin, Juan Manuel; Aceves Fernandez, Marco A.; Sotomayor-Olmedo, Artemio

    2009-01-01

    An improved method which considers the use of Fourier and wavelet transform based analysis to infer and extract 3D information from an object by fringe projection on it is presented. This method requires a single image which contains a sinusoidal white light fringe pattern projected on it, and this pattern has a known spatial frequency and its information is used to avoid any discontinuities in the fringes with high frequency. Several computer simulations and experiments have been carried out to verify the analysis. The comparison between numerical simulations and experiments has proved the validity of this proposed method. PMID:22303176

  17. Computational approaches to 3D modeling of RNA.

    PubMed

    Laing, Christian; Schlick, Tamar

    2010-07-21

    Many exciting discoveries have recently revealed the versatility of RNA and its importance in a variety of functions within the cell. Since the structural features of RNA are of major importance to their biological function, there is much interest in predicting RNA structure, either in free form or in interaction with various ligands, including proteins, metabolites and other molecules. In recent years, an increasing number of researchers have developed novel RNA algorithms for predicting RNA secondary and tertiary structures. In this review, we describe current experimental and computational advances and discuss recent ideas that are transforming the traditional view of RNA folding. To evaluate the performance of the most recent RNA 3D folding algorithms, we provide a comparative study in order to test the performance of available 3D structure prediction algorithms for an RNA data set of 43 structures of various lengths and motifs. We find that the algorithms vary widely in terms of prediction quality across different RNA lengths and topologies; most predictions have very large root mean square deviations from the experimental structure. We conclude by outlining some suggestions for future RNA folding research. PMID:21399271

  18. Evaluation of 3D pre-treatment verification for volumetric modulated arc therapy plan in head region

    NASA Astrophysics Data System (ADS)

    Ruangchan, S.; Oonsiri, S.; Suriyapee, S.

    2016-03-01

    The development of pre-treatment QA tools contributes to the three dimension (3D) dose verification using the calculation software with the measured planar dose distribution. This research is aimed to evaluate the Sun Nuclear 3DVH software with Thermo luminescence dosimeter (TLD) measurement. The two VMAT patient plans (2.5 arcs) of 6 MV photons with different PTV locations were transferred to the Rando phantom images. The PTV of the first plan located in homogeneous area and vice versa in the second plan. For treatment planning process, the Rando phantom images were employed in optimization and calculation with the PTV, brain stem, lens and TLD position contouring. The verification plans were created, transferred to the ArcCHECK for measurement and calculated the 3D dose using 3DVH software. The range of the percent dose differences in both PTV and organ at risk (OAR) between TLD and 3DVH software of the first and the second plans were -2.09 to 3.87% and -1.39 to 6.88%, respectively. The mean percent dose differences for the PTV were 1.62% and 3.93% for the first and the second plans, respectively. In conclusion, the 3DVH software results show good agreement with TLD when the tumor located in the homogeneous area.

  19. Alpha shape theory for 3D visualization and volumetric measurement of brain tumor progression using magnetic resonance images.

    PubMed

    Hamoud Al-Tamimi, Mohammed Sabbih; Sulong, Ghazali; Shuaib, Ibrahim Lutfi

    2015-07-01

    Resection of brain tumors is a tricky task in surgery due to its direct influence on the patients' survival rate. Determining the tumor resection extent for its complete information via-à-vis volume and dimensions in pre- and post-operative Magnetic Resonance Images (MRI) requires accurate estimation and comparison. The active contour segmentation technique is used to segment brain tumors on pre-operative MR images using self-developed software. Tumor volume is acquired from its contours via alpha shape theory. The graphical user interface is developed for rendering, visualizing and estimating the volume of a brain tumor. Internet Brain Segmentation Repository dataset (IBSR) is employed to analyze and determine the repeatability and reproducibility of tumor volume. Accuracy of the method is validated by comparing the estimated volume using the proposed method with that of gold-standard. Segmentation by active contour technique is found to be capable of detecting the brain tumor boundaries. Furthermore, the volume description and visualization enable an interactive examination of tumor tissue and its surrounding. Admirable features of our results demonstrate that alpha shape theory in comparison to other existing standard methods is superior for precise volumetric measurement of tumor. PMID:25865822

  20. Retrospective evaluation of dosimetric quality for prostate carcinomas treated with 3D conformal, intensity modulated and volumetric modulated arc radiotherapy

    SciTech Connect

    Crowe, Scott B; Kairn, Tanya; Middlebrook, Nigel; Hill, Brendan; Christie, David R H; Knight, Richard T; Kenny, John; Langton, Christian M; Trapp, Jamie V

    2013-12-15

    This study examines and compares the dosimetric quality of radiotherapy treatment plans for prostate carcinoma across a cohort of 163 patients treated across five centres: 83 treated with three-dimensional conformal radiotherapy (3DCRT), 33 treated with intensity modulated radiotherapy (IMRT) and 47 treated with volumetric modulated arc therapy (VMAT). Treatment plan quality was evaluated in terms of target dose homogeneity and organs at risk (OAR), through the use of a set of dose metrics. These included the mean, maximum and minimum doses; the homogeneity and conformity indices for the target volumes; and a selection of dose coverage values that were relevant to each OAR. Statistical significance was evaluated using two-tailed Welch's T-tests. The Monte Carlo DICOM ToolKit software was adapted to permit the evaluation of dose metrics from DICOM data exported from a commercial radiotherapy treatment planning system. The 3DCRT treatment plans offered greater planning target volume dose homogeneity than the other two treatment modalities. The IMRT and VMAT plans offered greater dose reduction in the OAR: with increased compliance with recommended OAR dose constraints, compared to conventional 3DCRT treatments. When compared to each other, IMRT and VMAT did not provide significantly different treatment plan quality for like-sized tumour volumes. This study indicates that IMRT and VMAT have provided similar dosimetric quality, which is superior to the dosimetric quality achieved with 3DCRT.

  1. Retrospective evaluation of dosimetric quality for prostate carcinomas treated with 3D conformal, intensity modulated and volumetric modulated arc radiotherapy

    PubMed Central

    Crowe, Scott B; Kairn, Tanya; Middlebrook, Nigel; Hill, Brendan; Christie, David R H; Knight, Richard T; Kenny, John; Langton, Christian M; Trapp, Jamie V

    2013-01-01

    Introduction This study examines and compares the dosimetric quality of radiotherapy treatment plans for prostate carcinoma across a cohort of 163 patients treated across five centres: 83 treated with three-dimensional conformal radiotherapy (3DCRT), 33 treated with intensity modulated radiotherapy (IMRT) and 47 treated with volumetric modulated arc therapy (VMAT). Methods Treatment plan quality was evaluated in terms of target dose homogeneity and organs at risk (OAR), through the use of a set of dose metrics. These included the mean, maximum and minimum doses; the homogeneity and conformity indices for the target volumes; and a selection of dose coverage values that were relevant to each OAR. Statistical significance was evaluated using two-tailed Welch's T-tests. The Monte Carlo DICOM ToolKit software was adapted to permit the evaluation of dose metrics from DICOM data exported from a commercial radiotherapy treatment planning system. Results The 3DCRT treatment plans offered greater planning target volume dose homogeneity than the other two treatment modalities. The IMRT and VMAT plans offered greater dose reduction in the OAR: with increased compliance with recommended OAR dose constraints, compared to conventional 3DCRT treatments. When compared to each other, IMRT and VMAT did not provide significantly different treatment plan quality for like-sized tumour volumes. Conclusions This study indicates that IMRT and VMAT have provided similar dosimetric quality, which is superior to the dosimetric quality achieved with 3DCRT. PMID:26229621

  2. Correlation between gamma index passing rate and clinical dosimetric difference for pre-treatment 2D and 3D volumetric modulated arc therapy dosimetric verification

    PubMed Central

    Jin, X; Yan, H; Han, C; Zhou, Y; Yi, J

    2015-01-01

    Objective: To investigate comparatively the percentage gamma passing rate (%GP) of two-dimensional (2D) and three-dimensional (3D) pre-treatment volumetric modulated arc therapy (VMAT) dosimetric verification and their correlation and sensitivity with percentage dosimetric errors (%DE). Methods: %GP of 2D and 3D pre-treatment VMAT quality assurance (QA) with different acceptance criteria was obtained by ArcCHECK® (Sun Nuclear Corporation, Melbourne, FL) for 20 patients with nasopharyngeal cancer (NPC) and 20 patients with oesophageal cancer. %DE were calculated from planned dose–volume histogram (DVH) and patients' predicted DVH calculated by 3DVH® software (Sun Nuclear Corporation). Correlation and sensitivity between %GP and %DE were investigated using Pearson's correlation coefficient (r) and receiver operating characteristics (ROCs). Results: Relatively higher %DE on some DVH-based metrics were observed for both patients with NPC and oesophageal cancer. Except for 2%/2 mm criterion, the average %GPs for all patients undergoing VMAT were acceptable with average rates of 97.11% ± 1.54% and 97.39% ± 1.37% for 2D and 3D 3%/3 mm criteria, respectively. The number of correlations for 3D was higher than that for 2D (21 vs 8). However, the general correlation was still poor for all the analysed metrics (9 out of 26 for 3D 3%/3 mm criterion). The average area under the curve (AUC) of ROCs was 0.66 ± 0.12 and 0.71 ± 0.21 for 2D and 3D evaluations, respectively. Conclusions: There is a lack of correlation between %GP and %DE for both 2D and 3D pre-treatment VMAT dosimetric evaluation. DVH-based dose metrics evaluation obtained from 3DVH will provide more useful analysis. Advances in knowledge: Correlation and sensitivity of %GP with %DE for VMAT QA were studied for the first time. PMID:25494412

  3. 3D pre-stack depth migration of receiver functions with the fast marching method: a Kirchhoff approach

    NASA Astrophysics Data System (ADS)

    Cheng, Cheng; Bodin, Thomas; Allen, Richard M.

    2016-02-01

    We present a novel 3D pre-stack Kirchhoff depth migration (PKDM) method for teleseismic receiver functions. The proposed algorithm considers the effects of diffraction, scattering, and travel time alteration caused by 3D volumetric heterogeneities. It is therefore particularly useful for imaging complex 3D structures such as dipping discontinuities, which is hard to accomplish with traditional methods. The scheme is based on the acoustic wave migration principle, where at each time step of the receiver function, the energy is migrated back to the ensemble of potential conversion points in the image, given a smooth 3D reference model. Travel times for P and S waves are computed with an efficient Eikonal solver, the Fast Marching Method. We also consider elastic scattering patterns, where the amplitude of converted S waves depends on the angle between the incident P wave, and the scattered S wave. Synthetic experiments demonstrate the validity of the method for a variety of dipping angle discontinuities. Comparison with the widely used Common Conversion Point (CCP) stacking method reveals that our migration shows considerable improvement. For example, the effect of multiple reflections that usually produce apparent discontinuities is avoided. The proposed approach is practical, computationally efficient, and is therefore a potentially powerful alternative to standard CCP methods for imaging large-scale continental structure under dense networks.

  4. An initial study on the estimation of time-varying volumetric treatment images and 3D tumor localization from single MV cine EPID images

    SciTech Connect

    Mishra, Pankaj Mak, Raymond H.; Rottmann, Joerg; Bryant, Jonathan H.; Williams, Christopher L.; Berbeco, Ross I.; Lewis, John H.; Li, Ruijiang

    2014-08-15

    Purpose: In this work the authors develop and investigate the feasibility of a method to estimate time-varying volumetric images from individual MV cine electronic portal image device (EPID) images. Methods: The authors adopt a two-step approach to time-varying volumetric image estimation from a single cine EPID image. In the first step, a patient-specific motion model is constructed from 4DCT. In the second step, parameters in the motion model are tuned according to the information in the EPID image. The patient-specific motion model is based on a compact representation of lung motion represented in displacement vector fields (DVFs). DVFs are calculated through deformable image registration (DIR) of a reference 4DCT phase image (typically peak-exhale) to a set of 4DCT images corresponding to different phases of a breathing cycle. The salient characteristics in the DVFs are captured in a compact representation through principal component analysis (PCA). PCA decouples the spatial and temporal components of the DVFs. Spatial information is represented in eigenvectors and the temporal information is represented by eigen-coefficients. To generate a new volumetric image, the eigen-coefficients are updated via cost function optimization based on digitally reconstructed radiographs and projection images. The updated eigen-coefficients are then multiplied with the eigenvectors to obtain updated DVFs that, in turn, give the volumetric image corresponding to the cine EPID image. Results: The algorithm was tested on (1) Eight digital eXtended CArdiac-Torso phantom datasets based on different irregular patient breathing patterns and (2) patient cine EPID images acquired during SBRT treatments. The root-mean-squared tumor localization error is (0.73 ± 0.63 mm) for the XCAT data and (0.90 ± 0.65 mm) for the patient data. Conclusions: The authors introduced a novel method of estimating volumetric time-varying images from single cine EPID images and a PCA-based lung motion model

  5. 3-D volumetric computed tomographic scoring as an objective outcome measure for chronic rhinosinusitis: Clinical correlations and comparison to Lund-Mackay scoring

    PubMed Central

    Pallanch, John; Yu, Lifeng; Delone, David; Robb, Rich; Holmes, David R.; Camp, Jon; Edwards, Phil; McCollough, Cynthia H.; Ponikau, Jens; Dearking, Amy; Lane, John; Primak, Andrew; Shinkle, Aaron; Hagan, John; Frigas, Evangelo; Ocel, Joseph J.; Tombers, Nicole; Siwani, Rizwan; Orme, Nicholas; Reed, Kurtis; Jerath, Nivedita; Dhillon, Robinder; Kita, Hirohito

    2014-01-01

    Background We aimed to test the hypothesis that 3-D volume-based scoring of computed tomographic (CT) images of the paranasal sinuses was superior to Lund-Mackay CT scoring of disease severity in chronic rhinosinusitis (CRS). We determined correlation between changes in CT scores (using each scoring system) with changes in other measures of disease severity (symptoms, endoscopic scoring, and quality of life) in patients with CRS treated with triamcinolone. Methods The study group comprised 48 adult subjects with CRS. Baseline symptoms and quality of life were assessed. Endoscopy and CT scans were performed. Patients received a single systemic dose of intramuscular triamcinolone and were reevaluated 1 month later. Strengths of the correlations between changes in CT scores and changes in CRS signs and symptoms and quality of life were determined. Results We observed some variability in degree of improvement for the different symptom, endoscopic, and quality-of-life parameters after treatment. Improvement of parameters was significantly correlated with improvement in CT disease score using both CT scoring methods. However, volumetric CT scoring had greater correlation with these parameters than Lund-Mackay scoring. Conclusion Volumetric scoring exhibited higher degree of correlation than Lund-Mackay scoring when comparing improvement in CT score with improvement in score for symptoms, endoscopic exam, and quality of life in this group of patients who received beneficial medical treatment for CRS. PMID:24106202

  6. Rapid dry-reagent immunomagnetic biosensing platform based on volumetric detection of nanoparticles on 3D structures.

    PubMed

    Orlov, Alexey V; Bragina, Vera A; Nikitin, Maxim P; Nikitin, Petr I

    2016-05-15

    A dry-reagent immunomagnetic (DRIM) biosensing platform is developed for rapid high-precision quantitative analyses for in vitro diagnostics. The platform combines the advantages of immunochromatography with highly sensitive quantification of 200-nm magnetic nanoparticles (MP) from the entire volume of lateral flow membranes. The MP are registered by their non-linear magnetization at combinatorial frequencies by a portable reader that offers the detection limit of 60 zeptomoles or 0.4 ng of magnetic nanolabels and extremely wide linear dynamic range of 7 orders. The efficient combination of small MP with large reaction surface of the 3D membranes has permitted the detection in human serum of as low as 25 pg/ml total prostate specific antigen (PSA) during 30-min assay. The featured 3-fold signal increase per every order of concentration within 3.5 orders of magnitude allows precise analysis of antigen concentrations in a wide range. The system also provides the first tool for quantitative MP mapping along the lateral flow strip for easy development and optimization of assays. The DRIM detection can be used for simple, rapid and sensitive quantification of protein biomarkers for in vitro diagnostics both in laboratory and near-patient conditions, for food analysis, environmental monitoring, security, and safety applications. PMID:26741530

  7. Hierarchical Approach to 'Atomistic' 3-D MOSFET Simulation

    NASA Technical Reports Server (NTRS)

    Asenov, Asen; Brown, Andrew R.; Davies, John H.; Saini, Subhash

    1999-01-01

    We present a hierarchical approach to the 'atomistic' simulation of aggressively scaled sub-0.1 micron MOSFET's. These devices are so small that their characteristics depend on the precise location of dopant atoms within them, not just on their average density. A full-scale three-dimensional drift-diffusion atomistic simulation approach is first described and used to verify more economical, but restricted, options. To reduce processor time and memory requirements at high drain voltage, we have developed a self-consistent option based on a solution of the current continuity equation restricted to a thin slab of the channel. This is coupled to the solution of the Poisson equation in the whole simulation domain in the Gummel iteration cycles. The accuracy of this approach is investigated in comparison to the full self-consistent solution. At low drain voltage, a single solution of the nonlinear Poisson equation is sufficient to extract the current with satisfactory accuracy. In this case, the current is calculated by solving the current continuity equation in a drift approximation only, also in a thin slab containing the MOSFET channel. The regions of applicability for the different components of this hierarchical approach are illustrated in example simulations covering the random dopant-induced threshold voltage fluctuations, threshold voltage lowering, threshold voltage asymmetry, and drain current fluctuations.

  8. Making of 3D extinction maps from population synthesis approach

    NASA Astrophysics Data System (ADS)

    Robin, A. C.; Marshall, D.; Reylé, C.; Montillaud, J.

    Interstellar extinction is critical when studying stellar populations and Galactic structure. By taking into account all informations on stellar populations on a given line of sight, the population synthesis approach is an efficient tool to derive the distribution of extinction. This approach has been shown to give reliable estimates in regions where the stars are numerous enough and well distributed in distance. This method has some limits due to dependency on model hypotheses. With other methods, some biases can appear close to the limiting magnitude, and to the maximum distance of detection, due to detection limits of the stars which depend on the extinction itself. We present the successes of this method as well as its limitations and compare with results of other methods.

  9. Lightning Modelling: From 3D to Circuit Approach

    NASA Astrophysics Data System (ADS)

    Moussa, H.; Abdi, M.; Issac, F.; Prost, D.

    2012-05-01

    The topic of this study is electromagnetic environment and electromagnetic interferences (EMI) effects, specifically the modelling of lightning indirect effects [1] on aircraft electrical systems present on deported and highly exposed equipments, such as nose landing gear (NLG) and nacelle, through a circuit approach. The main goal of the presented work, funded by a French national project: PREFACE, is to propose a simple equivalent electrical circuit to represent a geometrical structure, taking into account mutual, self inductances, and resistances, which play a fundamental role in the lightning current distribution. Then this model is intended to be coupled to a functional one, describing a power train chain composed of: a converter, a shielded power harness and a motor or a set of resistors used as a load for the converter. The novelty here, is to provide a pre-sizing qualitative approach allowing playing on integration in pre-design phases. This tool intends to offer a user-friendly way for replying rapidly to calls for tender, taking into account the lightning constraints. Two cases are analysed: first, a NLG that is composed of tubular pieces that can be easily approximated by equivalent cylindrical straight conductors. Therefore, passive R, L, M elements of the structure can be extracted through analytical engineer formulas such as those implemented in the partial element equivalent circuit (PEEC) [2] technique. Second, the same approach is intended to be applied on an electrical de-icing nacelle sub-system.

  10. Feasibility of Using Volumetric Contrast-Enhanced Ultrasound with a 3-D Transducer to Evaluate Therapeutic Response after Targeted Therapy in Rabbit Hepatic VX2 Carcinoma.

    PubMed

    Kim, Jeehyun; Kim, Jung Hoon; Yoon, Soon Ho; Choi, Won Seok; Kim, Young Jae; Han, Joon Koo; Choi, Byung-Ihn

    2015-12-01

    The aim of this study was to assess the feasibility of using dynamic contrast-enhanced ultrasound (DCE-US) with a 3-D transducer to evaluate therapeutic responses to targeted therapy. Rabbits with hepatic VX2 carcinomas, divided into a treatment group (n = 22, 30 mg/kg/d sorafenib) and a control group (n = 13), were evaluated with DCE-US using 2-D and 3-D transducers and computed tomography (CT) perfusion imaging at baseline and 1 d after the first treatment. Perfusion parameters were collected, and correlations between parameters were analyzed. In the treatment group, both volumetric and 2-D DCE-US perfusion parameters, including peak intensity (33.2 ± 19.9 vs. 16.6 ± 10.7, 63.7 ± 20.0 vs. 30.1 ± 19.8), slope (15.3 ± 12.4 vs. 5.7 ± 4.5, 37.3 ± 20.4 vs. 15.7 ± 13.0) and area under the curve (AUC; 1004.1 ± 560.3 vs. 611.4 ± 421.1, 1332.2 ± 708.3 vs. 670.4 ± 388.3), had significantly decreased 1 d after the first treatment (p = 0.00). In the control group, 2-D DCE-US revealed that peak intensity, time to peak and slope had significantly changed (p < 0.05); however, volumetric DCE-US revealed that peak intensity, time-intensity AUC, AUC during wash-in and AUC during wash-out had significantly changed (p = 0.00). CT perfusion imaging parameters, including blood flow, blood volume and permeability of the capillary vessel surface, had significantly decreased in the treatment group (p = 0.00); however, in the control group, peak intensity and blood volume had significantly increased (p = 0.00). It is feasible to use DCE-US with a 3-D transducer to predict early therapeutic response after targeted therapy because perfusion parameters, including peak intensity, slope and AUC, significantly decreased, which is similar to the trend observed for 2-D DCE-US and CT perfusion imaging parameters. PMID:26365926

  11. Continuous table acquisition MRI for radiotherapy treatment planning: Distortion assessment with a new extended 3D volumetric phantom

    SciTech Connect

    Walker, Amy Metcalfe, Peter; Liney, Gary; Holloway, Lois; Dowling, Jason; Rivest-Henault, David

    2015-04-15

    Purpose: Accurate geometry is required for radiotherapy treatment planning (RTP). When considering the use of magnetic resonance imaging (MRI) for RTP, geometric distortions observed in the acquired images should be considered. While scanner technology and vendor supplied correction algorithms provide some correction, large distortions are still present in images, even when considering considerably smaller scan lengths than those typically acquired with CT in conventional RTP. This study investigates MRI acquisition with a moving table compared with static scans for potential geometric benefits for RTP. Methods: A full field of view (FOV) phantom (diameter 500 mm; length 513 mm) was developed for measuring geometric distortions in MR images over volumes pertinent to RTP. The phantom consisted of layers of refined plastic within which vitamin E capsules were inserted. The phantom was scanned on CT to provide the geometric gold standard and on MRI, with differences in capsule location determining the distortion. MRI images were acquired with two techniques. For the first method, standard static table acquisitions were considered. Both 2D and 3D acquisition techniques were investigated. With the second technique, images were acquired with a moving table. The same sequence was acquired with a static table and then with table speeds of 1.1 mm/s and 2 mm/s. All of the MR images acquired were registered to the CT dataset using a deformable B-spline registration with the resulting deformation fields providing the distortion information for each acquisition. Results: MR images acquired with the moving table enabled imaging of the whole phantom length while images acquired with a static table were only able to image 50%–70% of the phantom length of 513 mm. Maximum distortion values were reduced across a larger volume when imaging with a moving table. Increased table speed resulted in a larger contribution of distortion from gradient nonlinearities in the through

  12. 3D Lorentzian loop quantum gravity and the spinor approach

    NASA Astrophysics Data System (ADS)

    Girelli, Florian; Sellaroli, Giuseppe

    2015-12-01

    We consider the generalization of the "spinor approach" to the Lorentzian case, in the context of three-dimensional loop quantum gravity with cosmological constant Λ =0 . The key technical tool that allows this generalization is the recoupling theory between unitary infinite-dimensional representations and nonunitary finite-dimensional ones, obtained in the process of generalizing the Wigner-Eckart theorem to SU(1,1). We use SU(1,1) tensor operators to build observables and a solvable quantum Hamiltonian constraint, analogous to the one introduced by V. Bonzom and his collaborators in the Euclidean case (with both Λ =0 and Λ ≠0 ). We show that the Lorentzian Ponzano-Regge amplitude is the solution of the quantum Hamiltonian constraint by recovering the Biedenharn-Elliott relation [generalized to the case where unitary and nonunitary SU(1,1) representations are coupled to each other]. Our formalism is sufficiently general that both the Lorentzian and the Euclidean case can be recovered (with Λ =0 ).

  13. A featureless approach to 3D polyhedral building modeling from aerial images.

    PubMed

    Hammoudi, Karim; Dornaika, Fadi

    2011-01-01

    This paper presents a model-based approach for reconstructing 3D polyhedral building models from aerial images. The proposed approach exploits some geometric and photometric properties resulting from the perspective projection of planar structures. Data are provided by calibrated aerial images. The novelty of the approach lies in its featurelessness and in its use of direct optimization based on image rawbrightness. The proposed framework avoids feature extraction and matching. The 3D polyhedral model is directly estimated by optimizing an objective function that combines an image-based dissimilarity measure and a gradient score over several aerial images. The optimization process is carried out by the Differential Evolution algorithm. The proposed approach is intended to provide more accurate 3D reconstruction than feature-based approaches. Fast 3D model rectification and updating can take advantage of the proposed method. Several results and evaluations of performance from real and synthetic images show the feasibility and robustness of the proposed approach. PMID:22346575

  14. A Featureless Approach to 3D Polyhedral Building Modeling from Aerial Images

    PubMed Central

    Hammoudi, Karim; Dornaika, Fadi

    2011-01-01

    This paper presents a model-based approach for reconstructing 3D polyhedral building models from aerial images. The proposed approach exploits some geometric and photometric properties resulting from the perspective projection of planar structures. Data are provided by calibrated aerial images. The novelty of the approach lies in its featurelessness and in its use of direct optimization based on image rawbrightness. The proposed framework avoids feature extraction and matching. The 3D polyhedral model is directly estimated by optimizing an objective function that combines an image-based dissimilarity measure and a gradient score over several aerial images. The optimization process is carried out by the Differential Evolution algorithm. The proposed approach is intended to provide more accurate 3D reconstruction than feature-based approaches. Fast 3D model rectification and updating can take advantage of the proposed method. Several results and evaluations of performance from real and synthetic images show the feasibility and robustness of the proposed approach. PMID:22346575

  15. A new approach towards image based virtual 3D city modeling by using close range photogrammetry

    NASA Astrophysics Data System (ADS)

    Singh, S. P.; Jain, K.; Mandla, V. R.

    2014-05-01

    3D city model is a digital representation of the Earth's surface and it's related objects such as building, tree, vegetation, and some manmade feature belonging to urban area. The demand of 3D city modeling is increasing day to day for various engineering and non-engineering applications. Generally three main image based approaches are using for virtual 3D city models generation. In first approach, researchers used Sketch based modeling, second method is Procedural grammar based modeling and third approach is Close range photogrammetry based modeling. Literature study shows that till date, there is no complete solution available to create complete 3D city model by using images. These image based methods also have limitations This paper gives a new approach towards image based virtual 3D city modeling by using close range photogrammetry. This approach is divided into three sections. First, data acquisition process, second is 3D data processing, and third is data combination process. In data acquisition process, a multi-camera setup developed and used for video recording of an area. Image frames created from video data. Minimum required and suitable video image frame selected for 3D processing. In second section, based on close range photogrammetric principles and computer vision techniques, 3D model of area created. In third section, this 3D model exported to adding and merging of other pieces of large area. Scaling and alignment of 3D model was done. After applying the texturing and rendering on this model, a final photo-realistic textured 3D model created. This 3D model transferred into walk-through model or in movie form. Most of the processing steps are automatic. So this method is cost effective and less laborious. Accuracy of this model is good. For this research work, study area is the campus of department of civil engineering, Indian Institute of Technology, Roorkee. This campus acts as a prototype for city. Aerial photography is restricted in many country

  16. Optimization approaches to volumetric modulated arc therapy planning.

    PubMed

    Unkelbach, Jan; Bortfeld, Thomas; Craft, David; Alber, Markus; Bangert, Mark; Bokrantz, Rasmus; Chen, Danny; Li, Ruijiang; Xing, Lei; Men, Chunhua; Nill, Simeon; Papp, Dávid; Romeijn, Edwin; Salari, Ehsan

    2015-03-01

    Volumetric modulated arc therapy (VMAT) has found widespread clinical application in recent years. A large number of treatment planning studies have evaluated the potential for VMAT for different disease sites based on the currently available commercial implementations of VMAT planning. In contrast, literature on the underlying mathematical optimization methods used in treatment planning is scarce. VMAT planning represents a challenging large scale optimization problem. In contrast to fluence map optimization in intensity-modulated radiotherapy planning for static beams, VMAT planning represents a nonconvex optimization problem. In this paper, the authors review the state-of-the-art in VMAT planning from an algorithmic perspective. Different approaches to VMAT optimization, including arc sequencing methods, extensions of direct aperture optimization, and direct optimization of leaf trajectories are reviewed. Their advantages and limitations are outlined and recommendations for improvements are discussed. PMID:25735291

  17. Optimization approaches to volumetric modulated arc therapy planning

    SciTech Connect

    Unkelbach, Jan Bortfeld, Thomas; Craft, David; Alber, Markus; Bangert, Mark; Bokrantz, Rasmus; Chen, Danny; Li, Ruijiang; Xing, Lei; Men, Chunhua; Nill, Simeon; Papp, Dávid; Romeijn, Edwin; Salari, Ehsan

    2015-03-15

    Volumetric modulated arc therapy (VMAT) has found widespread clinical application in recent years. A large number of treatment planning studies have evaluated the potential for VMAT for different disease sites based on the currently available commercial implementations of VMAT planning. In contrast, literature on the underlying mathematical optimization methods used in treatment planning is scarce. VMAT planning represents a challenging large scale optimization problem. In contrast to fluence map optimization in intensity-modulated radiotherapy planning for static beams, VMAT planning represents a nonconvex optimization problem. In this paper, the authors review the state-of-the-art in VMAT planning from an algorithmic perspective. Different approaches to VMAT optimization, including arc sequencing methods, extensions of direct aperture optimization, and direct optimization of leaf trajectories are reviewed. Their advantages and limitations are outlined and recommendations for improvements are discussed.

  18. Framework for quantitative evaluation of 3D vessel segmentation approaches using vascular phantoms in conjunction with 3D landmark localization and registration

    NASA Astrophysics Data System (ADS)

    Wörz, Stefan; Hoegen, Philipp; Liao, Wei; Müller-Eschner, Matthias; Kauczor, Hans-Ulrich; von Tengg-Kobligk, Hendrik; Rohr, Karl

    2016-03-01

    We introduce a framework for quantitative evaluation of 3D vessel segmentation approaches using vascular phantoms. Phantoms are designed using a CAD system and created with a 3D printer, and comprise realistic shapes including branches and pathologies such as abdominal aortic aneurysms (AAA). To transfer ground truth information to the 3D image coordinate system, we use a landmark-based registration scheme utilizing fiducial markers integrated in the phantom design. For accurate 3D localization of the markers we developed a novel 3D parametric intensity model that is directly fitted to the markers in the images. We also performed a quantitative evaluation of different vessel segmentation approaches for a phantom of an AAA.

  19. General approach for the description of optical 3D measuring systems

    NASA Astrophysics Data System (ADS)

    Andrae, Peter; Jueptner, Werner P. O.; Kebbel, Volker; Osten, Wolfgang

    1997-07-01

    In this paper a general geometric description of the optical methods for 3D coordinate measurement is presented. Similar to holographic interferometry this new approach is based on the concept of measuring sensitivity. As a special case the derived basic relation is applied to the fringe projection technique using a physical model of this measurement method. Moreover a geometric 3D model that contributes to a dramatic reduction of systematic distortions of measured 3D coordinates is presented. On the one hand this model is sufficiently general but on the other hand still easy to handle. It permits an explicit and direct determination of 3D coordinates from primary measuring data as well as a calibration of the measuring set-up using linear identification methods mainly. The described 3D model can be applied also with advantage to multiview registration tasks.

  20. Reactive Transport from Path3D: A Stream Tube Approach for Heterogeneous Aquifers

    NASA Astrophysics Data System (ADS)

    LI, L.

    2001-05-01

    Path3D (Zheng, 1991) is a popular computer program run in series with MODFLOW. Remediation engineers and hydrogeologist use it to track contaminant paths and to estimate solute travel time at heterogeneous sites. In order to predict fate and transport of multiple species at heterogeneous sites, numerical modeling packages, such as MT3D (Zheng,1990) or RT3D (Clement 1997) are often employed. These packages also are based on pre-processing with MODFLOW. However, for complex cases with aquifer heterogeneity, MT3D and RT3D often require very long computer run times. This paper addresses a new, stream-tube, approach that is both highly efficient and accurate to predict multi-species reactive transport at heterogeneous sites with steady flow. Our application of the stream tube approach is different from other stream tube approaches that apply the advection-dispersion-reaction equation in each stream tube (such as Ginn, 2000, Yabusaki, 1998, Charbeneau, 2000). In this work, the authors make use of properties of a linear system,working with decoupled reaction and sorption processes and mixing processes described by residence time distributions (RTDs). RTDs are abstracted from Path3D particle-tracking results and additional temporal and spatial dispersion (not caused by aquifer heterogeneity) is ignored. Reactions, including first order reactions and linear, reversible sorption, are applied through analytical transfer functions (called kinetic response functions). Convolution can then be applied to determine contaminant concentrations at monitoring points, using the RTDs determined from Path3D, kinetic transfer functions (expressed analytically), and expected trends of the source concentration. We are currently testing the approach and noting significant computational advantages for problems in three-dimensions, with first order reaction pathways and different retardation factors. We will demonstrate the method with several examples and compare the performance with MT3D and

  1. A new neural net approach to robot 3D perception and visuo-motor coordination

    NASA Technical Reports Server (NTRS)

    Lee, Sukhan

    1992-01-01

    A novel neural network approach to robot hand-eye coordination is presented. The approach provides a true sense of visual error servoing, redundant arm configuration control for collision avoidance, and invariant visuo-motor learning under gazing control. A 3-D perception network is introduced to represent the robot internal 3-D metric space in which visual error servoing and arm configuration control are performed. The arm kinematic network performs the bidirectional association between 3-D space arm configurations and joint angles, and enforces the legitimate arm configurations. The arm kinematic net is structured by a radial-based competitive and cooperative network with hierarchical self-organizing learning. The main goal of the present work is to demonstrate that the neural net representation of the robot 3-D perception net serves as an important intermediate functional block connecting robot eyes and arms.

  2. A simple approach for 3D reconstruction of the spine from biplanar radiography

    NASA Astrophysics Data System (ADS)

    Zhang, Junhua; Shi, Xinling; Lv, Liang; Guo, Fei; Zhang, Yufeng

    2014-04-01

    This paper proposed a simple approach for 3D spinal reconstruction from biplanar radiography. The proposed reconstruction consisted in reconstructing the 3D central curve of the spine based on the epipolar geometry and automatically aligning vertebrae under the constraint of this curve. The vertebral orientations were adjusted by matching the projections of the 3D pedicles with the 2D pedicles in biplanar radiographs. The user interaction time was within one minute for a thoracic spine. Sixteen pairs of radiographs of a thoracic spinal model were used to evaluate the precision and accuracy. The precision was within 3.1 mm for the location and 3.5° for the orientation. The accuracy was within 3.5 mm for the location and 3.9° for the orientation. These results demonstrate that this approach can be a promising tool to obtain the 3D spinal geometry with acceptable user interactions in scoliotic clinics.

  3. A hybrid approach for addressing ring flexibility in 3D database searching.

    PubMed

    Sadowski, J

    1997-01-01

    A hybrid approach for flexible 3D database searching is presented that addresses the problem of ring flexibility. It combines the explicit storage of up to 25 multiple conformations of rings, with up to eight atoms, generated by the 3D structure generator CORINA with the power of a torsional fitting technique implemented in the 3D database system UNITY. A comparison with the original UNITY approach, using a database with about 130,000 entries and five different pharmacophore queries, was performed. The hybrid approach scored, on an average, 10-20% more hits than the reference run. Moreover, specific problems with unrealistic hit geometries produced by the original approach can be excluded. In addition, the influence of the maximum number of ring conformations per molecule was investigated. An optimal number of 10 conformations per molecule is recommended. PMID:9139112

  4. Approach to Constructing 3d Virtual Scene of Irrigation Area Using Multi-Source Data

    NASA Astrophysics Data System (ADS)

    Cheng, S.; Dou, M.; Wang, J.; Zhang, S.; Chen, X.

    2015-10-01

    For an irrigation area that is often complicated by various 3D artificial ground features and natural environment, disadvantages of traditional 2D GIS in spatial data representation, management, query, analysis and visualization is becoming more and more evident. Building a more realistic 3D virtual scene is thus especially urgent for irrigation area managers and decision makers, so that they can carry out various irrigational operations lively and intuitively. Based on previous researchers' achievements, a simple, practical and cost-effective approach was proposed in this study, by adopting3D geographic information system (3D GIS), remote sensing (RS) technology. Based on multi-source data such as Google Earth (GE) high-resolution remote sensing image, ASTER G-DEM, hydrological facility maps and so on, 3D terrain model and ground feature models were created interactively. Both of the models were then rendered with texture data and integrated under ArcGIS platform. A vivid, realistic 3D virtual scene of irrigation area that has a good visual effect and possesses primary GIS functions about data query and analysis was constructed.Yet, there is still a long way to go for establishing a true 3D GIS for the irrigation are: issues of this study were deeply discussed and future research direction was pointed out in the end of the paper.

  5. SU-E-T-105: Development of 3D Dose Verification System for Volumetric Modulated Arc Therapy Using Improved Polyacrylamide-Based Gel Dosimeter

    SciTech Connect

    Ono, K; Fujimoto, S; Akagi, Y; Hirokawa, Y; Hayashi, S; Miyazawa, M

    2014-06-01

    Purpose: The aim of this dosimetric study was to develop 3D dose verification system for volumetric modulated arc therapy (VMAT) using polyacrylamide-based gel (PAGAT) dosimeter improved the sensitivity by magnesium chloride (MgCl{sub 2}). Methods: PAGAT gel containing MgCl{sub 2} as a sensitizer was prepared in this study. Methacrylic-acid-based gel (MAGAT) was also prepared to compare the dosimetric characteristics with PAGAT gel. The cylindrical glass vials (4 cm diameter, 12 cm length) filled with each polymer gel were irradiated with 6 MV photon beam using Novalis Tx linear accelerator (Varian/BrainLAB). The irradiated polymer gel dosimeters were scanned with Signa 1.5 T MRI system (GE), and dose calibration curves were obtained using T{sub 2} relaxation rate (R{sub 2} = 1/T{sub 2}). Dose rate (100-600 MU min{sup −1}) and fractionation (1-8 fractions) were varied. In addition, a cubic acrylic phantom (10 × 10 × 10 cm{sup 3}) filled with improved PAGAT gel inserted into the IMRT phantom (IBA) was irradiated with VMAT (RapidArc). C-shape structure was used for the VMAT planning by the Varian Eclipse treatment planning system (TPS). The dose comparison of TPS and measurements with the polymer gel dosimeter was accomplished by the gamma index analysis, overlaying the dose profiles for a set of data on selected planes using in-house developed software. Results: Dose rate and fractionation dependence of improved PAGAT gel were smaller than MAGAT gel. A high similarity was found by overlaying the dose profiles measured with improved PAGAT gel dosimeter and the TPS dose, and the mean pass rate of the gamma index analysis using 3%/3 mm criteria was achieved 90% on orthogonal planes for VMAT using improved PAGAT gel dosimeter. Conclusion: In-house developed 3D dose verification system using improved polyacrylamide-based gel dosimeter had a potential as an effective tool for VMAT QA.

  6. Metabolic approach for tumor delineation in glioma surgery: 3D MR spectroscopy image-guided resection.

    PubMed

    Zhang, Jie; Zhuang, Dong-Xiao; Yao, Cheng-Jun; Lin, Ching-Po; Wang, Tian-Liang; Qin, Zhi-Yong; Wu, Jin-Song

    2016-06-01

    OBJECT The extent of resection is one of the most essential factors that influence the outcomes of glioma resection. However, conventional structural imaging has failed to accurately delineate glioma margins because of tumor cell infiltration. Three-dimensional proton MR spectroscopy ((1)H-MRS) can provide metabolic information and has been used in preoperative tumor differentiation, grading, and radiotherapy planning. Resection based on glioma metabolism information may provide for a more extensive resection and yield better outcomes for glioma patients. In this study, the authors attempt to integrate 3D (1)H-MRS into neuronavigation and assess the feasibility and validity of metabolically based glioma resection. METHODS Choline (Cho)-N-acetylaspartate (NAA) index (CNI) maps were calculated and integrated into neuronavigation. The CNI thresholds were quantitatively analyzed and compared with structural MRI studies. Glioma resections were performed under 3D (1)H-MRS guidance. Volumetric analyses were performed for metabolic and structural images from a low-grade glioma (LGG) group and high-grade glioma (HGG) group. Magnetic resonance imaging and neurological assessments were performed immediately after surgery and 1 year after tumor resection. RESULTS Fifteen eligible patients with primary cerebral gliomas were included in this study. Three-dimensional (1)H-MRS maps were successfully coregistered with structural images and integrated into navigational system. Volumetric analyses showed that the differences between the metabolic volumes with different CNI thresholds were statistically significant (p < 0.05). For the LGG group, the differences between the structural and the metabolic volumes with CNI thresholds of 0.5 and 1.5 were statistically significant (p = 0.0005 and 0.0129, respectively). For the HGG group, the differences between the structural and metabolic volumes with CNI thresholds of 0.5 and 1.0 were statistically significant (p = 0.0027 and 0

  7. New approach to the perception of 3D shape based on veridicality, complexity, symmetry and volume.

    PubMed

    Pizlo, Zygmunt; Sawada, Tadamasa; Li, Yunfeng; Kropatsch, Walter G; Steinman, Robert M

    2010-01-01

    This paper reviews recent progress towards understanding 3D shape perception made possible by appreciating the significant role that veridicality and complexity play in the natural visual environment. The ability to see objects as they really are "out there" is derived from the complexity inherent in the 3D object's shape. The importance of both veridicality and complexity was ignored in most prior research. Appreciating their importance made it possible to devise a computational model that recovers the 3D shape of an object from only one of its 2D images. This model uses a simplicity principle consisting of only four a priori constraints representing properties of 3D shapes, primarily their symmetry and volume. The model recovers 3D shapes from a single 2D image as well, and sometimes even better, than a human being. In the rare recoveries in which errors are observed, the errors made by the model and human subjects are very similar. The model makes no use of depth, surfaces or learning. Recent elaborations of this model include: (i) the recovery of the shapes of natural objects, including human and animal bodies with limbs in varying positions (ii) providing the model with two input images that allowed it to achieve virtually perfect shape constancy from almost all viewing directions. The review concludes with a comparison of some of the highlights of our novel, successful approach to the recovery of 3D shape from a 2D image with prior, less successful approaches. PMID:19800910

  8. Server-based approach to web visualization of integrated 3-D medical image data.

    PubMed Central

    Poliakov, A. V.; Albright, E.; Corina, D.; Ojemann, G.; Martin, R. F.; Brinkley, J. F.

    2001-01-01

    Although computer processing power and network bandwidth are rapidly increasing, the average desktop is still not able to rapidly process large datasets such as 3-D medical image volumes. We have therefore developed a server side approach to this problem, in which a high performance graphics server accepts commands from web clients to load, process and render 3-D image volumes and models. The renderings are saved as 2-D snapshots on the server, where they are uploaded and displayed on the client. User interactions with the graphic interface on the client side are translated into additional commands to manipulate the 3-D scene, after which the server re-renders the scene and sends a new image to the client. Example forms-based and Java-based clients are described for a brain mapping application, but the techniques should be applicable to multiple domains where 3-D medical image visualization is of interest. PMID:11825248

  9. Mobile 3D quality of experience evaluation: a hybrid data collection and analysis approach

    NASA Astrophysics Data System (ADS)

    Utriainen, Timo; Häyrynen, Jyrki; Jumisko-Pyykkö, Satu; Boev, Atanas; Gotchev, Atanas; Hannuksela, Miska M.

    2011-02-01

    The paper presents a hybrid approach to study the user's experienced quality of 3D visual content on mobile autostereoscopic displays. It combines extensive subjective tests with collection and objective analysis of eye-tracked data. 3D cues which are significant for mobiles are simulated in the generated 3D test content. The methodology for conducting subjective quality evaluation includes hybrid data-collection of quantitative quality preferences, qualitative impressions, and binocular eye-tracking. We present early results of the subjective tests along with eye movement reaction times, areas of interest and heatmaps obtained from raw eye-tracked data after statistical analysis. The study contributes to the question what is important to be visualized on portable auto-stereoscopic displays and how to maintain and visually enhance the quality of 3D content for such displays.

  10. Visualization of boundaries in volumetric data sets through a what material you pick is what boundary you see approach.

    PubMed

    Li, Lu; Peng, Hu; Chen, Xun; Cheng, Juan; Gao, Dayong

    2016-04-01

    Transfer function design is a key issue in direct volume rendering. Many sophisticated transfer functions have been proposed to visualize boundaries in volumetric data sets such as computed tomography and magnetic resonance imaging. However, it is still conventionally challenging to reliably detect boundaries. Meanwhile, the interactive strategy is complicated for new users or even experts. In this paper, we first propose the human-centric boundary extraction criteria and our boundary model. Based on the model we present a boundary visualization method through a what material you pick is what boundary you see approach. Users can pick out the material of interest to directly convey semantics. In addition, the 3-D canny edge detection is utilized to ensure the good localization of boundaries. Furthermore, we establish a point-to-material distance measure to guarantee the accuracy and integrity of boundaries. The proposed boundary visualization is intuitive and flexible for the exploration of volumetric data. PMID:26796353

  11. Comparison Between Two Generic 3d Building Reconstruction Approaches - Point Cloud Based VS. Image Processing Based

    NASA Astrophysics Data System (ADS)

    Dahlke, D.; Linkiewicz, M.

    2016-06-01

    This paper compares two generic approaches for the reconstruction of buildings. Synthesized and real oblique and vertical aerial imagery is transformed on the one hand into a dense photogrammetric 3D point cloud and on the other hand into photogrammetric 2.5D surface models depicting a scene from different cardinal directions. One approach evaluates the 3D point cloud statistically in order to extract the hull of structures, while the other approach makes use of salient line segments in 2.5D surface models, so that the hull of 3D structures can be recovered. With orders of magnitudes more analyzed 3D points, the point cloud based approach is an order of magnitude more accurate for the synthetic dataset compared to the lower dimensioned, but therefor orders of magnitude faster, image processing based approach. For real world data the difference in accuracy between both approaches is not significant anymore. In both cases the reconstructed polyhedra supply information about their inherent semantic and can be used for subsequent and more differentiated semantic annotations through exploitation of texture information.

  12. Standards-based approaches to 3D and multiview video coding

    NASA Astrophysics Data System (ADS)

    Sullivan, Gary J.

    2009-08-01

    The extension of video applications to enable 3D perception, which typically is considered to include a stereo viewing experience, is emerging as a mass market phenomenon, as is evident from the recent prevalence of 3D major cinema title releases. For high quality 3D video to become a commonplace user experience beyond limited cinema distribution, adoption of an interoperable coded 3D digital video format will be needed. Stereo-view video can also be studied as a special case of the more general technologies of multiview and "free-viewpoint" video systems. The history of standardization work on this topic is actually richer than people may typically realize. The ISO/IEC Moving Picture Experts Group (MPEG), in particular, has been developing interoperability standards to specify various such coding schemes since the advent of digital video as we know it. More recently, the ITU-T Visual Coding Experts Group (VCEG) has been involved as well in the Joint Video Team (JVT) work on development of 3D features for H.264/14496-10 Advanced Video Coding, including Multiview Video Coding (MVC) extensions. This paper surveys the prior, ongoing, and anticipated future standardization efforts on this subject to provide an overview and historical perspective on feasible approaches to 3D and multiview video coding.

  13. A first approach of 3D Geostrophic Currents based on GOCE, altimetry and ARGO data

    NASA Astrophysics Data System (ADS)

    Sempere Beneyto, M. Dolores; Vigo, Isabel; Chao, Ben F.

    2016-04-01

    The most recent advances in the geoid determination, provided by the Gravity Field and Steady-State Ocean Circulation Explorer (GOCE) mission, together with the continuous monitoring of the sea surface height by the altimeters on board of satellites and Argo data makes possible to estimate the ocean geostrophy in 3D. In this work, we present a first approach of the 3D geostrophic circulation for North Atlantic region, from the surface down to 1500 m depth. It has been computed for a 10 years period (2004-2014), using an observation-based approach that combines altimetry with temperature and salinity through the thermal wind equation gridded at one degree longitude and latitude resolution. For validation of the results, the estimated 3D geostrophic circulation is compared with Ocean Circulation Models simulations and/or in-situ data, showing in all cases similar patterns.

  14. Individualized Surgical Approach Planning for Petroclival Tumors Using a 3D Printer.

    PubMed

    Muelleman, Thomas John; Peterson, Jeremy; Chowdhury, Naweed Iffat; Gorup, Jason; Camarata, Paul; Lin, James

    2016-06-01

    Objectives To determine the utility of three-dimensional (3D) printed models in individualized petroclival tumor resection planning by measuring the fidelity of printed anatomical structures and comparing tumor exposure afforded by different approaches. Design Case series and review of the literature. Setting Tertiary care center. Participants Three patients with petroclival lesions. Main Outcome Measures Subjective opinion of access by neuro-otologists and neurosurgeons as well as surface area of tumor exposure. Results Surgeons found the 3D models of each patient's skull and tumor useful for preoperative planning. Limitations of individual surgical approaches not identified through preoperative imaging were apparent after 3D models were evaluated. Significant variability in exposure was noted between models for similar or identical approaches. A notable drawback is that our printing process did not replicate mastoid air cells. Conclusions We found that 3D modeling is useful for individualized preoperative planning for approaching petroclival tumors. Our printing techniques did produce authentic replicas of the tumors in relation to bony structures. PMID:27175320

  15. On the Dynamic Programming Approach for the 3D Navier-Stokes Equations

    SciTech Connect

    Manca, Luigi

    2008-06-15

    The dynamic programming approach for the control of a 3D flow governed by the stochastic Navier-Stokes equations for incompressible fluid in a bounded domain is studied. By a compactness argument, existence of solutions for the associated Hamilton-Jacobi-Bellman equation is proved. Finally, existence of an optimal control through the feedback formula and of an optimal state is discussed.

  16. Dosimetric validation and clinical implementation of two 3D dose verification systems for quality assurance in volumetric-modulated arc therapy techniques.

    PubMed

    Clemente-Gutiérrez, Francisco; Pérez-Vara, Consuelo

    2015-01-01

    A pretreatment quality assurance program for volumetric techniques should include redundant calculations and measurement-based verifications. The patient-specific quality assurance process must be based in clinically relevant metrics. The aim of this study was to show the commission, clinical implementation, and comparison of two systems that allow performing a 3D redundant dose calculation. In addition, one of them is capable of reconstructing the dose on patient anatomy from measurements taken with a 2D ion chamber array. Both systems were compared in terms of reference calibration data (absolute dose, output factors, percentage depth-dose curves, and profiles). Results were in good agreement for absolute dose values (discrepancies were below 0.5%) and output factors (mean differences were below 1%). Maximum mean discrepancies were located between 10 and 20 cm of depth for PDDs (-2.7%) and in the penumbra region for profiles (mean DTA of 1.5 mm). Validation of the systems was performed by comparing point-dose measurements with values obtained by the two systems for static, dynamic fields from AAPM TG-119 report, and 12 real VMAT plans for different anatomical sites (differences better than 1.2%). Comparisons between measurements taken with a 2D ion chamber array and results obtained by both systems for real VMAT plans were also performed (mean global gamma passing rates better than 87.0% and 97.9% for the 2%/2 mm and 3%/3 mm criteria). Clinical implementation of the systems was evaluated by comparing dose-volume parameters for all TG-119 tests and real VMAT plans with TPS values (mean differences were below 1%). In addition, comparisons between dose distributions calculated by TPS and those extracted by the two systems for real VMAT plans were also performed (mean global gamma passing rates better than 86.0% and 93.0% for the 2%/2 mm and 3%/ 3 mm criteria). The clinical use of both systems was successfully evaluated. PMID:26103189

  17. A universal approach for automatic organ segmentations on 3D CT images based on organ localization and 3D GrabCut

    NASA Astrophysics Data System (ADS)

    Zhou, Xiangrong; Ito, Takaaki; Zhou, Xinxin; Chen, Huayue; Hara, Takeshi; Yokoyama, Ryujiro; Kanematsu, Masayuki; Hoshi, Hiroaki; Fujita, Hiroshi

    2014-03-01

    This paper describes a universal approach to automatic segmentation of different internal organ and tissue regions in three-dimensional (3D) computerized tomography (CT) scans. The proposed approach combines object localization, a probabilistic atlas, and 3D GrabCut techniques to achieve automatic and quick segmentation. The proposed method first detects a tight 3D bounding box that contains the target organ region in CT images and then estimates the prior of each pixel inside the bounding box belonging to the organ region or background based on a dynamically generated probabilistic atlas. Finally, the target organ region is separated from the background by using an improved 3D GrabCut algorithm. A machine-learning method is used to train a detector to localize the 3D bounding box of the target organ using template matching on a selected feature space. A content-based image retrieval method is used for online generation of a patient-specific probabilistic atlas for the target organ based on a database. A 3D GrabCut algorithm is used for final organ segmentation by iteratively estimating the CT number distributions of the target organ and backgrounds using a graph-cuts algorithm. We applied this approach to localize and segment twelve major organ and tissue regions independently based on a database that includes 1300 torso CT scans. In our experiments, we randomly selected numerous CT scans and manually input nine principal types of inner organ regions for performance evaluation. Preliminary results showed the feasibility and efficiency of the proposed approach for addressing automatic organ segmentation issues on CT images.

  18. DC-Electrical Resistivity Imaging for embankment dike investigation: A 3D extended normalisation approach

    NASA Astrophysics Data System (ADS)

    Fargier, Yannick; Lopes, Sérgio Palma; Fauchard, Cyrille; François, Daniel; Côte, Philippe

    2014-04-01

    Levee, dike and earth embankment dam structures are difficult to assess because of their length and complexity. Managers often include geophysical investigations in the overall dike condition assessment and the DC-Electrical Resistivity Imaging (ERI) method is particularly applicable owing to its cost-effectiveness and its potential sensitivity to internal erosion. However, due to the truly 3D nature of embankment dikes, implementing inline longitudinal tomographies along with conventional 2D inversion is likely to yield image artefacts. 3D effects from external causes (geometry, water reservoir) can be predicted and therefore we present a new approach based on redefining the normalisation principle to derive apparent resistivities from the measured data. The aim is to provide a set of pre-processed apparent resistivities that are not contaminated by external 3D effects and that yield more reliable results when processed within a 2D conventional inversion scheme. The presented approach is successfully applied to synthetic and real data sets, proving superior to the conventional 2D approach, although data acquisition approach is the same thus keeping the same cost-effectiveness.

  19. 3D deformable image matching: a hierarchical approach over nested subspaces

    NASA Astrophysics Data System (ADS)

    Musse, Olivier; Heitz, Fabrice; Armspach, Jean-Paul

    2000-06-01

    This paper presents a fast hierarchical method to perform dense deformable inter-subject matching of 3D MR Images of the brain. To recover the complex morphological variations in neuroanatomy, a hierarchy of 3D deformations fields is estimated, by minimizing a global energy function over a sequence of nested subspaces. The nested subspaces, generated from a single scaling function, consist of deformation fields constrained at different scales. The highly non linear energy function, describing the interactions between the target and the source images, is minimized using a coarse-to-fine continuation strategy over this hierarchy. The resulting deformable matching method shows low sensitivity to local minima and is able to track large non-linear deformations, with moderate computational load. The performances of the approach are assessed both on simulated 3D transformations and on a real data base of 3D brain MR Images from different individuals. The method has shown efficient in putting into correspondence the principle anatomical structures of the brain. An application to atlas-based MRI segmentation, by transporting a labeled segmentation map on patient data, is also presented.

  20. 3D tensor factorization approach to single-frame model-free blind-image deconvolution.

    PubMed

    Kopriva, Ivica

    2009-09-15

    By applying a bank of 2D Gabor filters to a blurred image, single-frame blind-image deconvolution (SF BID) is formulated as a 3D tensor factorization (TF) problem, with the key contribution that neither origin nor size of the spatially invariant blurring kernel is required to be known or estimated. Mixing matrix, the original image, and its spatial derivatives are identified from the factors in the Tucker3 model of the multichannel version of the blurred image. Previous approaches to 2D Gabor-filter-bank-based SF BID relied on 2D representation of the multichannel version of the blurred image and matrix factorization methods such as nonnegative matrix factorization (NMF) and independent component analysis (ICA). Unlike matrix factorization-based methods 3D TF preserves local structure in the image. Moreover, 3D TF based on the PARAFAC model is unique up to permutation and scales under very mild conditions. To achieve this, NMF and ICA respectively require enforcement of sparseness and statistical independence constraints on the original image and its spatial derivatives. These constraints are generally not satisfied. The 3D TF-based SF BID method is demonstrated on an experimental defocused red-green-blue image. PMID:19756121

  1. A reduced-coordinate approach to modeling RNA 3-D structures

    SciTech Connect

    Tung, Chang-Shung

    1997-09-01

    With the realization of RNA molecules capable of performing very specific functions (e.g., catalytic RNAs and RNAs that bind ligand with affinity and specificity of an anti-body) and contrary to the traditional view that structure of RNA molecules being functionally passive, it has become clear that studying the 3-dimensional (3-D) folding of RNA molecules is a very important task. In the absence of sufficient number of experimentally determined RNA structures available up-to-date, folding of RNA structures computationally provides an alternative approach in studying the 3-D structure of RNA molecules. We have developed a computational approach for folding RNA 3-D structures. The method is conceptually simple and general. It consists of two major components. The first being the arrangement of all helices in space. Once the helices are positioned and oriented in space, structures of the connecting loops are modeled and inserted between the helices. Any number of structural constraints derived either experimentally or theoretically can be used to guide the folding processes. A conformational sampling approach is developed with structural equilibration using the Metropolis Monte Carlo simulation. The lengths of various loop sizes (ranging from 1 base to 7 bases) are calculated based on a set of RNA structures deposited in PDB as well as a set of loop structures constructed using our method. The validity of using the averaged loop lengths of the connecting loops as distance constraints for arranging the helices in space is studied.

  2. An efficient multimodal 2D-3D hybrid approach to automatic face recognition.

    PubMed

    Mian, Ajmal S; Bennamoun, Mohammed; Owens, Robyn

    2007-11-01

    We present a fully automatic face recognition algorithm and demonstrate its performance on the FRGC v2.0 data. Our algorithm is multimodal (2D and 3D) and performs hybrid (feature-based and holistic) matching in order to achieve efficiency and robustness to facial expressions. The pose of a 3D face along with its texture is automatically corrected using a novel approach based on a single automatically detected point and the Hotelling transform. A novel 3D Spherical Face Representation (SFR) is used in conjunction with the SIFT descriptor to form a rejection classifier which quickly eliminates a large number of candidate faces at an early stage for efficient recognition in case of large galleries. The remaining faces are then verified using a novel region-based matching approach which is robust to facial expressions. This approach automatically segments the eyes-forehead and the nose regions, which are relatively less sensitive to expressions, and matches them separately using a modified ICP algorithm. The results of all the matching engines are fused at the metric level to achieve higher accuracy. We use the FRGC benchmark to compare our results to other algorithms which used the same database. Our multimodal hybrid algorithm performed better than others by achieving 99.74% and 98.31% verification rates at 0.001 FAR and identification rates of 99.02% and 95.37% for probes with neutral and non-neutral expression respectively. PMID:17848775

  3. A simple approach for the fabrication of 3D microelectrodes for impedimetric sensing

    NASA Astrophysics Data System (ADS)

    Tahsin Guler, Mustafa; Bilican, Ismail; Agan, Sedat; Elbuken, Caglar

    2015-09-01

    In this paper, we present a very simple method to fabricate three-dimensional (3D) microelectrodes integrated with microfluidic devices. We form the electrodes by etching a microwire placed across a microchannel. For precise control of the electrode spacing, we employ a hydrodynamic focusing microfluidic device and control the width of the etching solution stream. The focused widths of the etchant solution and the etching time determine the gap formed between the electrodes. Using the same microfluidic device, we can fabricate integrated 3D electrodes with different electrode gaps. We have demonstrated the functionality of these electrodes using an impedimetric particle counting setup. Using 3D microelectrodes with a diameter of 25 μm, we have detected 6 μm-diameter polystyrene beads in a buffer solution as well as erythrocytes in a PBS solution. We study the effect of electrode spacing on the signal-to-noise ratio of the impedance signal and we demonstrate that the smaller the electrode spacing the higher the signal obtained from a single microparticle. The sample stream is introduced to the system using the same hydrodynamic focusing device, which ensures the alignment of the sample in between the electrodes. Utilising a 3D hydrodynamic focusing approach, we force all the particles to go through the sensing region of the electrodes. This fabrication scheme not only provides a very low-cost and easy method for rapid prototyping, but which can also be used for applications requiring 3D electric field focused through a narrow section of the microchannel.

  4. An intelligent, robust approach to volumetric aircraft sizing

    NASA Astrophysics Data System (ADS)

    Upton, Eric

    Advances in computational power have produced great strides in the later design and production portions of an aircraft's life cycle, and these advances have included the internal layout component of the design and manufacturing process. However, conceptual and preliminary design tools for internal layout remain primarily based on historical regressions and estimations---a situation that becomes untenable when considering revolutionary designs or component technologies. Bringing internal layout information forward in the design process can encourage the same level of benefits enjoyed by other disciplines as advances in aerodynamics, structures and other fields propagate forward in the design of complex systems. Accurate prediction of the volume required to contain all of an aircraft's internal components results in a more accurate prediction of aircraft specifications, mission effectiveness, and costs, helping determine if an aircraft is the best choice for continued development. This is not a computationally simple problem, however, and great care must be taken to ensure the efficiency of any proposed solution. Any solution must also address the uncertainty inherent in describing internal components early in the design process. Implementing a methodology that applies notions of an intelligent search for a solution, as well as deals robustly with component sizing, produces a high chance of success. Development of a robust, rapid method for assessing the volumetric characteristics of an aircraft in the context of the conceptual and preliminary design processes can offer many of the benefits of a complete internal layout without the immense assignment of resources typical in the detail phase of the design process. A simplified methodology for volumetrically sizing an aircraft is presented here as well as an assessment of the state-of-the-art techniques for volumetric considerations used in current aircraft design literature. A prototype tool using a combination of

  5. A Generalized Approach to the Modeling and Analysis of 3D Surface Morphology in Organisms

    PubMed Central

    Pappas, Janice L.; Miller, Daniel J.

    2013-01-01

    The surface geometry of an organism represents the boundary of its three-dimensional (3D) form and can be used as a proxy for the phenotype. A mathematical approach is presented that describes surface morphology using parametric 3D equations with variables expressed as x, y, z in terms of parameters u, v. Partial differentiation of variables with respect to parameters yields elements of the Jacobian representing tangent lines and planes of every point on the surface. Jacobian elements provide a compact size-free summary of the entire surface, and can be used as variables in principal components analysis to produce a morphospace. Mollusk and echinoid models are generated to demonstrate that whole organisms can be represented in a common morphospace, regardless of differences in size, geometry, and taxonomic affinity. Models can be used to simulate theoretical forms, novel morphologies, and patterns of phenotypic variation, and can also be empirically-based by designing them with reference to actual forms using reverse engineering principles. Although this study uses the Jacobian to summarize models, they can also be analyzed with 3D methods such as eigensurface, spherical harmonics, wavelet analysis, and geometric morphometrics. This general approach should prove useful for exploring broad questions regarding morphological evolution and variation. PMID:24204866

  6. Coarse integral holography approach for real 3D color video displays.

    PubMed

    Chen, J S; Smithwick, Q Y J; Chu, D P

    2016-03-21

    A colour holographic display is considered the ultimate apparatus to provide the most natural 3D viewing experience. It encodes a 3D scene as holographic patterns that then are used to reproduce the optical wavefront. The main challenge at present is for the existing technologies to cope with the full information bandwidth required for the computation and display of holographic video. We have developed a dynamic coarse integral holography approach using opto-mechanical scanning, coarse integral optics and a low space-bandwidth-product high-bandwidth spatial light modulator to display dynamic holograms with a large space-bandwidth-product at video rates, combined with an efficient rendering algorithm to reduce the information content. This makes it possible to realise a full-parallax, colour holographic video display with a bandwidth of 10 billion pixels per second, and an adequate image size and viewing angle, as well as all relevant 3D cues. Our approach is scalable and the prototype can achieve even better performance with continuing advances in hardware components. PMID:27136858

  7. Functional Stereology for 3D Particle Size Distributions from 2D Observations: a Practical Approach

    NASA Astrophysics Data System (ADS)

    Proussevitch, A. A.; Sahagian, D. L.; Jutzeler, M.

    2010-12-01

    Functional stereology applies known deconvolution techniques to obtain 3D size distributions from 2D cross-section data based on an assumption that both 2D and 3D statistics have known distribution functions with unknown parameters. A new stereological approach enables us to solve this problem by utilizing function minimization to find parameters of the distribution functions. There is no limit to continuous distribution function types that could be used, such as Gaussian, Logistic, Weibull, Gamma, and others. As compared to previously known 2D to 3D conversion methods (e.g. Sahagian and Proussevitch, 1998), functional stereology has much greater practical application to non-spherical particles/objects because it is free of uncontrollable error propagation for all particles shapes. The new practical method of functional stereology has been implemented in Stereonet software adapted for both a) direct logarithmic scales of particle/voids volumes, and b) Phi units of linear dimensions (-log2 of size). Applications of the method include distribution of voids/bubbles in all types of volcanic rocks, pore networks in sedimentary rocks, mineral and grain sizes, volcanic clasts, breccia, and texture features of a wide range of rock formations. Such applications demonstrate utility of this functional stereology approach.

  8. Towards the design of 3D multiscale instructive tissue engineering constructs: Current approaches and trends.

    PubMed

    Oliveira, Sara M; Reis, Rui L; Mano, João F

    2015-11-01

    The design of 3D constructs with adequate properties to instruct and guide cells both in vitro and in vivo is one of the major focuses of tissue engineering. Successful tissue regeneration depends on the favorable crosstalk between the supporting structure, the cells and the host tissue so that a balanced matrix production and degradation are achieved. Herein, the major occurring events and players in normal and regenerative tissue are overviewed. These have been inspiring the selection or synthesis of instructive cues to include into the 3D constructs. We further highlight the importance of a multiscale perception of the range of features that can be included on the biomimetic structures. Lastly, we focus on the current and developing tissue-engineering approaches for the preparation of such 3D constructs: top-down, bottom-up and integrative. Bottom-up and integrative approaches present a higher potential for the design of tissue engineering devices with multiscale features and higher biochemical control than top-down strategies, and are the main focus of this review. PMID:26025038

  9. Sustainable approach toward synthesis of green functional carbonaceous 3-D micro/nanostructures from biomass

    NASA Astrophysics Data System (ADS)

    Tavangar, Amirhossein; Tan, Bo; Venkatakrishnan, Krishnan

    2013-08-01

    This study proposes a novel technique to synthesize functional carbonaceous three-dimensional (3-D) micro/nanocompounds from agricultural by-products using femtosecond laser irradiation. Biowastes of rice husk and wheat straw are value-engineered to carbonaceous structures in a single-step process under ambient conditions. Our results demonstrate that by controlling the laser fluence, structures with a variety of different morphologies from nanostructures to microstructures can be achieved. Also, the results indicate that altering the laser processing parameters influences the chemical composition of the synthesized structures. This sustainable approach presents an important step towards synthesizing 3-D micro/nanofibrous compounds from biowaste materials. These structures, as-synthesized or as nanocomposite fillers, can have practical uses in electronic, sensing, biological, and environmental applications.

  10. Sustainable approach toward synthesis of green functional carbonaceous 3-D micro/nanostructures from biomass.

    PubMed

    Tavangar, Amirhossein; Tan, Bo; Venkatakrishnan, Krishnan

    2013-01-01

    This study proposes a novel technique to synthesize functional carbonaceous three-dimensional (3-D) micro/nanocompounds from agricultural by-products using femtosecond laser irradiation. Biowastes of rice husk and wheat straw are value-engineered to carbonaceous structures in a single-step process under ambient conditions. Our results demonstrate that by controlling the laser fluence, structures with a variety of different morphologies from nanostructures to microstructures can be achieved. Also, the results indicate that altering the laser processing parameters influences the chemical composition of the synthesized structures. This sustainable approach presents an important step towards synthesizing 3-D micro/nanofibrous compounds from biowaste materials. These structures, as-synthesized or as nanocomposite fillers, can have practical uses in electronic, sensing, biological, and environmental applications. PMID:23924310

  11. A 3D clustering approach for point clouds to detect and quantify changes at a rock glacier front

    NASA Astrophysics Data System (ADS)

    Micheletti, Natan; Tonini, Marj; Lane, Stuart N.

    2016-04-01

    points (i) at a maximum distance (ii) around each core-point. Under this condition, seed points are said to be density-reachable by a core point delimiting a cluster around it. A chain of intermediate seed-points can connect contiguous clusters allowing clusters of arbitrary shape to be defined. The novelty of the proposed approach consists in the implementation of the DBSCAN 3D-module, where the xyz-coordinates identify each point and the density of points within a sphere is considered. This allows detecting volumetric features with a higher accuracy, depending only on actual sampling resolution. The approach is truly 3D and exploits all TLS measurements without the need of interpolation or data reduction. Using this method, enhanced geomorphological activity during the summer of 2015 in respect to the previous two years was observed. We attribute this result to the exceptionally high temperatures of that summer, which we deem responsible for accelerating the melting process at the rock glacier front and probably also increasing creep velocities. References: - Tonini, M. and Abellan, A. (2014). Rockfall detection from terrestrial LiDAR point clouds: A clustering approach using R. Journal of Spatial Information Sciences. Number 8, pp95-110 - Hennig, C. Package fpc: Flexible procedures for clustering. https://cran.r-project.org/web/packages/fpc/index.html, 2015. Accessed 2016-01-12.

  12. 2D approaches to 3D watermarking: state-of-the-art and perspectives

    NASA Astrophysics Data System (ADS)

    Mitrea, M.; Duţă, S.; Prêteux, F.

    2006-02-01

    With the advent of the Information Society, video, audio, speech, and 3D media represent the source of huge economic benefits. Consequently, there is a continuously increasing demand for protecting their related intellectual property rights. The solution can be provided by robust watermarking, a research field which exploded in the last 7 years. However, the largest part of the scientific effort was devoted to video and audio protection, the 3D objects being quite neglected. In the absence of any standardisation attempt, the paper starts by summarising the approaches developed in this respect and by further identifying the main challenges to be addressed in the next years. Then, it describes an original oblivious watermarking method devoted to the protection of the 3D objects represented by NURBS (Non uniform Rational B Spline) surfaces. Applied to both free form objects and CAD models, the method exhibited very good transparency (no visible differences between the marked and the unmarked model) and robustness (with respect to both traditional attacks and to NURBS processing).

  13. Diaphragm dome surface segmentation in CT data sets: a 3D active appearance model approach

    NASA Astrophysics Data System (ADS)

    Beichel, Reinhard; Gotschuli, Georg; Sorantin, Erich; Leberl, Franz W.; Sonka, Milan

    2002-05-01

    Knowledge about the location of the diaphragm dome surface, which separates the lungs and the heart from the abdominal cavity, is of vital importance for applications like automated segmentation of adjacent organs (e.g., liver) or functional analysis of the respiratory cycle. We present a new 3D Active Appearance Model (AAM) approach to segmentation of the top layer of the diaphragm dome. The 3D AAM consists of three parts: a 2D closed curve (reference curve), an elevation image and texture layers. The first two parts combined represent 3D shape information and the third part image intensity of the diaphragm dome and the surrounding layers. Differences in height between dome voxels and a reference plane are stored in the elevation image. The reference curve is generated by a parallel projection of the diaphragm dome outline in the axial direction. Landmark point placement is only done on the (2D) reference curve, which can be seen as the bounding curve of the elevation image. Matching is based on a gradient-descent optimization process and uses image intensity appearance around the actual dome shape. Results achieved in 60 computer generated phantom data sets show a high degree of accuracy (positioning error -0.07+/-1.29 mm). Validation using real CT data sets yielded a positioning error of -0.16+/-2.95 mm. Additional training and testing on in-vivo CT image data is ongoing.

  14. An approach to 3D model fusion in GIS systems and its application in a future ECDIS

    NASA Astrophysics Data System (ADS)

    Liu, Tao; Zhao, Depeng; Pan, Mingyang

    2016-04-01

    Three-dimensional (3D) computer graphics technology is widely used in various areas and causes profound changes. As an information carrier, 3D models are becoming increasingly important. The use of 3D models greatly helps to improve the cartographic expression and design. 3D models are more visually efficient, quicker and easier to understand and they can express more detailed geographical information. However, it is hard to efficiently and precisely fuse 3D models in local systems. The purpose of this study is to propose an automatic and precise approach to fuse 3D models in geographic information systems (GIS). It is the basic premise for subsequent uses of 3D models in local systems, such as attribute searching, spatial analysis, and so on. The basic steps of our research are: (1) pose adjustment by principal component analysis (PCA); (2) silhouette extraction by simple mesh silhouette extraction and silhouette merger; (3) size adjustment; (4) position matching. Finally, we implement the above methods in our system Automotive Intelligent Chart (AIC) 3D Electronic Chart Display and Information Systems (ECDIS). The fusion approach we propose is a common method and each calculation step is carefully designed. This approach solves the problem of cross-platform model fusion. 3D models can be from any source. They may be stored in the local cache or retrieved from Internet, or may be manually created by different tools or automatically generated by different programs. The system can be any kind of 3D GIS system.

  15. Volumetric (3D) bladder dose parameters are more reproducible than point (2D) dose parameters in vaginal vault high-dose-rate brachytherapy

    PubMed Central

    Sapienza, Lucas Gomes; Flosi, Adriana; Aiza, Antonio; de Assis Pellizzon, Antonio Cassio; Chojniak, Rubens; Baiocchi, Glauco

    2016-01-01

    There is no consensus on the use of computed tomography in vaginal cuff brachytherapy (VCB) planning. The purpose of this study was to prospectively determine the reproducibility of point bladder dose parameters (DICRU and maximum dose), compared with volumetric-based parameters. Twenty-two patients who were treated with high-dose-rate (HDR) VCB underwent simulation by computed tomography (CT-scan) with a Foley catheter at standard tension (position A) and extra tension (position B). CT-scan determined the bladder ICRU dose point in both positions and compared the displacement and recorded dose. Volumetric parameters (D0.1cc, D1.0cc, D2.0cc, D4.0cc and D50%) and point dose parameters were compared. The average spatial shift in ICRU dose point in the vertical, longitudinal and lateral directions was 2.91 mm (range: 0.10–9.00), 12.04 mm (range: 4.50–24.50) and 2.65 mm (range: 0.60–8.80), respectively. The DICRU ratio for positions A and B was 1.64 (p < 0.001). Moreover, a decrease in Dmax was observed (p = 0.016). Tension level of the urinary catheter did not affect the volumetric parameters. Our data suggest that point parameters (DICRU and Dmax) are not reproducible and are not the ideal choice for dose reporting. PMID:27296459

  16. Computing 3-D steady supersonic flow via a new Lagrangian approach

    NASA Technical Reports Server (NTRS)

    Loh, C. Y.; Liou, M.-S.

    1993-01-01

    The new Lagrangian method introduced by Loh and Hui (1990) is extended for 3-D steady supersonic flow computation. Details of the conservation form, the implementation of the local Riemann solver, and the Godunov and the high resolution TVD schemes are presented. The new approach is robust yet accurate, capable of handling complicated geometry and reactions between discontinuous waves. It keeps all the advantages claimed in the 2-D method of Loh and Hui, e.g., crisp resolution for a slip surface (contact discontinuity) and automatic grid generation along the stream.

  17. Controlled Positioning of Cells in Biomaterials—Approaches Towards 3D Tissue Printing

    PubMed Central

    Wüst, Silke; Müller, Ralph; Hofmann, Sandra

    2011-01-01

    Current tissue engineering techniques have various drawbacks: they often incorporate uncontrolled and imprecise scaffold geometries, whereas the current conventional cell seeding techniques result mostly in random cell placement rather than uniform cell distribution. For the successful reconstruction of deficient tissue, new material engineering approaches have to be considered to overcome current limitations. An emerging method to produce complex biological products including cells or extracellular matrices in a controlled manner is a process called bioprinting or biofabrication, which effectively uses principles of rapid prototyping combined with cell-loaded biomaterials, typically hydrogels. 3D tissue printing is an approach to manufacture functional tissue layer-by-layer that could be transplanted in vivo after production. This method is especially advantageous for stem cells since a controlled environment can be created to influence cell growth and differentiation. Using printed tissue for biotechnological and pharmacological needs like in vitro drug-testing may lead to a revolution in the pharmaceutical industry since animal models could be partially replaced by biofabricated tissues mimicking human physiology and pathology. This would not only be a major advancement concerning rising ethical issues but would also have a measureable impact on economical aspects in this industry of today, where animal studies are very labor-intensive and therefore costly. In this review, current controlled material and cell positioning techniques are introduced highlighting approaches towards 3D tissue printing. PMID:24956301

  18. The continuous molecular fields approach to building 3D-QSAR models.

    PubMed

    Baskin, Igor I; Zhokhova, Nelly I

    2013-05-01

    The continuous molecular fields (CMF) approach is based on the application of continuous functions for the description of molecular fields instead of finite sets of molecular descriptors (such as interaction energies computed at grid nodes) commonly used for this purpose. These functions can be encapsulated into kernels and combined with kernel-based machine learning algorithms to provide a variety of novel methods for building classification and regression structure-activity models, visualizing chemical datasets and conducting virtual screening. In this article, the CMF approach is applied to building 3D-QSAR models for 8 datasets through the use of five types of molecular fields (the electrostatic, steric, hydrophobic, hydrogen-bond acceptor and donor ones), the linear convolution molecular kernel with the contribution of each atom approximated with a single isotropic Gaussian function, and the kernel ridge regression data analysis technique. It is shown that the CMF approach even in this simplest form provides either comparable or enhanced predictive performance in comparison with state-of-the-art 3D-QSAR methods. PMID:23719959

  19. Single-arc volumetric-modulated arc therapy (sVMAT) as adjuvant treatment for gastric cancer: Dosimetric comparisons with three-dimensional conformal radiotherapy (3D-CRT) and intensity-modulated radiotherapy (IMRT)

    SciTech Connect

    Wang, Xin; Li, Guangjun; Zhang, Yingjie; Bai, Sen; Xu, Feng; Wei, Yuquan; Gong, Youling

    2013-01-01

    To compare the dosimetric differences between the single-arc volumetric-modulated arc therapy (sVMAT), 3-dimensional conformal radiotherapy (3D-CRT), and intensity-modulated radiotherapy (IMRT) techniques in treatment planning for gastric cancer as adjuvant radiotherapy. Twelve patients were retrospectively analyzed. In each patient's case, the parameters were compared based on the dose-volume histogram (DVH) of the sVMAT, 3D-CRT, and IMRT plans, respectively. Three techniques showed similar target dose coverage. The maximum and mean doses of the target were significantly higher in the sVMAT plans than that in 3D-CRT plans and in the 3D-CRT/IMRT plans, respectively, but these differences were clinically acceptable. The IMRT and sVMAT plans successfully achieved better target dose conformity, reduced the V{sub 20/30}, and mean dose of the left kidney, as well as the V{sub 20/30} of the liver, compared with the 3D-CRT plans. And the sVMAT technique reduced the V{sub 20} of the liver much significantly. Although the maximum dose of the spinal cord were much higher in the IMRT and sVMAT plans, respectively (mean 36.4 vs 39.5 and 40.6 Gy), these data were still under the constraints. Not much difference was found in the analysis of the parameters of the right kidney, intestine, and heart. The IMRT and sVMAT plans achieved similar dose distribution to the target, but superior to the 3D-CRT plans, in adjuvant radiotherapy for gastric cancer. The sVMAT technique improved the dose sparings of the left kidney and liver, compared with the 3D-CRT technique, but showed few dosimetric advantages over the IMRT technique. Studies are warranted to evaluate the clinical benefits of the VMAT treatment for patients with gastric cancer after surgery in the future.

  20. Digital breast tomosynthesis: computerized detection of microcalcifications in reconstructed breast volume using a 3D approach

    NASA Astrophysics Data System (ADS)

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

    2010-03-01

    We are developing a computer-aided detection (CAD) system for clustered microcalcifications in digital breast tomosynthesis (DBT). In this preliminary study, we investigated the approach of detecting microcalcifications in the tomosynthesized volume. The DBT volume is first enhanced by 3D multi-scale filtering and analysis of the eigenvalues of Hessian matrices with a calcification response function and signal-to-noise ratio enhancement filtering. Potential signal sites are identified in the enhanced volume and local analysis is performed to further characterize each object. A 3D dynamic clustering procedure is designed to locate potential clusters using hierarchical criteria. We collected a pilot data set of two-view DBT mammograms of 39 breasts containing microcalcification clusters (17 malignant, 22 benign) with IRB approval. A total of 74 clusters were identified by an experienced radiologist in the 78 DBT views. Our prototype CAD system achieved view-based sensitivity of 90% and 80% at an average FP rate of 7.3 and 2.0 clusters per volume, respectively. At the same levels of case-based sensitivity, the FP rates were 3.6 and 1.3 clusters per volume, respectively. For the subset of malignant clusters, the view-based detection sensitivity was 94% and 82% at an average FP rate of 6.0 and 1.5 FP clusters per volume, respectively. At the same levels of case-based sensitivity, the FP rates were 1.2 and 0.9 clusters per volume, respectively. This study demonstrated that computerized microcalcification detection in 3D is a promising approach to the development of a CAD system for DBT. Study is underway to further improve the computer-vision methods and to optimize the processing parameters using a larger data set.

  1. Assessment of dry-stone terrace wall degradation with a 3D approach

    NASA Astrophysics Data System (ADS)

    Djuma, Hakan; Camera, Corrado; Faka, Marina; Bruggeman, Adriana; Hermon, Sorin

    2016-04-01

    displacements between 3 and 8 cm on 1% of the middle terrace wall. High displacement values (> 8-10 cm) were associated with presence or removal of vegetation and/or data gaps. On the second site, the 3D models indicated that the collapsed terrace had lost a volume of 1.9 m3, which was restored during the communal terrace building event. This digital 3D documentation approach is more economical than laser scanning and it is a promising method for assessment of terrace wall displacement and changes after terrace wall restoration.

  2. A CNN-based approach to integrate the 3-D turbolent diffusion equation

    NASA Astrophysics Data System (ADS)

    Nunnari, G.

    2003-04-01

    The paper deals with the integration of the 3-D turbulent diffusion equation. This problem is relevant in several application fields including fluid dynamics, air/water pollution, volcanic ash emissions and industrial hazard assessment. As it is well known numerical solution of such a kind of equation is very time consuming even by using modern digital computers and this represents a short-coming for on-line applications. To overcome this drawback a Cellular Neural Network Approach is proposed in this paper. CNN's proposed by Chua and Yang in 1988 are massive parallel analog non-linear circuits with local interconnections between the computing elements that allow very fast distributed computations. Nowadays several producers of semiconductors such as SGS-Thomson are producing on chip CNN's so that their massive use for heavy computing applications is expected in the near future. In the paper the methodological background of the proposed approach will be outlined. Further some results both in terms of accuracy and computation time will be presented also in comparison with traditional three-dimensional computation schemes. Some results obtained to model 3-D pollution problems in the industrial area of Siracusa (Italy), characterised by a large concentration of petrol-chemical plants, will be presented.

  3. Volume rendering segmented data using 3D textures: a practical approach for intra-operative visualization

    NASA Astrophysics Data System (ADS)

    Subramanian, Navneeth; Mullick, Rakesh; Vaidya, Vivek

    2006-03-01

    Volume rendering has high utility in visualization of segmented datasets. However, volume rendering of the segmented labels along with the original data causes undesirable intermixing/bleeding artifacts arising from interpolation at the sharp boundaries. This issue is further amplified in 3D textures based volume rendering due to the inaccessibility of the interpolation stage. We present an approach which helps minimize intermixing artifacts while maintaining the high performance of 3D texture based volume rendering - both of which are critical for intra-operative visualization. Our approach uses a 2D transfer function based classification scheme where label distinction is achieved through an encoding that generates unique gradient values for labels. This helps ensure that labelled voxels always map to distinct regions in the 2D transfer function, irrespective of interpolation. In contrast to previously reported algorithms, our algorithm does not require multiple passes for rendering and supports greater than 4 masks. It also allows for real-time modification of the colors/opacities of the segmented structures along with the original data. Additionally, these capabilities are available with minimal texture memory requirements amongst comparable algorithms. Results are presented on clinical and phantom data.

  4. Modular Approaches to Earth Science Scientific Computing: 3D Electromagnetic Induction Modeling as an Example

    NASA Astrophysics Data System (ADS)

    Tandon, K.; Egbert, G.; Siripunvaraporn, W.

    2003-12-01

    We are developing a modular system for three-dimensional inversion of electromagnetic (EM) induction data, using an object oriented programming approach. This approach allows us to modify the individual components of the inversion scheme proposed, and also reuse the components for variety of problems in earth science computing howsoever diverse they might be. In particular, the modularity allows us to (a) change modeling codes independently of inversion algorithm details; (b) experiment with new inversion algorithms; and (c) modify the way prior information is imposed in the inversion to test competing hypothesis and techniques required to solve an earth science problem. Our initial code development is for EM induction equations on a staggered grid, using iterative solution techniques in 3D. An example illustrated here is an experiment with the sensitivity of 3D magnetotelluric inversion to uncertainties in the boundary conditions required for regional induction problems. These boundary conditions should reflect the large-scale geoelectric structure of the study area, which is usually poorly constrained. In general for inversion of MT data, one fixes boundary conditions at the edge of the model domain, and adjusts the earth?s conductivity structure within the modeling domain. Allowing for errors in specification of the open boundary values is simple in principle, but no existing inversion codes that we are aware of have this feature. Adding a feature such as this is straightforward within the context of the modular approach. More generally, a modular approach provides an efficient methodology for setting up earth science computing problems to test various ideas. As a concrete illustration relevant to EM induction problems, we investigate the sensitivity of MT data near San Andreas Fault at Parkfield (California) to uncertainties in the regional geoelectric structure.

  5. 3D time series analysis of cell shape using Laplacian approaches

    PubMed Central

    2013-01-01

    Background Fundamental cellular processes such as cell movement, division or food uptake critically depend on cells being able to change shape. Fast acquisition of three-dimensional image time series has now become possible, but we lack efficient tools for analysing shape deformations in order to understand the real three-dimensional nature of shape changes. Results We present a framework for 3D+time cell shape analysis. The main contribution is three-fold: First, we develop a fast, automatic random walker method for cell segmentation. Second, a novel topology fixing method is proposed to fix segmented binary volumes without spherical topology. Third, we show that algorithms used for each individual step of the analysis pipeline (cell segmentation, topology fixing, spherical parameterization, and shape representation) are closely related to the Laplacian operator. The framework is applied to the shape analysis of neutrophil cells. Conclusions The method we propose for cell segmentation is faster than the traditional random walker method or the level set method, and performs better on 3D time-series of neutrophil cells, which are comparatively noisy as stacks have to be acquired fast enough to account for cell motion. Our method for topology fixing outperforms the tools provided by SPHARM-MAT and SPHARM-PDM in terms of their successful fixing rates. The different tasks in the presented pipeline for 3D+time shape analysis of cells can be solved using Laplacian approaches, opening the possibility of eventually combining individual steps in order to speed up computations. PMID:24090312

  6. 3D inversion based on multi-grid approach of magnetotelluric data from Northern Scandinavia

    NASA Astrophysics Data System (ADS)

    Cherevatova, M.; Smirnov, M.; Korja, T. J.; Egbert, G. D.

    2012-12-01

    In this work we investigate the geoelectrical structure of the cratonic margin of Fennoscandian Shield by means of magnetotelluric (MT) measurements carried out in Northern Norway and Sweden during summer 2011-2012. The project Magnetotellurics in the Scandes (MaSca) focuses on the investigation of the crust, upper mantle and lithospheric structure in a transition zone from a stable Precambrian cratonic interior to a passive continental margin beneath the Caledonian Orogen and the Scandes Mountains in western Fennoscandia. Recent MT profiles in the central and southern Scandes indicated a large contrast in resistivity between Caledonides and Precambrian basement. The alum shales as a highly conductive layers between the resistive Precambrian basement and the overlying Caledonian nappes are revealed from this profiles. Additional measurements in the Northern Scandes were required. All together data from 60 synchronous long period (LMT) and about 200 broad band (BMT) sites were acquired. The array stretches from Lofoten and Bodo (Norway) in the west to Kiruna and Skeleftea (Sweden) in the east covering an area of 500x500 square kilometers. LMT sites were occupied for about two months, while most of the BMT sites were measured during one day. We have used new multi-grid approach for 3D electromagnetic (EM) inversion and modelling. Our approach is based on the OcTree discretization where the spatial domain is represented by rectangular cells, each of which might be subdivided (recursively) into eight sub-cells. In this simplified implementation the grid is refined only in the horizontal direction, uniformly in each vertical layer. Using multi-grid we manage to have a high grid resolution near the surface (for instance, to tackle with galvanic distortions) and lower resolution at greater depth as the EM fields decay in the Earth according to the diffusion equation. We also have a benefit in computational costs as number of unknowns decrease. The multi-grid forward

  7. A Reconstruction Approach for Imaging in 3D Cone Beam Vector Field Tomography

    PubMed Central

    Schuster, T.; Theis, D.; Louis, A. K.

    2008-01-01

    3D cone beam vector field tomography (VFT) aims for reconstructing and visualizing the velocity field of a moving fluid by measuring line integrals of projections of the vector field. The data are obtained by ultrasound measurements along a scanning curve which surrounds the object. From a mathematical point of view, we have to deal with the inversion of the vectorial cone beam transform. Since the vectorial cone beam transform of any gradient vector field with compact support is identically equal to zero, we can only hope to reconstruct the solenoidal part of an arbitrary vector field. In this paper we will at first summarize important properties of the cone beam transform for three-dimensional solenoidal vector fields and then propose a solution approach based on the method of approximate inverse. In this context, we intensively make use of results from scalar 3D computerized tomography. The findings presented in the paper will continuously be illustrated by pictures from first numerical experiments done with exact, simulated data. PMID:19197391

  8. Thin-dielectric-layer engineering for 3D nanostructure integration using an innovative planarization approach

    NASA Astrophysics Data System (ADS)

    Guerfi, Y.; Doucet, J. B.; Larrieu, G.

    2015-10-01

    Three-dimensional (3D) nanostructures are emerging as promising building blocks for a large spectrum of applications. One critical issue in integration regards mastering the thin, flat, and chemically stable insulating layer that must be implemented on the nanostructure network in order to build striking nano-architectures. In this letter, we report an innovative method for nanoscale planarization on 3D nanostructures by using hydrogen silesquioxane as a spin-on-glass (SOG) dielectric material. To decouple the thickness of the final layer from the height of the nanostructure, we propose to embed the nanowire network in the insulator layer by exploiting the planarizing properties of the SOG approach. To achieve the desired dielectric thickness, the structure is chemically etched back with a highly diluted solution to control the etch rate precisely. The roughness of the top surface was less than 2 nm. There were no surface defects and the planarity was excellent, even in the vicinity of the nanowires. This newly developed process was used to realize a multilevel stack architecture with sub-deca-nanometer-range layer thickness.

  9. High performance computing approaches for 3D reconstruction of complex biological specimens.

    PubMed

    da Silva, M Laura; Roca-Piera, Javier; Fernández, José-Jesús

    2010-01-01

    Knowledge of the structure of specimens is crucial to determine the role that they play in cellular and molecular biology. To yield the three-dimensional (3D) reconstruction by means of tomographic reconstruction algorithms, we need the use of large projection images and high processing time. Therefore, we propose the use of the high performance computing (HPC) to cope with the huge computational demands of this problem. We have implemented a HPC strategy where the distribution of tasks follows the master-slave paradigm. The master processor distributes a slab of slices, a piece of the final 3D structure to reconstruct, among the slave processors and receives reconstructed slices of the volume. We have evaluated the performance of our HPC approach using different sizes of the slab. We have observed that it is possible to find out an optimal size of the slab for the number of processor used that minimize communications time while maintaining a reasonable grain of parallelism to be exploited by the set of processors. PMID:20865517

  10. 3-D-numerical approach to simulate an avalanche impact into a reservoir

    NASA Astrophysics Data System (ADS)

    Gabl, R.; Seibl, J.; Gems, B.; Aufleger, M.

    2015-06-01

    The impact of an avalanche into a reservoir induces an impulse wave, which poses a threat to population and infrastructure. For a good approximation of the generated wave height and length as well as the resulting outflow volume over structures and dams, formulas, which base on different simplifying assumptions, can be used. Further project-specific investigations by means of a scale model test or numerical simulations are advisable for complex reservoirs as well as the inclusion of hydraulic structures such as spillways. The paper presents a new approach for a 3-D-numerical simulation of an avalanche impact into a reservoir. In this model concept the energy and mass of the avalanche are represented by accelerated water on the real hill slope. Instead of snow, only water and air are used to simulate the moving avalanche with the software FLOW-3D. A significant advantage of this assumption is the self-adaptation of the model avalanche onto the terrain. In order to reach good comparability of the results with existing research at the ETH Zürich, a simplified reservoir geometry is investigated. Thus, a reference case has been analysed including a variation of three geometry parameters (still water depth in the reservoir, freeboard of the dam and reservoir width).

  11. Body image, shape, and volumetric assessments using 3D whole body laser scanning and 2D digital photography in females with a diagnosed eating disorder: preliminary novel findings.

    PubMed

    Stewart, Arthur D; Klein, Susan; Young, Julie; Simpson, Susan; Lee, Amanda J; Harrild, Kirstin; Crockett, Philip; Benson, Philip J

    2012-05-01

    We piloted three-dimensional (3D) body scanning in eating disorder (ED) patients. Assessments of 22 ED patients (including nine anorexia nervosa (AN) patients, 12 bulimia nervosa (BN) patients, and one patient with eating disorder not otherwise specified) and 22 matched controls are presented. Volunteers underwent visual screening, two-dimensional (2D) digital photography to assess perception and dissatisfaction (via computerized image distortion), and adjunctive 3D full-body scanning. Patients and controls perceived themselves as bigger than their true shape (except in the chest region for controls and anorexia patients). All participants wished to be smaller across all body regions. Patients had poorer veridical perception and greater dissatisfaction than controls. Perception was generally poorer and dissatisfaction greater in bulimia compared with anorexia patients. 3D-volume:2D-area relationships showed that anorexia cases had least tissue on the torso and most on the arms and legs relative to frontal area. The engagement of patients with the scanning process suggests a validation study is viable. This would enable mental constructs of body image to be aligned with segmental volume of body areas, overcoming limitations, and errors associated with 2D instruments restricted to frontal (coronal) shapes. These novel data could inform the design of clinical trials in adjunctive treatments for eating disorders. PMID:22506746

  12. Optimising GPR modelling: A practical, multi-threaded approach to 3D FDTD numerical modelling

    NASA Astrophysics Data System (ADS)

    Millington, T. M.; Cassidy, N. J.

    2010-09-01

    The demand for advanced interpretational tools has lead to the development of highly sophisticated, computationally demanding, 3D GPR processing and modelling techniques. Many of these methods solve very large problems with stepwise methods that utilise numerically similar functions within iterative computational loops. Problems of this nature are readily parallelised by splitting the computational domain into smaller, independent chunks for direct use on cluster-style, multi-processor supercomputers. Unfortunately, the implications of running such facilities, as well as time investment needed to develop the parallel codes, means that for most researchers, the use of these advanced methods is too impractical. In this paper, we propose an alternative method of parallelisation which exploits the capabilities of the modern multi-core processors (upon which today's desktop PCs are built) by multi-threading the calculation of a problem's individual sub-solutions. To illustrate the approach, we have applied it to an advanced, 3D, finite-difference time-domain (FDTD) GPR modelling tool in which the calculation of the individual vector field components is multi-threaded. To be of practical use, the FDTD scheme must be able to deliver accurate results with short execution times and we, therefore, show that the performance benefits of our approach can deliver runtimes less than half those of the more conventional, serial programming techniques. We evaluate implementations of the technique using different programming languages (e.g., Matlab, Java, C++), which will facilitate the construction of a flexible modelling tool for use in future GPR research. The implementations are compared on a variety of typical hardware platforms, having between one and eight processing cores available, and also a modern Graphical Processing Unit (GPU)-based computer. Our results show that a multi-threaded xyz modelling approach is easy to implement and delivers excellent results when implemented

  13. Volumetric Modulation Arc Radiotherapy With Flattening Filter-Free Beams Compared With Static Gantry IMRT and 3D Conformal Radiotherapy for Advanced Esophageal Cancer: A Feasibility Study

    SciTech Connect

    Nicolini, Giorgia; Ghosh-Laskar, Sarbani; Shrivastava, Shyam Kishore; Banerjee, Sushovan; Chaudhary, Suresh; Agarwal, Jai Prakash; Munshi, Anusheel; Clivio, Alessandro; Fogliata, Antonella; Mancosu, Pietro; Vanetti, Eugenio; Cozzi, Luca

    2012-10-01

    Purpose: A feasibility study was performed to evaluate RapidArc (RA), and the potential benefit of flattening filter-free beams, on advanced esophageal cancer against intensity-modulated radiotherapy (IMRT) and three-dimensional conformal radiotherapy (3D-CRT). Methods and Materials: The plans for 3D-CRT and IMRT with three to seven and five to seven fixed beams were compared against double-modulated arcs with avoidance sectors to spare the lungs for 10 patients. All plans were optimized for 6-MV photon beams. The RA plans were studied for conventional and flattening filter-free (FFF) beams. The objectives for the planning target volume were the volume receiving {>=}95% or at most 107% of the prescribed dose of <1% with a dose prescription of 59.4 Gy. For the organs at risk, the lung volume (minus the planning target volume) receiving {>=}5 Gy was <60%, that receiving 20 Gy was <20%-30%, and the mean lung dose was <15.0 Gy. The heart volume receiving 45 Gy was <20%, volume receiving 30 Gy was <50%. The spinal dose received by 1% was <45 Gy. The technical delivery parameters for RA were assessed to compare the normal and FFF beam characteristics. Results: RA and IMRT provided equivalent coverage and homogeneity, slightly superior to 3D-CRT. The conformity index was 1.2 {+-} 0.1 for RA and IMRT and 1.5 {+-} 0.2 for 3D-CRT. The mean lung dose was 12.2 {+-} 4.5 for IMRT, 11.3 {+-} 4.6 for RA, and 10.8 {+-} 4.4 for RA with FFF beams, 18.2 {+-} 8.5 for 3D-CRT. The percentage of volume receiving {>=}20 Gy ranged from 23.6% {+-} 9.1% to 21.1% {+-} 9.7% for IMRT and RA (FFF beams) and 39.2% {+-} 17.0% for 3D-CRT. The heart and spine objectives were met by all techniques. The monitor units for IMRT and RA were 457 {+-} 139, 322 {+-} 20, and 387 {+-} 40, respectively. RA with FFF beams showed, compared with RA with normal beams, a {approx}20% increase in monitor units per Gray, a 90% increase in the average dose rate, and 20% reduction in beam on time (owing to different

  14. Deconvolution approach for 3D scanning microscopy with helical phase engineering.

    PubMed

    Roider, Clemens; Heintzmann, Rainer; Piestun, Rafael; Jesacher, Alexander

    2016-07-11

    RESCH (refocusing after scanning using helical phase engineering) microscopy is a scanning technique using engineered point spread functions which provides volumetric information. We present a strategy for processing the collected raw data with a multi-view maximum likelihood deconvolution algorithm, which inherently comprises the resolution gain of pixel-reassignment microscopy. The method, which we term MD-RESCH (for multi-view deconvolved RESCH), achieves in our current implementation a 20% resolution advantage along all three axes compared to RESCH and confocal microscopy. Along the axial direction, the resolution is comparable to that of image scanning microscopy. However, because the method inherently reconstructs a volume from a single 2D scan, a significantly higher optical sectioning becomes directly visible to the user, which would otherwise require collecting multiple 2D scans taken at a series of axial positions. Further, we introduce the use of a single-helical detection PSF to obtain an increased post-acquisition refocusing range. We present data from numerical simulations as well as experiments to confirm the validity of our approach. PMID:27410820

  15. Glasses-free 3D display based on micro-nano-approach and system

    NASA Astrophysics Data System (ADS)

    Lou, Yimin; Ye, Yan; Shen, Su; Pu, Donglin; Chen, Linsen

    2014-11-01

    Micro-nano optics and digital dot matrix hologram (DDMH) technique has been combined to code and fabricate glassfree 3D image. Two kinds of true color 3D DDMH have been designed. One of the design releases the fabrication complexity and the other enlarges the view angle of 3D DDMH. Chromatic aberration has been corrected using rainbow hologram technique. A holographic printing system combined the interference and projection lithography technique has been demonstrated. Fresnel lens and large view angle 3D DDMH have been outputted, excellent color performance of 3D image has been realized.

  16. A 3D approach for object recognition in illuminated scenes with adaptive correlation filters

    NASA Astrophysics Data System (ADS)

    Picos, Kenia; Díaz-Ramírez, Víctor H.

    2015-09-01

    In this paper we solve the problem of pose recognition of a 3D object in non-uniformly illuminated and noisy scenes. The recognition system employs a bank of space-variant correlation filters constructed with an adaptive approach based on local statistical parameters of the input scene. The position and orientation of the target are estimated with the help of the filter bank. For an observed input frame, the algorithm computes the correlation process between the observed image and the bank of filters using a combination of data and task parallelism by taking advantage of a graphics processing unit (GPU) architecture. The pose of the target is estimated by finding the template that better matches the current view of target within the scene. The performance of the proposed system is evaluated in terms of recognition accuracy, location and orientation errors, and computational performance.

  17. Extracting 3-D information from SEM and TEM images: Approaches and applications in the physical sciences

    SciTech Connect

    L`Esperance, G.; Dionne, M.; Tremblay, S.

    1996-12-31

    Techniques for extracting 3-D information from TEM samples in life sciences have considerably progressed in recent years. One approach has been the use of serial prepared by ultramicrotomy from which the volume of the sample and of various constituents can be reconstructed. In the case of engineering materials, however, ultramicrotomy generally induces severe deformation resulting in a large density of structural defects (dislocations, stacking faults etc.). This leads to significant diffraction contrast effects which mask microstructural features such as second phase particles, precipitates etc. Recently, a series of TEM bright field images taken at different tilts have been used in combination with image analysis to determine the volume fraction (V{sub f}) of second phase particles in thin foils of aluminum alloys. Although the technique was successful to remove most of the diffraction contrast effects and to make the particles visible, the need to acquire and process a large number of images makes the technique laborious and can lead to artefacts.

  18. 3D mapping of airway wall thickening in asthma with MSCT: a level set approach

    NASA Astrophysics Data System (ADS)

    Fetita, Catalin; Brillet, Pierre-Yves; Hartley, Ruth; Grenier, Philippe A.; Brightling, Christopher

    2014-03-01

    Assessing the airway wall thickness in multi slice computed tomography (MSCT) as image marker for airway disease phenotyping such asthma and COPD is a current trend and challenge for the scientific community working in lung imaging. This paper addresses the same problem from a different point of view: considering the expected wall thickness-to-lumen-radius ratio for a normal subject as known and constant throughout the whole airway tree, the aim is to build up a 3D map of airway wall regions of larger thickness and to define an overall score able to highlight a pathological status. In this respect, the local dimension (caliber) of the previously segmented airway lumen is obtained on each point by exploiting the granulometry morphological operator. A level set function is defined based on this caliber information and on the expected wall thickness ratio, which allows obtaining a good estimate of the airway wall throughout all segmented lumen generations. Next, the vascular (or mediastinal dense tissue) contact regions are automatically detected and excluded from analysis. For the remaining airway wall border points, the real wall thickness is estimated based on the tissue density analysis in the airway radial direction; thick wall points are highlighted on a 3D representation of the airways and several quantification scores are defined. The proposed approach is fully automatic and was evaluated (proof of concept) on a patient selection coming from different databases including mild, severe asthmatics and normal cases. This preliminary evaluation confirms the discriminative power of the proposed approach regarding different phenotypes and is currently extending to larger cohorts.

  19. Reliability of MR-Based Volumetric 3-D Analysis of Pelvic Muscles among Subjects with Low Back with Leg Pain and Healthy Volunteers

    PubMed Central

    Skorupska, Elżbieta; Keczmer, Przemysław; Łochowski, Rafał M.; Tomal, Paulina; Rychlik, Michał; Samborski, Włodzimierz

    2016-01-01

    Aim Lately, the diagnostic value of magnetic resonance imaging, Lasègue sign and classic neurological signs have been considered not accurate enough to distinguish the radicular from non-radicular low back with leg pain (LBLP) and a calculation of the symptomatic side muscle volume has been indicated as a probable valuable marker. However, only the multifidus muscle volume has been calculated so far. The main objective of the study was to verify whether LBLP subjects presented symptomatic side pelvic muscle atrophy compared to healthy volunteers. The second aim was to assess the inter-rater reliability of 3-D manual method for segmenting and measuring the volume of the gluteus maximus, gluteus medius, gluteus minimus and piriformis muscles in both LBLP patients and healthy subjects. Method Two independent raters analyzed MR images of LBLP and healthy subjects towards muscle volume of four pelvic muscles, i.e. the piriformis, gluteus minimus, gluteus medius and gluteus maximus. For both sides, the MR images of the muscles without adipose tissue infiltration were manually segmented in 3-D medical images. Results Symptomatic muscle atrophy was confirmed in only over 50% of LBLP subjects (gluteus maximus (p<0.001), gluteus minimus (p<0.01) and piriformis (p<0.05)). The ICC values indicated that the inter-rater reproducibility was greater than 0.90 for all measurements (LBLP and healthy subjects), except for the measurement of the right gluteus medius muscle in LBLP patients, which was equal to 0.848. Conclusion More than 50% of LBLP subjects presented symptomatic gluteus maximus, gluteus minimus and piriformis muscle atrophy. 3-D manual segmentation reliably measured muscle volume in all the measured pelvic muscles in both healthy and LBLP subjects. To answer the question of what kind of muscle atrophy is indicative of radicular or non-radicular pain further studies are required. PMID:27459688

  20. Accurate 3D point cloud comparison and volumetric change analysis of Terrestrial Laser Scan data in a hard rock coastal cliff environment

    NASA Astrophysics Data System (ADS)

    Earlie, C. S.; Masselink, G.; Russell, P.; Shail, R.; Kingston, K.

    2013-12-01

    Our understanding of the evolution of hard rock coastlines is limited due to the episodic nature and ';slow' rate at which changes occur. High-resolution surveying techniques, such as Terrestrial Laser Scanning (TLS), have just begun to be adopted as a method of obtaining detailed point cloud data to monitor topographical changes over short periods of time (weeks to months). However, the difficulties involved in comparing consecutive point cloud data sets in a complex three-dimensional plane, such as occlusion due to surface roughness and positioning of data capture point as a result of a consistently changing environment (a beach profile), mean that comparing data sets can lead to errors in the region of 10 - 20 cm. Meshing techniques are often used for point cloud data analysis for simple surfaces, but in surfaces such as rocky cliff faces, this technique has been found to be ineffective. Recession rates of hard rock coastlines in the UK are typically determined using aerial photography or airborne LiDAR data, yet the detail of the important changes occurring to the cliff face and toe are missed using such techniques. In this study we apply an algorithm (M3C2 - Multiscale Model to Model Cloud Comparison), initially developed for analysing fluvial morphological change, that directly compares point to point cloud data using surface normals that are consistent with surface roughness and measure the change that occurs along the normal direction (Lague et al., 2013). The surfaces changes are analysed using a set of user defined scales based on surface roughness and registration error. Once the correct parameters are defined, the volumetric cliff face changes are calculated by integrating the mean distance between the point clouds. The analysis has been undertaken at two hard rock sites identified for their active erosion located on the UK's south west peninsular at Porthleven in south west Cornwall and Godrevy in north Cornwall. Alongside TLS point cloud data, in

  1. FRACTURED RESERVOIR E&P IN ROCKY MOUNTAIN BASINS: A 3-D RTM MODELING APPROACH

    SciTech Connect

    P. Ortoleva; J. Comer; A. Park; D. Payne; W. Sibo; K. Tuncay

    2001-11-26

    Key natural gas reserves in Rocky Mountain and other U.S. basins are in reservoirs with economic producibility due to natural fractures. In this project, we evaluate a unique technology for predicting fractured reservoir location and characteristics ahead of drilling based on a 3-D basin/field simulator, Basin RTM. Recommendations are made for making Basin RTM a key element of a practical E&P strategy. A myriad of reaction, transport, and mechanical (RTM) processes underlie the creation, cementation and preservation of fractured reservoirs. These processes are often so strongly coupled that they cannot be understood individually. Furthermore, sedimentary nonuniformity, overall tectonics and basement heat flux histories make a basin a fundamentally 3-D object. Basin RTM is the only 3-D, comprehensive, fully coupled RTM basin simulator available for the exploration of fractured reservoirs. Results of Basin RTM simulations are presented, that demonstrate its capabilities and limitations. Furthermore, it is shown how Basin RTM is a basis for a revolutionary automated methodology for simultaneously using a range of remote and other basin datasets to locate reservoirs and to assess risk. Characteristics predicted by our model include reserves and composition, matrix and fracture permeability, reservoir rock strength, porosity, in situ stress and the statistics of fracture aperture, length and orientation. Our model integrates its input data (overall sedimentation, tectonic and basement heat flux histories) via the laws of physics and chemistry that describe the RTM processes to predict reservoir location and characteristics. Basin RTM uses 3-D, finite element solutions of the equations of rock mechanics, organic and inorganic diagenesis and multi-phase hydrology to make its predictions. As our model predicts reservoir characteristics, it can be used to optimize production approaches (e.g., assess the stability of horizontal wells or vulnerability of fractures to

  2. Joint 3D inversion of gravity and magnetic data with geological constraints - an alternative approach

    NASA Astrophysics Data System (ADS)

    Prutkin, Ilya; Vajda, Peter; Jentzsch, Gerhard

    2016-04-01

    Quite a popular approach now by interpretation of gravity data is a linear one - an attempt is made to find a density distribution d(x,y,z) below the Earth's surface. This approach has clear disadvantages. First, we face the problem of dimensionality: one looks for 3D function based on 2D data set (measurements on the Earth's surface), the degree of non-uniqueness is extremely high, and no regularization can save the situation. The number of unknowns is many times higher than the number of observations; otherwise, we obtain a very rough model of the lower half-space. Second, the linear approach is not reasonable from the geological point of view. It implies that density varies from one point to another. Usually, we assume big volumes with nearly homogeneous density - layers, blocks, intrusions. It looks more understandable, to search for geometry of density interfaces: 3D topography of contact surfaces and shapes of restricted bodies (intrusions). Third, in the framework of the linear approach even for a synthetic field of two separate objects we obtain clouds of points with slightly increased density. It is hardly ever possible, to isolate objects, particularly when one of them is located above another one. We suggest an alternative approach for the linear one. Our approach has been successfully applied for several case histories including a local gravity anomaly Kolarovo and a bigger area of the Thuringian Basin, where both gravity and magnetic data are inverted. First, we separate sources into deep, intermediate and shallow ones, using subsequent upward and downward continuation. All components are inverted separately. We address a problem which we name the problem of low frequencies: deep objects generate long wavelengths, but the converse implication is not necessarily true. For instance, the effect of the basin structure contributes substantially into low frequencies, though it is caused by shallow sources. However, our numerical experiments with intermediate

  3. Comparison between 3D volumetric rendering and multiplanar slices on the reliability of linear measurements on CBCT images: an in vitro study

    PubMed Central

    FERNANDES, Thais Maria Freire; ADAMCZYK, Julie; POLETI, Marcelo Lupion; HENRIQUES, José Fernando Castanha; FRIEDLAND, Bernard; GARIB, Daniela Gamba

    2015-01-01

    Objective The purpose of this study was to determine the accuracy and reliability of two methods of measurements of linear distances (multiplanar 2D and tridimensional reconstruction 3D) obtained from cone-beam computed tomography (CBCT) with different voxel sizes. Material and Methods Ten dry human mandibles were scanned at voxel sizes of 0.2 and 0.4 mm. Craniometric anatomical landmarks were identified twice by two independent operators on the multiplanar reconstructed and on volume rendering images that were generated by the software Dolphin®. Subsequently, physical measurements were performed using a digital caliper. Analysis of variance (ANOVA), intraclass correlation coefficient (ICC) and Bland-Altman were used for evaluating accuracy and reliability (p<0.05). Results Excellent intraobserver reliability and good to high precision interobserver reliability values were found for linear measurements from CBCT 3D and multiplanar images. Measurements performed on multiplanar reconstructed images were more accurate than measurements in volume rendering compared with the gold standard. No statistically significant difference was found between voxel protocols, independently of the measurement method. Conclusions Linear measurements on multiplanar images of 0.2 and 0.4 voxel are reliable and accurate when compared with direct caliper measurements. Caution should be taken in the volume rendering measurements, because the measurements were reliable, but not accurate for all variables. An increased voxel resolution did not result in greater accuracy of mandible measurements and would potentially provide increased patient radiation exposure. PMID:25004053

  4. A Block Copolymer Self-Assembly Approach for 3D Nanoconfined Dopants in Semiconductors

    NASA Astrophysics Data System (ADS)

    Popere, Bhooshan; Russ, Boris; Chang, William; Heitsch, Andrew; Trefonas, Peter; Segalman, Rachel

    2015-03-01

    Continuous shrinking of electronic circuits presents a new challenge to demonstrate reliable, uniform nanoscale doping. Directed self-assembly (DSA) of block copolymers (BCP) has proved critical in meeting the technology nodes by enabling excellent pitch control for lithography. Yet, controlling the 3D dopant distribution remains a fundamental design challenge. To this end, we have utilized BCP self-assembly in a novel approach to confine dopants to nanoscopic domains within a semiconductor. The periodic nature of these domains affords precise control over the dosage and spatial positions of dopant atoms. Dopant incorporation within the block copolymer domains via hydrogen bonding eliminates the need for tailored synthesis, making the approach highly modular. Rapid thermal annealing of the self-assembled films effectively drives the dopants into the underlying substrate, thus confining them to within 10-20 nm in all dimensions. Additionally, the size, pitch, dopant dosage and the junction depth can be independently varied for a wide range of dopants. Compositional and electronic measurements indicate that the domains are indeed discrete and nanoconfined. Our approach, thereby, enables a facile method for controlled nanoscopic doping in semiconductors.

  5. Modelling of 3D Attenuation Structure in the Mantle Using a Waveform Approach: Successes and Challenges

    NASA Astrophysics Data System (ADS)

    Romanowicz, B. A.; Gung, Y.

    2003-12-01

    The study of lateral variations in Q in the upper mantle at the global scale is generally addressed using isolated phases in the seismogram (for example fundamental mode surface wave spectra), which limits the sampling and therefore the resolution of Q structure that can be achieved. The use of isolated phases has the advantage of working directly with amplitudes, thus making it easier to detect contamination of the anelastic attenuation signal by elastic focusing and scattering, a key problem in attenuation tomography. We here discuss recent progress on a waveform modeling approach, which allows us to work with entire seismograms and exploit the information contained both in fundamental mode surface waves, overtones and body waves. The method is based on a normal mode approach and proceeds iteratively. In the first step, we invert for 3D elastic structure using the NACT approach (Non-linear Asymptotic Coupling Theory; Li and Romanowicz, 1995), which aligns the phase part of the observed and synthetic seismograms. In the second step, we invert for Q. The crucial issue is how to account for elastic effects in the amplitudes (focusing)- we discuss asymptotic versus more exact methods to address this problem and illustrate the effects on the resulting models. We discuss prominent features in the lateral variations in Q in the upper mantle, their evolution with depth, and their relation with elastic structure, in particular from the point of view of resolving upwellings and the large scale signature of plumes.

  6. i3DP, a robust 3D printing approach enabling genetic post-printing surface modification.

    PubMed

    Wang, Xiaolong; Cai, Xiaobing; Guo, Qiuquan; Zhang, Tengyuan; Kobe, Brad; Yang, Jun

    2013-10-01

    Initiator integrated 3D printing, namely i3DP, was developed by incorporating a vinyl-terminated initiator into UV curable resin to make functional structural materials that enable genetic post-printing surface-initiated modification. Taking advantage of 3D printing and surface-initiated ATRP, the feasible i3DP makes 3D printed complex architectures possible for nearly any desired surface modification for various applications, for example, even pouring water into a sieve was readily achieved. PMID:24002351

  7. A Novel Multiparametric Approach to 3D Quantitative MRI of the Brain

    PubMed Central

    Palma, Giuseppe; Tedeschi, Enrico; Borrelli, Pasquale; Cocozza, Sirio; Russo, Carmela; Liu, Saifeng; Ye, Yongquan; Comerci, Marco; Alfano, Bruno; Salvatore, Marco; Haacke, E. Mark; Mancini, Marcello

    2015-01-01

    Magnetic Resonance properties of tissues can be quantified in several respects: relaxation processes, density of imaged nuclei, magnetism of environmental molecules, etc. In this paper, we propose a new comprehensive approach to obtain 3D high resolution quantitative maps of arbitrary body districts, mainly focusing on the brain. The theory presented makes it possible to map longitudinal (R1), pure transverse (R2) and free induction decay (R2*) rates, along with proton density (PD) and magnetic susceptibility (χ), from a set of fast acquisition sequences in steady-state that are highly insensitive to flow phenomena. A novel denoising scheme is described and applied to the acquired datasets to enhance the signal to noise ratio of the derived maps and an information theory approach compensates for biases from radio frequency (RF) inhomogeneities, if no direct measure of the RF field is available. Finally, the results obtained on sample brain scans of healthy controls and multiple sclerosis patients are presented and discussed. PMID:26284778

  8. Validation of a Parametric Approach for 3d Fortification Modelling: Application to Scale Models

    NASA Astrophysics Data System (ADS)

    Jacquot, K.; Chevrier, C.; Halin, G.

    2013-02-01

    Parametric modelling approach applied to cultural heritage virtual representation is a field of research explored for years since it can address many limitations of digitising tools. For example, essential historical sources for fortification virtual reconstructions like plans-reliefs have several shortcomings when they are scanned. To overcome those problems, knowledge based-modelling can be used: knowledge models based on the analysis of theoretical literature of a specific domain such as bastioned fortification treatises can be the cornerstone of the creation of a parametric library of fortification components. Implemented in Grasshopper, these components are manually adjusted on the data available (i.e. 3D surveys of plans-reliefs or scanned maps). Most of the fortification area is now modelled and the question of accuracy assessment is raised. A specific method is used to evaluate the accuracy of the parametric components. The results of the assessment process will allow us to validate the parametric approach. The automation of the adjustment process can finally be planned. The virtual model of fortification is part of a larger project aimed at valorising and diffusing a very unique cultural heritage item: the collection of plans-reliefs. As such, knowledge models are precious assets when automation and semantic enhancements will be considered.

  9. An efficient approach to 3D single tree-crown delineation in LiDAR data

    NASA Astrophysics Data System (ADS)

    Mongus, Domen; Žalik, Borut

    2015-10-01

    This paper proposes a new method for 3D delineation of single tree-crowns in LiDAR data by exploiting the complementaries of treetop and tree trunk detections. A unified mathematical framework is provided based on the graph theory, allowing for all the segmentations to be achieved using marker-controlled watersheds. Treetops are defined by detecting concave neighbourhoods within the canopy height model using locally fitted surfaces. These serve as markers for watershed segmentation of the canopy layer where possible oversegmentation is reduced by merging the regions based on their heights, areas, and shapes. Additional tree crowns are delineated from mid- and under-storey layers based on tree trunk detection. A new approach for estimating the verticalities of the points' distributions is proposed for this purpose. The watershed segmentation is then applied on a density function within the voxel space, while boundaries of delineated trees from the canopy layer are used to prevent the overspreading of regions. The experiments show an approximately 6% increase in the efficiency of the proposed treetop definition based on locally fitted surfaces in comparison with the traditionally used local maxima of the smoothed canopy height model. In addition, 4% increase in the efficiency is achieved by the proposed tree trunk detection. Although the tree trunk detection alone is dependent on the data density, supplementing it with the treetop detection the proposed approach is efficient even when dealing with low density point-clouds.

  10. Personalized Medicine Approaches in Prostate Cancer Employing Patient Derived 3D Organoids and Humanized Mice

    PubMed Central

    Bartucci, Monica; Ferrari, Anna C.; Kim, Isaac Yi; Ploss, Alexander; Yarmush, Martin; Sabaawy, Hatem E.

    2016-01-01

    Prostate cancer (PCa) is the most common malignancy and the second most common cause of cancer death in Western men. Despite its prevalence, PCa has proven very difficult to propagate in vitro. PCa represents a complex organ-like multicellular structure maintained by the dynamic interaction of tumoral cells with parenchymal stroma, endothelial and immune cells, and components of the extracellular matrix (ECM). The lack of PCa models that recapitulate this intricate system has hampered progress toward understanding disease progression and lackluster therapeutic responses. Tissue slices, monolayer cultures and genetically engineered mouse models (GEMM) fail to mimic the complexities of the PCa microenvironment or reproduce the diverse mechanisms of therapy resistance. Moreover, patient derived xenografts (PDXs) are expensive, time consuming, difficult to establish for prostate cancer, lack immune cell-tumor regulation, and often tumors undergo selective engraftments. Here, we describe an interdisciplinary approach using primary PCa and tumor initiating cells (TICs), three-dimensional (3D) tissue engineering, genetic and morphometric profiling, and humanized mice to generate patient-derived organoids for examining personalized therapeutic responses in vitro and in mice co-engrafted with a human immune system (HIS), employing adaptive T-cell- and chimeric antigen receptor- (CAR) immunotherapy. The development of patient specific therapies targeting the vulnerabilities of cancer, when combined with antiproliferative and immunotherapy approaches could help to achieve the full transformative power of cancer precision medicine. PMID:27446916

  11. Personalized Medicine Approaches in Prostate Cancer Employing Patient Derived 3D Organoids and Humanized Mice.

    PubMed

    Bartucci, Monica; Ferrari, Anna C; Kim, Isaac Yi; Ploss, Alexander; Yarmush, Martin; Sabaawy, Hatem E

    2016-01-01

    Prostate cancer (PCa) is the most common malignancy and the second most common cause of cancer death in Western men. Despite its prevalence, PCa has proven very difficult to propagate in vitro. PCa represents a complex organ-like multicellular structure maintained by the dynamic interaction of tumoral cells with parenchymal stroma, endothelial and immune cells, and components of the extracellular matrix (ECM). The lack of PCa models that recapitulate this intricate system has hampered progress toward understanding disease progression and lackluster therapeutic responses. Tissue slices, monolayer cultures and genetically engineered mouse models (GEMM) fail to mimic the complexities of the PCa microenvironment or reproduce the diverse mechanisms of therapy resistance. Moreover, patient derived xenografts (PDXs) are expensive, time consuming, difficult to establish for prostate cancer, lack immune cell-tumor regulation, and often tumors undergo selective engraftments. Here, we describe an interdisciplinary approach using primary PCa and tumor initiating cells (TICs), three-dimensional (3D) tissue engineering, genetic and morphometric profiling, and humanized mice to generate patient-derived organoids for examining personalized therapeutic responses in vitro and in mice co-engrafted with a human immune system (HIS), employing adaptive T-cell- and chimeric antigen receptor- (CAR) immunotherapy. The development of patient specific therapies targeting the vulnerabilities of cancer, when combined with antiproliferative and immunotherapy approaches could help to achieve the full transformative power of cancer precision medicine. PMID:27446916

  12. Embedding SAS approach into conjugate gradient algorithms for asymmetric 3D elasticity problems

    SciTech Connect

    Chen, Hsin-Chu; Warsi, N.A.; Sameh, A.

    1996-12-31

    In this paper, we present two strategies to embed the SAS (symmetric-and-antisymmetric) scheme into conjugate gradient (CG) algorithms to make solving 3D elasticity problems, with or without global reflexive symmetry, more efficient. The SAS approach is physically a domain decomposition scheme that takes advantage of reflexive symmetry of discretized physical problems, and algebraically a matrix transformation method that exploits special reflexivity properties of the matrix resulting from discretization. In addition to offering large-grain parallelism, which is valuable in a multiprocessing environment, the SAS scheme also has the potential for reducing arithmetic operations in the numerical solution of a reasonably wide class of scientific and engineering problems. This approach can be applied directly to problems that have global reflexive symmetry, yielding smaller and independent subproblems to solve, or indirectly to problems with partial symmetry, resulting in loosely coupled subproblems. The decomposition is achieved by separating the reflexive subspace from the antireflexive one, possessed by a special class of matrices A, A {element_of} C{sup n x n} that satisfy the relation A = PAP where P is a reflection matrix (symmetric signed permutation matrix).

  13. The modular approach enables a fully ab initio simulation of the contacts between 3D and 2D materials.

    PubMed

    Fediai, Artem; Ryndyk, Dmitry A; Cuniberti, Gianaurelio

    2016-10-01

    Up to now, the electrical properties of the contacts between 3D metals and 2D materials have never been computed at a fully ab initio level due to the huge number of atomic orbitals involved in a current path from an electrode to a pristine 2D material. As a result, there are still numerous open questions and controversial theories on the electrical properties of systems with 3D/2D interfaces-for example, the current path and the contact length scalability. Our work provides a first-principles solution to this long-standing problem with the use of the modular approach, a method which rigorously combines a Green function formalism with the density functional theory (DFT) for this particular contact type. The modular approach is a general approach valid for any 3D/2D contact. As an example, we apply it to the most investigated among 3D/2D contacts-metal/graphene contacts-and show its abilities and consistency by comparison with existing experimental data. As it is applicable to any 3D/2D interface, the modular approach allows the engineering of 3D/2D contacts with the pre-defined electrical properties. PMID:27502169

  14. A modular cross-platform GPU-based approach for flexible 3D video playback

    NASA Astrophysics Data System (ADS)

    Olsson, Roger; Andersson, Håkan; Sjöström, Mårten

    2011-03-01

    Different compression formats for stereo and multiview based 3D video is being standardized and software players capable of decoding and presenting these formats onto different display types is a vital part in the commercialization and evolution of 3D video. However, the number of publicly available software video players capable of decoding and playing multiview 3D video is still quite limited. This paper describes the design and implementation of a GPU-based real-time 3D video playback solution, built on top of cross-platform, open source libraries for video decoding and hardware accelerated graphics. A software architecture is presented that efficiently process and presents high definition 3D video in real-time and in a flexible manner support both current 3D video formats and emerging standards. Moreover, a set of bottlenecks in the processing of 3D video content in a GPU-based real-time 3D video playback solution is identified and discussed.

  15. LayTracks3D: A new approach for meshing general solids using medial axis transform

    SciTech Connect

    Quadros, William Roshan

    2015-08-22

    This study presents an extension of the all-quad meshing algorithm called LayTracks to generate high quality hex-dominant meshes of general solids. LayTracks3D uses the mapping between the Medial Axis (MA) and the boundary of the 3D domain to decompose complex 3D domains into simpler domains called Tracks. Tracks in 3D have no branches and are symmetric, non-intersecting, orthogonal to the boundary, and the shortest path from the MA to the boundary. These properties of tracks result in desired meshes with near cube shape elements at the boundary, structured mesh along the boundary normal with any irregular nodes restricted to the MA, and sharp boundary feature preservation. The algorithm has been tested on a few industrial CAD models and hex-dominant meshes are shown in the Results section. Work is underway to extend LayTracks3D to generate all-hex meshes.

  16. An edge-from-focus approach to 3D inspection and metrology

    NASA Astrophysics Data System (ADS)

    Deng, Fuqin; Chen, Jia; Liu, Jianyang; Zhang, Zhijun; Deng, Jiangwen; Fung, Kenneth S. M.; Lam, Edmund Y.

    2015-02-01

    We propose an edge-based depth-from-focus technique for high-precision non-contact industrial inspection and metrology applications. In our system, an objective lens with a large numerical aperture is chosen to resolve the edge details of the measured object. By motorizing this imaging system, we capture the high-resolution edges within every narrow depth of field. We can therefore extend the measured range and keep a high resolution at the same time. Yet, on the surfaces with a large depth variation, a significant amount of data around each measured point are out of focus within the captured images. Then, it is difficult to extract the valuable information from these out-of-focus data due to the depth-variant blur. Moreover, these data impede the extraction of continuous contours for the measurement objects in high-level machine vision applications. The proposed approach however makes use of the out-of-focus data to synthesize a depth-invariant smoothed image, and then robustly locates the positions of high contrast edges based on non-maximum suppression and hysteresis thresholding. Furthermore, by focus analysis of both the in-focus and the out-of-focus data, we reconstruct the high-precision 3D edges for metrology applications.

  17. 3D resolution tests of two-plane wave approach using synthetic seismograms

    NASA Astrophysics Data System (ADS)

    Ceylan, S.; Larmat, C. S.; Sandvol, E. A.

    2012-12-01

    Two-plane wave tomography (TPWT) is becoming a standard approach to obtain fundamental mode Rayleigh wave phase velocities for a variety of tectonic settings. A recent study by Ceylan et al. (2012) has applied this method to eastern Tibet, using data from INDEPTH-IV and Namche-Barwa seismic experiments. The TPWT assumes that distortion of wavefronts at each station can be expressed as the sum of two plane waves. However, there is currently no robust or complete resolution test for TPWT, to address its limitations such as wavefront healing. In this study, we test the capabilities of TPWT and resolution of INDEPTH-IV seismic experiment, by performing 3D resolution tests using synthetic seismograms. Utilizing SPECFEM3D software, we compute synthetic data sets resolving periods down to ~30 s. We implement a checkerboard upper mantle (for depths between 50 and 650 km) with variable cell sizes, superimposed to PREM as the background model. We then calculate fundamental mode surface wave phase velocities using TPWT for periods between 33-143 seconds, using synthetic seismograms computed from our three dimensional hypothetical model. Assuming a constant Poisson's ratio, we use partial derivatives from Saito (1988) to invert for shear wave velocities. We show that the combination of TPWT and Saito (1988) methods is capable of retrieving anomalies down to depths of ~200 km for Rayleigh waves. Below these depths, we observe evidence of both lateral and vertical smearing. We also find that the traditional method for estimating the resolution of TPWT consistently overestimates phase velocity resolutions. Love waves exhibit adequate resolution down to depths of ~100 km. At depths greater than 100 km, smearing is more evident in SH wave results than those of SV waves. Increased smearing of SH waves is most probably due to propagation characteristics and shallower sensitivity of Love waves. Our results imply that TPWT can be applied to Love waves, making future investigations of

  18. A 2D range Hausdorff approach for 3D face recognition.

    SciTech Connect

    Koch, Mark William; Russ, Trina Denise; Little, Charles Quentin

    2005-04-01

    This paper presents a 3D facial recognition algorithm based on the Hausdorff distance metric. The standard 3D formulation of the Hausdorff matching algorithm has been modified to operate on a 2D range image, enabling a reduction in computation from O(N2) to O(N) without large storage requirements. The Hausdorff distance is known for its robustness to data outliers and inconsistent data between two data sets, making it a suitable choice for dealing with the inherent problems in many 3D datasets due to sensor noise and object self-occlusion. For optimal performance, the algorithm assumes a good initial alignment between probe and template datasets. However, to minimize the error between two faces, the alignment can be iteratively refined. Results from the algorithm are presented using 3D face images from the Face Recognition Grand Challenge database version 1.0.

  19. A 2D range Hausdorff approach to 3D facial recognition.

    SciTech Connect

    Koch, Mark William; Russ, Trina Denise; Little, Charles Quentin

    2004-11-01

    This paper presents a 3D facial recognition algorithm based on the Hausdorff distance metric. The standard 3D formulation of the Hausdorff matching algorithm has been modified to operate on a 2D range image, enabling a reduction in computation from O(N2) to O(N) without large storage requirements. The Hausdorff distance is known for its robustness to data outliers and inconsistent data between two data sets, making it a suitable choice for dealing with the inherent problems in many 3D datasets due to sensor noise and object self-occlusion. For optimal performance, the algorithm assumes a good initial alignment between probe and template datasets. However, to minimize the error between two faces, the alignment can be iteratively refined. Results from the algorithm are presented using 3D face images from the Face Recognition Grand Challenge database version 1.0.

  20. Optimal Surface Segmentation in Volumetric Images—A Graph-Theoretic Approach

    PubMed Central

    Li, Kang; Wu, Xiaodong; Chen, Danny Z.; Sonka, Milan

    2008-01-01

    Efficient segmentation of globally optimal surfaces representing object boundaries in volumetric data sets is important and challenging in many medical image analysis applications. We have developed an optimal surface detection method capable of simultaneously detecting multiple interacting surfaces, in which the optimality is controlled by the cost functions designed for individual surfaces and by several geometric constraints defining the surface smoothness and interrelations. The method solves the surface segmentation problem by transforming it into computing a minimum s-t cut in a derived arc-weighted directed graph. The proposed algorithm has a low-order polynomial time complexity and is computationally efficient. It has been extensively validated on more than 300 computer-synthetic volumetric images, 72 CT-scanned data sets of different-sized plexiglas tubes, and tens of medical images spanning various imaging modalities. In all cases, the approach yielded highly accurate results. Our approach can be readily extended to higher-dimensional image segmentation. PMID:16402624

  1. Automatic left-atrial segmentation from cardiac 3D ultrasound: a dual-chamber model-based approach

    NASA Astrophysics Data System (ADS)

    Almeida, Nuno; Sarvari, Sebastian I.; Orderud, Fredrik; Gérard, Olivier; D'hooge, Jan; Samset, Eigil

    2016-04-01

    In this paper, we present an automatic solution for segmentation and quantification of the left atrium (LA) from 3D cardiac ultrasound. A model-based framework is applied, making use of (deformable) active surfaces to model the endocardial surfaces of cardiac chambers, allowing incorporation of a priori anatomical information in a simple fashion. A dual-chamber model (LA and left ventricle) is used to detect and track the atrio-ventricular (AV) plane, without any user input. Both chambers are represented by parametric surfaces and a Kalman filter is used to fit the model to the position of the endocardial walls detected in the image, providing accurate detection and tracking during the whole cardiac cycle. This framework was tested in 20 transthoracic cardiac ultrasound volumetric recordings of healthy volunteers, and evaluated using manual traces of a clinical expert as a reference. The 3D meshes obtained with the automatic method were close to the reference contours at all cardiac phases (mean distance of 0.03+/-0.6 mm). The AV plane was detected with an accuracy of -0.6+/-1.0 mm. The LA volumes assessed automatically were also in agreement with the reference (mean +/-1.96 SD): 0.4+/-5.3 ml, 2.1+/-12.6 ml, and 1.5+/-7.8 ml at end-diastolic, end-systolic and pre-atrial-contraction frames, respectively. This study shows that the proposed method can be used for automatic volumetric assessment of the LA, considerably reducing the analysis time and effort when compared to manual analysis.

  2. Machine learning and synthetic aperture refocusing approach for more accurate masking of fish bodies in 3D PIV data

    NASA Astrophysics Data System (ADS)

    Ford, Logan; Bajpayee, Abhishek; Techet, Alexandra

    2015-11-01

    3D particle image velocimetry (PIV) is becoming a popular technique to study biological flows. PIV images that contain fish or other animals around which flow is being studied, need to be appropriately masked in order to remove the animal body from the 3D reconstructed volumes prior to calculating particle displacement vectors. Presented here is a machine learning and synthetic aperture (SA) refocusing based approach for more accurate masking of fish from reconstructed intensity fields for 3D PIV purposes. Using prior knowledge about the 3D shape and appearance of the fish along with SA refocused images at arbitrarily oriented focal planes, the location and orientation of a fish in a reconstructed volume can be accurately determined. Once the location and orientation of a fish in a volume is determined, it can be masked out.

  3. 3d-4f magnetic interaction with density functional theory plus u approach: local Coulomb correlation and exchange pathways.

    PubMed

    Zhang, Yachao; Yang, Yang; Jiang, Hong

    2013-12-12

    The 3d-4f exchange interaction plays an important role in many lanthanide based molecular magnetic materials such as single-molecule magnets and magnetic refrigerants. In this work, we study the 3d-4f magnetic exchange interactions in a series of Cu(II)-Gd(III) (3d(9)-4f(7)) dinuclear complexes based on the numerical atomic basis-norm-conserving pseudopotential method and density functional theory plus the Hubbard U correction approach (DFT+U). We obtain improved description of the 4f electrons by including the semicore 5s5p states in the valence part of the Gd-pseudopotential. The Hubbard U correction is employed to treat the strongly correlated Cu-3d and Gd-4f electrons, which significantly improve the agreement of the predicted exchange constants, J, with experiment, indicating the importance of accurate description of the local Coulomb correlation. The high efficiency of the DFT+U approach enables us to perform calculations with molecular crystals, which in general improve the agreement between theory and experiment, achieving a mean absolute error smaller than 2 cm(-1). In addition, through analyzing the physical effects of U, we identify two magnetic exchange pathways. One is ferromagnetic and involves an interaction between the Cu-3d, O-2p (bridge ligand), and the majority-spin Gd-5d orbitals. The other one is antiferromagnetic and involves Cu-3d, O-2p, and the empty minority-spin Gd-4f orbitals, which is suppressed by the planar Cu-O-O-Gd structure. This study demonstrates the accuracy of the DFT+U method for evaluating the 3d-4f exchange interactions, provides a better understanding of the exchange mechanism in the Cu(II)-Gd(III) complexes, and paves the way for exploiting the magnetic properties of the 3d-4f compounds containing lanthanides other than Gd. PMID:24274078

  4. Tracking of cracks in bridges using GPR: a 3D approach

    NASA Astrophysics Data System (ADS)

    Benedetto, A.

    2012-04-01

    Corrosion associated with reinforcing bars is the most significant contributor to bridge deficiencies. The corrosion is usually caused by moisture and chloride ion exposure. In particular, corrosion products FeO, Fe2O3, Fe3O4 and other oxides along reinforcement bars. The reinforcing bars are attacked by corrosion and yield expansive corrosion products. These oxidation products occupy a larger volume than the original intact steel and internal expansive stresses lead to cracking and debonding. There are some conventional inspection methods for detection of reinforcing bar corrosion but they can be invasive and destructive, often laborious, lane closures is required and it is difficult or unreliable any quantification of corrosion. For these reasons, bridge engineers are always more preferring to use the Ground Penetrating Radar (GPR) technique. In this work a novel numerical approach for three dimensional tracking and mapping of cracks in the bridge is proposed. The work starts from some interesting results based on the use of the 3D imaging technique in order to improve the potentiality of GPR to detect voids, cracks or buried object. The numerical approach has been tested on data acquired on some bridges using a pulse GPR system specifically designed for bridge deck and pavement inspection that is called RIS Hi Bright. The equipment integrates two arrays of Ultra Wide Band ground coupled antennas, having a main working frequency of 2 GHz. The two arrays within the RIS Hi Bright are using antennas arranged with different polarization. One array includes sensors with parallel polarization with respect to the scanning direction (VV array), the other has sensors in orthogonal polarization (HH array). Overall the system collects 16 profiles within a single scan (8 HH + 8 VV). The cracks, associated often to moisture increasing and higher values of the dielectric constant, produce a not negligible increasing of the signal amplitude. Following this, the algorithm

  5. TOBAGO — a semi-automated approach for the generation of 3-D building models

    NASA Astrophysics Data System (ADS)

    Gruen, Armin

    3-D city models are in increasing demand for a great number of applications. Photogrammetry is a relevant technology that can provide an abundance of geometric, topologic and semantic information concerning these models. The pressure to generate a large amount of data with high degree of accuracy and completeness poses a great challenge to phtogrammetry. The development of automated and semi-automated methods for the generation of those data sets is therefore a key issue in photogrammetric research. We present in this article a strategy and methodology for an efficient generation of even fairly complex building models. Within this concept we request the operator to measure the house roofs from a stereomodel in form of an unstructured point cloud. According to our experience this can be done very quickly. Even a non-experienced operator can measure several hundred roofs or roof units per day. In a second step we fit generic building models fully automatically to these point clouds. The structure information is inherently included in these building models. In such a way geometric, topologic and even semantic data can be handed over to a CAD-system, in our case AutoCad, for further visualization and manipulation. The structuring is achieved in three steps. In a first step a classifier is initiated which recognizes the class of houses a particular roof point cloud belongs to. This recognition step is primarily based on the analysis of the number of ridge points. In the second and third steps the concrete topological relations between roof points are investigated and generic building models are fitted to the point clouds. Based on the technique of constraint-based reasoning two geometrical parsers are solving this problem. We have tested the methodology under a variety of different conditions in several pilot projects. The results will indicate the good performance of our approach. In addition we will demonstrate how the results can be used for visualization (texture

  6. [A new approach to the tricuspid valve in Ebstein's anomaly by real time 3D echocardiography].

    PubMed

    Taktak, A; Acar, P; Dulac, Y; Abadir, S; Chilon, T; Roux, D; Glock, Y; Fournial, G

    2005-05-01

    Ebstein's anomaly affects the tricuspid valve with a large range of anatomical forms. Successful tricuspid valvuloplasty depends mainly on the ability to mobilise the leaflets. Evaluation of the leaflet surface is difficult with 2D echocardiography whereas 3D echocardiography provides intracardiac views of the valve. The authors used this method in 10 patients with 3 modes of imaging: biplane, real time and total volume. The study population (age: 1 day to 30 years) included: 1 prenatal diagnosis, 1 neonate with refractory cyanosis, 5 patients with mild tricuspid regurgitation, 3 patients with severe tricuspid regurgitation, 2 of whom underwent valvuloplasty. 3D echocardiography was disappointing in the foetus and neonate because of poor spatial resolution. The ventricular view of the tricuspid valve in older children and adults allowed analysis of tricuspid leaflet coaptation and of the mechanism of regurgitation. The commissures and leaflet surfaces were assessed. The results of surgical valvuloplasty could be evaluated by 3D echocardiography. 3D echocardiography is now transthoracic and a real time investigation. Technical advances are required before it comes into routine usage: a more manoeuvrable matricial probe (integrating pulsed and continuous wave Doppler) and larger volume real time 3D imaging with better resolution. Its role in the assessment of Ebstein's anomaly should be evaluated in a larger series of patients. PMID:15966604

  7. Evolution, Interaction, and Intrinsic Properties of Dislocations in Intermetallics: Anisotropic 3D Dislocation Dynamics Approach

    SciTech Connect

    Qian Chen

    2008-08-18

    The generation, motion, and interaction of dislocations play key roles during the plastic deformation process of crystalline solids. 3D Dislocation Dynamics has been employed as a mesoscale simulation algorithm to investigate the collective and cooperative behavior of dislocations. Most current research on 3D Dislocation Dynamics is based on the solutions available in the framework of classical isotropic elasticity. However, due to some degree of elastic anisotropy in almost all crystalline solids, it is very necessary to extend 3D Dislocation Dynamics into anisotropic elasticity. In this study, first, the details of efficient and accurate incorporation of the fully anisotropic elasticity into 3D discrete Dislocation Dynamics by numerically evaluating the derivatives of Green's functions are described. Then the intrinsic properties of perfect dislocations, including their stability, their core properties and disassociation characteristics, in newly discovered rare earth-based intermetallics and in conventional intermetallics are investigated, within the framework of fully anisotropic elasticity supplemented with the atomistic information obtained from the ab initio calculations. Moreover, the evolution and interaction of dislocations in these intermetallics as well as the role of solute segregation are presented by utilizing fully anisotropic 3D dislocation dynamics. The results from this work clearly indicate the role and the importance of elastic anisotropy on the evolution of dislocation microstructures, the overall ductility and the hardening behavior in these systems.

  8. LayTracks3D: A new approach for meshing general solids using medial axis transform

    DOE PAGESBeta

    Quadros, William Roshan

    2015-08-22

    This study presents an extension of the all-quad meshing algorithm called LayTracks to generate high quality hex-dominant meshes of general solids. LayTracks3D uses the mapping between the Medial Axis (MA) and the boundary of the 3D domain to decompose complex 3D domains into simpler domains called Tracks. Tracks in 3D have no branches and are symmetric, non-intersecting, orthogonal to the boundary, and the shortest path from the MA to the boundary. These properties of tracks result in desired meshes with near cube shape elements at the boundary, structured mesh along the boundary normal with any irregular nodes restricted to themore » MA, and sharp boundary feature preservation. The algorithm has been tested on a few industrial CAD models and hex-dominant meshes are shown in the Results section. Work is underway to extend LayTracks3D to generate all-hex meshes.« less

  9. Reliable Gait Recognition Using 3D Reconstructions and Random Forests - An Anthropometric Approach.

    PubMed

    Sandau, Martin; Heimbürger, Rikke V; Jensen, Karl E; Moeslund, Thomas B; Aanaes, Henrik; Alkjaer, Tine; Simonsen, Erik B

    2016-05-01

    Photogrammetric measurements of bodily dimensions and analysis of gait patterns in CCTV are important tools in forensic investigations but accurate extraction of the measurements are challenging. This study tested whether manual annotation of the joint centers on 3D reconstructions could provide reliable recognition. Sixteen participants performed normal walking where 3D reconstructions were obtained continually. Segment lengths and kinematics from the extremities were manually extracted by eight expert observers. The results showed that all the participants were recognized, assuming the same expert annotated the data. Recognition based on data annotated by different experts was less reliable achieving 72.6% correct recognitions as some parameters were heavily affected by interobserver variability. This study verified that 3D reconstructions are feasible for forensic gait analysis as an improved alternative to conventional CCTV. However, further studies are needed to account for the use of different clothing, field conditions, etc. PMID:27122399

  10. Fatigue life estimation for different notched specimens based on the volumetric approach

    NASA Astrophysics Data System (ADS)

    Zehsaz, M.; Hassanifard, S.; Esmaeili, F.

    2010-06-01

    In this paper, the effects of notch radius for different notched specimens has been studied on the values of stress concentration factor, notch strength reduction factor, and fatigue life duration of the specimens. The material which has been selected for this investigation is Al 2024T3 . Volumetric approach has been applied to obtain the values of notch strength reduction factor and results have been compared with those obtained from the Neuber and Peterson methods. Load controlled fatigue tests of mentioned specimens have been conducted on the 250kN servo-hydraulic Zwick/Amsler fatigue testing machine with the frequency of 10Hz. The fatigue lives of the specimens have also been predicted based on the available smooth S-N curve of Al2024-T3 and also the amounts of notch strength reduction factor which have been obtained from volumetric, Neuber and Peterson methods. The values of stress and strain around the notch roots are required to predict the fatigue life of notched specimens, so Ansys finite element code has been used and non-linear analyses have been performed to obtain the stress and strain distributions around the notches. The plastic deformations of the material have been simulated using multi-linear kinematic hardening and cyclic stress-strain relation. The work here shows that the volumetric approach does a very good job for predicting the fatigue life of the notched specimens.

  11. Heads-up 3D Microscopy: An Ergonomic and Educational Approach to Microsurgery.

    PubMed

    Mendez, Bernardino M; Chiodo, Michael V; Vandevender, Darl; Patel, Parit A

    2016-05-01

    Traditional microsurgery can lead surgeons to use postures that cause musculoskeletal fatigue, leaving them more prone to work-related injuries. A new technology from TrueVision transmits the microscopic image onto a 3-dimensional (3D) monitor, allowing surgeons to operate while sitting/standing in a heads-up position. The purpose of this study was to evaluate the feasibility of performing heads-up 3D microscopy as a more ergonomic alternative to traditional microsurgery. A feasibility study was conducted comparing heads-up 3D microscopy and traditional microscopy by performing femoral artery anastomoses on 8 Sprague-Dawley rats. Operative times and patency rates for each technology were compared. The 8 microsurgeons completed a questionnaire comparing image quality, comfort, technical feasibility, and educational value of the 2 technologies. Rat femoral artery anastomoses were successfully carried out by all 8 microsurgeons with each technology. There was no significant difference in anastomosis time between heads-up 3D and traditional microscopy (average times, 34.5 and 33.8 minutes, respectively; P = 0.66). Heads-up 3D microscopy was rated superior in neck and back comfort by 75% of participants. Image resolution, field of view, and technical feasibility were found to be superior or equivalent in 75% of participants, whereas 63% evaluated depth perception to be superior or equivalent. Heads-up 3D microscopy is a new technology that improves comfort for the microsurgeon without compromising image quality or technical feasibility. Its use has become prevalent in the field of ophthalmology and may also have utility in plastic and reconstructive surgery. PMID:27579241

  12. Heads-up 3D Microscopy: An Ergonomic and Educational Approach to Microsurgery

    PubMed Central

    Mendez, Bernardino M.; Chiodo, Michael V.; Vandevender, Darl

    2016-01-01

    Summary: Traditional microsurgery can lead surgeons to use postures that cause musculoskeletal fatigue, leaving them more prone to work-related injuries. A new technology from TrueVision transmits the microscopic image onto a 3-dimensional (3D) monitor, allowing surgeons to operate while sitting/standing in a heads-up position. The purpose of this study was to evaluate the feasibility of performing heads-up 3D microscopy as a more ergonomic alternative to traditional microsurgery. A feasibility study was conducted comparing heads-up 3D microscopy and traditional microscopy by performing femoral artery anastomoses on 8 Sprague-Dawley rats. Operative times and patency rates for each technology were compared. The 8 microsurgeons completed a questionnaire comparing image quality, comfort, technical feasibility, and educational value of the 2 technologies. Rat femoral artery anastomoses were successfully carried out by all 8 microsurgeons with each technology. There was no significant difference in anastomosis time between heads-up 3D and traditional microscopy (average times, 34.5 and 33.8 minutes, respectively; P = 0.66). Heads-up 3D microscopy was rated superior in neck and back comfort by 75% of participants. Image resolution, field of view, and technical feasibility were found to be superior or equivalent in 75% of participants, whereas 63% evaluated depth perception to be superior or equivalent. Heads-up 3D microscopy is a new technology that improves comfort for the microsurgeon without compromising image quality or technical feasibility. Its use has become prevalent in the field of ophthalmology and may also have utility in plastic and reconstructive surgery. PMID:27579241

  13. Mechanical Modelling of Pultrusion Process: 2D and 3D Numerical Approaches

    NASA Astrophysics Data System (ADS)

    Baran, Ismet; Hattel, Jesper H.; Akkerman, Remko; Tutum, Cem C.

    2015-02-01

    The process induced variations such as residual stresses and distortions are a critical issue in pultrusion, since they affect the structural behavior as well as the mechanical properties and geometrical precision of the final product. In order to capture and investigate these variations, a mechanical analysis should be performed. In the present work, the two dimensional (2D) quasi-static plane strain mechanical model for the pultrusion of a thick square profile developed by the authors is further improved using generalized plane strain elements. In addition to that, a more advanced 3D thermo-chemical-mechanical analysis is carried out using 3D quadratic elements which is a novel application for the numerical modelling of the pultrusion process. It is found that the 2D mechanical models give relatively reasonable and accurate stress and displacement evolutions in the transverse direction as compared to the 3D model. Moreover, the generalized plane strain model predicts the longitudinal process induced stresses more similar to the ones calculated in the 3D model as compared with the plane strain model.

  14. An improved parallel SPH approach to solve 3D transient generalized Newtonian free surface flows

    NASA Astrophysics Data System (ADS)

    Ren, Jinlian; Jiang, Tao; Lu, Weigang; Li, Gang

    2016-08-01

    In this paper, a corrected parallel smoothed particle hydrodynamics (C-SPH) method is proposed to simulate the 3D generalized Newtonian free surface flows with low Reynolds number, especially the 3D viscous jets buckling problems are investigated. The proposed C-SPH method is achieved by coupling an improved SPH method based on the incompressible condition with the traditional SPH (TSPH), that is, the improved SPH with diffusive term and first-order Kernel gradient correction scheme is used in the interior of the fluid domain, and the TSPH is used near the free surface. Thus the C-SPH method possesses the advantages of two methods. Meanwhile, an effective and convenient boundary treatment is presented to deal with 3D multiple-boundary problem, and the MPI parallelization technique with a dynamic cells neighbor particle searching method is considered to improve the computational efficiency. The validity and the merits of the C-SPH are first verified by solving several benchmarks and compared with other results. Then the viscous jet folding/coiling based on the Cross model is simulated by the C-SPH method and compared with other experimental or numerical results. Specially, the influences of macroscopic parameters on the flow are discussed. All the numerical results agree well with available data, and show that the C-SPH method has higher accuracy and better stability for solving 3D moving free surface flows over other particle methods.

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

    PubMed

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

    2015-09-01

    In the single particle reconstruction, the initial 3D structure often suffers from the limited angular sampling artifact. Selecting 2D class averages of particle images generally improves the accuracy and efficiency of the reference-free 3D angle estimation, but causes an insufficient angular sampling to fill the information of the target object in the 3D frequency space. Similarly, the initial 3D structure by the random-conical tilt reconstruction has the well-known "missing cone" artifact. Here, we attempted to solve the limited angular sampling problem by sequentially applying maximum a posteriori estimate with expectation maximization algorithm (sMAP-EM). Using both simulated and experimental cryo-electron microscope images, the sMAP-EM was compared to the direct Fourier method on the basis of reconstruction error and resolution. To establish selection criteria of the final regularization weight for the sMAP-EM, the effects of noise level and sampling sparseness on the reconstructions were examined with evenly distributed sampling simulations. The frequency information filled in the missing cone of the conical tilt sampling simulations was assessed by developing new quantitative measurements. All the results of visual and numerical evaluations showed the sMAP-EM performed better than the direct Fourier method, regardless of the sampling method, noise level, and sampling sparseness. Furthermore, the frequency domain analysis demonstrated that the sMAP-EM can fill the meaningful information in the unmeasured angular space without detailed a priori knowledge of the objects. The current research demonstrated that the sMAP-EM has a high potential to facilitate the determination of 3D protein structures at near atomic-resolution. PMID:26193484

  16. Designing Spatial Visualisation Tasks for Middle School Students with a 3D Modelling Software: An Instrumental Approach

    ERIC Educational Resources Information Center

    Turgut, Melih; Uygan, Candas

    2015-01-01

    In this work, certain task designs to enhance middle school students' spatial visualisation ability, in the context of an instrumental approach, have been developed. 3D modelling software, SketchUp®, was used. In the design process, software tools were focused on and, thereafter, the aim was to interpret the instrumental genesis and spatial…

  17. Bound state solution of Dirac equation for 3D harmonics oscillator plus trigonometric scarf noncentral potential using SUSY QM approach

    SciTech Connect

    Cari, C. Suparmi, A.

    2014-09-30

    Dirac equation of 3D harmonics oscillator plus trigonometric Scarf non-central potential for spin symmetric case is solved using supersymmetric quantum mechanics approach. The Dirac equation for exact spin symmetry reduces to Schrodinger like equation. The relativistic energy and wave function for spin symmetric case are simply obtained using SUSY quantum mechanics method and idea of shape invariance.

  18. A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.

    PubMed

    Fletcher, P Thomas; Tao, Ran; Jeong, Won-Ki; Whitaker, Ross T

    2007-01-01

    In this paper we present a volumetric approach for quantitatively studying white matter connectivity from diffusion tensor magnetic resonance imaging (DT-MRI). The proposed method is based on a minimization of path cost between two regions, defined as the integral of local costs that are derived from the full tensor data along the path. We solve the minimal path problem using a Hamilton-Jacobi formulation of the problem and a new, fast iterative method that computes updates on the propagating front of the cost function at every point. The solutions for the fronts emanating from the two initial regions are combined, giving a voxel-wise connectivity measurement of the optimal paths between the regions that pass through those voxels. The resulting high-connectivity voxels provide a volumetric representation of the white matter pathway between the terminal regions. We quantify the tensor data along these pathways using nonparametric regression of the tensors and of derived measures as a function of path length. In this way we can obtain volumetric measures on white-matter tracts between regions without any explicit integration of tracts. We demonstrate the proposed method on several fiber tracts from DT-MRI data of the normal human brain. PMID:17633712

  19. Multiple 3D reference system analyses for Phobos grooves, a novel approach

    NASA Astrophysics Data System (ADS)

    Simioni, Emanuele; Pajola, Maurizio; Massironi, Matteo; Cremonese, Gabriele

    2015-04-01

    Grooves analysis has represented in the last decade a robust method for geomorphological study of small bodies, as is the case for asteroids 951 Gaspra (Veverka et al., 1994), 243 Ida (Belton et al., 1994), 433 Eros (Thomas et al., (2002), Buczkowski et al., 2008), 21 Lutetia (Massironi et al., 2011, *Besse et al., 2014*) and 4 Vesta (Buczkowski et al., 2*012). Hence, such source of information can be deeper used for a novel approach presented on Phobos with the aim of providing more hints on its harshly debated origin. Stereo-plots and cyclographs represent two methods, unified under the name of stereographic projections, commonly used to describe the statistic of the orientations (dip-angle and dip-direction) of different planes with respect to cardinal points and a reference horizontal plane (Bucher, 1944; Phillips, 1954; Ragan, 1985). However this reference system is ambiguous for any applications on small irregular bodies such as asteroids or comets since it does not permit to highlight systems of parallel anisotropies and to have an idea of their distribution with respect to a given surface feature (for example an impact crater). In this work we show a novel approach for stereographic projections focusing to a multi-reference system. The multi-reference system can be centered on a specific surface feature such as a crater and can alternatively use an absolute reference plane containing the center of figure of the body (to retrieve systems of parallel anisotropies) or a relative horizontal plane (to understand the distribution of the anisotropies with respect to the central feature). In this way we are able to well define the distribution of the grooves expected to be originated from a impact cratering event in a small body. Following this methodology, we have extracted 352 3D fracture planes from the attitudes of the grooves over the surface topography of Phobos and, for each plane, the local surface versor has been defined. Consequently, stereo-plots on

  20. Using Pressure and Volumetric Approaches to Estimate CO2 Storage Capacity in Deep Saline Aquifers

    DOE PAGESBeta

    Thibeau, Sylvain; Bachu, Stefan; Birkholzer, Jens; Holloway, Sam; Neele, Filip; Zhou, Quanlin

    2014-12-31

    Various approaches are used to evaluate the capacity of saline aquifers to store CO2, resulting in a wide range of capacity estimates for a given aquifer. The two approaches most used are the volumetric “open aquifer” and “closed aquifer” approaches. We present four full-scale aquifer cases, where CO2 storage capacity is evaluated both volumetrically (with “open” and/or “closed” approaches) and through flow modeling. These examples show that the “open aquifer” CO2 storage capacity estimation can strongly exceed the cumulative CO2 injection from the flow model, whereas the “closed aquifer” estimates are a closer approximation to the flow-model derived capacity. Anmore » analogy to oil recovery mechanisms is presented, where the primary oil recovery mechanism is compared to CO2 aquifer storage without producing formation water; and the secondary oil recovery mechanism (water flooding) is compared to CO2 aquifer storage performed simultaneously with extraction of water for pressure maintenance. This analogy supports the finding that the “closed aquifer” approach produces a better estimate of CO2 storage without water extraction, and highlights the need for any CO2 storage estimate to specify whether it is intended to represent CO2 storage capacity with or without water extraction.« less

  1. Using Pressure and Volumetric Approaches to Estimate CO2 Storage Capacity in Deep Saline Aquifers

    SciTech Connect

    Thibeau, Sylvain; Bachu, Stefan; Birkholzer, Jens; Holloway, Sam; Neele, Filip; Zhou, Quanlin

    2014-12-31

    Various approaches are used to evaluate the capacity of saline aquifers to store CO2, resulting in a wide range of capacity estimates for a given aquifer. The two approaches most used are the volumetric “open aquifer” and “closed aquifer” approaches. We present four full-scale aquifer cases, where CO2 storage capacity is evaluated both volumetrically (with “open” and/or “closed” approaches) and through flow modeling. These examples show that the “open aquifer” CO2 storage capacity estimation can strongly exceed the cumulative CO2 injection from the flow model, whereas the “closed aquifer” estimates are a closer approximation to the flow-model derived capacity. An analogy to oil recovery mechanisms is presented, where the primary oil recovery mechanism is compared to CO2 aquifer storage without producing formation water; and the secondary oil recovery mechanism (water flooding) is compared to CO2 aquifer storage performed simultaneously with extraction of water for pressure maintenance. This analogy supports the finding that the “closed aquifer” approach produces a better estimate of CO2 storage without water extraction, and highlights the need for any CO2 storage estimate to specify whether it is intended to represent CO2 storage capacity with or without water extraction.

  2. An approach to quantifying 3D responses of cells to extreme strain

    PubMed Central

    Li, Yuhui; Huang, Guoyou; Li, Moxiao; Wang, Lin; Elson, Elliot L.; Jian Lu, Tian; Genin, Guy M.; Xu, Feng

    2016-01-01

    The tissues of hollow organs can routinely stretch up to 2.5 times their length. Although significant pathology can arise if relatively large stretches are sustained, the responses of cells are not known at these levels of sustained strain. A key challenge is presenting cells with a realistic and well-defined three-dimensional (3D) culture environment that can sustain such strains. Here, we describe an in vitro system called microscale, magnetically-actuated synthetic tissues (micro-MASTs) to quantify these responses for cells within a 3D hydrogel matrix. Cellular strain-threshold and saturation behaviors were observed in hydrogel matrix, including strain-dependent proliferation, spreading, polarization, and differentiation, and matrix adhesion retained at strains sufficient for apoptosis. More broadly, the system shows promise for defining and controlling the effects of mechanical environment upon a broad range of cells. PMID:26887698

  3. Reconstruction Accuracy Assessment of Surface and Underwater 3D Motion Analysis: A New Approach

    PubMed Central

    de Jesus, Kelly; de Jesus, Karla; Figueiredo, Pedro; Vilas-Boas, João Paulo; Fernandes, Ricardo Jorge; Machado, Leandro José

    2015-01-01

    This study assessed accuracy of surface and underwater 3D reconstruction of a calibration volume with and without homography. A calibration volume (6000 × 2000 × 2500 mm) with 236 markers (64 above and 88 underwater control points—with 8 common points at water surface—and 92 validation points) was positioned on a 25 m swimming pool and recorded with two surface and four underwater cameras. Planar homography estimation for each calibration plane was computed to perform image rectification. Direct linear transformation algorithm for 3D reconstruction was applied, using 1600000 different combinations of 32 and 44 points out of the 64 and 88 control points for surface and underwater markers (resp.). Root Mean Square (RMS) error with homography of control and validations points was lower than without it for surface and underwater cameras (P ≤ 0.03). With homography, RMS errors of control and validation points were similar between surface and underwater cameras (P ≥ 0.47). Without homography, RMS error of control points was greater for underwater than surface cameras (P ≤ 0.04) and the opposite was observed for validation points (P ≤ 0.04). It is recommended that future studies using 3D reconstruction should include homography to improve swimming movement analysis accuracy. PMID:26175796

  4. Low-cost approach of a 3D display for general aviation aircraft

    NASA Astrophysics Data System (ADS)

    Sachs, Gottfried; Sperl, Roman; Karl, Wunibald

    2001-08-01

    A low cost 3D-display and navigation system is described which presents guidance information in a 3-dimensional format to the pilot. For achieving the low cost goal, Commercial-off-the-Shelf components are used. The visual information provided by the 3D-display includes a presentation of the future flight path and other guidance elements as well as an image of the outside world. For generating the displayed information, a PC will be used. An appropriate computer software is available to generate the displayed information in real-time with an adequately high update rate. Precision navigation data which is required for accurately adjusting the displayed guidance information are provided by an integrated low cost navigation system. This navigation system consists of a differential global positioning system and an inertial measurement unit. Data from the navigation system is fed into an onboard-computer, using terrain elevation and feature analysis data to generate a synthetic image of the outside world. The system is intended to contribute to the safety of General Aviation aircraft, providing an affordable guidance and navigation aid for this type of aircraft. The low cost 3D display and navigation system will be installed in a two-seat Grob 109B aircraft which is operated by the Institute of Flight Mechanics and Flight Control of the Technische Universitchen as a research vehicle.

  5. An approach to architecture 3D scaffold with interconnective microchannel networks inducing angiogenesis for tissue engineering.

    PubMed

    Sun, Jiaoxia; Wang, Yuanliang; Qian, Zhiyong; Hu, Chenbo

    2011-11-01

    The angiogenesis of 3D scaffold is one of the major current limitations in clinical practice tissue engineering. The new strategy of construction 3D scaffold with microchannel circulation network may improve angiogenesis. In this study, 3D poly(D: ,L: -lactic acid) scaffolds with controllable microchannel structures were fabricated using sacrificial sugar structures. Melt drawing sugar-fiber network produced by a modified filament spiral winding method was used to form the microchannel with adjustable diameters and porosity. This fabrication process was rapid, inexpensive, and highly scalable. The porosity, microchannel diameter, interconnectivity and surface topographies of the scaffold were characterized by scanning electron microscopy. Mechanical properties were evaluated by compression tests. The mean porosity values of the scaffolds were in the 65-78% and the scaffold exhibited microchannel structure with diameter in the 100-200 μm range. The results showed that the scaffolds exhibited an adequate porosity, interconnective microchannel network, and mechanical properties. The cell culture studies with endothelial cells (ECs) demonstrated that the scaffold allowed cells to proliferate and penetrate into the volume of the entire scaffold. Overall, these findings suggest that the fabrication process offers significant advantages and flexibility in generating a variety of non-cytotoxic tissue engineering scaffolds with controllable distributions of porosity and physical properties that could provide the necessary physical cues for ECs and further improve angiogenesis for tissue engineering. PMID:21861076

  6. Statistical shape analysis using 3D Poisson equation-A quantitatively validated approach.

    PubMed

    Gao, Yi; Bouix, Sylvain

    2016-05-01

    Statistical shape analysis has been an important area of research with applications in biology, anatomy, neuroscience, agriculture, paleontology, etc. Unfortunately, the proposed methods are rarely quantitatively evaluated, and as shown in recent studies, when they are evaluated, significant discrepancies exist in their outputs. In this work, we concentrate on the problem of finding the consistent location of deformation between two population of shapes. We propose a new shape analysis algorithm along with a framework to perform a quantitative evaluation of its performance. Specifically, the algorithm constructs a Signed Poisson Map (SPoM) by solving two Poisson equations on the volumetric shapes of arbitrary topology, and statistical analysis is then carried out on the SPoMs. The method is quantitatively evaluated on synthetic shapes and applied on real shape data sets in brain structures. PMID:26874288

  7. Comparison of Existing Response Criteria in Patients with Hepatocellular Carcinoma Treated with Transarterial Chemoembolization Using a 3D Quantitative Approach

    PubMed Central

    Tacher, Vania; Lin, MingDe; Duran, Rafael; Yarmohammadi, Hooman; Lee, Howard; Chapiro, Julius; Chao, Michael; Wang, Zhijun; Frangakis, Constantine; Sohn, Jae Ho; Maltenfort, Mitchell Gil; Pawlik, Timothy; Geschwind, Jean-François

    2015-01-01

    Purpose To compare currently available non-three-dimensional methods (Response Evaluation Criteria in Solid Tumors [RECIST], European Association for Study of the Liver [EASL], modified RECIST [mRECIST[) with three-dimensional (3D) quantitative methods of the index tumor as early response markers in predicting patient survival after initial transcatheter arterial chemoembolization (TACE). Materials and Methods This was a retrospective single-institution HIPAA-compliant and institutional review board–approved study. From November 2001 to November 2008, 491 consecutive patients underwent intraarterial therapy for liver cancer with either conventional TACE or TACE with drug-eluting beads. A diagnosis of hepatocellular carcinoma (HCC) was made in 290 of these patients. The response of the index tumor on pre- and post-TACE magnetic resonance images was assessed retrospectively in 78 treatment-naïve patients with HCC (63 male; mean age, 63 years ± 11 [standard deviation]). Each response assessment method (RECIST, mRECIST, EASL, and 3D methods of volumetric RECIST [vRECIST] and quantitative EASL [qEASL]) was used to classify patients as responders or nonresponders by following standard guidelines for the uni- and bidimensional measurements and by using the formula for a sphere for the 3D measurements. The Kaplan-Meier method with the log-rank test was performed for each method to evaluate its ability to help predict survival of responders and nonresponders. Uni- and multivariate Cox proportional hazard ratio models were used to identify covariates that had significant association with survival. Results The uni- and bidimensional measurements of RECIST (hazard ratio, 0.6; 95% confidence interval [CI]: 0.3, 1.0; P = .09), mRECIST (hazard ratio, 0.6; 95% CI: 0.6, 1.0; P = .05), and EASL (hazard ratio, 1.1; 95% CI: 0.6, 2.2; P = .75) did not show a significant difference in survival between responders and nonresponders, whereas vRECIST (hazard ratio, 0.6; 95% CI: 0.3, 1

  8. Microfluidic volumetric flow determination using optical coherence tomography speckle: An autocorrelation approach

    NASA Astrophysics Data System (ADS)

    De Pretto, Lucas R.; Nogueira, Gesse E. C.; Freitas, Anderson Z.

    2016-04-01

    Functional modalities of Optical Coherence Tomography (OCT) based on speckle analysis are emerging in the literature. We propose a simple approach to the autocorrelation of OCT signal to enable volumetric flow rate differentiation, based on decorrelation time. Our results show that this technique could distinguish flows separated by 3 μl/min, limited by the acquisition speed of the system. We further perform a B-scan of gradient flow inside a microchannel, enabling the visualization of the drag effect on the walls.

  9. Analysis of Approximations and Aperture Distortion for 3D Migration of Bistatic Radar Data with the Two-Step Approach

    NASA Astrophysics Data System (ADS)

    Zanzi, Luigi; Lualdi, Maurizio

    2010-12-01

    The two-step approach is a fast algorithm for 3D migration originally introduced to process zero-offset seismic data. Its application to monostatic GPR (Ground Penetrating Radar) data is straightforward. A direct extension of the algorithm for the application to bistatic radar data is possible provided that the TX-RX azimuth is constant. As for the zero-offset case, the two-step operator is exactly equivalent to the one-step 3D operator for a constant velocity medium and is an approximation of the one-step 3D operator for a medium where the velocity varies vertically. Two methods are explored for handling a heterogeneous medium; both are suitable for the application of the two-step approach, and they are compared in terms of accuracy of the final 3D operator. The aperture of the two-step operator is discussed, and a solution is proposed to optimize its shape. The analysis is of interest for any NDT application where the medium is expected to be heterogeneous, or where the antenna is not in direct contact with the medium (e.g., NDT of artworks, humanitarian demining, radar with air-launched antennas).

  10. A novel and stable approach to anatomical structure morphing for enhanced intraoperative 3D visualization

    NASA Astrophysics Data System (ADS)

    Rajamani, Kumar T.; Gonzalez Ballester, Miguel A.; Nolte, Lutz-Peter; Styner, Martin

    2005-04-01

    The use of three dimensional models in planning and navigating computer assisted surgeries is now well established. These models provide intuitive visualization to the surgeons contributing to significantly better surgical outcomes. Models obtained from specifically acquired CT scans have the disadvantage that they induce high radiation dose to the patient. In this paper we propose a novel and stable method to construct a patient-specific model that provides an appropriate intra-operative 3D visualization without the need for a pre or intra-operative imaging. Patient specific data consists of digitized landmarks and surface points that are obtained intra-operatively. The 3D model is reconstructed by fitting a statistical deformable model to the minimal sparse digitized data. The statistical model is constructed using Principal Component Analysis from training objects. Our morphing scheme efficiently and accurately computes a Mahalanobis distance weighted least square fit of the deformable model to the 3D data model by solving a linear equation system. Relaxing the Mahalanobis distance term as additional points are incorporated enables our method to handle small and large sets of digitized points efficiently. Our novel incorporation of M-estimator based weighting of the digitized points enables us to effectively reject outliers and compute stable models. Normalization of the input model data and the digitized points makes our method size invariant and hence applicable directly to any anatomical shape. The method also allows incorporation of non-spatial data such as patient height and weight. The predominant applications are hip and knee surgeries.

  11. An approach to 3D magnetic field calculation using numerical and differential algebra methods

    SciTech Connect

    Caspi, S.; Helm, M.; Laslett, L.J.; Brady, V.O.

    1992-07-17

    Motivated by the need for new means for specification and determination of 3D fields that are produced by electromagnetic lens elements in the region interior to coil windings and seeking to obtain techniques that will be convenient for accurate conductor placement and dynamical study of particle motion, we have conveniently gene the representation of a 2D magnetic field to 3D. We have shown that the 3 dimensioal magnetic field components of a multipole magnet in the curl-fire divergence-fire region near the axis r=0 can be derived from one dimensional functions A{sub n}(z) and their derivatives (part 1). In the region interior to coil windings of accelerator magnets the three spatial components of magnet fields can be expressed in terms of harmonic components'' proportional to functions sin (n{theta}) or cos (n{theta}) of the azimuthal angle. The r,z dependence of any such component can then be expressed in terms of powers of r times functions A{sub n}(z) and their derivatives. For twodimensional configurations B{sub z} of course is identically zero, the derivatives of A{sub n}(z) vanish, and the harmonic components of the transverse field then acquire a simple proportionality B{sub r,n} {proportional to} r{sup n-1} sin (n{theta}),B{sub {theta},n} {proportional to} r{sup n-1} cos (n{theta}), whereas in a 3-D configuration the more complex nature of the field gives rise to additional so-called psuedomultipole'' components as judged by additional powers of r required in the development of the field. Computation of the 3-D magnetic field arising at a sequence of field points, as a direct result of a specified current configuration or coil geometry, can be calculated explicitly through use of the Biot-Savart law and from such data the coefficients can then be derived for a general development of the type indicated above. We indicate, discuss, and illustrate two means by which this development may be performed.

  12. Interactive 3D-PDF Presentations for the Simulation and Quantification of Extended Endoscopic Endonasal Surgical Approaches.

    PubMed

    Mavar-Haramija, Marija; Prats-Galino, Alberto; Méndez, Juan A Juanes; Puigdelívoll-Sánchez, Anna; de Notaris, Matteo

    2015-10-01

    A three-dimensional (3D) model of the skull base was reconstructed from the pre- and post-dissection head CT images and embedded in a Portable Document Format (PDF) file, which can be opened by freely available software and used offline. The CT images were segmented using a specific 3D software platform for biomedical data, and the resulting 3D geometrical models of anatomical structures were used for dual purpose: to simulate the extended endoscopic endonasal transsphenoidal approaches and to perform the quantitative analysis of the procedures. The analysis consisted of bone removal quantification and the calculation of quantitative parameters (surgical freedom and exposure area) of each procedure. The results are presented in three PDF documents containing JavaScript-based functions. The 3D-PDF files include reconstructions of the nasal structures (nasal septum, vomer, middle turbinates), the bony structures of the anterior skull base and maxillofacial region and partial reconstructions of the optic nerve, the hypoglossal and vidian canals and the internal carotid arteries. Alongside the anatomical model, axial, sagittal and coronal CT images are shown. Interactive 3D presentations were created to explain the surgery and the associated quantification methods step-by-step. The resulting 3D-PDF files allow the user to interact with the model through easily available software, free of charge and in an intuitive manner. The files are available for offline use on a personal computer and no previous specialized knowledge in informatics is required. The documents can be downloaded at http://hdl.handle.net/2445/55224 . PMID:26306875

  13. A 3D modeling approach to complex faults with multi-source data

    NASA Astrophysics Data System (ADS)

    Wu, Qiang; Xu, Hua; Zou, Xukai; Lei, Hongzhuan

    2015-04-01

    Fault modeling is a very important step in making an accurate and reliable 3D geological model. Typical existing methods demand enough fault data to be able to construct complex fault models, however, it is well known that the available fault data are generally sparse and undersampled. In this paper, we propose a workflow of fault modeling, which can integrate multi-source data to construct fault models. For the faults that are not modeled with these data, especially small-scale or approximately parallel with the sections, we propose the fault deduction method to infer the hanging wall and footwall lines after displacement calculation. Moreover, using the fault cutting algorithm can supplement the available fault points on the location where faults cut each other. Increasing fault points in poor sample areas can not only efficiently construct fault models, but also reduce manual intervention. By using a fault-based interpolation and remeshing the horizons, an accurate 3D geological model can be constructed. The method can naturally simulate geological structures no matter whether the available geological data are sufficient or not. A concrete example of using the method in Tangshan, China, shows that the method can be applied to broad and complex geological areas.

  14. Virtual Boutique: a 3D modeling and content-based management approach to e-commerce

    NASA Astrophysics Data System (ADS)

    Paquet, Eric; El-Hakim, Sabry F.

    2000-12-01

    The Virtual Boutique is made out of three modules: the decor, the market and the search engine. The decor is the physical space occupied by the Virtual Boutique. It can reproduce any existing boutique. For this purpose, photogrammetry is used. A set of pictures of a real boutique or space is taken and a virtual 3D representation of this space is calculated from them. Calculations are performed with software developed at NRC. This representation consists of meshes and texture maps. The camera used in the acquisition process determines the resolution of the texture maps. Decorative elements are added like painting, computer generated objects and scanned objects. The objects are scanned with laser scanner developed at NRC. This scanner allows simultaneous acquisition of range and color information based on white laser beam triangulation. The second module, the market, is made out of all the merchandises and the manipulators, which are used to manipulate and compare the objects. The third module, the search engine, can search the inventory based on an object shown by the customer in order to retrieve similar objects base don shape and color. The items of interest are displayed in the boutique by reconfiguring the market space, which mean that the boutique can be continuously customized according to the customer's needs. The Virtual Boutique is entirely written in Java 3D and can run in mono and stereo mode and has been optimized in order to allow high quality rendering.

  15. Automated Segmentation of the Right Ventricle in 3D Echocardiography: A Kalman Filter State Estimation Approach.

    PubMed

    Bersvendsen, Jorn; Orderud, Fredrik; Massey, Richard John; Fosså, Kristian; Gerard, Olivier; Urheim, Stig; Samset, Eigil

    2016-01-01

    As the right ventricle's (RV) role in cardiovascular diseases is being more widely recognized, interest in RV imaging, function and quantification is growing. However, there are currently few RV quantification methods for 3D echocardiography presented in the literature or commercially available. In this paper we propose an automated RV segmentation method for 3D echocardiographic images. We represent the RV geometry by a Doo-Sabin subdivision surface with deformation modes derived from a training set of manual segmentations. The segmentation is then represented as a state estimation problem and solved with an extended Kalman filter by combining the RV geometry with a motion model and edge detection. Validation was performed by comparing surface-surface distances, volumes and ejection fractions in 17 patients with aortic insufficiency between the proposed method, magnetic resonance imaging (MRI), and a manual echocardiographic reference. The algorithm was efficient with a mean computation time of 2.0 s. The mean absolute distances between the proposed and manual segmentations were 3.6 ± 0.7 mm. Good agreements of end diastolic volume, end systolic volume and ejection fraction with respect to MRI ( -26±24 mL , -16±26 mL and 0 ± 10%, respectively) and a manual echocardiographic reference (7 ± 30 mL, 13 ± 17 mL and -5±7% , respectively) were observed. PMID:26168434

  16. A Bayesian approach to real-time 3D tumor localization via monoscopic x-ray imaging during treatment delivery

    SciTech Connect

    Li, Ruijiang; Fahimian, Benjamin P.; Xing, Lei

    2011-07-15

    Purpose: Monoscopic x-ray imaging with on-board kV devices is an attractive approach for real-time image guidance in modern radiation therapy such as VMAT or IMRT, but it falls short in providing reliable information along the direction of imaging x-ray. By effectively taking consideration of projection data at prior times and/or angles through a Bayesian formalism, the authors develop an algorithm for real-time and full 3D tumor localization with a single x-ray imager during treatment delivery. Methods: First, a prior probability density function is constructed using the 2D tumor locations on the projection images acquired during patient setup. Whenever an x-ray image is acquired during the treatment delivery, the corresponding 2D tumor location on the imager is used to update the likelihood function. The unresolved third dimension is obtained by maximizing the posterior probability distribution. The algorithm can also be used in a retrospective fashion when all the projection images during the treatment delivery are used for 3D localization purposes. The algorithm does not involve complex optimization of any model parameter and therefore can be used in a ''plug-and-play'' fashion. The authors validated the algorithm using (1) simulated 3D linear and elliptic motion and (2) 3D tumor motion trajectories of a lung and a pancreas patient reproduced by a physical phantom. Continuous kV images were acquired over a full gantry rotation with the Varian TrueBeam on-board imaging system. Three scenarios were considered: fluoroscopic setup, cone beam CT setup, and retrospective analysis. Results: For the simulation study, the RMS 3D localization error is 1.2 and 2.4 mm for the linear and elliptic motions, respectively. For the phantom experiments, the 3D localization error is < 1 mm on average and < 1.5 mm at 95th percentile in the lung and pancreas cases for all three scenarios. The difference in 3D localization error for different scenarios is small and is not

  17. Personalized development of human organs using 3D printing technology.

    PubMed

    Radenkovic, Dina; Solouk, Atefeh; Seifalian, Alexander

    2016-02-01

    3D printing is a technique of fabricating physical models from a 3D volumetric digital image. The image is sliced and printed using a specific material into thin layers, and successive layering of the material produces a 3D model. It has already been used for printing surgical models for preoperative planning and in constructing personalized prostheses for patients. The ultimate goal is to achieve the development of functional human organs and tissues, to overcome limitations of organ transplantation created by the lack of organ donors and life-long immunosuppression. We hypothesized a precision medicine approach to human organ fabrication using 3D printed technology, in which the digital volumetric data would be collected by imaging of a patient, i.e. CT or MRI images followed by mathematical modeling to create a digital 3D image. Then a suitable biocompatible material, with an optimal resolution for cells seeding and maintenance of cell viability during the printing process, would be printed with a compatible printer type and finally implanted into the patient. Life-saving operations with 3D printed implants were already performed in patients. However, several issues need to be addressed before translational application of 3D printing into clinical medicine. These are vascularization, innervation, and financial cost of 3D printing and safety of biomaterials used for the construct. PMID:26826637

  18. The role of mechanical heterogeneities during continental breakup: a 3D lithospheric-scale modelling approach

    NASA Astrophysics Data System (ADS)

    Duclaux, Guillaume; Huismans, Ritske S.; May, Dave

    2015-04-01

    How and why do continents break? More than two decades of analogue and 2D plane-strain numerical experiments have shown that despite the origin of the forces driving extension, the geometry of continental rifts falls into three categories - or modes: narrow rift, wide rift, or core complex. The mode of extension itself is strongly influenced by the rheology (and rheological behaviour) of the modelled layered system. In every model, an initial thermal or mechanical heterogeneity, such as a weak seed or a notch, is imposed to help localise the deformation and avoid uniform stretching of the lithosphere by pure shear. While it is widely accepted that structural inheritance is a key parameter for controlling rift localisation - as implied by the Wilson Cycle - modelling the effect of lithospheric heterogeneities on the long-term tectonic evolution of an extending plate in full 3D remains challenging. Recent progress in finite-element methods applied to computational tectonics along with the improved accessibility to high performance computers, now enable to switch from plane strain thermo-mechanical experiments to full 3D high-resolution experiments. Here we investigate the role of mechanical heterogeneities on rift opening, linkage and propagation during extension of a layered lithospheric systems with pTatin3d, a geodynamics modeling package utilising the material-point-method for tracking material composition, combined with a multigrid finite-element method to solve heterogeneous, incompressible visco-plastic Stokes problems. The initial model setup consists in a box of 1200 km horizontally by 250 km deep. It includes a 35 km layer of continental crust, underlaid by 85 km of sub-continental lithospheric mantle, and an asthenospheric mantle. Crust and mantle have visco-plastic rheologies with a pressure dependent yielding, which includes strain weakening, and a temperature, stress, strain-rate-dependent viscosity based on wet quartzite rheology for the crust, and wet

  19. Engineering approaches to study fibrosis in 3-D in vitro systems.

    PubMed

    Porras, Ana M; Hutson, Heather N; Berger, Anthony J; Masters, Kristyn S

    2016-08-01

    Fibrotic diseases occur in virtually every tissue of the body and are a major cause of mortality, yet they remain largely untreatable and poorly understood on a mechanistic level. The development of anti-fibrotic agents has been hampered, in part, by the insufficient fibrosis biomimicry provided by traditional in vitro platforms. This review focuses on recent advancements toward creating 3-D platforms that mimic key features of fibrosis, as well as the application of novel imaging and sensor techniques to analyze dynamic extracellular matrix remodeling. Several opportunities are highlighted to apply new tools from the fields of biomaterials, imaging, and systems biology to yield pathophysiologically relevant in vitro platforms that improve our understanding of fibrosis and may enable identification of potential treatment targets. PMID:26926460

  20. Size-Controlled Fabrication of Polyaniline Microfibers Based on 3D Hydrodynamic Focusing Approach.

    PubMed

    Yoo, Imsung; Song, Simon; Uh, Kyungchan; Lee, Chan Woo; Kim, Jong-Man

    2015-07-01

    Owing to the relatively high conductivity and unique redox behavior, polyaniline (PANI) has been one of the most technologically promising conducting polymers. Although various methodologies have been developed, fabrication of PANI microfibers has been a challenging task owing to the poor solubility in most organic solvents. By taking advantage of a microfluidic technology and organic soluble acid labile t-Boc-protected PANI (t-Boc-PANI) as the conducting polymer precursor, fabrication of PANI microfibers in a size-controlled manner is possible. Introduction of a THF solution containing t-Boc-PANI, and dodecylbenzenesulfonic acid (DBSA) as a core flow, and water as a sheath flow into a microfluidic channel with a 3D hydrodynamic focusing effect results in crystallization of the polymer fiber. By changing the flow rate, linear PANI microfibers that range from 16.2 to 39.4 μm in diameter are readily obtained. PMID:25882095

  1. 3D Modeling of Spectra and Light Curves of Hot Jupiters with PHOENIX; a First Approach

    NASA Astrophysics Data System (ADS)

    Jiménez-Torres, J. J.

    2016-04-01

    A detailed global circulation model was used to feed the PHOENIX code and calculate 3D spectra and light curves of hot Jupiters. Cloud free and dusty radiative fluxes for the planet HD179949b were modeled to show differences between them. The PHOENIX simulations can explain the broad features of the observed 8 μm light curves, including the fact that the planet-star flux ratio peaks before the secondary eclipse. The PHOENIX reflection spectrum matches the Spitzer secondary-eclipse depth at 3.6 μm and underpredicts eclipse depths at 4.5, 5.8 and 8.0 μm. These discrepancies result from the chemical composition and suggest the incorporation of different metallicities in future studies.

  2. Hard and soft probe medium interactions in a 3D hydro+micro approach at RHIC

    NASA Astrophysics Data System (ADS)

    Bass, S. A.; Renk, T.; Ruppert, J.; Nonaka, C.

    2007-08-01

    We utilize a 3D hybrid hydro+micro model for a comprehensive and consistent description of soft and hard particle production in ultra-relativistic heavy-ion collisions at RHIC. In the soft sector we focus on the dynamics of (multi-) strange baryons, where a clear strangeness dependence of their collision rates and freeze-out is observed. In the hard sector we study the radiative energy loss of hard partons in a soft medium in the multiple soft scattering approximation. While the nuclear suppression factor RAA does not reflect the high quality of the medium description (except in a reduced systematic uncertainty in extracting the quenching power of the medium), the hydrodynamical model also allows us to study different centralities and in particular the angular variation of RAA with respect to the reaction plane, allowing for a controlled variation of the in-medium path length.

  3. Mass Movement Susceptibility in the Western San Juan Mountains, Colorado: A Preliminary 3-D Mapping Approach

    NASA Astrophysics Data System (ADS)

    Kelkar, K. A.; Giardino, J. R.

    2015-12-01

    Mass movement is a major activity that impacts lives of humans and their infrastructure. Human activity in steep, mountainous regions is especially at risk to this potential hazard. Thus, the identification and quantification of risk by mapping and determining mass movement susceptibility are fundamental in protecting lives, resources and ensuring proper land use regulation and planning. Specific mass-movement processes including debris flows, rock falls, snow avalanches and landslides continuously modify the landscape of the San Juan Mountains. Historically, large-magnitude slope failures have repeatedly occurred in the region. Common triggers include intense, long-duration precipitation, freeze-thaw processes, human activity and various volcanic lithologies overlying weaker sedimentary formations. Predicting mass movement is challenging because of its episodic and spatially, discontinuous occurrence. Landslides in mountain terrain are characterized as widespread, highly mobile and have a long duration of activity. We developed a 3-D model for landslide susceptibility using Geographic Information Systems Technology (GIST). The study area encompasses eight USGS quadrangles: Ridgway, Dallas, Mount Sneffels, Ouray, Telluride, Ironton, Ophir and Silverton. Fieldwork consisted of field reconnaissance mapping at 1:5,000 focusing on surficial geomorphology. Field mapping was used to identify potential locations, which then received additional onsite investigation and photographic documentation of features indicative of slope failure. A GIS module was created using seven terrain spatial databases: geology, surficial geomorphology (digitized), slope aspect, slope angle, vegetation, soils and distance to infrastructure to map risk. The GIS database will help determine risk zonation for the study area. Correlations between terrain parameters leading to slope failure were determined through the GIS module. This 3-D model will provide a spatial perspective of the landscape to

  4. 3D models mapping optimization through an integrated parameterization approach: cases studies from Ravenna

    NASA Astrophysics Data System (ADS)

    Cipriani, L.; Fantini, F.; Bertacchi, S.

    2014-06-01

    Image-based modelling tools based on SfM algorithms gained great popularity since several software houses provided applications able to achieve 3D textured models easily and automatically. The aim of this paper is to point out the importance of controlling models parameterization process, considering that automatic solutions included in these modelling tools can produce poor results in terms of texture utilization. In order to achieve a better quality of textured models from image-based modelling applications, this research presents a series of practical strategies aimed at providing a better balance between geometric resolution of models from passive sensors and their corresponding (u,v) map reference systems. This aspect is essential for the achievement of a high-quality 3D representation, since "apparent colour" is a fundamental aspect in the field of Cultural Heritage documentation. Complex meshes without native parameterization have to be "flatten" or "unwrapped" in the (u,v) parameter space, with the main objective to be mapped with a single image. This result can be obtained by using two different strategies: the former automatic and faster, while the latter manual and time-consuming. Reverse modelling applications provide automatic solutions based on splitting the models by means of different algorithms, that produce a sort of "atlas" of the original model in the parameter space, in many instances not adequate and negatively affecting the overall quality of representation. Using in synergy different solutions, ranging from semantic aware modelling techniques to quad-dominant meshes achieved using retopology tools, it is possible to obtain a complete control of the parameterization process.

  5. 3D topography measurements on correlation cells—a new approach to forensic ballistics identifications

    NASA Astrophysics Data System (ADS)

    Song, John; Chu, Wei; Tong, Mingsi; Soons, Johannes

    2014-06-01

    Based on three-dimensional (3D) topography measurements on correlation cells, the National Institute of Standards and Technology (NIST) has developed the ‘NIST Ballistics Identification System (NBIS)’ aimed at accurate ballistics identifications and fast ballistics evidence searches. The 3D topographies are divided into arrays of correlation cells to identify ‘valid correlation areas’ and eliminate ‘invalid correlation areas’ from the matching and identification procedure. A ‘congruent matching cells’ (CMC)’ method using three types of identification parameters of the paired correlation cells (cross correlation function maximum CCFmax, spatial registration position in x-y and registration angle θ) is used for high accuracy ballistics identifications. ‘Synchronous processing’ is proposed for correlating multiple cell pairs at the same time to increase the correlation speed. The proposed NBIS can be used for correlations of both geometrical topographies and optical intensity images. All the correlation parameters and algorithms are in the public domain and subject to open tests. An error rate reporting procedure has been developed that can greatly add to the scientific support for the firearm and toolmark identification specialty, and give confidence to the trier of fact in court proceedings. The NBIS is engineered to employ transparent identification parameters and criteria, statistical models and correlation algorithms. In this way, interoperability between different ballistics identification systems can be more easily achieved. This interoperability will make the NBIS suitable for ballistics identifications and evidence searches with large national databases, such as the National Integrated Ballistic Information Network in the United States.

  6. 5D Modelling: An Efficient Approach for Creating Spatiotemporal Predictive 3D Maps of Large-Scale Cultural Resources

    NASA Astrophysics Data System (ADS)

    Doulamis, A.; Doulamis, N.; Ioannidis, C.; Chrysouli, C.; Grammalidis, N.; Dimitropoulos, K.; Potsiou, C.; Stathopoulou, E.-K.; Ioannides, M.

    2015-08-01

    Outdoor large-scale cultural sites are mostly sensitive to environmental, natural and human made factors, implying an imminent need for a spatio-temporal assessment to identify regions of potential cultural interest (material degradation, structuring, conservation). On the other hand, in Cultural Heritage research quite different actors are involved (archaeologists, curators, conservators, simple users) each of diverse needs. All these statements advocate that a 5D modelling (3D geometry plus time plus levels of details) is ideally required for preservation and assessment of outdoor large scale cultural sites, which is currently implemented as a simple aggregation of 3D digital models at different time and levels of details. The main bottleneck of such an approach is its complexity, making 5D modelling impossible to be validated in real life conditions. In this paper, a cost effective and affordable framework for 5D modelling is proposed based on a spatial-temporal dependent aggregation of 3D digital models, by incorporating a predictive assessment procedure to indicate which regions (surfaces) of an object should be reconstructed at higher levels of details at next time instances and which at lower ones. In this way, dynamic change history maps are created, indicating spatial probabilities of regions needed further 3D modelling at forthcoming instances. Using these maps, predictive assessment can be made, that is, to localize surfaces within the objects where a high accuracy reconstruction process needs to be activated at the forthcoming time instances. The proposed 5D Digital Cultural Heritage Model (5D-DCHM) is implemented using open interoperable standards based on the CityGML framework, which also allows the description of additional semantic metadata information. Visualization aspects are also supported to allow easy manipulation, interaction and representation of the 5D-DCHM geometry and the respective semantic information. The open source 3DCity

  7. Unequal-period combination approach of gray code and phase-shifting for 3-D visual measurement

    NASA Astrophysics Data System (ADS)

    Yu, Shuang; Zhang, Jing; Yu, Xiaoyang; Sun, Xiaoming; Wu, Haibin

    2016-09-01

    Combination of Gray code and phase-shifting is the most practical and advanced approach for the structured light 3-D measurement so far, which is able to measure objects with complex and discontinuous surface. However, for the traditional combination of the Gray code and phase-shifting, the captured Gray code images are not always sharp cut-off in the black-white conversion boundaries, which may lead to wrong decoding analog code orders. Moreover, during the actual measurement, there also exists local decoding error for the wrapped analog code obtained with the phase-shifting approach. Therefore, for the traditional approach, the wrong analog code orders and the local decoding errors will consequently introduce the errors which are equivalent to a fringe period when the analog code is unwrapped. In order to avoid one-fringe period errors, we propose an approach which combines Gray code with phase-shifting according to unequal period. With theoretical analysis, we build the measurement model of the proposed approach, determine the applicable condition and optimize the Gray code encoding period and phase-shifting fringe period. The experimental results verify that the proposed approach can offer a reliable unwrapped analog code, which can be used in 3-D shape measurement.

  8. Handling and quantifying uncertainty in geological 3D models: A methodological approach based on remote-sensing and field work.

    NASA Astrophysics Data System (ADS)

    Baumberger, Roland; Wehrens, Philip; Herwegh, Marco

    2013-04-01

    Geological 3D models are always just an approximation of a complex natural situation. This is especially true in regions, where hard underground data (e.g. bore holes, tunnel mappings and seismic data) is lacking. One of the key problems while developing valid geological 3D models is the three-dimensional spatial distribution of geological structures, particularly with increasing distance from the surface. In our study, we investigate the Alpine 3D Deformation of the crystalline rocks of the Aar massif (Haslital valley, Central Switzerland). Deformation in this area is dominated by different sets of large-scale shear zones, which acted under both ductile and brittle deformation conditions. The goal of our study is the prediction of the geometry and the evolution of the structures in 3D space and time. A key point in our project is the generation of a reliable 3D model of today's structures. In this sense, estimation of the reliability of the surface information for the extrapolation to depth is mandatory. Based on our data, a method will be presented that contributes to a possible solution of the questions addressed above. The basic idea consists of the fact that (i) mechanical anisotropies as shear zones and faults show prominent three-dimensional information in the landscape, (ii) these geometries can be used as input data for a geological 3D model and (iii) that the 3D information mentioned allows a projection to depth. As a great advantage of the study area, a large number of underground tunnels exist, which allow to evaluate the quality of the aforementioned extrapolations. The method is based on a combined remote-sensing and field work approach: morphological incisions recognized on digital elevation models as well as on aerial photos on the computer screen were evaluated, described and attributed in detail in the field. Our approach is based on a six step workflow: (1) Elaboration of a large-scale structural map of geological structures by means of remote

  9. Novel 3D Approach to Flare Modeling via Interactive IDL Widget Tools

    NASA Astrophysics Data System (ADS)

    Nita, G. M.; Fleishman, G. D.; Gary, D. E.; Kuznetsov, A.; Kontar, E. P.

    2011-12-01

    Currently, and soon-to-be, available sophisticated 3D models of particle acceleration and transport in solar flares require a new level of user-friendly visualization and analysis tools allowing quick and easy adjustment of the model parameters and computation of realistic radiation patterns (images, spectra, polarization, etc). We report the current state of the art of these tools in development, already proved to be highly efficient for the direct flare modeling. We present an interactive IDL widget application intended to provide a flexible tool that allows the user to generate spatially resolved radio and X-ray spectra. The object-based architecture of this application provides full interaction with imported 3D magnetic field models (e.g., from an extrapolation) that may be embedded in a global coronal model. Various tools provided allow users to explore the magnetic connectivity of the model by generating magnetic field lines originating in user-specified volume positions. Such lines may serve as reference lines for creating magnetic flux tubes, which are further populated with user-defined analytical thermal/non thermal particle distribution models. By default, the application integrates IDL callable DLL and Shared libraries containing fast GS emission codes developed in FORTRAN and C++ and soft and hard X-ray codes developed in IDL. However, the interactive interface allows interchanging these default libraries with any user-defined IDL or external callable codes designed to solve the radiation transfer equation in the same or other wavelength ranges of interest. To illustrate the tool capacity and generality, we present a step-by-step real-time computation of microwave and X-ray images from realistic magnetic structures obtained from a magnetic field extrapolation preceding a real event, and compare them with the actual imaging data obtained by NORH and RHESSI instruments. We discuss further anticipated developments of the tools needed to accommodate

  10. Robust and scalable 3-D geo-electromagnetic modelling approach using the finite element method

    NASA Astrophysics Data System (ADS)

    Grayver, Alexander V.; Bürg, Markus

    2014-07-01

    We present a robust and scalable solver for time-harmonic Maxwell's equations for problems with large conductivity contrasts, wide range of frequencies, stretched grids and locally refined meshes. The solver is part of the fully distributed adaptive 3-D electromagnetic modelling scheme which employs the finite element method and unstructured non-conforming hexahedral meshes for spatial discretization using the open-source software deal.II. We use the complex-valued electric field formulation and split it into two real-valued equations for which we utilize an optimal block-diagonal pre-conditioner. Application of this pre-conditioner requires the solution of two smaller real-valued symmetric problems. We solve them by using either a direct solver or the conjugate gradient method pre-conditioned with the recently introduced auxiliary space technique. The auxiliary space pre-conditioner reformulates the original problem in form of several simpler ones, which are then solved using highly efficient algebraic multigrid methods. In this paper, we consider the magnetotelluric case and verify our numerical scheme by using COMMEMI 3-D models. Afterwards, we run a series of numerical experiments and demonstrate that the solver converges in a small number of iterations for a wide frequency range and variable problem sizes. The number of iterations is independent of the problem size, but exhibits a mild dependency on frequency. To test the stability of the method on locally refined meshes, we have implemented a residual-based a posteriori error estimator and compared it with uniform mesh refinement for problems up to 200 million unknowns. We test the scalability of the most time consuming parts of our code and show that they fulfill the strong scaling assumption as long as each MPI process possesses enough degrees of freedom to alleviate communication overburden. Finally, we refer back to a direct solver-based pre-conditioner and analyse its complexity in time. The results show

  11. A Chemical Approach to 3-D Lithographic Patterning of Si and GeNanocrystals

    SciTech Connect

    Sharp, I.D.; Xu, Q.; Yi, D.O.; Liao, C.Y.; Ager III, J.W.; Beeman, J.W.; Yu, K.M.; Robinson, J.T.; Dubon, O.D.; Chrzan, D.C.; Haller, E.E.

    2005-12-12

    Ion implantation into silica followed by thermal annealingis an established growth method for Si and Ge nanocrystals. Wedemonstrate that growth of Group IV semiconductor nanocrystals can besuppressed by co-implantation of oxygen prior to annealing. For Sinanocrystals, at low Si/O dose ratios, oxygen co-implantation leads to areduction of the average nanocrystal size and a blue-shift of thephotoluminescence emission energy. For both Si and Ge nanocrystals, atlarger Si/O or Ge/O dose ratios, the implanted specie is oxidized andnanocrystals do not form. This chemical deactivation was utilized toachieve patterned growth of Si and Ge nanocrystals. Si was implanted intoa thin SiO2 film on a Si substrate followed by oxygen implantationthrough an electron beam lithographically defined stencil mask. Thermalannealing of the co-implanted structure yields two-dimensionallypatterned growth of Si nanocrystals under the masked regions. We applieda previously developed process to obtain exposed nanocrystals byselective HF etching of the silica matrix to these patterned structures.Atomic force microscopy (AFM) of etched structures revealed that exposednanocrystals are not laterally displaced from their original positionsduring the etching process. Therefore, this process provides a means ofachieving patterned structures of exposed nanocrystals. The possibilitiesfor scaling this chemical-based lithography process to smaller featuresand for extending it to 3-D patterning is discussed.

  12. Stage acoustics for musicians: A multidimensional approach using 3D ambisonic technology

    NASA Astrophysics Data System (ADS)

    Guthrie, Anne

    In this research, a method was outlined and tested for the use of 3D Ambisonic technology to inform stage acoustics research and design. Stage acoustics for musicians as a field has yet to benefit from recent advancements in auralization and spatial acoustic analysis. This research attempts to address common issues in stage acoustics: subjective requirements for performers in relation to feelings of support, quality of sound, and ease of ensemble playing in relation to measurable, objective characteristics that can be used to design better stage enclosures. While these issues have been addressed in previous work, this research attempts to use technological advancements to improve the resolution and realism of the testing and analysis procedures. Advancements include measurement of spatial impulse responses using a spherical microphone array, higher-order ambisonic encoding and playback for real-time performer auralization, high-resolution spatial beamforming for analysis of onstage impulse responses, and multidimensional scaling procedures to determine subjective musician preferences. The methodology for implementing these technologies into stage acoustics research is outlined in this document and initial observations regarding implications for stage enclosure design are proposed. This research provides a robust method for measuring and analyzing performer experiences on multiple stages without the costly and time-intensive process of physically surveying orchestras on different stages, with increased repeatability while maintaining a high level of immersive realism and spatial resolution. Along with implications for physical design, this method provides possibilities for virtual teaching and rehearsal, parametric modeling and co-located performance.

  13. A hierarchical Bayesian approach for earthquake location and data uncertainty estimation in 3D heterogeneous media

    NASA Astrophysics Data System (ADS)

    Arroucau, Pierre; Custódio, Susana

    2015-04-01

    Solving inverse problems requires an estimate of data uncertainties. This usually takes the form of a data covariance matrix, which determines the shape of the model posterior distribution. Those uncertainties are yet not always known precisely and it is common practice to simply set them to a fixed, reasonable value. In the case of earthquake location, the hypocentral parameters (longitude, latitude, depth and origin time) are typically inverted for using seismic phase arrival times. But quantitative data variance estimates are rarely provided. Instead, arrival time catalogs usually associate phase picks with a quality factor, which is subsequently interpreted more or less arbitrarily in terms of data uncertainty in the location procedure. Here, we present a hierarchical Bayesian algorithm for earthquake location in 3D heterogeneous media, in which not only the earthquake hypocentral parameters, but also the P- and S-wave arrival time uncertainties, are inverted for, hence allowing more realistic posterior model covariance estimates. Forward modeling is achieved by means of the Fast Marching Method (FMM), an eikonal solver which has the ability to take interfaces into account, so direct, reflected and refracted phases can be used in the inversion. We illustrate the ability of our algorithm to retrieve earthquake hypocentral parameters as well as data uncertainties through synthetic examples and using a subset of arrival time catalogs for mainland Portugal and its Atlantic margin.

  14. A synthetic modular approach for modeling the role of the 3D microenvironment in tumor progression.

    PubMed

    Singh, S P; Schwartz, M P; Tokuda, E Y; Luo, Y; Rogers, R E; Fujita, M; Ahn, N G; Anseth, K S

    2015-01-01

    Here, we demonstrate the flexibility of peptide-functionalized poly(ethylene glycol) (PEG) hydrogels for modeling tumor progression. The PEG hydrogels were formed using thiol-ene chemistry to incorporate a matrix metalloproteinase-degradable peptide crosslinker (KKCGGPQG↓IWGQGCKK) permissive to proteolytic remodeling and the adhesive CRGDS peptide ligand. Tumor cell function was investigated by culturing WM239A melanoma cells on PEG hydrogel surfaces or encapsulating cells within the hydrogels, and either as monocultures or indirect (non-contact) cocultures with primary human dermal fibroblasts (hDFs). WM239A cluster size and proliferation rate depended on the shear elastic modulus for cells cultured on PEG hydrogels, while growth was inhibited by coculture with hDFs regardless of hydrogel stiffness. Cluster size was also suppressed by hDFs for WM239A cells encapsulated in PEG hydrogels, which is consistent with cells seeded on top of hydrogels. Notably, encapsulated WM239A clusters and single cells adopted invasive phenotypes in the hDF coculture model, which included single cell and collective migration modes that resembled invasion from human melanoma patient-derived xenograft tumors encapsulated in equivalent PEG hydrogels. Our combined results demonstrate that peptide-functionalized PEG hydrogels provide a useful platform for investigating aspects of tumor progression in 2D and 3D microenvironments, including single cell migration, cluster growth and invasion. PMID:26638791

  15. Automated analysis of barley organs using 3D laser scanning: an approach for high throughput phenotyping.

    PubMed

    Paulus, Stefan; Dupuis, Jan; Riedel, Sebastian; Kuhlmann, Heiner

    2014-01-01

    Due to the rise of laser scanning the 3D geometry of plant architecture is easy to acquire. Nevertheless, an automated interpretation and, finally, the segmentation into functional groups are still difficult to achieve. Two barley plants were scanned in a time course, and the organs were separated by applying a histogram-based classification algorithm. The leaf organs were represented by meshing algorithms, while the stem organs were parameterized by a least-squares cylinder approximation. We introduced surface feature histograms with an accuracy of 96% for the separation of the barley organs, leaf and stem. This enables growth monitoring in a time course for barley plants. Its reliability was demonstrated by a comparison with manually fitted parameters with a correlation R(2) = 0:99 for the leaf area and R(2) = 0:98 for the cumulated stem height. A proof of concept has been given for its applicability for the detection of water stress in barley, where the extension growth of an irrigated and a non-irrigated plant has been monitored. PMID:25029283

  16. A synthetic modular approach for modeling the role of the 3D microenvironment in tumor progression

    PubMed Central

    Singh, S. P.; Schwartz, M. P.; Tokuda, E. Y.; Luo, Y.; Rogers, R. E.; Fujita, M.; Ahn, N. G.; Anseth, K. S.

    2015-01-01

    Here, we demonstrate the flexibility of peptide-functionalized poly(ethylene glycol) (PEG) hydrogels for modeling tumor progression. The PEG hydrogels were formed using thiol-ene chemistry to incorporate a matrix metalloproteinase-degradable peptide crosslinker (KKCGGPQG↓IWGQGCKK) permissive to proteolytic remodeling and the adhesive CRGDS peptide ligand. Tumor cell function was investigated by culturing WM239A melanoma cells on PEG hydrogel surfaces or encapsulating cells within the hydrogels, and either as monocultures or indirect (non-contact) cocultures with primary human dermal fibroblasts (hDFs). WM239A cluster size and proliferation rate depended on the shear elastic modulus for cells cultured on PEG hydrogels, while growth was inhibited by coculture with hDFs regardless of hydrogel stiffness. Cluster size was also suppressed by hDFs for WM239A cells encapsulated in PEG hydrogels, which is consistent with cells seeded on top of hydrogels. Notably, encapsulated WM239A clusters and single cells adopted invasive phenotypes in the hDF coculture model, which included single cell and collective migration modes that resembled invasion from human melanoma patient-derived xenograft tumors encapsulated in equivalent PEG hydrogels. Our combined results demonstrate that peptide-functionalized PEG hydrogels provide a useful platform for investigating aspects of tumor progression in 2D and 3D microenvironments, including single cell migration, cluster growth and invasion. PMID:26638791

  17. Automated Analysis of Barley Organs Using 3D Laser Scanning: An Approach for High Throughput Phenotyping

    PubMed Central

    Paulus, Stefan; Dupuis, Jan; Riedel, Sebastian; Kuhlmann, Heiner

    2014-01-01

    Due to the rise of laser scanning the 3D geometry of plant architecture is easy to acquire. Nevertheless, an automated interpretation and, finally, the segmentation into functional groups are still difficult to achieve. Two barley plants were scanned in a time course, and the organs were separated by applying a histogram-based classification algorithm. The leaf organs were represented by meshing algorithms, while the stem organs were parameterized by a least-squares cylinder approximation. We introduced surface feature histograms with an accuracy of 96% for the separation of the barley organs, leaf and stem. This enables growth monitoring in a time course for barley plants. Its reliability was demonstrated by a comparison with manually fitted parameters with a correlation R2 = 0.99 for the leaf area and R2 = 0.98 for the cumulated stem height. A proof of concept has been given for its applicability for the detection of water stress in barley, where the extension growth of an irrigated and a non-irrigated plant has been monitored. PMID:25029283

  18. A Computationally-Efficient Kinetic Approach for Gas/Particle Mass Transfer Treatments: Development, Testing, and 3-D Application

    NASA Astrophysics Data System (ADS)

    Hu, X.; Zhang, Y.

    2007-05-01

    The Weather Research and Forecast/Chemistry Model (WRF/Chem) that simulates chemistry simultaneously with meteorology has recently been developed for real-time forecasting by the U.S. National Center for Atmospheric Research (NCAR) and National Oceanic & Atmospheric Administration (NOAA). As one of the six air quality models, WRF/Chem with a modal aerosol module has been applied for ozone and PM2.5 ensemble forecasts over eastern North America as part of the 2004 New England Air Quality Study (NEAQS) program (NEAQS-2004). Significant differences exist in the partitioning of volatile species (e.g., ammonium and nitrate) simulated by the six models. Model biases are partially attributed to the equilibrium assumption used in the gas/particles mass transfer approach in some models. Development of a more accurate, yet computationally- efficient gas/particle mass transfer approach for three-dimensional (3-D) applications, in particular, real-time forecasting, is therefore warranted. Model of Aerosol Dynamics, Reaction, Ionization, and Dissolution (MADRID) has been implemented into WRF/Chem (referred to as WRF/Chem-MADRID). WRF/Chem-MADRID offers three gas/particle partitioning treatments: equilibrium, kinetic, and hybrid approaches. The equilibrium approach is computationally-efficient and commonly used in 3-D air quality models but less accurate under certain conditions (e.g., in the presence of coarse, reactive particles such as PM containing sea-salts in the coastal areas). The kinetic approach is accurate but computationally-expensive, limiting its 3-D applications. The hybrid approach attempts to provide a compromise between merits and drawbacks of the two approaches by treating fine PM (typically < ~ 1 μm) with the equilibrium approach and coarse PM with the kinetic approach. A computationally-efficient kinetic gas/particle mass transfer approach in MADRID has recently been developed for 3-D applications based on an Analytical Predictor of Condensation (referred

  19. Early Earth plume-lid tectonics: A high-resolution 3D numerical modelling approach

    NASA Astrophysics Data System (ADS)

    Fischer, Ria; Gerya, Taras

    2016-04-01

    Early Earth had a higher amount of radiogenic elements as well as a higher amount of leftover primordial heat. Both contribute to the increased temperature in the Earth's interior and it is mainly this increased mantle potential temperature Tp that controls the dynamics of the crust and upper mantle and the predominant style of tectonics in the Archean Earth. We conduct 3D petrological-magmatic-thermomechanical numerical modelling experiments of the crust and upper mantle under Archean conditions using a plume-lid tectonics model setup. For varying crustal compositions and a mantle potential temperature increase ΔTp = 250K (compared to present day conditions), a hot lower thermal boundary layer introduces spontaneously developing mantle plumes and after repeated melt removal, depleted mantle lithosphere is formed self-consistently. New crust is produced in the form of both volcanic and plutonic magmatism. Models show large amounts of subcrustal decompression melting and production of new crust which in turn influences the dynamics. On short-term (10 ‑ 20Myr) rising diapirs and sinking basaltic crust lead to crustal overturn and to the formation of the typical Archean dome-and-keel pattern. On long-term a long (˜ 80Myr) passive 'growth phase' with strong growth of crust and lithosphere is observed. Both crust and lithosphere thickness are regulated by thermochemical instabilities assisted by lower crustal eclogitisation and a subcrustal small-scale convection area. Delamination of lower crust and lithosphere is initiated by linear or cylindrical eclogite drips and occurs as one 'catastrophic' event within a 20Myr 'removal phase'.

  20. Early Earth tectonics: A high-resolution 3D numerical modelling approach

    NASA Astrophysics Data System (ADS)

    Fischer, R.; Gerya, T.

    2015-12-01

    Early Earth had a higher amount of radiogenic elements as well as a higher amount of leftover primordial heat. Both contribute to the increased temperature in the Earth's interior and it is mainly this increased mantle potential temperature Tp that controls the dynamics of the crust and upper mantle and the predominant style of tectonics in the Early Earth. We conduct 3D petrological-magmatic-thermomechanical numerical modelling experiments of the crust and upper mantle under Early Earth conditions using a plume tectonics model setup. For varying crustal structures and a mantle potential temperature increase (ΔTp, compared to present day conditions), a hot lower thermal boundary layer introduces spontaneously developing mantle plumes and after repeated melt removal, depleted mantle lithosphere is formed self-consistently. New crust is produced in the form of both volcanics and plutonics. For an increase in mantle potential temperature ΔTp= 250 K, presumably corresponding to an Archean mantle, models show large amounts of subcrustal decompression melting and consequently large amounts of magmatism, which in turn influence the dynamics. In a first active phase (10-20 Ma) rising diapirs within the crust lead to the formation of the typical dome and keel pattern (e.g. Kaapvaal craton in South Africa, Pilbara craton in northwest Australia). A long passive phase follows with strong growth of crust and lithosphere. Both crust and lithosphere thickness are regulated by thermal-chemical instabilities assisted by lower crust eclogitization. Eclogitization depth is reached after ~80 Ma and linear or cylindrical drips originate at the crust or lithosphere bottom. Delamination of lower crust and lithosphere then occurs as one 'catastrophic' event within the next 20 Ma.

  1. Early Earth tectonics: A high-resolution 3D numerical modelling approach

    NASA Astrophysics Data System (ADS)

    Fischer, R.; Gerya, T.

    2014-12-01

    Early Earth had a higher amount of remaining radiogenic elements as well as a higher amount of leftover primordial heat. Both contributed to the increased temperature in the Earth's interior and it is mainly this increased mantle potential temperature ΔTp that controls the dynamics of the crust and upper mantle and the style of Early Earth tectonics. For a minor increase in temperature ΔTp < 175 K a subduction-collision style ensues which is largely similar to present day plate tectonics. For a moderate increase in ΔTp = 175-250 K subduction can still occur, however plates are strongly weakened and buckling, delamination and Rayleigh-Taylor style dripping of the plate is observed in addition. For higher temperatures ΔTp > 250 K no subduction can be observed anymore and tectonics is dominated by delamination and Rayleigh-Taylor instabilities. We conduct 3D petrological-thermomechanical numerical modelling experiments of the crust and upper mantle under Early Earth conditions and a plume tectonics model setup. For varying crustal structures and an increased mantle potential temperature ΔTp, a thermal anomaly in the bottom temperature boundary introduces a plume. The model is able to self-sufficiently form depleted mantle lithosphere after repeated melt removal. New crust can be produced in the form of volcanics or plutonics. To simulate differentiation the newly formed crust can have a range in composition from basaltic over dacitic to granitic depending on its source rock. Models show large amounts of subcrustal decompression melting and consequently large amounts of new formed crust which in turn influences the dynamics. Mantle and crust are convecting separately. Dome-shaped plutons of mafic or felsic composition can be observed in the crust. Between these domes elongated belts of upper crust, volcanics and sediments are formed. These structures look similar to, for example, the Kaapvaal craton in South Africa where the elongated shape of the Barberton

  2. Automated breast mass detection in 3D reconstructed tomosynthesis volumes: a featureless approach.

    PubMed

    Singh, Swatee; Tourassi, Georgia D; Baker, Jay A; Samei, Ehsan; Lo, Joseph Y

    2008-08-01

    The purpose of this study was to propose and implement a computer aided detection (CADe) tool for breast tomosynthesis. This task was accomplished in two stages-a highly sensitive mass detector followed by a false positive (FP) reduction stage. Breast tomosynthesis data from 100 human subject cases were used, of which 25 subjects had one or more mass lesions and the rest were normal. For stage 1, filter parameters were optimized via a grid search. The CADe identified suspicious locations were reconstructed to yield 3D CADe volumes of interest. The first stage yielded a maximum sensitivity of 93% with 7.7 FPs/breast volume. Unlike traditional CADe algorithms in which the second stage FP reduction is done via feature extraction and analysis, instead information theory principles were used with mutual information as a similarity metric. Three schemes were proposed, all using leave-one-case-out cross validation sampling. The three schemes, A, B, and C, differed in the composition of their knowledge base of regions of interest (ROIs). Scheme A's knowledge base was comprised of all the mass and FP ROIs generated by the first stage of the algorithm. Scheme B had a knowledge base that contained information from mass ROIs and randomly extracted normal ROIs. Scheme C had information from three sources of information-masses, FPs, and normal ROIs. Also, performance was assessed as a function of the composition of the knowledge base in terms of the number of FP or normal ROIs needed by the system to reach optimal performance. The results indicated that the knowledge base needed no more than 20 times as many FPs and 30 times as many normal ROIs as masses to attain maximal performance. The best overall system performance was 85% sensitivity with 2.4 FPs per breast volume for scheme A, 3.6 FPs per breast volume for scheme B, and 3 FPs per breast volume for scheme C. PMID:18777923

  3. Analyzing Remodeling of Cardiac Tissue: A Comprehensive Approach Based on Confocal Microscopy and 3D Reconstructions.

    PubMed

    Seidel, Thomas; Edelmann, J-C; Sachse, Frank B

    2016-05-01

    Microstructural characterization of cardiac tissue and its remodeling in disease is a crucial step in many basic research projects. We present a comprehensive approach for three-dimensional characterization of cardiac tissue at the submicrometer scale. We developed a compression-free mounting method as well as labeling and imaging protocols that facilitate acquisition of three-dimensional image stacks with scanning confocal microscopy. We evaluated the approach with normal and infarcted ventricular tissue. We used the acquired image stacks for segmentation, quantitative analysis and visualization of important tissue components. In contrast to conventional mounting, compression-free mounting preserved cell shapes, capillary lumens and extracellular laminas. Furthermore, the new approach and imaging protocols resulted in high signal-to-noise ratios at depths up to 60 µm. This allowed extensive analyzes revealing major differences in volume fractions and distribution of cardiomyocytes, blood vessels, fibroblasts, myofibroblasts and extracellular space in control vs. infarct border zone. Our results show that the developed approach yields comprehensive data on microstructure of cardiac tissue and its remodeling in disease. In contrast to other approaches, it allows quantitative assessment of all major tissue components. Furthermore, we suggest that the approach will provide important data for physiological models of cardiac tissue at the submicrometer scale. PMID:26399990

  4. [3-D ultrasound in gastroenterology].

    PubMed

    Zoller, W G; Liess, H

    1994-06-01

    Three-dimensional (3D) sonography represents a development of noninvasive diagnostic imaging by real-time two-dimensional (2D) sonography. The use of transparent rotating scans, comparable to a block of glass, generates a 3D effect. The objective of the present study was to optimate 3D presentation of abdominal findings. Additional investigations were made with a new volumetric program to determine the volume of selected findings of the liver. The results were compared with the estimated volumes of 2D sonography and 2D computer tomography (CT). For the processing of 3D images, typical parameter constellations were found for the different findings, which facilitated processing of 3D images. In more than 75% of the cases examined we found an optimal 3D presentation of sonographic findings with respect to the evaluation criteria developed by us for the 3D imaging of processed data. Great differences were found for the estimated volumes of the findings of the liver concerning the three different techniques applied. 3D ultrasound represents a valuable method to judge morphological appearance in abdominal findings. The possibility of volumetric measurements enlarges its potential diagnostic significance. Further clinical investigations are necessary to find out if definite differentiation between benign and malign findings is possible. PMID:7919882

  5. A Comprehensive Automated 3D Approach for Building Extraction, Reconstruction, and Regularization from Airborne Laser Scanning Point Clouds

    PubMed Central

    Dorninger, Peter; Pfeifer, Norbert

    2008-01-01

    Three dimensional city models are necessary for supporting numerous management applications. For the determination of city models for visualization purposes, several standardized workflows do exist. They are either based on photogrammetry or on LiDAR or on a combination of both data acquisition techniques. However, the automated determination of reliable and highly accurate city models is still a challenging task, requiring a workflow comprising several processing steps. The most relevant are building detection, building outline generation, building modeling, and finally, building quality analysis. Commercial software tools for building modeling require, generally, a high degree of human interaction and most automated approaches described in literature stress the steps of such a workflow individually. In this article, we propose a comprehensive approach for automated determination of 3D city models from airborne acquired point cloud data. It is based on the assumption that individual buildings can be modeled properly by a composition of a set of planar faces. Hence, it is based on a reliable 3D segmentation algorithm, detecting planar faces in a point cloud. This segmentation is of crucial importance for the outline detection and for the modeling approach. We describe the theoretical background, the segmentation algorithm, the outline detection, and the modeling approach, and we present and discuss several actual projects.

  6. Early Earth tectonics: A high-resolution 3D numerical modelling approach

    NASA Astrophysics Data System (ADS)

    Fischer, Ria; Gerya, Taras

    2015-04-01

    Early Earth had a higher amount of remaining radiogenic elements as well as a higher amount of leftover primordial heat. Both contributed to the increased temperature in the Earth's interior and it is mainly this increased mantle potential temperature ΔTp that controls the dynamics of the crust and upper mantle and the style of Early Earth tectonics. We conduct 3D petrological-thermomechanical numerical modelling experiments of the crust and upper mantle under Early Earth conditions using a plume tectonics model setup. For varying crustal structures and an increased mantle potential temperature ΔTp, a hot lower thermal boundary layer is used to introduce spontaneously developing mantle plumes. The model is able to self-sufficiently form depleted mantle lithosphere after repeated melt removal. New crust can be produced in the form of volcanics and/or plutonics. To simulate differentiation the newly formed crust can have a range in composition from basaltic to granitic depending on its source rock. For a major increase in the mantle temperature, presumably corresponding to an Archean mantle (ΔTp = 200 - 300K compared to present day conditions), models show large amounts of subcrustal decompression melting and consequently large amounts of volcanics, which in turn influence the dynamics. Mantle and crust are convecting separately. Dome-shaped felsic plutons can be observed in the crust. Between these domes elongated belts of downwelling basalt and sediments are formed. Both crust and lithosphere thickness are regulated by thermo-chemical instabilities assisted by lower crust eclogitization: linear or cylindrical drips originating at the crust or lithosphere bottom or delamination of lower crust or lithosphere. Very similar examples of dome and belt structures are still preserved in Archean cratons. One example is the Kaapvaal craton is South Africa where the elongated shape of the Barberton Greenstone Belt, mainly built from mafic rocks and sediments, is surrounded

  7. A Survey on Model Based Approaches for 2D and 3D Visual Human Pose Recovery

    PubMed Central

    Perez-Sala, Xavier; Escalera, Sergio; Angulo, Cecilio; Gonzàlez, Jordi

    2014-01-01

    Human Pose Recovery has been studied in the field of Computer Vision for the last 40 years. Several approaches have been reported, and significant improvements have been obtained in both data representation and model design. However, the problem of Human Pose Recovery in uncontrolled environments is far from being solved. In this paper, we define a general taxonomy to group model based approaches for Human Pose Recovery, which is composed of five main modules: appearance, viewpoint, spatial relations, temporal consistence, and behavior. Subsequently, a methodological comparison is performed following the proposed taxonomy, evaluating current SoA approaches in the aforementioned five group categories. As a result of this comparison, we discuss the main advantages and drawbacks of the reviewed literature. PMID:24594613

  8. Near field 3D displacement of El Mayor-Cupapah Earthquake: A hybrid approach. (Invited)

    NASA Astrophysics Data System (ADS)

    Hinojosa-Corona, A.; Limon, F. J.; Nissen, E.; Glennie, C. L.; Krishnan, A.; Oskin, M. E.; Arrowsmith, R.; Leprince, S.; Saripalli, S.; Arregui, S. M.; Borsa, A. A.; Kreylos, O.; Banesh, D.; Fletcher, J. M.

    2013-12-01

    The surface rupture produced on April 4th of 2010 by the M 7.2 El Mayor-Cucapah Earthquake is an ideal target to be analyzed by remote sensing techniques. It produced over 100 km of scarps, with vertical and horizontal slip on the order of 2 to 3 m in scarcely vegetated, rugged terrain underlain by mostly igneous rocks. A 3D displacement field (DF) was calculated by matching pre- to post-event airborne LiDAR point clouds through the Iterative Closest Point (ICP) algorithm, which first segments the point clouds into discrete windows, and for each, iteratively converges on a rigid body transformation comprising a translation and a rotation that best aligns the pre- to post-event point clouds. After testing different window sizes, we used a square window 100m a side. The El Mayor-Cucapah LiDAR data sets present special challenges for the ICP technique. The point clouds differ considerably in point density, by ~1:700. This, and the lower precision of the pre-earthquake data, limit the accuracy of the DF results. Despite these issues, the vertical and East-West (E-W) components of the DF from ICP very clearly delineate the trace of the surface rupture, showing east-side down dextral-normal motion in agreement with field measurements and the focal mechanism reported for this event. A systematic error in the LiDAR instrument used for the pre-event survey caused severe distortion of the North-South (N-S) component of the LiDAR returns. After reprocessing the source pre-event point cloud in various ways to correct for the systematic error, a more plausible pattern for the N-S component was obtained for the DF. To have another perspective for the horizontal DF, a subpixel correlation analysis of optical satellite images (SPOT 2.5 m panchromatic images) before and after the earthquake, was performed using the COSI-Corr software. We combined the N-S component from this analysis with the E-W and vertical components of the ICP results, and present the analysis of the resulting

  9. Fully automated 3D prostate central gland segmentation in MR images: a LOGISMOS based approach

    NASA Astrophysics Data System (ADS)

    Yin, Yin; Fotin, Sergei V.; Periaswamy, Senthil; Kunz, Justin; Haldankar, Hrishikesh; Muradyan, Naira; Turkbey, Baris; Choyke, Peter

    2012-02-01

    One widely accepted classification of a prostate is by a central gland (CG) and a peripheral zone (PZ). In some clinical applications, separating CG and PZ from the whole prostate is useful. For instance, in prostate cancer detection, radiologist wants to know in which zone the cancer occurs. Another application is for multiparametric MR tissue characterization. In prostate T2 MR images, due to the high intensity variation between CG and PZ, automated differentiation of CG and PZ is difficult. Previously, we developed an automated prostate boundary segmentation system, which tested on large datasets and showed good performance. Using the results of the pre-segmented prostate boundary, in this paper, we proposed an automated CG segmentation algorithm based on Layered Optimal Graph Image Segmentation of Multiple Objects and Surfaces (LOGISMOS). The designed LOGISMOS model contained both shape and topology information during deformation. We generated graph cost by training classifiers and used coarse-to-fine search. The LOGISMOS framework guarantees optimal solution regarding to cost and shape constraint. A five-fold cross-validation approach was applied to training dataset containing 261 images to optimize the system performance and compare with a voxel classification based reference approach. After the best parameter settings were found, the system was tested on a dataset containing another 261 images. The mean DSC of 0.81 for the test set indicates that our approach is promising for automated CG segmentation. Running time for the system is about 15 seconds.

  10. A new approach for magnetic curves in 3D Riemannian manifolds

    SciTech Connect

    Bozkurt, Zehra Gök, Ismail Yaylı, Yusuf Ekmekci, F. Nejat

    2014-05-15

    A magnetic field is defined by the property that its divergence is zero in a three-dimensional oriented Riemannian manifold. Each magnetic field generates a magnetic flow whose trajectories are curves called as magnetic curves. In this paper, we give a new variational approach to study the magnetic flow associated with the Killing magnetic field in a three-dimensional oriented Riemann manifold, (M{sup 3}, g). And then, we investigate the trajectories of the magnetic fields called as N-magnetic and B-magnetic curves.

  11. New 3D-Culture Approaches to Study Interactions of Bone Marrow Adipocytes with Metastatic Prostate Cancer Cells

    PubMed Central

    Herroon, Mackenzie Katheryn; Diedrich, Jonathan Driscoll; Podgorski, Izabela

    2016-01-01

    Adipocytes are a major component of the bone marrow that can critically affect metastatic progression in bone. Understanding how the marrow fat cells influence growth, behavior, and survival of tumor cells requires utilization of in vitro cell systems that can closely mimic the physiological microenvironment. Herein, we present two new three-dimensional (3D) culture approaches to study adipocyte–tumor cell interactions in vitro. The first is a transwell-based system composed of the marrow-derived adipocytes in 3D collagen I gels and reconstituted basement membrane-overlayed prostate tumor cell spheroids. Tumor cells cultured under these 3D conditions are continuously exposed to adipocyte-derived factors, and their response can be evaluated by morphological and immunohistochemical analyses. We show via immunofluorescence analysis of metabolism-associated proteins that under 3D conditions tumor cells have significantly different metabolic response to adipocytes than tumor cells grown in 2D culture. We also demonstrate that this model allows for incorporation of other cell types, such as bone marrow macrophages, and utilization of dye-quenched collagen substrates for examination of proteolysis-driven responses to adipocyte- and macrophage-derived factors. Our second 3D culture system is designed to study tumor cell invasion toward the adipocytes and the consequent interaction between the two cell types. In this model, marrow adipocytes are separated from the fluorescently labeled tumor cells by a layer of collagen I. At designated time points, adipocytes are stained with BODIPY and confocal z-stacks are taken through the depth of the entire culture to determine the distance traveled between the two cell types over time. We demonstrate that this system can be utilized to study effects of candidate factors on tumor invasion toward the adipocytes. We also show that immunohistochemical analyses can be performed to evaluate the impact of direct interaction of prostate

  12. Magmatic Systems in 3-D

    NASA Astrophysics Data System (ADS)

    Kent, G. M.; Harding, A. J.; Babcock, J. M.; Orcutt, J. A.; Bazin, S.; Singh, S.; Detrick, R. S.; Canales, J. P.; Carbotte, S. M.; Diebold, J.

    2002-12-01

    Multichannel seismic (MCS) images of crustal magma chambers are ideal targets for advanced visualization techniques. In the mid-ocean ridge environment, reflections originating at the melt-lens are well separated from other reflection boundaries, such as the seafloor, layer 2A and Moho, which enables the effective use of transparency filters. 3-D visualization of seismic reflectivity falls into two broad categories: volume and surface rendering. Volumetric-based visualization is an extremely powerful approach for the rapid exploration of very dense 3-D datasets. These 3-D datasets are divided into volume elements or voxels, which are individually color coded depending on the assigned datum value; the user can define an opacity filter to reject plotting certain voxels. This transparency allows the user to peer into the data volume, enabling an easy identification of patterns or relationships that might have geologic merit. Multiple image volumes can be co-registered to look at correlations between two different data types (e.g., amplitude variation with offsets studies), in a manner analogous to draping attributes onto a surface. In contrast, surface visualization of seismic reflectivity usually involves producing "fence" diagrams of 2-D seismic profiles that are complemented with seafloor topography, along with point class data, draped lines and vectors (e.g. fault scarps, earthquake locations and plate-motions). The overlying seafloor can be made partially transparent or see-through, enabling 3-D correlations between seafloor structure and seismic reflectivity. Exploration of 3-D datasets requires additional thought when constructing and manipulating these complex objects. As numbers of visual objects grow in a particular scene, there is a tendency to mask overlapping objects; this clutter can be managed through the effective use of total or partial transparency (i.e., alpha-channel). In this way, the co-variation between different datasets can be investigated

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

    PubMed

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

    2014-01-01

    The aim of this study is to investigate the use of computational fluid dynamics (CFD) to predict the solid separation efficiency of a hydrodynamic separator. The numerical difficulty concerns the discretization of the geometry to simulate both the global behavior and the local phenomena that occur near the screen. In this context, a CFD multiscale approach was used: a global model (at the scale of the device) is used to observe the hydrodynamic behavior within the device; a local model (portion of the screen) is used to determine the local phenomena that occur near the screen. The Eulerian-Lagrangian approach was used to model the particle trajectories in both models. The global model shows the influence of the particles' characteristics on the trapping efficiency. A high density favors the sedimentation. In contrast, particles with small densities (1,040 kg/m(3)) are steered by the hydrodynamic behavior and can potentially be trapped by the separator. The use of the local model allows us to observe the particle trajectories near the screen. A comparison between two types of screens (perforated plate vs expanded metal) highlights the turbulent effects created by the shape of the screen. PMID:24622557

  14. RGB color calibration for quantitative image analysis: the "3D thin-plate spline" warping approach.

    PubMed

    Menesatti, Paolo; Angelini, Claudio; Pallottino, Federico; Antonucci, Francesca; Aguzzi, Jacopo; Costa, Corrado

    2012-01-01

    In the last years the need to numerically define color by its coordinates in n-dimensional space has increased strongly. Colorimetric calibration is fundamental in food processing and other biological disciplines to quantitatively compare samples' color during workflow with many devices. Several software programmes are available to perform standardized colorimetric procedures, but they are often too imprecise for scientific purposes. In this study, we applied the Thin-Plate Spline interpolation algorithm to calibrate colours in sRGB space (the corresponding Matlab code is reported in the Appendix). This was compared with other two approaches. The first is based on a commercial calibration system (ProfileMaker) and the second on a Partial Least Square analysis. Moreover, to explore device variability and resolution two different cameras were adopted and for each sensor, three consecutive pictures were acquired under four different light conditions. According to our results, the Thin-Plate Spline approach reported a very high efficiency of calibration allowing the possibility to create a revolution in the in-field applicative context of colour quantification not only in food sciences, but also in other biological disciplines. These results are of great importance for scientific color evaluation when lighting conditions are not controlled. Moreover, it allows the use of low cost instruments while still returning scientifically sound quantitative data. PMID:22969337

  15. Assessing a novel approach for predicting local 3D protein structures from sequence.

    PubMed

    Benros, Cristina; de Brevern, Alexandre G; Etchebest, Catherine; Hazout, Serge

    2006-03-01

    We developed a novel approach for predicting local protein structure from sequence. It relies on the Hybrid Protein Model (HPM), an unsupervised clustering method we previously developed. This model learns three-dimensional protein fragments encoded into a structural alphabet of 16 protein blocks (PBs). Here, we focused on 11-residue fragments encoded as a series of seven PBs and used HPM to cluster them according to their local similarities. We thus built a library of 120 overlapping prototypes (mean fragments from each cluster), with good three-dimensional local approximation, i.e., a mean accuracy of 1.61 A Calpha root-mean-square distance. Our prediction method is intended to optimize the exploitation of the sequence-structure relations deduced from this library of long protein fragments. This was achieved by setting up a system of 120 experts, each defined by logistic regression to optimize the discrimination from sequence of a given prototype relative to the others. For a target sequence window, the experts computed probabilities of sequence-structure compatibility for the prototypes and ranked them, proposing the top scorers as structural candidates. Predictions were defined as successful when a prototype <2.5 A from the true local structure was found among those proposed. Our strategy yielded a prediction rate of 51.2% for an average of 4.2 candidates per sequence window. We also proposed a confidence index to estimate prediction quality. Our approach predicts from sequence alone and will thus provide valuable information for proteins without structural homologs. Candidates will also contribute to global structure prediction by fragment assembly. PMID:16385557

  16. High-throughput morphometric analysis of pulmonary airways in MSCT via a mixed 3D/2D approach

    NASA Astrophysics Data System (ADS)

    Ortner, Margarete; Fetita, Catalin; Brillet, Pierre-Yves; Pr"teux, Françoise; Grenier, Philippe

    2011-03-01

    Asthma and COPD are complex airway diseases with an increased incidence estimated for the next decade. Today, the mechanisms and relationships between airway structure/physiology and the clinical phenotype and genotype are not completely understood. We thus lack the tools to predict disease progression or therapeutic responses. One of the main causes is our limited ability to assess the complexity of airway diseases in large populations of patients with appropriate controls. Multi-slice computed tomography (MSCT) imaging opened the way to the non-invasive assessment of airway physiology and structure, but the use of such technology in large cohorts requires a high degree of automation of the measurements. This paper develops an investigation framework and the associated image quantification tools for high-throughput analysis of airways in MSCT. A mixed approach is proposed, combining 3D and cross-section measurements of the airway tree where the user-interaction is limited to the choice of the desired analysis patterns. Such approach relies on the fully-automated segmentation of the 3D airway tree, caliber estimation and visualization based on morphologic granulometry, central axis computation and tree segment selection, cross-section morphometry of airway lumen and wall, and bronchus longitudinal shape analysis for stenosis/bronciectasis detection and measure validation. The developed methodology has been successfully applied to a cohort of 96 patients from a multi-center clinical study of asthma control in moderate and persistent asthma.

  17. A maximum likelihood approach to diffeomorphic speckle tracking for 3D strain estimation in echocardiography.

    PubMed

    Curiale, Ariel H; Vegas-Sánchez-Ferrero, Gonzalo; Bosch, Johan G; Aja-Fernández, Santiago

    2015-08-01

    The strain and strain-rate measures are commonly used for the analysis and assessment of regional myocardial function. In echocardiography (EC), the strain analysis became possible using Tissue Doppler Imaging (TDI). Unfortunately, this modality shows an important limitation: the angle between the myocardial movement and the ultrasound beam should be small to provide reliable measures. This constraint makes it difficult to provide strain measures of the entire myocardium. Alternative non-Doppler techniques such as Speckle Tracking (ST) can provide strain measures without angle constraints. However, the spatial resolution and the noisy appearance of speckle still make the strain estimation a challenging task in EC. Several maximum likelihood approaches have been proposed to statistically characterize the behavior of speckle, which results in a better performance of speckle tracking. However, those models do not consider common transformations to achieve the final B-mode image (e.g. interpolation). This paper proposes a new maximum likelihood approach for speckle tracking which effectively characterizes speckle of the final B-mode image. Its formulation provides a diffeomorphic scheme than can be efficiently optimized with a second-order method. The novelty of the method is threefold: First, the statistical characterization of speckle generalizes conventional speckle models (Rayleigh, Nakagami and Gamma) to a more versatile model for real data. Second, the formulation includes local correlation to increase the efficiency of frame-to-frame speckle tracking. Third, a probabilistic myocardial tissue characterization is used to automatically identify more reliable myocardial motions. The accuracy and agreement assessment was evaluated on a set of 16 synthetic image sequences for three different scenarios: normal, acute ischemia and acute dyssynchrony. The proposed method was compared to six speckle tracking methods. Results revealed that the proposed method is the most

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

    SciTech Connect

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

    2012-11-15

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

  19. One-eyed stereo: a general approach to modeling 3-d scene geometry.

    PubMed

    Strat, T M; Fischler, M A

    1986-06-01

    A single two-dimensional image is an ambiguous representation of the three-dimensional world¿many different scenes could have produced the same image¿yet the human visual system is ex-tremely successful at recovering a qualitatively correct depth model from this type of representation. Workers in the field of computational vision have devised a number of distinct schemes that attempt to emulate this human capability; these schemes are collectively known as ``shape from...'' methods (e.g., shape from shading, shape from texture, or shape from contour). In this paper we contend that the distinct assumptions made in each of these schemes is tantamount to providing a second (virtual) image of the original scene, and that each of these approaches can be translated into a conventional stereo formalism. In particular, we show that it is frequently possible to structure the problem as one of recovering depth from a stereo pair consisting of the supplied perspective image (the original image) and an hypothesized orthographic image (the virtual image). We present a new algorithm of the form required to accomplish this type of stereo reconstruction task. PMID:21869368

  20. A general approach for DC apparent resistivity evaluation on arbitrarily shaped 3D structures

    NASA Astrophysics Data System (ADS)

    Marescot, Laurent; Rigobert, Stéphane; Palma Lopes, Sérgio; Lagabrielle, Richard; Chapellier, Dominique

    2006-09-01

    This paper presents a general and comprehensive way to evaluate the geometric factors used for the computation of apparent resistivities in the context of DC resistivity mapping and non-destructive investigations, in laboratory or in the field. This technique enables one to consider 3-dimensional objects with arbitrary shape. The expression of the geometric factor results from the early definition of apparent resistivitiy. It is expressed as the ratio of the resistances obtained from measurements to the resistances induced in the medium with unitary resistivity considering the same object geometry and electrode set-up. In this work, a finite element code is used for the computation of the geometric factor. In this code, the electrodes do not need to be located on the nodes of the mesh. This option makes the finite element mesh generation task easier. A first synthetical example illustrates how the present approach could be applied to apparent resistivity mapping in an environment with a complex underground topography. A second example, based on real data in a water tank, illustrates the simulation of a resistivity survey on a structure with finite extent, e.g. a laboratory sample. In both examples, topographic artefacts and effects of material sample shapes are successfully taken into account and reliable apparent resistivity descriptions of the structures are obtained. The effectiveness of the method for the detection of heterogeneities in apparent resistivity maps is highlighted.

  1. Flexible range finding applied to 3D surface synthesis: A pseudo-trinocular approach

    NASA Astrophysics Data System (ADS)

    Hong, Tongminh

    An important area in machine vision and computer graphics is surface modeling, which involves the issue of data acquisition. A new range finding system is proposed which exploits perspective invariance (cross ratio), the targeting capability of structural lighting (slide projector), and epipolar planes' geometry (trinocular strategy). The system allows a fully autonomous calibration process and is highly efficient in terms of speed and accuracy. The system eliminates the ambiguity in disparity matching experienced in stereopsis, the extra image processing encountered in the trinocular system, the tedious reorganization of range data into a rectangular domain for surface modeling, and the scanning process of most active range finders that are not suitable for moving objects. Research described includes the development of several new camera calibration techniques, reformulation of the epipolar lines geometry method, and a rigorous study of the orientation constraints of the sensors (cameras and projector) in order to enhance the robustness of the vision system. The superiority of this new pseudo trinocular approach over the active structural lighting method and the passive binocular and/or trinocular techniques is convincing. It is believed that the proposed range finder has considerable potential for surface modeling.

  2. A modular hierarchical approach to 3D electron microscopy image segmentation.

    PubMed

    Liu, Ting; Jones, Cory; Seyedhosseini, Mojtaba; Tasdizen, Tolga

    2014-04-15

    The study of neural circuit reconstruction, i.e., connectomics, is a challenging problem in neuroscience. Automated and semi-automated electron microscopy (EM) image analysis can be tremendously helpful for connectomics research. In this paper, we propose a fully automatic approach for intra-section segmentation and inter-section reconstruction of neurons using EM images. A hierarchical merge tree structure is built to represent multiple region hypotheses and supervised classification techniques are used to evaluate their potentials, based on which we resolve the merge tree with consistency constraints to acquire final intra-section segmentation. Then, we use a supervised learning based linking procedure for the inter-section neuron reconstruction. Also, we develop a semi-automatic method that utilizes the intermediate outputs of our automatic algorithm and achieves intra-segmentation with minimal user intervention. The experimental results show that our automatic method can achieve close-to-human intra-segmentation accuracy and state-of-the-art inter-section reconstruction accuracy. We also show that our semi-automatic method can further improve the intra-segmentation accuracy. PMID:24491638

  3. Electron scattering from large molecules: a 3d finite element R-matrix approach

    NASA Astrophysics Data System (ADS)

    Tonzani, Stefano; Greene, Chris H.

    2005-05-01

    To solve the Schr"odinger equation for scattering of a low energy electron from a molecule, we present a three-dimensional finite element R-matrix method [S. Tonzani and C. H. Greene, J. Chem. Phys. 122 01411, (2005)]. Using the static exchange and local density approximations, we can use directly the molecular potentials extracted from ab initio codes (GAUSSIAN 98 in the work described here). A local polarization potential based on density functional theory [F. A. Gianturco and A. Rodriguez-Ruiz, Phys. Rev. A 47, 1075 (1993)] approximately describes the long range attraction to the molecular target induced by the scattering electron without adjustable parameters. We have used this approach successfully in calculations of cross sections for small and medium sized molecules (like SF6, XeF6, C60 and Uracil). This method will be useful to treat the electron-induced dynamics of extended molecular systems, possibly of biological interest, where oth er more complex ab initio methods are difficult to apply.

  4. Transferring Multi-Scale Approaches from 3d City Modeling to Ifc-Based Tunnel Modeling

    NASA Astrophysics Data System (ADS)

    Borrmann, A.; Kolbe, T. H.; Donaubauer, A.; Steuer, H.; Jubierre, J. R.

    2013-09-01

    A multi-scale representation of the built environment is required to provide information with the adequate level of detail (LoD) for different use cases and objectives. This applies not only to the visualization of city and building models, but in particular to their use in the context of planning and analysis tasks. While in the field of Geographic Information Systems, the handling of multi-scale representations is well established and understood, no formal approaches for incorporating multi-scale methods exist in the field of Building Information Modeling (BIM) so far. However, these concepts are much needed to better support highly dynamic planning processes that make use of very rough information about the facility under design in the early stages and provide increasingly detailed and fine-grained information in later stages. To meet these demands, this paper presents a comprehensive concept for incorporating multi-scale representations with infrastructural building information models, with a particular focus on the representation of shield tunnels. Based on a detailed analysis of the data modeling methods used in CityGML for capturing multiscale representations and the requirements present in the context of infrastructure planning projects, we discuss potential extensions to the BIM data model Industry Foundation Classes (IFC). Particular emphasis is put on providing means for preserving the consistency of the representation across the different Levels-of-Detail (LoD). To this end we make use of a procedural geometry description which makes it possible to define explicit dependencies between geometric entities on different LoDs. The modification of an object on a coarse level consequently results in an automated update of all dependent objects on the finer levels. Finally we discuss the transformation of the IFC-based multi-scale tunnel model into a CityGML compliant tunnel representation.

  5. A robust and efficient approach to detect 3D rectal tubes from CT colonography

    SciTech Connect

    Yang Xiaoyun; Slabaugh, Greg

    2011-11-15

    Purpose: The rectal tube (RT) is a common source of false positives (FPs) in computer-aided detection (CAD) systems for CT colonography. A robust and efficient detection of RT can improve CAD performance by eliminating such ''obvious'' FPs and increase radiologists' confidence in CAD. Methods: In this paper, we present a novel and robust bottom-up approach to detect the RT. Probabilistic models, trained using kernel density estimation on simple low-level features, are employed to rank and select the most likely RT tube candidate on each axial slice. Then, a shape model, robustly estimated using random sample consensus (RANSAC), infers the global RT path from the selected local detections. Subimages around the RT path are projected into a subspace formed from training subimages of the RT. A quadratic discriminant analysis (QDA) provides a classification of a subimage as RT or non-RT based on the projection. Finally, a bottom-top clustering method is proposed to merge the classification predictions together to locate the tip position of the RT. Results: Our method is validated using a diverse database, including data from five hospitals. On a testing data with 21 patients (42 volumes), 99.5% of annotated RT paths have been successfully detected. Evaluated with CAD, 98.4% of FPs caused by the RT have been detected and removed without any loss of sensitivity. Conclusions: The proposed method demonstrates a high detection rate of the RT path, and when tested in a CAD system, reduces FPs caused by the RT without the loss of sensitivity.

  6. Temperature predictions for geothermal exploration - a lithospheric-scale 3D approach applied to the northern Upper Rhine Graben

    NASA Astrophysics Data System (ADS)

    Freymark, Jessica; Sippel, Judith; Scheck-Wenderoth, Magdalena; Bär, Kristian; Fritsche, Johann-Gerhard; Kracht, Matthias; Stiller, Manfred

    2015-04-01

    The Upper Rhine Graben and its prolongation, the Hessian depression, were formed as part of the European Cenozoic Rift System in a complex extensional to transtensional setting. At present-day, the Upper Rhine Graben is one of the regions in Germany that are well suitable for deep geothermal exploitation. In the framework of the EU-funded project "IMAGE" (Integrated Methods for Advanced Geothermal Exploration) we aim to contribute to the development of an integrated and multidisciplinary approach for the exploration of geothermal reservoirs by understanding the processes and properties controlling the spatial distribution of key parameters such as the underground temperature. Typically, reservoir-scale numerical models are developed for predictions on the subsurface hydrothermal conditions and for reducing the risk of drilling non-productive geothermal wells. One major problem related to such models is setting appropriate boundary conditions that define, for instance, how much heat enters the reservoir from greater depths. To understand the deep thermal field of the northern Upper Rhine Graben in the federal state of Hessen, we first develop a 3D structural model that differentiates the main geological units of the lithosphere including the shallow sedimentary fill. This model allows to solve the steady-state conductive heat equation and understand the first-order controlling factors of the regional thermal field. We present the database (e.g. seismic reflection data) and the methodological workflow (involving, e.g., 3D gravity modelling) that were used to develop the lithospheric-scale 3D structural model. Furthermore, we show how certain features of the structural model such as thickness variations of the radiogenic-heat-producing crystalline crust control the temperature distribution in the subsurface.

  7. The AERO system: a 3D-like approach for recording gene expression patterns in the whole mouse embryo.

    PubMed

    Shimizu, Hirohito; Kubo, Atsushi; Uchibe, Kenta; Hashimoto, Megumi; Yokoyama, Shigetoshi; Takada, Shuji; Mitsuoka, Kazuhiko; Asahara, Hiroshi

    2013-01-01

    We have recently constructed a web-based database of gene expression in the mouse whole embryo, EMBRYS (http://embrys.jp/embrys/html/MainMenu.html). To allow examination of gene expression patterns to the fullest extent possible, this database provides both photo images and annotation data. However, since embryos develop via an intricate process of morphogenesis, it would be of great value to track embryonic gene expression from a three dimensional perspective. In fact, several methods have been developed to achieve this goal, but highly laborious procedures and specific operational skills are generally required. We utilized a novel microscopic technique that enables the easy capture of rotational, 3D-like images of the whole embryo. In this method, a rotary head equipped with two mirrors that are designed to obtain an image tilted at 45 degrees to the microscope stage captures serial images at 2-degree intervals. By a simple operation, 180 images are automatically collected. These 2D images obtained at multiple angles are then used to reconstruct 3D-like images, termed AERO images. By means of this system, over 800 AERO images of 191 gene expression patterns were captured. These images can be easily rotated on the computer screen using the EMBRYS database so that researchers can view an entire embryo by a virtual viewing on a computer screen in an unbiased or non-predetermined manner. The advantages afforded by this approach make it especially useful for generating data viewed in public databases. PMID:24146773

  8. The AERO System: A 3D-Like Approach for Recording Gene Expression Patterns in the Whole Mouse Embryo

    PubMed Central

    Hashimoto, Megumi; Yokoyama, Shigetoshi; Takada, Shuji; Mitsuoka, Kazuhiko; Asahara, Hiroshi

    2013-01-01

    We have recently constructed a web-based database of gene expression in the mouse whole embryo, EMBRYS (http://embrys.jp/embrys/html/MainMenu.html). To allow examination of gene expression patterns to the fullest extent possible, this database provides both photo images and annotation data. However, since embryos develop via an intricate process of morphogenesis, it would be of great value to track embryonic gene expression from a three dimensional perspective. In fact, several methods have been developed to achieve this goal, but highly laborious procedures and specific operational skills are generally required. We utilized a novel microscopic technique that enables the easy capture of rotational, 3D-like images of the whole embryo. In this method, a rotary head equipped with two mirrors that are designed to obtain an image tilted at 45 degrees to the microscope stage captures serial images at 2-degree intervals. By a simple operation, 180 images are automatically collected. These 2D images obtained at multiple angles are then used to reconstruct 3D-like images, termed AERO images. By means of this system, over 800 AERO images of 191 gene expression patterns were captured. These images can be easily rotated on the computer screen using the EMBRYS database so that researchers can view an entire embryo by a virtual viewing on a computer screen in an unbiased or non-predetermined manner. The advantages afforded by this approach make it especially useful for generating data viewed in public databases. PMID:24146773

  9. A Unified Approach to Diffusion Direction Sensitive Slice Registration and 3-D DTI Reconstruction From Moving Fetal Brain Anatomy

    PubMed Central

    Fogtmann, Mads; Seshamani, Sharmishtaa; Kroenke, Christopher; Cheng, Xi; Chapman, Teresa; Wilm, Jakob; Rousseau, François

    2014-01-01

    This paper presents an approach to 3-D diffusion tensor image (DTI) reconstruction from multi-slice diffusion weighted (DW) magnetic resonance imaging acquisitions of the moving fetal brain. Motion scatters the slice measurements in the spatial and spherical diffusion domain with respect to the underlying anatomy. Previous image registration techniques have been described to estimate the between slice fetal head motion, allowing the reconstruction of 3-D a diffusion estimate on a regular grid using interpolation. We propose Approach to Unified Diffusion Sensitive Slice Alignment and Reconstruction (AUDiSSAR) that explicitly formulates a process for diffusion direction sensitive DW-slice-to-DTI-volume alignment. This also incorporates image resolution modeling to iteratively deconvolve the effects of the imaging point spread function using the multiple views provided by thick slices acquired in different anatomical planes. The algorithm is implemented using a multi-resolution iterative scheme and multiple real and synthetic data are used to evaluate the performance of the technique. An accuracy experiment using synthetically created motion data of an adult head and a experiment using synthetic motion added to sedated fetal monkey dataset show a significant improvement in motion-trajectory estimation compared to a state-of-the-art approaches. The performance of the method is then evaluated on challenging but clinically typical in utero fetal scans of four different human cases, showing improved rendition of cortical anatomy and extraction of white matter tracts. While the experimental work focuses on DTI reconstruction (second-order tensor model), the proposed reconstruction framework can employ any 5-D diffusion volume model that can be represented by the spatial parameterizations of an orientation distribution function. PMID:24108711

  10. 3d-modelling workflows for trans-nationally shared geological models - first approaches from the project GeoMol

    NASA Astrophysics Data System (ADS)

    Rupf, Isabel

    2013-04-01

    To meet the EU's ambitious targets for carbon emission reduction, renewable energy production has to be strongly upgraded and made more efficient for grid energy storage. Alpine Foreland Basins feature a unique geological inventory which can contribute substantially to tackle these challenges. They offer a geothermal potential and storage capacity for compressed air, as well as space for underground storage of CO2. Exploiting these natural subsurface resources will strongly compete with existing oil and gas claims and groundwater issues. The project GeoMol will provide consistent 3-dimensional subsurface information about the Alpine Foreland Basins based on a holistic and transnational approach. Core of the project GeoMol is a geological framework model for the entire Northern Molasse Basin, complemented by five detailed models in pilot areas, also in the Po Basin, which are dedicated to specific questions of subsurface use. The models will consist of up to 13 litho-stratigraphic horizons ranging from the Cenozoic basin fill down to Mesozoic and late Paleozoic sedimentary rocks and the crystalline basement. More than 5000 wells and 28 000 km seismic lines serve as input data sets for the geological subsurface model. The data have multiple sources and various acquisition dates, and their interpretations have gone through several paradigm changes. Therefore, it is necessary to standardize the data with regards to technical parameters and content prior to further analysis (cf. Capar et al. 2013, EGU2013-5349). Each partner will build its own geological subsurface model with different software solutions for seismic interpretation and 3d-modelling. Therefore, 3d-modelling follows different software- and partner-specific workflows. One of the main challenges of the project is to ensure a seamlessly fitting framework model. It is necessary to define several milestones for cross border checks during the whole modelling process. Hence, the main input data set of the

  11. Genetic approach to reconstruct complex regional geological setting of the Baltic basin in 3D geological model

    NASA Astrophysics Data System (ADS)

    Popovs, K.; Saks, T.; Ukass, J.; Jatnieks, J.

    2012-04-01

    Interpretation of geological structures in 3D geological models is a relatively new research topic that is already standardized in many geological branches. Due to its wide practical application, these models are indispensable and become one of the dominant interpretation methods in reducing geological uncertainties in many geology fields. Traditionally, geological concepts complement quantitative as much as qualitative data to obtain a model deemed acceptable, however, available data very often is insufficient and modeling methods primarily focus on spatial data but geological history usually is mostly neglected for the modeling of large sedimentary basins. A need to better integrate the long and often complex geological history and geological knowledge into modeling procedure is very acute to gain geological insight and improve the quality of geological models. During this research, 3D geological model of the Baltic basin (BB) was created. Because of its complex regional geological setting - wide range of the data sources with multiple scales, resolution and density as well as its various source formats, the study area provides a challenge for the 3D geological modeling. In order to create 3D regional geometrical model for the study area algorithmic genetic approach for model geometry reconstruction was applied. The genetic approach is based on the assumption that post-depositional deformation produce no significant change in sedimentary strata volume, assuming that the strata thickness and its length in a cross sectional plane remains unchanged except as a result of erosion. Assuming that the tectonic deformation occurred in sequential cycles and subsequent tectonic stage strata is separated by regional unconformity as is the case of the BB, there is an opportunity for algorithmic approach in reconstructing these conditions by sequentially reconstructing the layer original thickness. Layer thicknesses were sliced along fault lines, where applicable layer

  12. Edge-based finite element approach to the simulation of geoelectromagnetic induction in a 3-D sphere

    NASA Astrophysics Data System (ADS)

    Yoshimura, Ryokei; Oshiman, Naoto

    2002-02-01

    We present a new simulator based on an edge-based finite element method (FEM) for computing the global-scale electromagnetic (EM) induction responses in a 3-D conducting sphere excited by an external source current for a variety of frequencies. The formulation is in terms of the magnetic vector potential. The edge-element approach assigns the degrees of freedom to the edges rather than to the nodes of the element. This edge-element strictly satisfies the discontinuity of the normal boundary conditions without considering the enforced normal boundary conditions that are usually practiced in a node-based FEM. To verify our simulation code, we compare our results with those of other solvers for two test computations, corresponding to azimuthally symmetric and asymmetric models. The results are in good agreement with one another.

  13. Predictive Modeling of Antioxidant Coumarin Derivatives Using Multiple Approaches: Descriptor-Based QSAR, 3D-Pharmacophore Mapping, and HQSAR.

    PubMed

    Mitra, Indrani; Saha, Achintya; Roy, Kunal

    2013-03-01

    The inability of the systemic antioxidants to alleviate the exacerbation of free radical formation from metabolic outputs and environmental pollutants claims an urgent demand for the identification and design of new chemical entities with potent antioxidant activity. In the present work, different QSAR approaches have been utilized for identifying the essential structural attributes imparting a potential antioxidant activity profile of the coumarin derivatives. The descriptor-based QSAR model provides a quantitative outline regarding the structural prerequisites of the molecules, while 3D pharmacophore and HQSAR models emphasize the favourable spatial arrangement of the various chemical features and the crucial molecular fragments, respectively. All the models infer that the fused benzene ring and the oxygen atom of the pyran ring constituting the parent coumarin nucleus capture the prime pharmacophoric features, imparting superior antioxidant activity to the molecules. The developed models may serve as indispensable query tools for screening untested molecules belonging to the class of coumarin derivatives. PMID:23641329

  14. Real-time rendering method and performance evaluation of composable 3D lenses for interactive VR.

    PubMed

    Borst, Christoph W; Tiesel, Jan-Phillip; Best, Christopher M

    2010-01-01

    We present and evaluate a new approach for real-time rendering of composable 3D lenses for polygonal scenes. Such lenses, usually called "volumetric lenses," are an extension of 2D Magic Lenses to 3D volumes in which effects are applied to scene elements. Although the composition of 2D lenses is well known, 3D composition was long considered infeasible due to both geometric and semantic complexity. Nonetheless, for a scene with multiple interactive 3D lenses, the problem of intersecting lenses must be considered. Intersecting 3D lenses in meaningful ways supports new interfaces such as hierarchical 3D windows, 3D lenses for managing and composing visualization options, or interactive shader development by direct manipulation of lenses providing component effects. Our 3D volumetric lens approach differs from other approaches and is one of the first to address efficient composition of multiple lenses. It is well-suited to head-tracked VR environments because it requires no view-dependent generation of major data structures, allowing caching and reuse of full or partial results. A Composite Shader Factory module composes shader programs for rendering composite visual styles and geometry of intersection regions. Geometry is handled by Boolean combinations of region tests in fragment shaders, which allows both convex and nonconvex CSG volumes for lens shape. Efficiency is further addressed by a Region Analyzer module and by broad-phase culling. Finally, we consider the handling of order effects for composed 3D lenses. PMID:20224135

  15. Steady-state first pass perfusion (SSFPP): A new approach to 3D first-pass myocardial perfusion imaging

    PubMed Central

    Giri, Shivraman; Xue, Hui; Maiseyeu, Andrei; Kroeker, Randall; Rajagopalan, Sanjay; White, Richard D.; Zuehlsdorff, Sven; Raman, Subha V.; Simonetti, Orlando P

    2013-01-01

    Purpose To describe and characterize a new approach to first-pass myocardial perfusion utilizing balanced steady-state free precession acquisition without the use of saturation recovery or other magnetization preparation. Theory The balanced steady-state free precession sequence is inherently sensitive to contrast agent enhancement of the myocardium. This sensitivity can be used to advantage in first-pass myocardial perfusion imaging by eliminating the need for magnetization preparation. Methods Bloch equation simulations, phantom experiments, and in vivo 2D imaging studies were run comparing the proposed technique with three other methods: saturation recovery spoiled gradient echo, saturation recovery steady-state free precession, and steady-state spoiled gradient echo without magnetization preparation. Additionally, an acquisition-reconstruction strategy for 3D perfusion imaging is proposed and initial experience with this approach is demonstrated in healthy subjects and one patient. Results Phantom experiments verified simulation results showing the sensitivity of the balanced steady-state free precession sequence to contrast agent enhancement in solid tissue is similar to that of magnetization-prepared acquisitions. Images acquired in normal volunteers showed the proposed technique provided superior signal and signal-to-noise ratio compared with all other sequences at baseline as well as post-contrast. Conclusion A new approach to first-pass myocardial perfusion is presented that obviates the need for magnetization preparation and provides high signal-to-noise ratio. PMID:23440705

  16. Numerical Simulation of 3D Thermo-Elastic Fatigue Crack Growth Problems Using Coupled FE-EFG Approach

    NASA Astrophysics Data System (ADS)

    Pathak, Himanshu; Singh, Akhilendra; Singh, Indra Vir

    2016-06-01

    In this work, finite element method (FEM) and element free Galerkin method (EFGM) are coupled for solving 3D crack domains subjected to cyclic thermal load of constant amplitude. Crack growth contours and fatigue life have been obtained for each of the considered numerical examples. Thermo-elastic problems are decoupled into thermal and elastic problems . Firstly, the unknown temperature field is obtained by solving heat conduction equation, then, it is used as the input load in the elastic problem to calculate the displacement and stress fields. The geometrical discontinuity across crack surface is modelled by extrinsically enriched EFGM and the remaining part of the domain is approximated by standard finite element method. At the crack interface, a ramp function based interpolation scheme has been implemented. This coupled approach combines the advantages of both EFGM and FEM. A linear successive crack increment approach is used to model crack growth. The growing crack surface is traced by level set function. Standard Paris law is used for life estimation of the three-dimensional crack models. Different cases of planar and non-planar crack problems have been solved and their results are compared with the results obtained using extended finite element method to check accuracy, efficiency and robustness of the coupled FE-EFG approach implemented in this study.

  17. Hierarchical Statistical 3D ' Atomistic' Simulation of Decanano MOSFETs: Drift-Diffusion, Hydrodynamic and Quantum Mechanical Approaches

    NASA Technical Reports Server (NTRS)

    Asenov, Asen; Brown, A. R.; Slavcheva, G.; Davies, J. H.

    2000-01-01

    When MOSFETs are scaled to deep submicron dimensions the discreteness and randomness of the dopant charges in the channel region introduces significant fluctuations in the device characteristics. This effect, predicted 20 year ago, has been confirmed experimentally and in simulation studies. The impact of the fluctuations on the functionality, yield, and reliability of the corresponding systems shifts the paradigm of the numerical device simulation. It becomes insufficient to simulate only one device representing one macroscopical design in a continuous charge approximation. An ensemble of macroscopically identical but microscopically different devices has to be characterized by simulation of statistically significant samples. The aims of the numerical simulations shift from predicting the characteristics of a single device with continuous doping towards estimating the mean values and the standard deviations of basic design parameters such as threshold voltage, subthreshold slope, transconductance, drive current, etc. for the whole ensemble of 'atomistically' different devices in the system. It has to be pointed out that even the mean values obtained from 'atomistic' simulations are not identical to the values obtained from continuous doping simulations. In this paper we present a hierarchical approach to the 'atomistic' simulation of aggressively scaled decanano MOSFETs. A full scale 3D drift-diffusion'atomostic' simulation approach is first described and used for verification of the more economical, but also more restricted, options. To reduce the processor time and memory requirements at high drain voltage we have developed a self-consistent option based on a thin slab solution of the current continuity equation only in the channel region. This is coupled to the Poisson's equation solution in the whole simulation domain in the Gummel iteration cycles. The accuracy of this approach is investigated in comparison with the full self-consistent solution. At low drain

  18. An Approach to Develop 3d Geo-Dbms Topological Operators by Re-Using Existing 2d Operators

    NASA Astrophysics Data System (ADS)

    Xu, D.; Zlatanova, S.

    2013-09-01

    Database systems are continuously extending their capabilities to store, process and analyse 3D data. Topological relationships which describe the interaction of objects in space is one of the important spatial issues. However, spatial operators for 3D objects are still insufficient. In this paper we present the development of a new 3D topological function to distinguish intersections of 3D planar polygons. The development uses existing 2D functions in the DBMS and two geometric transformations (rotation and projection). This function is tested for a real dataset to detect overlapping 3D city objects. The paper presents the algorithms and analyses the challenges. Suggestions for improvements of the current algorithm as well as possible extensions to handle more 3D topological cases are discussed at the end.

  19. A volume of intersection approach for on-the-fly system matrix calculation in 3D PET image reconstruction

    NASA Astrophysics Data System (ADS)

    Lougovski, A.; Hofheinz, F.; Maus, J.; Schramm, G.; Will, E.; van den Hoff, J.

    2014-02-01

    The aim of this study is the evaluation of on-the-fly volume of intersection computation for system’s geometry modelling in 3D PET image reconstruction. For this purpose we propose a simple geometrical model in which the cubic image voxels on the given Cartesian grid are approximated with spheres and the rectangular tubes of response (ToRs) are approximated with cylinders. The model was integrated into a fully 3D list-mode PET reconstruction for performance evaluation. In our model the volume of intersection between a voxel and the ToR is only a function of the impact parameter (the distance between voxel centre to ToR axis) but is independent of the relative orientation of voxel and ToR. This substantially reduces the computational complexity of the system matrix calculation. Based on phantom measurements it was determined that adjusting the diameters of the spherical voxel size and the ToR in such a way that the actual voxel and ToR volumes are conserved leads to the best compromise between high spatial resolution, low noise, and suppression of Gibbs artefacts in the reconstructed images. Phantom as well as clinical datasets from two different PET systems (Siemens ECAT HR+ and Philips Ingenuity-TF PET/MR) were processed using the developed and the respective vendor-provided (line of intersection related) reconstruction algorithms. A comparison of the reconstructed images demonstrated very good performance of the new approach. The evaluation showed the respective vendor-provided reconstruction algorithms to possess 34-41% lower resolution compared to the developed one while exhibiting comparable noise levels. Contrary to explicit point spread function modelling our model has a simple straight-forward implementation and it should be easy to integrate into existing reconstruction software, making it competitive to other existing resolution recovery techniques.

  20. Iso-sciatic point: novel approach to distinguish shadowing 3-D mask effects from scanner aberrations in extreme ultraviolet lithography

    NASA Astrophysics Data System (ADS)

    Leunissen, Leonardus H. A.; Gronheid, Roel; Gao, Weimin

    2006-06-01

    Extreme ultraviolet lithography (EUVL) uses a reflective mask with a multilayer coating. Therefore, the illumination is an off-axis ring field system that is non-telecentric on the mask side. This non-zero angle of incidence combined with the three-dimensional mask topography results in the so-called "shadowing effect". The shadowing causes the printed CD to depend on the orientation as well as on the position in the slit and it will significantly influence the image formation [1,2]. In addition, simulations show that the Bossung curves are asymmetrical due to 3-D mask effects and their best focus depends on the shadowing angle [3]. Such tilts in the Bossung curves are usually associated with aberrations in the optical system. In this paper, we describe an approach in which both properties can be disentangled. Bossung curve simulations with varying effective angles of incidence (between 0 and 6 degrees) show that at discrete defocus offsets, the printed linewidth is independent of the incident angle (and thus independent of the shadowing effect), the so-called iso-sciatic (constant shadowing) point. For an ideal optical system this means that the size of a printed feature with a given mask-CD and orientation does not change through slit. With a suitable test structure it is possible to use this effect to distinguish between mask topography and imaging effects from aberrations through slit. Simulations for the following aberrations tested the approach: spherical, coma and astigmatism.

  1. Modeling Semantic Emotion Space Using a 3D Hypercube-Projection: An Innovative Analytical Approach for the Psychology of Emotions

    PubMed Central

    Trnka, Radek; Lačev, Alek; Balcar, Karel; Kuška, Martin; Tavel, Peter

    2016-01-01

    The widely accepted two-dimensional circumplex model of emotions posits that most instances of human emotional experience can be understood within the two general dimensions of valence and activation. Currently, this model is facing some criticism, because complex emotions in particular are hard to define within only these two general dimensions. The present theory-driven study introduces an innovative analytical approach working in a way other than the conventional, two-dimensional paradigm. The main goal was to map and project semantic emotion space in terms of mutual positions of various emotion prototypical categories. Participants (N = 187; 54.5% females) judged 16 discrete emotions in terms of valence, intensity, controllability and utility. The results revealed that these four dimensional input measures were uncorrelated. This implies that valence, intensity, controllability and utility represented clearly different qualities of discrete emotions in the judgments of the participants. Based on this data, we constructed a 3D hypercube-projection and compared it with various two-dimensional projections. This contrasting enabled us to detect several sources of bias when working with the traditional, two-dimensional analytical approach. Contrasting two-dimensional and three-dimensional projections revealed that the 2D models provided biased insights about how emotions are conceptually related to one another along multiple dimensions. The results of the present study point out the reductionist nature of the two-dimensional paradigm in the psychological theory of emotions and challenge the widely accepted circumplex model. PMID:27148130

  2. A methodological approach for 3-D Vs inversion from ambient noise tomography in a very heterogeneous crust

    NASA Astrophysics Data System (ADS)

    Macquet, M.; Paul, A.; Pedersen, H.

    2013-12-01

    A 3-D Vs model is the output of ambient noise tomography with the greatest add-on value. Computing this model is however difficult, especially in regions with very heterogeneous crustal structure. We propose here a new approach to invert group velocity data from ambient noise tomography for 3-D Vs structure, which gives good result even with strong lateral variations of the seismic structure. The study region is the Pyrenees mountain range s.l., at the border between France and Spain, as it includes 2 thick sedimentary basins surrounded by crystalline outcrops in the Pyrenees and the Massif Central. We use data of a dense temporary seismic broadband array of 49 stations installed in southwestern France at the end of 2010 in the framework of the PYROPE (PYRenean Observational Portable Experiment) project. The dataset also includes records of 70 broadband stations of the third leg of the IberArray project installed at the same time period in northern Spain. The two dense arrays with 60 km average inter-station distance make it possible to obtain high-resolution images of the lithosphere of the Pyrenees, the Ebro and Aquitaine basins and the Bay of Biscay. To complement the two temporary arrays and avoid smearing effects along their edges, we also used records of the French and Catalan permanent broadband networks. As a whole, the dataset includes records of 158 broadband stations. Using one year of data, we computed 12324 two-station correlations of ambient seismic noise records. We applied the processing in two overlapping period intervals: 5s-50s and 30s-75s, the latter to extend the subsequent measurement of group velocities to periods outside the first and secondary microseismic peak. We merged the common part of the 2 dispersion curves using a linear weighting to obtain, for each station pair, a single dispersion curve in the 5-75s period range. These group velocity curves are subsequently used to obtain 2-D group velocity maps using the tomographic method of

  3. Representing surface and subsurface hydrology at hyperresolution for Earth system models: Development of a hybrid 3-D approach

    NASA Astrophysics Data System (ADS)

    Hazenberg, P.; Broxton, P. D.; Brunke, M.; Gochis, D. J.; Lawrence, D. M.; Niu, G. Y.; Pelletier, J. D.; Troch, P. A. A.; Zeng, X.

    2014-12-01

    Traditionally, LSMs for use in Earth system models (ESMs) only account for one-dimensional (1-D) vertical hydrological processes at very coarse resolutions (~100 km). Recently, there has been interest in simulating lateral exchange of surface and subsurface water, as the grid resolution of ESMs increases (currently towards ~20 km) due to advances in computational power.In the current work, we present a new physically-based hydrological model capable of simulating lateral flow at a hyperresolution (1 km pixels) coupled with the vertical soil column of the Community Land Model (CLM), which has a much coarser resolution. Our new approach also uses sub-pixel topographic information to represent small scale lateral-flow processes. As input to our model, we use 1 km data of required surface and subsurface information, such depth to bedrock, hillslope width functions, fractional coverage of hillslopes/wetlands/riparian zones within each 1 km pixel, and a river network. Such data are largely derived from higher-resolution (30 m) topographic data, and will be made available to the community as global products.We have tested our model against measurements over a well instrumented, artificial hillslope at the University of Arizona's Biosphere 2 and found that both our approach and a full 3-D physically-based hydrological model can realistically simulate hydrological states and fluxes. However, computationally, our approach is 2 - 3 orders of magnitude faster than the latter. We are currently testing it for an ESM grid box that covers much of southeastern New York State, which includes the headwaters of the Delaware River, the Susquehana River, and parts of the Mohawk River Basin. Our approach improves upon the 1-D hydrological representation in CLM by representing the subgrid topographic and geomorphological variability in the grid box. The impact of representing such subgrid variability on surface water and energy fluxes will be discussed in our presentation.

  4. 3-D frequency-domain seismic wave modelling in heterogeneous, anisotropic media using a Gaussian Quadrature Grid (GQG) approach

    NASA Astrophysics Data System (ADS)

    Greenhalgh, Stewart; Zhou, Bing; Maurer, Hansruedi

    2010-05-01

    We have developed a modified version of the spectral element method (SEM), called the Gaussian Quadrature Grid (GQG) approach, for frequency domain 3D seismic modelling in arbitrary heterogeneous, anisotropic media. The model may incorporate an arbitrary free-surface topography and irregular subsurface interfaces. Unlike the SEM ,it does not require a powerful mesh generator such as the Delauney Triangular or TetGen. Rather, the GQG approach replaces the element mesh with Gaussian quadrature abscissae to directly sample the physical properties of the model parameters and compute the weighted residual or variational integral. This renders the model discretisation simple and easily matched to the model topography, as well as direct control of the model paramterisation for subsequent inversion. In addition, it offers high accuracy in numerical modelling provided that an appropriate density of the Gaussian quadrature abscissae is employed. The second innovation of the GQG is the incorporation of a new implementation of perfectly matched layers to suppress artificial reflections from the domain margins. We employ PML model parameters (specified complex valued density and elastic moduli) rather than explicitly solving the governing wave equation with a complex co-ordinate system as in conventional approaches. Such an implementation is simple, general, effective and easily extendable to any class of anisotropy and other numerical modelling methods. The accuracy of the GQG approach is controlled by the number of Gaussian quadrature points per minimum wavelength, the so-called sampling density. The optimal sampling density should be the one which enables high definition of geological characteristics and high precision of the variational integral evaluation and spatial differentiation. Our experiments show that satisfactory results can be obtained using sampling densities of 5 points per minimum wavelength. Efficiency of the GQG approach mainly depends on the linear

  5. Automatic Reconstruction of Spacecraft 3D Shape from Imagery

    NASA Astrophysics Data System (ADS)

    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.

  6. 3D Visualisation and Artistic Imagery to Enhance Interest in "Hidden Environments"--New Approaches to Soil Science

    ERIC Educational Resources Information Center

    Gilford, J.; Falconer, R. E.; Wade, R.; Scott-Brown, K. C.

    2014-01-01

    Interactive Virtual Environments (VEs) have the potential to increase student interest in soil science. Accordingly a bespoke "soil atlas" was created using Java3D as an interactive 3D VE, to show soil information in the context of (and as affected by) the over-lying landscape. To display the below-ground soil characteristics, four sets…

  7. A New Approach to Sap Flow Measurement Using 3D Printed Gauges and Open-source Electronics

    NASA Astrophysics Data System (ADS)

    Ham, J. M.; Miner, G. L.; Kluitenberg, G. J.

    2015-12-01

    A new type of sap flow gauge was developed to measure transpiration from herbaceous plants using a modified heat pulse technique. Gauges were fabricated using 3D-printing technology and low-cost electronics to keep the materials cost under $20 (U.S.) per sensor. Each gauge consisted of small-diameter needle probes fastened to a 3D-printed frame. One needle contained a resistance heater to provide a 6 to 8 second heat pulse while the other probes measured the resultant temperature increase at two distances from the heat source. The data acquisition system for the gauges was built from a low-cost Arduino microcontroller. The system read the gauges every 10 minutes and stored the results on a SD card. Different numerical techniques were evaluated for estimating sap velocity from the heat pulse data - including analytical solutions and parameter estimation approaches . Prototype gauges were tested in the greenhouse on containerized corn and sunflower. Sap velocities measured by the gauges were compared to independent gravimetric measurements of whole plant transpiration. Results showed the system could measure daily transpiration to within 3% of the gravimetric measurements. Excellent agreement was observed when two gauges were attached the same stem. Accuracy was not affected by rapidly changing transpiration rates observed under partly cloudy conditions. The gauge-based estimates of stem thermal properties suggested the system may also detect the onset of water stress. A field study showed the gauges could run for 1 to 2 weeks on a small battery pack. Sap flow measurements on multiple corn stems were scaled up by population to estimate field-scale transpiration. During full canopy cover, excellent agreement was observed between the scaled-up sap flow measurements and reference crop evapotranspiration calculated from weather data. Data also showed promise as a way to estimate real-time canopy resistance required for model verification and development. Given the low

  8. Improved vision in forensic documentation: forensic 3D/CAD-supported photogrammetry of bodily injury external surfaces combined with volumetric radiologic scanning of bodily injury internal structures provides more investigative leads and stronger forensic evidence

    NASA Astrophysics Data System (ADS)

    Thali, Michael J.; Braun, Marcel; Kneubuehl, Beat P.; Brueschweiler, Walter; Vock, Peter; Dirnhofer, Richard

    2000-05-01

    In the field of the documentation of forensics-relevant injuries, from the reconstructive point of view, the Forensic, 3D/CAD-supported Photometry plays an important role; particularly so when a detailed 3D reconstruction is vital. This was demonstrated with an experimentally-produced 'injury' to a head model, the 'skin-skull-brain model'. The injury-causing instrument, drawn from a real forensic case, was a specifically formed weapon.

  9. The Effect of Flattening Filter Free on Three-dimensional Conformal Radiation Therapy (3D-CRT), Intensity-Modulated Radiation Therapy (IMRT), and Volumetric Modulated Arc Therapy (VMAT) Plans for Metastatic Brain Tumors from Non-small Cell Lung Cancer.

    PubMed

    Shi, Li-Wan; Lai, You-Qun; Lin, Qin; Ha, Hui-Ming; Fu, Li-Rong

    2015-07-01

    Flattening filter free (FFF) may affect outcome measures of radiotherapy. The objective of this study is to compare the dosimetric parameters in three types of radiotherapy plans, three-dimensional conformal radiation therapy (3D-CRT), intensity-modulated radiation therapy (IMRT), and volumetric modulated arc therapy (VMAT), with or without the flattening filter (FF), developed for the treatment of metastatic brain tumors from non-small cell lung cancer (NSCLC). From July 2013 to October 2013, 3D-CRT, IMRT, and VMAT treatment plans were designed using 6 MV and 10 MV, with and without FF, for 10 patients with brain metastasis from NSCLC. The evaluation of the treatment plans included homogeneity index (HI), conformity index (CI), monitor units (MU), mean dose (Dmean), treatment time, and the influence of FFF on volumes. There was no difference in CI or HI between FFF and FF models with 3D-CRT, IMRT, and VMAT plans. At 6 MV, a lower Dmean was seen in the FFF model of 3D-CRT and in the VMAT plan at 10 MV. In the IMRT 6 MV, IMRT 10 MV, and VMAT 10 MV plans, higher MUs were seen in the FFF models. FFF treatments are similar in quality to FF plans, generally lead to more monitor units, and are associated with shorter treatment times. FFF plans ranked by the order of superiority in terms of a time advantage are VMAT, 3D-CRT, and IMRT. PMID:26011493

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

    NASA Astrophysics Data System (ADS)

    Li, Zhenwei; Sun, Jianyong; Zhang, Jianguo

    2012-02-01

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

  11. Particle acceleration in 3D single current sheets formed in the solar corona and heliosphere: PIC approach

    NASA Astrophysics Data System (ADS)

    Zharkova, V. V.; Siversky, T.

    2015-09-01

    Acceleration of protons and electrons in a reconnecting current sheet (RCS) is investigated with the test particle and particle-in-cell (PIC) approaches in a 3D magnetic topology. PIC simulations confirm a spatial separation of electrons and protons with respect to the midplane depending on the guiding field. Simulation reveals that the separation occurs in magnetic topologies with strong guiding fields and lasts as long as the particles are kept dragged into a current sheet. This separation produces a polarisation electric field induced by the plasma feedback to a presence of accelerated particles, which shape can change from symmetric towards the midplane (for weak guiding field) to fully asymmetric (for strong guiding field). Particles are found accelerated at a midplane of any current sheets present in the heliosphere to the energies up to hundred keV for electrons and hundred MeV for protons. The maximum energy gained by particles during their motion inside the current sheet is defined by its magnetic field topology (the ratio of magnetic field components), the side and location from the X-nullpoint, where the particles enter a current sheet. In strong magnetic fields of the solar corona with weaker guiding fields, electrons are found circulating about the midplane to large distances where proton are getting accelerated, creating about the current sheet midplane clouds of high energy electrons, which can be the source of hard X-ray emission in the coronal sources of flares. These electrons are ejected into the same footpoint as protons after the latter reach the energy sufficicent to break from a current sheet. In a weaker magnetic field of the heliosphere the bounced electrons with lower energies cannot reach the midplane turning instead at some distance D before the current sheet midplane by 180 degrees from their initial motion. Also the beams of accelerated transit and bounced particles are found to generate turbulent electric fields in a form of Langmuir

  12. Efficient framework for deformable 2D-3D registration

    NASA Astrophysics Data System (ADS)

    Fluck, Oliver; Aharon, Shmuel; Khamene, Ali

    2008-03-01

    Using 2D-3D registration it is possible to extract the body transformation between the coordinate systems of X-ray and volumetric CT images. Our initial motivation is the improvement of accuracy of external beam radiation therapy, an effective method for treating cancer, where CT data play a central role in radiation treatment planning. Rigid body transformation is used to compute the correct patient setup. The drawback of such approaches is that the rigidity assumption on the imaged object is not valid for most of the patient cases, mainly due to respiratory motion. In the present work, we address this limitation by proposing a flexible framework for deformable 2D-3D registration consisting of a learning phase incorporating 4D CT data sets and hardware accelerated free form DRR generation, 2D motion computation, and 2D-3D back projection.

  13. A volumetric approach to path-length measurements is essential when treating radiotherapy with modulated beams

    SciTech Connect

    Forde, Elizabeth; Booth, Jeremy; Leech, Michelle

    2014-07-01

    The established dosimetric benefits of intensity-modulated radiation therapy (IMRT) and volumetric-modulated arc therapy have lead to their increased use in prostate radiotherapy. Complimenting these techniques, volumetric image guidance has supported increased positional accuracy. In addition, 3-dimensional image guidance has also allowed for assessment of potential dosimetric variation that can be attributed to a deformation of either internal or external structures, such as rectal distension or body contour. Compounding these issues is the variation of tissue density through which the new field position passes and also the variation of dose across a modulated beam. Despite the growing level of interest in this area, there are only a limited number of articles that examine the effect of a variation in beam path length, particularly across a modulated field. IMRT and volumetric-modulated radiation therapy (VMAT) fields are dynamic in nature, and the dose gradient within these fields is variable. Assessment of variation of path length away from the beam's central axis and across the entire field is vital where there is considerable variation of dose within the field, such as IMRT and VMAT. In these cases, reliance on the traditional central axis to focus skin distances is no longer appropriate. This article discusses these more subtle challenges that may have a significant clinical effect if left unrecognized and undervalued.

  14. Using 1-to-3D modeling approach to constrain thermomechanical evolution of the Dead Sea Transform region

    NASA Astrophysics Data System (ADS)

    Petrunin, Alexey G.; Meneses Rioseco, Ernesto; Sobolev, Stephan V.

    2010-05-01

    (BBS) approach (Petrunin and Sobolev, Geology 2006, PEPI 2008) and estimate the present-day thickness of the brittle layer near the DST as 20-22 km. As a result of the 2.5 D modeling, we significantly narrow down the ranges of model parameters. At the final stage we check the obtained parameters using the 3D model of the Dead Sea basin similar to (Petrunin and Sobolev, Geology 2006) that gives good correlation with the sedimentary subsidence rate and present-day geometry of the basin.

  15. A multiscale approach for the reconstruction of the fiber architecture of the human brain based on 3D-PLI.

    PubMed

    Reckfort, Julia; Wiese, Hendrik; Pietrzyk, Uwe; Zilles, Karl; Amunts, Katrin; Axer, Markus

    2015-01-01

    Structural connectivity of the brain can be conceptionalized as a multiscale organization. The present study is built on 3D-Polarized Light Imaging (3D-PLI), a neuroimaging technique targeting the reconstruction of nerve fiber orientations and therefore contributing to the analysis of brain connectivity. Spatial orientations of the fibers are derived from birefringence measurements of unstained histological sections that are interpreted by means of a voxel-based analysis. This implies that a single fiber orientation vector is obtained for each voxel, which reflects the net effect of all comprised fibers. We have utilized two polarimetric setups providing an object space resolution of 1.3 μm/px (microscopic setup) and 64 μm/px (macroscopic setup) to carry out 3D-PLI and retrieve fiber orientations of the same tissue samples, but at complementary voxel sizes (i.e., scales). The present study identifies the main sources which cause a discrepancy of the measured fiber orientations observed when measuring the same sample with the two polarimetric systems. As such sources the differing optical resolutions and diverging retardances of the implemented waveplates were identified. A methodology was implemented that enables the compensation of measured different systems' responses to the same birefringent sample. This opens up new ways to conduct multiscale analysis in brains by means of 3D-PLI and to provide a reliable basis for the transition between different scales of the nerve fiber architecture. PMID:26388744

  16. Skeletonization approach for characterization of benign vs. malignant single thyroid nodules using 3D contrast enhanced ultrasound

    NASA Astrophysics Data System (ADS)

    Molinari, Filippo; Mantovani, Alice; Deandrea, Maurilio; Limone, Paolo; Garberoglio, Roberto; Suri, Jasjit S.

    2011-03-01

    High-resolution ultrasonography (HRUS) has potentialities in differential diagnosis between malignant and benign thyroid lesions, but interpretative pitfalls remain and accuracy is still poor. We developed an image processing technique for characterizing the intra-nodular vascularization of thyroid lesions. Twenty nodules (ten malignant) were analyzed by 3-D contrast-enhanced ultrasound imaging. The 3-D volumes were preprocessed and skeletonized. Seven vascular parameters were computed on the skeletons: number of vascular trees (NT); vascular density (VD); number of branching nodes (or branching points) (NB); mean vessel radius (MR); 2-D (DM) and 3-D (SOAM) tortuosity; and inflection count metric (ICM). Results showed that the malignant nodules had higher values of NT (83.1 vs. 18.1), VD (00.4 vs. 0.01), NB (1453 vs. 552), DM (51 vs. 18), ICM (19.9 vs. 8.7), and SOAM (26 vs. 11). Quantification of nodular vascularization based on 3-D contrast-enhanced ultrasound and skeletonization could help differential diagnosis of thyroid lesions.

  17. A linear programming approach to reconstructing subcellular structures from confocal images for automated generation of representative 3D cellular models

    PubMed Central

    Wood, Scott T.; Dean, Brian C.; Dean, Delphine

    2013-01-01

    This paper presents a novel computer vision algorithm to analyze 3D stacks of confocal images of fluorescently stained single cells. The goal of the algorithm is to create representative in silico model structures that can be imported into finite element analysis software for mechanical characterization. Segmentation of cell and nucleus boundaries is accomplished via standard thresholding methods. Using novel linear programming methods, a representative actin stress fiber network is generated by computing a linear superposition of fibers having minimum discrepancy compared with an experimental 3D confocal image. Qualitative validation is performed through analysis of seven 3D confocal image stacks of adherent vascular smooth muscle cells (VSMCs) grown in 2D culture. The presented method is able to automatically generate 3D geometries of the cell's boundary, nucleus, and representative F-actin network based on standard cell microscopy data. These geometries can be used for direct importation and implementation in structural finite element models for analysis of the mechanics of a single cell to potentially speed discoveries in the fields of regenerative medicine, mechanobiology, and drug discovery. PMID:23395283

  18. A multiscale approach for the reconstruction of the fiber architecture of the human brain based on 3D-PLI

    PubMed Central

    Reckfort, Julia; Wiese, Hendrik; Pietrzyk, Uwe; Zilles, Karl; Amunts, Katrin; Axer, Markus

    2015-01-01

    Structural connectivity of the brain can be conceptionalized as a multiscale organization. The present study is built on 3D-Polarized Light Imaging (3D-PLI), a neuroimaging technique targeting the reconstruction of nerve fiber orientations and therefore contributing to the analysis of brain connectivity. Spatial orientations of the fibers are derived from birefringence measurements of unstained histological sections that are interpreted by means of a voxel-based analysis. This implies that a single fiber orientation vector is obtained for each voxel, which reflects the net effect of all comprised fibers. We have utilized two polarimetric setups providing an object space resolution of 1.3 μm/px (microscopic setup) and 64 μm/px (macroscopic setup) to carry out 3D-PLI and retrieve fiber orientations of the same tissue samples, but at complementary voxel sizes (i.e., scales). The present study identifies the main sources which cause a discrepancy of the measured fiber orientations observed when measuring the same sample with the two polarimetric systems. As such sources the differing optical resolutions and diverging retardances of the implemented waveplates were identified. A methodology was implemented that enables the compensation of measured different systems' responses to the same birefringent sample. This opens up new ways to conduct multiscale analysis in brains by means of 3D-PLI and to provide a reliable basis for the transition between different scales of the nerve fiber architecture. PMID:26388744

  19. Future Mission Concept for 3-D Aerosol Monitoring From Space Based on Fusion of Remote Sensing Approaches

    NASA Astrophysics Data System (ADS)

    Diner, D. J.; Kahn, R. A.; Hostetler, C. A.; Ferrare, R. A.; Hair, J. W.; Cairns, B.; Torres, O.

    2006-05-01

    extinction independently along with vertically resolved estimates of microphysical properties, thus representing a significant advance relative to simpler backscatter systems such as GLAS and CALIPSO. This fusion of satellite-based approaches is aimed at observing the 3-D distribution of aerosol abundances, sizes, shapes, and absorption, and would represent a major technological advance in our ability to monitor and characterize near-surface particulate matter from space.

  20. A discriminative model-constrained EM approach to 3D MRI brain tissue classification and intensity non-uniformity correction

    NASA Astrophysics Data System (ADS)

    Wels, Michael; Zheng, Yefeng; Huber, Martin; Hornegger, Joachim; Comaniciu, Dorin

    2011-06-01

    We describe a fully automated method for tissue classification, which is the segmentation into cerebral gray matter (GM), cerebral white matter (WM), and cerebral spinal fluid (CSF), and intensity non-uniformity (INU) correction in brain magnetic resonance imaging (MRI) volumes. It combines supervised MRI modality-specific discriminative modeling and unsupervised statistical expectation maximization (EM) segmentation into an integrated Bayesian framework. While both the parametric observation models and the non-parametrically modeled INUs are estimated via EM during segmentation itself, a Markov random field (MRF) prior model regularizes segmentation and parameter estimation. Firstly, the regularization takes into account knowledge about spatial and appearance-related homogeneity of segments in terms of pairwise clique potentials of adjacent voxels. Secondly and more importantly, patient-specific knowledge about the global spatial distribution of brain tissue is incorporated into the segmentation process via unary clique potentials. They are based on a strong discriminative model provided by a probabilistic boosting tree (PBT) for classifying image voxels. It relies on the surrounding context and alignment-based features derived from a probabilistic anatomical atlas. The context considered is encoded by 3D Haar-like features of reduced INU sensitivity. Alignment is carried out fully automatically by means of an affine registration algorithm minimizing cross-correlation. Both types of features do not immediately use the observed intensities provided by the MRI modality but instead rely on specifically transformed features, which are less sensitive to MRI artifacts. Detailed quantitative evaluations on standard phantom scans and standard real-world data show the accuracy and robustness of the proposed method. They also demonstrate relative superiority in comparison to other state-of-the-art approaches to this kind of computational task: our method achieves average

  1. 3D Spectroscopy in Astronomy

    NASA Astrophysics Data System (ADS)

    Mediavilla, Evencio; Arribas, Santiago; Roth, Martin; Cepa-Nogué, Jordi; Sánchez, Francisco

    2011-09-01

    Preface; Acknowledgements; 1. Introductory review and technical approaches Martin M. Roth; 2. Observational procedures and data reduction James E. H. Turner; 3. 3D Spectroscopy instrumentation M. A. Bershady; 4. Analysis of 3D data Pierre Ferruit; 5. Science motivation for IFS and galactic studies F. Eisenhauer; 6. Extragalactic studies and future IFS science Luis Colina; 7. Tutorials: how to handle 3D spectroscopy data Sebastian F. Sánchez, Begona García-Lorenzo and Arlette Pécontal-Rousset.

  2. Speaking Volumes About 3-D

    NASA Technical Reports Server (NTRS)

    2002-01-01

    In 1999, Genex submitted a proposal to Stennis Space Center for a volumetric 3-D display technique that would provide multiple users with a 360-degree perspective to simultaneously view and analyze 3-D data. The futuristic capabilities of the VolumeViewer(R) have offered tremendous benefits to commercial users in the fields of medicine and surgery, air traffic control, pilot training and education, computer-aided design/computer-aided manufacturing, and military/battlefield management. The technology has also helped NASA to better analyze and assess the various data collected by its satellite and spacecraft sensors. Genex capitalized on its success with Stennis by introducing two separate products to the commercial market that incorporate key elements of the 3-D display technology designed under an SBIR contract. The company Rainbow 3D(R) imaging camera is a novel, three-dimensional surface profile measurement system that can obtain a full-frame 3-D image in less than 1 second. The third product is the 360-degree OmniEye(R) video system. Ideal for intrusion detection, surveillance, and situation management, this unique camera system offers a continuous, panoramic view of a scene in real time.

  3. A novel approach for a 2D/3D image registration routine for medical tool navigation in minimally invasive vascular interventions.

    PubMed

    Schwerter, Michael; Lietzmann, Florian; Schad, Lothar R

    2016-09-01

    Minimally invasive interventions are frequently aided by 2D projective image guidance. To facilitate the navigation of medical tools within the patient, information from preoperative 3D images can supplement interventional data. This work describes a novel approach to perform a 3D CT data registration to a single interventional native fluoroscopic frame. The goal of this procedure is to recover and visualize a current 2D interventional tool position in its corresponding 3D dataset. A dedicated routine was developed and tested on a phantom. The 3D position of a guidewire inserted into the phantom could successfully be reconstructed for varying 2D image acquisition geometries. The scope of the routine includes projecting the CT data into the plane of the fluoroscopy. A subsequent registration of the real and virtual projections is performed with an accuracy within the range of 1.16±0.17mm for fixed landmarks. The interventional tool is extracted from the fluoroscopy and matched to the corresponding part of the projected and transformed arterial vasculature. A root mean square error of up to 0.56mm for matched point pairs is reached. The desired 3D view is provided by backprojecting the matched guidewire through the CT array. Due to its potential to reduce patient dose and treatment times, the proposed routine has the capability of reducing patient stress at lower overall treatment costs. PMID:27157275

  4. A statistical approach to estimate the 3D size distribution of spheres from 2D size distributions

    USGS Publications Warehouse

    Kong, M.; Bhattacharya, R.N.; James, C.; Basu, A.

    2005-01-01

    Size distribution of rigidly embedded spheres in a groundmass is usually determined from measurements of the radii of the two-dimensional (2D) circular cross sections of the spheres in random flat planes of a sample, such as in thin sections or polished slabs. Several methods have been devised to find a simple factor to convert the mean of such 2D size distributions to the actual 3D mean size of the spheres without a consensus. We derive an entirely theoretical solution based on well-established probability laws and not constrained by limitations of absolute size, which indicates that the ratio of the means of measured 2D and estimated 3D grain size distribution should be r/4 (=.785). Actual 2D size distribution of the radii of submicron sized, pure Fe0 globules in lunar agglutinitic glass, determined from backscattered electron images, is tested to fit the gamma size distribution model better than the log-normal model. Numerical analysis of 2D size distributions of Fe0 globules in 9 lunar soils shows that the average mean of 2D/3D ratio is 0.84, which is very close to the theoretical value. These results converge with the ratio 0.8 that Hughes (1978) determined for millimeter-sized chondrules from empirical measurements. We recommend that a factor of 1.273 (reciprocal of 0.785) be used to convert the determined 2D mean size (radius or diameter) of a population of spheres to estimate their actual 3D size. ?? 2005 Geological Society of America.

  5. Visualization and volumetric structures from MR images of the brain

    SciTech Connect

    Parvin, B.; Johnston, W.; Robertson, D.

    1994-03-01

    Pinta is a system for segmentation and visualization of anatomical structures obtained from serial sections reconstructed from magnetic resonance imaging. The system approaches the segmentation problem by assigning each volumetric region to an anatomical structure. This is accomplished by satisfying constraints at the pixel level, slice level, and volumetric level. Each slice is represented by an attributed graph, where nodes correspond to regions and links correspond to the relations between regions. These regions are obtained by grouping pixels based on similarity and proximity. The slice level attributed graphs are then coerced to form a volumetric attributed graph, where volumetric consistency can be verified. The main novelty of our approach is in the use of the volumetric graph to ensure consistency from symbolic representations obtained from individual slices. In this fashion, the system allows errors to be made at the slice level, yet removes them when the volumetric consistency cannot be verified. Once the segmentation is complete, the 3D surfaces of the brain can be constructed and visualized.

  6. Estimating the subsurface temperature of Hessen/Germany based on a GOCAD 3D structural model - a comparison of numerical and geostatistical approaches

    NASA Astrophysics Data System (ADS)

    Rühaak, W.; Bär, K.; Sass, I.

    2012-04-01

    Based on a 3D structural GOCAD model of the German federal state Hessen the subsurface temperature distribution is computed. Since subsurface temperature data for greater depth are typically sparse, two different approaches for estimating the spatial subsurface temperature distribution are tested. One approach is the numerical computation of a 3D purely conductive steady state temperature distribution. This numerical model is based on measured thermal conductivity data for all relevant geological units, together with heat flow measurements and surface temperatures. The model is calibrated using continuous temperature-logs. Here only conductive heat transfer is considered as data for convective heat transport at great depth are currently not available. The other approach is by 3D ordinary Kriging; applying a modified approach where the quality of the temperature measurements is taken into account. A difficult but important part here is to derive good variograms for the horizontal and vertical direction. The variograms give necessary information about the spatial dependence. Both approaches are compared and discussed. Differences are mainly related due to convective processes, which are reflected by the interpolation result, but not by the numerical model. Therefore, a comparison of the two results is a good way to obtain information about flow processes in such great depth. This way an improved understanding of this mid enthalpy geothermal reservoir (1000 - 6000 m) is possible. Future work will be the reduction of the small but - especially for depth up to approximately 1000 m - relevant paleoclimate signal.

  7. True 3D chemical dosimetry (gels, plastics): Development and clinical role

    NASA Astrophysics Data System (ADS)

    Schreiner, L. J.

    2015-01-01

    Since the introduction of volumetric chemical dosimetry with Fricke gel dosimeters in the 1980s, three-dimensional (3D) dosimetry has been a promising technique for the clinic, since it provides a unique methodology for 3D dose measurement of the complex conformal dose distributions achieved by modern techniques such as Intensity Modulated and Volumetric Arc Radiation Therapy. In the last decade, the potential for improved clinical applicability has been advanced by the development of improved 3D dosimeters such as normoxic polymer gel systems, radiochromic plastics (such as PRESAGE) and, recently, newer radiochromic gel dosimeters. Some of these new 3D dosimetry systems were enabled by the availability of optical computed tomography imaging systems for fast dose readout. However, despite its promise, true 3D dosimetry is still not widely practiced in the community. Its use has been confined primarily to select centres of expertise and to specialised quality assurance or commissioning roles where other dosimetry techniques are difficult to implement. In this paper I review some of the current 3D chemical dosimeters available, discuss the requirements for their use and briefly review the roles that these systems can provide to complement the other dose delivery validation approaches available in the clinic. I conclude by describing two roles that may be uniquely served by 3D chemical dosimetry in end-to-end process testing and validation in the complex environment coming into play with the development of Image Guided Adaptive Radiation Therapy.

  8. 3D visualisation and artistic imagery to enhance interest in `hidden environments' - new approaches to soil science

    NASA Astrophysics Data System (ADS)

    Gilford, J.; Falconer, R. E.; Wade, R.; Scott-Brown, K. C.

    2014-09-01

    Interactive Virtual Environments (VEs) have the potential to increase student interest in soil science. Accordingly a bespoke 'soil atlas' was created using Java3D as an interactive 3D VE, to show soil information in the context of (and as affected by) the over-lying landscape. To display the below-ground soil characteristics, four sets of artistic illustrations were produced, each set showing the effects of soil organic-matter density and water content on fungal density, to determine potential for visualisations and interactivity in stimulating interest in soil and soil illustrations, interest being an important factor in facilitating learning. The illustrations were created using 3D modelling packages, and a wide range of styles were produced. This allowed a preliminary study of the relative merits of different artistic styles, scientific-credibility, scale, abstraction and 'realism' (e.g. photo-realism or realism of forms), and any relationship between these and the level of interest indicated by the study participants in the soil visualisations and VE. The study found significant differences in mean interest ratings for different soil illustration styles, as well as in the perception of scientific-credibility of these styles, albeit for both measures there was considerable difference of attitude between participants about particular styles. There was also found to be a highly significant positive correlation between participants rating styles highly for interest and highly for scientific-credibility. There was furthermore a particularly high interest rating among participants for seeing temporal soil processes illustrated/animated, suggesting this as a particularly promising method for further stimulating interest in soil illustrations and soil itself.

  9. A direct approach for instantaneous 3D density field reconstruction from background-oriented schlieren (BOS) measurements

    NASA Astrophysics Data System (ADS)

    Nicolas, F.; Todoroff, V.; Plyer, A.; Le Besnerais, G.; Donjat, D.; Micheli, F.; Champagnat, F.; Cornic, P.; Le Sant, Y.

    2016-01-01

    We present a new numerical method for reconstruction of instantaneous density volume from 3D background-oriented schlieren (3DBOS) measurements, with a validation on a dedicated flexible experimental BOS bench. In contrast to previous works, we use a direct formulation where density is estimated from measured deviation fields without the intermediate step of density gradient reconstruction. Regularization techniques are implemented to deal with the ill-posed problem encountered. The resulting high-dimensional optimization is conducted by conjugate gradient techniques. A parallel algorithm, implemented on graphics processing unit, helps to speed up the calculation. The resulting software is validated on synthetic BOS images of a 3D density field issued from a numerical simulation. Then, we describe a dedicated 3DBOS experimental facility which has been built to study various BOS settings and to assess the performance of the proposed numerical reconstruction process. Results on various datasets illustrate the potential of the method for flow characterization and measurement in real-world conditions.

  10. A Multi-Resolution Approach for an Automated Fusion of Different Low-Cost 3D Sensors

    PubMed Central

    Dupuis, Jan; Paulus, Stefan; Behmann, Jan; Plümer, Lutz; Kuhlmann, Heiner

    2014-01-01

    The 3D acquisition of object structures has become a common technique in many fields of work, e.g., industrial quality management, cultural heritage or crime scene documentation. The requirements on the measuring devices are versatile, because spacious scenes have to be imaged with a high level of detail for selected objects. Thus, the used measuring systems are expensive and require an experienced operator. With the rise of low-cost 3D imaging systems, their integration into the digital documentation process is possible. However, common low-cost sensors have the limitation of a trade-off between range and accuracy, providing either a low resolution of single objects or a limited imaging field. Therefore, the use of multiple sensors is desirable. We show the combined use of two low-cost sensors, the Microsoft Kinect and the David laserscanning system, to achieve low-resolved scans of the whole scene and a high level of detail for selected objects, respectively. Afterwards, the high-resolved David objects are automatically assigned to their corresponding Kinect object by the use of surface feature histograms and SVM-classification. The corresponding objects are fitted using an ICP-implementation to produce a multi-resolution map. The applicability is shown for a fictional crime scene and the reconstruction of a ballistic trajectory. PMID:24763255

  11. Fuzzy logic-based approach to wavelet denoising of 3D images produced by time-of-flight cameras.

    PubMed

    Jovanov, Ljubomir; Pižurica, Aleksandra; Philips, Wilfried

    2010-10-25

    In this paper we present a new denoising method for the depth images of a 3D imaging sensor, based on the time-of-flight principle. We propose novel ways to use luminance-like information produced by a time-of flight camera along with depth images. Firstly, we propose a wavelet-based method for estimating the noise level in depth images, using luminance information. The underlying idea is that luminance carries information about the power of the optical signal reflected from the scene and is hence related to the signal-to-noise ratio for every pixel within the depth image. In this way, we can efficiently solve the difficult problem of estimating the non-stationary noise within the depth images. Secondly, we use luminance information to better restore object boundaries masked with noise in the depth images. Information from luminance images is introduced into the estimation formula through the use of fuzzy membership functions. In particular, we take the correlation between the measured depth and luminance into account, and the fact that edges (object boundaries) present in the depth image are likely to occur in the luminance image as well. The results on real 3D images show a significant improvement over the state-of-the-art in the field. PMID:21164605

  12. Visualization of the Links Between Rainfall, Soil Water, Groundwater and Subsurface Stormflow: A Physics-Based 3-D Simulation Approach

    NASA Astrophysics Data System (ADS)

    James, A. L.; McDonnell, J. J.; Tromp-van Meerveld, H.

    2006-12-01

    Recent experimental work at the Panola Mountain Experimental Watershed trenched hillslope (Atlanta, GA) has shown that formation of transient groundwater in bedrock depressions during storm events is a precondition for the generation of subsurface stormflow. While there are clear threshold relations between subsurface stormflow and storm total precipitation, resolving the linkages between rainfall input, soil water recharge, transient groundwater formation and resulting subsurface stormflow has been difficult. Part of the problem is that we lack observational capabilities to interrogate the distributed internal slope response to storm rainfall. Even more problematic is our inability to quantify key boundary conditions like the permeability contrast at the soil-bedrock interface and its spatial variability. This paper uses a 3-D physically-based distributed model of the Panola hillslope (the TOUGH2 simulator) to model and visualize the linkages between storm rainfall, soil water recharge, transient groundwater development and resulting subsurface stormflow. We explore the effect of the bedrock permeability on the development of transient saturation within the hillslope in response to observed storm events. Preliminary results indicate that an increase in the estimated characteristic bedrock permeability at the Panola hillslope can deteriorate and even eliminate the connected patterns of transient saturation developed during a storm event that result in subsurface storm runoff. Our 3-D visualizations and virtual experiments with different bedrock permeability values provide insight into how bedrock permeability, antecedent soil moisture and storm conditions conspire to create the patterns of transient groundwater and resulting subsurface stormflow.

  13. Seasonal dynamics and stoichiometry of the planktonic community in the NW Mediterranean Sea: a 3D modeling approach

    NASA Astrophysics Data System (ADS)

    Alekseenko, Elena; Raybaud, Virginie; Espinasse, Boris; Carlotti, François; Queguiner, Bernard; Thouvenin, Bénédicte; Garreau, Pierre; Baklouti, Melika

    2014-01-01

    The 3D hydrodynamic Model for Applications at Regional Scale (MARS3D) was coupled with a biogeochemical model developed with the Ecological Modular Mechanistic Modelling (Eco3M) numerical tool. The three-dimensional coupled model was applied to the NW Mediterranean Sea to study the dynamics of the key biogeochemical processes in the area in relation with hydrodynamic constraints. In particular, we focused on the temporal and spatial variability of intracellular contents of living and non-living compartments. The conceptual scheme of the biogeochemical model accounts for the complex food web of the NW Mediterranean Sea (34 state variables), using flexible plankton stoichiometry. We used mechanistic formulations to describe most of the biogeochemical processes involved in the dynamics of marine pelagic ecosystems. Simulations covered the period from September 1, 2009 to January 31, 2011 (17 months), which enabled comparison of model outputs with situ measurements made during two oceanographic cruises in the region (Costeau-4: April 27-May 2, 2010 and Costeau-6: January 23-January 27, 2011).

  14. Comparison of different approaches of estimating effective dose from reported exposure data in 3D imaging with interventional fluoroscopy systems

    NASA Astrophysics Data System (ADS)

    Svalkvist, Angelica; Hansson, Jonny; Bâth, Magnus

    2014-03-01

    Three-dimensional (3D) imaging with interventional fluoroscopy systems is today a common examination. The examination includes acquisition of two-dimensional projection images, used to reconstruct section images of the patient. The aim of the present study was to investigate the difference in resulting effective dose obtained using different levels of complexity in calculations of effective doses from these examinations. In the study the Siemens Artis Zeego interventional fluoroscopy system (Siemens Medical Solutions, Erlangen, Germany) was used. Images of anthropomorphic chest and pelvis phantoms were acquired. The exposure values obtained were used to calculate the resulting effective doses from the examinations, using the computer software PCXMC (STUK, Helsinki, Finland). The dose calculations were performed using three different methods: 1. using individual exposure values for each projection image, 2. using the mean tube voltage and the total DAP value, evenly distributed over the projection images, and 3. using the mean kV and the total DAP value, evenly distributed over smaller selection of projection images. The results revealed that the difference in resulting effective dose between the first two methods was smaller than 5%. When only a selection of projection images were used in the dose calculations the difference increased to over 10%. Given the uncertainties associated with the effective dose concept, the results indicate that dose calculations based on average exposure values distributed over a smaller selection of projection angles can provide reasonably accurate estimations of the radiation doses from 3D imaging using interventional fluoroscopy systems.

  15. Volumetric magnetic induction tomography

    NASA Astrophysics Data System (ADS)

    Wei, H.-Y.; Ma, L.; Soleimani, M.

    2012-05-01

    Magnetic induction tomography (MIT) is a new and emerging type of tomography technique that is able to map the passive electromagnetic properties (in particular conductivity) of an object. Because of its non-invasive feature, it becomes a suitable technique for many industries, such as metal processing and mining. This paper presents a volumetric MIT (VMIT) system based on an existing measurement setup in our 2D system (MIT Mk-I). By increasing the number of sensors in the axial direction, volumetric imaging can be realized and hence can improve the spatial resolution of the reconstructed images. All of the system control, data acquisition and signal demodulation are accomplished by a commercial data acquisition card and the National Instruments graphical programming language. In this paper, both the system architecture and the forward 3D sensitivity model will be presented. The image reconstruction scheme is modified by introducing a 3D sensitivity map to replace the previous 2D sensitivity map used for the MIT Mk-I system. The iterative Landweber technique was implemented as the inverse solver to reconstruct the images. Several laboratory-based experimental results are demonstrated in this paper, with different shapes of imaging objects. The reconstructed images are satisfactory showing for the first time volumetric conductivity reconstruction using a multi-layer MIT system. The results indicate the high-quality image reconstruction using our novel VMIT system for potential use in industrial applications, such as metal flow imaging.

  16. Survey on RGB, 3D, Thermal, and Multimodal Approaches for Facial Expression Recognition: History, Trends, and Affect-Related Applications.

    PubMed

    Corneanu, Ciprian Adrian; Simon, Marc Oliu; Cohn, Jeffrey F; Guerrero, Sergio Escalera

    2016-08-01

    Facial expressions are an important way through which humans interact socially. Building a system capable of automatically recognizing facial expressions from images and video has been an intense field of study in recent years. Interpreting such expressions remains challenging and much research is needed about the way they relate to human affect. This paper presents a general overview of automatic RGB, 3D, thermal and multimodal facial expression analysis. We define a new taxonomy for the field, encompassing all steps from face detection to facial expression recognition, and describe and classify the state of the art methods accordingly. We also present the important datasets and the bench-marking of most influential methods. We conclude with a general discussion about trends, important questions and future lines of research. PMID:26761193

  17. Three Dimensional Rover/Lander/Orbiter Mission-Planning (3D-ROMPS) System: A Modern Approach to Mission Planning

    NASA Technical Reports Server (NTRS)

    Scharfe, Nathan D.

    2005-01-01

    NASA's current mission planning system is based on point design, two-dimensional display, spread sheets, and report technology. This technology does not enable engineers to analyze the results of parametric studies of missions plans. This technology will not support the increased observational complexity and data volume of missions like Cassini, Mars Reconnaissance Orbiter (MRO), Mars Science Laboratory (MSL), and Mars Sample Return (MSR). The goal of the 3D-ROMPS task has been to establish a set of operational mission planning and analysis tools in the Image Processing Laboratory (IPL) Mission Support Area (MSA) that will respond to engineering requirements for planning future Solar System Exploration (SSE) missions using a three-dimensional display.

  18. A 3-D tomographic retrieval approach with advection compensation for the air-borne limb-imager GLORIA

    NASA Astrophysics Data System (ADS)

    Ungermann, J.; Blank, J.; Lotz, J.; Leppkes, K.; Hoffmann, L.; Guggenmoser, T.; Kaufmann, M.; Preusse, P.; Naumann, U.; Riese, M.

    2011-11-01

    Infrared limb sounding from aircraft can provide 2-D curtains of multiple trace gas species. However, conventional limb sounders view perpendicular to the aircraft axis and are unable to resolve the observed airmass along their line-of-sight. GLORIA (Gimballed Limb Observer for Radiance Imaging of the Atmosphere) is a new remote sensing instrument that is able to adjust its horizontal view angle with respect to the aircraft flight direction from 45° to 135°. This will allow for tomographic measurements of mesoscale structures for a wide variety of atmospheric constituents. Many flights of the GLORIA instrument will not follow closed curves that allow measuring an airmass from all directions. Consequently, it is examined by means of simulations, what spatial resolution can be expected under ideal conditions from tomographic evaluation of measurements made during a straight flight. It is demonstrated that the achievable horizontal resolution in the line-of-sight direction could be reduced from over 200 km to around 70 km compared to conventional retrievals and that the tomographic retrieval is also more robust against horizontal gradients in retrieved quantities in this direction. In a second step, it is shown that the incorporation of channels exhibiting different optical depth can further enhance the spatial resolution of 3-D retrievals enabling the exploitation of spectral samples usually not used for limb sounding due to their opacity. A second problem for tomographic retrievals is that advection, which can be neglected for conventional retrievals, plays an important role for the time-scales involved in a tomographic measurement flight. This paper presents a method to diagnose the effect of a time-varying atmosphere on a 3-D retrieval and demonstrates an effective way to compensate for effects of advection by incorporating wind-fields from meteorological datasets as a priori information.

  19. General fusion approaches for the age determination of latent fingerprint traces: results for 2D and 3D binary pixel feature fusion

    NASA Astrophysics Data System (ADS)

    Merkel, Ronny; Gruhn, Stefan; Dittmann, Jana; Vielhauer, Claus; Bräutigam, Anja

    2012-03-01

    Determining the age of latent fingerprint traces found at crime scenes is an unresolved research issue since decades. Solving this issue could provide criminal investigators with the specific time a fingerprint trace was left on a surface, and therefore would enable them to link potential suspects to the time a crime took place as well as to reconstruct the sequence of events or eliminate irrelevant fingerprints to ensure privacy constraints. Transferring imaging techniques from different application areas, such as 3D image acquisition, surface measurement and chemical analysis to the domain of lifting latent biometric fingerprint traces is an upcoming trend in forensics. Such non-destructive sensor devices might help to solve the challenge of determining the age of a latent fingerprint trace, since it provides the opportunity to create time series and process them using pattern recognition techniques and statistical methods on digitized 2D, 3D and chemical data, rather than classical, contact-based capturing techniques, which alter the fingerprint trace and therefore make continuous scans impossible. In prior work, we have suggested to use a feature called binary pixel, which is a novel approach in the working field of fingerprint age determination. The feature uses a Chromatic White Light (CWL) image sensor to continuously scan a fingerprint trace over time and retrieves a characteristic logarithmic aging tendency for 2D-intensity as well as 3D-topographic images from the sensor. In this paper, we propose to combine such two characteristic aging features with other 2D and 3D features from the domains of surface measurement, microscopy, photography and spectroscopy, to achieve an increase in accuracy and reliability of a potential future age determination scheme. Discussing the feasibility of such variety of sensor devices and possible aging features, we propose a general fusion approach, which might combine promising features to a joint age determination scheme

  20. 3-D numerical approach to simulate the overtopping volume caused by an impulse wave comparable to avalanche impact in a reservoir

    NASA Astrophysics Data System (ADS)

    Gabl, R.; Seibl, J.; Gems, B.; Aufleger, M.

    2015-12-01

    The impact of an avalanche in a reservoir induces impulse waves, which pose a threat to population and infrastructure. For a good approximation of the generated wave height and length as well as the resulting overtopping volume over structures and dams, formulas, which are based on different simplifying assumptions, can be used. Further project-specific investigations by means of a scale model test or numerical simulations are advisable for complex reservoirs as well as the inclusion of hydraulic structures such as spillways. This paper presents a new approach for a 3-D numerical simulation of the avalanche impact in a reservoir. In this model concept the energy and mass of the avalanche are represented by accelerated water on the actual hill slope. Instead of snow, only water and air are used to simulate the moving avalanche with the software FLOW-3D. A significant advantage of this assumption is the self-adaptation of the model avalanche onto the terrain. In order to reach good comparability of the results with existing research at ETH Zürich, a simplified reservoir geometry is investigated. Thus, a reference case has been analysed including a variation of three geometry parameters (still water depth in the reservoir, freeboard of the dam and reservoir width). There was a good agreement of the overtopping volume at the dam between the presented 3-D numerical approach and the literature equations. Nevertheless, an extended parameter variation as well as a comparison with natural data should be considered as further research topics.

  1. Europeana and 3D

    NASA Astrophysics Data System (ADS)

    Pletinckx, D.

    2011-09-01

    The current 3D hype creates a lot of interest in 3D. People go to 3D movies, but are we ready to use 3D in our homes, in our offices, in our communication? Are we ready to deliver real 3D to a general public and use interactive 3D in a meaningful way to enjoy, learn, communicate? The CARARE project is realising this for the moment in the domain of monuments and archaeology, so that real 3D of archaeological sites and European monuments will be available to the general public by 2012. There are several aspects to this endeavour. First of all is the technical aspect of flawlessly delivering 3D content over all platforms and operating systems, without installing software. We have currently a working solution in PDF, but HTML5 will probably be the future. Secondly, there is still little knowledge on how to create 3D learning objects, 3D tourist information or 3D scholarly communication. We are still in a prototype phase when it comes to integrate 3D objects in physical or virtual museums. Nevertheless, Europeana has a tremendous potential as a multi-facetted virtual museum. Finally, 3D has a large potential to act as a hub of information, linking to related 2D imagery, texts, video, sound. We describe how to create such rich, explorable 3D objects that can be used intuitively by the generic Europeana user and what metadata is needed to support the semantic linking.

  2. A Simple Approach for an Eggshell-Based 3D-Printed Osteoinductive Multiphasic Calcium Phosphate Scaffold.

    PubMed

    Dadhich, Prabhash; Das, Bodhisatwa; Pal, Pallabi; Srivas, Pavan K; Dutta, Joy; Ray, Sabyasachi; Dhara, Santanu

    2016-05-18

    Natural origin bioceramics are widely used for bone grafts. In the present study, an eggshell-derived bioceramic scaffold is fabricated by 3D printing as a potential bone-graft analogue. The eggshell, a biological waste material, was mixed with a specific ratio of phosphoric acid and chitosan to form a precursor toward the fabrication of an osteoinductive multiphasic calcium phosphate scaffold via a coagulation-assisted extrusion and sintering for a multiscalar hierarchical porous structure with improved mechanical properties. Physicochemical characterization of the formed scaffolds was carried out for phase analysis, surface morphology, and mechanical properties. A similar scaffold was prepared using a chemically synthesized calcium phosphate powder that was compared with the natural origin one. The higher surface area associated with the interconnected porosity along with multiple phases of the natural origin scaffold facilitated higher cell adhesion and proliferation compared to the chemically synthesized one. Further, the natural origin scaffold displayed relatively higher cell differentiation activity, as is evident by protein and gene expression studies. On subcutaneous implantation for 30 days, promising vascular tissue in-growth was observed, circumventing a major foreign body response. Collagen-rich vascular extracellular matrix deposition and osteocalcin secretion indicated bonelike tissue formation. Finally, the eggshell-derived multiphasic calcium phosphate scaffold displayed improvement in the mechanical properties with higher porosity and osteoinductivity compared to the chemically derived apatite and unveiled a new paradigm for utilization of biological wastes in bone-graft application. PMID:26853051

  3. Development of 3D-QSAR Model for Acetylcholinesterase Inhibitors Using a Combination of Fingerprint, Molecular Docking, and Structure-Based Pharmacophore Approaches.

    PubMed

    Lee, Sehan; Barron, Mace G

    2015-11-01

    Acetylcholinesterase (AChE), a serine hydrolase vital for regulating the neurotransmitter acetylcholine in animals, has been used as a target for drugs and pesticides. With the increasing availability of AChE crystal structures, with or without ligands bound, structure-based approaches have been successfully applied to AChE inhibitors (AChEIs). The major limitation of these approaches has been the small applicability domain due to the lack of structural diversity in the training set. In this study, we developed a 3 dimensional quantitative structure-activity relationship (3D-QSAR) for inhibitory activity of 89 reversible and irreversible AChEIs including drugs and insecticides. A 3D-fingerprint descriptor encoding protein-ligand interactions was developed using molecular docking and structure-based pharmacophore to rationalize the structural requirements responsible for the activity of these compounds. The obtained 3D-QSAR model exhibited high correlation value (R(2) = 0.93) and low mean absolute error (MAE = 0.32 log units) for the training set (n = 63). The model was predictive across a range of structures as shown by the leave-one-out cross-validated correlation coefficient (Q(2) = 0.89) and external validation results (n = 26, R(2) = 0.89, and MAE = 0.38 log units). The model revealed that the compounds with high inhibition potency had proper conformation in the active site gorge and interacted with key amino acid residues, in particular Trp84 and Phe330 at the catalytic anionic site, Trp279 at the peripheral anionic site, and Gly118, Gly119, and Ala201 at the oxyanion hole. The resulting universal 3D-QSAR model provides insight into the multiple molecular interactions determining AChEI potency that may guide future chemical design and regulation of toxic AChEIs. PMID:26202430

  4. [Real time 3D echocardiography].

    PubMed

    Bauer, F; Shiota, T; Thomas, J D

    2001-07-01

    Three-dimensional representation of the heart is an old concern. Usually, 3D reconstruction of the cardiac mass is made by successive acquisition of 2D sections, the spatial localisation and orientation of which require complex guiding systems. More recently, the concept of volumetric acquisition has been introduced. A matricial emitter-receiver probe complex with parallel data processing provides instantaneous of a pyramidal 64 degrees x 64 degrees volume. The image is restituted in real time and is composed of 3 planes (planes B and C) which can be displaced in all spatial directions at any time during acquisition. The flexibility of this system of acquisition allows volume and mass measurement with greater accuracy and reproducibility, limiting inter-observer variability. Free navigation of the planes of investigation allows reconstruction for qualitative and quantitative analysis of valvular heart disease and other pathologies. Although real time 3D echocardiography is ready for clinical usage, some improvements are still necessary to improve its conviviality. Then real time 3D echocardiography could be the essential tool for understanding, diagnosis and management of patients. PMID:11494630

  5. [Real time 3D echocardiography

    NASA Technical Reports Server (NTRS)

    Bauer, F.; Shiota, T.; Thomas, J. D.

    2001-01-01

    Three-dimensional representation of the heart is an old concern. Usually, 3D reconstruction of the cardiac mass is made by successive acquisition of 2D sections, the spatial localisation and orientation of which require complex guiding systems. More recently, the concept of volumetric acquisition has been introduced. A matricial emitter-receiver probe complex with parallel data processing provides instantaneous of a pyramidal 64 degrees x 64 degrees volume. The image is restituted in real time and is composed of 3 planes (planes B and C) which can be displaced in all spatial directions at any time during acquisition. The flexibility of this system of acquisition allows volume and mass measurement with greater accuracy and reproducibility, limiting inter-observer variability. Free navigation of the planes of investigation allows reconstruction for qualitative and quantitative analysis of valvular heart disease and other pathologies. Although real time 3D echocardiography is ready for clinical usage, some improvements are still necessary to improve its conviviality. Then real time 3D echocardiography could be the essential tool for understanding, diagnosis and management of patients.

  6. A 3D nanoscale approach to nebular paleomagnetism in the Semarkona LL3.0 ordinary chondrite

    NASA Astrophysics Data System (ADS)

    Einsle, J. F.; Fu, R. R.; Weiss, B. P.; Kasama, T.; Midgley, P. A.; Harrison, R. J.

    2014-12-01

    Solar nebular models suggest that magnetic fields are central to the redistribution of mass and angular momentum in the protoplanetary disk. Using individual chondrules with patches of dusty olivine the strength of these magnetic fields can be measured due to presence of nanoscale Fe inclusions. Since chondrules formed by rapid heating and cooling in the early solar nebula, individual chondrules have the potential to record the magnetic field that was present during their formation, and retain this signal for several billion years. Recently the first robust paleointensity measurement of nebular fields was compleated by measureing dusty olivine grains from the Semarkona LL3.0 ordinary chondrite meteorite in a SQUID microscope. (Fu et al. this meeting) Extracting quantitative information from the paleomagnetic meaurements requires a full understanding of the underlying physical mechanisms producing the measured magnetic signal. Here we characterise the magnetic behaviour of the same dusty olivine chondrules, using a variety of electron microscopy techniques. Electron holography and Lorentz imaging confirm the dominance of single vortex (SV) states in the majority of the remanence carriers. In-field measurements demonstrate the high stability of this SV state, making them suitable carriers of paleomagnetic information. We present a 3D volume reconstruction of the dusty olivine using Focussed-Ion-Beam (FIB) slice-and-view tomography. Combining the selective milling properties of FIB with the high spatial resolution of the Scanning Electron Microscope we are able to capture images as we make successive slices through a selected region of the sample. For this initial study we present a collection of 400 images taken every 10 nm as we slice through an 10 μm x 10 μm x 4 μm volume of the dusty olivine patch within a single chondrule. Each image possesses resolution around 10 nm allowing us to resolve particles in both the single domain and single vortex size ranges. Once

  7. The Collaboratory for MS3D: A New Cyberinfrastructure for the Structural Elucidation of Biological Macromolecules and their Assemblies Using Mass Spectrometry-based Approaches

    PubMed Central

    Yu, Eizadora T.; Hawkins, Arie; Kuntz, Irwin D.; Rahn, Larry A.; Rothfuss, Andrew; Sale, Kenneth; Young, Malin M.; Yang, Christine L.; Pancerella, Carmen M.; Fabris, Daniele

    2009-01-01

    Modern biomedical research is evolving with the rapid growth of diverse data types, biophysical characterization methods, computational tools and extensive collaboration among researchers spanning various communities and having complementary backgrounds and expertise. Collaborating researchers are increasingly dependent on shared data and tools made available by other investigators with common interests, thus forming communities that transcend the traditional boundaries of the single research lab or institution. Barriers, however, remain to the formation of these virtual communities, usually due to the steep learning curve associated with becoming familiar with new tools, or with the difficulties associated with transferring data between tools. Recognizing the need for shared reference data and analysis tools, we are developing an integrated knowledge environment that supports productive interactions among researchers. Here we report on our current collaborative environment, which focuses on bringing together structural biologists working in the area of mass spectrometric based methods for the analysis of tertiary and quaternary macromolecular structures (MS3D) called the Collaboratory for MS3D (C-MS3D). C-MS3D is a web-portal designed to provide collaborators with a shared work environment that integrates data storage and management with data analysis tools. Files are stored and archived along with pertinent meta data in such a way as to allow file handling to be tracked (data provenance) and data files to be searched using keywords and modification dates. While at this time the portal is designed around a specific application, the shared work environment is a general approach to building collaborative work groups. The goal of which is to not only provide a common data sharing and archiving system but also to assist in the building of new collaborations and to spur the development of new tools and technologies. PMID:18817429

  8. 3d-3d correspondence revisited

    NASA Astrophysics Data System (ADS)

    Chung, Hee-Joong; Dimofte, Tudor; Gukov, Sergei; Sułkowski, Piotr

    2016-04-01

    In fivebrane compactifications on 3-manifolds, we point out the importance of all flat connections in the proper definition of the effective 3d {N}=2 theory. The Lagrangians of some theories with the desired properties can be constructed with the help of homological knot invariants that categorify colored Jones polynomials. Higgsing the full 3d theories constructed this way recovers theories found previously by Dimofte-Gaiotto-Gukov. We also consider the cutting and gluing of 3-manifolds along smooth boundaries and the role played by all flat connections in this operation.

  9. Incorporation of texture-based features in optimal graph-theoretic approach with application to the 3D segmentation of intraretinal surfaces in SD-OCT volumes

    NASA Astrophysics Data System (ADS)

    Antony, Bhavna J.; Abràmoff, Michael D.; Sonka, Milan; Kwon, Young H.; Garvin, Mona K.

    2012-02-01

    While efficient graph-theoretic approaches exist for the optimal (with respect to a cost function) and simultaneous segmentation of multiple surfaces within volumetric medical images, the appropriate design of cost functions remains an important challenge. Previously proposed methods have used simple cost functions or optimized a combination of the same, but little has been done to design cost functions using learned features from a training set, in a less biased fashion. Here, we present a method to design cost functions for the simultaneous segmentation of multiple surfaces using the graph-theoretic approach. Classified texture features were used to create probability maps, which were incorporated into the graph-search approach. The efficiency of such an approach was tested on 10 optic nerve head centered optical coherence tomography (OCT) volumes obtained from 10 subjects that presented with glaucoma. The mean unsigned border position error was computed with respect to the average of manual tracings from two independent observers and compared to our previously reported results. A significant improvement was noted in the overall means which reduced from 9.25 +/- 4.03μm to 6.73 +/- 2.45μm (p < 0.01) and is also comparable with the inter-observer variability of 8.85 +/- 3.85μm.

  10. Automated 3-D Segmentation of Lungs With Lung Cancer in CT Data Using a Novel Robust Active Shape Model Approach

    PubMed Central

    Sun, Shanhui; Bauer, Christian; Beichel, Reinhard

    2013-01-01

    Segmentation of lungs with (large) lung cancer regions is a nontrivial problem. We present a new fully automated approach for segmentation of lungs with such high-density pathologies. Our method consists of two main processing steps. First, a novel robust active shape model (RASM) matching method is utilized to roughly segment the outline of the lungs. The initial position of the RASM is found by means of a rib cage detection method. Second, an optimal surface finding approach is utilized to further adapt the initial segmentation result to the lung. Left and right lungs are segmented individually. An evaluation on 30 data sets with 40 abnormal (lung cancer) and 20 normal left/right lungs resulted in an average Dice coefficient of 0.975 ± 0.006 and a mean absolute surface distance error of 0.84 ± 0.23 mm, respectively. Experiments on the same 30 data sets showed that our methods delivered statistically significant better segmentation results, compared to two commercially available lung segmentation approaches. In addition, our RASM approach is generally applicable and suitable for large shape models. PMID:21997248

  11. Nitrogen transfers off Walvis Bay: a 3-D coupled physical/biogeochemical modeling approach in the Namibian upwelling system

    NASA Astrophysics Data System (ADS)

    Gutknecht, E.; Dadou, I.; Marchesiello, P.; Cambon, G.; Le Vu, B.; Sudre, J.; Garçon, V.; Machu, E.; Rixen, T.; Kock, A.; Flohr, A.; Paulmier, A.; Lavik, G.

    2013-06-01

    Eastern boundary upwelling systems (EBUS) are regions of high primary production often associated with oxygen minimum zones (OMZs). They represent key regions for the oceanic nitrogen (N) cycle. By exporting organic matter (OM) and nutrients produced in the coastal region to the open ocean, EBUS can play an important role in sustaining primary production in subtropical gyres. However, losses of fixed inorganic N through denitrification and anammox processes take place in oxygen depleted environments such as EBUS, and can potentially mitigate the role of these regions as a source of N to the open ocean. EBUS can also represent a considerable source of nitrous oxide (N2O) to the atmosphere, affecting the atmospheric budget of N2O. In this paper a 3-D coupled physical/biogeochemical model (ROMS/BioEBUS) is used to investigate the N budget in the Namibian upwelling system. The main processes linked to EBUS and associated OMZs are taken into account. The study focuses on the northern part of the Benguela upwelling system (BUS), especially the Walvis Bay area (between 22° S and 24° S) where the OMZ is well developed. Fluxes of N off the Walvis Bay area are estimated in order to understand and quantify (1) the total N offshore export from the upwelling area, representing a possible N source that sustains primary production in the South Atlantic subtropical gyre; (2) export production and subsequent losses of fixed N via denitrification and anammox under suboxic conditions (O2 < 25 mmol O2 m-3); and (3) the N2O emission to the atmosphere in the upwelling area. In the mixed layer, the total N offshore export is estimated as 8.5 ± 3.9 × 1010 mol N yr-1 at 10° E off the Walvis Bay area, with a mesoscale contribution of 20%. Extrapolated to the whole BUS, the coastal N source for the subtropical gyre corresponds to 0.1 ± 0.04 mol N m-2 yr-1. This N flux represents a major source of N for the gyre compared with other N sources, and contributes 28% of the new primary

  12. Does fluid infiltration affect the motion of sediment grains? - A 3-D numerical modelling approach using SPH

    NASA Astrophysics Data System (ADS)

    Bartzke, Gerhard; Rogers, Benedict D.; Fourtakas, Georgios; Mokos, Athanasios; Huhn, Katrin

    2016-04-01

    The processes that cause the creation of a variety of sediment morphological features, e.g. laminated beds, ripples, or dunes, are based on the initial motion of individual sediment grains. However, with experimental techniques it is difficult to measure the flow characteristics, i.e., the velocity of the pore water flow in sediments, at a sufficient resolution and in a non-intrusive way. As a result, the role of fluid infiltration at the surface and in the interior affecting the initiation of motion of a sediment bed is not yet fully understood. Consequently, there is a strong need for numerical models, since these are capable of quantifying fluid driven sediment transport processes of complex sediment beds composed of irregular shapes. The numerical method Smoothed Particle Hydrodynamics (SPH) satisfies this need. As a meshless and Lagrangian technique, SPH is ideally suited to simulating flows in sediment beds composed of various grain shapes, but also flow around single grains at a high temporal and spatial resolution. The solver chosen is DualSPHysics (www.dual.sphysics.org) since this is validated for a range of flow conditions. For the present investigation a 3-D numerical flume model was generated using SPH with a length of 4.0 cm, a width of 0.05 cm and a height of 0.2 cm where mobile sediment particles were deposited in a recess. An experimental setup was designed to test sediment configurations composed of irregular grain shapes (grain diameter, D50=1000 μm). Each bed consisted of 3500 mobile objects. After the bed generation process, the entire domain was flooded with 18 million fluid particles. To drive the flow, an oscillating motion perpendicular to the bed was applied to the fluid, reaching a peak value of 0.3 cm/s, simulating 4 seconds of real time. The model results showed that flow speeds decreased logarithmically from the top of the domain towards the surface of the beds, indicating a fully developed boundary layer. Analysis of the fluid

  13. Efficient computation of the spontaneous decay rate of arbitrarily shaped 3D nanosized resonators: a Krylov model-order reduction approach

    NASA Astrophysics Data System (ADS)

    Zimmerling, Jörn; Wei, Lei; Urbach, Paul; Remis, Rob

    2016-03-01

    We present a Krylov model-order reduction approach to efficiently compute the spontaneous decay (SD) rate of arbitrarily shaped 3D nanosized resonators. We exploit the symmetry of Maxwell's equations to efficiently construct so-called reduced-order models that approximate the SD rate of a quantum emitter embedded in a resonating nanostructure. The models allow for frequency sweeps, meaning that a single model provides SD rate approximations over an entire spectral interval of interest. Field approximations and dominant quasinormal modes can be determined at low cost as well.

  14. Fast and robust extraction of centerlines in 3D tubular structures using a scattered-snakelet approach

    NASA Astrophysics Data System (ADS)

    Spuhler, Christoph; Harders, Matthias; Székely, Gábor

    2006-03-01

    We present a fast and robust approach for automatic centerline extraction of tubular structures. The underlying idea is to cut traditional snakes into a set of shorter, independent segments - so-called snakelets. Following the same variational principles, each snakelet acts locally and extracts a subpart of the overall structure. After a parallel optimization step, outliers are detected and the remaining segments then form an implicit centerline. No manual initialization of the snakelets is necessary, which represents one advantage of the method. Moreover, computational complexity does not directly depend on dataset size, but on the number of snake segments necessary to cover the structure of interest, resulting in short computation times. Lastly, the approach is robust even for very complex datasets such as the small intestine. Our approach was tested on several medical datasets (CT datasets of colon, small bowel, and blood vessels) and yielded smooth, connected centerlines with few or no branches. The computation time needed is less than a minute using standard computing hardware.

  15. 3D multi-object segmentation of cardiac MSCT imaging by using a multi-agent approach.

    PubMed

    Fleureau, Julien; Garreau, Mireille; Boulmier, Dominique; Hernández, Alfredo

    2007-01-01

    We propose a new technique for general purpose, semi-interactive and multi-object segmentation in N-dimensional images, applied to the extraction of cardiac structures in MultiSlice Computed Tomography (MSCT) imaging. The proposed approach makes use of a multi-agent scheme combined with a supervised classification methodology allowing the introduction of a priori information and presenting fast computing times. The multi-agent system is organised around a communicating agent which manages a population of situated agents which segment the image through cooperative and competitive interactions. The proposed technique has been tested on several patient data sets. Some typical results are finally presented and discussed. PMID:18003382

  16. 3D Multi-Object Segmentation of Cardiac MSCT Imaging by using a Multi-Agent Approach

    PubMed Central

    Fleureau, Julien; Garreau, Mireille; Boulmier, Dominique; Hernandez, Alfredo

    2007-01-01

    We propose a new technique for general purpose, semi-interactive and multi-object segmentation in N-dimensional images, applied to the extraction of cardiac structures in MultiSlice Computed Tomography (MSCT) imaging. The proposed approach makes use of a multi-agent scheme combined with a supervised classification methodology allowing the introduction of a priori information and presenting fast computing times. The multi-agent system is organised around a communicating agent which manages a population of situated agents which segment the image through cooperative and competitive interactions. The proposed technique has been tested on several patient data sets. Some typical results are finally presented and discussed. PMID:18003382

  17. RGB Color Calibration for Quantitative Image Analysis: The “3D Thin-Plate Spline” Warping Approach

    PubMed Central

    Menesatti, Paolo; Angelini, Claudio; Pallottino, Federico; Antonucci, Francesca; Aguzzi, Jacopo; Costa, Corrado

    2012-01-01

    In the last years the need to numerically define color by its coordinates in n-dimensional space has increased strongly. Colorimetric calibration is fundamental in food processing and other biological disciplines to quantitatively compare samples' color during workflow with many devices. Several software programmes are available to perform standardized colorimetric procedures, but they are often too imprecise for scientific purposes. In this study, we applied the Thin-Plate Spline interpolation algorithm to calibrate colours in sRGB space (the corresponding Matlab code is reported in the Appendix). This was compared with other two approaches. The first is based on a commercial calibration system (ProfileMaker) and the second on a Partial Least Square analysis. Moreover, to explore device variability and resolution two different cameras were adopted and for each sensor, three consecutive pictures were acquired under four different light conditions. According to our results, the Thin-Plate Spline approach reported a very high efficiency of calibration allowing the possibility to create a revolution in the in-field applicative context of colour quantification not only in food sciences, but also in other biological disciplines. These results are of great importance for scientific color evaluation when lighting conditions are not controlled. Moreover, it allows the use of low cost instruments while still returning scientifically sound quantitative data. PMID:22969337

  18. 3D and Education

    NASA Astrophysics Data System (ADS)

    Meulien Ohlmann, Odile

    2013-02-01

    Today the industry offers a chain of 3D products. Learning to "read" and to "create in 3D" becomes an issue of education of primary importance. 25 years professional experience in France, the United States and Germany, Odile Meulien set up a personal method of initiation to 3D creation that entails the spatial/temporal experience of the holographic visual. She will present some different tools and techniques used for this learning, their advantages and disadvantages, programs and issues of educational policies, constraints and expectations related to the development of new techniques for 3D imaging. Although the creation of display holograms is very much reduced compared to the creation of the 90ies, the holographic concept is spreading in all scientific, social, and artistic activities of our present time. She will also raise many questions: What means 3D? Is it communication? Is it perception? How the seeing and none seeing is interferes? What else has to be taken in consideration to communicate in 3D? How to handle the non visible relations of moving objects with subjects? Does this transform our model of exchange with others? What kind of interaction this has with our everyday life? Then come more practical questions: How to learn creating 3D visualization, to learn 3D grammar, 3D language, 3D thinking? What for? At what level? In which matter? for whom?

  19. A topology-oriented and tissue-specific approach to detect pleural thickenings from 3D CT data

    NASA Astrophysics Data System (ADS)

    Buerger, C.; Chaisaowong, K.; Knepper, A.; Kraus, T.; Aach, T.

    2009-02-01

    Pleural thickenings are caused by asbestos exposure and may evolve into malignant pleural mesothelioma. The detection of pleural thickenings is today mostly done by a visual inspection of CT data, which is time-consuming and underlies the physician's subjective judgment. We propose a new detection algorithm within our computer-assisted diagnosis (CAD) system to automatically detect pleural thickenings within CT data. First, pleura contours are identified by thresholding and contour relaxation with a probabilistic model. Subsequently, the approach to automatically detect pleural thickenings is proposed as a two-step procedure. Step one; since pleural thickenings appear as fine-scale occurrences on the rather large-scale pleura contour, a surface-based smoothing algorithm is developed. Pleural thickenings are initially detected as the difference between the original contours and the resulting "healthy" model of the pleura. Step two; as pleural thickenings can expand into the surrounding thoracic tissue, a subsequent tissue-specific segmentation for the initially detected pleural thickenings is performed in order to separate pleural thickenings from the surrounding thoracic tissue. For this purpose, a probabilistic Hounsfield model for pleural thickenings as a mixture of Gaussian distributions has been constructed. The parameters were estimated by applying the Expectation-Maximization (EM) algorithm. A model fitting technique in combination with the application of a Gibbs-Markov random field (GMRF) model then allows the tissuespecific segmentation of pleural thickenings with high precision. With these methods, a new approach is presented in order to assure a precise and reproducible detection of pleural mesothelioma in its early stage.

  20. Particle tracking approach for transport in three-dimensional discrete fracture networks: Particle tracking in 3-D DFNs

    DOE PAGESBeta

    Makedonska, Nataliia; Painter, Scott L.; Bui, Quan M.; Gable, Carl W.; Karra, Satish

    2015-09-16

    The discrete fracture network (DFN) model is a method to mimic discrete pathways for fluid flow through a fractured low-permeable rock mass, and may be combined with particle tracking simulations to address solute transport. However, experience has shown that it is challenging to obtain accurate transport results in three-dimensional DFNs because of the high computational burden and difficulty in constructing a high-quality unstructured computational mesh on simulated fractures. We present a new particle tracking capability, which is adapted to control volume (Voronoi polygons) flow solutions on unstructured grids (Delaunay triangulations) on three-dimensional DFNs. The locally mass-conserving finite-volume approach eliminates massmore » balance-related problems during particle tracking. The scalar fluxes calculated for each control volume face by the flow solver are used to reconstruct a Darcy velocity at each control volume centroid. The groundwater velocities can then be continuously interpolated to any point in the domain of interest. The control volumes at fracture intersections are split into four pieces, and the velocity is reconstructed independently on each piece, which results in multiple groundwater velocities at the intersection, one for each fracture on each side of the intersection line. This technique enables detailed particle transport representation through a complex DFN structure. Verified for small DFNs, the new simulation capability enables numerical experiments on advective transport in large DFNs to be performed. As a result, we demonstrate this particle transport approach on a DFN model using parameters similar to those of crystalline rock at a proposed geologic repository for spent nuclear fuel in Forsmark, Sweden.« less

  1. Particle tracking approach for transport in three-dimensional discrete fracture networks: Particle tracking in 3-D DFNs

    SciTech Connect

    Makedonska, Nataliia; Painter, Scott L.; Bui, Quan M.; Gable, Carl W.; Karra, Satish

    2015-09-16

    The discrete fracture network (DFN) model is a method to mimic discrete pathways for fluid flow through a fractured low-permeable rock mass, and may be combined with particle tracking simulations to address solute transport. However, experience has shown that it is challenging to obtain accurate transport results in three-dimensional DFNs because of the high computational burden and difficulty in constructing a high-quality unstructured computational mesh on simulated fractures. We present a new particle tracking capability, which is adapted to control volume (Voronoi polygons) flow solutions on unstructured grids (Delaunay triangulations) on three-dimensional DFNs. The locally mass-conserving finite-volume approach eliminates mass balance-related problems during particle tracking. The scalar fluxes calculated for each control volume face by the flow solver are used to reconstruct a Darcy velocity at each control volume centroid. The groundwater velocities can then be continuously interpolated to any point in the domain of interest. The control volumes at fracture intersections are split into four pieces, and the velocity is reconstructed independently on each piece, which results in multiple groundwater velocities at the intersection, one for each fracture on each side of the intersection line. This technique enables detailed particle transport representation through a complex DFN structure. Verified for small DFNs, the new simulation capability enables numerical experiments on advective transport in large DFNs to be performed. As a result, we demonstrate this particle transport approach on a DFN model using parameters similar to those of crystalline rock at a proposed geologic repository for spent nuclear fuel in Forsmark, Sweden.

  2. A multiscale 0-D/3-D approach to patient-specific adaptation of a cerebral autoregulation model for computational fluid dynamics studies of cardiopulmonary bypass.

    PubMed

    Neidlin, Michael; Steinseifer, Ulrich; Kaufmann, Tim A S

    2014-06-01

    Neurological complication often occurs during cardiopulmonary bypass (CPB). One of the main causes is hypoperfusion of the cerebral tissue affected by the position of the cannula tip and diminished cerebral autoregulation (CA). Recently, a lumped parameter approach could describe the baroreflex, one of the main mechanisms of cerebral autoregulation, in a computational fluid dynamics (CFD) study of CPB. However, the cerebral blood flow (CBF) was overestimated and the physiological meaning of the variables and their impact on the model was unknown. In this study, we use a 0-D control circuit representation of the Baroreflex mechanism, to assess the parameters with respect to their physiological meaning and their influence on CBF. Afterwards the parameters are transferred to 3D-CFD and the static and dynamic behavior of cerebral autoregulation is investigated. The parameters of the baroreflex mechanism can reproduce normotensive, hypertensive and impaired autoregulation behavior. Further on, the proposed model can mimic the effects of anesthetic agents and other factors controlling dynamic CA. The CFD simulations deliver similar results of static and dynamic CBF as the 0-D control circuit. This study shows the feasibility of a multiscale 0-D/3-D approach to include patient-specific cerebral autoregulation into CFD studies. PMID:24746017

  3. Visualization of liver in 3-D

    NASA Astrophysics Data System (ADS)

    Chen, Chin-Tu; Chou, Jin-Shin; Giger, Maryellen L.; Kahn, Charles E., Jr.; Bae, Kyongtae T.; Lin, Wei-Chung

    1991-05-01

    Visualization of the liver in three dimensions (3-D) can improve the accuracy of volumetric estimation and also aid in surgical planning. We have developed a method for 3-D visualization of the liver using x-ray computed tomography (CT) or magnetic resonance (MR) images. This method includes four major components: (1) segmentation algorithms for extracting liver data from tomographic images; (2) interpolation techniques for both shape and intensity; (3) schemes for volume rendering and display, and (4) routines for electronic surgery and image analysis. This method has been applied to cases from a living-donor liver transplant project and appears to be useful for surgical planning.

  4. Waveform Modeling of 3D Structure of D" Region Using A Coupled SEM/Normal Mode Approach

    NASA Astrophysics Data System (ADS)

    To, A.; Gung, Y.; Capadeville, Y.; Romanowicz, B.

    2003-12-01

    The presence of strong lateral heterogeneity in D" is now well documented and presents challenges for seismic modeling. The main challenges are the limited global sampling of D" and the theoretical limits of validity of the present modeling tools, such as standard ray theory and mode approaches. We use coupled normal mode/Spectral Element Method (SEM) to compute synthetic seismograms of Sdiff in the D" part of a tomographic model(SAW24b16, Mégnin and Romanowicz, 2000) down to corner frequency 1/12s. SEM allows to take into account strong heterogeneity in a rigorous manner. The coupled method is much faster than standard SEM, when the numerical part of the computation is restricted to the D" region. In the rest of the mantle, the wave field is computed using efficient normal mode summation. As a first step, we consider a radially symmetric model outside of the D" region, and compare Sdiff synthetics with observed waveforms for a collection of deep earthquakes, for which the effect of strong heterogeneity in the crust and upper mantle is avoided. Observed and synthetic travel time trends are very consistent and in many cases the observed residuals are significantly larger. This indicates that the tomographic model only represents the smooth features of the real structure. Observed waveform amplitudes and SEM synthetics are somewhat less consistent. We compare the predictions for 800 Sdiff phases using SEM with those obtained by more approximate methods : ray theory and NACT (Non-linear asymptotic coupling theory, a normal mode perturbation approach). We discuss systematic trends in the travel times predicted by the different methods, compared to observations. Starting with the tomographic model, and correcting for mantle structure outside of D" using approximate NACT predictions, we next invert for perturbations to the tomographic model, using the coupled SEM/mode computation for the forward part of the modeling, in several regions of D" under the Pacific, which are

  5. Top-Down and Bottom-Up Approaches in 3D Printing Technologies for Drug Delivery Challenges.

    PubMed

    Katakam, Prakash; Dey, Baishakhi; Assaleh, Fathi H; Hwisa, Nagiat Tayeb; Adiki, Shanta Kumari; Chandu, Babu Rao; Mitra, Analava

    2015-01-01

    3-Dimensional printing (3DP) constitutes a raft of technologies, based on different physical mechanisms, that generate a 3-dimensional physical object from a digital model. Because of its rapid fabrication and precise geometry, 3DP has gained a prominent focus in biomedical and nanobiomaterials research. Despite advancements in targeted, controlled, and pulsatile drug delivery, the achievement of site-specific and disease-responsive drug release and stringent control over in vivo biodistribution, are still some of the important, challenging areas for pharmaceutical research and development and existing drug delivery techniques. Microelectronic industries are capable of generating nano-/microdrug delivery devices at high throughputs with a highly precise control over design. Successful miniaturizations of micro-pumps with multireservoir architectures for delivery of pharmaceuticals developed by micro-electromechanical systems technology were more acceptable than implantable devices. Inkjet printing technologies, which dispense a precise amount of polymer ink solutions, find applications in controlled drug delivery. Bioelectronic products have revolutionized drug delivery technologies. Designing nanoparticles by nanoimprint lithography showed a controlled drug release pattern, biodistribution, and in vivo transport. This review highlights the "top-down" and "bottom-up" approaches of the most promising 3DP technologies and their broader applications in biomedical and therapeutic drug delivery, with critical assessment of its merits, demerits, and intellectual property rights challenges. PMID:25746205

  6. Personalized x-ray reconstruction of the proximal femur via a non-rigid 2D-3D registration

    NASA Astrophysics Data System (ADS)

    Yu, Weimin; Zysset, Philippe; Zheng, Guoyan

    2015-03-01

    In this paper we present a new approach for a personalized X-ray reconstruction of the proximal femur via a non-rigid registration of a 3D volumetric template to 2D calibrated C-arm images. The 2D-3D registration is done with a hierarchical two-stage strategy: the global scaled rigid registration stage followed by a regularized deformable b-spline registration stage. In both stages, a set of control points with uniform spacing are placed over the domain of the 3D volumetric template and the registrations are driven by computing updated positions of these control points, which then allows to accurately register the 3D volumetric template to the reference space of the C-arm images. Comprehensive experiments on simulated images, on images of cadaveric femurs and on clinical datasets are designed and conducted to evaluate the performance of the proposed approach. Quantitative and qualitative evaluation results are given, which demonstrate the efficacy of the present approach.

  7. High Resolution Dsm and Classified Volumetric Generation: AN Operational Approach to the Improvement of Geospatial Intelligence

    NASA Astrophysics Data System (ADS)

    Boccardo, P.; Gentili, G.

    2011-09-01

    As mentioned by Bacastow and Bellafiore, Geospatial Intelligence (GEOINT) is a field of knowledge, a process, and a profession. As knowledge, it is information integrated in a coherent space-time context that supports descriptions, explanations, or forecasts of human activities with which decision makers take action. As a process, it is the means by which data and information are collected, manipulated, geospatially reasoned, and disseminated to decision-makers. The geospatial intelligence professional establishes the scope of activities, interdisciplinary associations, competencies, and standards in academe, government, and the private sectors. Taking into account the fact that GEOINT is crucial for broad organizations, BLOM Group, a leading International provider within acquisition, processing and modeling of geographic information and ITHACA, a non-profit organization devoted to products and services delivering to the UN System in the field of geomatics, set up and provided GEOINT data to the main Italian companies operating in the field of mobile phone networking. This data, extremely useful for telecom network planning, have derived and produced using a standardized and effective (from the production point of view) approach. In this paper, all the procedures used for the production are described and tested with the aim to investigate the suitability of the data and the procedures themselves to any others possible fields of application.

  8. Integrated approach for quantification of fractured tight reservoir rocks: Porosity, permeability analyses and 3D fracture network characterisation on fractured dolomite samples

    NASA Astrophysics Data System (ADS)

    Voorn, Maarten; Barnhoorn, Auke; Exner, Ulrike; Baud, Patrick; Reuschlé, Thierry

    2015-04-01

    Fractured reservoir rocks make up an important part of the hydrocarbon reservoirs worldwide. A detailed analysis of fractures and fracture networks in reservoir rock samples is thus essential to determine the potential of these fractured reservoirs. However, common analyses on drill core and plug samples taken from such reservoirs (including hand specimen analysis, thin section analysis and laboratory porosity and permeability determination) suffer from various problems, such as having a limited resolution, providing only 2D and no internal structure information, being destructive on the samples and/or not being representative for full fracture networks. In this study, we therefore explore the use of an additional method - non-destructive 3D X-ray micro-Computed Tomography (μCT) - to obtain more information on such fractured samples. Seven plug-sized samples were selected from narrowly fractured rocks of the Hauptdolomit formation, taken from wellbores in the Vienna Basin, Austria. These samples span a range of different fault rocks in a fault zone interpretation, from damage zone to fault core. 3D μCT data is used to extract porosity, fracture aperture, fracture density and fracture orientations - in bulk as well as locally. The 3D analyses are complemented with thin sections made to provide some 2D information with a much higher detail than the μCT data. Finally, gas- and water permeability measurements under confining pressure provide an important link (at least in order of magnitude) of the µCT results towards more realistic reservoir conditions. Our results show that 3D μCT can be applied efficiently on plug-sized samples of naturally fractured rocks, and that several important parameters can be extracted. μCT can therefore be a useful addition to studies on such reservoir rocks, and provide valuable input for modelling and simulations. Also permeability experiments under confining pressure provide important additional insights. Combining these and other

  9. Reservoir geology using 3D modelling tools

    SciTech Connect

    Dubrule, O.; Samson, P.; Segonds, D.

    1996-12-31

    The last decade has seen tremendous developments in the area of quantitative geological modelling. These developments have a significant impact on the current practice of constructing reservoir models. A structural model can first be constructed on the basis of depth-converted structural interpretations produced on a seismic interpretation workstation. Surfaces and faults can be represented as geological objects, and interactively modified. Once the tectonic framework has been obtained, intermediate stratigraphic surfaces can be constructed between the main structural surfaces. Within each layer, reservoir attributes can be represented using various techniques. Examples show how the distribution of different facies (i.e. from fine to coarse grain) can be represented, or how various depositional units (for instance channels, crevasses and lobes in a turbidite setting) can be modelled as geological {open_quotes}objects{close_quotes} with complex geometries. Elf Aquitaine, in close co-operation with the GOCAD project in Nancy (France) is investigating how geological models can be made more realistic by developing interactive functionalities. Examples show that, contrary to standard deterministic or geostatistical modelling techniques (which tend to be difficult to control) the use of new 3D tools allows the geologist to interactively modify geological surfaces (including faults) or volumetric properties. Thus, the sensitivity of various economic parameters (oil in place, connected volumes, reserves) to major geological uncertainties can be evaluated. It is argued that future breakthroughs in geological modelling techniques are likely to happen in the development of interactive approaches rather than in the research of new mathematical algorithms.

  10. Reservoir geology using 3D modelling tools

    SciTech Connect

    Dubrule, O. ); Samson, P. ); Segonds, D. )

    1996-01-01

    The last decade has seen tremendous developments in the area of quantitative geological modelling. These developments have a significant impact on the current practice of constructing reservoir models. A structural model can first be constructed on the basis of depth-converted structural interpretations produced on a seismic interpretation workstation. Surfaces and faults can be represented as geological objects, and interactively modified. Once the tectonic framework has been obtained, intermediate stratigraphic surfaces can be constructed between the main structural surfaces. Within each layer, reservoir attributes can be represented using various techniques. Examples show how the distribution of different facies (i.e. from fine to coarse grain) can be represented, or how various depositional units (for instance channels, crevasses and lobes in a turbidite setting) can be modelled as geological [open quotes]objects[close quotes] with complex geometries. Elf Aquitaine, in close co-operation with the GOCAD project in Nancy (France) is investigating how geological models can be made more realistic by developing interactive functionalities. Examples show that, contrary to standard deterministic or geostatistical modelling techniques (which tend to be difficult to control) the use of new 3D tools allows the geologist to interactively modify geological surfaces (including faults) or volumetric properties. Thus, the sensitivity of various economic parameters (oil in place, connected volumes, reserves) to major geological uncertainties can be evaluated. It is argued that future breakthroughs in geological modelling techniques are likely to happen in the development of interactive approaches rather than in the research of new mathematical algorithms.

  11. Left-ventricle segmentation in real-time 3D echocardiography using a hybrid active shape model and optimal graph search approach

    NASA Astrophysics Data System (ADS)

    Zhang, Honghai; Abiose, Ademola K.; Campbell, Dwayne N.; Sonka, Milan; Martins, James B.; Wahle, Andreas

    2010-03-01

    Quantitative analysis of the left ventricular shape and motion patterns associated with left ventricular mechanical dyssynchrony (LVMD) is essential for diagnosis and treatment planning in congestive heart failure. Real-time 3D echocardiography (RT3DE) used for LVMD analysis is frequently limited by heavy speckle noise or partially incomplete data, thus a segmentation method utilizing learned global shape knowledge is beneficial. In this study, the endocardial surface of the left ventricle (LV) is segmented using a hybrid approach combining active shape model (ASM) with optimal graph search. The latter is used to achieve landmark refinement in the ASM framework. Optimal graph search translates the 3D segmentation into the detection of a minimum-cost closed set in a graph and can produce a globally optimal result. Various information-gradient, intensity distributions, and regional-property terms-are used to define the costs for the graph search. The developed method was tested on 44 RT3DE datasets acquired from 26 LVMD patients. The segmentation accuracy was assessed by surface positioning error and volume overlap measured for the whole LV as well as 16 standard LV regions. The segmentation produced very good results that were not achievable using ASM or graph search alone.

  12. Molecular modelling on small molecular CDK2 inhibitors: an integrated approach using a combination of molecular docking, 3D-QSAR and pharmacophore modelling.

    PubMed

    Yuan, H; Liu, H; Tai, W; Wang, F; Zhang, Y; Yao, S; Ran, T; Lu, S; Ke, Z; Xiong, X; Xu, J; Chen, Y; Lu, T

    2013-10-01

    Cyclin-dependent kinase 2 (CDK2) has been identified as an important target for developing novel anticancer agents. Molecular docking, three-dimensional quantitative structure-activity relationship (3D-QSAR) and pharmacophore modelling were combined with the ultimate goal of studying the structure-activity relationship of CDK2 inhibitors. The comparative molecular similarity indices analysis (CoMSIA) model constructed based on a set of 3-aminopyrazole derivatives as CDK2 inhibitors gave statistically significant results (q (2) = 0.700; r (2) = 0.982). A HypoGen pharmacophore model, constructed using diverse CDK2 inhibitors, also showed significant statistics ([Formula: see text]Cost = 61.483; RMSD = 0.53; Correlation coefficient = 0.98). The small residues and error values between the estimated and experimental activities of the training and test set compounds proved their strong capability of activity prediction. The structural insights obtained from these two models were consistent with each other. The pharmacophore model summarized the important pharmacophoric features required for protein-ligand binding. The 3D contour maps in combination with the comprehensive pharmacophoric features helped to better interpret the structure-activity relationship. The results will be beneficial for the discovery and design of novel CDK2 inhibitors. The simplicity of this approach provides expansion to its applicability in optimizing other classes of small molecular CDK2 inhibitors. PMID:23941641

  13. 3D integration approaches for MEMS and CMOS sensors based on a Cu through-silicon-via technology and wafer level bonding

    NASA Astrophysics Data System (ADS)

    Hofmann, L.; Dempwolf, S.; Reuter, D.; Ecke, R.; Gottfried, K.; Schulz, S. E.; Knechtel, R.; Geßner, T.

    2015-05-01

    Technologies for the 3D integration are described within this paper with respect to devices that have to retain a specific minimum wafer thickness for handling purposes (CMOS) and integrity of mechanical elements (MEMS). This implies Through-Silicon Vias (TSVs) with large dimensions and high aspect ratios (HAR). Moreover, as a main objective, the aspired TSV technology had to be universal and scalable with the designated utilization in a MEMS/CMOS foundry. Two TSV approaches are investigated and discussed, in which the TSVs were fabricated either before or after wafer thinning. One distinctive feature is an incomplete TSV Cu-filling, which avoids long processing and complex process control, while minimizing the thermomechanical stress between Cu and Si and related adverse effects in the device. However, the incomplete filling also includes various challenges regarding process integration. A method based on pattern plating is described, in which TSVs are metalized at the same time as the redistribution layer and which eliminates the need for additional planarization and patterning steps. For MEMS, the realization of a protective hermetically sealed capping is crucial, which is addressed in this paper by glass frit wafer level bonding and is discussed for hermetic sealing of MEMS inertial sensors. The TSV based 3D integration technologies are demonstrated on CMOS like test vehicle and on a MEMS device fabricated in Air Gap Insulated Microstructure (AIM) technology.

  14. 3D Imaging.

    ERIC Educational Resources Information Center

    Hastings, S. K.

    2002-01-01

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

  15. 3-D CFD Simulation and Validation of Oxygen-Rich Hydrocarbon Combustion in a Gas-Centered Swirl Coaxial Injector using a Flamelet-Based Approach

    NASA Technical Reports Server (NTRS)

    Richardson, Brian; Kenny, Jeremy

    2015-01-01

    Injector design is a critical part of the development of a rocket Thrust Chamber Assembly (TCA). Proper detailed injector design can maximize propulsion efficiency while minimizing the potential for failures in the combustion chamber. Traditional design and analysis methods for hydrocarbon-fuel injector elements are based heavily on empirical data and models developed from heritage hardware tests. Using this limited set of data produces challenges when trying to design a new propulsion system where the operating conditions may greatly differ from heritage applications. Time-accurate, Three-Dimensional (3-D) Computational Fluid Dynamics (CFD) modeling of combusting flows inside of injectors has long been a goal of the fluid analysis group at Marshall Space Flight Center (MSFC) and the larger CFD modeling community. CFD simulation can provide insight into the design and function of an injector that cannot be obtained easily through testing or empirical comparisons to existing hardware. However, the traditional finite-rate chemistry modeling approach utilized to simulate combusting flows for complex fuels, such as Rocket Propellant-2 (RP-2), is prohibitively expensive and time consuming even with a large amount of computational resources. MSFC has been working, in partnership with Streamline Numerics, Inc., to develop a computationally efficient, flamelet-based approach for modeling complex combusting flow applications. In this work, a flamelet modeling approach is used to simulate time-accurate, 3-D, combusting flow inside a single Gas Centered Swirl Coaxial (GCSC) injector using the flow solver, Loci-STREAM. CFD simulations were performed for several different injector geometries. Results of the CFD analysis helped guide the design of the injector from an initial concept to a tested prototype. The results of the CFD analysis are compared to data gathered from several hot-fire, single element injector tests performed in the Air Force Research Lab EC-1 test facility

  16. A computerized framework for monitoring four-dimensional dose distributions during stereotactic body radiation therapy using a portal dose image-based 2D/3D registration approach.

    PubMed

    Nakamoto, Takahiro; Arimura, Hidetaka; Nakamura, Katsumasa; Shioyama, Yoshiyuki; Mizoguchi, Asumi; Hirose, Taka-Aki; Honda, Hiroshi; Umezu, Yoshiyuki; Nakamura, Yasuhiko; Hirata, Hideki

    2015-03-01

    A computerized framework for monitoring four-dimensional (4D) dose distributions during stereotactic body radiation therapy based on a portal dose image (PDI)-based 2D/3D registration approach has been proposed in this study. Using the PDI-based registration approach, simulated 4D "treatment" CT images were derived from the deformation of 3D planning CT images so that a 2D planning PDI could be similar to a 2D dynamic clinical PDI at a breathing phase. The planning PDI was calculated by applying a dose calculation algorithm (a pencil beam convolution algorithm) to the geometry of the planning CT image and a virtual water equivalent phantom. The dynamic clinical PDIs were estimated from electronic portal imaging device (EPID) dynamic images including breathing phase data obtained during a treatment. The parameters of the affine transformation matrix were optimized based on an objective function and a gamma pass rate using a Levenberg-Marquardt (LM) algorithm. The proposed framework was applied to the EPID dynamic images of ten lung cancer patients, which included 183 frames (mean: 18.3 per patient). The 4D dose distributions during the treatment time were successfully obtained by applying the dose calculation algorithm to the simulated 4D "treatment" CT images. The mean±standard deviation (SD) of the percentage errors between the prescribed dose and the estimated dose at an isocenter for all cases was 3.25±4.43%. The maximum error for the ten cases was 14.67% (prescribed dose: 1.50Gy, estimated dose: 1.72Gy), and the minimum error was 0.00%. The proposed framework could be feasible for monitoring the 4D dose distribution and dose errors within a patient's body during treatment. PMID:25592290

  17. 3D EIT image reconstruction with GREIT.

    PubMed

    Grychtol, Bartłomiej; Müller, Beat; Adler, Andy

    2016-06-01

    Most applications of thoracic EIT use a single plane of electrodes on the chest from which a transverse image 'slice' is calculated. However, interpretation of EIT images is made difficult by the large region above and below the electrode plane to which EIT is sensitive. Volumetric EIT images using two (or more) electrode planes should help compensate, but are little used currently. The Graz consensus reconstruction algorithm for EIT (GREIT) has become popular in lung EIT. One shortcoming of the original formulation of GREIT is its restriction to reconstruction onto a 2D planar image. We present an extension of the GREIT algorithm to 3D and develop open-source tools to evaluate its performance as a function of the choice of stimulation and measurement pattern. Results show 3D GREIT using two electrode layers has significantly more uniform sensitivity profiles through the chest region. Overall, the advantages of 3D EIT are compelling. PMID:27203184

  18. patGPCR: A Multitemplate Approach for Improving 3D Structure Prediction of Transmembrane Helices of G-Protein-Coupled Receptors

    PubMed Central

    Wu, Hongjie; Lü, Qiang; Quan, Lijun; Qian, Peide; Xia, Xiaoyan

    2013-01-01

    The structures of the seven transmembrane helices of G-protein-coupled receptors are critically involved in many aspects of these receptors, such as receptor stability, ligand docking, and molecular function. Most of the previous multitemplate approaches have built a “super” template with very little merging of aligned fragments from different templates. Here, we present a parallelized multitemplate approach, patGPCR, to predict the 3D structures of transmembrane helices of G-protein-coupled receptors. patGPCR, which employs a bundle-packing related energy function that extends on the RosettaMem energy, parallelizes eight pipelines for transmembrane helix refinement and exchanges the optimized helix structures from multiple templates. We have investigated the performance of patGPCR on a test set containing eight determined G-protein-coupled receptors. The results indicate that patGPCR improves the TM RMSD of the predicted models by 33.64% on average against a single-template method. Compared with other homology approaches, the best models for five of the eight targets built by patGPCR had a lower TM RMSD than that obtained from SWISS-MODEL; patGPCR also showed lower average TM RMSD than single-template and multiple-template MODELLER. PMID:23554839

  19. TRACE 3-D documentation

    SciTech Connect

    Crandall, K.R.

    1987-08-01

    TRACE 3-D is an interactive beam-dynamics program that calculates the envelopes of a bunched beam, including linear space-charge forces, through a user-defined transport system. TRACE 3-D provides an immediate graphics display of the envelopes and the phase-space ellipses and allows nine types of beam-matching options. This report describes the beam-dynamics calculations and gives detailed instruction for using the code. Several examples are described in detail.

  20. Self consistent particles dynamics in/out of the cusp region by using back tracking technics; a global 3D PIC simulation approach

    NASA Astrophysics Data System (ADS)

    Esmaeili, A.; Cai, D.; Lembege, B.; Nishikawa, K.

    2013-12-01

    Large scale three dimensionbal PIC (particle in cell) simulations are presently used in order to analyze the global solar wind-terrestrial magnetosphere intreraction within a full self-consistent approach, and where both electrons and ions are treated as an assembly of individual particles. This 3D kinetic approach allows us to analyze in particular the dynamics and the fine structures of the cusp region when including self consistently not only its whole neighborhood (in the terrestrial magnetosphere) but also the impact of the solar wind and the interplanetary field (IMF) features. Herein, we focuss our attention on the cusp region and in particular on the acceleration and precipitation of particles (both ions and electrons) within the cusp. In present simulations, the IMF is chosen northward, (i.e. where the X -reconnection region is just above the cusp, in the meridian plane). Back-trackings of self-consistent particles are analyzed in details in order to determine (i) which particles (just above the cusp) are precipitated deeply into the cusp, (ii) which populations are injected from the cusp into the nearby tail, (iii) where the particles suffer the largest energisation along their self-consistent trajectories, (iv) where these populations accumulate, and (v) where the most energetic particles are originally coming from. This approach allows to make a traking of particles within the scenario "solar wind-magnetosheath- cusp -nearbytail"; moreover it strongly differs from the standard test particles technics and allows to provide informations not accessible when using full MHD approach. Keywords: Tracing Particles, Particle In Cell (PIC) simulation, double cusp, test particles method, IMF, Solar wind, Magnetosphere

  1. Resolution-limited optical recording in 3D.

    PubMed

    Orlic, Susanna; Dietz, Enrico; Frohmann, Sven; Rass, Jens

    2011-08-15

    We present an optical write/read system for high density optical data storage in 3-D. The microholographic approach relies on submicron-sized reflection gratings that encode the digital data. As in conventional optical data storage, the physical limitations are imposed by both the diffraction of light and resolution of the recording material. We demonstrate resolution-limited volume recording in photopolymer materials sensitive in the green and violet spectral range. The volume occupied by a micrograting scales down by the transition in the write/read wavelength. Readout yields a micrograting width of 306 nm at 532 nm and 197 nm at 405 nm. To our knowledge these are the smallest volume holograms ever recorded. The recordings demonstrate the potential of the technique for volumetric optical structuring, data storage and encryption. PMID:21934972

  2. 3D laptop for defense applications

    NASA Astrophysics Data System (ADS)

    Edmondson, Richard; Chenault, David

    2012-06-01

    Polaris Sensor Technologies has developed numerous 3D display systems using a US Army patented approach. These displays have been developed as prototypes for handheld controllers for robotic systems and closed hatch driving, and as part of a TALON robot upgrade for 3D vision, providing depth perception for the operator for improved manipulation and hazard avoidance. In this paper we discuss the prototype rugged 3D laptop computer and its applications to defense missions. The prototype 3D laptop combines full temporal and spatial resolution display with the rugged Amrel laptop computer. The display is viewed through protective passive polarized eyewear, and allows combined 2D and 3D content. Uses include robot tele-operation with live 3D video or synthetically rendered scenery, mission planning and rehearsal, enhanced 3D data interpretation, and simulation.

  3. 3D detection of colonic polyps by CT colonography: accuracy, pitfalls, and solutions by adjunct 2D workup.

    PubMed

    Schmidt, S A; Ernst, A S; Beer, M; Juchems, M S

    2015-10-01

    Computed tomography colonography (CTC) enables evaluation of the colon with minimal invasiveness. In spite of advances in multidetector CT (MDCT) technology and advanced software features, including electronic bowel cleansing (digital removal and tagging of fluid and debris), a number of potential pitfalls in the evaluation of the 3D volumetric dataset persist. The purpose of this article is to illustrate the strengths and potential pitfalls in the detection of colorectal polyps using CTC via a primary three-dimensional (3D) approach for evaluation. PMID:26220124

  4. Radiochromic 3D Detectors

    NASA Astrophysics Data System (ADS)

    Oldham, Mark

    2015-01-01

    Radiochromic materials exhibit a colour change when exposed to ionising radiation. Radiochromic film has been used for clinical dosimetry for many years and increasingly so recently, as films of higher sensitivities have become available. The two principle advantages of radiochromic dosimetry include greater tissue equivalence (radiologically) and the lack of requirement for development of the colour change. In a radiochromic material, the colour change arises direct from ionising interactions affecting dye molecules, without requiring any latent chemical, optical or thermal development, with important implications for increased accuracy and convenience. It is only relatively recently however, that 3D radiochromic dosimetry has become possible. In this article we review recent developments and the current state-of-the-art of 3D radiochromic dosimetry, and the potential for a more comprehensive solution for the verification of complex radiation therapy treatments, and 3D dose measurement in general.

  5. Bootstrapping 3D fermions

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  6. 3D ultrafast laser scanner

    NASA Astrophysics Data System (ADS)

    Mahjoubfar, A.; Goda, K.; Wang, C.; Fard, A.; Adam, J.; Gossett, D. R.; Ayazi, A.; Sollier, E.; Malik, O.; Chen, E.; Liu, Y.; Brown, R.; Sarkhosh, N.; Di Carlo, D.; Jalali, B.

    2013-03-01

    Laser scanners are essential for scientific research, manufacturing, defense, and medical practice. Unfortunately, often times the speed of conventional laser scanners (e.g., galvanometric mirrors and acousto-optic deflectors) falls short for many applications, resulting in motion blur and failure to capture fast transient information. Here, we present a novel type of laser scanner that offers roughly three orders of magnitude higher scan rates than conventional methods. Our laser scanner, which we refer to as the hybrid dispersion laser scanner, performs inertia-free laser scanning by dispersing a train of broadband pulses both temporally and spatially. More specifically, each broadband pulse is temporally processed by time stretch dispersive Fourier transform and further dispersed into space by one or more diffractive elements such as prisms and gratings. As a proof-of-principle demonstration, we perform 1D line scans at a record high scan rate of 91 MHz and 2D raster scans and 3D volumetric scans at an unprecedented scan rate of 105 kHz. The method holds promise for a broad range of scientific, industrial, and biomedical applications. To show the utility of our method, we demonstrate imaging, nanometer-resolved surface vibrometry, and high-precision flow cytometry with real-time throughput that conventional laser scanners cannot offer due to their low scan rates.

  7. SU-E-J-141: Activity-Equivalent Path Length Approach for the 3D PET-Based Dose Reconstruction in Proton Therapy

    SciTech Connect

    Attili, A; Vignati, A; Giordanengo, S; Kraan, A; Dalmasso, F; Battistoni, G

    2015-06-15

    Purpose: Ion beam therapy is sensitive to uncertainties from treatment planning and dose delivery. PET imaging of induced positron emitter distributions is a practical approach for in vivo, in situ verification of ion beam treatments. Treatment verification is usually done by comparing measured activity distributions with reference distributions, evaluated in nominal conditions. Although such comparisons give valuable information on treatment quality, a proper clinical evaluation of the treatment ultimately relies on the knowledge of the actual delivered dose. Analytical deconvolution methods relating activity and dose have been studied in this context, but were not clinically applied. In this work we present a feasibility study of an alternative approach for dose reconstruction from activity data, which is based on relating variations in accumulated activity to tissue density variations. Methods: First, reference distributions of dose and activity were calculated from the treatment plan and CT data. Then, the actual measured activity data were cumulatively matched with the reference activity distributions to obtain a set of activity-equivalent path lengths (AEPLs) along the rays of the pencil beams. Finally, these AEPLs were used to deform the original dose distribution, yielding the actual delivered dose. The method was tested by simulating a proton therapy treatment plan delivering 2 Gy on a homogeneous water phantom (the reference), which was compared with the same plan delivered on a phantom containing inhomogeneities. Activity and dose distributions were were calculated by means of the FLUKA Monte Carlo toolkit. Results: The main features of the observed dose distribution in the inhomogeneous situation were reproduced using the AEPL approach. Variations in particle range were reproduced and the positions, where these deviations originated, were properly identified. Conclusions: For a simple inhomogeneous phantom the 3D dose reconstruction from PET

  8. Accuracy in Quantitative 3D Image Analysis

    PubMed Central

    Bassel, George W.

    2015-01-01

    Quantitative 3D imaging is becoming an increasingly popular and powerful approach to investigate plant growth and development. With the increased use of 3D image analysis, standards to ensure the accuracy and reproducibility of these data are required. This commentary highlights how image acquisition and postprocessing can introduce artifacts into 3D image data and proposes steps to increase both the accuracy and reproducibility of these analyses. It is intended to aid researchers entering the field of 3D image processing of plant cells and tissues and to help general readers in understanding and evaluating such data. PMID:25804539

  9. 3D Printed Block Copolymer Nanostructures

    ERIC Educational Resources Information Center

    Scalfani, Vincent F.; Turner, C. Heath; Rupar, Paul A.; Jenkins, Alexander H.; Bara, Jason E.

    2015-01-01

    The emergence of 3D printing has dramatically advanced the availability of tangible molecular and extended solid models. Interestingly, there are few nanostructure models available both commercially and through other do-it-yourself approaches such as 3D printing. This is unfortunate given the importance of nanotechnology in science today. In this…

  10. 3D microscope

    NASA Astrophysics Data System (ADS)

    Iizuka, Keigo

    2008-02-01

    In order to circumvent the fact that only one observer can view the image from a stereoscopic microscope, an attachment was devised for displaying the 3D microscopic image on a large LCD monitor for viewing by multiple observers in real time. The principle of operation, design, fabrication, and performance are presented, along with tolerance measurements relating to the properties of the cellophane half-wave plate used in the design.

  11. Automated detection, 3D segmentation and analysis of high resolution spine MR images using statistical shape models

    NASA Astrophysics Data System (ADS)

    Neubert, A.; Fripp, J.; Engstrom, C.; Schwarz, R.; Lauer, L.; Salvado, O.; Crozier, S.

    2012-12-01

    Recent advances in high resolution magnetic resonance (MR) imaging of the spine provide a basis for the automated assessment of intervertebral disc (IVD) and vertebral body (VB) anatomy. High resolution three-dimensional (3D) morphological information contained in these images may be useful for early detection and monitoring of common spine disorders, such as disc degeneration. This work proposes an automated approach to extract the 3D segmentations of lumbar and thoracic IVDs and VBs from MR images using statistical shape analysis and registration of grey level intensity profiles. The algorithm was validated on a dataset of volumetric scans of the thoracolumbar spine of asymptomatic volunteers obtained on a 3T scanner using the relatively new 3D T2-weighted SPACE pulse sequence. Manual segmentations and expert radiological findings of early signs of disc degeneration were used in the validation. There was good agreement between manual and automated segmentation of the IVD and VB volumes with the mean Dice scores of 0.89 ± 0.04 and 0.91 ± 0.02 and mean absolute surface distances of 0.55 ± 0.18 mm and 0.67 ± 0.17 mm respectively. The method compares favourably to existing 3D MR segmentation techniques for VBs. This is the first time IVDs have been automatically segmented from 3D volumetric scans and shape parameters obtained were used in preliminary analyses to accurately classify (100% sensitivity, 98.3% specificity) disc abnormalities associated with early degenerative changes.

  12. Stability of 3D Textile Composite Reinforcement Simulations: Solutions to Spurious Transverse Modes

    NASA Astrophysics Data System (ADS)

    Mathieu, S.; Hamila, N.; Dupé, F.; Descamps, C.; Boisse, P.

    2016-08-01

    The simulation of thick 3D composite reinforcement forming brings to light new modeling challenges. The specific anisotropic material behavior due to the possible slippage between fibers induces, among other phenomena, the development of spurious transverse modes in bending-dominated 3D simulations. To obtain coherent finite element responses, two solutions are proposed. The first one uses a simple assumed strain formulation usually prescribed to prevent volumetric locking. This solution avoids spurious transverse modes by stiffening of the hourglass modes. Nevertheless the deformation obtained by this approach still suffers from the inability of the standard continuum mechanics of Cauchy to describe fibrous material deformation. The second proposed approach is based on the introduction of a bending stiffness which both avoids the spurious transverse modes and also improves the global behavior of the element formulation by enriching the underlying continuum. To emphasize the differences between different formulations, element stiffnesses are explicitly calculated and compared.

  13. Stability of 3D Textile Composite Reinforcement Simulations: Solutions to Spurious Transverse Modes

    NASA Astrophysics Data System (ADS)

    Mathieu, S.; Hamila, N.; Dupé, F.; Descamps, C.; Boisse, P.

    2016-03-01

    The simulation of thick 3D composite reinforcement forming brings to light new modeling challenges. The specific anisotropic material behavior due to the possible slippage between fibers induces, among other phenomena, the development of spurious transverse modes in bending-dominated 3D simulations. To obtain coherent finite element responses, two solutions are proposed. The first one uses a simple assumed strain formulation usually prescribed to prevent volumetric locking. This solution avoids spurious transverse modes by stiffening of the hourglass modes. Nevertheless the deformation obtained by this approach still suffers from the inability of the standard continuum mechanics of Cauchy to describe fibrous material deformation. The second proposed approach is based on the introduction of a bending stiffness which both avoids the spurious transverse modes and also improves the global behavior of the element formulation by enriching the underlying continuum. To emphasize the differences between different formulations, element stiffnesses are explicitly calculated and compared.

  14. A high capacity 3D steganography algorithm.

    PubMed

    Chao, Min-Wen; Lin, Chao-hung; Yu, Cheng-Wei; Lee, Tong-Yee

    2009-01-01

    In this paper, we present a very high-capacity and low-distortion 3D steganography scheme. Our steganography approach is based on a novel multilayered embedding scheme to hide secret messages in the vertices of 3D polygon models. Experimental results show that the cover model distortion is very small as the number of hiding layers ranges from 7 to 13 layers. To the best of our knowledge, this novel approach can provide much higher hiding capacity than other state-of-the-art approaches, while obeying the low distortion and security basic requirements for steganography on 3D models. PMID:19147891

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

    NASA Astrophysics Data System (ADS)

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

    2012-07-01

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

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

    PubMed

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

    2012-07-01

    Image-guided alignment procedures in radiotherapy aim at minimizing discrepancies between the planned and the real patient setup. For that purpose, we developed a 2D/3D approach which rigidly registers a computed tomography (CT) with two x-rays by maximizing the agreement in pixel intensity between the x-rays and the corresponding reconstructed radiographs from the CT. Moreover, the algorithm selects regions of interest (masks) in the x-rays based on 3D segmentations from the pre-planning stage. For validation, orthogonal x-ray pairs from different viewing directions of 80 pelvic cone-beam CT (CBCT) raw data sets were used. The 2D/3D results were compared to corresponding standard 3D/3D CBCT-to-CT alignments. Outcome over 8400 2D/3D experiments showed that parametric errors in root mean square were <0.18° (rotations) and <0.73 mm (translations), respectively, using rank correlation as intensity metric. This corresponds to a mean target registration error, related to the voxels of the lesser pelvis, of <2 mm in 94.1% of the cases. From the results we conclude that 2D/3D registration based on sequentially acquired orthogonal x-rays of the pelvis is a viable alternative to CBCT-based approaches if rigid alignment on bony anatomy is sufficient, no volumetric intra-interventional data set is required and the expected error range fits the individual treatment prescription. PMID:22705709

  17. Diffusion approximation for modeling of 3-D radiation distributions

    SciTech Connect

    Zardecki, A.; Gerstl, S.A.W.; De Kinder, R.E. Jr.

    1985-01-01

    A three-dimensional transport code DIF3D, based on the diffusion approximation, is used to model the spatial distribution of radiation energy arising from volumetric isotropic sources. Future work will be concerned with the determination of irradiances and modeling of realistic scenarios, relevant to the battlefield conditions. 8 refs., 4 figs.

  18. Vascular endothelial growth factor receptor-2 (VEGFR-2) inhibitors: development and validation of predictive 3-D QSAR models through extensive ligand- and structure-based approaches.

    PubMed

    Ragno, Rino; Ballante, Flavio; Pirolli, Adele; Wickersham, Richard B; Patsilinakos, Alexandros; Hesse, Stéphanie; Perspicace, Enrico; Kirsch, Gilbert

    2015-08-01

    Vascular endothelial growth factor receptor-2, (VEGFR-2), is a key element in angiogenesis, the process by which new blood vessels are formed, and is thus an important pharmaceutical target. Here, 3-D quantitative structure-activity relationship (3-D QSAR) were used to build a quantitative screening and pharmacophore model of the VEGFR-2 receptors for design of inhibitors with improved activities. Most of available experimental data information has been used as training set to derive optimized and fully cross-validated eight mono-probe and a multi-probe quantitative models. Notable is the use of 262 molecules, aligned following both structure-based and ligand-based protocols, as external test set confirming the 3-D QSAR models' predictive capability and their usefulness in design new VEGFR-2 inhibitors. From a survey on literature, this is the first generation of a wide-ranging computational medicinal chemistry application on VEGFR2 inhibitors. PMID:26194852

  19. Multiviewer 3D monitor

    NASA Astrophysics Data System (ADS)

    Kostrzewski, Andrew A.; Aye, Tin M.; Kim, Dai Hyun; Esterkin, Vladimir; Savant, Gajendra D.

    1998-09-01

    Physical Optics Corporation has developed an advanced 3-D virtual reality system for use with simulation tools for training technical and military personnel. This system avoids such drawbacks of other virtual reality (VR) systems as eye fatigue, headaches, and alignment for each viewer, all of which are due to the need to wear special VR goggles. The new system is based on direct viewing of an interactive environment. This innovative holographic multiplexed screen technology makes it unnecessary for the viewer to wear special goggles.

  20. 3D Audio System

    NASA Technical Reports Server (NTRS)

    1992-01-01

    Ames Research Center research into virtual reality led to the development of the Convolvotron, a high speed digital audio processing system that delivers three-dimensional sound over headphones. It consists of a two-card set designed for use with a personal computer. The Convolvotron's primary application is presentation of 3D audio signals over headphones. Four independent sound sources are filtered with large time-varying filters that compensate for motion. The perceived location of the sound remains constant. Possible applications are in air traffic control towers or airplane cockpits, hearing and perception research and virtual reality development.

  1. 3D Surgical Simulation

    PubMed Central

    Cevidanes, Lucia; Tucker, Scott; Styner, Martin; Kim, Hyungmin; Chapuis, Jonas; Reyes, Mauricio; Proffit, William; Turvey, Timothy; Jaskolka, Michael

    2009-01-01

    This paper discusses the development of methods for computer-aided jaw surgery. Computer-aided jaw surgery allows us to incorporate the high level of precision necessary for transferring virtual plans into the operating room. We also present a complete computer-aided surgery (CAS) system developed in close collaboration with surgeons. Surgery planning and simulation include construction of 3D surface models from Cone-beam CT (CBCT), dynamic cephalometry, semi-automatic mirroring, interactive cutting of bone and bony segment repositioning. A virtual setup can be used to manufacture positioning splints for intra-operative guidance. The system provides further intra-operative assistance with the help of a computer display showing jaw positions and 3D positioning guides updated in real-time during the surgical procedure. The CAS system aids in dealing with complex cases with benefits for the patient, with surgical practice, and for orthodontic finishing. Advanced software tools for diagnosis and treatment planning allow preparation of detailed operative plans, osteotomy repositioning, bone reconstructions, surgical resident training and assessing the difficulties of the surgical procedures prior to the surgery. CAS has the potential to make the elaboration of the surgical plan a more flexible process, increase the level of detail and accuracy of the plan, yield higher operative precision and control, and enhance documentation of cases. Supported by NIDCR DE017727, and DE018962 PMID:20816308

  2. Topology dictionary for 3D video understanding.

    PubMed

    Tung, Tony; Matsuyama, Takashi

    2012-08-01

    This paper presents a novel approach that achieves 3D video understanding. 3D video consists of a stream of 3D models of subjects in motion. The acquisition of long sequences requires large storage space (2 GB for 1 min). Moreover, it is tedious to browse data sets and extract meaningful information. We propose the topology dictionary to encode and describe 3D video content. The model consists of a topology-based shape descriptor dictionary which can be generated from either extracted patterns or training sequences. The model relies on 1) topology description and classification using Reeb graphs, and 2) a Markov motion graph to represent topology change states. We show that the use of Reeb graphs as the high-level topology descriptor is relevant. It allows the dictionary to automatically model complex sequences, whereas other strategies would require prior knowledge on the shape and topology of the captured subjects. Our approach serves to encode 3D video sequences, and can be applied for content-based description and summarization of 3D video sequences. Furthermore, topology class labeling during a learning process enables the system to perform content-based event recognition. Experiments were carried out on various 3D videos. We showcase an application for 3D video progressive summarization using the topology dictionary. PMID:22745004

  3. Translating Response During Therapy into Ultimate Treatment Outcome: A Personalized 4-Dimensional MRI Tumor Volumetric Regression Approach in Cervical Cancer

    SciTech Connect

    Mayr, Nina A.; Wang, Jian Z.; Lo, Simon S.; Zhang Dongqing; Grecula, John C.; Lu Lanchun; Montebello, Joseph F.; Fowler, Jeffrey M.; Yuh, William T.C.

    2010-03-01

    Purpose: To assess individual volumetric tumor regression pattern in cervical cancer during therapy using serial four-dimensional MRI and to define the regression parameters' prognostic value validated with local control and survival correlation. Methods and Materials: One hundred and fifteen patients with Stage IB{sub 2}-IVA cervical cancer treated with radiation therapy (RT) underwent serial MRI before (MRI 1) and during RT, at 2-2.5 weeks (MRI 2, at 20-25 Gy), and at 4-5 weeks (MRI 3, at 40-50 Gy). Eighty patients had a fourth MRI 1-2 months post-RT. Mean follow-up was 5.3 years. Tumor volume was measured by MRI-based three-dimensional volumetry, and plotted as dose(time)/volume regression curves. Volume regression parameters were correlated with local control, disease-specific, and overall survival. Results: Residual tumor volume, slope, and area under the regression curve correlated significantly with local control and survival. Residual volumes >=20% at 40-50 Gy were independently associated with inferior 5-year local control (53% vs. 97%, p <0.001) and disease-specific survival rates (50% vs. 72%, p = 0.009) than smaller volumes. Patients with post-RT residual volumes >=10% had 0% local control and 17% disease-specific survival, compared with 91% and 72% for <10% volume (p <0.001). Conclusion: Using more accurate four-dimensional volumetric regression analysis, tumor response can now be directly translated into individual patients' outcome for clinical application. Our results define two temporal thresholds critically influencing local control and survival. In patients with >=20% residual volume at 40-50 Gy and >=10% post-RT, the risk for local failure and death are so high that aggressive intervention may be warranted.

  4. A Learner-Centered Approach for Training Science Teachers through Virtual Reality and 3D Visualization Technologies: Practical Experience for Sharing

    ERIC Educational Resources Information Center

    Yeung, Yau-Yuen

    2004-01-01

    This paper presentation will report on how some science educators at the Science Department of The Hong Kong Institute of Education have successfully employed an array of innovative learning media such as three-dimensional (3D) and virtual reality (VR) technologies to create seven sets of resource kits, most of which are being placed on the…

  5. A synergistic approach to the design, fabrication and evaluation of 3D printed micro and nano featured scaffolds for vascularized bone tissue repair

    NASA Astrophysics Data System (ADS)

    Holmes, Benjamin; Bulusu, Kartik; Plesniak, Michael; Zhang, Lijie Grace

    2016-02-01

    3D bioprinting has begun to show great promise in advancing the development of functional tissue/organ replacements. However, to realize the true potential of 3D bioprinted tissues for clinical use requires the fabrication of an interconnected and effective vascular network. Solving this challenge is critical, as human tissue relies on an adequate network of blood vessels to transport oxygen, nutrients, other chemicals, biological factors and waste, in and out of the tissue. Here, we have successfully designed and printed a series of novel 3D bone scaffolds with both bone formation supporting structures and highly interconnected 3D microvascular mimicking channels, for efficient and enhanced osteogenic bone regeneration as well as vascular cell growth. Using a chemical functionalization process, we have conjugated our samples with nano hydroxyapatite (nHA), for the creation of novel micro and nano featured devices for vascularized bone growth. We evaluated our scaffolds with mechanical testing, hydrodynamic measurements and in vitro human mesenchymal stem cell (hMSC) adhesion (4 h), proliferation (1, 3 and 5 d) and osteogenic differentiation (1, 2 and 3 weeks). These tests confirmed bone-like physical properties and vascular-like flow profiles, as well as demonstrated enhanced hMSC adhesion, proliferation and osteogenic differentiation. Additional in vitro experiments with human umbilical vein endothelial cells also demonstrated improved vascular cell growth, migration and organization on micro-nano featured scaffolds.

  6. A synergistic approach to the design, fabrication and evaluation of 3D printed micro and nano featured scaffolds for vascularized bone tissue repair.

    PubMed

    Holmes, Benjamin; Bulusu, Kartik; Plesniak, Michael; Zhang, Lijie Grace

    2016-02-12

    3D bioprinting has begun to show great promise in advancing the development of functional tissue/organ replacements. However, to realize the true potential of 3D bioprinted tissues for clinical use requires the fabrication of an interconnected and effective vascular network. Solving this challenge is critical, as human tissue relies on an adequate network of blood vessels to transport oxygen, nutrients, other chemicals, biological factors and waste, in and out of the tissue. Here, we have successfully designed and printed a series of novel 3D bone scaffolds with both bone formation supporting structures and highly interconnected 3D microvascular mimicking channels, for efficient and enhanced osteogenic bone regeneration as well as vascular cell growth. Using a chemical functionalization process, we have conjugated our samples with nano hydroxyapatite (nHA), for the creation of novel micro and nano featured devices for vascularized bone growth. We evaluated our scaffolds with mechanical testing, hydrodynamic measurements and in vitro human mesenchymal stem cell (hMSC) adhesion (4 h), proliferation (1, 3 and 5 d) and osteogenic differentiation (1, 2 and 3 weeks). These tests confirmed bone-like physical properties and vascular-like flow profiles, as well as demonstrated enhanced hMSC adhesion, proliferation and osteogenic differentiation. Additional in vitro experiments with human umbilical vein endothelial cells also demonstrated improved vascular cell growth, migration and organization on micro-nano featured scaffolds. PMID:26758780

  7. Weakly supervised automatic segmentation and 3D modeling of the knee joint from MR images

    NASA Astrophysics Data System (ADS)

    Amami, Amal; Ben Azouz, Zouhour

    2013-12-01

    Automatic segmentation and 3D modeling of the knee joint from MR images, is a challenging task. Most of the existing techniques require the tedious manual segmentation of a training set of MRIs. We present an approach that necessitates the manual segmentation of one MR image. It is based on a volumetric active appearance model. First, a dense tetrahedral mesh is automatically created on a reference MR image that is arbitrary selected. Second, a pairwise non-rigid registration between each MRI from a training set and the reference MRI is computed. The non-rigid registration is based on a piece-wise affine deformation using the created tetrahedral mesh. The minimum description length is then used to bring all the MR images into a correspondence. An average image and tetrahedral mesh, as well as a set of main modes of variations, are generated using the established correspondence. Any manual segmentation of the average MRI can be mapped to other MR images using the AAM. The proposed approach has the advantage of simultaneously generating 3D reconstructions of the surface as well as a 3D solid model of the knee joint. The generated surfaces and tetrahedral meshes present the interesting property of fulfilling a correspondence between different MR images. This paper shows preliminary results of the proposed approach. It demonstrates the automatic segmentation and 3D reconstruction of a knee joint obtained by mapping a manual segmentation of a reference image.

  8. 3D polarimetric purity

    NASA Astrophysics Data System (ADS)

    Gil, José J.; San José, Ignacio

    2010-11-01

    From our previous definition of the indices of polarimetric purity for 3D light beams [J.J. Gil, J.M. Correas, P.A. Melero and C. Ferreira, Monogr. Semin. Mat. G. de Galdeano 31, 161 (2004)], an analysis of their geometric and physical interpretation is presented. It is found that, in agreement with previous results, the first parameter is a measure of the degree of polarization, whereas the second parameter (called the degree of directionality) is a measure of the mean angular aperture of the direction of propagation of the corresponding light beam. This pair of invariant, non-dimensional, indices of polarimetric purity contains complete information about the polarimetric purity of a light beam. The overall degree of polarimetric purity is obtained as a weighted quadratic average of the degree of polarization and the degree of directionality.

  9. 3D field harmonics

    SciTech Connect

    Caspi, S.; Helm, M.; Laslett, L.J.

    1991-03-30

    We have developed an harmonic representation for the three dimensional field components within the windings of accelerator magnets. The form by which the field is presented is suitable for interfacing with other codes that make use of the 3D field components (particle tracking and stability). The field components can be calculated with high precision and reduced cup time at any location (r,{theta},z) inside the magnet bore. The same conductor geometry which is used to simulate line currents is also used in CAD with modifications more readily available. It is our hope that the format used here for magnetic fields can be used not only as a means of delivering fields but also as a way by which beam dynamics can suggest correction to the conductor geometry. 5 refs., 70 figs.

  10. 'Bonneville' in 3-D!

    NASA Technical Reports Server (NTRS)

    2004-01-01

    The Mars Exploration Rover Spirit took this 3-D navigation camera mosaic of the crater called 'Bonneville' after driving approximately 13 meters (42.7 feet) to get a better vantage point. Spirit's current position is close enough to the edge to see the interior of the crater, but high enough and far enough back to get a view of all of the walls. Because scientists and rover controllers are so pleased with this location, they will stay here for at least two more martian days, or sols, to take high resolution panoramic camera images of 'Bonneville' in its entirety. Just above the far crater rim, on the left side, is the rover's heatshield, which is visible as a tiny reflective speck.

  11. 3D non-rigid surface-based MR-TRUS registration for image-guided prostate biopsy

    NASA Astrophysics Data System (ADS)

    Sun, Yue; Qiu, Wu; Romagnoli, Cesare; Fenster, Aaron

    2014-03-01

    Two dimensional (2D) transrectal ultrasound (TRUS) guided prostate biopsy is the standard approach for definitive diagnosis of prostate cancer (PCa). However, due to the lack of image contrast of prostate tumors needed to clearly visualize early-stage PCa, prostate biopsy often results in false negatives, requiring repeat biopsies. Magnetic Resonance Imaging (MRI) has been considered to be a promising imaging modality for noninvasive identification of PCa, since it can provide a high sensitivity and specificity for the detection of early stage PCa. Our main objective is to develop and validate a registration method of 3D MR-TRUS images, allowing generation of volumetric 3D maps of targets identified in 3D MR images to be biopsied using 3D TRUS images. Our registration method first makes use of an initial rigid registration of 3D MR images to 3D TRUS images using 6 manually placed approximately corresponding landmarks in each image. Following the manual initialization, two prostate surfaces are segmented from 3D MR and TRUS images and then non-rigidly registered using a thin-plate spline (TPS) algorithm. The registration accuracy was evaluated using 4 patient images by measuring target registration error (TRE) of manually identified corresponding intrinsic fiducials (calcifications and/or cysts) in the prostates. Experimental results show that the proposed method yielded an overall mean TRE of 2.05 mm, which is favorably comparable to a clinical requirement for an error of less than 2.5 mm.

  12. 3D Printing for Tissue Engineering

    PubMed Central

    Jia, Jia; Yao, Hai; Mei, Ying

    2016-01-01

    Tissue engineering aims to fabricate functional tissue for applications in regenerative medicine and drug testing. More recently, 3D printing has shown great promise in tissue fabrication with a structural control from micro- to macro-scale by using a layer-by-layer approach. Whether through scaffold-based or scaffold-free approaches, the standard for 3D printed tissue engineering constructs is to provide a biomimetic structural environment that facilitates tissue formation and promotes host tissue integration (e.g., cellular infiltration, vascularization, and active remodeling). This review will cover several approaches that have advanced the field of 3D printing through novel fabrication methods of tissue engineering constructs. It will also discuss the applications of synthetic and natural materials for 3D printing facilitated tissue fabrication. PMID:26869728

  13. 3D whiteboard: collaborative sketching with 3D-tracked smart phones

    NASA Astrophysics Data System (ADS)

    Lue, James; Schulze, Jürgen P.

    2014-02-01

    We present the results of our investigation of the feasibility of a new approach for collaborative drawing in 3D, based on Android smart phones. Our approach utilizes a number of fiduciary markers, placed in the working area where they can be seen by the smart phones' cameras, in order to estimate the pose of each phone in the room. Our prototype allows two users to draw 3D objects with their smart phones by moving their phones around in 3D space. For example, 3D lines are drawn by recording the path of the phone as it is moved around in 3D space, drawing line segments on the screen along the way. Each user can see the virtual drawing space on their smart phones' displays, as if the display was a window into this space. Besides lines, our prototype application also supports 3D geometry creation, geometry transformation operations, and it shows the location of the other user's phone.

  14. Recording stereoscopic 3D neurosurgery with a head-mounted 3D camera system.

    PubMed

    Lee, Brian; Chen, Brian R; Chen, Beverly B; Lu, James Y; Giannotta, Steven L

    2015-06-01

    Stereoscopic three-dimensional (3D) imaging can present more information to the viewer and further enhance the learning experience over traditional two-dimensional (2D) video. Most 3D surgical videos are recorded from the operating microscope and only feature the crux, or the most important part of the surgery, leaving out other crucial parts of surgery including the opening, approach, and closing of the surgical site. In addition, many other surgeries including complex spine, trauma, and intensive care unit procedures are also rarely recorded. We describe and share our experience with a commercially available head-mounted stereoscopic 3D camera system to obtain stereoscopic 3D recordings of these seldom recorded aspects of neurosurgery. The strengths and limitations of using the GoPro(®) 3D system as a head-mounted stereoscopic 3D camera system in the operating room are reviewed in detail. Over the past several years, we have recorded in stereoscopic 3D over 50 cranial and spinal surgeries and created a library for education purposes. We have found the head-mounted stereoscopic 3D camera system to be a valuable asset to supplement 3D footage from a 3D microscope. We expect that these comprehensive 3D surgical videos will become an important facet of resident education and ultimately lead to improved patient care. PMID:25620087

  15. [Chaotic artificial bee colony algorithm: a new approach to the problem of minimization of energy of the 3D protein structure].

    PubMed

    Wang, Y; Guo, G D; Chen, L F

    2013-01-01

    Frediction of the three-dimensional structure of a protein from its amino acid sequence can be considered as a global optimization problem. In this paper, the Chaotic Artificial Bee Colony (CABC) algorithm was introduced and applied to 3D protein structure prediction. Based on the 3D off-lattice AB model, the CABC algorithm combines global search and local search of the Artificial Bee Colony (ABC) algorithm with the Chaotic search algorithm to avoid the problem of premature convergence and easily trapping the local optimum solution. The experiments carried out with the popular Fibonacci sequences demonstrate that the proposed algorithm provides an effective and high-performance method for protein structure prediction. PMID:25509864

  16. Full Three-Dimensional Approach: Seismic Structure of the Mantle Beneath Western Pacific Using 3-D Fréchet Kernels

    NASA Astrophysics Data System (ADS)

    Chen, L.; Zhao, L.; Jordan, T. H.

    2002-12-01

    We present a full three-dimensional (3-D) model of the shear-speed structure for the mantle beneath western Pacific Ocean. Over 800 three-component recordings of earthquakes (Mw > 5.5) from the seismic zones around the western Pacific rim to station HON/KIP in Hawaii, MIDW in Midway, MAT/MAJO and ERM in Japan, and GUMO in Mariana Island were processed to obtain ~20,000 frequency-dependent phase delays for various of seismic waves, including S, SS, upper-mantle guided and surface waves, and ScS reverberations. The 3-D Fréchet kernels for these delay times are computed by the coupled normal mode theory described by Zhao, Jordan, and Chapman (2000), and the measurements were inverted for a 3-D radially anisotropic shear-speed model using a linear Gaussian-Bayesian scheme. The model parameters include shear-speed variations throughout the mantle and perturbations to radial shear-wave anisotropy in the uppermost mantle. The resolving power of the inversion has been investigated through a series of checkerboard and other tests, which indicate that the horizontal and vertical resolving lengths of about 700 and 200 km or less in the upper mantle. Our results for the large-scale variations in the isotropic shear speeds are generally consistent with published global tomographic models. For example, the uppermost mantle (< 200 km depth) shows fast anomalies in the interior of the Pacific plate and slow anomalies in the marginal basins along the Pacific rim, while this pattern is reversed in the transition zone (400-700 km). Our model reveals greater lateral heterogeneity than the global models, especially in the 200-400 km depth range, suggesting a complex 3-D mantle flow in the western Pacific upper mantle.

  17. Rapid mapping of volumetric errors

    SciTech Connect

    Krulewich, D.; Hale, L.; Yordy, D.

    1995-09-13

    This paper describes a relatively inexpensive, fast, and easy to execute approach to mapping the volumetric errors of a machine tool, coordinate measuring machine, or robot. An error map is used to characterize a machine or to improve its accuracy by compensating for the systematic errors. The method consists of three steps: (1) modeling the relationship between the volumetric error and the current state of the machine; (2) acquiring error data based on length measurements throughout the work volume; and (3) optimizing the model to the particular machine.

  18. Interactive initialization of 2D/3D rigid registration

    SciTech Connect

    Gong, Ren Hui; Güler, Özgür; Kürklüoglu, Mustafa; Lovejoy, John; Yaniv, Ziv

    2013-12-15

    Purpose: Registration is one of the key technical components in an image-guided navigation system. A large number of 2D/3D registration algorithms have been previously proposed, but have not been able to transition into clinical practice. The authors identify the primary reason for the lack of adoption with the prerequisite for a sufficiently accurate initial transformation, mean target registration error of about 10 mm or less. In this paper, the authors present two interactive initialization approaches that provide the desired accuracy for x-ray/MR and x-ray/CT registration in the operating room setting. Methods: The authors have developed two interactive registration methods based on visual alignment of a preoperative image, MR, or CT to intraoperative x-rays. In the first approach, the operator uses a gesture based interface to align a volume rendering of the preoperative image to multiple x-rays. The second approach uses a tracked tool available as part of a navigation system. Preoperatively, a virtual replica of the tool is positioned next to the anatomical structures visible in the volumetric data. Intraoperatively, the physical tool is positioned in a similar manner and subsequently used to align a volume rendering to the x-ray images using an augmented reality (AR) approach. Both methods were assessed using three publicly available reference data sets for 2D/3D registration evaluation. Results: In the authors' experiments, the authors show that for x-ray/MR registration, the gesture based method resulted in a mean target registration error (mTRE) of 9.3 ± 5.0 mm with an average interaction time of 146.3 ± 73.0 s, and the AR-based method had mTREs of 7.2 ± 3.2 mm with interaction times of 44 ± 32 s. For x-ray/CT registration, the gesture based method resulted in a mTRE of 7.4 ± 5.0 mm with an average interaction time of 132.1 ± 66.4 s, and the AR-based method had mTREs of 8.3 ± 5.0 mm with interaction times of 58 ± 52 s. Conclusions: Based on the

  19. 3D tumor spheroid models for in vitro therapeutic screening: a systematic approach to enhance the biological relevance of data obtained.

    PubMed

    Zanoni, Michele; Piccinini, Filippo; Arienti, Chiara; Zamagni, Alice; Santi, Spartaco; Polico, Rolando; Bevilacqua, Alessandro; Tesei, Anna

    2016-01-01

    The potential of a spheroid tumor model composed of cells in different proliferative and metabolic states for the development of new anticancer strategies has been amply demonstrated. However, there is little or no information in the literature on the problems of reproducibility of data originating from experiments using 3D models. Our analyses, carried out using a novel open source software capable of performing an automatic image analysis of 3D tumor colonies, showed that a number of morphology parameters affect the response of large spheroids to treatment. In particular, we found that both spheroid volume and shape may be a source of variability. We also compared some commercially available viability assays specifically designed for 3D models. In conclusion, our data indicate the need for a pre-selection of tumor spheroids of homogeneous volume and shape to reduce data variability to a minimum before use in a cytotoxicity test. In addition, we identified and validated a cytotoxicity test capable of providing meaningful data on the damage induced in large tumor spheroids of up to diameter in 650 μm by different kinds of treatments. PMID:26752500

  20. Harnessing 3D models of mammary epithelial morphogenesis: An off the beaten path approach to identify candidate biomarkers of early stage breast cancer.

    PubMed

    Rossetti, Stefano; Bshara, Wiam; Reiners, Johanna A; Corlazzoli, Francesca; Miller, Austin; Sacchi, Nicoletta

    2016-10-01

    Regardless of the etiological factor, an aberrant morphology is the common hallmark of ductal carcinoma in situ (DCIS), which is a highly heterogeneous disease. To test if critical core morphogenetic mechanisms are compromised by different mutations, we performed proteomics analysis of five mammary epithelial HME1 mutant lines that develop a DCIS-like morphology in three dimensional (3D) culture. Here we show first, that all HME1 mutant lines share a common protein signature highlighting an inverse deregulation of two annexins, ANXA2 and ANXA8. Either ANXA2 downregulation or ANXA8 upregulation in the HME1 cell context are per se sufficient to confer a 3D DCIS-like morphology. Seemingly, different mutations impinged on a common mechanism that differentially regulates the two annexins. Second, we show that ANXA8 expression is significantly higher in DCIS tissue samples versus normal breast tissue and atypical ductal hyperplasia (ADH). Apparently, ANXA8 expression is significantly more upregulated in ER-negative versus ER-positive cases, and significantly correlates with tumor stage, grade and positive lymph node. Based on our study, 3D mammary morphogenesis models can be an alternate/complementary strategy for unraveling new DCIS mechanisms and biomarkers. PMID:27422542

  1. [A new 2D and 3D imaging approach to musculoskeletal physiology and pathology with low-dose radiation and the standing position: the EOS system].

    PubMed

    Dubousset, Jean; Charpak, Georges; Dorion, Irène; Skalli, Wafa; Lavaste, François; Deguise, Jacques; Kalifa, Gabriel; Ferey, Solène

    2005-02-01

    Close collaboration between multidisciplinary specialists (physicists, biomecanical engineers, medical radiologists and pediatric orthopedic surgeons) has led to the development of a new low-dose radiation device named EOS. EOS has three main advantages: The use of a gaseous X-ray detector, invented by Georges Charpak (Nobel Prizewinner 1992), the dose necessary to obtain a 2D image of the skeletal system has been reduced by 8 to 10 times, while that required to obtain a 3D reconstruction from CT slices has fallen by a factor of 800 to 1000. The accuracy of the 3D reconstruction obtained with EOS is as good as that obtained with CT. The patient is examined in the standing (or seated) position, and is scanned simultaneously from head to feet, both frontally and laterally. This is a major advantage over conventional CT which requires the patient to be placed horizontally. -The 3D reconstructions of each element of the osteo-articular system are as precise as those obtained by conventional CT. EOS is also rapid, taking only 15 to 30 minutes to image the entire spine. PMID:16114859

  2. 3D tumor spheroid models for in vitro therapeutic screening: a systematic approach to enhance the biological relevance of data obtained

    PubMed Central

    Zanoni, Michele; Piccinini, Filippo; Arienti, Chiara; Zamagni, Alice; Santi, Spartaco; Polico, Rolando; Bevilacqua, Alessandro; Tesei, Anna

    2016-01-01

    The potential of a spheroid tumor model composed of cells in different proliferative and metabolic states for the development of new anticancer strategies has been amply demonstrated. However, there is little or no information in the literature on the problems of reproducibility of data originating from experiments using 3D models. Our analyses, carried out using a novel open source software capable of performing an automatic image analysis of 3D tumor colonies, showed that a number of morphology parameters affect the response of large spheroids to treatment. In particular, we found that both spheroid volume and shape may be a source of variability. We also compared some commercially available viability assays specifically designed for 3D models. In conclusion, our data indicate the need for a pre-selection of tumor spheroids of homogeneous volume and shape to reduce data variability to a minimum before use in a cytotoxicity test. In addition, we identified and validated a cytotoxicity test capable of providing meaningful data on the damage induced in large tumor spheroids of up to diameter in 650 μm by different kinds of treatments. PMID:26752500

  3. 3D PDF - a means of public access to geological 3D - objects, using the example of GTA3D

    NASA Astrophysics Data System (ADS)

    Slaby, Mark-Fabian; Reimann, Rüdiger

    2013-04-01

    In geology, 3D modeling has become very important. In the past, two-dimensional data such as isolines, drilling profiles, or cross-sections based on those, were used to illustrate the subsurface geology, whereas now, we can create complex digital 3D models. These models are produced with special software, such as GOCAD ®. The models can be viewed, only through the software used to create them, or through viewers available for free. The platform-independent PDF (Portable Document Format), enforced by Adobe, has found a wide distribution. This format has constantly evolved over time. Meanwhile, it is possible to display CAD data in an Adobe 3D PDF file with the free Adobe Reader (version 7). In a 3D PDF, a 3D model is freely rotatable and can be assembled from a plurality of objects, which can thus be viewed from all directions on their own. In addition, it is possible to create moveable cross-sections (profiles), and to assign transparency to the objects. Based on industry-standard CAD software, 3D PDFs can be generated from a large number of formats, or even be exported directly from this software. In geoinformatics, different approaches to creating 3D PDFs exist. The intent of the Authority for Mining, Energy and Geology to allow free access to the models of the Geotectonic Atlas (GTA3D), could not be realized with standard software solutions. A specially designed code converts the 3D objects to VRML (Virtual Reality Modeling Language). VRML is one of the few formats that allow using image files (maps) as textures, and to represent colors and shapes correctly. The files were merged in Acrobat X Pro, and a 3D PDF was generated subsequently. A topographic map, a display of geographic directions and horizontal and vertical scales help to facilitate the use.

  4. Prominent rocks - 3D

    NASA Technical Reports Server (NTRS)

    1997-01-01

    Many prominent rocks near the Sagan Memorial Station are featured in this image, taken in stereo by the Imager for Mars Pathfinder (IMP) on Sol 3. 3D glasses are necessary to identify surface detail. Wedge is at lower left; Shark, Half-Dome, and Pumpkin are at center. Flat Top, about four inches high, is at lower right. The horizon in the distance is one to two kilometers away.

    Mars Pathfinder is the second in NASA's Discovery program of low-cost spacecraft with highly focused science goals. The Jet Propulsion Laboratory, Pasadena, CA, developed and manages the Mars Pathfinder mission for NASA's Office of Space Science, Washington, D.C. JPL is an operating division of the California Institute of Technology (Caltech). The Imager for Mars Pathfinder (IMP) was developed by the University of Arizona Lunar and Planetary Laboratory under contract to JPL. Peter Smith is the Principal Investigator.

    Click below to see the left and right views individually. [figure removed for brevity, see original site] Left [figure removed for brevity, see original site] Right

  5. 'Diamond' in 3-D

    NASA Technical Reports Server (NTRS)

    2004-01-01

    This 3-D, microscopic imager mosaic of a target area on a rock called 'Diamond Jenness' was taken after NASA's Mars Exploration Rover Opportunity ground into the surface with its rock abrasion tool for a second time.

    Opportunity has bored nearly a dozen holes into the inner walls of 'Endurance Crater.' On sols 177 and 178 (July 23 and July 24, 2004), the rover worked double-duty on Diamond Jenness. Surface debris and the bumpy shape of the rock resulted in a shallow and irregular hole, only about 2 millimeters (0.08 inch) deep. The final depth was not enough to remove all the bumps and leave a neat hole with a smooth floor. This extremely shallow depression was then examined by the rover's alpha particle X-ray spectrometer.

    On Sol 178, Opportunity's 'robotic rodent' dined on Diamond Jenness once again, grinding almost an additional 5 millimeters (about 0.2 inch). The rover then applied its Moessbauer spectrometer to the deepened hole. This double dose of Diamond Jenness enabled the science team to examine the rock at varying layers. Results from those grindings are currently being analyzed.

    The image mosaic is about 6 centimeters (2.4 inches) across.

  6. Computationally efficient storage of 3D particle intensity and position data for use in 3D PIV and 3D PTV

    NASA Astrophysics Data System (ADS)

    Atkinson, C.; Buchmann, N. A.; Soria, J.

    2013-11-01

    Three-dimensional (3D) volumetric velocity measurement techniques, such as tomographic or holographic particle image velocimetry (PIV), rely upon the computationally intensive formation, storage and localized interrogation of multiple 3D particle intensity fields. Calculation of a single velocity field typically requires the extraction of particle intensities into tens of thousands of 3D sub-volumes or discrete particle clusters, the processing of which can significantly affect the performance of 3D cross-correlation based PIV and 3D particle tracking velocimetry (PTV). In this paper, a series of popular and customized volumetric data formats are presented and investigated using synthetic particle volumes and experimental data arising from tomographic PIV measurements of a turbulent boundary layer. Results show that the use of a sub-grid ordered non-zero intensity format with a sub-grid size of 16 × 16 × 16 points provides the best performance for cross-correlation based PIV analysis, while a particle clustered non-zero intensity format provides the best format for PTV applications. In practical tomographic PIV measurements the sub-grid ordered non-zero intensity format offered a 29% improvement in reconstruction times, while providing a 93% reduction in volume data requirements and a 28% overall improvement in cross-correlation based velocity analysis and validation times.

  7. Adaptation of video game UVW mapping to 3D visualization of gene expression patterns

    NASA Astrophysics Data System (ADS)

    Vize, Peter D.; Gerth, Victor E.

    2007-01-01

    Analysis of gene expression patterns within an organism plays a critical role in associating genes with biological processes in both health and disease. During embryonic development the analysis and comparison of different gene expression patterns allows biologists to identify candidate genes that may regulate the formation of normal tissues and organs and to search for genes associated with congenital diseases. No two individual embryos, or organs, are exactly the same shape or size so comparing spatial gene expression in one embryo to that in another is difficult. We will present our efforts in comparing gene expression data collected using both volumetric and projection approaches. Volumetric data is highly accurate but difficult to process and compare. Projection methods use UV mapping to align texture maps to standardized spatial frameworks. This approach is less accurate but is very rapid and requires very little processing. We have built a database of over 180 3D models depicting gene expression patterns mapped onto the surface of spline based embryo models. Gene expression data in different models can easily be compared to determine common regions of activity. Visualization software, both Java and OpenGL optimized for viewing 3D gene expression data will also be demonstrated.

  8. High definition 3D ultrasound imaging.

    PubMed

    Morimoto, A K; Krumm, J C; Kozlowski, D M; Kuhlmann, J L; Wilson, C; Little, C; Dickey, F M; Kwok, K S; Rogers, B; Walsh, N

    1997-01-01

    We have demonstrated high definition and improved resolution using a novel scanning system integrated with a commercial ultrasound machine. The result is a volumetric 3D ultrasound data set that can be visualized using standard techniques. Unlike other 3D ultrasound images, image quality is improved from standard 2D data. Image definition and bandwidth is improved using patent pending techniques. The system can be used to image patients or wounded soldiers for general imaging of anatomy such as abdominal organs, extremities, and the neck. Although the risks associated with x-ray carcinogenesis are relatively low at diagnostic dose levels, concerns remain for individuals in high risk categories. In addition, cost and portability of CT and MRI machines can be prohibitive. In comparison, ultrasound can provide portable, low-cost, non-ionizing imaging. Previous clinical trials comparing ultrasound to CT were used to demonstrate qualitative and quantitative improvements of ultrasound using the Sandia technologies. Transverse leg images demonstrated much higher clarity and lower noise than is seen in traditional ultrasound images. An x-ray CT scan was provided of the same cross-section for comparison. The results of our most recent trials demonstrate the advantages of 3D ultrasound and motion compensation compared with 2D ultrasound. Metal objects can also be observed within the anatomy. PMID:10168958

  9. Seismic reflection data integrated in a combined 3D isostatic and gravity modelling approach - new insights into the lithospheric structure of the northern Upper Rhine Graben and Hessen (Germany)

    NASA Astrophysics Data System (ADS)

    Freymark, Jessica; Sippel, Judith; Scheck-Wenderoth, Magdalena; Stiller, Manfred; Bär, Kristian; Fritsche, Johann-Gerhard; Kracht, Matthias

    2015-04-01

    Seismic reflection and refraction profiles reveal information on first-order heterogeneities of the crust. After application of a suitable time-to-depth conversion we have re-interpreted near-vertical migrated seismic reflection data of the DEKORP project that image the deep subsurface of the northern Upper Rhine Graben and the federal state of Hessen. The most prominent feature in the crystalline crust, visible in these profiles, is a highly reflective lower crust differentiated from a 'transparent' upper crust showing considerably less continuous reflections. We present a workflow of integrating the seismic data into a combined 3D isostatic and gravity modelling approach. Basement depth as well as the thickness and lithological variations of the sediment fill are well known in the region. 3D isostatic calculations allow predicting the average density of the sub-sedimentary crystalline crust and thus the thickness distributions of the Upper and the Lower Crust for those parts of the study area where seismic information is missing. Finally, we calculate the 3D gravity response of the entire lithosphere of Hessen and interactively adjust the crustal density configuration to the measured gravity field while keeping the seismic information. The product of our approach, i.e. a lithospheric-scale observation-constrained 3D structural model, is used to numerically simulate heat transport processes for temperature predictions in this region of high potential for geothermal utilisation.

  10. Positional Awareness Map 3D (PAM3D)

    NASA Technical Reports Server (NTRS)

    Hoffman, Monica; Allen, Earl L.; Yount, John W.; Norcross, April Louise

    2012-01-01

    The Western Aeronautical Test Range of the National Aeronautics and Space Administration s Dryden Flight Research Center needed to address the aging software and hardware of its current situational awareness display application, the Global Real-Time Interactive Map (GRIM). GRIM was initially developed in the late 1980s and executes on older PC architectures using a Linux operating system that is no longer supported. Additionally, the software is difficult to maintain due to its complexity and loss of developer knowledge. It was decided that a replacement application must be developed or acquired in the near future. The replacement must provide the functionality of the original system, the ability to monitor test flight vehicles in real-time, and add improvements such as high resolution imagery and true 3-dimensional capability. This paper will discuss the process of determining the best approach to replace GRIM, and the functionality and capabilities of the first release of the Positional Awareness Map 3D.

  11. 3D Visualization Development of SIUE Campus

    NASA Astrophysics Data System (ADS)

    Nellutla, Shravya

    Geographic Information Systems (GIS) has progressed from the traditional map-making to the modern technology where the information can be created, edited, managed and analyzed. Like any other models, maps are simplified representations of real world. Hence visualization plays an essential role in the applications of GIS. The use of sophisticated visualization tools and methods, especially three dimensional (3D) modeling, has been rising considerably due to the advancement of technology. There are currently many off-the-shelf technologies available in the market to build 3D GIS models. One of the objectives of this research was to examine the available ArcGIS and its extensions for 3D modeling and visualization and use them to depict a real world scenario. Furthermore, with the advent of the web, a platform for accessing and sharing spatial information on the Internet, it is possible to generate interactive online maps. Integrating Internet capacity with GIS functionality redefines the process of sharing and processing the spatial information. Enabling a 3D map online requires off-the-shelf GIS software, 3D model builders, web server, web applications and client server technologies. Such environments are either complicated or expensive because of the amount of hardware and software involved. Therefore, the second objective of this research was to investigate and develop simpler yet cost-effective 3D modeling approach that uses available ArcGIS suite products and the free 3D computer graphics software for designing 3D world scenes. Both ArcGIS Explorer and ArcGIS Online will be used to demonstrate the way of sharing and distributing 3D geographic information on the Internet. A case study of the development of 3D campus for the Southern Illinois University Edwardsville is demonstrated.

  12. 3D Printed Bionic Ears

    PubMed Central

    Mannoor, Manu S.; Jiang, Ziwen; James, Teena; Kong, Yong Lin; Malatesta, Karen A.; Soboyejo, Winston O.; Verma, Naveen; Gracias, David H.; McAlpine, Michael C.

    2013-01-01

    The ability to three-dimensionally interweave biological tissue with functional electronics could enable the creation of bionic organs possessing enhanced functionalities over their human counterparts. Conventional electronic devices are inherently two-dimensional, preventing seamless multidimensional integration with synthetic biology, as the processes and materials are very different. Here, we present a novel strategy for overcoming these difficulties via additive manufacturing of biological cells with structural and nanoparticle derived electronic elements. As a proof of concept, we generated a bionic ear via 3D printing of a cell-seeded hydrogel matrix in the precise anatomic geometry of a human ear, along with an intertwined conducting polymer consisting of infused silver nanoparticles. This allowed for in vitro culturing of cartilage tissue around an inductive coil antenna in the ear, which subsequently enables readout of inductively-coupled signals from cochlea-shaped electrodes. The printed ear exhibits enhanced auditory sensing for radio frequency reception, and complementary left and right ears can listen to stereo audio music. Overall, our approach suggests a means to intricately merge biologic and nanoelectronic functionalities via 3D printing. PMID:23635097

  13. 3D printed bionic ears.

    PubMed

    Mannoor, Manu S; Jiang, Ziwen; James, Teena; Kong, Yong Lin; Malatesta, Karen A; Soboyejo, Winston O; Verma, Naveen; Gracias, David H; McAlpine, Michael C

    2013-06-12

    The ability to three-dimensionally interweave biological tissue with functional electronics could enable the creation of bionic organs possessing enhanced functionalities over their human counterparts. Conventional electronic devices are inherently two-dimensional, preventing seamless multidimensional integration with synthetic biology, as the processes and materials are very different. Here, we present a novel strategy for overcoming these difficulties via additive manufacturing of biological cells with structural and nanoparticle derived electronic elements. As a proof of concept, we generated a bionic ear via 3D printing of a cell-seeded hydrogel matrix in the anatomic geometry of a human ear, along with an intertwined conducting polymer consisting of infused silver nanoparticles. This allowed for in vitro culturing of cartilage tissue around an inductive coil antenna in the ear, which subsequently enables readout of inductively-coupled signals from cochlea-shaped electrodes. The printed ear exhibits enhanced auditory sensing for radio frequency reception, and complementary left and right ears can listen to stereo audio music. Overall, our approach suggests a means to intricately merge biologic and nanoelectronic functionalities via 3D printing. PMID:23635097

  14. Volumetric Topological Analysis: A Novel Approach for Trabecular Bone Classification on the Continuum between Plates and Rods

    PubMed Central

    Saha, Punam K; Xu, Yan; Duan, Hong; Heiner, Anneliese; Liang, Guoyuan

    2011-01-01

    Trabecular bone (TB) is a complex quasi-random network of interconnected plates and rods. TB constantly remodels to adapt to the stresses to which it is subjected (Wolff s Law). In osteoporosis, this dynamic equilibrium between bone formation and resorption is perturbed, leading to bone loss and structural deterioration, both increasing fracture risk. Bone s mechanical behavior can only be partially explained by variations in bone mineral density, which led to the notion of bone structural quality. Previously, we developed digital topological analysis (DTA) which classifies plates, rods, profiles, edges, and junctions in a TB skeletal representation. Although the method has become quite popular, a major limitation of DTA is that it provides only hard classifications of different topological entities, failing to distinguish between narrow and wide plates. Here, we present a new method called volumetric topological analysis (VTA) for regional quantification of TB topology. At each TB location, the method uniquely classifies its topology on the continuum between perfect plates and perfect rods, facilitating early detections of TB alterations from plates to rods according to the known etiology of osteoporotic bone loss. Several new ideas, including manifold distance transform, manifold scale, and feature propagation have been introduced here and combined with existing DTA and distance transform methods, leading to the new VTA technology. This method has been applied to multi-detector CT and μCT images of four cadaveric distal tibia and five distal radius specimens. Both intra- and inter-modality reproducibility of the method has been examined using repeat CT and μCT scans of distal tibia specimens. Also, the method s ability to predict experimental biomechanical properties of TB via CT imaging under in vivo conditions has been quantitatively examined and the results found are very encouraging. PMID:20562041

  15. Volumetric Forest Change Detection Through Vhr Satellite Imagery

    NASA Astrophysics Data System (ADS)

    Akca, Devrim; Stylianidis, Efstratios; Smagas, Konstantinos; Hofer, Martin; Poli, Daniela; Gruen, Armin; Sanchez Martin, Victor; Altan, Orhan; Walli, Andreas; Jimeno, Elisa; Garcia, Alejandro

    2016-06-01

    Quick and economical ways of detecting of planimetric and volumetric changes of forest areas are in high demand. A research platform, called FORSAT (A satellite processing platform for high resolution forest assessment), was developed for the extraction of 3D geometric information from VHR (very-high resolution) imagery from satellite optical sensors and automatic change detection. This 3D forest information solution was developed during a Eurostars project. FORSAT includes two main units. The first one is dedicated to the geometric and radiometric processing of satellite optical imagery and 2D/3D information extraction. This includes: image radiometric pre-processing, image and ground point measurement, improvement of geometric sensor orientation, quasiepipolar image generation for stereo measurements, digital surface model (DSM) extraction by using a precise and robust image matching approach specially designed for VHR satellite imagery, generation of orthoimages, and 3D measurements in single images using mono-plotting and in stereo images as well as triplets. FORSAT supports most of the VHR optically imagery commonly used for civil applications: IKONOS, OrbView - 3, SPOT - 5 HRS, SPOT - 5 HRG, QuickBird, GeoEye-1, WorldView-1/2, Pléiades 1A/1B, SPOT 6/7, and sensors of similar type to be expected in the future. The second unit of FORSAT is dedicated to 3D surface comparison for change detection. It allows users to import digital elevation models (DEMs), align them using an advanced 3D surface matching approach and calculate the 3D differences and volume changes between epochs. To this end our 3D surface matching method LS3D is being used. FORSAT is a single source and flexible forest information solution with a very competitive price/quality ratio, allowing expert and non-expert remote sensing users to monitor forests in three and four dimensions from VHR optical imagery for many forest information needs. The capacity and benefits of FORSAT have been tested in

  16. The Neighboring Column Approximation (NCA) - A fast approach for the calculation of 3D thermal heating rates in cloud resolving models

    NASA Astrophysics Data System (ADS)

    Klinger, Carolin; Mayer, Bernhard

    2016-01-01

    Due to computational costs, radiation is usually neglected or solved in plane parallel 1D approximation in today's numerical weather forecast and cloud resolving models. We present a fast and accurate method to calculate 3D heating and cooling rates in the thermal spectral range that can be used in cloud resolving models. The parameterization considers net fluxes across horizontal box boundaries in addition to the top and bottom boundaries. Since the largest heating and cooling rates occur inside the cloud, close to the cloud edge, the method needs in first approximation only the information if a grid box is at the edge of a cloud or not. Therefore, in order to calculate the heating or cooling rates of a specific grid box, only the directly neighboring columns are used. Our so-called Neighboring Column Approximation (NCA) is an analytical consideration of cloud side effects which can be considered a convolution of a 1D radiative transfer result with a kernel or radius of 1 grid-box (5 pt stencil) and which does usually not break the parallelization of a cloud resolving model. The NCA can be easily applied to any cloud resolving model that includes a 1D radiation scheme. Due to the neglect of horizontal transport of radiation further away than one model column, the NCA works best for model resolutions of about 100 m or lager. In this paper we describe the method and show a set of applications of LES cloud field snap shots. Correction terms, gains and restrictions of the NCA are described. Comprehensive comparisons to the 3D Monte Carlo Model MYSTIC and a 1D solution are shown. In realistic cloud fields, the full 3D simulation with MYSTIC shows cooling rates up to -150 K/d (100 m resolution) while the 1D solution shows maximum coolings of only -100 K/d. The NCA is capable of reproducing the larger 3D cooling rates. The spatial distribution of the heating and cooling is improved considerably. Computational costs are only a factor of 1.5-2 higher compared to a 1D

  17. 3D Time-domain wave modeling in fluid-solid coupled media: a cell-based finite-difference method approach

    NASA Astrophysics Data System (ADS)

    Lee, H.; Min, D.; Lim, S.; Yang, J.; Kwon, B.; Yoo, H.

    2009-12-01

    In a conventional marine seismic data analysis, pressure data have been usually interpreted on the basis of acoustic wave equation. The acoustic wave equation, however, only deals with P-wave propagation, and it cannot correctly describe the wave propagation in acoustic-elastic (fluid-solid) coupled media. Recently, in 4C OBC survey (4-component ocean bottom cable), it is possible to acquire both pressure and 3-component displacements (measured at the sea-bottom). Combining pressure and displacement data allows us to interpret subsurface structures more accurately. In order to accurately simulate wave propagation in fluid-solid coupled media, we need an acoustic-elastic coupled modeling algorithm, which deals with displacements in elastic region and pressure in acoustic region. For waveform inversion and reverse-time migration that require a great number of forward modeling, it is essential to develop an efficient scheme that reduces computing time and computer core memory. In this study, we present a 3D time-domain acoustic-elastic coupled modeling algorithm on the basis of the cell-based finite difference method. The cell-based method has proven to properly describe the free-surface boundary, which indicates that it will also properly describe the fluid-solid interface boundaries. In the acoustic-elastic coupled modeling, we first compose cell-based finite differences individually for the 3D acoustic and elastic media, and then combine the differences using the fluid-solid interface boundary conditions. Considering that the 2D acoustic-elastic coupled modeling algorithm gives numerical solutions comparable to analytic solutions, we expect that the 3D acoustic-elastic coupled modeling will correctly describe wave propagation in the fluid-solid coupled media. We apply our algorithm to 3D horizontal two- and three-layer models. Numerical experiments show that the cell-based coupled modeling algorithm properly describes S- and converted waves as well as P-waves. The

  18. 3D active surfaces for liver segmentation in multisequence MRI images.

    PubMed

    Bereciartua, Arantza; Picon, Artzai; Galdran, Adrian; Iriondo, Pedro

    2016-08-01

    Biopsies for diagnosis can sometimes be replaced by non-invasive techniques such as CT and MRI. Surgeons require accurate and efficient methods that allow proper segmentation of the organs in order to ensure the most reliable intervention planning. Automated liver segmentation is a difficult and open problem where CT has been more widely explored than MRI. MRI liver segmentation represents a challenge due to the presence of characteristic artifacts, such as partial volumes, noise and low contrast. In this paper, we present a novel method for multichannel MRI automatic liver segmentation. The proposed method consists of the minimization of a 3D active surface by means of the dual approach to the variational formulation of the underlying problem. This active surface evolves over a probability map that is based on a new compact descriptor comprising spatial and multisequence information which is further modeled by means of a liver statistical model. This proposed 3D active surface approach naturally integrates volumetric regularization in the statistical model. The advantages of the compact visual descriptor together with the proposed approach result in a fast and accurate 3D segmentation method. The method was tested on 18 healthy liver studies and results were compared to a gold standard made by expert radiologists. Comparisons with other state-of-the-art approaches are provided by means of nine well established quality metrics. The obtained results improve these methodologies, achieving a Dice Similarity Coefficient of 98.59. PMID:27282235

  19. Snapshot Hyperspectral Volumetric Microscopy.

    PubMed

    Wu, Jiamin; Xiong, Bo; Lin, Xing; He, Jijun; Suo, Jinli; Dai, Qionghai

    2016-01-01

    The comprehensive analysis of biological specimens brings about the demand for capturing the spatial, temporal and spectral dimensions of visual information together. However, such high-dimensional video acquisition faces major challenges in developing large data throughput and effective multiplexing techniques. Here, we report the snapshot hyperspectral volumetric microscopy that computationally reconstructs hyperspectral profiles for high-resolution volumes of ~1000 μm × 1000 μm × 500 μm at video rate by a novel four-dimensional (4D) deconvolution algorithm. We validated the proposed approach with both numerical simulations for quantitative evaluation and various real experimental results on the prototype system. Different applications such as biological component analysis in bright field and spectral unmixing of multiple fluorescence are demonstrated. The experiments on moving fluorescent beads and GFP labelled drosophila larvae indicate the great potential of our method for observing multiple fluorescent markers in dynamic specimens. PMID:27103155

  20. Snapshot Hyperspectral Volumetric Microscopy

    NASA Astrophysics Data System (ADS)

    Wu, Jiamin; Xiong, Bo; Lin, Xing; He, Jijun; Suo, Jinli; Dai, Qionghai

    2016-04-01

    The comprehensive analysis of biological specimens brings about the demand for capturing the spatial, temporal and spectral dimensions of visual information together. However, such high-dimensional video acquisition faces major challenges in developing large data throughput and effective multiplexing techniques. Here, we report the snapshot hyperspectral volumetric microscopy that computationally reconstructs hyperspectral profiles for high-resolution volumes of ~1000 μm × 1000 μm × 500 μm at video rate by a novel four-dimensional (4D) deconvolution algorithm. We validated the proposed approach with both numerical simulations for quantitative evaluation and various real experimental results on the prototype system. Different applications such as biological component analysis in bright field and spectral unmixing of multiple fluorescence are demonstrated. The experiments on moving fluorescent beads and GFP labelled drosophila larvae indicate the great potential of our method for observing multiple fluorescent markers in dynamic specimens.

  1. Snapshot Hyperspectral Volumetric Microscopy

    PubMed Central

    Wu, Jiamin; Xiong, Bo; Lin, Xing; He, Jijun; Suo, Jinli; Dai, Qionghai

    2016-01-01

    The comprehensive analysis of biological specimens brings about the demand for capturing the spatial, temporal and spectral dimensions of visual information together. However, such high-dimensional video acquisition faces major challenges in developing large data throughput and effective multiplexing techniques. Here, we report the snapshot hyperspectral volumetric microscopy that computationally reconstructs hyperspectral profiles for high-resolution volumes of ~1000 μm × 1000 μm × 500 μm at video rate by a novel four-dimensional (4D) deconvolution algorithm. We validated the proposed approach with both numerical simulations for quantitative evaluation and various real experimental results on the prototype system. Different applications such as biological component analysis in bright field and spectral unmixing of multiple fluorescence are demonstrated. The experiments on moving fluorescent beads and GFP labelled drosophila larvae indicate the great potential of our method for observing multiple fluorescent markers in dynamic specimens. PMID:27103155

  2. Efficient threshold for volumetric segmentation

    NASA Astrophysics Data System (ADS)

    Burdescu, Dumitru D.; Brezovan, Marius; Stanescu, Liana; Stoica Spahiu, Cosmin; Ebanca, Daniel

    2015-07-01

    Image segmentation plays a crucial role in effective understanding of digital images. However, the research on the existence of general purpose segmentation algorithm that suits for variety of applications is still very much active. Among the many approaches in performing image segmentation, graph based approach is gaining popularity primarily due to its ability in reflecting global image properties. Volumetric image segmentation can simply result an image partition composed by relevant regions, but the most fundamental challenge in segmentation algorithm is to precisely define the volumetric extent of some object, which may be represented by the union of multiple regions. The aim in this paper is to present a new method to detect visual objects from color volumetric images and efficient threshold. We present a unified framework for volumetric image segmentation and contour extraction that uses a virtual tree-hexagonal structure defined on the set of the image voxels. The advantage of using a virtual tree-hexagonal network superposed over the initial image voxels is that it reduces the execution time and the memory space used, without losing the initial resolution of the image.

  3. An efficient Volumetric Arc Therapy treatment planning approach for hippocampal-avoidance whole-brain radiation therapy (HA-WBRT)

    SciTech Connect

    Shen, Jin; Bender, Edward; Yaparpalvi, Ravindra; Kuo, Hsiang-Chi; Basavatia, Amar; Hong, Linda; Bodner, William; Garg, Madhur K.; Kalnicki, Shalom; Tomé, Wolfgang A.

    2015-10-01

    An efficient and simple class solution is proposed for hippocampal-avoidance whole-brain radiation therapy (HA-WBRT) planning using the Volumetric Arc Therapy (VMAT) delivery technique following the NRG Oncology protocol NRG-CC001 treatment planning guidelines. The whole-brain planning target volume (PTV) was subdivided into subplanning volumes that lie in plane and out of plane with the hippocampal-avoidance volume. To further improve VMAT treatment plans, a partial-field dual-arc technique was developed. Both the arcs were allowed to overlap on the in-plane subtarget volume, and in addition, one arc covered the superior out-of-plane sub-PTV, while the other covered the inferior out-of-plane subtarget volume. For all plans (n = 20), the NRG-CC001 protocol dose-volume criteria were met. Mean values of volumes for the hippocampus and the hippocampal-avoidance volume were 4.1 cm{sup 3} ± 1.0 cm{sup 3} and 28.52 cm{sup 3} ± 3.22 cm{sup 3}, respectively. For the PTV, the average values of D{sub 2%} and D{sub 98%} were 36.1 Gy ± 0.8 Gy and 26.2 Gy ± 0.6 Gy, respectively. The hippocampus D{sub 100%} mean value was 8.5 Gy ± 0.2 Gy and the maximum dose was 15.7 Gy ± 0.3 Gy. The corresponding plan quality indices were 0.30 ± 0.01 (homogeneity index), 0.94 ± 0.01 (target conformality), and 0.75 ± 0.02 (confirmation number). The median total monitor unit (MU) per fraction was 806 MU (interquartile range [IQR]: 792 to 818 MU) and the average beam total delivery time was 121.2 seconds (IQR: 120.6 to 121.35 seconds). All plans passed the gamma evaluation using the 5-mm, 4% criteria, with γ > 1 of not more than 9.1% data points for all fields. An efficient and simple planning class solution for HA-WBRT using VMAT has been developed that allows all protocol constraints of NRG-CC001 to be met.

  4. Use of 3D-computed tomography angiography for planning the surgical removal of pineal region meningiomas using Poppen's approach: a report of ten cases and a literature review

    PubMed Central

    2011-01-01

    Background There are several treatment approaches for pineal region meningiomas, such as Poppen's approach, Krause's approach and combinations of the two approaches. We present our experience with the use of 3D-computed tomography angiography for planning the surgical removal of pineal region meningiomas using a suboccipital transtentorial approach (Poppen's approach) and evaluate the role of Poppen's approach. Methods During the period from January 2005 to June 2010, ten patients presented to us with pineal region meningioma. MRI was routinely used to define the tumor size, position, and its relevant complications while 3D-CTA was applied to define the blood supply of the tumor and the venous complex (VC) shift before operations. Most of the meningiomas had developed at both sides of the tentorial plane and extended laterally with typical characteristics of a pineal region tumor. Results All tumors were completely removed surgically without any injury to the VC. Postoperative intracranial infection occurred in one case who recovered after antibiotics were given. Postoperative intraventricular hemorrhage and pneumocephalus were found in one case, but fully recovered after conservative treatment. In the nine cases of concurrent hydrocephalus, this was gradually relieved in eight patients and the single case that became aggravated was successfully treated with ventriculoperitoneal shunt. Moreover, the follow-up MRI examinations did not indicate any recurrence of the meningiomas. Conclusion We found that the use of Poppen's approach is strongly supported for the successful removal of pineal region meningiomas without serious complications. PMID:21676231

  5. Inflammation in 3D.

    PubMed

    Kobayashi, Scott D; DeLeo, Frank R

    2012-06-14

    Our view of the response to infection is limited by current methodologies, which provide minimal spatial information on the systemic inflammatory response. In this issue, Attia et al. (2012) describe a cutting-edge approach to image the inflammatory response to infection, which includes identification of host proteins in three dimensions. PMID:22704615

  6. New portable FELIX 3D display

    NASA Astrophysics Data System (ADS)

    Langhans, Knut; Bezecny, Daniel; Homann, Dennis; Bahr, Detlef; Vogt, Carsten; Blohm, Christian; Scharschmidt, Karl-Heinz

    1998-04-01

    An improved generation of our 'FELIX 3D Display' is presented. This system is compact, light, modular and easy to transport. The created volumetric images consist of many voxels, which are generated in a half-sphere display volume. In that way a spatial object can be displayed occupying a physical space with height, width and depth. The new FELIX generation uses a screen rotating with 20 revolutions per second. This target screen is mounted by an easy to change mechanism making it possible to use appropriate screens for the specific purpose of the display. An acousto-optic deflection unit with an integrated small diode pumped laser draws the images on the spinning screen. Images can consist of up to 10,000 voxels at a refresh rate of 20 Hz. Currently two different hardware systems are investigated. The first one is based on a standard PCMCIA digital/analog converter card as an interface and is controlled by a notebook. The developed software is provided with a graphical user interface enabling several animation features. The second, new prototype is designed to display images created by standard CAD applications. It includes the development of a new high speed hardware interface suitable for state-of-the- art fast and high resolution scanning devices, which require high data rates. A true 3D volume display as described will complement the broad range of 3D visualization tools, such as volume rendering packages, stereoscopic and virtual reality techniques, which have become widely available in recent years. Potential applications for the FELIX 3D display include imaging in the field so fair traffic control, medical imaging, computer aided design, science as well as entertainment.

  7. Electron Tomography of Cryo-Immobilized Plant Tissue: A Novel Approach to Studying 3D Macromolecular Architecture of Mature Plant Cell Walls In Situ

    PubMed Central

    Sarkar, Purbasha; Bosneaga, Elena; Yap, Edgar G.; Das, Jyotirmoy; Tsai, Wen-Ting; Cabal, Angelo; Neuhaus, Erica; Maji, Dolonchampa; Kumar, Shailabh; Joo, Michael; Yakovlev, Sergey; Csencsits, Roseann; Yu, Zeyun; Bajaj, Chandrajit; Downing, Kenneth H.; Auer, Manfred

    2014-01-01

    Cost-effective production of lignocellulosic biofuel requires efficient breakdown of cell walls present in plant biomass to retrieve the wall polysaccharides for fermentation. In-depth knowledge of plant cell wall composition is therefore essential for improving the fuel production process. The precise spatial three-dimensional (3D) organization of cellulose, hemicellulose, pectin and lignin within plant cell walls remains unclear to date since the microscopy techniques used so far have been limited to two-dimensional, topographic or low-resolution imaging, or required isolation or chemical extraction of the cell walls. In this paper we demonstrate that by cryo-immobilizing fresh tissue, then either cryo-sectioning or freeze-substituting and resin embedding, followed by cryo- or room temperature (RT) electron tomography, respectively, we can visualize previously unseen details of plant cell wall architecture in 3D, at macromolecular resolution (∼2 nm), and in near-native state. Qualitative and quantitative analyses showed that wall organization of cryo-immobilized samples were preserved remarkably better than conventionally prepared samples that suffer substantial extraction. Lignin-less primary cell walls were well preserved in both self-pressurized rapidly frozen (SPRF), cryo-sectioned samples as well as high-pressure frozen, freeze-substituted and resin embedded (HPF-FS-resin) samples. Lignin-rich secondary cell walls appeared featureless in HPF-FS-resin sections presumably due to poor stain penetration, but their macromolecular features could be visualized in unprecedented details in our cryo-sections. While cryo-tomography of vitreous tissue sections is currently proving to be instrumental in developing 3D models of lignin-rich secondary cell walls, here we confirm that the technically easier method of RT-tomography of HPF-FS-resin sections could be used immediately for routine study of low-lignin cell walls. As a proof of principle, we characterized the

  8. Electron tomography of cryo-immobilized plant tissue: a novel approach to studying 3D macromolecular architecture of mature plant cell walls in situ.

    PubMed

    Sarkar, Purbasha; Bosneaga, Elena; Yap, Edgar G; Das, Jyotirmoy; Tsai, Wen-Ting; Cabal, Angelo; Neuhaus, Erica; Maji, Dolonchampa; Kumar, Shailabh; Joo, Michael; Yakovlev, Sergey; Csencsits, Roseann; Yu, Zeyun; Bajaj, Chandrajit; Downing, Kenneth H; Auer, Manfred

    2014-01-01

    Cost-effective production of lignocellulosic biofuel requires efficient breakdown of cell walls present in plant biomass to retrieve the wall polysaccharides for fermentation. In-depth knowledge of plant cell wall composition is therefore essential for improving the fuel production process. The precise spatial three-dimensional (3D) organization of cellulose, hemicellulose, pectin and lignin within plant cell walls remains unclear to date since the microscopy techniques used so far have been limited to two-dimensional, topographic or low-resolution imaging, or required isolation or chemical extraction of the cell walls. In this paper we demonstrate that by cryo-immobilizing fresh tissue, then either cryo-sectioning or freeze-substituting and resin embedding, followed by cryo- or room temperature (RT) electron tomography, respectively, we can visualize previously unseen details of plant cell wall architecture in 3D, at macromolecular resolution (∼ 2 nm), and in near-native state. Qualitative and quantitative analyses showed that wall organization of cryo-immobilized samples were preserved remarkably better than conventionally prepared samples that suffer substantial extraction. Lignin-less primary cell walls were well preserved in both self-pressurized rapidly frozen (SPRF), cryo-sectioned samples as well as high-pressure frozen, freeze-substituted and resin embedded (HPF-FS-resin) samples. Lignin-rich secondary cell walls appeared featureless in HPF-FS-resin sections presumably due to poor stain penetration, but their macromolecular features could be visualized in unprecedented details in our cryo-sections. While cryo-tomography of vitreous tissue sections is currently proving to be instrumental in developing 3D models of lignin-rich secondary cell walls, here we confirm that the technically easier method of RT-tomography of HPF-FS-resin sections could be used immediately for routine study of low-lignin cell walls. As a proof of principle, we characterized the

  9. A frequency-based approach to locate common structure for 2D-3D intensity-based registration of setup images in prostate radiotherapy

    SciTech Connect

    Munbodh, Reshma; Chen Zhe; Jaffray, David A.; Moseley, Douglas J.; Knisely, Jonathan P. S.; Duncan, James S.

    2007-07-15

    In many radiotherapy clinics, geometric uncertainties in the delivery of 3D conformal radiation therapy and intensity modulated radiation therapy of the prostate are reduced by aligning the patient's bony anatomy in the planning 3D CT to corresponding bony anatomy in 2D portal images acquired before every treatment fraction. In this paper, we seek to determine if there is a frequency band within the portal images and the digitally reconstructed radiographs (DRRs) of the planning CT in which bony anatomy predominates over non-bony anatomy such that portal images and DRRs can be suitably filtered to achieve high registration accuracy in an automated 2D-3D single portal intensity-based registration framework. Two similarity measures, mutual information and the Pearson correlation coefficient were tested on carefully collected gold-standard data consisting of a kilovoltage cone-beam CT (CBCT) and megavoltage portal images in the anterior-posterior (AP) view of an anthropomorphic phantom acquired under clinical conditions at known poses, and on patient data. It was found that filtering the portal images and DRRs during the registration considerably improved registration performance. Without filtering, the registration did not always converge while with filtering it always converged to an accurate solution. For the pose-determination experiments conducted on the anthropomorphic phantom with the correlation coefficient, the mean (and standard deviation) of the absolute errors in recovering each of the six transformation parameters were {theta}{sub x}:0.18(0.19) deg., {theta}{sub y}:0.04(0.04) deg., {theta}{sub z}:0.04(0.02) deg., t{sub x}:0.14(0.15) mm, t{sub y}:0.09(0.05) mm, and t{sub z}:0.49(0.40) mm. The mutual information-based registration with filtered images also resulted in similarly small errors. For the patient data, visual inspection of the superimposed registered images showed that they were correctly aligned in all instances. The results presented in this

  10. 3D Elastic Wavefield Tomography

    NASA Astrophysics Data System (ADS)

    Guasch, L.; Warner, M.; Stekl, I.; Umpleby, A.; Shah, N.

    2010-12-01

    Wavefield tomography, or waveform inversion, aims to extract the maximum information from seismic data by matching trace by trace the response of the solid earth to seismic waves using numerical modelling tools. Its first formulation dates from the early 80's, when Albert Tarantola developed a solid theoretical basis that is still used today with little change. Due to computational limitations, the application of the method to 3D problems has been unaffordable until a few years ago, and then only under the acoustic approximation. Although acoustic wavefield tomography is widely used, a complete solution of the seismic inversion problem requires that we account properly for the physics of wave propagation, and so must include elastic effects. We have developed a 3D tomographic wavefield inversion code that incorporates the full elastic wave equation. The bottle neck of the different implementations is the forward modelling algorithm that generates the synthetic data to be compared with the field seismograms as well as the backpropagation of the residuals needed to form the direction update of the model parameters. Furthermore, one or two extra modelling runs are needed in order to calculate the step-length. Our approach uses a FD scheme explicit time-stepping by finite differences that are 4th order in space and 2nd order in time, which is a 3D version of the one developed by Jean Virieux in 1986. We chose the time domain because an explicit time scheme is much less demanding in terms of memory than its frequency domain analogue, although the discussion of wich domain is more efficient still remains open. We calculate the parameter gradients for Vp and Vs by correlating the normal and shear stress wavefields respectively. A straightforward application would lead to the storage of the wavefield at all grid points at each time-step. We tackled this problem using two different approaches. The first one makes better use of resources for small models of dimension equal

  11. Nonlaser-based 3D surface imaging

    SciTech Connect

    Lu, Shin-yee; Johnson, R.K.; Sherwood, R.J.

    1994-11-15

    3D surface imaging refers to methods that generate a 3D surface representation of objects of a scene under viewing. Laser-based 3D surface imaging systems are commonly used in manufacturing, robotics and biomedical research. Although laser-based systems provide satisfactory solutions for most applications, there are situations where non laser-based approaches are preferred. The issues that make alternative methods sometimes more attractive are: (1) real-time data capturing, (2) eye-safety, (3) portability, and (4) work distance. The focus of this presentation is on generating a 3D surface from multiple 2D projected images using CCD cameras, without a laser light source. Two methods are presented: stereo vision and depth-from-focus. Their applications are described.

  12. 3D-patterned polymer brush surfaces

    NASA Astrophysics Data System (ADS)

    Zhou, Xuechang; Liu, Xuqing; Xie, Zhuang; Zheng, Zijian

    2011-12-01

    Polymer brush-based three-dimensional (3D) structures are emerging as a powerful platform to engineer a surface by providing abundant spatially distributed chemical and physical properties. In this feature article, we aim to give a summary of the recent progress on the fabrication of 3D structures with polymer brushes, with a particular focus on the micro- and nanoscale. We start with a brief introduction on polymer brushes and the challenges to prepare their 3D structures. Then, we highlight the recent advances of the fabrication approaches on the basis of traditional polymerization time and grafting density strategies, and a recently developed feature density strategy. Finally, we provide some perspective outlooks on the future directions of engineering the 3D structures with polymer brushes.

  13. An Approach to 3d Digital Modeling of Surfaces with Poor Texture by Range Imaging Techniques. `SHAPE from Stereo' VS. `SHAPE from Silhouette' in Digitizing Jorge Oteiza's Sculptures

    NASA Astrophysics Data System (ADS)

    García Fernández, J.; Álvaro Tordesillas, A.; Barba, S.

    2015-02-01

    Despite eminent development of digital range imaging techniques, difficulties persist in the virtualization of objects with poor radiometric information, in other words, objects consisting of homogeneous colours (totally white, black, etc.), repetitive patterns, translucence, or materials with specular reflection. This is the case for much of the Jorge Oteiza's works, particularly in the sculpture collection of the Museo Fundación Jorge Oteiza (Navarra, Spain). The present study intend to analyse and asses the performance of two digital 3D-modeling methods based on imaging techniques, facing cultural heritage in singular cases, determined by radiometric characteristics as mentioned: Shape from Silhouette and Shape from Stereo. On the other hand, the text proposes the definition of a documentation workflow and presents the results of its application in the collection of sculptures created by Oteiza.

  14. A task-based parallelism and vectorized approach to 3D Method of Characteristics (MOC) reactor simulation for high performance computing architectures

    NASA Astrophysics Data System (ADS)

    Tramm, John R.; Gunow, Geoffrey; He, Tim; Smith, Kord S.; Forget, Benoit; Siegel, Andrew R.

    2016-05-01

    In this study we present and analyze a formulation of the 3D Method of Characteristics (MOC) technique applied to the simulation of full core nuclear reactors. Key features of the algorithm include a task-based parallelism model that allows independent MOC tracks to be assigned to threads dynamically, ensuring load balancing, and a wide vectorizable inner loop that takes advantage of modern SIMD computer architectures. The algorithm is implemented in a set of highly optimized proxy applications in order to investigate its performance characteristics on CPU, GPU, and Intel Xeon Phi architectures. Speed, power, and hardware cost efficiencies are compared. Additionally, performance bottlenecks are identified for each architecture in order to determine the prospects for continued scalability of the algorithm on next generation HPC architectures.

  15. An Experimental Approach to Assess the Impact of Post Processing Variables on the Mechanical Characteristics of 3D Printed (Powder Binding Process) Parts

    NASA Astrophysics Data System (ADS)

    Impens, David

    The study is designed to provide a robust understanding of the mechanical characteristic of a 3D printed part for selected post processing conditions. The `green' printed parts are generally very brittle and porous, therefore, infiltrates are introduced to alter the mechanical characteristics, which will introduce new opportunities for this technology. Exploratory testing is performed to shape the choices for post processing with the infiltrates. Specimen geometry, specific for tensile, compression and flexural testing were rendered in CAD software and printed on the Z-printer 450 (Zp150 powder / Zb59 binder) with three different build orientations (horizontal/ angled /vertical). Results show that infiltrates can significantly improve the mechanical characteristics and material-infiltrate performance varies per build orientation. It is now understood that this material does not react similar to other materials and cannot be easily predicted. Additional physical testing should be performed and this complete test set should be conducted for new infiltrates.

  16. Cognitive MMN and P300 in mild cognitive impairment and Alzheimer's disease: A high density EEG-3D vector field tomography approach.

    PubMed

    Papadaniil, Chrysa D; Kosmidou, Vasiliki E; Tsolaki, Anthoula; Tsolaki, Magda; Kompatsiaris, Ioannis Yiannis; Hadjileontiadis, Leontios J

    2016-10-01

    Precise preclinical detection of dementia for effective treatment and stage monitoring is of great importance. Miscellaneous types of biomarkers, e.g., biochemical, genetic, neuroimaging, and physiological, have been proposed to diagnose Alzheimer's disease (AD), the usual suspect behind manifested cognitive decline, and mild cognitive impairment (MCI), a neuropathology prior to AD that does not affect cognitive functions. Event related potential (ERP) methods constitute a non-invasive, inexpensive means of analysis and have been proposed as sensitive biomarkers of cognitive impairment; besides, various ERP components are strongly linked with working memory, attention, sensory processing and motor responses. In this study, an auditory oddball task is employed, to acquire high density electroencephalograhy recordings from healthy elderly controls, MCI and AD patients. The mismatch negativity (MMN) and P300 ERP components are then extracted and their relationship with neurodegeneration is examined. Then, the neural activation at these components is reconstructed using the 3D vector field tomography (3D-VFT) inverse solution. The results reveal a decline of both ERPs amplitude, and a statistically significant prolongation of their latency as cognitive impairment advances. For the MMN, higher brain activation is usually localized in the inferior frontal and superior temporal gyri in the controls. However, in AD, parietal sites exhibit strong activity. Stronger P300 generators are mostly found in the frontal lobe for the controls, but in AD they often shift to the temporal lobe. Reduction in inferior frontal source strength and the switch of the maximum intensity area to parietal and superior temporal sites suggest that these areas, especially the former, are of particular significance when neurodegenerative disorders are investigated. The modulation of MMN and P300 can serve to produce biomarkers of dementia and its progression, and brain imaging can further contribute

  17. Hybrid grid-particle methods and Penalization: A Sherman-Morrison-Woodbury approach to compute 3D viscous flows using FFT

    NASA Astrophysics Data System (ADS)

    Chatelin, Robin; Poncet, Philippe

    2014-07-01

    Particle methods are very convenient to compute transport equations in fluid mechanics as their computational cost is linear and they are not limited by convection stability conditions. To achieve large 3D computations the method must be coupled to efficient algorithms for velocity computations, including a good treatment of non-homogeneities and complex moving geometries. The Penalization method enables to consider moving bodies interaction by adding a term in the conservation of momentum equation. This work introduces a new computational algorithm to solve implicitly in the same step the Penalization term and the Laplace operators, since explicit computations are limited by stability issues, especially at low Reynolds number. This computational algorithm is based on the Sherman-Morrison-Woodbury formula coupled to a GMRES iterative method to reduce the computations to a sequence of Poisson problems: this allows to formulate a penalized Poisson equation as a large perturbation of a standard Poisson, by means of algebraic relations. A direct consequence is the possibility to use fast solvers based on Fast Fourier Transforms for this problem with good efficiency from both the computational and the memory consumption point of views, since these solvers are recursive and they do not perform any matrix assembling. The resulting fluid mechanics computations are very fast and they consume a small amount of memory, compared to a reference solver or a linear system resolution. The present applications focus mainly on a coupling between transport equation and 3D Stokes equations, for studying biological organisms motion in a highly viscous flows with variable viscosity.

  18. Identification of novel histone deacetylase 1 inhibitors by combined pharmacophore modeling, 3D-QSAR analysis, in silico screening and Density Functional Theory (DFT) approaches

    NASA Astrophysics Data System (ADS)

    Choubey, Sanjay K.; Mariadasse, Richard; Rajendran, Santhosh; Jeyaraman, Jeyakanthan

    2016-12-01

    Overexpression of HDAC1, a member of Class I histone deacetylase is reported to be implicated in breast cancer. Epigenetic alteration in carcinogenesis has been the thrust of research for few decades. Increased deacetylation leads to accelerated cell proliferation, cell migration, angiogenesis and invasion. HDAC1 is pronounced as the potential drug target towards the treatment of breast cancer. In this study, the biochemical potential of 6-aminonicotinamide derivatives was rationalized. Five point pharmacophore model with one hydrogen-bond acceptor (A3), two hydrogen-bond donors (D5, D6), one ring (R12) and one hydrophobic group (H8) was developed using 6-aminonicotinamide derivatives. The pharmacophore hypothesis yielded a 3D-QSAR model with correlation-coefficient (r2 = 0.977, q2 = 0.801) and it was externally validated with (r2pred = 0.929, r2cv = 0.850 and r2m = 0.856) which reveals the statistical significance of the model having high predictive power. The model was then employed as 3D search query for virtual screening against compound libraries (Zinc, Maybridge, Enamine, Asinex, Toslab, LifeChem and Specs) in order to identify novel scaffolds which can be experimentally validated to design future drug molecule. Density Functional Theory (DFT) at B3LYP/6-31G* level was employed to explore the electronic features of the ligands involved in charge transfer reaction during receptor ligand interaction. Binding free energy (ΔGbind) calculation was done using MM/GBSA which defines the affinity of ligands towards the receptor.

  19. Registration of 3D spectral OCT volumes using 3D SIFT feature point matching

    NASA Astrophysics Data System (ADS)

    Niemeijer, Meindert; Garvin, Mona K.; Lee, Kyungmoo; van Ginneken, Bram; Abràmoff, Michael D.; Sonka, Milan

    2009-02-01

    The recent introduction of next generation spectral OCT scanners has enabled routine acquisition of high resolution, 3D cross-sectional volumetric images of the retina. 3D OCT is used in the detection and management of serious eye diseases such as glaucoma and age-related macular degeneration. For follow-up studies, image registration is a vital tool to enable more precise, quantitative comparison of disease states. This work presents a registration method based on a recently introduced extension of the 2D Scale-Invariant Feature Transform (SIFT) framework1 to 3D.2 The SIFT feature extractor locates minima and maxima in the difference of Gaussian scale space to find salient feature points. It then uses histograms of the local gradient directions around each found extremum in 3D to characterize them in a 4096 element feature vector. Matching points are found by comparing the distance between feature vectors. We apply this method to the rigid registration of optic nerve head- (ONH) and macula-centered 3D OCT scans of the same patient that have only limited overlap. Three OCT data set pairs with known deformation were used for quantitative assessment of the method's robustness and accuracy when deformations of rotation and scaling were considered. Three-dimensional registration accuracy of 2.0+/-3.3 voxels was observed. The accuracy was assessed as average voxel distance error in N=1572 matched locations. The registration method was applied to 12 3D OCT scans (200 x 200 x 1024 voxels) of 6 normal eyes imaged in vivo to demonstrate the clinical utility and robustness of the method in a real-world environment.

  20. Volumetric PIV with a Plenoptic Camera

    NASA Astrophysics Data System (ADS)

    Thurow, Brian; Fahringer, Tim

    2012-11-01

    Plenoptic cameras have received attention recently due to their ability to computationally refocus an image after it has been acquired. We describe the development of a robust, economical and easy-to-use volumetric PIV technique using a unique plenoptic camera built in our laboratory. The tomographic MART algorithm is used to reconstruct pairs of 3D particle volumes with velocity determined using conventional cross-correlation techniques. 3D/3C velocity measurements (volumetric dimensions of 2 . 8 ' ' × 1 . 9 ' ' × 1 . 6 ' ') of a turbulent boundary layer produced on the wall of a conventional wind tunnel are presented. This work has been supported by the Air Force Office of Scientific Research,(Grant #FA9550-100100576).

  1. How 3D immersive visualization is changing medical diagnostics

    NASA Astrophysics Data System (ADS)

    Koning, Anton H. J.

    2011-03-01

    Originally the only way to look inside the human body without opening it up was by means of two dimensional (2D) images obtained using X-ray equipment. The fact that human anatomy is inherently three dimensional leads to ambiguities in interpretation and problems of occlusion. Three dimensional (3D) imaging modalities such as CT, MRI and 3D ultrasound remove these drawbacks and are now part of routine medical care. While most hospitals 'have gone digital', meaning that the images are no longer printed on film, they are still being viewed on 2D screens. However, this way valuable depth information is lost, and some interactions become unnecessarily complex or even unfeasible. Using a virtual reality (VR) system to present volumetric data means that depth information is presented to the viewer and 3D interaction is made possible. At the Erasmus MC we have developed V-Scope, an immersive volume visualization system for visualizing a variety of (bio-)medical volumetric datasets, ranging from 3D ultrasound, via CT and MRI, to confocal microscopy, OPT and 3D electron-microscopy data. In this talk we will address the advantages of such a system for both medical diagnostics as well as for (bio)medical research.

  2. 3D Elevation Program—Virtual USA in 3D

    USGS Publications Warehouse

    Lukas, Vicki; Stoker, J.M.

    2016-01-01

    The U.S. Geological Survey (USGS) 3D Elevation Program (3DEP) uses a laser system called ‘lidar’ (light detection and ranging) to create a virtual reality map of the Nation that is very accurate. 3D maps have many uses with new uses being discovered all the time.  

  3. Rapid, High-Throughput Tracking of Bacterial Motility in 3D via Phase-Contrast Holographic Video Microscopy

    PubMed Central

    Cheong, Fook Chiong; Wong, Chui Ching; Gao, YunFeng; Nai, Mui Hoon; Cui, Yidan; Park, Sungsu; Kenney, Linda J.; Lim, Chwee Teck

    2015-01-01

    Tracking fast-swimming bacteria in three dimensions can be extremely challenging with current optical techniques and a microscopic approach that can rapidly acquire volumetric information is required. Here, we introduce phase-contrast holographic video microscopy as a solution for the simultaneous tracking of multiple fast moving cells in three dimensions. This technique uses interference patterns formed between the scattered and the incident field to infer the three-dimensional (3D) position and size of bacteria. Using this optical approach, motility dynamics of multiple bacteria in three dimensions, such as speed and turn angles, can be obtained within minutes. We demonstrated the feasibility of this method by effectively tracking multiple bacteria species, including Escherichia coli, Agrobacterium tumefaciens, and Pseudomonas aeruginosa. In addition, we combined our fast 3D imaging technique with a microfluidic device to present an example of a drug/chemical assay to study effects on bacterial motility. PMID:25762336

  4. 3D-resolved fluorescence and phosphorescence lifetime imaging using temporal focusing wide-field two-photon excitation

    PubMed Central

    Choi, Heejin; Tzeranis, Dimitrios S.; Cha, Jae Won; Clémenceau, Philippe; de Jong, Sander J. G.; van Geest, Lambertus K.; Moon, Joong Ho; Yannas, Ioannis V.; So, Peter T. C.

    2012-01-01

    Fluorescence and phosphorescence lifetime imaging are powerful techniques for studying intracellular protein interactions and for diagnosing tissue pathophysiology. While lifetime-resolved microscopy has long been in the repertoire of the biophotonics community, current implementations fall short in terms of simultaneously providing 3D resolution, high throughput, and good tissue penetration. This report describes a new highly efficient lifetime-resolved imaging method that combines temporal focusing wide-field multiphoton excitation and simultaneous acquisition of lifetime information in frequency domain using a nanosecond gated imager from a 3D-resolved plane. This approach is scalable allowing fast volumetric imaging limited only by the available laser peak power. The accuracy and performance of the proposed method is demonstrated in several imaging studies important for understanding peripheral nerve regeneration processes. Most importantly, the parallelism of this approach may enhance the imaging speed of long lifetime processes such as phosphorescence by several orders of magnitude. PMID:23187477

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

    SciTech Connect

    Wong, S.T.C.

    1997-02-01

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

  6. Exploring Volumetrically Indexed Cups

    ERIC Educational Resources Information Center

    Jones, Dustin L.

    2011-01-01

    This article was inspired by a set of 12 cylindrical cups, which are volumetrically indexed; that is to say, the volume of cup "n" is equal to "n" times the volume of cup 1. Various sets of volumetrically indexed cylindrical cups are explored. I demonstrate how this children's toy is ripe for mathematical investigation, with connections to…

  7. Coupled 3D Time-Dependent Wave-Packet Approach in Hyperspherical Coordinates: The D(+)+H2 Reaction on the Triple-Sheeted DMBE Potential Energy Surface.

    PubMed

    Ghosh, Sandip; Sahoo, Tapas; Adhikari, Satrajit; Sharma, Rahul; Varandas, António J C

    2015-12-17

    We implement a coupled three-dimensional (3D) time-dependent wave packet formalism for the 4D reactive scattering problem in hyperspherical coordinates on the accurate double many body expansion (DMBE) potential energy surface (PES) for the ground and first two singlet states (1(1)A', 2(1)A', and 3(1)A') to account for nonadiabatic processes in the D(+) + H2 reaction for both zero and nonzero values of the total angular momentum (J). As the long-range interactions in D(+) + H2 contribute significantly due to nonadiabatic effects, the convergence profiles of reaction probabilities for the reactive noncharge transfer (RNCT), nonreactive charge transfer (NRCT), and reactive charge transfer (RCT) processes are shown for different collisional energies with respect to the helicity (K) and total angular momentum (J) quantum numbers. The total and state-to-state cross sections are presented as a function of the collision energy for the initial rovibrational state v = 0, j = 0 of the diatom, and the calculated cross sections compared with other theoretical and experimental results. PMID:26436891

  8. Registration of terrestrial mobile laser data on 2D or 3D geographic database by use of a non-rigid ICP approach.

    NASA Astrophysics Data System (ADS)

    Monnier, F.; Vallet, B.; Paparoditis, N.; Papelard, J.-P.; David, N.

    2013-10-01

    This article presents a generic and efficient method to register terrestrial mobile data with imperfect location on a geographic database with better overall accuracy but less details. The registration method proposed in this paper is based on a semi-rigid point to plane ICP ("Iterative Closest Point"). The main applications of such registration is to improve existing geographic databases, particularly in terms of accuracy, level of detail and diversity of represented objects. Other applications include fine geometric modelling and fine façade texturing, object extraction such as trees, poles, road signs marks, facilities, vehicles, etc. The geopositionning system of mobile mapping systems is affected by GPS masks that are only partially corrected by an Inertial Navigation System (INS) which can cause an important drift. As this drift varies non-linearly, but slowly in time, it will be modelled by a translation defined as a piecewise linear function of time which variation over time will be minimized (rigidity term). For each iteration of the ICP, the drift is estimated in order to minimise the distance between laser points and planar model primitives (data attachment term). The method has been tested on real data (a scan of the city of Paris of 3.6 million laser points registered on a 3D model of approximately 71,400 triangles).

  9. 3D QSAR STUDIES ON A SERIES OF QUINAZOLINE DERRIVATIVES AS TYROSINE KINASE (EGFR) INHIBITOR: THE K-NEAREST NEIGHBOR MOLECULAR FIELD ANALYSIS APPROACH

    PubMed Central

    Noolvi, Malleshappa N.; Patel, Harun M.

    2010-01-01

    Epidermal growth factor receptor (EGFR) protein tyrosine kinases (PTKs) are known for its role in cancer. Quinazoline have been reported to be the molecules of interest, with potent anticancer activity and they act by binding to ATP site of protein kinases. ATP binding site of protein kinases provides an extensive opportunity to design newer analogs. With this background, we report an attempt to discern the structural and physicochemical requirements for inhibition of EGFR tyrosine kinase. The k-Nearest Neighbor Molecular Field Analysis (kNN-MFA), a three dimensional quantitative structure activity relationship (3D- QSAR) method has been used in the present case to study the correlation between the molecular properties and the tyrosine kinase (EGFR) inhibitory activities on a series of quinazoline derivatives. kNNMFA calculations for both electrostatic and steric field were carried out. The master grid maps derived from the best model has been used to display the contribution of electrostatic potential and steric field. The statistical results showed significant correlation coefficient r2 (q2) of 0.846, r2 for external test set (pred_r2) 0.8029, coefficient of correlation of predicted data set (pred_r2se) of 0.6658, degree of freedom 89 and k nearest neighbor of 2. Therefore, this study not only casts light on binding mechanism between EGFR and its inhibitors, but also provides hints for the design of new EGFR inhibitors with observable structural diversity PMID:24825983

  10. Characterization of exudates released by the marine diatom Skeletonema costatum exposed to copper stress: a 3D-fluorescence spectroscopy approach.

    PubMed

    Herzi, Faouzi; Hlaili, Asma Sakka; Le Poupon, Christophe; Mabrouk, Hassine Hadj; Mounier, Stéphane

    2013-10-01

    In a laboratory study, metal contamination experiments were conducted to investigate the effects of two free copper concentrations (10(-9) and 10(-8) M) on cell growth and on dissolved organic matter exudation by a marine diatom Skeletonema costatum. Throughout incubation, the growth kinetics and exudation of extracellular molecules (i.e. dissolved organic carbon (DOC) and the fluorescent organic matter) were determined. Results revealed an inhibition of S. costatum growth when the free copper level increased (from 10(-9) to 10(-8)). Furthermore, DOC release was more significant in cultures contaminated by 10(-9) M Cu(2+) than in control, suggesting a coping mechanism developed by this species. In this study, samples were daily analysed by 3D-fluorescence and PARAFAC algorithm, in order to compare the fluorescent material produced during growth under different contaminations. PARAFAC treatment revealed two main contributions: one related to the biological activity (C1), the other linked to the marine organic matter (C2). The third component C3 was typically protein-like. This fluorophore was considered as a tryptophan-like fluorophore, whereas the C1 and the C2 components were associated to marine production such as humic matter. PMID:23868094

  11. Modeling of mass and charge transport in a solid oxide fuel cell anode structure by a 3D lattice Boltzmann approach

    NASA Astrophysics Data System (ADS)

    Paradis, Hedvig; Andersson, Martin; Sundén, Bengt

    2015-09-01

    A 3D model at microscale by the lattice Boltzmann method (LBM) is proposed for part of an anode of a solid oxide fuel cell (SOFC) to analyze the interaction between the transport and reaction processes and structural parameters. The equations of charge, momentum, heat and mass transport are simulated in the model. The modeling geometry is created with randomly placed spheres to resemble the part of the anode structure close to the electrolyte. The electrochemical reaction processes are captured at specific sites where spheres representing Ni and YSZ materials are present with void space. This work focuses on analyzing the effect of structural parameters such as porosity, and percentage of active reaction sites on the ionic current density and concentration of H2 using LBM. It is shown that LBM can be used to simulate an SOFC anode at microscale and evaluate the effect of structural parameters on the transport processes to improve the performance of the SOFC anode. It was found that increasing the porosity from 30 to 50 % decreased the ionic current density due to a reduction in the number of reaction sites. Also the consumption of H2 decreased with increasing porosity. When the percentage of active reaction sites was increased while the porosity was kept constant, the ionic current density increased. However, the H2 concentration was slightly reduced when the percentage of active reaction sites was increased. The gas flow tortuosity decreased with increasing porosity.

  12. Modeling of mass and charge transport in a solid oxide fuel cell anode structure by a 3D lattice Boltzmann approach

    NASA Astrophysics Data System (ADS)

    Paradis, Hedvig; Andersson, Martin; Sundén, Bengt

    2016-08-01

    A 3D model at microscale by the lattice Boltzmann method (LBM) is proposed for part of an anode of a solid oxide fuel cell (SOFC) to analyze the interaction between the transport and reaction processes and structural parameters. The equations of charge, momentum, heat and mass transport are simulated in the model. The modeling geometry is created with randomly placed spheres to resemble the part of the anode structure close to the electrolyte. The electrochemical reaction processes are captured at specific sites where spheres representing Ni and YSZ materials are present with void space. This work focuses on analyzing the effect of structural parameters such as porosity, and percentage of active reaction sites on the ionic current density and concentration of H2 using LBM. It is shown that LBM can be used to simulate an SOFC anode at microscale and evaluate the effect of structural parameters on the transport processes to improve the performance of the SOFC anode. It was found that increasing the porosity from 30 to 50 % decreased the ionic current density due to a reduction in the number of reaction sites. Also the consumption of H2 decreased with increasing porosity. When the percentage of active reaction sites was increased while the porosity was kept constant, the ionic current density increased. However, the H2 concentration was slightly reduced when the percentage of active reaction sites was increased. The gas flow tortuosity decreased with increasing porosity.

  13. Volumetric Echocardiographic Particle Image Velocimetry (V-Echo-PIV)

    NASA Astrophysics Data System (ADS)

    Falahatpisheh, Ahmad; Kheradvar, Arash

    2015-11-01

    Measurement of 3D flow field inside the cardiac chambers has proven to be a challenging task. Current laser-based 3D PIV methods estimate the third component of the velocity rather than directly measuring it and also cannot be used to image the opaque heart chambers. Modern echocardiography systems are equipped with 3D probes that enable imaging the entire 3D opaque field. However, this feature has not yet been employed for 3D vector characterization of blood flow. For the first time, we introduce a method that generates velocity vector field in 4D based on volumetric echocardiographic images. By assuming the conservation of brightness in 3D, blood speckles are tracked. A hierarchical 3D PIV method is used to account for large particle displacement. The discretized brightness transport equation is solved in a least square sense in interrogation windows of size 163 voxels. We successfully validate the method in analytical and experimental cases. Volumetric echo data of a left ventricle is then processed in the systolic phase. The expected velocity fields were successfully predicted by V-Echo-PIV. In this work, we showed a method to image blood flow in 3D based on volumetric images of human heart using no contrast agent.

  14. 3D fast wavelet network model-assisted 3D face recognition

    NASA Astrophysics Data System (ADS)

    Said, Salwa; Jemai, Olfa; Zaied, Mourad; Ben Amar, Chokri

    2015-12-01

    In last years, the emergence of 3D shape in face recognition is due to its robustness to pose and illumination changes. These attractive benefits are not all the challenges to achieve satisfactory recognition rate. Other challenges such as facial expressions and computing time of matching algorithms remain to be explored. In this context, we propose our 3D face recognition approach using 3D wavelet networks. Our approach contains two stages: learning stage and recognition stage. For the training we propose a novel algorithm based on 3D fast wavelet transform. From 3D coordinates of the face (x,y,z), we proceed to voxelization to get a 3D volume which will be decomposed by 3D fast wavelet transform and modeled after that with a wavelet network, then their associated weights are considered as vector features to represent each training face . For the recognition stage, an unknown identity face is projected on all the training WN to obtain a new vector features after every projection. A similarity score is computed between the old and the obtained vector features. To show the efficiency of our approach, experimental results were performed on all the FRGC v.2 benchmark.

  15. The rendering context for stereoscopic 3D web

    NASA Astrophysics Data System (ADS)

    Chen, Qinshui; Wang, Wenmin; Wang, Ronggang

    2014-03-01

    3D technologies on the Web has been studied for many years, but they are basically monoscopic 3D. With the stereoscopic technology gradually maturing, we are researching to integrate the binocular 3D technology into the Web, creating a stereoscopic 3D browser that will provide users with a brand new experience of human-computer interaction. In this paper, we propose a novel approach to apply stereoscopy technologies to the CSS3 3D Transforms. Under our model, each element can create or participate in a stereoscopic 3D rendering context, in which 3D Transforms such as scaling, translation and rotation, can be applied and be perceived in a truly 3D space. We first discuss the underlying principles of stereoscopy. After that we discuss how these principles can be applied to the Web. A stereoscopic 3D browser with backward compatibility is also created for demonstration purposes. We take advantage of the open-source WebKit project, integrating the 3D display ability into the rendering engine of the web browser. For each 3