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Sample records for 3d target localization

  1. 3-D target-based distributed smart camera network localization.

    PubMed

    Kassebaum, John; Bulusu, Nirupama; Feng, Wu-Chi

    2010-10-01

    For distributed smart camera networks to perform vision-based tasks such as subject recognition and tracking, every camera's position and orientation relative to a single 3-D coordinate frame must be accurately determined. In this paper, we present a new camera network localization solution that requires successively showing a 3-D feature point-rich target to all cameras, then using the known geometry of a 3-D target, cameras estimate and decompose projection matrices to compute their position and orientation relative to the coordinatization of the 3-D target's feature points. As each 3-D target position establishes a distinct coordinate frame, cameras that view more than one 3-D target position compute translations and rotations relating different positions' coordinate frames and share the transform data with neighbors to facilitate realignment of all cameras to a single coordinate frame. Compared to other localization solutions that use opportunistically found visual data, our solution is more suitable to battery-powered, processing-constrained camera networks because it requires communication only to determine simultaneous target viewings and for passing transform data. Additionally, our solution requires only pairwise view overlaps of sufficient size to see the 3-D target and detect its feature points, while also giving camera positions in meaningful units. We evaluate our algorithm in both real and simulated smart camera networks. In the real network, position error is less than 1 ('') when the 3-D target's feature points fill only 2.9% of the frame area. PMID:20679031

  2. Action Enhances Acoustic Cues for 3-D Target Localization by Echolocating Bats.

    PubMed

    Wohlgemuth, Melville J; Kothari, Ninad B; Moss, Cynthia F

    2016-09-01

    Under natural conditions, animals encounter a barrage of sensory information from which they must select and interpret biologically relevant signals. Active sensing can facilitate this process by engaging motor systems in the sampling of sensory information. The echolocating bat serves as an excellent model to investigate the coupling between action and sensing because it adaptively controls both the acoustic signals used to probe the environment and movements to receive echoes at the auditory periphery. We report here that the echolocating bat controls the features of its sonar vocalizations in tandem with the positioning of the outer ears to maximize acoustic cues for target detection and localization. The bat's adaptive control of sonar vocalizations and ear positioning occurs on a millisecond timescale to capture spatial information from arriving echoes, as well as on a longer timescale to track target movement. Our results demonstrate that purposeful control over sonar sound production and reception can serve to improve acoustic cues for localization tasks. This finding also highlights the general importance of movement to sensory processing across animal species. Finally, our discoveries point to important parallels between spatial perception by echolocation and vision. PMID:27608186

  3. A novel method of target recognition based on 3D-color-space locally adaptive regression kernels model

    NASA Astrophysics Data System (ADS)

    Liu, Jiaqi; Han, Jing; Zhang, Yi; Bai, Lianfa

    2015-10-01

    Locally adaptive regression kernels model can describe the edge shape of images accurately and graphic trend of images integrally, but it did not consider images' color information while the color is an important element of an image. Therefore, we present a novel method of target recognition based on 3-D-color-space locally adaptive regression kernels model. Different from the general additional color information, this method directly calculate the local similarity features of 3-D data from the color image. The proposed method uses a few examples of an object as a query to detect generic objects with incompact, complex and changeable shapes. Our method involves three phases: First, calculating the novel color-space descriptors from the RGB color space of query image which measure the likeness of a voxel to its surroundings. Salient features which include spatial- dimensional and color -dimensional information are extracted from said descriptors, and simplifying them to construct a non-similar local structure feature set of the object class by principal components analysis (PCA). Second, we compare the salient features with analogous features from the target image. This comparison is done using a matrix generalization of the cosine similarity measure. Then the similar structures in the target image are obtained using local similarity structure statistical matching. Finally, we use the method of non-maxima suppression in the similarity image to extract the object position and mark the object in the test image. Experimental results demonstrate that our approach is effective and accurate in improving the ability to identify targets.

  4. Automatic localization of target vertebrae in spine surgery using fast CT-to-fluoroscopy (3D-2D) image registration

    NASA Astrophysics Data System (ADS)

    Otake, Y.; Schafer, S.; Stayman, J. W.; Zbijewski, W.; Kleinszig, G.; Graumann, R.; Khanna, A. J.; Siewerdsen, J. H.

    2012-02-01

    Localization of target vertebrae is an essential step in minimally invasive spine surgery, with conventional methods relying on "level counting" - i.e., manual counting of vertebrae under fluoroscopy starting from readily identifiable anatomy (e.g., the sacrum). The approach requires an undesirable level of radiation, time, and is prone to counting errors due to the similar appearance of vertebrae in projection images; wrong-level surgery occurs in 1 of every ~3000 cases. This paper proposes a method to automatically localize target vertebrae in x-ray projections using 3D-2D registration between preoperative CT (in which vertebrae are preoperatively labeled) and intraoperative fluoroscopy. The registration uses an intensity-based approach with a gradient-based similarity metric and the CMA-ES algorithm for optimization. Digitally reconstructed radiographs (DRRs) and a robust similarity metric are computed on GPU to accelerate the process. Evaluation in clinical CT data included 5,000 PA and LAT projections randomly perturbed to simulate human variability in setup of mobile intraoperative C-arm. The method demonstrated 100% success for PA view (projection error: 0.42mm) and 99.8% success for LAT view (projection error: 0.37mm). Initial implementation on GPU provided automatic target localization within about 3 sec, with further improvement underway via multi-GPU. The ability to automatically label vertebrae in fluoroscopy promises to streamline surgical workflow, improve patient safety, and reduce wrong-site surgeries, especially in large patients for whom manual methods are time consuming and error prone.

  5. NIF Ignition Target 3D Point Design

    SciTech Connect

    Jones, O; Marinak, M; Milovich, J; Callahan, D

    2008-11-05

    We have developed an input file for running 3D NIF hohlraums that is optimized such that it can be run in 1-2 days on parallel computers. We have incorporated increasing levels of automation into the 3D input file: (1) Configuration controlled input files; (2) Common file for 2D and 3D, different types of capsules (symcap, etc.); and (3) Can obtain target dimensions, laser pulse, and diagnostics settings automatically from NIF Campaign Management Tool. Using 3D Hydra calculations to investigate different problems: (1) Intrinsic 3D asymmetry; (2) Tolerance to nonideal 3D effects (e.g. laser power balance, pointing errors); and (3) Synthetic diagnostics.

  6. Improved robustness study of a shock ignited target, with DUED code including non-local electron transport and 3D laser ray-tracing

    NASA Astrophysics Data System (ADS)

    Atzeni, Stefano; Marocchino, Alberto; Schiavi, Angelo

    2016-03-01

    Accurate descriptions of laser power coupling to the plasma and electron energy transport are crucial for designing shock-ignition targets and assessing their robustness (in particular with regard to laser and positioning errors). To this purpose, the 2D DUED laser fusion code has been improved with the inclusion of a 3D laser ray-tracing scheme and a model for non-local electron transport. 2D simulations with the upgraded code are presented; the dependence of the fusion yield vs target displacement is studied. Two different irradiation configurations are considered.

  7. Local Diagnosis of Reconnection in 3D

    NASA Astrophysics Data System (ADS)

    Scudder, J. D.; Karimabadi, H.; Daughton, W. S.; Roytershteyn, V.

    2014-12-01

    We demonstrate (I,II) an approach to find reconnection sites in 3D where there is no flux function for guidance, and where local observational signatures for the ``violation of frozen flux'' are under developed, if not non-existent. We use 2D and 3D PIC simulations of asymmetric guide field reconnection to test our observational hierarchy of single spacecraft kinetic diagnostics - all possible with present state of the art instrumentation. The proliferation of turbulent, electron inertial scale layers in the realistic 3D case demonstrates that electron demagnetization, while necessary, is not sufficient to identify reconnection sites. An excellent local, observable, single spacecraft proxy is demonstrated for the size of the theoretical frozen flux violation. Since even frozen flux violations need not imply reconnection is at hand, a new calibrated dimensionless method is used to determine the importance of such violations. This measure is available in 2D and 3D to help differentiate reconnection layers from weaker frozen flux violating layers. We discuss the possibility that this technique can be implemented on MMS. A technique to highlight flow geometries conducive to reconnection in 3D simulations is also suggested, that may also be implementable with the MMS flotilla. We use local analysis with multiple necessary, but theoretically independent electron kinetic conditions to help reduce the probability of misidentification of any given layer as a reconnection site. Since these local conditions are all necessary for the site, but none is known to be sufficient, the multiple tests help to greatly reduce false positive identifications. The selectivity of the results of this approach using PIC simulations of 3D asymmetric guide field reconnection will be shown using varying numbers of simultaneous conditions. Scudder, J.D., H. Karimabadi, W. Daughton and V. Roytershteyn I, II, submitted Phys. Plasma., 2014

  8. Experimental investigation of a general real-time 3D target localization method using sequential kV imaging combined with respiratory monitoring

    NASA Astrophysics Data System (ADS)

    Cho, Byungchul; Poulsen, Per; Ruan, Dan; Sawant, Amit; Keall, Paul J.

    2012-11-01

    The goal of this work was to experimentally quantify the geometric accuracy of a novel real-time 3D target localization method using sequential kV imaging combined with respiratory monitoring for clinically realistic arc and static field treatment delivery and target motion conditions. A general method for real-time target localization using kV imaging and respiratory monitoring was developed. Each dimension of internal target motion T(x, y, z; t) was estimated from the external respiratory signal R(t) through the correlation between R(ti) and the projected marker positions p(xp, yp; ti) on kV images by a state-augmented linear model: T(x, y, z; t) = aR(t) + bR(t - τ) + c. The model parameters, a, b, c, were determined by minimizing the squared fitting error ∑‖p(xp, yp; ti) - P(θi) · (aR(ti) + bR(ti - τ) + c)‖2 with the projection operator P(θi). The model parameters were first initialized based on acquired kV arc images prior to MV beam delivery. This method was implemented on a trilogy linear accelerator consisting of an OBI x-ray imager (operating at 1 Hz) and real-time position monitoring (RPM) system (30 Hz). Arc and static field plans were delivered to a moving phantom programmed with measured lung tumour motion from ten patients. During delivery, the localization method determined the target position and the beam was adjusted in real time via dynamic multileaf collimator (DMLC) adaptation. The beam-target alignment error was quantified by segmenting the beam aperture and a phantom-embedded fiducial marker on MV images and analysing their relative position. With the localization method, the root-mean-squared errors of the ten lung tumour traces ranged from 0.7-1.3 mm and 0.8-1.4 mm during the single arc and five-field static beam delivery, respectively. Without the localization method, these errors ranged from 3.1-7.3 mm. In summary, a general method for real-time target localization using kV imaging and respiratory monitoring has been

  9. 2D/3D Image fusion for accurate target localization and evaluation of a mask based stereotactic system in fractionated stereotactic radiotherapy of cranial lesions

    SciTech Connect

    Jin, J.-Y.; Ryu, Samuel; Faber, Kathleen; Mikkelsen, Tom; Chen Qing; Li Shidong; Movsas, Benjamin

    2006-12-15

    The purpose of this study was to evaluate the accuracy of a two-dimensional (2D) to three-dimensional (3D) image-fusion-guided target localization system and a mask based stereotactic system for fractionated stereotactic radiotherapy (FSRT) of cranial lesions. A commercial x-ray image guidance system originally developed for extracranial radiosurgery was used for FSRT of cranial lesions. The localization accuracy was quantitatively evaluated with an anthropomorphic head phantom implanted with eight small radiopaque markers (BBs) in different locations. The accuracy and its clinical reliability were also qualitatively evaluated for a total of 127 fractions in 12 patients with both kV x-ray images and MV portal films. The image-guided system was then used as a standard to evaluate the overall uncertainty and reproducibility of the head mask based stereotactic system in these patients. The phantom study demonstrated that the maximal random error of the image-guided target localization was {+-}0.6 mm in each direction in terms of the 95% confidence interval (CI). The systematic error varied with measurement methods. It was approximately 0.4 mm, mainly in the longitudinal direction, for the kV x-ray method. There was a 0.5 mm systematic difference, primarily in the lateral direction, between the kV x-ray and the MV portal methods. The patient study suggested that the accuracy of the image-guided system in patients was comparable to that in the phantom. The overall uncertainty of the mask system was {+-}4 mm, and the reproducibility was {+-}2.9 mm in terms of 95% CI. The study demonstrated that the image guidance system provides accurate and precise target positioning.

  10. IFSAR processing for 3D target reconstruction

    NASA Astrophysics Data System (ADS)

    Austin, Christian D.; Moses, Randolph L.

    2005-05-01

    In this paper we investigate the use of interferometric synthetic aperture radar (IFSAR) processing for the 3D reconstruction of radar targets. A major source of reconstruction error is induced by multiple scattering responses in a resolution cell, giving rise to height errors. We present a model for multiple scattering centers and analyze the errors that result using traditional IFSAR height estimation. We present a simple geometric model that characterizes the height error and suggests tests for detecting or reducing this error. We consider the use of image magnitude difference as a test statistic to detect multiple scattering responses in a resolution cell, and we analyze the resulting height error reduction and hypothesis test performance using this statistic. Finally, we consider phase linearity test statistics when three or more IFSAR images are available. Examples using synthetic Xpatch backhoe imagery are presented.

  11. 3-D SAR image formation from sparse aperture data using 3-D target grids

    NASA Astrophysics Data System (ADS)

    Bhalla, Rajan; Li, Junfei; Ling, Hao

    2005-05-01

    The performance of ATR systems can potentially be improved by using three-dimensional (3-D) SAR images instead of the traditional two-dimensional SAR images or one-dimensional range profiles. 3-D SAR image formation of targets from radar backscattered data collected on wide angle, sparse apertures has been identified by AFRL as fundamental to building an object detection and recognition capability. A set of data has been released as a challenge problem. This paper describes a technique based on the concept of 3-D target grids aimed at the formation of 3-D SAR images of targets from sparse aperture data. The 3-D target grids capture the 3-D spatial and angular scattering properties of the target and serve as matched filters for SAR formation. The results of 3-D SAR formation using the backhoe public release data are presented.

  12. SU-E-J-13: Six Degree of Freedom Image Fusion Accuracy for Cranial Target Localization On the Varian Edge Stereotactic Radiosurgery System: Comparison Between 2D/3D and KV CBCT Image Registration

    SciTech Connect

    Xu, H; Song, K; Chetty, I; Kim, J; Wen, N

    2015-06-15

    Purpose: To determine the 6 degree of freedom systematic deviations between 2D/3D and CBCT image registration with various imaging setups and fusion algorithms on the Varian Edge Linac. Methods: An anthropomorphic head phantom with radio opaque targets embedded was scanned with CT slice thicknesses of 0.8, 1, 2, and 3mm. The 6 DOF systematic errors were assessed by comparing 2D/3D (kV/MV with CT) with 3D/3D (CBCT with CT) image registrations with different offset positions, similarity measures, image filters, and CBCT slice thicknesses (1 and 2 mm). The 2D/3D registration accuracy of 51 fractions for 26 cranial SRS patients was also evaluated by analyzing 2D/3D pre-treatment verification taken after 3D/3D image registrations. Results: The systematic deviations of 2D/3D image registration using kV- kV, MV-kV and MV-MV image pairs were within ±0.3mm and ±0.3° for translations and rotations with 95% confidence interval (CI) for a reference CT with 0.8 mm slice thickness. No significant difference (P>0.05) on target localization was observed between 0.8mm, 1mm, and 2mm CT slice thicknesses with CBCT slice thicknesses of 1mm and 2mm. With 3mm CT slice thickness, both 2D/3D and 3D/3D registrations performed less accurately in longitudinal direction than thinner CT slice thickness (0.60±0.12mm and 0.63±0.07mm off, respectively). Using content filter and using similarity measure of pattern intensity instead of mutual information, improved the 2D/3D registration accuracy significantly (P=0.02 and P=0.01, respectively). For the patient study, means and standard deviations of residual errors were 0.09±0.32mm, −0.22±0.51mm and −0.07±0.32mm in VRT, LNG and LAT directions, respectively, and 0.12°±0.46°, −0.12°±0.39° and 0.06°±0.28° in RTN, PITCH, and ROLL directions, respectively. 95% CI of translational and rotational deviations were comparable to those in phantom study. Conclusion: 2D/3D image registration provided on the Varian Edge radiosurgery, 6 DOF

  13. 3D structure and nuclear targets

    NASA Astrophysics Data System (ADS)

    Dupré, Raphaël; Scopetta, Sergio

    2016-06-01

    Recent experimental and theoretical ideas are laying the ground for a new era in the knowledge of the parton structure of nuclei. We report on two promising directions beyond inclusive deep inelastic scattering experiments, aimed at, among other goals, unveiling the three-dimensional structure of the bound nucleon. The 3D structure in coordinate space can be accessed through deep exclusive processes, whose non-perturbative content is parametrized in terms of generalized parton distributions. In this way the distribution of partons in the transverse plane will be obtained, providing a pictorial view of the realization of the European Muon Collaboration effect. In particular, we show how, through the generalized parton distribution framework, non-nucleonic degrees of freedom in nuclei can be unveiled. Analogously, the momentum space 3D structure can be accessed by studying transverse-momentum-dependent parton distributions in semi-inclusive deep inelastic scattering processes. The status of measurements is also summarized, in particular novel coincidence measurements at high-luminosity facilities, such as Jefferson Laboratory. Finally the prospects for the next years at future facilities, such as the 12GeV Jefferson Laboratory and the Electron Ion Collider, are presented.

  14. 3D-2D image registration for target localization in spine surgery: investigation of similarity metrics providing robustness to content mismatch.

    PubMed

    De Silva, T; Uneri, A; Ketcha, M D; Reaungamornrat, S; Kleinszig, G; Vogt, S; Aygun, N; Lo, S-F; Wolinsky, J-P; Siewerdsen, J H

    2016-04-21

    In image-guided spine surgery, robust three-dimensional to two-dimensional (3D-2D) registration of preoperative computed tomography (CT) and intraoperative radiographs can be challenged by the image content mismatch associated with the presence of surgical instrumentation and implants as well as soft-tissue resection or deformation. This work investigates image similarity metrics in 3D-2D registration offering improved robustness against mismatch, thereby improving performance and reducing or eliminating the need for manual masking. The performance of four gradient-based image similarity metrics (gradient information (GI), gradient correlation (GC), gradient information with linear scaling (GS), and gradient orientation (GO)) with a multi-start optimization strategy was evaluated in an institutional review board-approved retrospective clinical study using 51 preoperative CT images and 115 intraoperative mobile radiographs. Registrations were tested with and without polygonal masks as a function of the number of multistarts employed during optimization. Registration accuracy was evaluated in terms of the projection distance error (PDE) and assessment of failure modes (PDE  >  30 mm) that could impede reliable vertebral level localization. With manual polygonal masking and 200 multistarts, the GC and GO metrics exhibited robust performance with 0% gross failures and median PDE  <  6.4 mm (±4.4 mm interquartile range (IQR)) and a median runtime of 84 s (plus upwards of 1-2 min for manual masking). Excluding manual polygonal masks and decreasing the number of multistarts to 50 caused the GC-based registration to fail at a rate of  >14%; however, GO maintained robustness with a 0% gross failure rate. Overall, the GI, GC, and GS metrics were susceptible to registration errors associated with content mismatch, but GO provided robust registration (median PDE  =  5.5 mm, 2.6 mm IQR) without manual masking and with an improved

  15. 3D-2D image registration for target localization in spine surgery: investigation of similarity metrics providing robustness to content mismatch

    NASA Astrophysics Data System (ADS)

    De Silva, T.; Uneri, A.; Ketcha, M. D.; Reaungamornrat, S.; Kleinszig, G.; Vogt, S.; Aygun, N.; Lo, S.-F.; Wolinsky, J.-P.; Siewerdsen, J. H.

    2016-04-01

    In image-guided spine surgery, robust three-dimensional to two-dimensional (3D-2D) registration of preoperative computed tomography (CT) and intraoperative radiographs can be challenged by the image content mismatch associated with the presence of surgical instrumentation and implants as well as soft-tissue resection or deformation. This work investigates image similarity metrics in 3D-2D registration offering improved robustness against mismatch, thereby improving performance and reducing or eliminating the need for manual masking. The performance of four gradient-based image similarity metrics (gradient information (GI), gradient correlation (GC), gradient information with linear scaling (GS), and gradient orientation (GO)) with a multi-start optimization strategy was evaluated in an institutional review board-approved retrospective clinical study using 51 preoperative CT images and 115 intraoperative mobile radiographs. Registrations were tested with and without polygonal masks as a function of the number of multistarts employed during optimization. Registration accuracy was evaluated in terms of the projection distance error (PDE) and assessment of failure modes (PDE  >  30 mm) that could impede reliable vertebral level localization. With manual polygonal masking and 200 multistarts, the GC and GO metrics exhibited robust performance with 0% gross failures and median PDE  <  6.4 mm (±4.4 mm interquartile range (IQR)) and a median runtime of 84 s (plus upwards of 1-2 min for manual masking). Excluding manual polygonal masks and decreasing the number of multistarts to 50 caused the GC-based registration to fail at a rate of  >14% however, GO maintained robustness with a 0% gross failure rate. Overall, the GI, GC, and GS metrics were susceptible to registration errors associated with content mismatch, but GO provided robust registration (median PDE  =  5.5 mm, 2.6 mm IQR) without manual masking and with an improved

  16. R3D Align: global pairwise alignment of RNA 3D structures using local superpositions

    PubMed Central

    Rahrig, Ryan R.; Leontis, Neocles B.; Zirbel, Craig L.

    2010-01-01

    Motivation: Comparing 3D structures of homologous RNA molecules yields information about sequence and structural variability. To compare large RNA 3D structures, accurate automatic comparison tools are needed. In this article, we introduce a new algorithm and web server to align large homologous RNA structures nucleotide by nucleotide using local superpositions that accommodate the flexibility of RNA molecules. Local alignments are merged to form a global alignment by employing a maximum clique algorithm on a specially defined graph that we call the ‘local alignment’ graph. Results: The algorithm is implemented in a program suite and web server called ‘R3D Align’. The R3D Align alignment of homologous 3D structures of 5S, 16S and 23S rRNA was compared to a high-quality hand alignment. A full comparison of the 16S alignment with the other state-of-the-art methods is also provided. The R3D Align program suite includes new diagnostic tools for the structural evaluation of RNA alignments. The R3D Align alignments were compared to those produced by other programs and were found to be the most accurate, in comparison with a high quality hand-crafted alignment and in conjunction with a series of other diagnostics presented. The number of aligned base pairs as well as measures of geometric similarity are used to evaluate the accuracy of the alignments. Availability: R3D Align is freely available through a web server http://rna.bgsu.edu/R3DAlign. The MATLAB source code of the program suite is also freely available for download at that location. Supplementary information: Supplementary data are available at Bioinformatics online. Contact: r-rahrig@onu.edu PMID:20929913

  17. Characterizing targets and backgrounds for 3D laser radars

    NASA Astrophysics Data System (ADS)

    Steinvall, Ove K.; Larsson, Hakan; Gustafsson, Frank; Chevalier, Tomas R.; Persson, Asa; Klasen, Lena M.

    2004-12-01

    Exciting development is taking place in 3 D sensing laser radars. Scanning systems are well established for mapping from airborne and ground sensors. 3 D sensing focal plane arrays (FPAs) enable a full range and intensity image can be captured in one laser shot. Gated viewing systems also produces 3 D target information. Many applications for 3 D laser radars are found in robotics, rapid terrain visualization, augmented vision, reconnaissance and target recognition, weapon guidance including aim point selection and others. The net centric warfare will demand high resolution geo-data for a common description of the environment. At FOI we have a measurement program to collect data relevant for 3 D laser radars using airborne and tripod mounted equipment for data collection. Data collection spans from single pixel waveform collection (1 D) over 2 D using range gated imaging to full 3 D imaging using scanning systems. This paper will describe 3 D laser data from different campaigns with emphasis on range distribution and reflections properties for targets and background during different seasonal conditions. Example of the use of the data for system modeling, performance prediction and algorithm development will be given. Different metrics to characterize the data set will also be discussed.

  18. Target surface finding using 3D SAR data

    NASA Astrophysics Data System (ADS)

    Ruiter, Jason R.; Burns, Joseph W.; Subotic, Nikola S.

    2005-05-01

    Methods of generating more literal, easily interpretable imagery from 3-D SAR data are being studied to provide all weather, near-visual target identification and/or scene interpretation. One method of approaching this problem is to automatically generate shape-based geometric renderings from the SAR data. In this paper we describe the application of the Marching Tetrahedrons surface finding algorithm to 3-D SAR data. The Marching Tetrahedrons algorithm finds a surface through the 3-D data cube, which provides a recognizable representation of the target surface. This algorithm was applied to the public-release X-patch simulations of a backhoe, which provided densely sampled 3-D SAR data sets. The performance of the algorithm to noise and spatial resolution were explored. Surface renderings were readily recognizable over a range of spatial resolution, and maintained their fidelity even under relatively low Signal-to-Noise Ratio (SNR) conditions.

  19. Fast and precise 3D fluorophore localization by gradient fitting

    NASA Astrophysics Data System (ADS)

    Ma, Hongqiang; Xu, Jianquan; Jin, Jingyi; Gao, Ying; Lan, Li; Liu, Yang

    2016-02-01

    Astigmatism imaging is widely used to encode the 3D position of fluorophore in single-particle tracking and super-resolution localization microscopy. Here, we present a fast and precise localization algorithm based on gradient fitting to decode the 3D subpixel position of the fluorophore. This algorithm determines the center of the emitter by finding the position with the best-fit gradient direction distribution to the measured point spread function (PSF), and can retrieve the 3D subpixel position of the emitter in a single iteration. Through numerical simulation and experiments with mammalian cells, we demonstrate that our algorithm yields comparable localization precision to the traditional iterative Gaussian function fitting (GF) based method, while exhibits over two orders-of-magnitude faster execution speed. Our algorithm is a promising online reconstruction method for 3D super-resolution microscopy.

  20. FR3D: finding local and composite recurrent structural motifs in RNA 3D structures.

    PubMed

    Sarver, Michael; Zirbel, Craig L; Stombaugh, Jesse; Mokdad, Ali; Leontis, Neocles B

    2008-01-01

    New methods are described for finding recurrent three-dimensional (3D) motifs in RNA atomic-resolution structures. Recurrent RNA 3D motifs are sets of RNA nucleotides with similar spatial arrangements. They can be local or composite. Local motifs comprise nucleotides that occur in the same hairpin or internal loop. Composite motifs comprise nucleotides belonging to three or more different RNA strand segments or molecules. We use a base-centered approach to construct efficient, yet exhaustive search procedures using geometric, symbolic, or mixed representations of RNA structure that we implement in a suite of MATLAB programs, "Find RNA 3D" (FR3D). The first modules of FR3D preprocess structure files to classify base-pair and -stacking interactions. Each base is represented geometrically by the position of its glycosidic nitrogen in 3D space and by the rotation matrix that describes its orientation with respect to a common frame. Base-pairing and base-stacking interactions are calculated from the base geometries and are represented symbolically according to the Leontis/Westhof basepairing classification, extended to include base-stacking. These data are stored and used to organize motif searches. For geometric searches, the user supplies the 3D structure of a query motif which FR3D uses to find and score geometrically similar candidate motifs, without regard to the sequential position of their nucleotides in the RNA chain or the identity of their bases. To score and rank candidate motifs, FR3D calculates a geometric discrepancy by rigidly rotating candidates to align optimally with the query motif and then comparing the relative orientations of the corresponding bases in the query and candidate motifs. Given the growing size of the RNA structure database, it is impossible to explicitly compute the discrepancy for all conceivable candidate motifs, even for motifs with less than ten nucleotides. The screening algorithm that we describe finds all candidate motifs whose

  1. VISRAD, 3-D Target Design and Radiation Simulation Code

    NASA Astrophysics Data System (ADS)

    Li, Yingjie; Macfarlane, Joseph; Golovkin, Igor

    2015-11-01

    The 3-D view factor code VISRAD is widely used in designing HEDP experiments at major laser and pulsed-power facilities, including NIF, OMEGA, OMEGA-EP, ORION, LMJ, Z, and PLX. It simulates target designs by generating a 3-D grid of surface elements, utilizing a variety of 3-D primitives and surface removal algorithms, and can be used to compute the radiation flux throughout the surface element grid by computing element-to-element view factors and solving power balance equations. Target set-up and beam pointing are facilitated by allowing users to specify positions and angular orientations using a variety of coordinates systems (e.g., that of any laser beam, target component, or diagnostic port). Analytic modeling for laser beam spatial profiles for OMEGA DPPs and NIF CPPs is used to compute laser intensity profiles throughout the grid of surface elements. We will discuss recent improvements to the software package and plans for future developments.

  2. FR3D: finding local and composite recurrent structural motifs in RNA 3D structures

    PubMed Central

    Sarver, Michael; Stombaugh, Jesse; Mokdad, Ali; Leontis, Neocles B.

    2010-01-01

    New methods are described for finding recurrent three-dimensional (3D) motifs in RNA atomic-resolution structures. Recurrent RNA 3D motifs are sets of RNA nucleotides with similar spatial arrangements. They can be local or composite. Local motifs comprise nucleotides that occur in the same hairpin or internal loop. Composite motifs comprise nucleotides belonging to three or more different RNA strand segments or molecules. We use a base-centered approach to construct efficient, yet exhaustive search procedures using geometric, symbolic, or mixed representations of RNA structure that we implement in a suite of MATLAB programs, “Find RNA 3D” (FR3D). The first modules of FR3D preprocess structure files to classify base-pair and -stacking interactions. Each base is represented geometrically by the position of its glycosidic nitrogen in 3D space and by the rotation matrix that describes its orientation with respect to a common frame. Base-pairing and base-stacking interactions are calculated from the base geometries and are represented symbolically according to the Leontis/Westhof basepairing classification, extended to include base-stacking. These data are stored and used to organize motif searches. For geometric searches, the user supplies the 3D structure of a query motif which FR3D uses to find and score geometrically similar candidate motifs, without regard to the sequential position of their nucleotides in the RNA chain or the identity of their bases. To score and rank candidate motifs, FR3D calculates a geometric discrepancy by rigidly rotating candidates to align optimally with the query motif and then comparing the relative orientations of the corresponding bases in the query and candidate motifs. Given the growing size of the RNA structure database, it is impossible to explicitly compute the discrepancy for all conceivable candidate motifs, even for motifs with less than ten nucleotides. The screening algorithm that we describe finds all candidate motifs

  3. Context-driven automated target detection in 3D data

    NASA Astrophysics Data System (ADS)

    West, Karen F.; Webb, Brian N.; Lersch, James R.; Pothier, Steven; Triscari, Joseph M.; Iverson, A. E.

    2004-09-01

    This paper summarizes a system, and its component algorithms, for context-driven target vehicle detection in 3-D data that was developed under the Defense Advanced Research Projects Agency (DARPA) Exploitation of 3-D Data (E3D) Program. In order to determine the power of shape and geometry for the extraction of context objects and the detection of targets, our algorithm research and development concentrated on the geometric aspects of the problem and did not utilize intensity information. Processing begins with extraction of context information and initial target detection at reduced resolution, followed by a detailed, full-resolution analysis of candidate targets. Our reduced-resolution processing includes a probabilistic procedure for finding the ground that is effective even in rough terrain; a hierarchical, graph-based approach for the extraction of context objects and potential vehicle hide sites; and a target detection process that is driven by context-object and hide-site locations. Full-resolution processing includes statistical false alarm reduction and decoy mitigation. When results are available from previously collected data, we also perform object-level change detection, which affects the probabilities that objects are context objects or targets. Results are presented for both synthetic and collected LADAR data.

  4. Measurement of the mobility edge for 3D Anderson localization

    NASA Astrophysics Data System (ADS)

    Semeghini, Giulia; Landini, Manuele; Castilho, Patricia; Roy, Sanjukta; Spagnolli, Giacomo; Trenkwalder, Andreas; Fattori, Marco; Inguscio, Massimo; Modugno, Giovanni

    2016-05-01

    An outstanding problem of Anderson localization (AL) in 3D systems is the determination of the mobility edge, i.e. the energy threshold that separates localized and extended states. In our experiment we use a Bose-Einstein condensate of 39 K atoms and study its transport properties in a disordered optical potential. By tuning the inter-particle interactions to zero via magnetic Feshbach resonances, we study the single-particle phenomenon of AL. A novel technique to measure and control the atomic energy distribution allows us to measure for the first time the position of the localization threshold as a function of the disorder strength. We also study how the addition of finite repulsive or attractive interactions breaks the localized regime and triggers subdiffusive expansion of the atoms. In the future, similar experiments might also probe the existence of many-body localization in 3D.

  5. Localization of liver tumors in freehand 3D laparoscopic ultrasound

    NASA Astrophysics Data System (ADS)

    Shahin, O.; Martens, V.; Besirevic, A.; Kleemann, M.; Schlaefer, A.

    2012-02-01

    The aim of minimally invasive laparoscopic liver interventions is to completely resect or ablate tumors while minimizing the trauma caused by the operation. However, restrictions such as limited field of view and reduced depth perception can hinder the surgeon's capabilities to precisely localize the tumor. Typically, preoperative data is acquired to find the tumor(s) and plan the surgery. Nevertheless, determining the precise position of the tumor is required, not only before but also during the operation. The standard use of ultrasound in hepatic surgery is to explore the liver and identify tumors. Meanwhile, the surgeon mentally builds a 3D context to localize tumors. This work aims to upgrade the use of ultrasound in laparoscopic liver surgery. We propose an approach to segment and localize tumors intra-operatively in 3D ultrasound. We reconstruct a 3D laparoscopic ultrasound volume containing a tumor. The 3D image is then preprocessed and semi-automatically segmented using a level set algorithm. During the surgery, for each subsequent reconstructed volume, a fast update of the tumor position is accomplished via registration using the previously segmented and localized tumor as a prior knowledge. The approach was tested on a liver phantom with artificial tumors. The tumors were localized in approximately two seconds with a mean error of less than 0.5 mm. The strengths of this technique are that it can be performed intra-operatively, it helps the surgeon to accurately determine the location, shape and volume of the tumor, and it is repeatable throughout the operation.

  6. 3-D model-based tracking for UAV indoor localization.

    PubMed

    Teulière, Céline; Marchand, Eric; Eck, Laurent

    2015-05-01

    This paper proposes a novel model-based tracking approach for 3-D localization. One main difficulty of standard model-based approach lies in the presence of low-level ambiguities between different edges. In this paper, given a 3-D model of the edges of the environment, we derive a multiple hypotheses tracker which retrieves the potential poses of the camera from the observations in the image. We also show how these candidate poses can be integrated into a particle filtering framework to guide the particle set toward the peaks of the distribution. Motivated by the UAV indoor localization problem where GPS signal is not available, we validate the algorithm on real image sequences from UAV flights. PMID:25099967

  7. 3D target array for pulsed multi-sourced radiography

    DOEpatents

    Le Galloudec, Nathalie Joelle

    2016-02-23

    The various technologies presented herein relate to the generation of x-rays and other charged particles. A plurality of disparate source materials can be combined on an array to facilitate fabrication of co-located mixed tips (point sources) which can be utilized to form a polychromatic cloud, e.g., a plurality of x-rays having a range of energies and or wavelengths, etc. The tips can be formed such that the x-rays are emitted in a direction different to other charged particles to facilitate clean x-ray sourcing. Particles, such as protons, can be directionally emitted to facilitate generation of neutrons at a secondary target. The various particles can be generated by interaction of a laser irradiating the array of tips. The tips can be incorporated into a plurality of 3D conical targets, the conical target sidewall(s) can be utilized to microfocus a portion of a laser beam onto the tip material.

  8. Saliency detection for videos using 3D FFT local spectra

    NASA Astrophysics Data System (ADS)

    Long, Zhiling; AlRegib, Ghassan

    2015-03-01

    Bottom-up spatio-temporal saliency detection identifies perceptually important regions of interest in video sequences. The center-surround model proves to be useful for visual saliency detection. In this work, we explore using 3D FFT local spectra as features for saliency detection within the center-surround framework. We develop a spectral location based decomposition scheme to divide a 3D FFT cube into two components, one related to temporal changes and the other related to spatial changes. Temporal saliency and spatial saliency are detected separately using features derived from each spectral component through a simple center-surround comparison method. The two detection results are then combined to yield a saliency map. We apply the same detection algorithm to different color channels (YIQ) and incorporate the results into the final saliency determination. The proposed technique is tested with the public CRCNS database. Both visual and numerical evaluations verify the promising performance of our technique.

  9. 3D studies of the NIF symmetry tuning targets

    NASA Astrophysics Data System (ADS)

    Milovich, J.; Jones, O.; Edwards, M.; Weber, S.; Dewald, E.; Landen, O.; Marinak, M.

    2009-11-01

    Minimizing radiation drive asymmetries is necessary for a successful ignition campaign. Since the ignition capsule symmetry is most sensitive to the foot (first 2 ns) and the peak of the laser pulse, two different targets will be fielded on the NIF: re-emit and symmetry capsules (Sym-Caps). The first measures the incoming flux asymmetries during the foot by observing the re-radiated flux of a high-Z ball in place of the ignition capsule. The Sym-Caps resemble the ignition target with the frozen DT layer replaced by an equivalent mass of ablator material, thus preserving the hydrodynamic implosion properties. By measuring the x-ray self-emission near peak compression the ignition capsule core shape can be tuned. Simulations with 2D radiation-hydrodynamic simulations codes omit 3D effects in the hohlraum such as diagnostic holes, capsule roughness, shot-to-shot variations caused by laser beam power imbalances and pointing errors. We study these effects by performing 3D simulations using HYDRA and found that tuning the laser pulse using a finite number of shots is not substantially compromised.

  10. Coverage Assessment and Target Tracking in 3D Domains

    PubMed Central

    Boudriga, Noureddine; Hamdi, Mohamed; Iyengar, Sitharama

    2011-01-01

    Recent advances in integrated electronic devices motivated the use of Wireless Sensor Networks (WSNs) in many applications including domain surveillance and mobile target tracking, where a number of sensors are scattered within a sensitive region to detect the presence of intruders and forward related events to some analysis center(s). Obviously, sensor deployment should guarantee an optimal event detection rate and should reduce coverage holes. Most of the coverage control approaches proposed in the literature deal with two-dimensional zones and do not develop strategies to handle coverage in three-dimensional domains, which is becoming a requirement for many applications including water monitoring, indoor surveillance, and projectile tracking. This paper proposes efficient techniques to detect coverage holes in a 3D domain using a finite set of sensors, repair the holes, and track hostile targets. To this end, we use the concepts of Voronoi tessellation, Vietoris complex, and retract by deformation. We show in particular that, through a set of iterative transformations of the Vietoris complex corresponding to the deployed sensors, the number of coverage holes can be computed with a low complexity. Mobility strategies are also proposed to repair holes by moving appropriately sensors towards the uncovered zones. The tracking objective is to set a non-uniform WSN coverage within the monitored domain to allow detecting the target(s) by the set of sensors. We show, in particular, how the proposed algorithms adapt to cope with obstacles. Simulation experiments are carried out to analyze the efficiency of the proposed models. To our knowledge, repairing and tracking is addressed for the first time in 3D spaces with different sensor coverage schemes. PMID:22163733

  11. Resolution improvement by 3D particle averaging in localization microscopy

    PubMed Central

    Broeken, Jordi; Johnson, Hannah; Lidke, Diane S.; Liu, Sheng; Nieuwenhuizen, Robert P.J.; Stallinga, Sjoerd; Lidke, Keith A.; Rieger, Bernd

    2015-01-01

    Inspired by recent developments in localization microscopy that applied averaging of identical particles in 2D for increasing the resolution even further, we discuss considerations for alignment (registration) methods for particles in general and for 3D in particular. We detail that traditional techniques for particle registration from cryo electron microscopy based on cross-correlation are not suitable, as the underlying image formation process is fundamentally different. We argue that only localizations, i.e. a set of coordinates with associated uncertainties, are recorded and not a continuous intensity distribution. We present a method that owes to this fact and that is inspired by the field of statistical pattern recognition. In particular we suggest to use an adapted version of the Bhattacharyya distance as a merit function for registration. We evaluate the method in simulations and demonstrate it on three-dimensional super-resolution data of Alexa 647 labelled to the Nup133 protein in the nuclear pore complex of Hela cells. From the simulations we find suggestions that for successful registration the localization uncertainty must be smaller than the distance between labeling sites on a particle. These suggestions are supported by theoretical considerations concerning the attainable resolution in localization microscopy and its scaling behavior as a function of labeling density and localization precision. PMID:25866640

  12. 3D photoacoustic imaging of a moving target

    NASA Astrophysics Data System (ADS)

    Ephrat, Pinhas; Roumeliotis, Michael; Prato, Frank S.; Carson, Jeffrey J. L.

    2009-02-01

    We have developed a fast 3D photoacoustic imaging system based on a sparse array of ultrasound detectors and iterative image reconstruction. To investigate the high frame rate capabilities of our system in the context of rotational motion, flow, and spectroscopy, we performed high frame-rate imaging on a series of targets, including a rotating graphite rod, a bolus of methylene blue flowing through a tube, and hyper-spectral imaging of a tube filled with methylene blue under a no flow condition. Our frame-rate for image acquisition was 10 Hz, which was limited by the laser repetition rate. We were able to track the rotation of the rod and accurately estimate its rotational velocity, at a rate of 0.33 rotations-per-second. The flow of contrast in the tube, at a flow rate of 180 μL/min, was also well depicted, and quantitative analysis suggested a potential method for estimating flow velocity from such measurements. The spectrum obtained did not provide accurate results, but depicted the spectral absorption signature of methylene blue , which may be sufficient for identification purposes. These preliminary results suggest that our high frame-rate photoacoustic imaging system could be used for identifying contrast agents and monitoring kinetics as an agent propagates through specific, simple structures such as blood vessels.

  13. 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.

  14. Test target for characterizing 3D resolution of optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Hu, Zhixiong; Hao, Bingtao; Liu, Wenli; Hong, Baoyu; Li, Jiao

    2014-12-01

    Optical coherence tomography (OCT) is a non-invasive 3D imaging technology which has been applied or investigated in many diagnostic fields including ophthalmology, dermatology, dentistry, cardiovasology, endoscopy, brain imaging and so on. Optical resolution is an important characteristic that can describe the quality and utility of an image acquiring system. We employ 3D printing technology to design and fabricate a test target for characterizing 3D resolution of optical coherence tomography. The test target which mimics USAF 1951 test chart was produced with photopolymer. By measuring the 3D test target, axial resolution as well as lateral resolution of a spectral domain OCT system was evaluated. For comparison, conventional microscope and surface profiler were employed to characterize the 3D test targets. The results demonstrate that the 3D resolution test targets have the potential of qualitatively and quantitatively validating the performance of OCT systems.

  15. Flash trajectory imaging of target 3D motion

    NASA Astrophysics Data System (ADS)

    Wang, Xinwei; Zhou, Yan; Fan, Songtao; He, Jun; Liu, Yuliang

    2011-03-01

    We present a flash trajectory imaging technique which can directly obtain target trajectory and realize non-contact measurement of motion parameters by range-gated imaging and time delay integration. Range-gated imaging gives the range of targets and realizes silhouette detection which can directly extract targets from complex background and decrease the complexity of moving target image processing. Time delay integration increases information of one single frame of image so that one can directly gain the moving trajectory. In this paper, we have studied the algorithm about flash trajectory imaging and performed initial experiments which successfully obtained the trajectory of a falling badminton. Our research demonstrates that flash trajectory imaging is an effective approach to imaging target trajectory and can give motion parameters of moving targets.

  16. Targeted infill drilling at Stratton field using 3-D seismic

    SciTech Connect

    Suydam, J.R.; Reitz, D.T.

    1994-12-31

    Stratton field is located on the Vicksburg flexure trend in Nueces and Kleberg Counties, South Texas. It has produced more than 2.8 Tcf of gas since 1937 from Frio fluvial/deltaic sandstones and Vicksburg shallow-marine sandstones. The field is a combination stratigraphic and faulted structural trap, and contains numerous highly compartmentalized sandstone reservoirs. Continuous infield drilling is required to keep the field producing, and 3-D seismic data have been used to select the best locations for these wells. In 1992, an 8-mi{sup 2} seismic survey was completed in the southern end of the field, and the resulting structural interpretation presented many more fault traps than were apparent in the 2-D seismic interpretation. So far, all of the new wells drilled within the survey have encountered untapped compartments enclosed by fault traps. Furthermore, fault cuts in the new wells have always been within 20 ft of the position predicted by seismic data.

  17. Targeted infill drilling at Stratton Field using 3-D seismic

    SciTech Connect

    Suydam, J.; Reitz, D.

    1994-09-01

    Stratton field is located on the Vicksburg flexure trend in Nueces and Kleberg counties, south Texas. It has produced over 2.8 tcf of gas since 1937 from Frio fluvial/deltaic sandstones and Vicksburg shallow marine sandstones. The field is a combination stratigraphic and faulted structural trap, and contains numerous highly compartmentalized sandstone reservoirs. Continuous infield drilling is required to keep the field producing, and 3-D seismic data have been used to select the best locations for these wells. In 1992, the Bureau of Economic Geology shot an 8-mi{sup 2} survey in the southern end of the field, and the resulting structural interpretation presented many more fault traps that were not apparent in the 2-D seismic interpretation. So far, all of the new wells drilled within the survey have encountered untapped compartments enclosed by fault traps. Furthermore, fault cuts in the new wells have always been within 20 ft of the position predicted by seismic data.

  18. Localizing Protein in 3D Neural Stem Cell Culture: a Hybrid Visualization Methodology

    PubMed Central

    Fai, Stephen; Bennett, Steffany A.L.

    2010-01-01

    The importance of 3-dimensional (3D) topography in influencing neural stem and progenitor cell (NPC) phenotype is widely acknowledged yet challenging to study. When dissociated from embryonic or post-natal brain, single NPCs will proliferate in suspension to form neurospheres. Daughter cells within these cultures spontaneously adopt distinct developmental lineages (neurons, oligodendrocytes, and astrocytes) over the course of expansion despite being exposed to the same extracellular milieu. This progression recapitulates many of the stages observed over the course of neurogenesis and gliogenesis in post-natal brain and is often used to study basic NPC biology within a controlled environment. Assessing the full impact of 3D topography and cellular positioning within these cultures on NPC fate is, however, difficult. To localize target proteins and identify NPC lineages by immunocytochemistry, free-floating neurospheres must be plated on a substrate or serially sectioned. This processing is required to ensure equivalent cell permeabilization and antibody access throughout the sphere. As a result, 2D epifluorescent images of cryosections or confocal reconstructions of 3D Z-stacks can only provide spatial information about cell position within discrete physical or digital 3D slices and do not visualize cellular position in the intact sphere. Here, to reiterate the topography of the neurosphere culture and permit spatial analysis of protein expression throughout the entire culture, we present a protocol for isolation, expansion, and serial sectioning of post-natal hippocampal neurospheres suitable for epifluorescent or confocal immunodetection of target proteins. Connexin29 (Cx29) is analyzed as an example. Next, using a hybrid of graphic editing and 3D modelling softwares rigorously applied to maintain biological detail, we describe how to re-assemble the 3D structural positioning of these images and digitally map labelled cells within the complete neurosphere. This

  19. "Stereo Compton cameras" for the 3-D localization of radioisotopes

    NASA Astrophysics Data System (ADS)

    Takeuchi, K.; Kataoka, J.; Nishiyama, T.; Fujita, T.; Kishimoto, A.; Ohsuka, S.; Nakamura, S.; Adachi, S.; Hirayanagi, M.; Uchiyama, T.; Ishikawa, Y.; Kato, T.

    2014-11-01

    The Compton camera is a viable and convenient tool used to visualize the distribution of radioactive isotopes that emit gamma rays. After the nuclear disaster in Fukushima in 2011, there is a particularly urgent need to develop "gamma cameras", which can visualize the distribution of such radioisotopes. In response, we propose a portable Compton camera, which comprises 3-D position-sensitive GAGG scintillators coupled with thin monolithic MPPC arrays. The pulse-height ratio of two MPPC-arrays allocated at both ends of the scintillator block determines the depth of interaction (DOI), which dramatically improves the position resolution of the scintillation detectors. We report on the detailed optimization of the detector design, based on Geant4 simulation. The results indicate that detection efficiency reaches up to 0.54%, or more than 10 times that of other cameras being tested in Fukushima, along with a moderate angular resolution of 8.1° (FWHM). By applying the triangular surveying method, we also propose a new concept for the stereo measurement of gamma rays by using two Compton cameras, thus enabling the 3-D positional measurement of radioactive isotopes for the first time. From one point source simulation data, we ensured that the source position and the distance to the same could be determined typically to within 2 meters' accuracy and we also confirmed that more than two sources are clearly separated by the event selection from two point sources of simulation data.

  20. 3-D Target Location from Stereoscopic SAR Images

    SciTech Connect

    DOERRY,ARMIN W.

    1999-10-01

    SAR range-Doppler images are inherently 2-dimensional. Targets with a height offset lay over onto offset range and azimuth locations. Just which image locations are laid upon depends on the imaging geometry, including depression angle, squint angle, and target bearing. This is the well known layover phenomenon. Images formed with different aperture geometries will exhibit different layover characteristics. These differences can be exploited to ascertain target height information, in a stereoscopic manner. Depending on the imaging geometries, height accuracy can be on the order of horizontal position accuracies, thereby rivaling the best IFSAR capabilities in fine resolution SAR images. All that is required for this to work are two distinct passes with suitably different geometries from any plain old SAR.

  1. Mechanisms of DNA damage response to targeted irradiation in organotypic 3D skin cultures.

    PubMed

    Acheva, Anna; Ghita, Mihaela; Patel, Gaurang; Prise, Kevin M; Schettino, Giuseppe

    2014-01-01

    DNA damage (caused by direct cellular exposure and bystander signaling) and the complex pathways involved in its repair are critical events underpinning cellular and tissue response following radiation exposures. There are limited data addressing the dynamics of DNA damage induction and repair in the skin particularly in areas not directly exposed. Here we investigate the mechanisms regulating DNA damage, repair, intracellular signalling and their impact on premature differentiation and development of inflammatory-like response in the irradiated and surrounding areas of a 3D organotypic skin model. Following localized low-LET irradiation (225 kVp X-rays), low levels of 53BP1 foci were observed in the 3D model (3.8±0.28 foci/Gy/cell) with foci persisting and increasing in size up to 48 h post irradiation. In contrast, in cell monolayers 14.2±0.6 foci/Gy/cell and biphasic repair kinetics with repair completed before 24 h was observed. These differences are linked to differences in cellular status with variable level of p21 driving apoptotic signalling in 2D and accelerated differentiation in both the directly irradiated and bystander areas of the 3D model. The signalling pathways utilized by irradiated keratinocytes to induce DNA damage in non-exposed areas of the skin involved the NF-κB transcription factor and its downstream target COX-2. PMID:24505255

  2. 3D cell culture systems modeling tumor growth determinants in cancer target discovery.

    PubMed

    Thoma, Claudio R; Zimmermann, Miriam; Agarkova, Irina; Kelm, Jens M; Krek, Wilhelm

    2014-04-01

    Phenotypic heterogeneity of cancer cells, cell biological context, heterotypic crosstalk and the microenvironment are key determinants of the multistep process of tumor development. They sign responsible, to a significant extent, for the limited response and resistance of cancer cells to molecular-targeted therapies. Better functional knowledge of the complex intra- and intercellular signaling circuits underlying communication between the different cell types populating a tumor tissue and of the systemic and local factors that shape the tumor microenvironment is therefore imperative. Sophisticated 3D multicellular tumor spheroid (MCTS) systems provide an emerging tool to model the phenotypic and cellular heterogeneity as well as microenvironmental aspects of in vivo tumor growth. In this review we discuss the cellular, chemical and physical factors contributing to zonation and cellular crosstalk within tumor masses. On this basis, we further describe 3D cell culture technologies for growth of MCTS as advanced tools for exploring molecular tumor growth determinants and facilitating drug discovery efforts. We conclude with a synopsis on technological aspects for on-line analysis and post-processing of 3D MCTS models. PMID:24636868

  3. Novel Target Fabrication Using 3D Printing Developed at University of Michigan

    NASA Astrophysics Data System (ADS)

    Klein, Sallee R.; Deininger, Michael; Gillespie, Robb S.; Di Stefano, Carlos A.; MacDonald, Michael J.; J-E Manuel, Mario; Young, Rachel P.; Kuranz, Carolyn C.; Keiter, Paul A.; Drake, R. Paul

    2016-04-01

    The University of Michigan has been fabricating targets for high-energy-density experiments for the past decade. We utilize the technique of machined acrylic bodies and mating components acting as constraints to build repeatable targets. Combining 3D printing with traditional machining, we are able to take advantage of the very best part of both aspects of manufacturing. Here we present several recent campaigns to act as showcase and introduction of our techniques and our experience with 3D printing, effecting how we utilize 3D printing in our target builds.

  4. Geofencing-Based Localization for 3d Data Acquisition Navigation

    NASA Astrophysics Data System (ADS)

    Nakagawa, M.; Kamio, T.; Yasojima, H.; Kobayashi, T.

    2016-06-01

    Users require navigation for many location-based applications using moving sensors, such as autonomous robot control, mapping route navigation and mobile infrastructure inspection. In indoor environments, indoor positioning systems using GNSSs can provide seamless indoor-outdoor positioning and navigation services. However, instabilities in sensor position data acquisition remain, because the indoor environment is more complex than the outdoor environment. On the other hand, simultaneous localization and mapping processing is better than indoor positioning for measurement accuracy and sensor cost. However, it is not easy to estimate position data from a single viewpoint directly. Based on these technical issues, we focus on geofencing techniques to improve position data acquisition. In this research, we propose a methodology to estimate more stable position or location data using unstable position data based on geofencing in indoor environments. We verify our methodology through experiments in indoor environments.

  5. 3D target tracking in infrared imagery by SIFT-based distance histograms

    NASA Astrophysics Data System (ADS)

    Yan, Ruicheng; Cao, Zhiguo

    2011-11-01

    SIFT tracking algorithm is an excellent point-based tracking algorithm, which has high tracking performance and accuracy due to its robust capability against rotation, scale change and occlusion. However, when tracking a huge 3D target in complicated real scenarios in a forward-looking infrared (FLIR) image sequence taken from an airborne moving platform, the tracked point locating in the vertical surface usually shifts away from the correct position. In this paper, we propose a novel algorithm for 3D target tracking in FLIR image sequences. Our approach uses SIFT keypoints detected in consecutive frames for point correspondence. The candidate position of the tracked point is firstly estimated by computing the affine transformation using local corresponding SIFT keypoints. Then the correct position is located via an optimal method. Euclidean distances between a candidate point and SIFT keypoints nearby are calculated and formed into a SIFT-based distance histogram. The distance histogram is defined a cost of associating each candidate point to a correct tracked point using the constraint based on the topology of each candidate point with its surrounding SIFT keypoints. Minimization of the cost is formulated as a combinatorial optimization problem. Experiments demonstrate that the proposed algorithm efficiently improves the tracking performance and accuracy.

  6. Opti-acoustic stereo imaging: on system calibration and 3-D target reconstruction.

    PubMed

    Negahdaripour, Shahriar; Sekkati, Hicham; Pirsiavash, Hamed

    2009-06-01

    Utilization of an acoustic camera for range measurements is a key advantage for 3-D shape recovery of underwater targets by opti-acoustic stereo imaging, where the associated epipolar geometry of optical and acoustic image correspondences can be described in terms of conic sections. In this paper, we propose methods for system calibration and 3-D scene reconstruction by maximum likelihood estimation from noisy image measurements. The recursive 3-D reconstruction method utilized as initial condition a closed-form solution that integrates the advantages of two other closed-form solutions, referred to as the range and azimuth solutions. Synthetic data tests are given to provide insight into the merits of the new target imaging and 3-D reconstruction paradigm, while experiments with real data confirm the findings based on computer simulations, and demonstrate the merits of this novel 3-D reconstruction paradigm. PMID:19380272

  7. Fast and Precise 3D Fluorophore Localization based on Gradient Fitting

    NASA Astrophysics Data System (ADS)

    Ma, Hongqiang; Xu, Jianquan; Jin, Jingyi; Gao, Ying; Lan, Li; Liu, Yang

    2015-09-01

    Astigmatism imaging approach has been widely used to encode the fluorophore’s 3D position in single-particle tracking and super-resolution localization microscopy. Here, we present a new high-speed localization algorithm based on gradient fitting to precisely decode the 3D subpixel position of the fluorophore. This algebraic algorithm determines the center of the fluorescent emitter by finding the position with the best-fit gradient direction distribution to the measured point spread function (PSF), and can retrieve the 3D subpixel position of the fluorophore in a single iteration. Through numerical simulation and experiments with mammalian cells, we demonstrate that our algorithm yields comparable localization precision to the traditional iterative Gaussian function fitting (GF) based method, while exhibits over two orders-of-magnitude faster execution speed. Our algorithm is a promising high-speed analyzing method for 3D particle tracking and super-resolution localization microscopy.

  8. Fast and Precise 3D Fluorophore Localization based on Gradient Fitting

    PubMed Central

    Ma, Hongqiang; Xu, Jianquan; Jin, Jingyi; Gao, Ying; Lan, Li; Liu, Yang

    2015-01-01

    Astigmatism imaging approach has been widely used to encode the fluorophore’s 3D position in single-particle tracking and super-resolution localization microscopy. Here, we present a new high-speed localization algorithm based on gradient fitting to precisely decode the 3D subpixel position of the fluorophore. This algebraic algorithm determines the center of the fluorescent emitter by finding the position with the best-fit gradient direction distribution to the measured point spread function (PSF), and can retrieve the 3D subpixel position of the fluorophore in a single iteration. Through numerical simulation and experiments with mammalian cells, we demonstrate that our algorithm yields comparable localization precision to the traditional iterative Gaussian function fitting (GF) based method, while exhibits over two orders-of-magnitude faster execution speed. Our algorithm is a promising high-speed analyzing method for 3D particle tracking and super-resolution localization microscopy. PMID:26390959

  9. Local 3D matrix microenvironment regulates cell migration through spatiotemporal dynamics of contractility-dependent adhesions.

    PubMed

    Doyle, Andrew D; Carvajal, Nicole; Jin, Albert; Matsumoto, Kazue; Yamada, Kenneth M

    2015-01-01

    The physical properties of two-dimensional (2D) extracellular matrices (ECMs) modulate cell adhesion dynamics and motility, but little is known about the roles of local microenvironmental differences in three-dimensional (3D) ECMs. Here we generate 3D collagen gels of varying matrix microarchitectures to characterize their regulation of 3D adhesion dynamics and cell migration. ECMs containing bundled fibrils demonstrate enhanced local adhesion-scale stiffness and increased adhesion stability through balanced ECM/adhesion coupling, whereas highly pliable reticular matrices promote adhesion retraction. 3D adhesion dynamics are locally regulated by ECM rigidity together with integrin/ECM association and myosin II contractility. Unlike 2D migration, abrogating contractility stalls 3D migration regardless of ECM pore size. We find force is not required for clustering of activated integrins on 3D native collagen fibrils. We propose that efficient 3D migration requires local balancing of contractility with ECM stiffness to stabilize adhesions, which facilitates the detachment of activated integrins from ECM fibrils. PMID:26548801

  10. Local 3D matrix microenvironment regulates cell migration through spatiotemporal dynamics of contractility-dependent adhesions

    PubMed Central

    Doyle, Andrew D.; Carvajal, Nicole; Jin, Albert; Matsumoto, Kazue; Yamada, Kenneth M.

    2015-01-01

    The physical properties of two-dimensional (2D) extracellular matrices (ECMs) modulate cell adhesion dynamics and motility, but little is known about the roles of local microenvironmental differences in three-dimensional (3D) ECMs. Here we generate 3D collagen gels of varying matrix microarchitectures to characterize their regulation of 3D adhesion dynamics and cell migration. ECMs containing bundled fibrils demonstrate enhanced local adhesion-scale stiffness and increased adhesion stability through balanced ECM/adhesion coupling, whereas highly pliable reticular matrices promote adhesion retraction. 3D adhesion dynamics are locally regulated by ECM rigidity together with integrin/ECM association and myosin II contractility. Unlike 2D migration, abrogating contractility stalls 3D migration regardless of ECM pore size. We find force is not required for clustering of activated integrins on 3D native collagen fibrils. We propose that efficient 3D migration requires local balancing of contractility with ECM stiffness to stabilize adhesions, which facilitates the detachment of activated integrins from ECM fibrils. PMID:26548801

  11. Local 3D matrix microenvironment regulates cell migration through spatiotemporal dynamics of contractility-dependent adhesions

    NASA Astrophysics Data System (ADS)

    Doyle, Andrew D.; Carvajal, Nicole; Jin, Albert; Matsumoto, Kazue; Yamada, Kenneth M.

    2015-11-01

    The physical properties of two-dimensional (2D) extracellular matrices (ECMs) modulate cell adhesion dynamics and motility, but little is known about the roles of local microenvironmental differences in three-dimensional (3D) ECMs. Here we generate 3D collagen gels of varying matrix microarchitectures to characterize their regulation of 3D adhesion dynamics and cell migration. ECMs containing bundled fibrils demonstrate enhanced local adhesion-scale stiffness and increased adhesion stability through balanced ECM/adhesion coupling, whereas highly pliable reticular matrices promote adhesion retraction. 3D adhesion dynamics are locally regulated by ECM rigidity together with integrin/ECM association and myosin II contractility. Unlike 2D migration, abrogating contractility stalls 3D migration regardless of ECM pore size. We find force is not required for clustering of activated integrins on 3D native collagen fibrils. We propose that efficient 3D migration requires local balancing of contractility with ECM stiffness to stabilize adhesions, which facilitates the detachment of activated integrins from ECM fibrils.

  12. 3D Chemical Similarity Networks for Structure-Based Target Prediction and Scaffold Hopping.

    PubMed

    Lo, Yu-Chen; Senese, Silvia; Damoiseaux, Robert; Torres, Jorge Z

    2016-08-19

    Target identification remains a major challenge for modern drug discovery programs aimed at understanding the molecular mechanisms of drugs. Computational target prediction approaches like 2D chemical similarity searches have been widely used but are limited to structures sharing high chemical similarity. Here, we present a new computational approach called chemical similarity network analysis pull-down 3D (CSNAP3D) that combines 3D chemical similarity metrics and network algorithms for structure-based drug target profiling, ligand deorphanization, and automated identification of scaffold hopping compounds. In conjunction with 2D chemical similarity fingerprints, CSNAP3D achieved a >95% success rate in correctly predicting the drug targets of 206 known drugs. Significant improvement in target prediction was observed for HIV reverse transcriptase (HIVRT) compounds, which consist of diverse scaffold hopping compounds targeting the nucleotidyltransferase binding site. CSNAP3D was further applied to a set of antimitotic compounds identified in a cell-based chemical screen and identified novel small molecules that share a pharmacophore with Taxol and display a Taxol-like mechanism of action, which were validated experimentally using in vitro microtubule polymerization assays and cell-based assays. PMID:27285961

  13. A physical model eye with 3D resolution test targets for optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Hu, Zhixiong; Liu, Wenli; Hong, Baoyu; Hao, Bingtao; Wang, Lele; Li, Jiao

    2014-09-01

    Optical coherence tomography (OCT) has been widely employed as non-invasive 3D imaging diagnostic instrument, particularly in the field of ophthalmology. Although OCT has been approved for use in clinic in USA, Europe and Asia, international standardization of this technology is still in progress. Validation of OCT imaging capabilities is considered extremely important to ensure its effective use in clinical diagnoses. Phantom with appropriate test targets can assist evaluate and calibrate imaging performance of OCT at both installation and throughout lifetime of the instrument. In this paper, we design and fabricate a physical model eye with 3D resolution test targets to characterize OCT imaging performance. The model eye was fabricated with transparent resin to simulate realistic ophthalmic testing environment, and most key optical elements including cornea, lens and vitreous body were realized. The test targets which mimic USAF 1951 test chart were fabricated on the fundus of the model eye by 3D printing technology. Differing from traditional two dimensional USAF 1951 test chart, a group of patterns which have different thickness in depth were fabricated. By measuring the 3D test targets, axial resolution as well as lateral resolution of an OCT system can be evaluated at the same time with this model eye. To investigate this specialized model eye, it was measured by a scientific spectral domain OCT instrument and a clinical OCT system respectively. The results demonstrate that the model eye with 3D resolution test targets have the potential of qualitatively and quantitatively validating the performance of OCT systems.

  14. Image-based indoor localization system based on 3D SfM model

    NASA Astrophysics Data System (ADS)

    Lu, Guoyu; Kambhamettu, Chandra

    2013-12-01

    Indoor localization is an important research topic for both of the robot and signal processing communities. In recent years, image-based localization is also employed in indoor environment for the easy availability of the necessary equipment. After capturing an image and sending it to an image database, the best matching image is returned with the navigation information. By allowing further camera pose estimation, the image-based localization system with the use of Structure-from-Motion reconstruction model can achieve higher accuracy than the methods of searching through a 2D image database. However, this emerging technique is still only on the use of outdoor environment. In this paper, we introduce the 3D SfM model based image-based localization system into the indoor localization task. We capture images of the indoor environment and reconstruct the 3D model. On the localization task, we simply use the images captured by a mobile to match the 3D reconstructed model to localize the image. In this process, we use the visual words and the approximate nearest neighbor methods to accelerate the process of nding the query feature's correspondences. Within the visual words, we conduct linear search in detecting the correspondences. From the experiments, we nd that the image-based localization method based on 3D SfM model gives good localization result based on both accuracy and speed.

  15. A 3D interactive multi-object segmentation tool using local robust statistics driven active contours.

    PubMed

    Gao, Yi; Kikinis, Ron; Bouix, Sylvain; Shenton, Martha; Tannenbaum, Allen

    2012-08-01

    Extracting anatomical and functional significant structures renders one of the important tasks for both the theoretical study of the medical image analysis, and the clinical and practical community. In the past, much work has been dedicated only to the algorithmic development. Nevertheless, for clinical end users, a well designed algorithm with an interactive software is necessary for an algorithm to be utilized in their daily work. Furthermore, the software would better be open sourced in order to be used and validated by not only the authors but also the entire community. Therefore, the contribution of the present work is twofolds: first, we propose a new robust statistics based conformal metric and the conformal area driven multiple active contour framework, to simultaneously extract multiple targets from MR and CT medical imagery in 3D. Second, an open source graphically interactive 3D segmentation tool based on the aforementioned contour evolution is implemented and is publicly available for end users on multiple platforms. In using this software for the segmentation task, the process is initiated by the user drawn strokes (seeds) in the target region in the image. Then, the local robust statistics are used to describe the object features, and such features are learned adaptively from the seeds under a non-parametric estimation scheme. Subsequently, several active contours evolve simultaneously with their interactions being motivated by the principles of action and reaction-this not only guarantees mutual exclusiveness among the contours, but also no longer relies upon the assumption that the multiple objects fill the entire image domain, which was tacitly or explicitly assumed in many previous works. In doing so, the contours interact and converge to equilibrium at the desired positions of the desired multiple objects. Furthermore, with the aim of not only validating the algorithm and the software, but also demonstrating how the tool is to be used, we provide

  16. Novel 3-D laparoscopic magnetic ultrasound image guidance for lesion targeting

    PubMed Central

    Sindram, David; McKillop, Iain H; Martinie, John B; Iannitti, David A

    2010-01-01

    Objectives: Accurate laparoscopic liver lesion targeting for biopsy or ablation depends on the ability to merge laparoscopic and ultrasound images with proprioceptive instrument positioning, a skill that can be acquired only through extensive experience. The aim of this study was to determine whether using magnetic positional tracking to provide three-dimensional, real-time guidance improves accuracy during laparoscopic needle placement. Methods: Magnetic sensors were embedded into a needle and laparoscopic ultrasound transducer. These sensors interrupted the magnetic fields produced by an electromagnetic field generator, allowing for real-time, 3-D guidance on a stereoscopic monitor. Targets measuring 5 mm were embedded 3–5 cm deep in agar and placed inside a laparoscopic trainer box. Two novices (a college student and an intern) and two experts (hepatopancreatobiliary surgeons) targeted the lesions out of the ultrasound plane using either traditional or 3-D guidance. Results: Each subject targeted 22 lesions, 11 with traditional and 11 with the novel guidance (n = 88). Hit rates of 32% (14/44) and 100% (44/44) were observed with the traditional approach and the 3-D magnetic guidance approach, respectively. The novices were essentially unable to hit the targets using the traditional approach, but did not miss using the novel system. The hit rate of experts improved from 59% (13/22) to 100% (22/22) (P < 0.0001). Conclusions: The novel magnetic 3-D laparoscopic ultrasound guidance results in perfect targeting of 5-mm lesions, even by surgical novices. PMID:21083797

  17. Automatic loop closure detection using multiple cameras for 3D indoor localization

    NASA Astrophysics Data System (ADS)

    Kua, John; Corso, Nicholas; Zakhor, Avideh

    2012-03-01

    Automated 3D modeling of building interiors is useful in applications such as virtual reality and environment mapping. We have developed a human operated backpack data acquisition system equipped with a variety of sensors such as cameras, laser scanners, and orientation measurement sensors to generate 3D models of building interiors, including uneven surfaces and stairwells. An important intermediate step in any 3D modeling system, including ours, is accurate 6 degrees of freedom localization over time. In this paper, we propose two approaches to improve localization accuracy over our previously proposed methods. First, we develop an adaptive localization algorithm which takes advantage of the environment's floor planarity whenever possible. Secondly, we show that by including all the loop closures resulting from two cameras facing away from each other, it is possible to reduce localization error in scenarios where parts of the acquisition path is retraced. We experimentally characterize the performance gains due to both schemes.

  18. Modeling of Localized Neutral Particle Sources in 3D Edge Plasmas

    SciTech Connect

    Umansky, M V; Rognlien, T D; Fenstermacher, M E; Borchardt, M; Mutzke, A; Riemann, J; Schneider, R; Owen, L W

    2002-05-23

    A new edge plasma code BoRiS [1] has a fully 3D fluid plasma model. We supplement BoRiS with a 3D fluid neutral model including equations for parallel momentum and collisional perpendicular diffusion. This makes BoRiS an integrated plasma-neutral model suitable for a variety of applications. We present modeling results for a localized gas source in the geometry of the NCSX stellarator.

  19. Wide-field hyperspectral 3D imaging of functionalized gold nanoparticles targeting cancer cells by reflected light microscopy.

    PubMed

    Patskovsky, Sergiy; Bergeron, Eric; Rioux, David; Meunier, Michel

    2015-05-01

    We present a new hyperspectral reflected light microscopy system with a scanned broadband supercontinuum light source. This wide-field and low phototoxic hyperspectral imaging system has been successful for performing spectral three-dimensional (3D) localization and spectroscopic identification of CD44-targeted PEGylated AuNPs in fixed cell preparations. Such spatial and spectral information is essential for the improvement of nanoplasmonic-based imaging, disease detection and treatment in complex biological environment. The presented system can be used for real-time 3D NP tracking as spectral sensors, thus providing new avenues in the spatio-temporal characterization and detection of bioanalytes. 3D image of the distribution of functionalized AuNPs attached to CD44-expressing MDA-MB-231 human cancer cells. PMID:24961507

  20. Toward 3D-guided prostate biopsy target optimization: an estimation of tumor sampling probabilities

    NASA Astrophysics Data System (ADS)

    Martin, Peter R.; Cool, Derek W.; Romagnoli, Cesare; Fenster, Aaron; Ward, Aaron D.

    2014-03-01

    Magnetic resonance imaging (MRI)-targeted, 3D transrectal ultrasound (TRUS)-guided "fusion" prostate biopsy aims to reduce the ~23% false negative rate of clinical 2D TRUS-guided sextant biopsy. Although it has been reported to double the positive yield, MRI-targeted biopsy still yields false negatives. Therefore, we propose optimization of biopsy targeting to meet the clinician's desired tumor sampling probability, optimizing needle targets within each tumor and accounting for uncertainties due to guidance system errors, image registration errors, and irregular tumor shapes. We obtained multiparametric MRI and 3D TRUS images from 49 patients. A radiologist and radiology resident contoured 81 suspicious regions, yielding 3D surfaces that were registered to 3D TRUS. We estimated the probability, P, of obtaining a tumor sample with a single biopsy. Given an RMS needle delivery error of 3.5 mm for a contemporary fusion biopsy system, P >= 95% for 21 out of 81 tumors when the point of optimal sampling probability was targeted. Therefore, more than one biopsy core must be taken from 74% of the tumors to achieve P >= 95% for a biopsy system with an error of 3.5 mm. Our experiments indicated that the effect of error along the needle axis on the percentage of core involvement (and thus the measured tumor burden) was mitigated by the 18 mm core length.

  1. Automatic organ localizations on 3D CT images by using majority-voting of multiple 2D detections based on local binary patterns and Haar-like features

    NASA Astrophysics Data System (ADS)

    Zhou, Xiangrong; Yamaguchi, Shoutarou; Zhou, Xinxin; Chen, Huayue; Hara, Takeshi; Yokoyama, Ryujiro; Kanematsu, Masayuki; Fujita, Hiroshi

    2013-02-01

    This paper describes an approach to accomplish the fast and automatic localization of the different inner organ regions on 3D CT scans. The proposed approach combines object detections and the majority voting technique to achieve the robust and quick organ localization. The basic idea of proposed method is to detect a number of 2D partial appearances of a 3D target region on CT images from multiple body directions, on multiple image scales, by using multiple feature spaces, and vote all the 2D detecting results back to the 3D image space to statistically decide one 3D bounding rectangle of the target organ. Ensemble learning was used to train the multiple 2D detectors based on template matching on local binary patterns and Haar-like feature spaces. A collaborative voting was used to decide the corner coordinates of the 3D bounding rectangle of the target organ region based on the coordinate histograms from detection results in three body directions. Since the architecture of the proposed method (multiple independent detections connected to a majority voting) naturally fits the parallel computing paradigm and multi-core CPU hardware, the proposed algorithm was easy to achieve a high computational efficiently for the organ localizations on a whole body CT scan by using general-purpose computers. We applied this approach to localization of 12 kinds of major organ regions independently on 1,300 torso CT scans. In our experiments, we randomly selected 300 CT scans (with human indicated organ and tissue locations) for training, and then, applied the proposed approach with the training results to localize each of the target regions on the other 1,000 CT scans for the performance testing. The experimental results showed the possibility of the proposed approach to automatically locate different kinds of organs on the whole body CT scans.

  2. A Multiscale Constraints Method Localization of 3D Facial Feature Points

    PubMed Central

    Li, Hong-an; Zhang, Yongxin; Li, Zhanli; Li, Huilin

    2015-01-01

    It is an important task to locate facial feature points due to the widespread application of 3D human face models in medical fields. In this paper, we propose a 3D facial feature point localization method that combines the relative angle histograms with multiscale constraints. Firstly, the relative angle histogram of each vertex in a 3D point distribution model is calculated; then the cluster set of the facial feature points is determined using the cluster algorithm. Finally, the feature points are located precisely according to multiscale integral features. The experimental results show that the feature point localization accuracy of this algorithm is better than that of the localization method using the relative angle histograms. PMID:26539244

  3. Local 3D matrix confinement determines division axis through cell shape

    PubMed Central

    He, Lijuan; Chen, Weitong; Wu, Pei-Hsun; Jimenez, Angela; Wong, Bin Sheng; San, Angela; Konstantopoulos, Konstantinos; Wirtz, Denis

    2016-01-01

    How the division axis is determined in mammalian cells embedded in three-dimensional (3D) matrices remains elusive, despite that many types of cells divide in 3D environments. Cells on two-dimensional (2D) substrates typically round up completely to divide. Here, we show that in 3D collagen matrices, mammalian cells such as HT1080 human fibrosarcoma and MDA-MB-231 breast cancer cells exhibit division modes distinct from their Counterparts on 2D substrates, with a markedly higher fraction of cells remaining highly elongated through mitosis in 3D matrices. The long axis of elongated mitotic cells accurately predicts the division axis, independently of matrix density and cell-matrix interactions. This 3D-specific elongated division mode is determined by the local confinement produced by the matrix and the ability of cells to protrude and locally remodel the matrix via β1 integrin. Elongated division is readily recapitulated using collagen-coated microfabricated channels. Cells depleted of β1 integrin still divide in the elongated mode in microchannels, suggesting that 3D confinement is sufficient to induce the elongated cell-division phenotype. PMID:26515603

  4. 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.

  5. Universal gates based on targeted phase shifts in a 3D neutral atom array

    NASA Astrophysics Data System (ADS)

    Kumar, Aishwarya; Wang, Yang; Wu, Tsung-Yao; Weiss, David

    2016-05-01

    We demonstrate a new approach to making targeted single qubit gates using Cesium atoms in a 5x5x5 3D neutral atom array. It combines targeted AC Zeeman phase shifts with global microwave pulses to produce arbitrary single qubit gates. Non-targeted atoms are left virtually untouched by the gates. We have addressed 48 sites, targeted individually, in a 40% full array. We have also performed Randomized Benchmarking to characterize the fidelity and crosstalk errors of this gate. These gates are highly insensitive to addressing beam imperfections and can be applied to other systems and geometries. Supported by NSF.

  6. 3D numerical thermal stress analysis of the high power target for the SLC Positron Source

    SciTech Connect

    Reuter, E.M.; Hodgson, J.A.

    1991-05-01

    The volumetrically nonuniform power deposition of the incident 33 GeV electron beam in the SLC Positron Source Target is hypothesized to be the most likely cause target failure. The resultant pulsed temperature distributions are known to generate complicated stress fields with no known closed-form analytical solution. 3D finite element analyses of these temperature distributions and associated thermal stress fields in the new High Power Target are described here. Operational guidelines based on the results of these analyses combined with assumptions made about the fatigue characteristics of the exotic target material are proposed. 6 refs., 4 figs.

  7. 3D modelling of the electromagnetic response of geophysical targets using the FDTD method

    SciTech Connect

    Debroux, P.S.

    1996-05-01

    A publicly available and maintained electromagnetic finite-difference time domain (FDTD) code has been applied to the forward modelling of the response of 1D, 2D and 3D geophysical targets to a vertical magnetic dipole excitation. The FDTD method is used to analyze target responses in the 1 MHz to 100 MHz range, where either conduction or displacement currents may have the controlling role. The response of the geophysical target to the excitation is presented as changes in the magnetic field ellipticity. The results of the FDTD code compare favorably with previously published integral equation solutions of the response of 1D targets, and FDTD models calculated with different finite-difference cell sizes are compared to find the effect of model discretization on the solution. The discretization errors, calculated as absolute error in ellipticity, are presented for the different ground geometry models considered, and are, for the most part, below 10% of the integral equation solutions. Finally, the FDTD code is used to calculate the magnetic ellipticity response of a 2D survey and a 3D sounding of complicated geophysical targets. The response of these 2D and 3D targets are too complicated to be verified with integral equation solutions, but show the proper low- and high-frequency responses.

  8. A new look at spotlight mode synthetic aperture radar as tomography: imaging 3-D targets.

    PubMed

    Jakowatz, C V; Thompson, P A

    1995-01-01

    A new 3D tomographic formulation of spotlight mode synthetic aperture radar (SAR) is developed. This extends the pioneering work of Munson et al. (1983), who first formally described SAR in terms of tomography but who made the simplifying assumption that the target scene was 2D. The present authors treat the more general and practical case in which the radar target reflectivities comprise a 3D function. The main goal is to demonstrate that the demodulated radar return data from a spotlight mode collection represent a certain set of samples of the 3D Fourier transform of the target reflectivity function and to do so using a tomographic paradigm instead of traditional range-Doppler analysis. They also show that the tomographic approach is useful in interpreting the reconstructed 2D SAR image corresponding to a 3D scene. Specifically, the well-known SAR phenomenon of layover is easily explained in terms of tomographic projections and is shown to be analogous to the projection effect in conventional optical imaging. PMID:18290021

  9. Automated Identification and Localization of Hematopoietic Stem Cells in 3D Intravital Microscopy Data

    PubMed Central

    Khorshed, Reema A.; Hawkins, Edwin D.; Duarte, Delfim; Scott, Mark K.; Akinduro, Olufolake A.; Rashidi, Narges M.; Spitaler, Martin; Lo Celso, Cristina

    2015-01-01

    Summary Measuring three-dimensional (3D) localization of hematopoietic stem cells (HSCs) within the bone marrow microenvironment using intravital microscopy is a rapidly expanding research theme. This approach holds the key to understanding the detail of HSC-niche interactions, which are critical for appropriate stem cell function. Due to the complex tissue architecture of the bone marrow and to the progressive introduction of scattering and signal loss at increasing imaging depths, there is no ready-made software to handle efficient segmentation and unbiased analysis of the data. To address this, we developed an automated image analysis tool that simplifies and standardizes the biological interpretation of 3D HSC microenvironment images. The algorithm identifies HSCs and measures their localization relative to surrounding osteoblast cells and bone collagen. We demonstrate here the effectiveness, consistency, and accuracy of the proposed approach compared to current manual analysis and its wider applicability to analyze other 3D bone marrow components. PMID:26120058

  10. Eccentricity in Images of Circular and Spherical Targets and its Impact to 3D Object Reconstruction

    NASA Astrophysics Data System (ADS)

    Luhmann, T.

    2014-06-01

    This paper discusses a feature of projective geometry which causes eccentricity in the image measurement of circular and spherical targets. While it is commonly known that flat circular targets can have a significant displacement of the elliptical image centre with respect to the true imaged circle centre, it can also be shown that the a similar effect exists for spherical targets. Both types of targets are imaged with an elliptical contour. As a result, if measurement methods based on ellipses are used to detect the target (e.g. best-fit ellipses), the calculated ellipse centre does not correspond to the desired target centre in 3D space. This paper firstly discusses the use and measurement of circular and spherical targets. It then describes the geometrical projection model in order to demonstrate the eccentricity in image space. Based on numerical simulations, the eccentricity in the image is further quantified and investigated. Finally, the resulting effect in 3D space is estimated for stereo and multi-image intersections. It can be stated that the eccentricity is larger than usually assumed, and must be compensated for high-accuracy applications. Spherical targets do not show better results than circular targets. The paper is an updated version of Luhmann (2014) new experimental investigations on the effect of length measurement errors.

  11. SU-E-J-231: Comparison of 3D Angiogram and MRI in Delineating the AVM Target for Frameless Stereotactic Radiosurgery

    SciTech Connect

    Avkshtol, V; Tanny, S; Reddy, K; Chen, C; Parsai, E

    2014-06-01

    Purpose: Stereotactic radiation therapy (SRT) provides an excellent alternative to embolization and surgical excision for the management of appropriately selected cerebral arteriovenous malformations (AVMs). The currently accepted standard for delineating AVMs is planar digital subtraction angiography (DSA). DSA can be used to acquire a 3D data set that preserves osseous structures (3D-DA) at the time of the angiography for SRT planning. Magnetic resonance imaging (MRI) provides an alternative noninvasive method of visualizing the AVM nidus with comparable spatial resolution. We utilized 3D-DA and T1 post-contrast MRI data to evaluate the differences in SRT target volumes. Methods: Four patients underwent 3D-DA and high-resolution MRI. 3D T1 post-contrast images were obtained in all three reconstruction planes. A planning CT was fused with MRI and 3D-DA data sets. The AVMs were contoured utilizing one of the image sets at a time. Target volume, centroid, and maximum and minimum dimensions were analyzed for each patient. Results: Targets delineated using post-contrast MRI demonstrated a larger mean volume. AVMs >2 cc were found to have a larger difference between MRI and 3D-DA volumes. Larger AVMs also demonstrated a smaller relative uncertainty in contour centroid position (1 mm). AVM targets <2 cc had smaller absolute differences in volume, but larger differences in contour centroid position (2.5 mm). MRI targets demonstrated a more irregular shape compared to 3D-DA targets. Conclusions: Our preliminary data supports the use of MRI alone to delineate AVM targets >2 cc. The greater centroid stability for AVMs >2 cc ensures accurate target localization during image fusion. The larger MRI target volumes did not result in prohibitively greater volumes of normal brain tissue receiving the prescription dose. The larger centroid instability for AVMs <2 cc precludes the use of MRI alone for target delineation. We recommend incorporating a 3D-DA for these patients.

  12. Relativistic Laser Pulse Intensification with 3D Printed Micro-Tube Plasma Target

    NASA Astrophysics Data System (ADS)

    Ji, Liangliang; Snyder, Joseph; Pukhov, Alexander; Akli, Kramer

    2015-11-01

    The potential and applications of laser-plasma interactions (LPI) are restricted by the parameter space of existing lasers and targets. Advancing the laser intensity to the extreme regime is motivated by the production of energetic particle beams and by the quest to explore the exotic regimes of light-matter interaction. Target density and dimensions can always be varied to optimize the outcome. Here, we propose to create another degree of freedom in the parameter space of LPI using recent advances in 3D printing of materials. Fine structures at nm scale with high repetition and accuracy can nowadays be manufactured, allowing for a full precise control of the target. We demonstrate, via particle-in-cell (PIC) simulations, that 3D-printed micro-tube plasma (MTP) targets yield an intensity enhancement factor of 2-5. The novel MTP targets not only act as a plasma optical device to reach the 1023W/cm2 threshold based on today's intensities, but can also boost the generation of secondary particle and radiation sources. This work demonstrates that the combination of high contrast high power lasers and nano-3D printing techniques opens new paths in the intensity frontier and LPI micro-engineering.

  13. Bone segmentation and fracture detection in ultrasound using 3D local phase features.

    PubMed

    Hacihaliloglu, Ilker; Abugharbieh, Rafeef; Hodgson, Antony; Rohling, Robert

    2008-01-01

    3D ultrasound (US) is increasingly considered as a viable alternative imaging modality in computer-assisted orthopaedic surgery (CAOS) applications. Automatic bone segmentation from US images, however, remains a challenge due to speckle noise and various other artifacts inherent to US. In this paper, we present intensity invariant three dimensional (3D) local image phase features, obtained using 3D Log-Gabor filter banks, for extracting ridge-like features similar to those that occur at soft tissue/bone interfaces. Our contributions include the novel extension of 2D phase symmetry features to 3D and their use in automatic extraction of bone surfaces and fractured fragments in 3D US. We validate our technique using phantom, in vitro, and in vivo experiments. Qualitative and quantitative results demonstrate remarkably clear segmentations results of bone surfaces with a localization accuracy of better than 0.62 mm and mean errors in estimating fracture displacements below 0.65 mm, which will likely be of strong clinical utility. PMID:18979759

  14. 3D laser scanning microscopy of hypervelocity impact features in metal and aerogel targets

    NASA Astrophysics Data System (ADS)

    Hillier, J. K.; Postberg, F.; Price, M. C.; Trieloff, M.; Li, Y. W.; Srama, R.

    2012-09-01

    We present the results of a study into the mapping of hypervelocity impact features using a Keyence VK-X200 3D laser scanning microscope. The impact features observed are impact craters in a variety of different metal targets (Al, Au and Cu) and impact tracks in aerogel targets, similar to those used in the Stardust mission. Differences in crater morphology between different target materials and impact velocities, as well as differences in track depth and diameter in aerogel, for particles of known constant dimensions, are discussed.

  15. 3D graph segmentation for target detection in FOPEN LiDAR data

    NASA Astrophysics Data System (ADS)

    Shorter, Nicholas; Locke, Judson; Smith, O'Neil; Keating, Emma; Smith, Philip

    2013-05-01

    A novel use of Felzenszwalb's graph based efficient image segmentation algorithm* is proposed for segmenting 3D volumetric foliage penetrating (FOPEN) Light Detection and Ranging (LiDAR) data for automated target detection. The authors propose using an approximate nearest neighbors algorithm to establish neighbors of points in 3D and thus form the graph for segmentation. Following graph formation, the angular difference in the points' estimated normal vectors is proposed for the graph edge weights. Then the LiDAR data is segmented, in 3D, and metrics are calculated from the segments to determine their geometrical characteristics and thus likelihood of being a target. Finally, the bare earth within the scene is automatically identified to avoid confusion of flat bare earth with flat targets. The segmentation, the calculated metrics, and the bare earth all culminate in a target detection system deployed for FOPEN LiDAR. General purpose graphics processing units (GPGPUs) are leveraged to reduce processing times for the approximate nearest neighbors and point normal estimation algorithms such that the application can be run in near real time. Results are presented on several data sets.

  16. 3D Geometry and Motion Estimations of Maneuvering Targets for Interferometric ISAR With Sparse Aperture.

    PubMed

    Xu, Gang; Xing, Mengdao; Xia, Xiang-Gen; Zhang, Lei; Chen, Qianqian; Bao, Zheng

    2016-05-01

    In the current scenario of high-resolution inverse synthetic aperture radar (ISAR) imaging, the non-cooperative targets may have strong maneuverability, which tends to cause time-variant Doppler modulation and imaging plane in the echoed data. Furthermore, it is still a challenge to realize ISAR imaging of maneuvering targets from sparse aperture (SA) data. In this paper, we focus on the problem of 3D geometry and motion estimations of maneuvering targets for interferometric ISAR (InISAR) with SA. For a target of uniformly accelerated rotation, the rotational modulation in echo is formulated as chirp sensing code under a chirp-Fourier dictionary to represent the maneuverability. In particular, a joint multi-channel imaging approach is developed to incorporate the multi-channel data and treat the multi-channel ISAR image formation as a joint-sparsity constraint optimization. Then, a modified orthogonal matching pursuit (OMP) algorithm is employed to solve the optimization problem to produce high-resolution range-Doppler (RD) images and chirp parameter estimation. The 3D target geometry and the motion estimations are followed by using the acquired RD images and chirp parameters. Herein, a joint estimation approach of 3D geometry and rotation motion is presented to realize outlier removing and error reduction. In comparison with independent single-channel processing, the proposed joint multi-channel imaging approach performs better in 2D imaging, 3D imaging, and motion estimation. Finally, experiments using both simulated and measured data are performed to confirm the effectiveness of the proposed algorithm. PMID:26930684

  17. Local-global alignment for finding 3D similarities in protein structures

    DOEpatents

    Zemla, Adam T.

    2011-09-20

    A method of finding 3D similarities in protein structures of a first molecule and a second molecule. The method comprises providing preselected information regarding the first molecule and the second molecule. Comparing the first molecule and the second molecule using Longest Continuous Segments (LCS) analysis. Comparing the first molecule and the second molecule using Global Distance Test (GDT) analysis. Comparing the first molecule and the second molecule using Local Global Alignment Scoring function (LGA_S) analysis. Verifying constructed alignment and repeating the steps to find the regions of 3D similarities in protein structures.

  18. Improvement of 3d Monte Carlo Localization Using a Depth Camera and Terrestrial Laser Scanner

    NASA Astrophysics Data System (ADS)

    Kanai, S.; Hatakeyama, R.; Date, H.

    2015-05-01

    Effective and accurate localization method in three-dimensional indoor environments is a key requirement for indoor navigation and lifelong robotic assistance. So far, Monte Carlo Localization (MCL) has given one of the promising solutions for the indoor localization methods. Previous work of MCL has been mostly limited to 2D motion estimation in a planar map, and a few 3D MCL approaches have been recently proposed. However, their localization accuracy and efficiency still remain at an unsatisfactory level (a few hundreds millimetre error at up to a few FPS) or is not fully verified with the precise ground truth. Therefore, the purpose of this study is to improve an accuracy and efficiency of 6DOF motion estimation in 3D MCL for indoor localization. Firstly, a terrestrial laser scanner is used for creating a precise 3D mesh model as an environment map, and a professional-level depth camera is installed as an outer sensor. GPU scene simulation is also introduced to upgrade the speed of prediction phase in MCL. Moreover, for further improvement, GPGPU programming is implemented to realize further speed up of the likelihood estimation phase, and anisotropic particle propagation is introduced into MCL based on the observations from an inertia sensor. Improvements in the localization accuracy and efficiency are verified by the comparison with a previous MCL method. As a result, it was confirmed that GPGPU-based algorithm was effective in increasing the computational efficiency to 10-50 FPS when the number of particles remain below a few hundreds. On the other hand, inertia sensor-based algorithm reduced the localization error to a median of 47mm even with less number of particles. The results showed that our proposed 3D MCL method outperforms the previous one in accuracy and efficiency.

  19. Block design enhances classification of 3D reach targets from electroencephalographic signals.

    PubMed

    Sosnik, Ronen; Tadipatri, Vijay Aditya; Tewfik, Ahmed H; Pellizzer, Giuseppe

    2016-08-01

    To date, decoding accuracy of actual or imagined pointing movements to targets in 3D space from electroencephalographic (EEG) signals has remained modest. The reason may pertain to the fact that these movements activate essentially the same neural networks. In this study, we aimed at testing whether repetitive pointing movements to each of the targets promotes the development of segregated neural patterns, resulting in enhanced decoding accuracy. Six human subjects generated slow or fast repetitive pointing movements with their right dominant arm to one of five targets distributed in 3D space, followed by repetitive imagery of movements to the same target or to a different target. Nine naive subjects generated both repetitive and non-repetitive slow actual movements to each of the five targets to test the effect of block design on decoding accuracy. In order to assure that base line drift and low frequency motion artifacts do not contaminate the data, the data were high-pass filtered in 4-30Hz, leaving out the delta and gamma band. For the repetitive trials, the model decoded target location with 81% accuracy, which is significantly higher than chance level. The average decoding rate of target location was only 30% for the non-repetitive trials, which is not significantly different than chance level. A subset of electrodes, mainly over the contralateral sensorimotor areas, was found to provide most of the discriminative features for all tested conditions. Time proximity between trained and tested blocks was found to enhance decoding accuracy of target location both by target non-specific and specific mechanisms. Our findings suggest that movement repetition promotes the development of distinct neural patterns, presumably by the formation of target-specific kinesthetic memory. PMID:27223628

  20. Nodes Localization in 3D Wireless Sensor Networks Based on Multidimensional Scaling Algorithm

    PubMed Central

    2014-01-01

    In the recent years, there has been a huge advancement in wireless sensor computing technology. Today, wireless sensor network (WSN) has become a key technology for different types of smart environment. Nodes localization in WSN has arisen as a very challenging problem in the research community. Most of the applications for WSN are not useful without a priory known nodes positions. Adding GPS receivers to each node is an expensive solution and inapplicable for indoor environments. In this paper, we implemented and evaluated an algorithm based on multidimensional scaling (MDS) technique for three-dimensional (3D) nodes localization in WSN using improved heuristic method for distance calculation. Using extensive simulations we investigated our approach regarding various network parameters. We compared the results from the simulations with other approaches for 3D-WSN localization and showed that our approach outperforms other techniques in terms of accuracy.

  1. 3D Ultrasound Can Contribute to Planning CT to Define the Target for Partial Breast Radiotherapy

    SciTech Connect

    Berrang, Tanya S.; Truong, Pauline T. Popescu, Carmen; Drever, Laura; Kader, Hosam A.; Hilts, Michelle L.; Mitchell, Tracy; Soh, S.Y.; Sands, Letricia; Silver, Stuart; Olivotto, Ivo A.

    2009-02-01

    Purpose: The role of three-dimensional breast ultrasound (3D US) in planning partial breast radiotherapy (PBRT) is unknown. This study evaluated the accuracy of coregistration of 3D US to planning computerized tomography (CT) images, the seroma contouring consistency of radiation oncologists using the two imaging modalities and the clinical situations in which US was associated with improved contouring consistency compared to CT. Materials and Methods: Twenty consecutive women with early-stage breast cancer were enrolled prospectively after breast-conserving surgery. Subjects underwent 3D US at CT simulation for adjuvant RT. Three radiation oncologists independently contoured the seroma on separate CT and 3D US image sets. Seroma clarity, seroma volumes, and interobserver contouring consistency were compared between the imaging modalities. Associations between clinical characteristics and seroma clarity were examined using Pearson correlation statistics. Results: 3D US and CT coregistration was accurate to within 2 mm or less in 19/20 (95%) cases. CT seroma clarity was reduced with dense breast parenchyma (p = 0.035), small seroma volume (p < 0.001), and small volume of excised breast tissue (p = 0.01). US seroma clarity was not affected by these factors (p = NS). US was associated with improved interobserver consistency compared with CT in 8/20 (40%) cases. Of these 8 cases, 7 had low CT seroma clarity scores and 4 had heterogeneously to extremely dense breast parenchyma. Conclusion: 3D US can be a useful adjunct to CT in planning PBRT. Radiation oncologists were able to use US images to contour the seroma target, with improved interobserver consistency compared with CT in cases with dense breast parenchyma and poor CT seroma clarity.

  2. Photon-counting passive 3D image sensing and processing for automatic target recognition

    NASA Astrophysics Data System (ADS)

    Yeom, Seokwon; Javidi, Bahram; Watson, Edward

    2008-04-01

    In this paper we overview the nonlinear matched filtering for photon counting recognition with 3D passive sensing. The first and second order statistical properties of the nonlinear matched filtering can improve the recognition performance compared to the linear matched filtering. Automatic target reconstruction and recognition are addressed for partially occluded objects. The recognition performance is shown to be improved significantly in the reconstruction space. The discrimination capability is analyzed in terms of Fisher ratio (FR) and receiver operating characteristic (ROC) curves.

  3. Multisensor fusion for 3D target tracking using track-before-detect particle filter

    NASA Astrophysics Data System (ADS)

    Moshtagh, Nima; Romberg, Paul M.; Chan, Moses W.

    2015-05-01

    This work presents a novel fusion mechanism for estimating the three-dimensional trajectory of a moving target using images collected by multiple imaging sensors. The proposed projective particle filter avoids the explicit target detection prior to fusion. In projective particle filter, particles that represent the posterior density (of target state in a high-dimensional space) are projected onto the lower-dimensional observation space. Measurements are generated directly in the observation space (image plane) and a marginal (sensor) likelihood is computed. The particles states and their weights are updated using the joint likelihood computed from all the sensors. The 3D state estimate of target (system track) is then generated from the states of the particles. This approach is similar to track-before-detect particle filters that are known to perform well in tracking dim and stealthy targets in image collections. Our approach extends the track-before-detect approach to 3D tracking using the projective particle filter. The performance of this measurement-level fusion method is compared with that of a track-level fusion algorithm using the projective particle filter. In the track-level fusion algorithm, the 2D sensor tracks are generated separately and transmitted to a fusion center, where they are treated as measurements to the state estimator. The 2D sensor tracks are then fused to reconstruct the system track. A realistic synthetic scenario with a boosting target was generated, and used to study the performance of the fusion mechanisms.

  4. Characterizing the effects of droplines on target acquisition performance on a 3-D perspective display

    NASA Technical Reports Server (NTRS)

    Liao, Min-Ju; Johnson, Walter W.

    2004-01-01

    The present study investigated the effects of droplines on target acquisition performance on a 3-D perspective display in which participants were required to move a cursor into a target cube as quickly as possible. Participants' performance and coordination strategies were characterized using both Fitts' law and acquisition patterns of the 3 viewer-centered target display dimensions (azimuth, elevation, and range). Participants' movement trajectories were recorded and used to determine movement times for acquisitions of the entire target and of each of its display dimensions. The goodness of fit of the data to a modified Fitts function varied widely among participants, and the presence of droplines did not have observable impacts on the goodness of fit. However, droplines helped participants navigate via straighter paths and particularly benefited range dimension acquisition. A general preference for visually overlapping the target with the cursor prior to capturing the target was found. Potential applications of this research include the design of interactive 3-D perspective displays in which fast and accurate selection and manipulation of content residing at multiple ranges may be a challenge.

  5. The Donegal Sign Tree: A Local Legend Confirmed with Holographic Radar and 3-D Magnetics

    NASA Astrophysics Data System (ADS)

    Bechtel, T.; Cassidy, M.; Inagaki, M.; Windsor, C.; Capineri, L.; Falorni, P.; Bulleti, A.; Valentini, S.; Borgioli, G.; Ivashov, S.; Zhuravlev, A.; Razewig, V.; Vasiliev, I.; Bechtel, E.

    2009-05-01

    A tree at a crossroad in Historic Donegal, PA (founded 1722) bears unusual burls. Two are similar in size, and lie on opposite sides of the trunk at a height of six feet. Locals say that the tree engulfed an old road sign, and the geometry of the burls gives this appearance. However, the trunk between these two burls bears no welt where it sealed after swallowing the sign. In addition, there are other burls farther up the tree, which are not consistent with engulfed signs. Although the locals all know the legend of the swallowed sign, none ever actually saw the sign; not even an octogenarian who has lived at the crossroad his entire life, and recalls the tree as a child just as it is today. In order to test the veracity of the legend, this study performed subsurface imaging of the tree using holographic subsurface radar (Rascan), and 3-D measurements of the magnetic field about the tree using cesium vapor sensors. The Rascan system used is a continuous wave subsurface radar that operates at 5 discrete frequencies between 1.5 and 2.0 GHz. Reflections from subsurface objects are recorded as the phase difference pattern between an internal reference signal, and the reflected signal. Thus, it is a microwave analogy for optical holography. Rascan records reflections with two receiving antennae - parallel and perpendicular to the transmitter - so a single set of scans provides ten images; five frequencies at two polarizations. This ensures that an object at arbitrary depth will produce a strong phase difference in one of the images. As a consequence, elongate objects that are angled from the plane of scanning (e.g. a dipping sheet) produce "zebra stripes" of contrast values that vary cyclically with depth. The presence of stripes, and their relative positions in the different frequency images (the movement of which has been dubbed the "zebra shift") is useful for determining the relative depth of different portions of a dipping planar, or curved subsurface object. Rascan

  6. 3-D crustal velocity model for Lithuania and its application to local event studies

    NASA Astrophysics Data System (ADS)

    Kozlovskaya, Elena; Budraitis, Mantas; Janutyte, Ilma; Motuza, Gediminas; Lazauskiene, Jurga; Passeq-Working Group

    2010-05-01

    PASSEQ 2006-2008 project (PASsive Seismic Experiment in TESZ) aimed at studying the lithosphere-asthenosphere system around the TransEuropean Suture Zone (TESZ)- the transition between old Proterozoic platform of north and east Europe and younger Phanerozoic platform in central and western Europe. The experiment was a seismic array research aiming to retrieve the structure of the crust and Earth's mantle down to the mantle transition zone, including mapping of upper mantle seismic velocity variations and discontinuities (Moho, lithosphere-asthenosphere boundary, mantle transition zone) using all available techniques. During the experiment 26 seismic stations (including four broadband stations) were installed in Lithuania. One of the main targets of PASSEQ deployment in Lithuania was identification and characterization of the local seismic activity. The PASSEQ stations in Lithuania were in operation since June, 2006 till January, 2008. During this period a number of local seismic events was recorded and preliminary event location was made using the LocSat algorithm and 1-D velocity model. This standard procedure is not enough precise for Lithuania, however, because the thickness of the crust varies significantly in the region (from 45 to 55 km). In order to improve event location, we separated the events into several groups and located each group separately using a VELEST algorithms and own 1-D velocity model for each group. We also compiled a 3-D seismic velocity of the crust down to a depth of 60 km. The model, consisting of four major layers (sediments, upper crust, middle crust, lower crust and uppermost mantle) was interpolated from 2-D velocity models along previous wide-angle reflection and refraction profiles into a regular grid. The quality of the approximation was analysed using comparison of travel times of P-waves recorded along previous controlled source profiles and synthetic travel times calculated using the 3-D velocity model. The model was converted

  7. Uniform Local Binary Pattern Based Texture-Edge Feature for 3D Human Behavior Recognition

    PubMed Central

    Ming, Yue; Wang, Guangchao; Fan, Chunxiao

    2015-01-01

    With the rapid development of 3D somatosensory technology, human behavior recognition has become an important research field. Human behavior feature analysis has evolved from traditional 2D features to 3D features. In order to improve the performance of human activity recognition, a human behavior recognition method is proposed, which is based on a hybrid texture-edge local pattern coding feature extraction and integration of RGB and depth videos information. The paper mainly focuses on background subtraction on RGB and depth video sequences of behaviors, extracting and integrating historical images of the behavior outlines, feature extraction and classification. The new method of 3D human behavior recognition has achieved the rapid and efficient recognition of behavior videos. A large number of experiments show that the proposed method has faster speed and higher recognition rate. The recognition method has good robustness for different environmental colors, lightings and other factors. Meanwhile, the feature of mixed texture-edge uniform local binary pattern can be used in most 3D behavior recognition. PMID:25942404

  8. Uniform Local Binary Pattern Based Texture-Edge Feature for 3D Human Behavior Recognition.

    PubMed

    Ming, Yue; Wang, Guangchao; Fan, Chunxiao

    2015-01-01

    With the rapid development of 3D somatosensory technology, human behavior recognition has become an important research field. Human behavior feature analysis has evolved from traditional 2D features to 3D features. In order to improve the performance of human activity recognition, a human behavior recognition method is proposed, which is based on a hybrid texture-edge local pattern coding feature extraction and integration of RGB and depth videos information. The paper mainly focuses on background subtraction on RGB and depth video sequences of behaviors, extracting and integrating historical images of the behavior outlines, feature extraction and classification. The new method of 3D human behavior recognition has achieved the rapid and efficient recognition of behavior videos. A large number of experiments show that the proposed method has faster speed and higher recognition rate. The recognition method has good robustness for different environmental colors, lightings and other factors. Meanwhile, the feature of mixed texture-edge uniform local binary pattern can be used in most 3D behavior recognition. PMID:25942404

  9. 2D image classification for 3D anatomy localization: employing deep convolutional neural networks

    NASA Astrophysics Data System (ADS)

    de Vos, Bob D.; Wolterink, Jelmer M.; de Jong, Pim A.; Viergever, Max A.; Išgum, Ivana

    2016-03-01

    Localization of anatomical regions of interest (ROIs) is a preprocessing step in many medical image analysis tasks. While trivial for humans, it is complex for automatic methods. Classic machine learning approaches require the challenge of hand crafting features to describe differences between ROIs and background. Deep convolutional neural networks (CNNs) alleviate this by automatically finding hierarchical feature representations from raw images. We employ this trait to detect anatomical ROIs in 2D image slices in order to localize them in 3D. In 100 low-dose non-contrast enhanced non-ECG synchronized screening chest CT scans, a reference standard was defined by manually delineating rectangular bounding boxes around three anatomical ROIs -- heart, aortic arch, and descending aorta. Every anatomical ROI was automatically identified using a combination of three CNNs, each analyzing one orthogonal image plane. While single CNNs predicted presence or absence of a specific ROI in the given plane, the combination of their results provided a 3D bounding box around it. Classification performance of each CNN, expressed in area under the receiver operating characteristic curve, was >=0.988. Additionally, the performance of ROI localization was evaluated. Median Dice scores for automatically determined bounding boxes around the heart, aortic arch, and descending aorta were 0.89, 0.70, and 0.85 respectively. The results demonstrate that accurate automatic 3D localization of anatomical structures by CNN-based 2D image classification is feasible.

  10. Multi-Camera Sensor System for 3D Segmentation and Localization of Multiple Mobile Robots

    PubMed Central

    Losada, Cristina; Mazo, Manuel; Palazuelos, Sira; Pizarro, Daniel; Marrón, Marta

    2010-01-01

    This paper presents a method for obtaining the motion segmentation and 3D localization of multiple mobile robots in an intelligent space using a multi-camera sensor system. The set of calibrated and synchronized cameras are placed in fixed positions within the environment (intelligent space). The proposed algorithm for motion segmentation and 3D localization is based on the minimization of an objective function. This function includes information from all the cameras, and it does not rely on previous knowledge or invasive landmarks on board the robots. The proposed objective function depends on three groups of variables: the segmentation boundaries, the motion parameters and the depth. For the objective function minimization, we use a greedy iterative algorithm with three steps that, after initialization of segmentation boundaries and depth, are repeated until convergence. PMID:22319297

  11. Multi-camera sensor system for 3D segmentation and localization of multiple mobile robots.

    PubMed

    Losada, Cristina; Mazo, Manuel; Palazuelos, Sira; Pizarro, Daniel; Marrón, Marta

    2010-01-01

    This paper presents a method for obtaining the motion segmentation and 3D localization of multiple mobile robots in an intelligent space using a multi-camera sensor system. The set of calibrated and synchronized cameras are placed in fixed positions within the environment (intelligent space). The proposed algorithm for motion segmentation and 3D localization is based on the minimization of an objective function. This function includes information from all the cameras, and it does not rely on previous knowledge or invasive landmarks on board the robots. The proposed objective function depends on three groups of variables: the segmentation boundaries, the motion parameters and the depth. For the objective function minimization, we use a greedy iterative algorithm with three steps that, after initialization of segmentation boundaries and depth, are repeated until convergence. PMID:22319297

  12. Injectable 3-D Fabrication of Medical Electronics at the Target Biological Tissues

    NASA Astrophysics Data System (ADS)

    Jin, Chao; Zhang, Jie; Li, Xiaokang; Yang, Xueyao; Li, Jingjing; Liu, Jing

    2013-12-01

    Conventional transplantable biomedical devices generally request sophisticated surgery which however often causes big trauma and serious pain to the patients. Here, we show an alternative way of directly making three-dimensional (3-D) medical electronics inside the biological body through sequential injections of biocompatible packaging material and liquid metal ink. As the most typical electronics, a variety of medical electrodes with different embedded structures were demonstrated to be easily formed at the target tissues. Conceptual in vitro experiments provide strong evidences for the excellent performances of the injectable electrodes. Further in vivo animal experiments disclosed that the formed electrode could serve as both highly efficient ECG (Electrocardiograph) electrode and stimulator electrode. These findings clarified the unique features and practicability of the liquid metal based injectable 3-D fabrication of medical electronics. The present strategy opens the way for directly manufacturing electrophysiological sensors or therapeutic devices in situ via a truly minimally invasive approach.

  13. Injectable 3-D Fabrication of Medical Electronics at the Target Biological Tissues

    PubMed Central

    Jin, Chao; Zhang, Jie; Li, Xiaokang; Yang, Xueyao; Li, Jingjing; Liu, Jing

    2013-01-01

    Conventional transplantable biomedical devices generally request sophisticated surgery which however often causes big trauma and serious pain to the patients. Here, we show an alternative way of directly making three-dimensional (3-D) medical electronics inside the biological body through sequential injections of biocompatible packaging material and liquid metal ink. As the most typical electronics, a variety of medical electrodes with different embedded structures were demonstrated to be easily formed at the target tissues. Conceptual in vitro experiments provide strong evidences for the excellent performances of the injectable electrodes. Further in vivo animal experiments disclosed that the formed electrode could serve as both highly efficient ECG (Electrocardiograph) electrode and stimulator electrode. These findings clarified the unique features and practicability of the liquid metal based injectable 3-D fabrication of medical electronics. The present strategy opens the way for directly manufacturing electrophysiological sensors or therapeutic devices in situ via a truly minimally invasive approach. PMID:24309385

  14. Metric Calibration of a Focused Plenoptic Camera Based on a 3d Calibration Target

    NASA Astrophysics Data System (ADS)

    Zeller, N.; Noury, C. A.; Quint, F.; Teulière, C.; Stilla, U.; Dhome, M.

    2016-06-01

    In this paper we present a new calibration approach for focused plenoptic cameras. We derive a new mathematical projection model of a focused plenoptic camera which considers lateral as well as depth distortion. Therefore, we derive a new depth distortion model directly from the theory of depth estimation in a focused plenoptic camera. In total the model consists of five intrinsic parameters, the parameters for radial and tangential distortion in the image plane and two new depth distortion parameters. In the proposed calibration we perform a complete bundle adjustment based on a 3D calibration target. The residual of our optimization approach is three dimensional, where the depth residual is defined by a scaled version of the inverse virtual depth difference and thus conforms well to the measured data. Our method is evaluated based on different camera setups and shows good accuracy. For a better characterization of our approach we evaluate the accuracy of virtual image points projected back to 3D space.

  15. Local Metric Learning in 2D/3D Deformable Registration With Application in the Abdomen

    PubMed Central

    Chou, Chen-Rui; Mageras, Gig; Pizer, Stephen

    2015-01-01

    In image-guided radiotherapy (IGRT) of disease sites subject to respiratory motion, soft tissue deformations can affect localization accuracy. We describe the application of a method of 2D/3D deformable registration to soft tissue localization in abdomen. The method, called registration efficiency and accuracy through learning a metric on shape (REALMS), is designed to support real-time IGRT. In a previously developed version of REALMS, the method interpolated 3D deformation parameters for any credible deformation in a deformation space using a single globally-trained Riemannian metric for each parameter. We propose a refinement of the method in which the metric is trained over a particular region of the deformation space, such that interpolation accuracy within that region is improved. We report on the application of the proposed algorithm to IGRT in abdominal disease sites, which is more challenging than in lung because of low intensity contrast and nonrespiratory deformation. We introduce a rigid translation vector to compensate for nonrespiratory deformation, and design a special region-of-interest around fiducial markers implanted near the tumor to produce a more reliable registration. Both synthetic data and actual data tests on abdominal datasets show that the localized approach achieves more accurate 2D/3D deformable registration than the global approach. PMID:24771575

  16. Simulation and testing of a multichannel system for 3D sound localization

    NASA Astrophysics Data System (ADS)

    Matthews, Edward Albert

    Three-dimensional (3D) audio involves the ability to localize sound anywhere in a three-dimensional space. 3D audio can be used to provide the listener with the perception of moving sounds and can provide a realistic listening experience for applications such as gaming, video conferencing, movies, and concerts. The purpose of this research is to simulate and test 3D audio by incorporating auditory localization techniques in a multi-channel speaker system. The objective is to develop an algorithm that can place an audio event in a desired location by calculating and controlling the gain factors of each speaker. A MATLAB simulation displays the location of the speakers and perceived sound, which is verified through experimentation. The scenario in which the listener is not equidistant from each of the speakers is also investigated and simulated. This research is envisioned to lead to a better understanding of human localization of sound, and will contribute to a more realistic listening experience.

  17. Calibration target reconstruction for 3-D vision inspection system of large-scale engineering objects

    NASA Astrophysics Data System (ADS)

    Yin, Yongkai; Peng, Xiang; Guan, Yingjian; Liu, Xiaoli; Li, Ameng

    2010-11-01

    It is usually difficult to calibrate the 3-D vision inspection system that may be employed to measure the large-scale engineering objects. One of the challenges is how to in-situ build-up a large and precise calibration target. In this paper, we present a calibration target reconstruction strategy to solve such a problem. First, we choose one of the engineering objects to be inspected as a calibration target, on which we paste coded marks on the object surface. Next, we locate and decode marks to get homologous points. From multiple camera images, the fundamental matrix between adjacent images can be estimated, and then the essential matrix can be derived with priori known camera intrinsic parameters and decomposed to obtain camera extrinsic parameters. Finally, we are able to obtain the initial 3D coordinates with binocular stereo vision reconstruction, and then optimize them with the bundle adjustment by considering the lens distortions, leading to a high-precision calibration target. This reconstruction strategy has been applied to the inspection of an industrial project, from which the proposed method is successfully validated.

  18. Model fitting using RANSAC for surgical tool localization in 3-D ultrasound images.

    PubMed

    Uhercík, Marián; Kybic, Jan; Liebgott, Hervé; Cachard, Christian

    2010-08-01

    Ultrasound guidance is used for many surgical interventions such as biopsy and electrode insertion. We present a method to localize a thin surgical tool such as a biopsy needle or a microelectrode in a 3-D ultrasound image. The proposed method starts with thresholding and model fitting using random sample consensus for robust localization of the axis. Subsequent local optimization refines its position. Two different tool image models are presented: one is simple and fast and the second uses learned a priori information about the tool's voxel intensities and the background. Finally, the tip of the tool is localized by finding an intensity drop along the axis. The simulation study shows that our algorithm can localize the tool at nearly real-time speed, even using a MATLAB implementation, with accuracy better than 1 mm. In an experimental comparison with several alternative localization methods, our method appears to be the fastest and the most robust one. We also show the results on real 3-D ultrasound data from a PVA cryogel phantom, turkey breast, and breast biopsy. PMID:20483680

  19. Freehand photoacoustic tomography for 3D angiography using local gradient information

    NASA Astrophysics Data System (ADS)

    Kirchner, Thomas; Wild, Esther; Maier-Hein, Klaus H.; Maier-Hein, Lena

    2016-03-01

    Photo-acoustic tomography (PAT) is capable of imaging optical absorption in depths beyond the diffusion limit. As blood is one of the main absorbers in tissue, one important application is the visualization of vasculature, which can provide important clues for diagnosing diseases like cancer. While the state-of-the-art work in photo-acoustic 3D angiography has focused on computed tomography systems involving complex setups, we propose an approach based on optically tracking a freehand linear ultrasound probe that can be smoothly integrated into the clinical workflow. To this end, we present a method for calibration of a PAT system using an N-wire phantom specifically designed for PAT and show how to use local gradient information in the 3D reconstructed volume to significantly enhance the signal. According to experiments performed with a tissue mimicking intra-lipid phantom, the signal-to-noise ratio, contrast and contrast-to-noise ratio measured in the full field of view of the linear probe can be improved by factors of 1.7+/-0.7, 14.6+/-5.8 and 2.8+/-1.2 respectively, when comparing the post envelope detection reconstructed 3D volume with the processed one. Qualitative validation performed in tissue mimicking gelatin phantoms further showed good agreement of the reconstructed vasculature with corresponding structures extracted from X-ray computed tomographies. As our method provides high contrast 3D images of the vasculature despite a low hardware complexity its potential for clinical application is high.

  20. Multilevel local refinement and multigrid methods for 3-D turbulent flow

    SciTech Connect

    Liao, C.; Liu, C.; Sung, C.H.; Huang, T.T.

    1996-12-31

    A numerical approach based on multigrid, multilevel local refinement, and preconditioning methods for solving incompressible Reynolds-averaged Navier-Stokes equations is presented. 3-D turbulent flow around an underwater vehicle is computed. 3 multigrid levels and 2 local refinement grid levels are used. The global grid is 24 x 8 x 12. The first patch is 40 x 16 x 20 and the second patch is 72 x 32 x 36. 4th order artificial dissipation are used for numerical stability. The conservative artificial compressibility method are used for further improvement of convergence. To improve the accuracy of coarse/fine grid interface of local refinement, flux interpolation method for refined grid boundary is used. The numerical results are in good agreement with experimental data. The local refinement can improve the prediction accuracy significantly. The flux interpolation method for local refinement can keep conservation for a composite grid, therefore further modify the prediction accuracy.

  1. Technical Note: Immunohistochemical evaluation of mouse brain irradiation targeting accuracy with 3D-printed immobilization device

    SciTech Connect

    Zarghami, Niloufar Jensen, Michael D.; Talluri, Srikanth; Dick, Frederick A.; Foster, Paula J.; Chambers, Ann F.; Wong, Eugene

    2015-11-15

    Purpose: Small animal immobilization devices facilitate positioning of animals for reproducible imaging and accurate focal radiation therapy. In this study, the authors demonstrate the use of three-dimensional (3D) printing technology to fabricate a custom-designed mouse head restraint. The authors evaluate the accuracy of this device for the purpose of mouse brain irradiation. Methods: A mouse head holder was designed for a microCT couch using CAD software and printed in an acrylic based material. Ten mice received half-brain radiation while positioned in the 3D-printed head holder. Animal placement was achieved using on-board image guidance and computerized asymmetric collimators. To evaluate the precision of beam localization for half-brain irradiation, mice were sacrificed approximately 30 min after treatment and brain sections were stained for γ-H2AX, a marker for DNA breaks. The distance and angle of the γ-H2AX radiation beam border to longitudinal fissure were measured on histological samples. Animals were monitored for any possible trauma from the device. Results: Visualization of the radiation beam on ex vivo brain sections with γ-H2AX immunohistochemical staining showed a sharp radiation field within the tissue. Measurements showed a mean irradiation targeting error of 0.14 ± 0.09 mm (standard deviation). Rotation between the beam axis and mouse head was 1.2° ± 1.0° (standard deviation). The immobilization device was easily adjusted to accommodate different sizes of mice. No signs of trauma to the mice were observed from the use of tooth block and ear bars. Conclusions: The authors designed and built a novel 3D-printed mouse head holder with many desired features for accurate and reproducible radiation targeting. The 3D printing technology was found to be practical and economical for producing a small animal imaging and radiation restraint device and allows for customization for study specific needs.

  2. Automated localization of implanted seeds in 3D TRUS images used for prostate brachytherapy

    SciTech Connect

    Wei Zhouping; Gardi, Lori; Downey, Donal B.; Fenster, Aaron

    2006-07-15

    An algorithm has been developed in this paper to localize implanted radioactive seeds in 3D ultrasound images for a dynamic intraoperative brachytherapy procedure. Segmentation of the seeds is difficult, due to their small size in relatively low quality of transrectal ultrasound (TRUS) images. In this paper, intraoperative seed segmentation in 3D TRUS images is achieved by performing a subtraction of the image before the needle has been inserted, and the image after the seeds have been implanted. The seeds are searched in a 'local' space determined by the needle position and orientation information, which are obtained from a needle segmentation algorithm. To test this approach, 3D TRUS images of the agar and chicken tissue phantoms were obtained. Within these phantoms, dummy seeds were implanted. The seed locations determined by the seed segmentation algorithm were compared with those obtained from a volumetric cone-beam flat-panel micro-CT scanner and human observers. Evaluation of the algorithm showed that the rms error in determining the seed locations using the seed segmentation algorithm was 0.98 mm in agar phantoms and 1.02 mm in chicken phantoms.

  3. Enhanced Optical Transmission Mediated by Localized Plasmons in Anisotropic, 3D Nanohole Arrays

    PubMed Central

    Yang, Jiun-Chan; Gao, Hanwei; Suh, Jae Yong; Zhou, Wei; Lee, Min Hyung; Odom, Teri W.

    2010-01-01

    This paper describes 3D nanohole arrays whose high optical transmission is mediated more by localized surface plasmon (LSP) excitations than by surface plasmon polaritons (SPPs). First, LSPs on 3D hole arrays lead to optical transmission an order of magnitude higher than 2D planar hole arrays. Second, LSP-mediated transmission is broadband and more tunable than SPP-enhanced transmission which is restricted by Bragg coupling. Third, for the first time, two types of surface plasmons can be selectively excited and manipulated on the same plasmonic substrate. This new plasmonic substrate fabricated by high-throughput nanolithography techniques paves the way for cutting-edge optoelectronic and biomedical applications. PMID:20698633

  4. Local intersection volume: a new 3D descriptor applied to develop a 3D-QSAR pharmacophore model for benzodiazepine receptor ligands.

    PubMed

    Verli, Hugo; Albuquerque, Magaly Girão; Bicca de Alencastro, Ricardo; Barreiro, Eliezer J

    2002-03-01

    In this work, we have developed a new descriptor, named local intersection volume (LIV), in order to compose a 3D-QSAR pharmacophore model for benzodiazepine receptor ligands. The LIV can be classified as a 3D local shape descriptor in contraposition to the global shape descriptors. We have selected from the literature 49 non-benzodiazepine compounds as a training data set and the model was obtained and evaluated by genetic algorithms (GA) and partial least-squares (PLS) methods using LIVs as descriptors. The LIV 3D-QSAR model has a good predictive capacity according the cross-validation test by "leave-one-out" procedure (Q(2)=0.72). The developed model was compared to a comprehensive and extensive SAR pharmacophore model, recently proposed by Cook and co-workers, for benzodiazepine receptor ligands [J. Med. Chem. 43 (2000) 71]. It showed a relevant correlation with the pharmacophore groups pointed out in that work. Our LIV 3D-QSAR model was also able to predict affinity values for a series of nine compounds (test data set) that was not included into the training data set. PMID:11900866

  5. 3-D inversion of airborne electromagnetic data parallelized and accelerated by local mesh and adaptive soundings

    NASA Astrophysics Data System (ADS)

    Yang, Dikun; Oldenburg, Douglas W.; Haber, Eldad

    2014-03-01

    Airborne electromagnetic (AEM) methods are highly efficient tools for assessing the Earth's conductivity structures in a large area at low cost. However, the configuration of AEM measurements, which typically have widely distributed transmitter-receiver pairs, makes the rigorous modelling and interpretation extremely time-consuming in 3-D. Excessive overcomputing can occur when working on a large mesh covering the entire survey area and inverting all soundings in the data set. We propose two improvements. The first is to use a locally optimized mesh for each AEM sounding for the forward modelling and calculation of sensitivity. This dedicated local mesh is small with fine cells near the sounding location and coarse cells far away in accordance with EM diffusion and the geometric decay of the signals. Once the forward problem is solved on the local meshes, the sensitivity for the inversion on the global mesh is available through quick interpolation. Using local meshes for AEM forward modelling avoids unnecessary computing on fine cells on a global mesh that are far away from the sounding location. Since local meshes are highly independent, the forward modelling can be efficiently parallelized over an array of processors. The second improvement is random and dynamic down-sampling of the soundings. Each inversion iteration only uses a random subset of the soundings, and the subset is reselected for every iteration. The number of soundings in the random subset, determined by an adaptive algorithm, is tied to the degree of model regularization. This minimizes the overcomputing caused by working with redundant soundings. Our methods are compared against conventional methods and tested with a synthetic example. We also invert a field data set that was previously considered to be too large to be practically inverted in 3-D. These examples show that our methodology can dramatically reduce the processing time of 3-D inversion to a practical level without losing resolution

  6. High-resolution 3D simulations of NIF ignition targets performed on Sequoia with HYDRA

    NASA Astrophysics Data System (ADS)

    Marinak, M. M.; Clark, D. S.; Jones, O. S.; Kerbel, G. D.; Sepke, S.; Patel, M. V.; Koning, J. M.; Schroeder, C. R.

    2015-11-01

    Developments in the multiphysics ICF code HYDRA enable it to perform large-scale simulations on the Sequoia machine at LLNL. With an aggregate computing power of 20 Petaflops, Sequoia offers an unprecedented capability to resolve the physical processes in NIF ignition targets for a more complete, consistent treatment of the sources of asymmetry. We describe modifications to HYDRA that enable it to scale to over one million processes on Sequoia. These include new options for replicating parts of the mesh over a subset of the processes, to avoid strong scaling limits. We consider results from a 3D full ignition capsule-only simulation performed using over one billion zones run on 262,000 processors which resolves surface perturbations through modes l = 200. We also report progress towards a high-resolution 3D integrated hohlraum simulation performed using 262,000 processors which resolves surface perturbations on the ignition capsule through modes l = 70. These aim for the most complete calculations yet of the interactions and overall impact of the various sources of asymmetry for NIF ignition targets. This work was performed under the auspices of the Lawrence Livermore National Security, LLC, (LLNS) under Contract No. DE-AC52-07NA27344.

  7. 3-D P Wave Velocity Structure of Marmara Region Using Local Earthquake Tomography

    NASA Astrophysics Data System (ADS)

    Işık, S. E.; Gurbuz, C.

    2014-12-01

    The 3D P wave velocity model of upper and lower crust of the Marmara Region between 40.200- 41.200N and 26.500- 30.500E is obtained by tomographic inversion (Simulps) of 47034 P wave arrivals of local earthquakes recorded at 90 land stations between October 2009 and December 2012 and 30 OBO stations and 14162 shot arrivals recorded at 35 OBO stations (Seismarmara Survey, 2001). We first obtained a 1D minimum model with Velest code in order to obtain an initial model for 3D inversion with 648 well located earthquakes located within the study area. After several 3D inversion trials we decided to create a more adequate initial model for 3D inversion. Choosing the initial model we estimated the 3D P wave velocity model representing the whole region both for land and sea. The results are tested by making Checkerboard , Restoring Resolution and Characteristic Tests, and the reliable areas of the resulting model is defined in terms of RDE, DWS, SF and Hit count distributions. By taking cross sections from the resulting model we observed the vertical velocity change along profiles crossing both land and sea. All the profiles crossing the basins showed that the high velocities of lower crust make extensions towards the basin area which looks like the force that gives a shape to the basins. These extensions of lower crust towards the basins appeared with an average velocity of 6.3 km/s which might be the result of the deformation due the shearing in the region. It is also interpreted that the development of these high velocities coincide with the development of the basins. Thus, both the basins and the high velocity zones around them might be resulted from the entrance of the NAF into the Marmara Sea and at the same time a shear regime was dominated due to the resistance of the northern Marmara Region (Yılmaz, 2010). The seismicity is observed between 5 km and 15 km after the 3D location of the earthquakes. The locations of the earthquakes improved and the seismogenic zone

  8. Sound localization with head movement: implications for 3-d audio displays

    PubMed Central

    McAnally, Ken I.; Martin, Russell L.

    2014-01-01

    Previous studies have shown that the accuracy of sound localization is improved if listeners are allowed to move their heads during signal presentation. This study describes the function relating localization accuracy to the extent of head movement in azimuth. Sounds that are difficult to localize were presented in the free field from sources at a wide range of azimuths and elevations. Sounds remained active until the participants' heads had rotated through windows ranging in width of 2, 4, 8, 16, 32, or 64° of azimuth. Error in determining sound-source elevation and the rate of front/back confusion were found to decrease with increases in azimuth window width. Error in determining sound-source lateral angle was not found to vary with azimuth window width. Implications for 3-d audio displays: the utility of a 3-d audio display for imparting spatial information is likely to be improved if operators are able to move their heads during signal presentation. Head movement may compensate in part for a paucity of spectral cues to sound-source location resulting from limitations in either the audio signals presented or the directional filters (i.e., head-related transfer functions) used to generate a display. However, head movements of a moderate size (i.e., through around 32° of azimuth) may be required to ensure that spatial information is conveyed with high accuracy. PMID:25161605

  9. Quantitative Assessment of Local Collagen Matrix Remodeling in 3-D Culture: The Role of Rho Kinase

    PubMed Central

    Kim, Areum; Lakshman, Neema; Petroll, W.Matthew

    2007-01-01

    The purpose of this study was to quantitatively assess the role of Rho kinase in modulating the pattern and amount of local cell-induced collagen matrix remodeling. Human corneal fibroblasts were plated inside 100 μm thick fibrillar collagen matrices and cultured for 24 hours in media with or without the Rho kinase inhibitor Y-27632. Cells were then fixed and stained with phalloidin. Fluorescent (for f-actin) and reflected light (for collagen fibrils) 3-D optical section images were acquired using laser confocal microscopy. Fourier transform analysis was used to assess collagen fibril alignment, and 3-D cell morphology and local collagen density were measured using MetaMorph. Culture in serum-containing media induced significant global matrix contraction, which was inhibited by blocking Rho kinase (p < 0.001). Fibroblasts generally had a bipolar morphology and intracellular stress fibers. Collagen fibrils were compacted and aligned parallel to stress fibers and pseudopodia. When Rho kinase was inhibited, cells had a more cortical f-actin distribution and dendritic morphology. Both local collagen fibril density and alignment were significantly reduced (p<0.01). Overall, the data suggests that Rho kinase dependent contractile force generation leads to co-alignment of cells and collagen fibrils along the plane of greatest resistance, and that this process contributes to global matrix contraction. PMID:16978606

  10. Local characterization of hindered Brownian motion by using digital video microscopy and 3D particle tracking.

    PubMed

    Dettmer, Simon L; Keyser, Ulrich F; Pagliara, Stefano

    2014-02-01

    In this article we present methods for measuring hindered Brownian motion in the confinement of complex 3D geometries using digital video microscopy. Here we discuss essential features of automated 3D particle tracking as well as diffusion data analysis. By introducing local mean squared displacement-vs-time curves, we are able to simultaneously measure the spatial dependence of diffusion coefficients, tracking accuracies and drift velocities. Such local measurements allow a more detailed and appropriate description of strongly heterogeneous systems as opposed to global measurements. Finite size effects of the tracking region on measuring mean squared displacements are also discussed. The use of these methods was crucial for the measurement of the diffusive behavior of spherical polystyrene particles (505 nm diameter) in a microfluidic chip. The particles explored an array of parallel channels with different cross sections as well as the bulk reservoirs. For this experiment we present the measurement of local tracking accuracies in all three axial directions as well as the diffusivity parallel to the channel axis while we observed no significant flow but purely Brownian motion. Finally, the presented algorithm is suitable also for tracking of fluorescently labeled particles and particles driven by an external force, e.g., electrokinetic or dielectrophoretic forces. PMID:24593372

  11. Local characterization of hindered Brownian motion by using digital video microscopy and 3D particle tracking

    NASA Astrophysics Data System (ADS)

    Dettmer, Simon L.; Keyser, Ulrich F.; Pagliara, Stefano

    2014-02-01

    In this article we present methods for measuring hindered Brownian motion in the confinement of complex 3D geometries using digital video microscopy. Here we discuss essential features of automated 3D particle tracking as well as diffusion data analysis. By introducing local mean squared displacement-vs-time curves, we are able to simultaneously measure the spatial dependence of diffusion coefficients, tracking accuracies and drift velocities. Such local measurements allow a more detailed and appropriate description of strongly heterogeneous systems as opposed to global measurements. Finite size effects of the tracking region on measuring mean squared displacements are also discussed. The use of these methods was crucial for the measurement of the diffusive behavior of spherical polystyrene particles (505 nm diameter) in a microfluidic chip. The particles explored an array of parallel channels with different cross sections as well as the bulk reservoirs. For this experiment we present the measurement of local tracking accuracies in all three axial directions as well as the diffusivity parallel to the channel axis while we observed no significant flow but purely Brownian motion. Finally, the presented algorithm is suitable also for tracking of fluorescently labeled particles and particles driven by an external force, e.g., electrokinetic or dielectrophoretic forces.

  12. Local characterization of hindered Brownian motion by using digital video microscopy and 3D particle tracking

    SciTech Connect

    Dettmer, Simon L.; Keyser, Ulrich F.; Pagliara, Stefano

    2014-02-15

    In this article we present methods for measuring hindered Brownian motion in the confinement of complex 3D geometries using digital video microscopy. Here we discuss essential features of automated 3D particle tracking as well as diffusion data analysis. By introducing local mean squared displacement-vs-time curves, we are able to simultaneously measure the spatial dependence of diffusion coefficients, tracking accuracies and drift velocities. Such local measurements allow a more detailed and appropriate description of strongly heterogeneous systems as opposed to global measurements. Finite size effects of the tracking region on measuring mean squared displacements are also discussed. The use of these methods was crucial for the measurement of the diffusive behavior of spherical polystyrene particles (505 nm diameter) in a microfluidic chip. The particles explored an array of parallel channels with different cross sections as well as the bulk reservoirs. For this experiment we present the measurement of local tracking accuracies in all three axial directions as well as the diffusivity parallel to the channel axis while we observed no significant flow but purely Brownian motion. Finally, the presented algorithm is suitable also for tracking of fluorescently labeled particles and particles driven by an external force, e.g., electrokinetic or dielectrophoretic forces.

  13. Assessing target design robustness for Shock Ignition using 3D laser raytracing

    NASA Astrophysics Data System (ADS)

    Schiavi, Angelo; Atzeni, Stefano; Marocchino, Alberto

    2014-10-01

    Shock ignition (SI) is a laser direct-drive Inertial Confinement Fusion scheme in which fuel compression and hot spot formation are separated. Shock ignition shows potential for high gain at laser energy below 1 MJ (see review Ref.), and could be tested on present large scale facilities. We produced an analytical model for SI which allows rescaling of target and laser drive parameters starting from a given point design. The goal is to redefine a laser-target configuration increasing the robustness while preserving its performance. We developed a metric for ignition margins specific to SI. We report on simulations of rescaled targets using 2D hydrodynamic fluid model with 3D laser raytracing. The robustness with respect to target fabrication parameters and laser facility fluctuations will be assessed for an original reference design as well as for a rescaled target, testing the accuracy of the ignition margin predictor just developed. Work supported by the Italian MIUR Project PRIN2012AY5LEL.

  14. Comparison of Phase-Based 3D Near-Field Source Localization Techniques for UHF RFID.

    PubMed

    Parr, Andreas; Miesen, Robert; Vossiek, Martin

    2016-01-01

    In this paper, we present multiple techniques for phase-based narrowband backscatter tag localization in three-dimensional space with planar antenna arrays or synthetic apertures. Beamformer and MUSIC localization algorithms, known from near-field source localization and direction-of-arrival estimation, are applied to the 3D backscatter scenario and their performance in terms of localization accuracy is evaluated. We discuss the impact of different transceiver modes known from the literature, which evaluate different send and receive antenna path combinations for a single localization, as in multiple input multiple output (MIMO) systems. Furthermore, we propose a new Singledimensional-MIMO (S-MIMO) transceiver mode, which is especially suited for use with mobile robot systems. Monte-Carlo simulations based on a realistic multipath error model ensure spatial correlation of the simulated signals, and serve to critically appraise the accuracies of the different localization approaches. A synthetic uniform rectangular array created by a robotic arm is used to evaluate selected localization techniques. We use an Ultra High Frequency (UHF) Radiofrequency Identification (RFID) setup to compare measurements with the theory and simulation. The results show how a mean localization accuracy of less than 30 cm can be reached in an indoor environment. Further simulations demonstrate how the distance between aperture and tag affects the localization accuracy and how the size and grid spacing of the rectangular array need to be adapted to improve the localization accuracy down to orders of magnitude in the centimeter range, and to maximize array efficiency in terms of localization accuracy per number of elements. PMID:27347976

  15. Comparison of Phase-Based 3D Near-Field Source Localization Techniques for UHF RFID

    PubMed Central

    Parr, Andreas; Miesen, Robert; Vossiek, Martin

    2016-01-01

    In this paper, we present multiple techniques for phase-based narrowband backscatter tag localization in three-dimensional space with planar antenna arrays or synthetic apertures. Beamformer and MUSIC localization algorithms, known from near-field source localization and direction-of-arrival estimation, are applied to the 3D backscatter scenario and their performance in terms of localization accuracy is evaluated. We discuss the impact of different transceiver modes known from the literature, which evaluate different send and receive antenna path combinations for a single localization, as in multiple input multiple output (MIMO) systems. Furthermore, we propose a new Singledimensional-MIMO (S-MIMO) transceiver mode, which is especially suited for use with mobile robot systems. Monte-Carlo simulations based on a realistic multipath error model ensure spatial correlation of the simulated signals, and serve to critically appraise the accuracies of the different localization approaches. A synthetic uniform rectangular array created by a robotic arm is used to evaluate selected localization techniques. We use an Ultra High Frequency (UHF) Radiofrequency Identification (RFID) setup to compare measurements with the theory and simulation. The results show how a mean localization accuracy of less than 30 cm can be reached in an indoor environment. Further simulations demonstrate how the distance between aperture and tag affects the localization accuracy and how the size and grid spacing of the rectangular array need to be adapted to improve the localization accuracy down to orders of magnitude in the centimeter range, and to maximize array efficiency in terms of localization accuracy per number of elements. PMID:27347976

  16. Can 3D light localization be reached in ‘white paint’?

    NASA Astrophysics Data System (ADS)

    Sperling, T.; Schertel, L.; Ackermann, M.; Aubry, G. J.; Aegerter, C. M.; Maret, G.

    2016-01-01

    When waves scatter multiple times in 3D random media, a disorder driven phase transition from diffusion to localization may occur (Anderson 1958 Phys. Rev. 109 1492-505 Abrahams et al 1979 Phys. Rev. Lett. 42 673-6). In ‘The question of classical localization: a theory of white paint?’ Anderson suggested the possibility to observe light localization in TiO2 samples (Anderson 1985 Phil. Mag. B 52 505-9). We recently claimed the observation of localization effects measuring photon time of flight (ToF) distributions (Störzer et al 2006 Phys. Rev. Lett. 96 063904) and evaluating transmission profiles (TPs) (Sperling et al 2013 Nat. Photonics 7 48-52) in such TiO2 samples. Here we present a careful study of the long time tail of ToF distributions and the long time behavior of the TP width for very thin samples and different turbidities that questions the localization interpretation. We further show new data that allow an alternative consistent explanation of these previous data by a fluorescence process. An adapted diffusion model including an appropriate exponential fluorescence decay accounts for the shape of the ToF distributions and the TP width. These observations question whether the strong localization regime can be reached with visible light scattering in polydisperse TiO2 samples, since the disorder parameter can hardly be increased any further in such a ‘white paint’ material.

  17. Recognizing Objects in 3D Point Clouds with Multi-Scale Local Features

    PubMed Central

    Lu, Min; Guo, Yulan; Zhang, Jun; Ma, Yanxin; Lei, Yinjie

    2014-01-01

    Recognizing 3D objects from point clouds in the presence of significant clutter and occlusion is a highly challenging task. In this paper, we present a coarse-to-fine 3D object recognition algorithm. During the phase of offline training, each model is represented with a set of multi-scale local surface features. During the phase of online recognition, a set of keypoints are first detected from each scene. The local surfaces around these keypoints are further encoded with multi-scale feature descriptors. These scene features are then matched against all model features to generate recognition hypotheses, which include model hypotheses and pose hypotheses. Finally, these hypotheses are verified to produce recognition results. The proposed algorithm was tested on two standard datasets, with rigorous comparisons to the state-of-the-art algorithms. Experimental results show that our algorithm was fully automatic and highly effective. It was also very robust to occlusion and clutter. It achieved the best recognition performance on all of these datasets, showing its superiority compared to existing algorithms. PMID:25517694

  18. Recognizing objects in 3D point clouds with multi-scale local features.

    PubMed

    Lu, Min; Guo, Yulan; Zhang, Jun; Ma, Yanxin; Lei, Yinjie

    2014-01-01

    Recognizing 3D objects from point clouds in the presence of significant clutter and occlusion is a highly challenging task. In this paper, we present a coarse-to-fine 3D object recognition algorithm. During the phase of offline training, each model is represented with a set of multi-scale local surface features. During the phase of online recognition, a set of keypoints are first detected from each scene. The local surfaces around these keypoints are further encoded with multi-scale feature descriptors. These scene features are then matched against all model features to generate recognition hypotheses, which include model hypotheses and pose hypotheses. Finally, these hypotheses are verified to produce recognition results. The proposed algorithm was tested on two standard datasets, with rigorous comparisons to the state-of-the-art algorithms. Experimental results show that our algorithm was fully automatic and highly effective. It was also very robust to occlusion and clutter. It achieved the best recognition performance on all of these datasets, showing its superiority compared to existing algorithms. PMID:25517694

  19. TRAIL protein localization in human primary T cells by 3D microscopy using 3D interactive surface plot: a new method to visualize plasma membrane.

    PubMed

    Gras, Christophe; Smith, Nikaïa; Sengmanivong, Lucie; Gandini, Mariana; Kubelka, Claire Fernandes; Herbeuval, Jean-Philippe

    2013-01-31

    The apoptotic ligand TNF-related apoptosis ligand (TRAIL) is expressed on the membrane of immune cells during HIV infection. The intracellular stockade of TRAIL in human primary CD4(+) T cells is not known. Here we investigated whether primary CD4(+) T cells expressed TRAIL in their intracellular compartment and whether TRAIL is relocalized on the plasma membrane under HIV activation. We found that TRAIL protein was stocked in intracellular compartment in non activated CD4(+) T cells and that the total level of TRAIL protein was not increased under HIV-1 stimulation. However, TRAIL was massively relocalized on plasma membrane when cells were cultured with HIV. Using three dimensional (3D) microscopy we localized TRAIL protein in human T cells and developed a new method to visualize plasma membrane without the need of a membrane marker. This method used the 3D interactive surface plot and bright light acquired images. PMID:23085529

  20. Forward-looking infrared 3D target tracking via combination of particle filter and SIFT

    NASA Astrophysics Data System (ADS)

    Li, Xing; Cao, Zhiguo; Yan, Ruicheng; Li, Tuo

    2013-10-01

    Aiming at the problem of tracking 3D target in forward-looking infrared (FLIR) image, this paper proposes a high-accuracy robust tracking algorithm based on SIFT and particle filter. The main contribution of this paper is the proposal of a new method of estimating the affine transformation matrix parameters based on Monte Carlo methods of particle filter. At first, we extract SIFT features on infrared image, and calculate the initial affine transformation matrix with optimal candidate key points. Then we take affine transformation parameters as particles, and use SIR (Sequential Importance Resampling) particle filter to estimate the best position, thus implementing our algorithm. The experiments demonstrate that our algorithm proves to be robust with high accuracy.

  1. Large-scale 3D simulations of ICF and HEDP targets

    NASA Astrophysics Data System (ADS)

    Marinak, Michael M.

    2000-10-01

    The radiation hydrodynamics code HYDRA continues to be developed and applied to 3D simulations of a variety of targets for both inertial confinement fusion (ICF) and high energy density physics. Several packages have been added enabling this code to perform ICF target simulations with similar accuracy as two-dimensional codes of long-time historical use. These include a laser ray trace and deposition package, a heavy ion deposition package, implicit Monte Carlo photonics, and non-LTE opacities, derived from XSN or the linearized response matrix approach.(R. More, T. Kato, Phys. Rev. Lett. 81, 814 (1998), S. Libby, F. Graziani, R. More, T. Kato, Proceedings of the 13th International Conference on Laser Interactions and Related Plasma Phenomena, (AIP, New York, 1997).) LTE opacities can also be calculated for arbitrary mixtures online by combining tabular values generated by different opacity codes. Thermonuclear burn, charged particle transport, neutron energy deposition, electron-ion coupling and conduction, and multigroup radiation diffusion packages are also installed. HYDRA can employ ALE hydrodynamics; a number of grid motion algorithms are available. Multi-material flows are resolved using material interface reconstruction. Results from large-scale simulations run on up to 1680 processors, using a combination of massively parallel processing and symmetric multiprocessing, will be described. A large solid angle simulation of Rayleigh-Taylor instability growth in a NIF ignition capsule has resolved simultaneously the full spectrum of the most dangerous modes that grow from surface roughness. Simulations of a NIF hohlraum illuminated with the initial 96 beam configuration have also been performed. The effect of the hohlraum’s 3D intrinsic drive asymmetry on the capsule implosion will be considered. We will also discuss results from a Nova experiment in which a copper sphere is crushed by a planar shock. Several interacting hydrodynamic instabilities, including

  2. Probing Local Mineralogy in 3D with Dual Energy X-Ray Microscopy

    NASA Astrophysics Data System (ADS)

    Gelb, J.; Yun, S.; Doerr, D.; Hunter, L.; Johnson, B.; Merkle, A.; Fahey, K.

    2013-12-01

    In recent years, 3D imaging of rock microstructures has become routine practice for determining pore-scale properties in the geosciences. X-Ray imaging techniques, such as X-Ray Microscopy (XRM), have demonstrated several unique capabilities: namely, the ability to characterize the same sample across a range of length scales and REVs (from millimeters to nanometers), and to perform these characterizations on the same sample over a range of times/treatments (e.g., to observe fluid transporting through the pore networks in a flow cell). While the XRM technique is a popular choice for structural (i.e., pore) characterization, historically it has provided little mineralogical information. This means that resulting simulations are either based on pore structure alone, or rely on correlative chemical mapping techniques for compositionally-sensitive models. Recent advancements in XRM techniques are now enabling compositional sensitivity for a variety of geological sample types. By collecting high-resolution 3D tomography data sets at two different source settings (energies), results may be mixed together to enhance the appearance (contrast) of specific materials. This approach is proving beneficial, for example, to mining applications to locate and identify precious metals, as well as for oil & gas applications to map local hydrophobicity. Here, we will introduce the technique of dual energy X-Ray microscopy, showing how it extends the capabilities of traditional XRM techniques, affording the same high resolution structural information while adding 3D compositional data. Application examples will be shown to illustrate its effectiveness at both the single to sub-micron length scale for mining applications as well as at the 150 nm length scale for shale rock analysis.

  3. Local ISM 3D Distribution and Soft X-ray Background Inferences for Nearby Hot Gas

    NASA Technical Reports Server (NTRS)

    Puspitarini, L.; Lallement, R.; Snowden, Steven L.; Vergely, J.-L.; Snowden, S.

    2014-01-01

    Three-dimensional (3D) interstellar medium (ISM) maps can be used to locate not only interstellar (IS) clouds, but also IS bubbles between the clouds that are blown by stellar winds and supernovae, and are filled by hot gas. To demonstrate this, and to derive a clearer picture of the local ISM, we compare our recent 3D IS dust distribution maps to the ROSAT diffuse Xray background maps after removal of heliospheric emission. In the Galactic plane, there is a good correspondence between the locations and extents of the mapped nearby cavities and the soft (0.25 keV) background emission distribution, showing that most of these nearby cavities contribute to this soft X-ray emission. Assuming a constant dust to gas ratio and homogeneous 106 K hot gas filling the cavities, we modeled in a simple way the 0.25 keV surface brightness along the Galactic plane as seen from the Sun, taking into account the absorption by the mapped clouds. The data-model comparison favors the existence of hot gas in the solar neighborhood, the so-called Local Bubble (LB). The inferred mean pressure in the local cavities is found to be approx.9,400/cu cm K, in agreement with previous studies, providing a validation test for the method. On the other hand, the model overestimates the emission from the huge cavities located in the third quadrant. Using CaII absorption data, we show that the dust to CaII ratio is very small in those regions, implying the presence of a large quantity of lower temperature (non-X-ray emitting) ionized gas and as a consequence a reduction of the volume filled by hot gas, explaining at least part of the discrepancy. In the meridian plane, the two main brightness enhancements coincide well with the LB's most elongated parts and chimneys connecting the LB to the halo, but no particular nearby cavity is found towards the enhancement in the direction of the bright North Polar Spur (NPS) at high latitude. We searched in the 3D maps for the source regions of the higher energy

  4. Discovery of previously unrecognised local faults in London, UK, using detailed 3D geological modelling

    NASA Astrophysics Data System (ADS)

    Aldiss, Don; Haslam, Richard

    2013-04-01

    In parts of London, faulting introduces lateral heterogeneity to the local ground conditions, especially where construction works intercept the Palaeogene Lambeth Group. This brings difficulties to the compilation of a ground model that is fully consistent with the ground investigation data, and so to the design and construction of engineering works. However, because bedrock in the London area is rather uniform at outcrop, and is widely covered by Quaternary deposits, few faults are shown on the geological maps of the area. This paper discusses a successful resolution of this problem at a site in east central London, where tunnels for a new underground railway station are planned. A 3D geological model was used to provide an understanding of the local geological structure, in faulted Lambeth Group strata, that had not been possible by other commonly-used methods. This model includes seven previously unrecognised faults, with downthrows ranging from about 1 m to about 12 m. The model was constructed in the GSI3D geological modelling software using about 145 borehole records, including many legacy records, in an area of 850 m by 500 m. The basis of a GSI3D 3D geological model is a network of 2D cross-sections drawn by a geologist, generally connecting borehole positions (where the borehole records define the level of the geological units that are present), and outcrop and subcrop lines for those units (where shown by a geological map). When the lines tracing the base of each geological unit within the intersecting cross-sections are complete and mutually consistent, the software is used to generate TIN surfaces between those lines, so creating a 3D geological model. Even where a geological model is constructed as if no faults were present, changes in apparent dip between two data points within a single cross-section can indicate that a fault is present in that segment of the cross-section. If displacements of similar size with the same polarity are found in a series

  5. 3-D crustal velocity model for Lithuania and its application to local event studies

    NASA Astrophysics Data System (ADS)

    Budraitis, M.; Kozlovskaya, E.; Janutyte, I.; Motuza, G.

    2009-12-01

    PASSEQ 2006-2008 project (PASsive Seismic Experiment in TESZ) aimed at studying the lithosphere-asthenosphere system around the TransEuropean Suture Zone (TESZ)- the transition between old Proterozoic platform of north and east Europe and younger Phanerozoic platform in central and western Europe. The experiment was a seismic array research aiming to retrieve the structure of the crust and Earth's mantle down to the mantle transition zone, including mapping of upper mantle seismic velocity variations and discontinuities (Moho, lithosphere-asthenosphere boundary, mantle transition zone) using all available techniques. During the experiment 26 seismic stations (including four broadband stations) were installed in Lithuania and operated since June, 2006 till January, 2008. One of the main reasons of PASSEQ deployment in Lithuania is identification and characterisation of the local seismic activity. During the data acquisition period a number of local seismic events was identified and preliminary event location was made using LocSat and VELEST algorithms and 1-D velocity models. These standard procedures is not enough precise for Lithuania, however, because the thickness of the crust varies significantly in the region (from 45 to 55 km). Another problem was low quality of S-wave arrivals due to thick (up to 2 km) sediments in most part of Lithuania. In order to improve event location, we compiled a 3-D seismic velocity model of the crust down to a depth of 60 km. The model, consisting of four major layers (sediments, upper crust, middle crust, lower crust and uppermost mantle) was interpolated from 2-D velocity models along previous wide-angle reflection and refraction profiles into a regular grid. The quality of the approximation was analysed using comparison of travel times of P-waves recorded by controlled source experiments and calculated travel times through the 3-D velocity model. The model was converted into a density model using a special procedure, in which

  6. 3D maps of the local ISM from inversion of individual color excess measurements

    NASA Astrophysics Data System (ADS)

    Lallement, R.; Vergely, J.-L.; Valette, B.; Puspitarini, L.; Eyer, L.; Casagrande, L.

    2014-01-01

    Aims: Three-dimensional (3D) maps of the Galactic interstellar matter (ISM) are a potential tool of wide use, but accurate and detailed maps are still lacking. One of the ways to construct the maps is to invert individual distance-limited ISM measurements, a method we have applied here to measurements of stellar color excess in the optical. Methods: We assembled color excess data together with the associated parallax or photometric distances to constitute a catalog of ≃23 000 sightlines for stars within 2.5 kpc. The photometric data are taken from Strömgren catalogs, the Geneva photometric database, and the Geneva-Copenhagen survey. We also included extinctions derived towards open clusters. We applied an inversion method based on a regularized Bayesian approach to this color excess dataset, a method previously used for mapping at closer distances. Results: We show the dust spatial distribution resulting from the inversion by means of planar cuts through the differential opacity 3D distribution, and by means of 2D maps of the integrated opacity from the Sun up to various distances. The mapping assigns locations to the nearby dense clouds and represents their distribution at the spatial resolution that is allowed by the dataset properties, i.e. ≃10 pc close to the Sun and increasing to ≃100 pc beyond 1 kpc. Biases toward nearby and/or weakly extincted stars make this dataset particularly appropriate to mapping the local and neighboring cavities and to locating faint, extended nearby clouds, which are both goals that are difficult or impossible with other mapping methods. The new maps reveal a ≃1 kpc wide empty region in the third quadrant in the continuation of the so-called CMa tunnel of the Local Cavity, a cavity that we identify as the Superbubble GSH238+00+09 detected in radio emission maps and that is found to be bounded by the Orion and Vela clouds. The maps also show an extended narrower tunnel in the opposite direction (l ≃ 70°) that also extends

  7. Localization of spots in FISH images of breast cancer using 3-D shape analysis.

    PubMed

    Les, T; Markiewicz, T; Osowski, S; Jesiotr, M; Kozlowski, W

    2016-06-01

    The fluorescence in situ (FISH) belongs to the most often used molecular cytogenetic techniques, applied in many areas of diagnosis and research. The analysis of FISH images relies on localization and counting the red and green spots in order to determine HER2 status of the breast cancer samples. The algorithm of spot localization presented in the paper is based on 3-D shape analysis of the image objects. The subsequent regions of the image are matched to the reference pattern and the results of this matching influence localization of spots. The paper compares different shapes of the reference pattern and their efficiency in spot localization. The numerical experiments have been performed on the basis of 12 cases (patients), each represented by three images. Few thousands of cells have been analysed. The quantitative analyses comparing different versions of algorithm are presented and compared to the expert results. The best version of the procedure provides the absolute relative difference to the expert results smaller than 3%. These results confirm high efficiency of the proposed approach to the spot identification. The proposed method of FISH image analysis improves the efficiency of detecting fluorescent signals in FISH images. The evaluation results are encouraging for further testing of the developed automatic system directed to application in medical practice. PMID:26694535

  8. Automated Foveola Localization in Retinal 3D-OCT Images Using Structural Support Vector Machine Prediction

    PubMed Central

    Liu, Yu-Ying; Ishikawa, Hiroshi; Chen, Mei; Wollstein, Gadi; Schuman, Joel S.; Rehg, James M.

    2013-01-01

    We develop an automated method to determine the foveola location in macular 3D-OCT images in either healthy or pathological conditions. Structural Support Vector Machine (S-SVM) is trained to directly predict the location of the foveola, such that the score at the ground truth position is higher than that at any other position by a margin scaling with the associated localization loss. This S-SVM formulation directly minimizes the empirical risk of localization error, and makes efficient use of all available training data. It deals with the localization problem in a more principled way compared to the conventional binary classifier learning that uses zero-one loss and random sampling of negative examples. A total of 170 scans were collected for the experiment. Our method localized 95.1% of testing scans within the anatomical area of the foveola. Our experimental results show that the proposed method can effectively identify the location of the foveola, facilitating diagnosis around this important landmark. PMID:23285565

  9. A method of 3D object recognition and localization in a cloud of points

    NASA Astrophysics Data System (ADS)

    Bielicki, Jerzy; Sitnik, Robert

    2013-12-01

    The proposed method given in this article is prepared for analysis of data in the form of cloud of points directly from 3D measurements. It is designed for use in the end-user applications that can directly be integrated with 3D scanning software. The method utilizes locally calculated feature vectors (FVs) in point cloud data. Recognition is based on comparison of the analyzed scene with reference object library. A global descriptor in the form of a set of spatially distributed FVs is created for each reference model. During the detection process, correlation of subsets of reference FVs with FVs calculated in the scene is computed. Features utilized in the algorithm are based on parameters, which qualitatively estimate mean and Gaussian curvatures. Replacement of differentiation with averaging in the curvatures estimation makes the algorithm more resistant to discontinuities and poor quality of the input data. Utilization of the FV subsets allows to detect partially occluded and cluttered objects in the scene, while additional spatial information maintains false positive rate at a reasonably low level.

  10. Vertical Corner Feature Based Precise Vehicle Localization Using 3D LIDAR in Urban Area.

    PubMed

    Im, Jun-Hyuck; Im, Sung-Hyuck; Jee, Gyu-In

    2016-01-01

    Tall buildings are concentrated in urban areas. The outer walls of buildings are vertically erected to the ground and almost flat. Therefore, the vertical corners that meet the vertical planes are present everywhere in urban areas. These corners act as convenient landmarks, which can be extracted by using the light detection and ranging (LIDAR) sensor. A vertical corner feature based precise vehicle localization method is proposed in this paper and implemented using 3D LIDAR (Velodyne HDL-32E). The vehicle motion is predicted by accumulating the pose increment output from the iterative closest point (ICP) algorithm based on the geometric relations between the scan data of the 3D LIDAR. The vertical corner is extracted using the proposed corner extraction method. The vehicle position is then corrected by matching the prebuilt corner map with the extracted corner. The experiment was carried out in the Gangnam area of Seoul, South Korea. In the experimental results, the maximum horizontal position error is about 0.46 m and the 2D Root Mean Square (RMS) horizontal error is about 0.138 m. PMID:27517936

  11. A formal classification of 3D medial axis points and their local geometry.

    PubMed

    Giblin, Peter; Kimia, Benjamin B

    2004-02-01

    This paper proposes a novel hypergraph skeletal representation for 3D shape based on a formal derivation of the generic structure of its medial axis. By classifying each skeletal point by its order of contact, we show that, generically, the medial axis consists of five types of points, which are then organized into sheets, curves, and points: 1) sheets (manifolds with boundary) which are the locus of bitangent spheres with regular tangency A1(2) (Ak(n) notation means n distinct k-fold tangencies of the sphere of contact, as explained in the text); two types of curves, 2) the intersection curve of three sheets and the locus of centers of tritangent spheres, A1(3), and 3) the boundary of sheets, which are the locus of centers of spheres whose radius equals the larger principal curvature, i.e., higher order contact A3 points; and two types of points, 4) centers of quad-tangent spheres, A1(4), and 5) centers of spheres with one regular tangency and one higher order tangency, A1A3. The geometry of the 3D medial axis thus consists of sheets (A1(2)) bounded by one type of curve (A3) on their free end, which corresponds to ridges on the surface, and attached to two other sheets at another type of curve (A1(3)), which support a generalized cylinder description. The A3 curves can only end in A1A3 points where they must meet an A1(3) curve. The A1(3) curves meet together in fours at an A1(4) point. This formal result leads to a compact representation for 3D shape, referred to as the medial axis hypergraph representation consisting of nodes (A1(4) and A1A3 points), links between pairs of nodes (A1(3) and A3 curves) and hyperlinks between groups of links (A1(2) sheets). The description of the local geometry at nodes by itself is sufficient to capture qualitative aspects of shapes, in analogy to 2D. We derive a pointwise reconstruction formula to reconstruct a surface from this medial axis hypergraph together with the radius function. Thus, this information completely

  12. An optimal sensing strategy for recognition and localization of 3-D natural quadric objects

    NASA Technical Reports Server (NTRS)

    Lee, Sukhan; Hahn, Hernsoo

    1991-01-01

    An optimal sensing strategy for an optical proximity sensor system engaged in the recognition and localization of 3-D natural quadric objects is presented. The optimal sensing strategy consists of the selection of an optimal beam orientation and the determination of an optimal probing plane that compose an optimal data collection operation known as an optimal probing. The decision of an optimal probing is based on the measure of discrimination power of a cluster of surfaces on a multiple interpretation image (MII), where the measure of discrimination power is defined in terms of a utility function computing the expected number of interpretations that can be pruned out by a probing. An object representation suitable for active sensing based on a surface description vector (SDV) distribution graph and hierarchical tables is presented. Experimental results are shown.

  13. Calibration of Panoramic Cameras with Coded Targets and a 3d Calibration Field

    NASA Astrophysics Data System (ADS)

    Tommaselli, A. M. G.; Marcato, J., Jr.; Moraes, M. V. A.; Silva, S. L. A.; Artero, A. O.

    2014-03-01

    The aim of this paper is to present results achieved with a 3D terrestrial calibration field, designed for calibrating digital cameras and omnidirectional sensors. This terrestrial calibration field is composed of 139 ARUCO coded targets. Some experiments were performed using a Nikon D3100 digital camera with 8mm Samyang Bower fisheye lens. The camera was calibrated in this terrestrial test field using a conventional bundle adjustment with the Collinearity and mathematical models specially designed for fisheye lenses. The CMC software (Calibration with Multiple Cameras), developed in-house, was used for the calibration trials. This software was modified to use fisheye models to which the Conrady-Brown distortion equations were added. The target identification and image measurements of its four corners were performed automatically with a public software. Several experiments were performed with 16 images and the results were presented and compared. Besides the calibration of fish-eye cameras, the field was designed for calibration of a catadrioptic system and brief informations on the calibration of this unit will be provided in the paper.

  14. A New Methodology for 3D Target Detection in Automotive Radar Applications.

    PubMed

    Baselice, Fabio; Ferraioli, Giampaolo; Lukin, Sergyi; Matuozzo, Gianfranco; Pascazio, Vito; Schirinzi, Gilda

    2016-01-01

    Today there is a growing interest in automotive sensor monitoring systems. One of the main challenges is to make them an effective and valuable aid in dangerous situations, improving transportation safety. The main limitation of visual aid systems is that they do not produce accurate results in critical visibility conditions, such as in presence of rain, fog or smoke. Radar systems can greatly help in overcoming such limitations. In particular, imaging radar is gaining interest in the framework of Driver Assistance Systems (DAS). In this manuscript, a new methodology able to reconstruct the 3D imaged scene and to detect the presence of multiple targets within each line of sight is proposed. The technique is based on the use of Compressive Sensing (CS) theory and produces the estimation of multiple targets for each line of sight, their range distance and their reflectivities. Moreover, a fast approach for 2D focus based on the FFT algorithm is proposed. After the description of the proposed methodology, different simulated case studies are reported in order to evaluate the performances of the proposed approach. PMID:27136558

  15. A New Methodology for 3D Target Detection in Automotive Radar Applications

    PubMed Central

    Baselice, Fabio; Ferraioli, Giampaolo; Lukin, Sergyi; Matuozzo, Gianfranco; Pascazio, Vito; Schirinzi, Gilda

    2016-01-01

    Today there is a growing interest in automotive sensor monitoring systems. One of the main challenges is to make them an effective and valuable aid in dangerous situations, improving transportation safety. The main limitation of visual aid systems is that they do not produce accurate results in critical visibility conditions, such as in presence of rain, fog or smoke. Radar systems can greatly help in overcoming such limitations. In particular, imaging radar is gaining interest in the framework of Driver Assistance Systems (DAS). In this manuscript, a new methodology able to reconstruct the 3D imaged scene and to detect the presence of multiple targets within each line of sight is proposed. The technique is based on the use of Compressive Sensing (CS) theory and produces the estimation of multiple targets for each line of sight, their range distance and their reflectivities. Moreover, a fast approach for 2D focus based on the FFT algorithm is proposed. After the description of the proposed methodology, different simulated case studies are reported in order to evaluate the performances of the proposed approach. PMID:27136558

  16. Study of a dense, coronal thick target source with the microwave data and 3D modeling

    NASA Astrophysics Data System (ADS)

    Fleishman, Gregory; Xu, Yan

    2015-04-01

    We present a detailed 3D modeling of a dense, coronal thick target X-ray flare using the GX Simulator tool, photospheric magnetic measurements, and microwave data. The developed model offers a remarkable agreement between the synthesized and observed spectra and images in both X-ray and microwave domains, which validates the entire model. The flaring loop parameters validated via the modeling are fully consistent with those derived from the X-ray spectral fit, but do not easily agree with those derived from the fit of the X-ray image sizes computed at various energies. Specifically, the plasma density obtained in the modeling is noticeably smaller than that derived from the size fit. The performed modeling suggests that the accelerated electrons are trapped at the coronal part of the flaring loop by a turbulence, while proves that the data are clearly inconsistent with the electron magnetic trapping in the weak diffusion regime mediated by the Coulomb collisions. Thus, the modeling confirms the interpretation of the coronal thick-target sources as the sites of electron acceleration in flares.This work was supported in part by NSF grants AGS-1250374, AGS-1262772, AGS-1153424, AGS-1348513, and AGS-1408703 and NASA grants NNX14AC87G and NNX-13AG13G to New Jersey Institute of Technology.

  17. 3D localization of electrophysiology catheters from a single x-ray cone-beam projection

    SciTech Connect

    Robert, Normand Polack, George G.; Sethi, Benu; Rowlands, John A.; Crystal, Eugene

    2015-10-15

    Purpose: X-ray images allow the visualization of percutaneous devices such as catheters in real time but inherently lack depth information. The provision of 3D localization of these devices from cone beam x-ray projections would be advantageous for interventions such as electrophysiology (EP), whereby the operator needs to return a device to the same anatomical locations during the procedure. A method to achieve real-time 3D single view localization (SVL) of an object of known geometry from a single x-ray image is presented. SVL exploits the change in the magnification of an object as its distance from the x-ray source is varied. The x-ray projection of an object of interest is compared to a synthetic x-ray projection of a model of said object as its pose is varied. Methods: SVL was tested with a 3 mm spherical marker and an electrophysiology catheter. The effect of x-ray acquisition parameters on SVL was investigated. An independent reference localization method was developed to compare results when imaging a catheter translated via a computer controlled three-axes stage. SVL was also performed on clinical fluoroscopy image sequences. A commercial navigation system was used in some clinical image sequences for comparison. Results: SVL estimates exhibited little change as x-ray acquisition parameters were varied. The reproducibility of catheter position estimates in phantoms denoted by the standard deviations, (σ{sub x}, σ{sub y}, σ{sub z}) = (0.099 mm,  0.093 mm,  2.2 mm), where x and y are parallel to the detector plane and z is the distance from the x-ray source. Position estimates (x, y, z) exhibited a 4% systematic error (underestimation) when compared to the reference method. The authors demonstrated that EP catheters can be tracked in clinical fluoroscopic images. Conclusions: It has been shown that EP catheters can be localized in real time in phantoms and clinical images at fluoroscopic exposure rates. Further work is required to characterize

  18. Modified fibrin hydrogel matrices: both, 3D-scaffolds and local and controlled release systems to stimulate angiogenesis.

    PubMed

    Hall, Heike

    2007-01-01

    Sufficient blood perfusion is essential for all tissues to guarantee nutrient- and gas exchange. As many diseases are induced by the reduction of blood perfusion such that these tissues gradually loose their ability to function properly, therapeutic angiogenesis aims to increase blood flow in ischemic tissues by stimulating the patient's endogenous capacity to develop new blood vessels. These studies include application of angiogenesis stimulating (growth) factors and adhesion sequences as well as local gene therapy. One approach is to rationally design 3D-fibrin hydrogel matrices that provide specific adhesion sequences such as a receptor for alpha v beta 3-integrin expressed on angiogenic endothelial cells and that, in addition, are able to store and release angiogenic growth factors such as VEGF-A(165) and bFGF that target cell type-specific responses. Moreover, these matrices can be modified to release complexed plasmid DNA that transfect surrounding cells and improve angiogenesis. During wound healing, cells infiltrate into the scaffold and degrade it, thereby releasing entrapped growth factors or complexed plasmid DNA, and with the speed of tissue regeneration the scaffold is completely removed when tissue healing is achieved. The long-term aim is to develop biomimetic 3D-matrices for applications in a biomaterials context that can be applied directly at the site of injury by minimal invasive surgery. 3D-fibrin matrices constitute a scaffold and release system for single or combined therapeutic biomolecules and may therefore be able to contribute to the patients' endogenous healing response resulting in the functional recovery of a diseased tissue or organ. PMID:18220797

  19. Intrafractional 3D localization using kilovoltage digital tomosynthesis for sliding-window intensity modulated radiation therapy.

    PubMed

    Zhang, Pengpeng; Hunt, Margie; Pham, Hai; Tang, Grace; Mageras, Gig

    2015-09-01

    To implement novel imaging sequences integrated into intensity modulated radiation therapy (IMRT) and determine 3D positions for intrafractional patient motion monitoring and management.In one method, we converted a static gantry IMRT beam into a series of arcs in which dose index and multileaf collimator positions for all control points were unchanged, but gantry angles were modified to oscillate ± 3° around the original angle. Kilovoltage (kV) projections were acquired continuously throughout delivery and reconstructed to provide a series of 6° arc digital tomosynthesis (DTS) images which served to evaluate the in-plane positions of embedded-fiducials/vertebral-body. To obtain out-of-plane positions via triangulation, a 20° gantry rotation with beam hold-off was inserted during delivery to produce a pair of 6° DTS images separated by 14°. In a second method, the gantry remained stationary, but both kV source and detector moved over a 15° longitudinal arc using pitch and translational adjustment of the robotic arms. Evaluation of localization accuracy in an anthropomorphic Rando phantom during simulated intrafractional motion used programmed couch translations from customized scripts. Purpose-built software was used to reconstruct DTS images, register them to reference template images and calculate 3D fiducial positions.No significant dose difference (<0.5%) was found between the original and converted IMRT beams. For a typical hypofractionated spine treatment, 200 single DTS (6° arc) and 10 paired DTS (20° arc) images were acquired for each IMRT beam, providing in-plane and out-of-plane monitoring every 1.6 and 34.5 s, respectively. Mean ± standard deviation error in predicted position was -0.3 ± 0.2 mm, -0.1 ± 0.1 mm in-plane, and 0.2 ± 0.4 mm out-of-plane with rotational gantry, 0.8 ± 0.1 mm, -0.7 ± 0.3 mm in-plane and 1.1 ± 0.1 mm out-of-plane with translational source/detector.Acquiring 3D fiducial positions from kV-DTS during fixed gantry

  20. Clean localization super-resolution microscopy for 3D biological imaging

    NASA Astrophysics Data System (ADS)

    Mondal, Partha P.; Curthoys, Nikki M.; Hess, Samuel T.

    2016-01-01

    We propose clean localization microscopy (a variant of fPALM) using a molecule filtering technique. Localization imaging involves acquiring a large number of images containing single molecule signatures followed by one-to-one mapping to render a super-resolution image. In principle, this process can be repeated for other z-planes to construct a 3D image. But, single molecules observed from off-focal planes result in false representation of their presence in the focal plane, resulting in incorrect quantification and analysis. We overcome this with a single molecule filtering technique that imposes constraints on the diffraction limited spot size of single molecules in the image plane. Calibration with sub-diffraction size beads puts a natural cutoff on the actual diffraction-limited size of single molecules in the focal plane. This helps in distinguishing beads present in the focal plane from those in the off-focal planes thereby providing an estimate of the single molecules in the focal plane. We study the distribution of actin (labeled with a photoactivatable CAGE 552 dye) in NIH 3T3 mouse fibroblast cells.

  1. 3-D statistical cancer atlas-based targeting of prostate biopsy using ultrasound image guidance

    NASA Astrophysics Data System (ADS)

    Narayanan, Ramkrishnan; Shen, Dinggang; Davatzikos, Christos A.; Crawford, E. David; Barqawi, Albaha; Werahera, Priya; Kumar, Dinesh; Suri, Jasjit S.

    2008-03-01

    Prostate cancer is a multifocal disease and lesions are not distributed uniformly within the gland. Several biopsy protocols concerning spatially specific targeting have been reported urology literature. Recently a statistical cancer atlas of the prostate was constructed providing voxelwise probabilities of cancers in the prostate. Additionally an optimized set of biopsy sites was computed with 94 - 96% detection accuracy was reported using only 6-7 needles. Here we discuss the warping of this atlas to prostate segmented side-fire ultrasound images of the patient. A shape model was used to speed up registration. The model was trained from over 38 expert segmented subjects off-line. This training yielded as few as 15-20 degrees of freedom that were optimized to warp the atlas surface to the patient's ultrasound image followed by elastic interpolation of the 3-D atlas. As a result the atlas is completely mapped to the patient's prostate anatomy along with optimal predetermined needle locations for biopsy. These do not preclude the use of additional biopsies if desired. A color overlay of the atlas is also displayed on the ultrasound image showing high cancer zones within the prostate. Finally current biopsy locations are saved in the atlas space and may be used to update the atlas based on the pathology report. In addition to the optimal atlas plan, previous biopsy locations and alternate plans can also be stored in the atlas space and warped to the patient with no additional time overhead.

  2. Improved EEG source localization employing 3D sensing by "Flying Triangulation"

    NASA Astrophysics Data System (ADS)

    Ettl, Svenja; Rampp, Stefan; Fouladi-Movahed, Sarah; Dalal, Sarang S.; Willomitzer, Florian; Arold, Oliver; Stefan, Hermann; Häusler, Gerd

    2013-04-01

    With electroencephalography (EEG), a person's brain activity can be monitored over time and sources of activity localized. With this information, brain regions showing pathological activity, such as epileptic spikes, can be delineated. In cases of severe drug-resistant epilepsy, surgical resection of these brain regions may be the only treatment option. This requires a precise localization of the responsible seizure generators. They can be reconstructed from EEG data when the electrode positions are known. The standard method employs a "digitization pen" and has severe drawbacks: It is time consuming, the result is user-dependent, and the patient has to hold still. We present a novel method which overcomes these drawbacks. It is based on the optical "Flying Triangulation" (FlyTri) sensor which allows a motion-robust acquisition of precise 3D data. To compare the two methods, the electrode positions were determined with each method for a real-sized head model with EEG electrodes and their deviation to the ground-truth data calculated. The standard deviation for the current method was 3.39 mm while it was 0.98 mm for the new method. The influence of these results on the final EEG source localization was investigated by simulating EEG data. The digitization pen result deviates substantially from the true source location and time series. In contrast, the FlyTri result agrees with the original information. Our findings suggest that FlyTri might become a valuable tool in the field of medical brain research, because of its improved precision and contactless handling. Future applications might include co-registration of multimodal information.

  3. The use of 3D shape models of Rosetta targets for morphological studies

    NASA Astrophysics Data System (ADS)

    Capanna, C.; Jorda, L.; Auger, A.-T.; Groussin, O.; Gaskell, R.; Hviid, S.; Lamy, P.

    2015-10-01

    New 3D reconstruction techniques have been developed during the last decade to retrieve the global and/or local topography of small solar system bodies from visible images. These techniques can be separated into two categories: the so-called "photoclinometric" and the so-called "photogrammetric" techniques. Two implementations of the photoclinometric technique are available: the SPC technique (StereoPhotoClinometry) which combines sparse stereo with a classical clinometry algorithm[1] and a more recent method called MSPCD (Multi- Resolution Stereo-PhotoClinometry by Deformation) which proceeds by iterative deformation of a triangular mesh in a multi-resolution scheme[2], using stereo points as a guide during the deformation[3]. Our study is based on the 3D shape models of the asteroid Lutetia and of the comet 67P/Churyumov- Gerasimenko retrieved by the SPC and MSPCD methods. More specifically, we describe how the models produced by these two techniques can contribute to detailed and quantitative studies of the morphological properties of small bodies through three test cases shortly described below.• Measurement of crater depth and depth-to-diameter distribution. We show that the reconstruction techniques can lead to systematic differences in the measurement of crater depth. This will be illustrated by a set of craters[4] identified in the Achaia region at the surface of the asteroid 21 Lutetia. • Calculation of the volume of large boulders at the surface of comet 67P/C-G. We show how the reconstruction technique affects significantly the volume determination of a large boulder named Cheops in the Imhotep region. • Measurement of gravitational slopes. We discuss the differences between the gravitational slope distributions in Seth obtained with the SPC and MSPCD models[5]. Since no ground control points are available on small bodies, we use the comparison of high-resolution images with the corresponding synthetic images generated with the models[6] to assess

  4. Automatic registration of optical imagery with 3d lidar data using local combined mutual information

    NASA Astrophysics Data System (ADS)

    Parmehr, E. G.; Fraser, C. S.; Zhang, C.; Leach, J.

    2013-10-01

    Automatic registration of multi-sensor data is a basic step in data fusion for photogrammetric and remote sensing applications. The effectiveness of intensity-based methods such as Mutual Information (MI) for automated registration of multi-sensor image has been previously reported for medical and remote sensing applications. In this paper, a new multivariable MI approach that exploits complementary information of inherently registered LiDAR DSM and intensity data to improve the robustness of registering optical imagery and LiDAR point cloud, is presented. LiDAR DSM and intensity information has been utilised in measuring the similarity of LiDAR and optical imagery via the Combined MI. An effective histogramming technique is adopted to facilitate estimation of a 3D probability density function (pdf). In addition, a local similarity measure is introduced to decrease the complexity of optimisation at higher dimensions and computation cost. Therefore, the reliability of registration is improved due to the use of redundant observations of similarity. The performance of the proposed method for registration of satellite and aerial images with LiDAR data in urban and rural areas is experimentally evaluated and the results obtained are discussed.

  5. Plane Localization in 3-D Fetal Neurosonography for Longitudinal Analysis of the Developing Brain.

    PubMed

    Yaqub, Mohammad; Rueda, Sylvia; Kopuri, Anil; Melo, Pedro; Papageorghiou, A T; Sullivan, Peter B; McCormick, Kenneth; Noble, J Alison

    2016-07-01

    The parasagittal (PS) plane is a 2-D diagnostic plane used routinely in cranial ultrasonography of the neonatal brain. This paper develops a novel approach to find the PS plane in a 3-D fetal ultrasound scan to allow image-based biomarkers to be tracked from prebirth through the first weeks of postbirth life. We propose an accurate plane-finding solution based on regression forests (RF). The method initially localizes the fetal brain and its midline automatically. The midline on several axial slices is used to detect the midsagittal plane, which is used as a constraint in the proposed RF framework to detect the PS plane. The proposed learning algorithm guides the RF learning method in a novel way by: 1) using informative voxels and voxel informative strength as a weighting within the training stage objective function, and 2) introducing regularization of the RF by proposing a geometrical feature within the training stage. Results on clinical data indicate that the new automated method is more reproducible than manual plane finding obtained by two clinicians. PMID:26011873

  6. Indoor Localization Algorithms for an Ambulatory Human Operated 3D Mobile Mapping System

    SciTech Connect

    Corso, N; Zakhor, A

    2013-12-03

    Indoor localization and mapping is an important problem with many applications such as emergency response, architectural modeling, and historical preservation. In this paper, we develop an automatic, off-line pipeline for metrically accurate, GPS-denied, indoor 3D mobile mapping using a human-mounted backpack system consisting of a variety of sensors. There are three novel contributions in our proposed mapping approach. First, we present an algorithm which automatically detects loop closure constraints from an occupancy grid map. In doing so, we ensure that constraints are detected only in locations that are well conditioned for scan matching. Secondly, we address the problem of scan matching with poor initial condition by presenting an outlier-resistant, genetic scan matching algorithm that accurately matches scans despite a poor initial condition. Third, we present two metrics based on the amount and complexity of overlapping geometry in order to vet the estimated loop closure constraints. By doing so, we automatically prevent erroneous loop closures from degrading the accuracy of the reconstructed trajectory. The proposed algorithms are experimentally verified using both controlled and real-world data. The end-to-end system performance is evaluated using 100 surveyed control points in an office environment and obtains a mean accuracy of 10 cm. Experimental results are also shown on three additional datasets from real world environments including a 1500 meter trajectory in a warehouse sized retail shopping center.

  7. 3-D localization of gamma ray sources with coded apertures for medical applications

    NASA Astrophysics Data System (ADS)

    Kaissas, I.; Papadimitropoulos, C.; Karafasoulis, K.; Potiriadis, C.; Lambropoulos, C. P.

    2015-09-01

    Several small gamma cameras for radioguided surgery using CdTe or CdZnTe have parallel or pinhole collimators. Coded aperture imaging is a well-known method for gamma ray source directional identification, applied in astrophysics mainly. The increase in efficiency due to the substitution of the collimators by the coded masks renders the method attractive for gamma probes used in radioguided surgery. We have constructed and operationally verified a setup consisting of two CdTe gamma cameras with Modified Uniform Redundant Array (MURA) coded aperture masks of rank 7 and 19 and a video camera. The 3-D position of point-like radioactive sources is estimated via triangulation using decoded images acquired by the gamma cameras. We have also developed code for both fast and detailed simulations and we have verified the agreement between experimental results and simulations. In this paper we present a simulation study for the spatial localization of two point sources using coded aperture masks with rank 7 and 19.

  8. Locally adaptive 2D-3D registration using vascular structure model for liver catheterization.

    PubMed

    Kim, Jihye; Lee, Jeongjin; Chung, Jin Wook; Shin, Yeong-Gil

    2016-03-01

    Two-dimensional-three-dimensional (2D-3D) registration between intra-operative 2D digital subtraction angiography (DSA) and pre-operative 3D computed tomography angiography (CTA) can be used for roadmapping purposes. However, through the projection of 3D vessels, incorrect intersections and overlaps between vessels are produced because of the complex vascular structure, which makes it difficult to obtain the correct solution of 2D-3D registration. To overcome these problems, we propose a registration method that selects a suitable part of a 3D vascular structure for a given DSA image and finds the optimized solution to the partial 3D structure. The proposed algorithm can reduce the registration errors because it restricts the range of the 3D vascular structure for the registration by using only the relevant 3D vessels with the given DSA. To search for the appropriate 3D partial structure, we first construct a tree model of the 3D vascular structure and divide it into several subtrees in accordance with the connectivity. Then, the best matched subtree with the given DSA image is selected using the results from the coarse registration between each subtree and the vessels in the DSA image. Finally, a fine registration is conducted to minimize the difference between the selected subtree and the vessels of the DSA image. In experimental results obtained using 10 clinical datasets, the average distance errors in the case of the proposed method were 2.34±1.94mm. The proposed algorithm converges faster and produces more correct results than the conventional method in evaluations on patient datasets. PMID:26824922

  9. Measurements of non-target organ doses using MOSFET dosemeters for selected IMRT and 3D CRT radiation treatment procedures.

    PubMed

    Wang, Brian; Xu, X George

    2008-01-01

    Many expressed concerns about the potential increase in second cancer risk from the widespread shift to intensity-modulated radiation therapy (IMRT) techniques from traditional 3-D conformal radiation treatment (3D CRT). This paper describes the study on in-phantom measurements of radiation doses in organ sites away from the primary tumour target. The measurements involved a RANDO((R)) phantom and Metal Oxide Semiconductor Field Effect Transistor dosemeters for selected 3D CRT and IMRT treatment plans. Three different treatment plans, 4-field 3D CRT, 6-field 3D CRT and 7-field IMRT for the prostate, were considered in this study. Steps to reconstruct organ doses from directly measured data were also presented. The dosemeter readings showed that the doses decrease as the distances increase for all treatment plans. At 40 cm from the prostate target, doses were <1% of the therapeutic dose. At this location, however, the IMRT plan resulted in an absorbed dose from photons, that is a factor of 3-5 higher than the 3D CRT treatment plans. This increase on absorbed dose is due to the increased exposure time for delivering the IMRT plan. The total monitor unit (MU) was 2850 for the IMRT case, while the MU was 1308 and 1260 for 6-field and 4-field 3D CRT cases, respectively. Findings from this case study involving the prostate treatments agree with those from previous studies that IMRT indeed delivers higher photon doses to locations that are away from the primary target. PMID:17627959

  10. Combined global 2D-local 3D modeling of the industrial Czochralski silicon crystal growth process

    NASA Astrophysics Data System (ADS)

    Jung, T.; Seebeck, J.; Friedrich, J.

    2013-04-01

    A global, axisymmetric thermal model of a Czochralski furnace is coupled to an external, local, 3D, time-dependent flow model of the melt via the inclusion of turbulent heat fluxes, extracted from the 3D melt model, into the 2D furnace model. Boundary conditions of the 3D model are updated using results from the 2D model. In the 3D model the boundary layers are resolved by aggressive mesh refinement towards the walls, and the Large Eddy Simulation approach is used to model the turbulent flow in the melt volume on a relatively coarse mesh to minimize calculation times. It is shown that by using this approach it is possible to reproduce fairly good results from Direct Numerical Simulations obtained on much finer meshes, as well as experimental results for interface shape and oxygen concentration in the case of growth of silicon crystals with 210 mm diameter for photovoltaics by the Czochralski method.

  11. Joint Cross-Range Scaling and 3D Geometry Reconstruction of ISAR Targets Based on Factorization Method.

    PubMed

    Lei Liu; Feng Zhou; Xue-Ru Bai; Ming-Liang Tao; Zi-Jing Zhang

    2016-04-01

    Traditionally, the factorization method is applied to reconstruct the 3D geometry of a target from its sequential inverse synthetic aperture radar images. However, this method requires performing cross-range scaling to all the sub-images and thus has a large computational burden. To tackle this problem, this paper proposes a novel method for joint cross-range scaling and 3D geometry reconstruction of steadily moving targets. In this method, we model the equivalent rotational angular velocity (RAV) by a linear polynomial with time, and set its coefficients randomly to perform sub-image cross-range scaling. Then, we generate the initial trajectory matrix of the scattering centers, and solve the 3D geometry and projection vectors by the factorization method with relaxed constraints. After that, the coefficients of the polynomial are estimated from the projection vectors to obtain the RAV. Finally, the trajectory matrix is re-scaled using the estimated rotational angle, and accurate 3D geometry is reconstructed. The two major steps, i.e., the cross-range scaling and the factorization, are performed repeatedly to achieve precise 3D geometry reconstruction. Simulation results have proved the effectiveness and robustness of the proposed method. PMID:26886991

  12. 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

  13. Applications of detailed 3D P-wave velocity crustal model in Poland for local, regional and global seismic tomography

    NASA Astrophysics Data System (ADS)

    Polkowski, Marcin; Grad, Marek

    2015-04-01

    The 3D P-wave seismic velocity model was obtained by combining data from multiple studies during past 50 years. Data sources included refraction seismology, reflection seismology, geological boreholes, vertical seismic profiling, magnetotellurics and gravimetry. Use of many data sources allowed creation of detailed 3D P-wave velocity model that reaches to depth of 60 km and includes 6-layers of sediments and 3-layers of the crust. Purpose of this study is to analyze how 3D model influences local (accuracy of location and source time estimation for local events), regional (identification of wide-angle seismic phases) and global (teleseismic tomography) seismic travel times. Additionally we compare results of forward seismic wave propagation with signals observed on short period and broadband stations. National Science Centre Poland provided financial support for this work by NCN grant DEC-2011/02/A/ST10/00284.

  14. A Generalized Functional Model Based Method for Vibration-Based Damage Precise Localization in 3D Structures

    NASA Astrophysics Data System (ADS)

    Sakaris, Christos S.; Sakellariou, John S.; Fassois, Spilios D.

    2015-07-01

    A Generalized Functional Model Based Method for vibration-based damage precise localization on structures consisting of 1D, 2D, or 3D elements is introduced. The method generalizes previous versions applicable to structures consisting of 1D elements, thus allowing for 2D and 3D elements as well. It is based on scalar (single sensor) or vector (multiple sensor) Functional Models which - in the inspection phase - incorporate the mathematical form of the specific structural topology. Precise localization is then based on coordinate estimation within this model structure, and confidence bounds are also obtained. The effectiveness of the method is demonstrated through experiments on a 3D truss structure where damage corresponds to single bolt loosening. Both the scalar and vector versions of the method are shown to be effective even within a very limited, low frequency, bandwidth of 3-59 Hz. The improvement achieved through the use of multiple sensors is also demonstrated.

  15. 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

  16. Joint azimuth and elevation localization estimates in 3D synthetic aperture radar scenarios

    NASA Astrophysics Data System (ADS)

    Pepin, Matthew

    2015-05-01

    The location of point scatterers in Synthetic Aperture Radar (SAR) data is exploited in several modern analyzes including persistent scatter tracking, terrain deformation, and object identification. The changes in scatterers over time (pulse-to-pulse including vibration and movement, or pass-to-pass including direct follow on, time of day, and season), can be used to draw more information about the data collection. Multiple pass and multiple antenna SAR scenarios have extended these analyzes to location in three dimensions. Either multiple passes at different elevation angles may be .own or an antenna array with an elevation baseline performs a single pass. Parametric spectral estimation in each dimension allows sub-pixel localization of point scatterers in some cases additionally exploiting the multiple samples in each cross dimension. The accuracy of parametric estimation is increased when several azimuth passes or elevations (snapshots) are summed to mitigate measurement noise. Inherent range curvature across the aperture however limits the accuracy in the range dimension to that attained from a single pulse. Unlike the stationary case where radar returns may be averaged the movement necessary to create the synthetic aperture is only approximately (to pixel level accuracy) removed to form SAR images. In parametric estimation increased accuracy is attained when two dimensions are used to jointly estimate locations. This paper involves jointly estimating azimuth and elevation to attain increased accuracy 3D location estimates. In this way the full 2D array of azimuth and elevation samples is used to obtain the maximum possible accuracy. In addition the independent dimension collection geometry requires choosing which dimension azimuth or elevation attains the highest accuracy while joint estimation increases accuracy in both dimensions. When maximum parametric estimation accuracy in azimuth is selected the standard interferometric SAR scenario results. When

  17. 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

  18. Identifying High Potential Well Targets with 3D Seismic and Mineralogy

    SciTech Connect

    Mellors, R. J.

    2015-10-30

    Seismic reflection the primary tool used in petroleum exploration and production, but use in geothermal exploration is less standard, in part due to cost but also due to the challenges in identifying the highly-permeable zones essential for economic hydrothermal systems [e.g. Louie et al., 2011; Majer, 2003]. Newer technology, such as wireless sensors and low-cost high performance computing, has helped reduce the cost and effort needed to conduct 3D surveys. The second difficulty, identifying permeable zones, has been less tractable so far. Here we report on the use of seismic attributes from a 3D seismic survey to identify and map permeable zones in a hydrothermal area.

  19. 3-D electromagnetic modeling for very early time sounding of shallow targets using integral equations

    SciTech Connect

    Xiong, Z.; Tripp, A.C.

    1994-12-31

    This paper presents an integral equation algorithm for 3D EM modeling at high frequencies for applications in engineering an environmental studies. The integral equation method remains the same for low and high frequencies, but the dominant roles of the displacements currents complicate both numerical treatments and interpretations. With singularity extraction technique they successively extended the application of the Hankel filtering technique to the computation of Hankel integrals occurring in high frequency EM modeling. Time domain results are calculated from frequency domain results via Fourier transforms. While frequency domain data are not obvious for interpretations, time domain data show wave-like pictures that resemble seismograms. Both 1D and 3D numerical results show clearly the layer interfaces.

  20. 3D Simulations of the NIF Indirect Drive Ignition Target Design

    SciTech Connect

    Jones, O S; Milovich, J L; Callahan, D A; Edwards, M J; Landen, O L; Salmonson, J D; Clark, D S; Haan, S W; Marinak, M M; Patel, M V; Langer, S H; Sepke, S M; Springer, P T; Hatchett, S P

    2010-01-05

    The radiation hydrodynamics code Hydra is used to quantify the sensitivity of different NIF ignition point designs to several 3D effects. Each of the 48 NIF quads is included in the calculations and is allowed to have different power. With this model they studied the effect on imploded core symmetry of discrete laser spots (as opposed to idealized azimuthally-averaged rings) and random variations in laser power.

  1. A cut-&-paste strategy for the 3-D inversion of helicopter-borne electromagnetic data - II. Combining regional 1-D and local 3-D inversion

    NASA Astrophysics Data System (ADS)

    Ullmann, A.; Scheunert, M.; Afanasjew, M.; Börner, R.-U.; Siemon, B.; Spitzer, K.

    2016-07-01

    As a standard procedure, multi-frequency helicopter-borne electromagnetic (HEM) data are inverted to conductivity-depth models using 1-D inversion methods, which may, however, fail in areas of strong lateral conductivity contrasts (so-called induction anomalies). Such areas require more realistic multi-dimensional modelling. Since the full 3-D inversion of an entire HEM data set is still extremely time consuming, our idea is to combine fast 1-D and accurate but numerically expensive 3-D inversion of HEM data in such a way that the full 3-D inversion is only carried out for those parts of a HEM survey which are affected by induction anomalies. For all other parts, a 1-D inversion method is sufficient. We present a newly developed algorithm for identification, selection, and extraction of induction anomalies in HEM data sets and show how the 3-D inversion model of the anomalous area is re-integrated into the quasi-1-D background. Our proposed method is demonstrated to work properly on a synthetic and a field HEM data set from the Cuxhaven tunnel valley in Germany. We show that our 1-D/3-D approach yields better results compared to 1-D inversions in areas where 3-D effects occur.

  2. Targets For Three-Dimensional (3-D) Tracking Of Human Impact Test Subjects

    NASA Astrophysics Data System (ADS)

    Muzzy, William H.; Prell, Arthur M.

    1982-02-01

    Lightweight targets mounted on the head and neck of human volunteers are photographed by high-speed cameras during impact acceleration tests. The targets must be capable of being tracked through a wide angular motion by at least two cameras to obtain three-dimens-ional displacement and orientation. Because the targets are tracked and digitized by a computerized photodigitizer, their pattern must be selected to maximize recognition and minimize crossover confusion. This pater discusses the target construction, orientation on the accelerometer mount, pattern selection, and paint scheme.

  3. Local plate/rod descriptors of 3D trabecular bone micro-CT images from medial axis topologic analysis

    SciTech Connect

    Peyrin, Francoise; Attali, Dominique; Chappard, Christine; Benhamou, Claude Laurent

    2010-08-15

    Purpose: Trabecular bone microarchitecture is made of a complex network of plate and rod structures evolving with age and disease. The purpose of this article is to propose a new 3D local analysis method for the quantitative assessment of parameters related to the geometry of trabecular bone microarchitecture. Methods: The method is based on the topologic classification of the medial axis of the 3D image into branches, rods, and plates. Thanks to the reversibility of the medial axis, the classification is next extended to the whole 3D image. Finally, the percentages of rods and plates as well as their mean thicknesses are calculated. The method was applied both to simulated test images and 3D micro-CT images of human trabecular bone. Results: The classification of simulated phantoms made of plates and rods shows that the maximum error in the quantitative percentages of plate and rods is less than 6% and smaller than with the structure model index (SMI). Micro-CT images of human femoral bone taken in osteoporosis and early or advanced osteoarthritis were analyzed. Despite the large physiological variability, the present method avoids the underestimation of rods observed with other local methods. The relative percentages of rods and plates were not significantly different between osteoarthritis and osteoporotic groups, whereas their absolute percentages were in relation to an increase of rod and plate thicknesses in advanced osteoarthritis with also higher relative and absolute number of nodes. Conclusions: The proposed method is model-independent, robust to surface irregularities, and enables geometrical characterization of not only skeletal structures but entire 3D images. Its application provided more accurate results than the standard SMI on simple simulated phantoms, but the discrepancy observed on the advanced osteoarthritis group raises questions that will require further investigations. The systematic use of such a local method in the characterization of

  4. Fourier-Space Nonlinear Rayleigh-Taylor Growth Measurements of 3D Laser-Imprinted Modulations in Planar Targets

    SciTech Connect

    Smalyuk, V.A.; Sadot, O.; Delettrez, J.A.; Meyerhofer, D.D.; Regan, S.P.; Sangster, T.C.

    2005-12-05

    Nonlinear growth of 3-D broadband nonuniformities was measured near saturation levels using x-ray radiography in planar foils accelerated by laser light. The initial target modulations were seeded by laser nonuniformities and later amplified during acceleration by Rayleigh-Taylor instability. The nonlinear saturation velocities are measured for the first time and are found to be in excellent agreement with Haan predictions. The measured growth of long-wavelength modes is consistent with enhanced, nonlinear, long-wavelength generation in ablatively driven targets.

  5. Detecting Distance between Injected Microspheres and Target Tumor via 3D Reconstruction of Tissue Sections

    SciTech Connect

    Carson, James P.; Kuprat, Andrew P.; Colby, Sean M.; Davis, Cassi A.; Basciano, Christopher; Greene, Kevin; Feo, John T.; Kennedy, Andrew

    2012-08-28

    One treatment increasing in use for solid tumors in the liver is radioembolization via the delivery of 90Y microspheres to the vascular bed within or near the location of the tumor. It is desirable as part of the treatment for the microspheres to embed preferentially in or near the tumor. This work details an approach for analyzing the deposition of microspheres with respect to the location of the tumor. The approach used is based upon thin-slice serial sectioning of the tissue sample, followed by high resolution imaging, microsphere detection, and 3-D reconstruction of the tumor surface. Distance from the microspheres to the tumor was calculated using a fast deterministic point inclusion method.

  6. RELAP5-3D thermal hydraulic analysis of the target cooling system in the SPES experimental facility

    NASA Astrophysics Data System (ADS)

    Giardina, M.; Castiglia, F.; Buffa, P.; Palermo, G.; Prete, G.

    2014-11-01

    The SPES (Selective Production of Exotic Species) experimental facility, under construction at the Italian National Institute of Nuclear Physics (INFN) Laboratories of Legnaro, Italy, is a second generation Isotope Separation On Line (ISOL) plant for advanced nuclear physic studies. The UCx target-ion source system works at temperature of about 2273 K, producing a high level of radiation (105 Sv/h), for this reason a careful risk analysis for the target chamber is among the major safety issues. In this paper, the obtained results of thermofluid-dynamics simulations of accidental transients in the SPES target cooling system are reported. The analysis, performed by using the RELAP5-3D 2.4.2 qualified thermal-hydraulic system code, proves good safety performance of this system during different accidental conditions.

  7. On FAST3D simulations of directly-driven inertial-fusion targets with high-Z layers for reducing laser imprint and surface non-uniformity growth

    NASA Astrophysics Data System (ADS)

    Bates, Jason; Schmitt, Andrew; Klapisch, Marcel; Karasik, Max; Obenschain, Steve

    2013-10-01

    Modifications to the FAST3D code have been made to enhance its ability to simulate the dynamics of plastic ICF targets with high-Z overcoats. This class of problems is challenging computationally due in part to plasma conditions that are not in a state of local thermodynamic equilibrium and to the presence of mixed computational cells containing more than one material. Recently, new opacity tables for gold, palladium and plastic have been generated with an improved version of the STA code. These improved tables provide smoother, higher-fidelity opacity data over a wider range of temperature and density states than before, and contribute to a more accurate treatment of radiative transfer processes in FAST3D simulations. Furthermore, a new, more efficient subroutine known as ``MMEOS'' has been installed in the FAST3D code for determining pressure and temperature equilibrium conditions within cells containing multiple materials. We will discuss these topics, and present new simulation results for high-Z planar-target experiments performed recently on the NIKE Laser Facility. Work supported by DOE/NNSA.

  8. Preservation of protein fluorescence in embedded human dendritic cells for targeted 3D light and electron microscopy.

    PubMed

    Höhn, K; Fuchs, J; Fröber, A; Kirmse, R; Glass, B; Anders-Össwein, M; Walther, P; Kräusslich, H-G; Dietrich, C

    2015-08-01

    In this study, we present a correlative microscopy workflow to combine detailed 3D fluorescence light microscopy data with ultrastructural information gained by 3D focused ion beam assisted scanning electron microscopy. The workflow is based on an optimized high pressure freezing/freeze substitution protocol that preserves good ultrastructural detail along with retaining the fluorescence signal in the resin embedded specimens. Consequently, cellular structures of interest can readily be identified and imaged by state of the art 3D confocal fluorescence microscopy and are precisely referenced with respect to an imprinted coordinate system on the surface of the resin block. This allows precise guidance of the focused ion beam assisted scanning electron microscopy and limits the volume to be imaged to the structure of interest. This, in turn, minimizes the total acquisition time necessary to conduct the time consuming ultrastructural scanning electron microscope imaging while eliminating the risk to miss parts of the target structure. We illustrate the value of this workflow for targeting virus compartments, which are formed in HIV-pulsed mature human dendritic cells. PMID:25786567

  9. Preservation of protein fluorescence in embedded human dendritic cells for targeted 3D light and electron microscopy

    PubMed Central

    HÖHN, K.; FUCHS, J.; FRÖBER, A.; KIRMSE, R.; GLASS, B.; ANDERS‐ÖSSWEIN, M.; WALTHER, P.; KRÄUSSLICH, H.‐G.

    2015-01-01

    Summary In this study, we present a correlative microscopy workflow to combine detailed 3D fluorescence light microscopy data with ultrastructural information gained by 3D focused ion beam assisted scanning electron microscopy. The workflow is based on an optimized high pressure freezing/freeze substitution protocol that preserves good ultrastructural detail along with retaining the fluorescence signal in the resin embedded specimens. Consequently, cellular structures of interest can readily be identified and imaged by state of the art 3D confocal fluorescence microscopy and are precisely referenced with respect to an imprinted coordinate system on the surface of the resin block. This allows precise guidance of the focused ion beam assisted scanning electron microscopy and limits the volume to be imaged to the structure of interest. This, in turn, minimizes the total acquisition time necessary to conduct the time consuming ultrastructural scanning electron microscope imaging while eliminating the risk to miss parts of the target structure. We illustrate the value of this workflow for targeting virus compartments, which are formed in HIV‐pulsed mature human dendritic cells. PMID:25786567

  10. 3D high-content screening for the identification of compounds that target cells in dormant tumor spheroid regions

    SciTech Connect

    Wenzel, Carsten; Riefke, Björn; Gründemann, Stephan; Krebs, Alice; Christian, Sven; Prinz, Florian; Osterland, Marc; Golfier, Sven; Räse, Sebastian; Ansari, Nariman; Esner, Milan; Bickle, Marc; Pampaloni, Francesco; Mattheyer, Christian; Stelzer, Ernst H.; Parczyk, Karsten; Prechtl, Stefan; Steigemann, Patrick

    2014-04-15

    Cancer cells in poorly vascularized tumor regions need to adapt to an unfavorable metabolic microenvironment. As distance from supplying blood vessels increases, oxygen and nutrient concentrations decrease and cancer cells react by stopping cell cycle progression and becoming dormant. As cytostatic drugs mainly target proliferating cells, cancer cell dormancy is considered as a major resistance mechanism to this class of anti-cancer drugs. Therefore, substances that target cancer cells in poorly vascularized tumor regions have the potential to enhance cytostatic-based chemotherapy of solid tumors. With three-dimensional growth conditions, multicellular tumor spheroids (MCTS) reproduce several parameters of the tumor microenvironment, including oxygen and nutrient gradients as well as the development of dormant tumor regions. We here report the setup of a 3D cell culture compatible high-content screening system and the identification of nine substances from two commercially available drug libraries that specifically target cells in inner MCTS core regions, while cells in outer MCTS regions or in 2D cell culture remain unaffected. We elucidated the mode of action of the identified compounds as inhibitors of the respiratory chain and show that induction of cell death in inner MCTS core regions critically depends on extracellular glucose concentrations. Finally, combinational treatment with cytostatics showed increased induction of cell death in MCTS. The data presented here shows for the first time a high-content based screening setup on 3D tumor spheroids for the identification of substances that specifically induce cell death in inner tumor spheroid core regions. This validates the approach to use 3D cell culture screening systems to identify substances that would not be detectable by 2D based screening in otherwise similar culture conditions. - Highlights: • Establishment of a novel method for 3D cell culture based high-content screening. • First reported high

  11. Optical Coherence Tomography Noise Reduction Using Anisotropic Local Bivariate Gaussian Mixture Prior in 3D Complex Wavelet Domain

    PubMed Central

    Sonka, Milan; Abramoff, Michael D.

    2013-01-01

    In this paper, MMSE estimator is employed for noise-free 3D OCT data recovery in 3D complex wavelet domain. Since the proposed distribution for noise-free data plays a key role in the performance of MMSE estimator, a priori distribution for the pdf of noise-free 3D complex wavelet coefficients is proposed which is able to model the main statistical properties of wavelets. We model the coefficients with a mixture of two bivariate Gaussian pdfs with local parameters which are able to capture the heavy-tailed property and inter- and intrascale dependencies of coefficients. In addition, based on the special structure of OCT images, we use an anisotropic windowing procedure for local parameters estimation that results in visual quality improvement. On this base, several OCT despeckling algorithms are obtained based on using Gaussian/two-sided Rayleigh noise distribution and homomorphic/nonhomomorphic model. In order to evaluate the performance of the proposed algorithm, we use 156 selected ROIs from 650 × 512 × 128 OCT dataset in the presence of wet AMD pathology. Our simulations show that the best MMSE estimator using local bivariate mixture prior is for the nonhomomorphic model in the presence of Gaussian noise which results in an improvement of 7.8 ± 1.7 in CNR. PMID:24222760

  12. Integrated WiFi/PDR/Smartphone Using an Unscented Kalman Filter Algorithm for 3D Indoor Localization

    PubMed Central

    Chen, Guoliang; Meng, Xiaolin; Wang, Yunjia; Zhang, Yanzhe; Tian, Peng; Yang, Huachao

    2015-01-01

    Because of the high calculation cost and poor performance of a traditional planar map when dealing with complicated indoor geographic information, a WiFi fingerprint indoor positioning system cannot be widely employed on a smartphone platform. By making full use of the hardware sensors embedded in the smartphone, this study proposes an integrated approach to a three-dimensional (3D) indoor positioning system. First, an improved K-means clustering method is adopted to reduce the fingerprint database retrieval time and enhance positioning efficiency. Next, with the mobile phone’s acceleration sensor, a new step counting method based on auto-correlation analysis is proposed to achieve cell phone inertial navigation positioning. Furthermore, the integration of WiFi positioning with Pedestrian Dead Reckoning (PDR) obtains higher positional accuracy with the help of the Unscented Kalman Filter algorithm. Finally, a hybrid 3D positioning system based on Unity 3D, which can carry out real-time positioning for targets in 3D scenes, is designed for the fluent operation of mobile terminals. PMID:26404314

  13. Integrated WiFi/PDR/Smartphone Using an Unscented Kalman Filter Algorithm for 3D Indoor Localization.

    PubMed

    Chen, Guoliang; Meng, Xiaolin; Wang, Yunjia; Zhang, Yanzhe; Tian, Peng; Yang, Huachao

    2015-01-01

    Because of the high calculation cost and poor performance of a traditional planar map when dealing with complicated indoor geographic information, a WiFi fingerprint indoor positioning system cannot be widely employed on a smartphone platform. By making full use of the hardware sensors embedded in the smartphone, this study proposes an integrated approach to a three-dimensional (3D) indoor positioning system. First, an improved K-means clustering method is adopted to reduce the fingerprint database retrieval time and enhance positioning efficiency. Next, with the mobile phone's acceleration sensor, a new step counting method based on auto-correlation analysis is proposed to achieve cell phone inertial navigation positioning. Furthermore, the integration of WiFi positioning with Pedestrian Dead Reckoning (PDR) obtains higher positional accuracy with the help of the Unscented Kalman Filter algorithm. Finally, a hybrid 3D positioning system based on Unity 3D, which can carry out real-time positioning for targets in 3D scenes, is designed for the fluent operation of mobile terminals. PMID:26404314

  14. 3D non-rigid registration using surface and local salient features for transrectal ultrasound image-guided prostate biopsy

    NASA Astrophysics Data System (ADS)

    Yang, Xiaofeng; Akbari, Hamed; Halig, Luma; Fei, Baowei

    2011-03-01

    We present a 3D non-rigid registration algorithm for the potential use in combining PET/CT and transrectal ultrasound (TRUS) images for targeted prostate biopsy. Our registration is a hybrid approach that simultaneously optimizes the similarities from point-based registration and volume matching methods. The 3D registration is obtained by minimizing the distances of corresponding points at the surface and within the prostate and by maximizing the overlap ratio of the bladder neck on both images. The hybrid approach not only capture deformation at the prostate surface and internal landmarks but also the deformation at the bladder neck regions. The registration uses a soft assignment and deterministic annealing process. The correspondences are iteratively established in a fuzzy-to-deterministic approach. B-splines are used to generate a smooth non-rigid spatial transformation. In this study, we tested our registration with pre- and postbiopsy TRUS images of the same patients. Registration accuracy is evaluated using manual defined anatomic landmarks, i.e. calcification. The root-mean-squared (RMS) of the difference image between the reference and floating images was decreased by 62.6+/-9.1% after registration. The mean target registration error (TRE) was 0.88+/-0.16 mm, i.e. less than 3 voxels with a voxel size of 0.38×0.38×0.38 mm3 for all five patients. The experimental results demonstrate the robustness and accuracy of the 3D non-rigid registration algorithm.

  15. 3D maps of the local interstellar medium: searching for the imprints of past events

    NASA Astrophysics Data System (ADS)

    Lallement, R.

    2015-01-01

    Inversion of interstellar (IS) gas or dust absorbing columns measured along the path to stars distributed in distance and direction allows reconstructing the distribution of interstellar matter (ISM) in three dimensions. A low resolution IS dust map based on reddening measurements towards 23,000 nearby stars is used to illustrate the potential of the more detailed maps that are expected within the next several years. The map reveals the location of the main IS cloud complexes up to distances on the order of 600 to 1200 pc depending on directions. Owing to target selection biases towards weakly reddened, brighter stars, the map is especially revealing in terms of regions devoid of IS matter. It traces the Local Bubble and its neighboring cavities, including a conspicuous, giant, >=1000 pc long cavity in the third quadrant located beyond the so-called βMa tunnel. This cavity is bordered by the main constituents of the Gould belt, the well-known and still unexplained rotating and expanding ring of clouds and young stars, inclined by ~ 20° to the galactic plane. Comparing the dust distribution with X-ray emission maps and IS gas observations shows that the giant cavity contains a large fraction of warm, fully ionized and dust-poor gas in addition to million K, X-ray bright gas. This set of structures must reflect the main events that occurred in the past; today however even the formation of the Gould belt is still a matter of controversy. It has been suggested recently that the Cretaceus-Tertiary (KT) mass extinction is potentially due to a gamma-ray burst (GRB) that occurred in the massive globular cluster (GC) 47 Tuc during its close encounter with the Sun ~70 Myrs ago. Such a hypothesis is based on computations of the cluster and Sun trajectories and the frequency of short GRBs in GC's. Given the mass, speed and size of 47 Tuc, wherever it crossed the Galactic plane it must have produced at the crossing site significant dynamical effects on the disk stars and IS

  16. Single-qubit gates based on targeted phase shifts in a 3D neutral atom array.

    PubMed

    Wang, Yang; Kumar, Aishwarya; Wu, Tsung-Yao; Weiss, David S

    2016-06-24

    Although the quality of individual quantum bits (qubits) and quantum gates has been steadily improving, the number of qubits in a single system has increased quite slowly. Here, we demonstrate arbitrary single-qubit gates based on targeted phase shifts, an approach that can be applied to atom, ion, or other atom-like systems. These gates are highly insensitive to addressing beam imperfections and have little cross-talk, allowing for a dramatic scaling up of qubit number. We have performed gates in series on 48 individually targeted sites in a 40% full 5 by 5 by 5 three-dimensional array created by an optical lattice. Using randomized benchmarking, we demonstrate an average gate fidelity of 0.9962(16), with an average cross-talk fidelity of 0.9979(2) (numbers in parentheses indicate the one standard deviation uncertainty in the final digits). PMID:27339984

  17. Connecting Global Measures of 3D Magnetic Reconnection to Local Kinetic Physics

    SciTech Connect

    Daughton, William Scott

    2015-07-16

    After giving the motivation for the work, slides present the topic under the following headings: Description of LAPD experiment; Actual simulation setup; Simple kinetic theory of ined-tied tearing; Diagnostics to characterizing 3D reconnection; Example #1 - short-tied system; and Example #2 - long line-tied system. Colorful simulations are shown for quasipotential vs field line exponentiation, field line integrated Ohms Law, and correlation with agyrotopy & energy conversion for example #1; and evolution of current density for largest case, field exponentiation vs quasi-potential, and time evolution of magnetic field lines for example #2. To satisfy line-tied boundary conditions, there is need for superposition of oblique modes--the simple two-mode approximation works surprisingly well. For force-free layers with bg >1, the fastest growing periodic modes are oblique with kxλ ~0.5. This implies a minimum length of Ly > 2πλbg. There are strong correlations between σ → Ξ → A0e (observable with spacecraft). Electron pressure tensor is the dominant non-ideal term.

  18. High-content 3D multicolor super-resolution localization microscopy.

    PubMed

    Pereira, Pedro M; Almada, Pedro; Henriques, Ricardo

    2015-01-01

    Super-resolution (SR) methodologies permit the visualization of cellular structures at near-molecular scale (1-30 nm), enabling novel mechanistic analysis of key events in cell biology not resolvable by conventional fluorescence imaging (∼300-nm resolution). When this level of detail is combined with computing power and fast and reliable analysis software, high-content screenings using SR becomes a practical option to address multiple biological questions. The importance of combining these powerful analytical techniques cannot be ignored, as they can address phenotypic changes on the molecular scale and in a statistically robust manner. In this work, we suggest an easy-to-implement protocol that can be applied to set up a high-content 3D SR experiment with user-friendly and freely available software. The protocol can be divided into two main parts: chamber and sample preparation, where a protocol to set up a direct STORM (dSTORM) sample is presented; and a second part where a protocol for image acquisition and analysis is described. We intend to take the reader step-by-step through the experimental process highlighting possible experimental bottlenecks and possible improvements based on recent developments in the field. PMID:25640426

  19. 3D source localization of interictal spikes in epilepsy patients with MRI lesions

    NASA Astrophysics Data System (ADS)

    Ding, Lei; Worrell, Gregory A.; Lagerlund, Terrence D.; He, Bin

    2006-08-01

    The present study aims to accurately localize epileptogenic regions which are responsible for epileptic activities in epilepsy patients by means of a new subspace source localization approach, i.e. first principle vectors (FINE), using scalp EEG recordings. Computer simulations were first performed to assess source localization accuracy of FINE in the clinical electrode set-up. The source localization results from FINE were compared with the results from a classic subspace source localization approach, i.e. MUSIC, and their differences were tested statistically using the paired t-test. Other factors influencing the source localization accuracy were assessed statistically by ANOVA. The interictal epileptiform spike data from three adult epilepsy patients with medically intractable partial epilepsy and well-defined symptomatic MRI lesions were then studied using both FINE and MUSIC. The comparison between the electrical sources estimated by the subspace source localization approaches and MRI lesions was made through the coregistration between the EEG recordings and MRI scans. The accuracy of estimations made by FINE and MUSIC was also evaluated and compared by R2 statistic, which was used to indicate the goodness-of-fit of the estimated sources to the scalp EEG recordings. The three-concentric-spheres head volume conductor model was built for each patient with three spheres of different radii which takes the individual head size and skull thickness into consideration. The results from computer simulations indicate that the improvement of source spatial resolvability and localization accuracy of FINE as compared with MUSIC is significant when simulated sources are closely spaced, deep, or signal-to-noise ratio is low in a clinical electrode set-up. The interictal electrical generators estimated by FINE and MUSIC are in concordance with the patients' structural abnormality, i.e. MRI lesions, in all three patients. The higher R2 values achieved by FINE than MUSIC

  20. Applicability of 3D Monte Carlo simulations for local values calculations in a PWR core

    NASA Astrophysics Data System (ADS)

    Bernard, Franck; Cochet, Bertrand; Jinaphanh, Alexis; Jacquet, Olivier

    2014-06-01

    As technical support of the French Nuclear Safety Authority, IRSN has been developing the MORET Monte Carlo code for many years in the framework of criticality safety assessment and is now working to extend its application to reactor physics. For that purpose, beside the validation for criticality safety (more than 2000 benchmarks from the ICSBEP Handbook have been modeled and analyzed), a complementary validation phase for reactor physics has been started, with benchmarks from IRPHEP Handbook and others. In particular, to evaluate the applicability of MORET and other Monte Carlo codes for local flux or power density calculations in large power reactors, it has been decided to contribute to the "Monte Carlo Performance Benchmark" (hosted by OECD/NEA). The aim of this benchmark is to monitor, in forthcoming decades, the performance progress of detailed Monte Carlo full core calculations. More precisely, it measures their advancement towards achieving high statistical accuracy in reasonable computation time for local power at fuel pellet level. A full PWR reactor core is modeled to compute local power densities for more than 6 million fuel regions. This paper presents results obtained at IRSN for this benchmark with MORET and comparisons with MCNP. The number of fuel elements is so large that source convergence as well as statistical convergence issues could cause large errors in local tallies, especially in peripheral zones. Various sampling or tracking methods have been implemented in MORET, and their operational effects on such a complex case have been studied. Beyond convergence issues, to compute local values in so many fuel regions could cause prohibitive slowing down of neutron tracking. To avoid this, energy grid unification and tallies preparation before tracking have been implemented, tested and proved to be successful. In this particular case, IRSN obtained promising results with MORET compared to MCNP, in terms of local power densities, standard

  1. A 3D Computational fluid dynamics model validation for candidate molybdenum-99 target geometry

    NASA Astrophysics Data System (ADS)

    Zheng, Lin; Dale, Greg; Vorobieff, Peter

    2014-11-01

    Molybdenum-99 (99Mo) is the parent product of technetium-99m (99mTc), a radioisotope used in approximately 50,000 medical diagnostic tests per day in the U.S. The primary uses of this product include detection of heart disease, cancer, study of organ structure and function, and other applications. The US Department of Energy seeks new methods for generating 99Mo without the use of highly enriched uranium, to eliminate proliferation issues and provide a domestic supply of 99mTc for medical imaging. For this project, electron accelerating technology is used by sending an electron beam through a series of 100Mo targets. During this process a large amount of heat is created, which directly affects the operating temperature dictated by the tensile stress limit of the wall material. To maintain the required temperature range, helium gas is used as a cooling agent that flows through narrow channels between the target disks. In our numerical study, we investigate the cooling performance on a series of new geometry designs of the cooling channel. This research is supported by Los Alamos National Laboratory.

  2. Quantify Plasma Response to Non-Axisymmetric (3D) Magnetic Fields in Tokamaks, Final Report for FES (Fusion Energy Sciences) FY2014 Joint Research Target

    SciTech Connect

    Strait, E. J.; Park, J. -K.; Marmar, E. S.; Ahn, J. -W.; Berkery, J. W.; Burrell, K. H.; Canik, J. M.; Delgado-Aparicio, L.; Ferraro, N. M.; Garofalo, A. M.; Gates, D. A.; Greenwald, M.; Kim, K.; King, J. D.; Lanctot, M. J.; Lazerson, S. A.; Liu, Y. Q.; Lore, J. D.; Menard, J. E.; Nazikian, R.; Shafer, M. W.; Paz-Soldan, C.; Reiman, A. H.; Rice, J. E.; Sabbagh, S. A.; Sugiyama, L.; Turnbull, A. D.; Volpe, F.; Wang, Z. R.; Wolfe, S. M.

    2014-09-30

    The goal of the 2014 Joint Research Target (JRT) has been to conduct experiments and analysis to investigate and quantify the response of tokamak plasmas to non-axisymmetric (3D) magnetic fields. Although tokamaks are conceptually axisymmetric devices, small asymmetries often result from inaccuracies in the manufacture and assembly of the magnet coils, or from nearby magnetized objects. In addition, non-axisymmetric fields may be deliberately applied for various purposes. Even at small amplitudes of order 10-4 of the main axisymmetric field, such “3D” fields can have profound impacts on the plasma performance. The effects are often detrimental (reduction of stabilizing plasma rotation, degradation of energy confinement, localized heat flux to the divertor, or excitation of instabilities) but may in some case be beneficial (maintenance of rotation, or suppression of instabilities). In general, the magnetic response of the plasma alters the 3D field, so that the magnetic field configuration within the plasma is not simply the sum of the external 3D field and the original axisymmetric field. Typically the plasma response consists of a mixture of local screening of the external field by currents induced at resonant surfaces in the plasma, and amplification of the external field by stable kink modes. Thus, validated magnetohydrodynamic (MHD) models of the plasma response to 3D fields are crucial to the interpretation of existing experiments and the prediction of plasma performance in future devices. The non-axisymmetric coil sets available at each facility allow well-controlled studies of the response to external 3D fields. The work performed in support of the 2014 Joint Research Target has included joint modeling and analysis of existing experimental data, and collaboration on new experiments designed to address the goals of the JRT. A major focus of the work was validation of numerical models through quantitative comparison to experimental data, in

  3. Global localization of 3D anatomical structures by pre-filtered Hough forests and discrete optimization.

    PubMed

    Donner, René; Menze, Bjoern H; Bischof, Horst; Langs, Georg

    2013-12-01

    The accurate localization of anatomical landmarks is a challenging task, often solved by domain specific approaches. We propose a method for the automatic localization of landmarks in complex, repetitive anatomical structures. The key idea is to combine three steps: (1) a classifier for pre-filtering anatomical landmark positions that (2) are refined through a Hough regression model, together with (3) a parts-based model of the global landmark topology to select the final landmark positions. During training landmarks are annotated in a set of example volumes. A classifier learns local landmark appearance, and Hough regressors are trained to aggregate neighborhood information to a precise landmark coordinate position. A non-parametric geometric model encodes the spatial relationships between the landmarks and derives a topology which connects mutually predictive landmarks. During the global search we classify all voxels in the query volume, and perform regression-based agglomeration of landmark probabilities to highly accurate and specific candidate points at potential landmark locations. We encode the candidates' weights together with the conformity of the connecting edges to the learnt geometric model in a Markov Random Field (MRF). By solving the corresponding discrete optimization problem, the most probable location for each model landmark is found in the query volume. We show that this approach is able to consistently localize the model landmarks despite the complex and repetitive character of the anatomical structures on three challenging data sets (hand radiographs, hand CTs, and whole body CTs), with a median localization error of 0.80 mm, 1.19 mm and 2.71 mm, respectively. PMID:23664450

  4. Intensity-modulated radiotherapy, not 3D conformal, is the preferred technique for treating locally advanced lung cancer

    PubMed Central

    Chang, Joe Y.

    2015-01-01

    When used to treat lung cancer, intensity-modulated radiotherapy (IMRT) can deliver higher dose to the targets and spare more critical organs in lung cancer than can 3D conformal radiotherapy (3DCRT). However, tumor-motion management and optimized radiotherapy planning based on four-dimensional computed tomography (4D CT) scanning are crucial to maximize the benefit of IMRT and to eliminate or minimize potential uncertainties. This article summarizes these strategies and reviews published findings supporting the safety and efficacy of IMRT for lung cancer. PMID:25771415

  5. 3D growth rates from tomographic images: local measurements for a better understanding of snow metamorphism

    NASA Astrophysics Data System (ADS)

    Flin, F.; Calonne, N.; Denis, R.; Caneill, R.; Bernard, L.; Anne, D.; Philip, A.; Roulle, J.; Rolland du Roscoat, S.; Geindreau, C.

    2015-12-01

    Once deposited on the ground, snow forms a complex porous material whose microstructure constantly transforms over time. These evolutions, which strongly impact the physical and mechanical properties of snow (e.g. Srivastava et al, 2010; Calonne et al, 2014) need to be considered in details for an accurate snowpack modeling. However, some of the physical mechanisms involved in metamorphism are still poorly understood.To address this problem, several investigations combining X-ray tomography and 3D micro-modeling have been carried out (e.g. Flin et al, 2003; Kämpfer and Plapp, 2009; Pinzer et al, 2012) but precise comparisons between experimentation and modeling remain difficult. One of the difficulties comes from the lack of high resolution time-lapse series for experiments occurring with very well-defined boundary conditions, and from which precise measurements of the interfacial growth rates can be done.Thanks to a recently developed cryogenic cell (Calonne et al, 2015), we conducted in situ time-lapse tomographic experiments on several snow and ice samples under various conditions (isothermal metamorphism at -7°C, temperature gradient metamorphism at -2°C under a TG of 18 K/m, air cavity migration in a single crystal at -4°C under a TG of 50 K/m). The non-destructive nature of X-ray microtomography yielded series of 8 micron resolution images that were acquired with a 2 to 12 h time step. An image analysis method was then developed to estimate the normal growth rates on each point of the ice-air interface and applied to the series obtained.The analysis of the results and their comparison to those of existing models (e.g. Flin et al, 2003; Flin and Brzoska, 2008) give interesting outlooks for the understanding of the physical mechanisms involved in snow metamorphism. References:Calonne, N., et al (2015), Geophys. Res. Lett., 42, 3911-3918.Calonne, N., et al (2014), The Cryosphere, 8, 2255-2274.Flin, F. and J.-B. Brzoska (2008), Ann. Glaciol., 49, 17-21.Flin

  6. Decoding 3-D Reach and Grasp Kinematics from High-Frequency Local Field Potentials in Primate Primary Motor Cortex

    PubMed Central

    Zhuang, Jun; Vargas-Irwin, Carlos; Donoghue, John P.

    2011-01-01

    Intracortical microelectrode array recordings generate a variety of neural signals with potential application as control signals in neural interface systems. Previous studies have focused on single and multiunit activity, as well as low frequency local field potentials (LFPs), but have not explored higher frequency (>200 Hz) LFPs. In addition, the potential to decode three dimensional (3-D) reach and grasp kinematics based on LFPs has not been demonstrated. Here, we use mutual information and decoding analyses to probe the information content about 3-D reaching and grasping of 7 different LFP frequency bands in the range of 0.3 Hz – 400 Hz. LFPs were recorded via 96-microelectrode arrays in primary motor cortex (M1) of two monkeys performing free reaching to grasp moving objects. Mutual information analyses revealed that higher frequency bands (e.g. 100 – 200 Hz and 200 – 400 Hz) carried the most information about the examined kinematics. Furthermore, Kalman filter decoding revealed that broadband high frequency LFPs, likely reflecting multiunit activity, provided the best decoding performance as well as substantial accuracy in reconstructing reach kinematics, grasp aperture and aperture velocity. These results indicate that LFPs, especially high frequency bands, could be useful signals for neural interfaces controlling 3-D reach and grasp kinematics. PMID:20403782

  7. Mechanical Simulation of the Localized Deformation in the Aluminum Foams: A Three-dimensional (3D) Structure Based Study

    NASA Astrophysics Data System (ADS)

    Kai, Zhu; Enyu, Guo; Wenqian, Zhou; Sansan, Shuai; Tao, Jing; Hongliang, Hou; Yanjin, Xu

    2015-06-01

    Metal-foam materials have been used increasingly in industry for their low-density, high-toughness and high impact resistance properties. Understanding the macro-scale mechanical properties of these materials is essential to evaluate their actual performance and thus to optimize the structures and properties accordingly. Synchrotron radiation X-ray microtomographytechnique is a promising method to study 3D structures at small length scales, which provides high spatial resolution and allows the researchers to observe the change of structures/features in situ without destroying the original objects. In this work, the real 3D structure of closed-cell aluminum foam was obtained by using synchrotron radiation X-ray microtomography. The reconstructed 3D model of the foam was further utilized as input for the subsequent mechanical study to investigate the localized deformation behaviors and evolution process of the foam under longitudinal quasi-static uniaxial compressive loading. By analyzing the simulated results, it is demonstrated that the deformation bands always initiate and propagate along the cell walls which are finally folded upon loading. And the large spherical cells are more susceptible to yielding, as well as to the stress concentration than the cells with other shapes. This finding is consistent with the experimental results.

  8. 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

  9. New 3D parallel GILD electromagnetic modeling and nonlinear inversion using global magnetic integral and local differential equation

    SciTech Connect

    Xie, G.; Li, J.; Majer, E.; Zuo, D.

    1998-07-01

    This paper describes a new 3D parallel GILD electromagnetic (EM) modeling and nonlinear inversion algorithm. The algorithm consists of: (a) a new magnetic integral equation instead of the electric integral equation to solve the electromagnetic forward modeling and inverse problem; (b) a collocation finite element method for solving the magnetic integral and a Galerkin finite element method for the magnetic differential equations; (c) a nonlinear regularizing optimization method to make the inversion stable and of high resolution; and (d) a new parallel 3D modeling and inversion using a global integral and local differential domain decomposition technique (GILD). The new 3D nonlinear electromagnetic inversion has been tested with synthetic data and field data. The authors obtained very good imaging for the synthetic data and reasonable subsurface EM imaging for the field data. The parallel algorithm has high parallel efficiency over 90% and can be a parallel solver for elliptic, parabolic, and hyperbolic modeling and inversion. The parallel GILD algorithm can be extended to develop a high resolution and large scale seismic and hydrology modeling and inversion in the massively parallel computer.

  10. Robust 3D object localization and pose estimation for random bin picking with the 3DMaMa algorithm

    NASA Astrophysics Data System (ADS)

    Skotheim, Øystein; Thielemann, Jens T.; Berge, Asbjørn; Sommerfelt, Arne

    2010-02-01

    Enabling robots to automatically locate and pick up randomly placed and oriented objects from a bin is an important challenge in factory automation, replacing tedious and heavy manual labor. A system should be able to recognize and locate objects with a predefined shape and estimate the position with the precision necessary for a gripping robot to pick it up. We describe a system that consists of a structured light instrument for capturing 3D data and a robust approach for object location and pose estimation. The method does not depend on segmentation of range images, but instead searches through pairs of 2D manifolds to localize candidates for object match. This leads to an algorithm that is not very sensitive to scene complexity or the number of objects in the scene. Furthermore, the strategy for candidate search is easily reconfigurable to arbitrary objects. Experiments reported in this paper show the utility of the method on a general random bin picking problem, in this paper exemplified by localization of car parts with random position and orientation. Full pose estimation is done in less than 380 ms per image. We believe that the method is applicable for a wide range of industrial automation problems where precise localization of 3D objects in a scene is needed.

  11. Fully Automatic Localization and Segmentation of 3D Vertebral Bodies from CT/MR Images via a Learning-Based Method

    PubMed Central

    Chu, Chengwen; Belavý, Daniel L.; Armbrecht, Gabriele; Bansmann, Martin; Felsenberg, Dieter; Zheng, Guoyan

    2015-01-01

    In this paper, we address the problems of fully automatic localization and segmentation of 3D vertebral bodies from CT/MR images. We propose a learning-based, unified random forest regression and classification framework to tackle these two problems. More specifically, in the first stage, the localization of 3D vertebral bodies is solved with random forest regression where we aggregate the votes from a set of randomly sampled image patches to get a probability map of the center of a target vertebral body in a given image. The resultant probability map is then further regularized by Hidden Markov Model (HMM) to eliminate potential ambiguity caused by the neighboring vertebral bodies. The output from the first stage allows us to define a region of interest (ROI) for the segmentation step, where we use random forest classification to estimate the likelihood of a voxel in the ROI being foreground or background. The estimated likelihood is combined with the prior probability, which is learned from a set of training data, to get the posterior probability of the voxel. The segmentation of the target vertebral body is then done by a binary thresholding of the estimated probability. We evaluated the present approach on two openly available datasets: 1) 3D T2-weighted spine MR images from 23 patients and 2) 3D spine CT images from 10 patients. Taking manual segmentation as the ground truth (each MR image contains at least 7 vertebral bodies from T11 to L5 and each CT image contains 5 vertebral bodies from L1 to L5), we evaluated the present approach with leave-one-out experiments. Specifically, for the T2-weighted MR images, we achieved for localization a mean error of 1.6 mm, and for segmentation a mean Dice metric of 88.7% and a mean surface distance of 1.5 mm, respectively. For the CT images we achieved for localization a mean error of 1.9 mm, and for segmentation a mean Dice metric of 91.0% and a mean surface distance of 0.9 mm, respectively. PMID:26599505

  12. Fully Automatic Localization and Segmentation of 3D Vertebral Bodies from CT/MR Images via a Learning-Based Method.

    PubMed

    Chu, Chengwen; Belavý, Daniel L; Armbrecht, Gabriele; Bansmann, Martin; Felsenberg, Dieter; Zheng, Guoyan

    2015-01-01

    In this paper, we address the problems of fully automatic localization and segmentation of 3D vertebral bodies from CT/MR images. We propose a learning-based, unified random forest regression and classification framework to tackle these two problems. More specifically, in the first stage, the localization of 3D vertebral bodies is solved with random forest regression where we aggregate the votes from a set of randomly sampled image patches to get a probability map of the center of a target vertebral body in a given image. The resultant probability map is then further regularized by Hidden Markov Model (HMM) to eliminate potential ambiguity caused by the neighboring vertebral bodies. The output from the first stage allows us to define a region of interest (ROI) for the segmentation step, where we use random forest classification to estimate the likelihood of a voxel in the ROI being foreground or background. The estimated likelihood is combined with the prior probability, which is learned from a set of training data, to get the posterior probability of the voxel. The segmentation of the target vertebral body is then done by a binary thresholding of the estimated probability. We evaluated the present approach on two openly available datasets: 1) 3D T2-weighted spine MR images from 23 patients and 2) 3D spine CT images from 10 patients. Taking manual segmentation as the ground truth (each MR image contains at least 7 vertebral bodies from T11 to L5 and each CT image contains 5 vertebral bodies from L1 to L5), we evaluated the present approach with leave-one-out experiments. Specifically, for the T2-weighted MR images, we achieved for localization a mean error of 1.6 mm, and for segmentation a mean Dice metric of 88.7% and a mean surface distance of 1.5 mm, respectively. For the CT images we achieved for localization a mean error of 1.9 mm, and for segmentation a mean Dice metric of 91.0% and a mean surface distance of 0.9 mm, respectively. PMID:26599505

  13. Scalable Fluidic Injector Arrays for Viral Targeting of Intact 3-D Brain Circuits

    PubMed Central

    Chan, Stephanie; Bernstein, Jacob; Boyden, Edward

    2010-01-01

    Our understanding of neural circuits--how they mediate the computations that subserve sensation, thought, emotion, and action, and how they are corrupted in neurological and psychiatric disorders--would be greatly facilitated by a technology for rapidly targeting genes to complex 3-dimensional neural circuits, enabling fast creation of "circuit-level transgenics." We have recently developed methods in which viruses encoding for light-sensitive proteins can sensitize specific cell types to millisecond-timescale activation and silencing in the intact brain. We here present the design and implementation of an injector array capable of delivering viruses (or other fluids) to dozens of defined points within the 3-dimensional structure of the brain (Figure. 1A, 1B). The injector array comprises one or more displacement pumps that each drive a set of syringes, each of which feeds into a polyimide/fused-silica capillary via a high-pressure-tolerant connector. The capillaries are sized, and then inserted into, desired locations specified by custom-milling a stereotactic positioning board, thus allowing viruses or other reagents to be delivered to the desired set of brain regions. To use the device, the surgeon first fills the fluidic subsystem entirely with oil, backfills the capillaries with the virus, inserts the device into the brain, and infuses reagents slowly (<0.1 microliters/min). The parallel nature of the injector array facilitates rapid, accurate, and robust labeling of entire neural circuits with viral payloads such as optical sensitizers to enable light-activation and silencing of defined brain circuits. Along with other technologies, such as optical fiber arrays for light delivery to desired sets of brain regions, we hope to create a toolbox that enables the systematic probing of causal neural functions in the intact brain. This technology may not only open up such systematic approaches to circuit-focused neuroscience in mammals, and facilitate labeling of

  14. STRUCTURE IN THE 3D GALAXY DISTRIBUTION. II. VOIDS AND WATERSHEDS OF LOCAL MAXIMA AND MINIMA

    SciTech Connect

    Way, M. J.; Gazis, P. R.; Scargle, Jeffrey D. E-mail: PGazis@sbcglobal.net

    2015-01-20

    The major uncertainties in studies of the multi-scale structure of the universe arise not from observational errors but from the variety of legitimate definitions and detection methods for individual structures. To facilitate the study of these methodological dependencies, we have carried out 12 different analyses defining structures in various ways. This has been done in a purely geometrical way by utilizing the HOP algorithm as a unique parameter-free method of assigning groups of galaxies to local density maxima or minima. From three density estimation techniques (smoothing kernels, Bayesian blocks, and self-organizing maps) applied to three data sets (the Sloan Digital Sky Survey Data Release 7, the Millennium simulation, and randomly distributed points) we tabulate information that can be used to construct catalogs of structures connected to local density maxima and minima. We also introduce a void finder that utilizes a method to assemble Delaunay tetrahedra into connected structures and characterizes regions empty of galaxies in the source catalog.

  15. Nonrigid motion correction in 3D using autofocusing with localized linear translations.

    PubMed

    Cheng, Joseph Y; Alley, Marcus T; Cunningham, Charles H; Vasanawala, Shreyas S; Pauly, John M; Lustig, Michael

    2012-12-01

    MR scans are sensitive to motion effects due to the scan duration. To properly suppress artifacts from nonrigid body motion, complex models with elements such as translation, rotation, shear, and scaling have been incorporated into the reconstruction pipeline. However, these techniques are computationally intensive and difficult to implement for online reconstruction. On a sufficiently small spatial scale, the different types of motion can be well approximated as simple linear translations. This formulation allows for a practical autofocusing algorithm that locally minimizes a given motion metric--more specifically, the proposed localized gradient-entropy metric. To reduce the vast search space for an optimal solution, possible motion paths are limited to the motion measured from multichannel navigator data. The novel navigation strategy is based on the so-called "Butterfly" navigators, which are modifications of the spin-warp sequence that provides intrinsic translational motion information with negligible overhead. With a 32-channel abdominal coil, sufficient number of motion measurements were found to approximate possible linear motion paths for every image voxel. The correction scheme was applied to free-breathing abdominal patient studies. In these scans, a reduction in artifacts from complex, nonrigid motion was observed. PMID:22307933

  16. Tools to Perform Local Dense 3D Reconstruction of Shallow Water Seabed.

    PubMed

    Avanthey, Loïca; Beaudoin, Laurent; Gademer, Antoine; Roux, Michel

    2016-01-01

    Tasks such as distinguishing or identifying individual objects of interest require the production of dense local clouds at the scale of these individual objects of interest. Due to the physical and dynamic properties of an underwater environment, the usual dense matching algorithms must be rethought in order to be adaptive. These properties also imply that the scene must be observed at close range. Classic robotized acquisition systems are oversized for local studies in shallow water while the systematic acquisition of data is not guaranteed with divers. We address these two major issues through a multidisciplinary approach. To efficiently acquire on-demand stereoscopic pairs using simple logistics in small areas of shallow water, we devised an agile light-weight dedicated system which is easy to reproduce. To densely match two views in a reliable way, we devised a reconstruction algorithm that automatically accounts for the dynamics, variability and light absorption of the underwater environment. Field experiments in the Mediterranean Sea were used to assess the results. PMID:27196913

  17. "SP-G", a putative new surfactant protein--tissue localization and 3D structure.

    PubMed

    Rausch, Felix; Schicht, Martin; Paulsen, Friedrich; Ngueya, Ivan; Bräuer, Lars; Brandt, Wolfgang

    2012-01-01

    Surfactant proteins (SP) are well known from human lung. These proteins assist the formation of a monolayer of surface-active phospholipids at the liquid-air interface of the alveolar lining, play a major role in lowering the surface tension of interfaces, and have functions in innate and adaptive immune defense. During recent years it became obvious that SPs are also part of other tissues and fluids such as tear fluid, gingiva, saliva, the nasolacrimal system, and kidney. Recently, a putative new surfactant protein (SFTA2 or SP-G) was identified, which has no sequence or structural identity to the already know surfactant proteins. In this work, computational chemistry and molecular-biological methods were combined to localize and characterize SP-G. With the help of a protein structure model, specific antibodies were obtained which allowed the detection of SP-G not only on mRNA but also on protein level. The localization of this protein in different human tissues, sequence based prediction tools for posttranslational modifications and molecular dynamic simulations reveal that SP-G has physicochemical properties similar to the already known surfactant proteins B and C. This includes also the possibility of interactions with lipid systems and with that, a potential surface-regulatory feature of SP-G. In conclusion, the results indicate SP-G as a new surfactant protein which represents an until now unknown surfactant protein class. PMID:23094088

  18. Tools to Perform Local Dense 3D Reconstruction of Shallow Water Seabed ‡

    PubMed Central

    Avanthey, Loïca; Beaudoin, Laurent; Gademer, Antoine; Roux, Michel

    2016-01-01

    Tasks such as distinguishing or identifying individual objects of interest require the production of dense local clouds at the scale of these individual objects of interest. Due to the physical and dynamic properties of an underwater environment, the usual dense matching algorithms must be rethought in order to be adaptive. These properties also imply that the scene must be observed at close range. Classic robotized acquisition systems are oversized for local studies in shallow water while the systematic acquisition of data is not guaranteed with divers. We address these two major issues through a multidisciplinary approach. To efficiently acquire on-demand stereoscopic pairs using simple logistics in small areas of shallow water, we devised an agile light-weight dedicated system which is easy to reproduce. To densely match two views in a reliable way, we devised a reconstruction algorithm that automatically accounts for the dynamics, variability and light absorption of the underwater environment. Field experiments in the Mediterranean Sea were used to assess the results. PMID:27196913

  19. Local Evaluation of a Fusion System for 3-D Tomographic Image Interpretation

    NASA Astrophysics Data System (ADS)

    Lamallem, Abdellah; Valet, Lionel; Coquin, Didier

    2010-11-01

    Information fusion has been studied in various domains of computer sciences and engineering, and these techniques have increasingly been used. Such systems aim to build new interesting information from much information. Over time, fusion systems have become complex systems integrating information extraction, representations, combinations and interpretations. The performance evaluation of such systems has become a real problem. The choices of methods and parameter values have a significant impact on the quality of the results. A global evaluation of the fused results does not allow the end-users to adjust the numerous parameters. We propose a local approach to evaluate the mission completeness of the fusion system subparts. In this article, we focus on the formulation of the mission of extraction subparts and we measure their degree of achievement. We aim at showing the end-users which subparts do not completely achieve the functionality they were designed for.

  20. Anderson localization of matter waves in 3D anisotropic disordered potentials

    NASA Astrophysics Data System (ADS)

    Piraud, Marie

    2016-05-01

    We study quantum transport and Anderson localization of matterwaves in 3 dimensional correlated disorder, focusing on the effects of the anisotropy. Indeed, understanding the anisotropy effects is fundamental for experiments with ultracold atoms as well as for several other systems, such as electrons in MOSFETs, light in biological medium, liquid crystals. A major challenge is to understand whether the anisotropy of the diffusion tensor is altered by the interference terms at the origin of Anderson localization. In particular, its anisotropy at the mobility edge remains to be investigated. So far, all theoretical analysis have assumed - more or less implicitly - that the anisotropy of the diffusion tensor is preserved by interference effects, and have focussed on the vanishing of diffusion as a whole. In this talk, I will start by presenting the usual description of matterwave transport in disordered medium. I will then present our method to go beyond the standard self-consistent theory, which includes in particular the full anisotropic structure of the spectral function. It thus avoids the infrared divergence of the usual self-consistent theory and, most importantly, does not make any assumption on the anisotropy of the renormalized diffusion tensor when including quantum interference terms. Using a generic model of disorder with elongated correlations, we find that the diffusion tensor is strongly affected by the quantum interference terms and that the anisotropy strongly diminishes in the vicinity of the mobility edge. Our work paves the way to further investigation with speckle potentials, which are directly relevant to ultracold-atom experiments. It will permit comparison with previous predictions for the mobility edge and shed new light on ongoing experiments in the field of ultracold atoms.

  1. Towards a magnetic localization system for 3-D tracking of tongue movements in speech-language therapy.

    PubMed

    Cheng, Chihwen; Huo, Xueliang; Ghovanloo, Maysam

    2009-01-01

    This paper presents a new magnetic localization system based on a compact triangular sensor setup and three different optimization algorithms, intended for tracking tongue motion in the 3-D oral space. A small permanent magnet, secured on the tongue by tissue adhesives, will be used as a tracer. The magnetic field variations due to tongue motion are detected by a 3-D magneto-inductive sensor array outside the mouth and wirelessly transmitted to a computer. The position and rotation angles of the tracer are reconstructed based on sensor outputs and magnetic dipole equation using DIRECT, Powell, and Nelder-Mead optimization algorithms. Localization accuracy and processing time of the three algorithms are compared using one data set collected in which source-sensor distance was changed from 40 to 150 mm. Powell algorithm showed the best performance with 0.92 mm accuracy in position and 0.7(o) in orientation. The average processing time was 43.9 ms/sample, which can satisfy real time tracking up to approximately 20 Hz. PMID:19964478

  2. A High-Resolution 3D Separated-Local-Field Experiment by Means of Magic-Angle Turning

    PubMed

    Hu; Alderman; Pugmire; Grant

    1997-05-01

    A 3D separated-local-field (SLF) experiment based on the 2D PHORMAT technique is described. In the 3D experiment, the conventional 2D SLF powder pattern for each chemically inequivalent carbon is separated according to their different isotropic chemical shifts. The dipolar coupling constant of a C-H pair, hence the bond distance, and the relative orientation of the chemical-shift tensor to the C-H vector can all be determined for the protonated carbons with a single measurement. As the sample turns at only about 30 Hz in a MAT experiment, the SLF patterns obtained approach those of a stationary sample, and an accuracy in the measurement similar to that obtained on a stationary sample is expected. The technique is demonstrated on 2,6-dimethoxynaphthalene, where the 13 C-1 H separated-local-field powder patterns for the six chemically inequivalent carbons are clearly identified and measured. The observed dipolar coupling for the methoxy carbon is effectively reduced by the fast rotation of the group about its C3 symmetry axis. The average angle between the C-H bond direction and the C3 rotation axis in the OCH3 group is found to be about 66°. PMID:9252281

  3. Estimation of aortic valve leaflets from 3D CT images using local shape dictionaries and linear coding

    NASA Astrophysics Data System (ADS)

    Liang, Liang; Martin, Caitlin; Wang, Qian; Sun, Wei; Duncan, James

    2016-03-01

    Aortic valve (AV) disease is a significant cause of morbidity and mortality. The preferred treatment modality for severe AV disease is surgical resection and replacement of the native valve with either a mechanical or tissue prosthetic. In order to develop effective and long-lasting treatment methods, computational analyses, e.g., structural finite element (FE) and computational fluid dynamic simulations, are very effective for studying valve biomechanics. These computational analyses are based on mesh models of the aortic valve, which are usually constructed from 3D CT images though many hours of manual annotation, and therefore an automatic valve shape reconstruction method is desired. In this paper, we present a method for estimating the aortic valve shape from 3D cardiac CT images, which is represented by triangle meshes. We propose a pipeline for aortic valve shape estimation which includes novel algorithms for building local shape dictionaries and for building landmark detectors and curve detectors using local shape dictionaries. The method is evaluated on real patient image dataset using a leave-one-out approach and achieves an average accuracy of 0.69 mm. The work will facilitate automatic patient-specific computational modeling of the aortic valve.

  4. 3D-printed hierarchical scaffold for localized isoniazid/rifampin drug delivery and osteoarticular tuberculosis therapy.

    PubMed

    Zhu, Min; Li, Kun; Zhu, Yufang; Zhang, Jianhua; Ye, Xiaojian

    2015-04-01

    After surgical treatment of osteoarticular tuberculosis (TB), it is necessary to fill the surgical defect with an implant, which combines the merits of osseous regeneration and local multi-drug therapy so as to avoid drug resistance and side effects. In this study, a 3D-printed macro/meso-porous composite scaffold is fabricated. High dosages of isoniazid (INH)/rifampin (RFP) anti-TB drugs are loaded into chemically modified mesoporous bioactive ceramics in advance, which are then bound with poly (3-hydroxybutyrate-co-3-hydroxyhexanoate) (PHBHHx) through a 3D printing procedure. The composite scaffolds show greatly prolonged drug release time compared to commercial calcium phosphate scaffolds either in vitro or in vivo. In addition, the drug concentrations on the periphery tissues of defect are maintained above INH/RFP minimal inhibitory concentrations even up to 12 weeks post-surgery, while they are extremely low in blood. Examinations of certain serum enzymes suggest no harm to hepatic or renal functions. Micro-CT evaluations and histology results also indicate partly degradation of the composite scaffolds and new bone growth in the cavity. These results suggest promising applications of our hierarchical composite scaffold in bone regeneration and local anti-TB therapy after osteoarticular TB debridement surgery. PMID:25653217

  5. New local potential useful for genome annotation and 3D modeling

    SciTech Connect

    Chandonia, John-Marc; Cohen, Fred E.

    2003-07-17

    A new potential energy function representing the conformational preferences of sequentially local regions of a protein backbone is presented. This potential is derived from secondary structure probabilities such as those produced by neural network-based prediction methods. The potential is applied to the problem of remote homolog identification, in combination with a distance dependent inter-residue potential and position-based scoring matrices. This fold recognition jury is implemented in a Java application called JThread. These methods are benchmarked on several test sets, including one released entirely after development and parameterization of JThread. In benchmark tests to identify known folds structurally similar (but not identical) to the native structure of a sequence, JThread performs significantly better than PSI-BLAST, with 10 percent more structures correctly identified as the most likely structural match in a fold library, and 20 percent more structures correctly narrowed down to a set of five possible candidates. JThread also significantly improves the average sequence alignment accuracy, from 53 percent to 62 percent of residues correctly aligned. Reliable fold assignments and alignments are identified, making the method useful for genome annotation. JThread is applied to predicted open reading frames (ORFs) from the genomes of Mycoplasma genitalium and Drosophila melanogaster, identifying 20 new structural annotations in the former and 801 in the latter.

  6. Efficient parallel seismic simulations including topography and 3-D material heterogeneities on locally refined composite grids

    NASA Astrophysics Data System (ADS)

    Petersson, Anders; Rodgers, Arthur

    2010-05-01

    The finite difference method on a uniform Cartesian grid is a highly efficient and easy to implement technique for solving the elastic wave equation in seismic applications. However, the spacing in a uniform Cartesian grid is fixed throughout the computational domain, whereas the resolution requirements in realistic seismic simulations usually are higher near the surface than at depth. This can be seen from the well-known formula h ≤ L-P which relates the grid spacing h to the wave length L, and the required number of grid points per wavelength P for obtaining an accurate solution. The compressional and shear wave lengths in the earth generally increase with depth and are often a factor of ten larger below the Moho discontinuity (at about 30 km depth), than in sedimentary basins near the surface. A uniform grid must have a grid spacing based on the small wave lengths near the surface, which results in over-resolving the solution at depth. As a result, the number of points in a uniform grid is unnecessarily large. In the wave propagation project (WPP) code, we address the over-resolution-at-depth issue by generalizing our previously developed single grid finite difference scheme to work on a composite grid consisting of a set of structured rectangular grids of different spacings, with hanging nodes on the grid refinement interfaces. The computational domain in a regional seismic simulation often extends to depth 40-50 km. Hence, using a refinement ratio of two, we need about three grid refinements from the bottom of the computational domain to the surface, to keep the local grid size in approximate parity with the local wave lengths. The challenge of the composite grid approach is to find a stable and accurate method for coupling the solution across the grid refinement interface. Of particular importance is the treatment of the solution at the hanging nodes, i.e., the fine grid points which are located in between coarse grid points. WPP implements a new, energy

  7. SU-D-9A-06: 3D Localization of Neurovascular Bundles Through MR-TRUS Registration in Prostate Radiotherapy

    SciTech Connect

    Yang, X; Rossi, P; Ogunleye, T; Jani, A; Curran, W; Liu, T

    2014-06-01

    Purpose: Erectile dysfunction (ED) is the most common complication of prostate-cancer radiotherapy (RT) and the major mechanism is radiation-induced neurovascular bundle (NVB) damage. However, the localization of the NVB remains challenging. This study's purpose is to accurately localize 3D NVB by integrating MR and transrectal ultrasound (TRUS) images through MR-TRUS fusion. Methods: T1 and T2-weighted MR prostate images were acquired using a Philips 1.5T MR scanner and a pelvic phase-array coil. The 3D TRUS images were captured with a clinical scanner and a 7.5 MHz biplane probe. The TRUS probe was attached to a stepper; the B-mode images were captured from the prostate base to apex at a 1-mm step and the Doppler images were acquired in a 5-mm step. The registration method modeled the prostate tissue as an elastic material, and jointly estimated the boundary condition (surface deformation) and the volumetric deformations under elastic constraint. This technique was validated with a clinical study of 7 patients undergoing RT treatment for prostate cancer. The accuracy of our approach was assessed through the locations of landmarks, as well as previous ultrasound Doppler images of patients. Results: MR-TRUS registration was successfully performed for all patients. The mean displacement of the landmarks between the post-registration MR and TRUS images was 1.37±0.42 mm, which demonstrated the precision of the registration based on the biomechanical model; and the NVB volume Dice Overlap Coefficient was 92.1±3.2%, which demonstrated the accuracy of the NVB localization. Conclusion: We have developed a novel approach to improve 3D NVB localization through MR-TRUS fusion for prostate RT, demonstrated its clinical feasibility, and validated its accuracy with ultrasound Doppler data. This technique could be a useful tool as we try to spare the NVB in prostate RT, monitor NBV response to RT, and potentially improve post-RT potency outcomes.

  8. The Complete (3-D) Co-Seismic Displacements Using Point-Like Targets Tracking With Ascending And Descending SAR Data

    NASA Astrophysics Data System (ADS)

    Hu, Xie; Wang, Teng; Liao, Mingsheng

    2013-12-01

    SAR Interferometry (InSAR) has its unique advantages, e.g., all weather/time accessibility, cm-level accuracy and large spatial coverage, however, it can only obtain one dimensional measurement along line-of-sight (LOS) direction. Offset tracking is an important complement to measure large and rapid displacements in both azimuth and range directions. Here we perform offset tracking on detected point-like targets (PT) by calculating the cross-correlation with a sinc-like template. And a complete 3-D displacement field can be derived using PT offset tracking from a pair of ascending and descending data. The presented case study on 2010 M7.2 El Mayor-Cucapah earthquake helps us better understand the rupture details.

  9. Accurate 3D rigid-body target motion and structure estimation by using GMTI/HRR with template information

    NASA Astrophysics Data System (ADS)

    Wu, Shunguang; Hong, Lang

    2008-04-01

    A framework of simultaneously estimating the motion and structure parameters of a 3D object by using high range resolution (HRR) and ground moving target indicator (GMTI) measurements with template information is given. By decoupling the motion and structure information and employing rigid-body constraints, we have developed the kinematic and measurement equations of the problem. Since the kinematic system is unobservable by using only one scan HRR and GMTI measurements, we designed an architecture to run the motion and structure filters in parallel by using multi-scan measurements. Moreover, to improve the estimation accuracy in large noise and/or false alarm environments, an interacting multi-template joint tracking (IMTJT) algorithm is proposed. Simulation results have shown that the averaged root mean square errors for both motion and structure state vectors have been significantly reduced by using the template information.

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

    NASA Astrophysics Data System (ADS)

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

    2010-01-01

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

  11. Magnetic resonance imaging-targeted, 3D transrectal ultrasound-guided fusion biopsy for prostate cancer: Quantifying the impact of needle delivery error on diagnosis

    SciTech Connect

    Martin, Peter R.; Cool, Derek W.; Romagnoli, Cesare; Fenster, Aaron; Ward, Aaron D.

    2014-07-15

    tumor was consistently greater when using spherical tumor shapes as opposed to no shape assumption. However, an assumption of spherical tumor shape for RMSE = 3.5 mm led to a mean overestimation of tumor sampling probabilities of 3%, implying that assuming spherical tumor shape may be reasonable for many prostate tumors. The authors also determined that a biopsy system would need to have a RMS needle delivery error of no more than 1.6 mm in order to sample 95% of tumors with one core. The authors’ experiments also indicated that the effect of axial-direction error on the measured tumor burden was mitigated by the 18 mm core length at 3.5 mm RMSE. Conclusions: For biopsy systems with RMSE ≥ 3.5 mm, more than one biopsy core must be taken from the majority of tumors to achieveP ≥ 95%. These observations support the authors’ perspective that some tumors of clinically significant sizes may require more than one biopsy attempt in order to be sampled during the first biopsy session. This motivates the authors’ ongoing development of an approach to optimize biopsy plans with the aim of achieving a desired probability of obtaining a sample from each tumor, while minimizing the number of biopsies. Optimized planning of within-tumor targets for MRI-3D TRUS fusion biopsy could support earlier diagnosis of prostate cancer while it remains localized to the gland and curable.

  12. Accurate quantification of local changes for carotid arteries in 3D ultrasound images using convex optimization-based deformable registration

    NASA Astrophysics Data System (ADS)

    Cheng, Jieyu; Qiu, Wu; Yuan, Jing; Fenster, Aaron; Chiu, Bernard

    2016-03-01

    Registration of longitudinally acquired 3D ultrasound (US) images plays an important role in monitoring and quantifying progression/regression of carotid atherosclerosis. We introduce an image-based non-rigid registration algorithm to align the baseline 3D carotid US with longitudinal images acquired over several follow-up time points. This algorithm minimizes the sum of absolute intensity differences (SAD) under a variational optical-flow perspective within a multi-scale optimization framework to capture local and global deformations. Outer wall and lumen were segmented manually on each image, and the performance of the registration algorithm was quantified by Dice similarity coefficient (DSC) and mean absolute distance (MAD) of the outer wall and lumen surfaces after registration. In this study, images for 5 subjects were registered initially by rigid registration, followed by the proposed algorithm. Mean DSC generated by the proposed algorithm was 79:3+/-3:8% for lumen and 85:9+/-4:0% for outer wall, compared to 73:9+/-3:4% and 84:7+/-3:2% generated by rigid registration. Mean MAD of 0:46+/-0:08mm and 0:52+/-0:13mm were generated for lumen and outer wall respectively by the proposed algorithm, compared to 0:55+/-0:08mm and 0:54+/-0:11mm generated by rigid registration. The mean registration time of our method per image pair was 143+/-23s.

  13. Spectrum simulation of rough and nanostructured targets from their 2D and 3D image by Monte Carlo methods

    NASA Astrophysics Data System (ADS)

    Schiettekatte, François; Chicoine, Martin

    2016-03-01

    Corteo is a program that implements Monte Carlo (MC) method to simulate ion beam analysis (IBA) spectra of several techniques by following the ions trajectory until a sufficiently large fraction of them reach the detector to generate a spectrum. Hence, it fully accounts for effects such as multiple scattering (MS). Here, a version of Corteo is presented where the target can be a 2D or 3D image. This image can be derived from micrographs where the different compounds are identified, therefore bringing extra information into the solution of an IBA spectrum, and potentially significantly constraining the solution. The image intrinsically includes many details such as the actual surface or interfacial roughness, or actual nanostructures shape and distribution. This can for example lead to the unambiguous identification of structures stoichiometry in a layer, or at least to better constraints on their composition. Because MC computes in details the trajectory of the ions, it simulates accurately many of its aspects such as ions coming back into the target after leaving it (re-entry), as well as going through a variety of nanostructures shapes and orientations. We show how, for example, as the ions angle of incidence becomes shallower than the inclination distribution of a rough surface, this process tends to make the effective roughness smaller in a comparable 1D simulation (i.e. narrower thickness distribution in a comparable slab simulation). Also, in ordered nanostructures, target re-entry can lead to replications of a peak in a spectrum. In addition, bitmap description of the target can be used to simulate depth profiles such as those resulting from ion implantation, diffusion, and intermixing. Other improvements to Corteo include the possibility to interpolate the cross-section in angle-energy tables, and the generation of energy-depth maps.

  14. Self-Localization of a Multi-Fisheye Camera Based Augmented Reality System in Textureless 3d Building Models

    NASA Astrophysics Data System (ADS)

    Urban, S.; Leitloff, J.; Wursthorn, S.; Hinz, S.

    2013-10-01

    Georeferenced images help planners to compare and document the progress of underground construction sites. As underground positioning can not rely on GPS/GNSS, we introduce a solely vision based localization method, that makes use of a textureless 3D CAD model of the construction site. In our analysis-by-synthesis approach, depth and normal fisheye images are rendered from presampled positions and gradient orientations are extracted to build a high dimensional synthetic feature space. Acquired camera images are then matched to those features by using a robust distance metric and fast nearest neighbor search. In this manner, initial poses can be obtained on a laptop in real-time using concurrent processing and the graphics processing unit.

  15. MRI data driven partial volume effects correction in PET imaging using 3D local multi-resolution analysis

    NASA Astrophysics Data System (ADS)

    Le Pogam, Adrien; Lamare, Frederic; Hatt, Mathieu; Fernandez, Philippe; Le Rest, Catherine Cheze; Visvikis, Dimitris

    2013-02-01

    PET partial volume effects (PVE) resulting from the limited resolution of PET scanners is still a quantitative issue that PET/MRI scanners do not solve by themselves. A recently proposed voxel-based locally adaptive 3D multi-resolution PVE correction based on the mutual analysis of wavelet decompositions was applied on 12 clinical 18F-FLT PET/T1 MRI images of glial tumors, and compared to a PET only voxel-wise iterative deconvolution approach. Quantitative and qualitative results demonstrated the interest of exploiting PET/MRI information with higher uptake increases (19±8% vs. 11±7%, p=0.02), as well as more convincing visual restoration of details within tumors with respect to deconvolution of the PET uptake only. Further studies are now required to demonstrate the accuracy of this restoration with histopathological validation of the uptake in tumors.

  16. About Non-Line-Of-Sight Satellite Detection and Exclusion in a 3D Map-Aided Localization Algorithm

    PubMed Central

    Peyraud, Sébastien; Bétaille, David; Renault, Stéphane; Ortiz, Miguel; Mougel, Florian; Meizel, Dominique; Peyret, François

    2013-01-01

    Reliable GPS positioning in city environment is a key issue actually, signals are prone to multipath, with poor satellite geometry in many streets. Using a 3D urban model to forecast satellite visibility in urban contexts in order to improve GPS localization is the main topic of the present article. A virtual image processing that detects and eliminates possible faulty measurements is the core of this method. This image is generated using the position estimated a priori by the navigation process itself, under road constraints. This position is then updated by measurements to line-of-sight satellites only. This closed-loop real-time processing has shown very first promising full-scale test results. PMID:23344379

  17. About Non-Line-Of-Sight satellite detection and exclusion in a 3D map-aided localization algorithm.

    PubMed

    Peyraud, Sébastien; Bétaille, David; Renault, Stéphane; Ortiz, Miguel; Mougel, Florian; Meizel, Dominique; Peyret, François

    2013-01-01

    Reliable GPS positioning in city environment is a key issue: actually, signals are prone to multipath, with poor satellite geometry in many streets. Using a 3D urban model to forecast satellite visibility in urban contexts in order to improve GPS localization is the main topic of the present article. A virtual image processing that detects and eliminates possible faulty measurements is the core of this method. This image is generated using the position estimated a priori by the navigation process itself, under road constraints. This position is then updated by measurements to line-of-sight satellites only. This closed-loop real-time processing has shown very first promising full-scale test results. PMID:23344379

  18. Local existence and Gevrey regularity of 3-D Navier-Stokes equations with ℓp initial data

    NASA Astrophysics Data System (ADS)

    Biswas, Animikh

    We obtain local existence and Gevrey regularity of 3-D periodic Navier-Stokes equations in case the sequence of Fourier coefficients of the initial data is in ℓp (p<3/2). The ℓp norm of the sequence of Fourier coefficients of the solution and its analogous Gevrey norm remains bounded on a time interval whose length depends only on the size of the body force and the ℓp norm of the Fourier coefficient sequence of the initial data. The control on the Gevrey norm produces explicit estimates on the analyticity radius of the solution as in Foias and Temam (J. Funct. Anal. 87 (1989) 359-369). The results provide an alternate approach in estimating the space-analyticity radius of solutions to Navier-Stokes equations than the one presented by Grujić and Kukavica (J. Funct. Anal. 152 (1998) 447-466).

  19. Automatic segmentation of solitary pulmonary nodules based on local intensity structure analysis and 3D neighborhood features in 3D chest CT images

    NASA Astrophysics Data System (ADS)

    Chen, Bin; Kitasaka, Takayuki; Honma, Hirotoshi; Takabatake, Hirotsugu; Mori, Masaki; Natori, Hiroshi; Mori, Kensaku

    2012-03-01

    This paper presents a solitary pulmonary nodule (SPN) segmentation method based on local intensity structure analysis and neighborhood feature analysis in chest CT images. Automated segmentation of SPNs is desirable for a chest computer-aided detection/diagnosis (CAS) system since a SPN may indicate early stage of lung cancer. Due to the similar intensities of SPNs and other chest structures such as blood vessels, many false positives (FPs) are generated by nodule detection methods. To reduce such FPs, we introduce two features that analyze the relation between each segmented nodule candidate and it neighborhood region. The proposed method utilizes a blob-like structure enhancement (BSE) filter based on Hessian analysis to augment the blob-like structures as initial nodule candidates. Then a fine segmentation is performed to segment much more accurate region of each nodule candidate. FP reduction is mainly addressed by investigating two neighborhood features based on volume ratio and eigenvector of Hessian that are calculates from the neighborhood region of each nodule candidate. We evaluated the proposed method by using 40 chest CT images, include 20 standard-dose CT images that we randomly chosen from a local database and 20 low-dose CT images that were randomly chosen from a public database: LIDC. The experimental results revealed that the average TP rate of proposed method was 93.6% with 12.3 FPs/case.

  20. An investigation of matching symmetry in the human pinnae with possible implications for 3D ear recognition and sound localization.

    PubMed

    Claes, Peter; Reijniers, Jonas; Shriver, Mark D; Snyders, Jonatan; Suetens, Paul; Nielandt, Joachim; De Tré, Guy; Vandermeulen, Dirk

    2015-01-01

    The human external ears, or pinnae, have an intriguing shape and, like most parts of the human external body, bilateral symmetry is observed between left and right. It is a well-known part of our auditory sensory system and mediates the spatial localization of incoming sounds in 3D from monaural cues due to its shape-specific filtering as well as binaural cues due to the paired bilateral locations of the left and right ears. Another less broadly appreciated aspect of the human pinna shape is its uniqueness from one individual to another, which is on the level of what is seen in fingerprints and facial features. This makes pinnae very useful in human identification, which is of great interest in biometrics and forensics. Anatomically, the type of symmetry observed is known as matching symmetry, with structures present as separate mirror copies on both sides of the body, and in this work we report the first such investigation of the human pinna in 3D. Within the framework of geometric morphometrics, we started by partitioning ear shape, represented in a spatially dense way, into patterns of symmetry and asymmetry, following a two-factor anova design. Matching symmetry was measured in all substructures of the pinna anatomy. However, substructures that 'stick out' such as the helix, tragus, and lobule also contained a fair degree of asymmetry. In contrast, substructures such as the conchae, antitragus, and antihelix expressed relatively stronger degrees of symmetric variation in relation to their levels of asymmetry. Insights gained from this study were injected into an accompanying identification setup exploiting matching symmetry where improved performance is demonstrated. Finally, possible implications of the results in the context of ear recognition as well as sound localization are discussed. PMID:25382291

  1. A proposal for combining mapping, localization and target recognition

    NASA Astrophysics Data System (ADS)

    Grönwall, Christina; Hendeby, Gustaf; Sinivaara, Kristian

    2015-10-01

    Simultaneous localization and mapping (SLAM) is a well-known positioning approach in GPS-denied environments such as urban canyons and inside buildings. Autonomous/aided target detection and recognition (ATR) is commonly used in military application to detect threats and targets in outdoor environments. This papers present approaches to combine SLAM with ATR in ways that compensate for the drawbacks in each method. The methods use physical objects that are recognizable by ATR as unambiguous features in SLAM, while SLAM provides the ATR with better position estimates. Landmarks in the form of 3D point features based on normal aligned radial features (NARF) are used in conjunction with identified objects and 3D object models that replace landmarks when possible. This leads to a more compact map representation with fewer landmarks, which partly compensates for the introduced cost of the ATR. We analyze three approaches to combine SLAM and 3D-data; point-point matching ignoring NARF features, point-point matching using the set of points that are selected by NARF feature analysis, and matching of NARF features using nearest neighbor analysis. The first two approaches are is similar to the common iterative closest point (ICP). We propose an algorithm that combines EKF-SLAM and ATR based on rectangle estimation. The intended application is to improve the positioning of a first responder moving through an indoor environment, where the map offers localization and simultaneously helps locate people, furniture and potentially dangerous objects such as gas canisters.

  2. MiR-10a* up-regulates coxsackievirus B3 biosynthesis by targeting the 3D-coding sequence

    PubMed Central

    Tong, Lei; Lin, Lexun; Wu, Shuo; Guo, Zhiwei; Wang, Tianying; Qin, Ying; Wang, Ruixue; Zhong, Xiaoyan; Wu, Xia; Wang, Yan; Luan, Tian; Wang, Qiang; Li, Yunxia; Chen, Xiaofeng; Zhang, Fengmin; Zhao, Wenran; Zhong, Zhaohua

    2013-01-01

    MicroRNAs (miRNAs) are small non-coding RNAs that can posttranscriptionally regulate gene expression by targeting messenger RNAs. During miRNA biogenesis, the star strand (miRNA*) is generally degraded to a low level in the cells. However, certain miRNA* express abundantly and can be recruited into the silencing complex to regulate gene expression. Most miRNAs function as suppressive regulators on gene expression. Group B coxsackieviruses (CVB) are the major pathogens of human viral myocarditis and dilated cardiomyopathy. CVB genome is a positive-sense, single-stranded RNA. Our previous study shows that miR-342-5p can suppress CVB biogenesis by targeting its 2C-coding sequence. In this study, we found that the miR-10a duplex could significantly up-regulate the biosynthesis of CVB type 3 (CVB3). Further study showed that it was the miR-10a star strand (miR-10a*) that augmented CVB3 biosynthesis. Site-directed mutagenesis showed that the miR-10a* target was located in the nt6818–nt6941 sequence of the viral 3D-coding region. MiR-10a* was detectable in the cardiac tissues of suckling Balb/c mice, suggesting that miR-10a* may impact CVB3 replication during its cardiac infection. Taken together, these data for the first time show that miRNA* can positively modulate gene expression. MiR-10a* might be involved in the CVB3 cardiac pathogenesis. PMID:23389951

  3. Local Genome Topology Can Exhibit an Incompletely Rewired 3D-Folding State during Somatic Cell Reprogramming.

    PubMed

    Beagan, Jonathan A; Gilgenast, Thomas G; Kim, Jesi; Plona, Zachary; Norton, Heidi K; Hu, Gui; Hsu, Sarah C; Shields, Emily J; Lyu, Xiaowen; Apostolou, Effie; Hochedlinger, Konrad; Corces, Victor G; Dekker, Job; Phillips-Cremins, Jennifer E

    2016-05-01

    Pluripotent genomes are folded in a topological hierarchy that reorganizes during differentiation. The extent to which chromatin architecture is reconfigured during somatic cell reprogramming is poorly understood. Here we integrate fine-resolution architecture maps with epigenetic marks and gene expression in embryonic stem cells (ESCs), neural progenitor cells (NPCs), and NPC-derived induced pluripotent stem cells (iPSCs). We find that most pluripotency genes reconnect to target enhancers during reprogramming. Unexpectedly, some NPC interactions around pluripotency genes persist in our iPSC clone. Pluripotency genes engaged in both "fully-reprogrammed" and "persistent-NPC" interactions exhibit over/undershooting of target expression levels in iPSCs. Additionally, we identify a subset of "poorly reprogrammed" interactions that do not reconnect in iPSCs and display only partially recovered, ESC-specific CTCF occupancy. 2i/LIF can abrogate persistent-NPC interactions, recover poorly reprogrammed interactions, reinstate CTCF occupancy, and restore expression levels. Our results demonstrate that iPSC genomes can exhibit imperfectly rewired 3D-folding linked to inaccurately reprogrammed gene expression. PMID:27152443

  4. Targeting Resources for Local Growth.

    ERIC Educational Resources Information Center

    Casto, James E.

    2001-01-01

    Focusing state and federal dollars on targeted areas, the Kentucky Appalachian Community Development Initiative helps communities in eastern Kentucky fund their own strategies for economic growth. In Hindman, the project focuses on creating the Kentucky School of Crafts, to train master artisans; supporting the Kentucky Appalachian Artisan Center;…

  5. Targeting p21 Degradation Locally

    PubMed Central

    Xiong, Yue

    2016-01-01

    Just as the activity of many multifunctional proteins is restricted by subcellular localization, so is their regulation. In this issue of Development Cell, Starostina et al. identify an E3 ubiquitin ligase, CRL2LRR1, for the cyclin-dependent kinase inhibitor p21 that specifically ubiquitylates cytoplasmic p21 to facilitate cell migration. PMID:21074711

  6. Orientation-weighted local Minkowski functionals in 3D for quantitative assessment of trabecular bone structure in the hip

    NASA Astrophysics Data System (ADS)

    Boehm, H. F.; Bitterling, H.; Weber, C.; Kuhn, V.; Eckstein, F.; Reiser, M.

    2007-03-01

    Fragility fractures or pathologic fractures of the hip, i.e. fractures with no apparent trauma, represent the worst complication in osteoporosis with a mortality close to 25% during the first post-traumatic year. Over 90% of hip fractures result from falls from standing height. A substantial number of femoral fractures are initiated in the femoral neck or the trochanteric regions which contain an internal architecture of trabeculae that are functionally highly specialized to withstand the complex pattern of external and internal forces associated with human gait. Prediction of the mechanical strength of bone tissue can be achieved by dedicated texture analysis of data obtained by high resolution imaging modalities, e.g. computed tomography (CT) or magnetic resonance tomography (MRI). Since in the case of the proximal femur, the connectivity, regional distribution and - most of all - the preferred orientation of individual trabeculae change considerably within narrow spatial limits, it seems most reasonable to evaluate the femoral bone structure on an orientation-weighted, local scale. In past studies, we could demonstrate the advantages of topological analysis of bone structure using the Minkowski Functionals in 3D on a global and on a local scale. The current study was designed to test the hypothesis that the prediction of the mechanical competence of the proximal femur by a new algorithm considering orientational changes of topological properties in the trabecular architecture is feasible and better suited than conventional methods based on the measurement of the mineral density of bone tissue (BMD).

  7. Local structures around 3d metal dopants in topological insulator Bi2Se3 studied by EXAFS measurements

    NASA Astrophysics Data System (ADS)

    Liu, Zhen; Wei, Xinyuan; Wang, Jiajia; Pan, Hong; Ji, Fuhao; Xi, Fuchun; Zhang, Jing; Hu, Tiandou; Zhang, Shuo; Jiang, Zheng; Wen, Wen; Huang, Yuying; Ye, Mao; Yang, Zhongqin; Qiao, Shan

    2014-09-01

    Transition-metal-doped Bi2Se3 crystals, X0.05Bi2Se3 (X =Cr, Co, Ni, and Cu), are prepared and studied by powder x-ray diffraction and extended x-ray absorption fine structure (EXAFS) measurements to get the local structures around the dopants. Cr atoms substitute Bi atoms and Co atoms may substitute Bi atoms or form Co3Se4 (C2/m) clusters. Cu is also found taking the Bi substitutional site, which differs from the reported superconductor phase of Cu-doped Bi2Se3, suggesting the dependence of site occupancy of Cu in Bi2Se3 on the process of sample growing. For Ni0.05Bi2Se3, Ni atoms form Ni3Se4 (C2/m) clusters. The nearest neighbors of X (X =Cr, Co, and Cu) are Se atoms, and the X-Se bond lengths are extracted from EXAFS as 2.50 Å for Cr-Se, 2.40 Å for Co-Se, and 2.38 Å for Cu-Se, which show the direct evidences of dramatic structural relaxations around 3d dopants. The bond information of local structures around dopants is valuable for subsequent theoretical studies, and can hardly be obtained from other techniques.

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-01-01

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

  10. Portable, Easy-to-Operate, and Antifouling Microcapsule Array Chips Fabricated by 3D Ice Printing for Visual Target Detection.

    PubMed

    Zhang, Hong-Ze; Zhang, Fang-Ting; Zhang, Xiao-Hui; Huang, Dong; Zhou, Ying-Lin; Li, Zhi-Hong; Zhang, Xin-Xiang

    2015-06-16

    Herein, we proposed a portable, easy-to-operate, and antifouling microcapsule array chip for target detection. This prepackaged chip was fabricated by innovative and cost-effective 3D ice printing integrating with photopolymerization sealing which could eliminate complicated preparation of wet chemistry and effectively resist outside contaminants. Only a small volume of sample (2 μL for each microcapsule) was consumed to fulfill the assay. All the reagents required for the analysis were stored in ice form within the microcapsule before use, which guaranteed the long-term stability of microcapsule array chips. Nitrite and glucose were chosen as models for proof of concept to achieve an instant quantitative detection by naked eyes without the need of external sophisticated instruments. The simplicity, low cost, and small sample consumption endowed ice-printing microcapsule array chips with potential commercial value in the fields of on-site environmental monitoring, medical diagnostics, and rapid high-throughput point-of-care quantitative assay. PMID:25970032

  11. Determination of Rectification Corrections for Semi Gantry Crane Rail Axes in the Local 3D Coordinate System

    NASA Astrophysics Data System (ADS)

    Filipiak, Daria; Kamiński, Waldemar

    2015-02-01

    Electronic tacheometers are currently the standard instruments used in geodetic work, including also geodetic engineering measurements. The main advantage connected with this equipment is among others high accuracy of the measurement and thus high accuracy of the final determinations represented for example by the points' coordinates. One of many applications of the tacheometers is the measurement of crane rail axes. This measurement is based on polar method and it allows to get the spatial coordinates of points in 3D local system. The standard technology of measurement of crane rail axes and development of its calculations' results is well-known and widely presented in the subject literature. At the same time new methods of observations results evaluation are developing. Some new proposals for the development of measurement results were already presented in (Kamiński, 2013). This paper is a generalisation of the paper quoted above. The authors developed the concept which was presented there by a proposal for determining rectification corrections for semi gantry crane rail axes. To carried out the task, the parametric method with conditions on parameters was used. Moreover the practical tests on simulated measurement results were conducted. The results obtained from alignment confirmed the theoretical assumptions. Despite the fact that analyses were carried out only on the simulated data, it is already possible to say that presented method for determination of rectification corrections for crane rail axes can be used for development of the observations from real measurement.

  12. A microwave imaging-based 3D localization algorithm for an in-body RF source as in wireless capsule endoscopes.

    PubMed

    Chandra, Rohit; Balasingham, Ilangko

    2015-08-01

    A microwave imaging-based technique for 3D localization of an in-body RF source is presented. Such a technique can be useful for localization of an RF source as in wireless capsule endoscopes for positioning of any abnormality in the gastrointestinal tract. Microwave imaging is used to determine the dielectric properties (relative permittivity and conductivity) of the tissues that are required for a precise localization. A 2D microwave imaging algorithm is used for determination of the dielectric properties. Calibration method is developed for removing any error due to the used 2D imaging algorithm on the imaging data of a 3D body. The developed method is tested on a simple 3D heterogeneous phantom through finite-difference-time-domain simulations. Additive white Gaussian noise at the signal-to-noise ratio of 30 dB is added to the simulated data to make them more realistic. The developed calibration method improves the imaging and the localization accuracy. Statistics on the localization accuracy are generated by randomly placing the RF source at various positions inside the small intestine of the phantom. The cumulative distribution function of the localization error is plotted. In 90% of the cases, the localization accuracy was found within 1.67 cm, showing the capability of the developed method for 3D localization. PMID:26737194

  13. Surface-based matching of 3D point clouds with variable coordinates in source and target system

    NASA Astrophysics Data System (ADS)

    Ge, Xuming; Wunderlich, Thomas

    2016-01-01

    The automatic co-registration of point clouds, representing three-dimensional (3D) surfaces, is an important technique in 3D reconstruction and is widely applied in many different disciplines. An alternative approach is proposed here that estimates the transformation parameters of one or more 3D search surfaces with respect to a 3D template surface. The approach uses the nonlinear Gauss-Helmert model, minimizing the quadratically constrained least squares problem. This approach has the ability to match arbitrarily oriented 3D surfaces captured from a number of different sensors, on different time-scales and at different resolutions. In addition to the 3D surface-matching paths, the mathematical model allows the precision of the point clouds to be assessed after adjustment. The error behavior of surfaces can also be investigated based on the proposed approach. Some practical examples are presented and the results are compared with the iterative closest point and the linear least-squares approaches to demonstrate the performance and benefits of the proposed technique.

  14. Planning and visualization methods for effective bronchoscopic target localization

    NASA Astrophysics Data System (ADS)

    Gibbs, Jason D.; Taeprasarsit, Pinyo; Higgins, William E.

    2012-02-01

    Bronchoscopic biopsy of lymph nodes is an important step in staging lung cancer. Lymph nodes, however, lie behind the airway walls and are near large vascular structures - all of these structures are hidden from the bronchoscope's field of view. Previously, we had presented a computer-based virtual bronchoscopic navigation system that provides reliable guidance for bronchoscopic sampling. While this system offers a major improvement over standard practice, bronchoscopists told us that target localization- lining up the bronchoscope before deploying a needle into the target - can still be challenging. We therefore address target localization in two distinct ways: (1) automatic computation of an optimal diagnostic sampling pose for safe, effective biopsies, and (2) a novel visualization of the target and surrounding major vasculature. The planning determines the final pose for the bronchoscope such that the needle, when extended from the tip, maximizes the tissue extracted. This automatically calculated local pose orientation is conveyed in endoluminal renderings by a 3D arrow. Additional visual cues convey obstacle locations and target depths-of-sample from arbitrary instantaneous viewing orientations. With the system, a physician can freely navigate in the virtual bronchoscopic world perceiving the depth-of-sample and possible obstacle locations at any endoluminal pose, not just one pre-determined optimal pose. We validated the system using mediastinal lymph nodes in eleven patients. The system successfully planned for 20 separate targets in human MDCT scans. In particular, given the patient and bronchoscope constraints, our method found that safe, effective biopsies were feasible in 16 of the 20 targets; the four remaining targets required more aggressive safety margins than a "typical" target. In all cases, planning computation took only a few seconds, while the visualizations updated in real time during bronchoscopic navigation.

  15. Density structure and geometry of the Costa Rican subduction zone from 3-D gravity modeling and local earthquake data

    NASA Astrophysics Data System (ADS)

    Lücke, O. H.; Arroyo, I. G.

    2015-10-01

    The eastern part of the oceanic Cocos Plate presents a heterogeneous crustal structure due to diverse origins and ages as well as plate-hot spot interactions which originated the Cocos Ridge, a structure that converges with the Caribbean Plate in southeastern Costa Rica. The complex structure of the oceanic plate directly influences the dynamics and geometry of the subduction zone along the Middle American Trench. In this paper an integrated interpretation of the slab geometry in Costa Rica is presented based on 3-D density modeling of combined satellite and surface gravity data, constrained by available geophysical and geological data and seismological information obtained from local networks. The results show the continuation of steep subduction geometry from the Nicaraguan margin into northwestern Costa Rica, followed by a moderate dipping slab under the Central Cordillera toward the end of the Central American Volcanic Arc. Contrary to commonly assumed, to the southeast end of the volcanic arc, our preferred model shows a steep, coherent slab that extends up to the landward projection of the Panama Fracture Zone. Overall, a gradual change in the depth of the intraplate seismicity is observed, reaching 220 km in the northwestern part, and becoming progressively shallower toward the southeast, where it reaches a maximum depth of 75 km. The changes in the terminal depth of the observed seismicity correlate with the increased density in the modeled slab. The absence of intermediate depth (> 75 km) intraplate seismicity in the southeastern section and the higher densities for the subducted slab in this area, support a model in which dehydration reactions in the subducted slab cease at a shallower depth, originating an anhydrous and thus aseismic slab.

  16. Electrostatic Contributions Drive the Interaction Between Staphylococcus aureus Protein Efb-C and its Complement Target C3d

    SciTech Connect

    Haspel, N.; Ricklin, D.; Geisbrecht, B.V.; Kavraki, L.E.; Lambris, J.D.

    2008-11-13

    The C3-inhibitory domain of Staphylococcus aureus extracellular fibrinogen-binding protein (Efb-C) defines a novel three-helix bundle motif that regulates complement activation. Previous crystallographic studies of Efb-C bound to its cognate subdomain of human C3 (C3d) identified Arg-131 and Asn-138 of Efb-C as key residues for its activity. In order to characterize more completely the physical and chemical driving forces behind this important interaction, we employed in this study a combination of structural, biophysical, and computational methods to analyze the interaction of C3d with Efb-C and the single-point mutants R131A and N138A. Our results show that while these mutations do not drastically affect the structure of the Efb-C/C3d recognition complex, they have significant adverse effects on both the thermodynamic and kinetic profiles of the resulting complexes. We also characterized other key interactions along the Efb-C/C3d binding interface and found an intricate network of salt bridges and hydrogen bonds that anchor Efb-C to C3d, resulting in its potent complement inhibitory properties.

  17. Electrostatic contributions drive the interaction between Staphylococcus aureus protein Efb-C and its complement target C3d

    PubMed Central

    Haspel, Nurit; Ricklin, Daniel; Geisbrecht, Brian V.; Kavraki, Lydia E.; Lambris, John D.

    2008-01-01

    The C3–inhibitory domain of Staphylococcus aureus extracellular fibrinogen-binding protein (Efb-C) defines a novel three-helix bundle motif that regulates complement activation. Previous crystallographic studies of Efb-C bound to its cognate subdomain of human C3 (C3d) identified Arg-131 and Asn-138 of Efb-C as key residues for its activity. In order to characterize more completely the physical and chemical driving forces behind this important interaction, we employed in this study a combination of structural, biophysical, and computational methods to analyze the interaction of C3d with Efb-C and the single-point mutants R131A and N138A. Our results show that while these mutations do not drastically affect the structure of the Efb-C/C3d recognition complex, they have significant adverse effects on both the thermodynamic and kinetic profiles of the resulting complexes. We also characterized other key interactions along the Efb-C/C3d binding interface and found an intricate network of salt bridges and hydrogen bonds that anchor Efb-C to C3d, resulting in its potent complement inhibitory properties. PMID:18687868

  18. Transorbital target localization in the porcine model

    NASA Astrophysics Data System (ADS)

    DeLisi, Michael P.; Mawn, Louise A.; Galloway, Robert L.

    2013-03-01

    Current pharmacological therapies for the treatment of chronic optic neuropathies such as glaucoma are often inadequate due to their inability to directly affect the optic nerve and prevent neuron death. While drugs that target the neurons have been developed, existing methods of administration are not capable of delivering an effective dose of medication along the entire length of the nerve. We have developed an image-guided system that utilizes a magnetically tracked flexible endoscope to navigate to the back of the eye and administer therapy directly to the optic nerve. We demonstrate the capabilities of this system with a series of targeted surgical interventions in the orbits of live pigs. Target objects consisted of NMR microspherical bulbs with a volume of 18 μL filled with either water or diluted gadolinium-based contrast, and prepared with either the presence or absence of a visible coloring agent. A total of 6 pigs were placed under general anesthesia and two microspheres of differing color and contrast content were blindly implanted in the fat tissue of each orbit. The pigs were scanned with T1-weighted MRI, image volumes were registered, and the microsphere containing gadolinium contrast was designated as the target. The surgeon was required to navigate the flexible endoscope to the target and identify it by color. For the last three pigs, a 2D/3D registration was performed such that the target's coordinates in the image volume was noted and its location on the video stream was displayed with a crosshair to aid in navigation. The surgeon was able to correctly identify the target by color, with an average intervention time of 20 minutes for the first three pigs and 3 minutes for the last three.

  19. Importance of protocol target definition on the ability to spare normal tissue: An IMRT and 3D-CRT planning comparison for intraorbital tumors

    SciTech Connect

    Hein, Patrick A.; Gladstone, David J.; Bellerive, Marc R.; Hug, Eugen B. . E-mail: Eugen.B.Hug@hitchcock.org

    2005-08-01

    Purpose: We selected five intraorbital tumor sites that are frequently found in clinical practice in children diagnosed with orbital rhabdomyosarcoma and performed three-dimensional conformal radiotherapy (3D-CRT) and intensity-modulated photon radiotherapy (IMRT) planning. Results of target coverage and doses to critical structures were compared. The goal of this study was to evaluate and to document realistic expectations as to organ-sparing capabilities of modern radiation therapy planning technologies with a focus on lens-sparing irradiation. Furthermore, we investigated potential added benefits of IMRT compared with 3D-CRT and the influence of protocol volume criteria definitions on the ability to obtain normal tissue dose sparing using the orbit as an example of a complex anatomic site. Methods and Materials: The five intraorbital tumor sites were placed retrobulbar, temporal, nasal, in the upper inner and upper outer quadrant, the latter two more complex in shape. Gross tumor volume (GTV), clinical target volume (CTV), and planning target volume (PTV) were defined in image-fused computed tomography and magnetic resonance data sets. 3D-CRT and IMRT photon plans, using equal beam angles and collimation for direct comparison, were designed to 45 Gy prescription dose according to Intergroup Rhabdomyosarcoma Study Group-D9602 (IRSG-D9602) protocol (Intergroup Rhabdomyosarcoma Study V [IRS-V] protocol) for Stage I, Clinical Group 3 orbital rhabdomyosarcoma. To compare the impact of changed target definitions in IMRT planning, additional IMRT plans were generated using modified volume and dose coverage criteria. The minimum dose constraint (95%) of the PTV was substituted by a required minimum volume coverage (95%) with the prescribed dose. Dose-volume histograms (DVHs) were obtained, including target volumes, lens, optic nerves, optic chiasm, lacrimal gland, bony orbit, pituitary gland, frontal and temporal lobes. Results: Protocol target volume coverage criteria

  20. Integrated-boost IMRT or 3-D-CRT using FET-PET based auto-contoured target volume delineation for glioblastoma multiforme - a dosimetric comparison

    PubMed Central

    2009-01-01

    Background Biological brain tumor imaging using O-(2-[18F]fluoroethyl)-L-tyrosine (FET)-PET combined with inverse treatment planning for locally restricted dose escalation in patients with glioblastoma multiforme seems to be a promising approach. The aim of this study was to compare inverse with forward treatment planning for an integrated boost dose application in patients suffering from a glioblastoma multiforme, while biological target volumes are based on FET-PET and MRI data sets. Methods In 16 glioblastoma patients an intensity-modulated radiotherapy technique comprising an integrated boost (IB-IMRT) and a 3-dimensional conventional radiotherapy (3D-CRT) technique were generated for dosimetric comparison. FET-PET, MRI and treatment planning CT (P-CT) were co-registrated. The integrated boost volume (PTV1) was auto-contoured using a cut-off tumor-to-brain ratio (TBR) of ≥ 1.6 from FET-PET. PTV2 delineation was MRI-based. The total dose was prescribed to 72 and 60 Gy for PTV1 and PTV2, using daily fractions of 2.4 and 2 Gy. Results After auto-contouring of PTV1 a marked target shape complexity had an impact on the dosimetric outcome. Patients with 3-4 PTV1 subvolumes vs. a single volume revealed a significant decrease in mean dose (67.7 vs. 70.6 Gy). From convex to complex shaped PTV1 mean doses decreased from 71.3 Gy to 67.7 Gy. The homogeneity and conformity for PTV1 and PTV2 was significantly improved with IB-IMRT. With the use of IB-IMRT the minimum dose within PTV1 (61.1 vs. 57.4 Gy) and PTV2 (51.4 vs. 40.9 Gy) increased significantly, and the mean EUD for PTV2 was improved (59.9 vs. 55.3 Gy, p < 0.01). The EUD for PTV1 was only slightly improved (68.3 vs. 67.3 Gy). The EUD for the brain was equal with both planning techniques. Conclusion In the presented planning study the integrated boost concept based on inversely planned IB-IMRT is feasible. The FET-PET-based automatically contoured PTV1 can lead to very complex geometric configurations, limiting the

  1. Local and systemic activation of the whole complement cascade in human leukocytoclastic cutaneous vasculitis; C3d,g and terminal complement complex as sensitive markers.

    PubMed Central

    Dauchel, H; Joly, P; Delpech, A; Thomine, E; Sauger, F; Le Loet, X; Lauret, P; Tron, F; Fontaine, M; Ripoche, J

    1993-01-01

    We have studied complement activation both in plasma samples and in lesional skin from patients with leukocytoclastic cutaneous vasculitis (LCV). Enzyme immunoassay (EIA) quantification of the complement activation markers, C3d,g and the terminal complement complex (TCC) in plasma, showed that their levels were significantly increased in 66% and 55% of the patients, respectively (n = 29) compared with healthy controls, whereas the standard measurements of C3, factor B, C1q, C4 and C2 were generally within normal range. Elevations of C3d,g and TCC levels in plasma were significantly correlated. Importantly, a significant correlation was found between the severity of the vasculitis and both C3d,g and TCC plasma levels. Immunofluorescence studies of skin biopsy specimens demonstrated simultaneous presence of perivascular dermal deposits of C3d,g and TCC in lesional skin from 96% and 80% respectively of the patients (n = 25). There was a significant correlation between the intensity of the deposits of both markers. Clusterin, a TCC inhibitory protein, was always found at the same sites of perivascular TCC deposits. Immunofluorescence studies at the epidermal basement membrane zone (BMZ) revealed in each case deposits of C3d,g which were accompanied by TCC deposits in 52% of the biopsy specimens. These data demonstrate that there is a local and systemic activation of the whole complement cascade in human LCV. The presence of both C3d,g and clusterin-associated TCC perivascular deposits suggests an intervention of a regulatory mechanism of local complement activation in LCV. Finally, measurement of plasma C3d,g and TCC appears to be a sensitive indicator of systemic complement activation and disease severity in LCV. Images Fig. 1 Fig. 2 PMID:8485913

  2. HER2 signaling pathway activation and response of breast cancer cells to HER2-targeting agents is dependent strongly on the 3D microenvironment

    SciTech Connect

    Weigelt, Britta; Lo, Alvin T; Park, Catherine C; Gray, Joe W; Bissell, Mina J

    2009-07-27

    Development of effective and durable breast cancer treatment strategies requires a mechanistic understanding of the influence of the microenvironment on response. Previous work has shown that cellular signaling pathways and cell morphology are dramatically influenced by three-dimensional (3D) cultures as opposed to traditional two-dimensional (2D) monolayers. Here, we compared 2D and 3D culture models to determine the impact of 3D architecture and extracellular matrix (ECM) on HER2 signaling and on the response of HER2-amplified breast cancer cell lines to the HER2-targeting agents Trastuzumab, Pertuzumab and Lapatinib. We show that the response of the HER2-amplified AU565, SKBR3 and HCC1569 cells to these anti-HER2 agents was highly dependent on whether the cells were cultured in 2D monolayer or 3D laminin-rich ECM gels. Inhibition of {beta}1 integrin, a major cell-ECM receptor subunit, significantly increased the sensitivity of the HER2-amplified breast cancer cell lines to the humanized monoclonal antibodies Trastuzumab and Pertuzumab when grown in a 3D environment. Finally, in the absence of inhibitors, 3D cultures had substantial impact on HER2 downstream signaling and induced a switch between PI3K-AKT- and RAS-MAPKpathway activation in all cell lines studied, including cells lacking HER2 amplification and overexpression. Our data provide direct evidence that breast cancer cells are able to rapidly adapt to different environments and signaling cues by activating alternative pathways that regulate proliferation and cell survival, events that may play a significant role in the acquisition of resistance to targeted therapies.

  3. A visual probe localization and calibration system for cost-effective computer-aided 3D ultrasound.

    PubMed

    Ali, Aziah; Logeswaran, Rajasvaran

    2007-08-01

    The 3D ultrasound systems produce much better reproductions than 2D ultrasound, but their prohibitively high cost deprives many less affluent organization this benefit. This paper proposes using the conventional 2D ultrasound equipment readily available in most hospitals, along with a single conventional digital camera, to construct 3D ultrasound images. The proposed system applies computer vision to extract position information of the ultrasound probe while the scanning takes place. The probe, calibrated in order to calculate the offset of the ultrasound scan from the position of the marker attached to it, is used to scan a number of geometrical objects. Using the proposed system, the 3D volumes of the objects were successfully reconstructed. The system was tested in clinical situations where human body parts were scanned. The results presented, and confirmed by medical staff, are very encouraging for cost-effective implementation of computer-aided 3D ultrasound using a simple setup with 2D ultrasound equipment and a conventional digital camera. PMID:17126314

  4. Targeted Business Incentives and Local Labor Markets

    ERIC Educational Resources Information Center

    Freedman, Matthew

    2013-01-01

    This paper uses a regression discontinuity design to examine the effects of geographically targeted business incentives on local labor markets. Unlike elsewhere in the United States, enterprise zone (EZ) designations in Texas are determined in part by a cutoff rule based on census block group poverty rates. Exploiting this discontinuity as a…

  5. NOTE: Adaptation of a 3D prostate cancer atlas for transrectal ultrasound guided target-specific biopsy

    NASA Astrophysics Data System (ADS)

    Narayanan, R.; Werahera, P. N.; Barqawi, A.; Crawford, E. D.; Shinohara, K.; Simoneau, A. R.; Suri, J. S.

    2008-10-01

    Due to lack of imaging modalities to identify prostate cancer in vivo, current TRUS guided prostate biopsies are taken randomly. Consequently, many important cancers are missed during initial biopsies. The purpose of this study was to determine the potential clinical utility of a high-speed registration algorithm for a 3D prostate cancer atlas. This 3D prostate cancer atlas provides voxel-level likelihood of cancer and optimized biopsy locations on a template space (Zhan et al 2007). The atlas was constructed from 158 expert annotated, 3D reconstructed radical prostatectomy specimens outlined for cancers (Shen et al 2004). For successful clinical implementation, the prostate atlas needs to be registered to each patient's TRUS image with high registration accuracy in a time-efficient manner. This is implemented in a two-step procedure, the segmentation of the prostate gland from a patient's TRUS image followed by the registration of the prostate atlas. We have developed a fast registration algorithm suitable for clinical applications of this prostate cancer atlas. The registration algorithm was implemented on a graphical processing unit (GPU) to meet the critical processing speed requirements for atlas guided biopsy. A color overlay of the atlas superposed on the TRUS image was presented to help pick statistically likely regions known to harbor cancer. We validated our fast registration algorithm using computer simulations of two optimized 7- and 12-core biopsy protocols to maximize the overall detection rate. Using a GPU, patient's TRUS image segmentation and atlas registration took less than 12 s. The prostate cancer atlas guided 7- and 12-core biopsy protocols had cancer detection rates of 84.81% and 89.87% respectively when validated on the same set of data. Whereas the sextant biopsy approach without the utility of 3D cancer atlas detected only 70.5% of the cancers using the same histology data. We estimate 10-20% increase in prostate cancer detection rates

  6. Targeting and Localization for Mars Rover Operations

    NASA Technical Reports Server (NTRS)

    Powell, Mark W.; Crockett, Thomas; Fox, Jason M.; Joswig, Joseph C.; Norris, Jeffrey S.; Rabe, Kenneth J.; McCurdy, Michael; Pyrzak, Guy

    2006-01-01

    In this work we discuss how the quality of localization knowledge impacts the remote operation of rovers on the surface of Mars. We look at the techniques of localization estimation used in the Mars Pathfinder and Mars Exploration Rover missions. We examine the motivation behind the modes of targeting for different types of activities, such as navigation, remote science, and in situ science. We discuss the virtues and shortcomings of existing approaches and new improvements in the latest operations tools used to support the Mars Exploration Rover missions and rover technology development tasks at the Jet Propulsion Laboratory. We conclude with future directions we plan to explore in improving the localization knowledge available for operations and more effective targeting of rovers and their instrument payloads.

  7. Targeting and Localization for Mars Rover Operations

    NASA Technical Reports Server (NTRS)

    Powell, Mark W.; Crockett, Thomas; Fox, Jason M.; Joswig, Joseph C.; Norris, Jeffrey S.; Rabe, Kenneth J.

    2008-01-01

    A design and a partially developed application framework were presented for improving localization and targeting for surface spacecraft. The program has value for the Mars Science Laboratory mission, and has been delivered to support the Mars Exploration Rovers as part of the latest version of the Maestro science planning tool. It also has applications for future missions involving either surface-based or low-altitude atmospheric robotic vehicles. The targeting and localization solutions solve the problem of how to integrate localization estimate updates into operational planning tools, operational data product generalizations, and flight software by adding expanded flexibility to flight software, the operations data product pipeline, and operations planning tools based on coordinate frame updates during a planning cycle.

  8. Impact of grain size evolution on the localization of deformation: 3D numerical simulations of mantle convection

    NASA Astrophysics Data System (ADS)

    Rozel, Antoine; Golabek, Gregor; Tackley, Paul

    2014-05-01

    Thermodynamically consistent models of single phase grain size evolution have been proposed in the past years [Austin and Evans (2007), Ricard and Bercovici (2009), Rozel et al. (2011), Rozel (2012)]. In a recently updated version [Bercovici and Ricard (2012), PEPI], the mechanics of two-phase grain aggregates has been formulated following the same physical approach. Several non-linear mechanisms such as dynamic recrystallization or Zener pinning are now available in a single non-equilibrium formulation of grain size distributions evolution. The self-consistent generation of localized plate boundaries is predicted in [Bercovici and Ricard (2012), EPSL] using this model, but it has not been tested in a dynamically consistent way. We propose the first set of three-dimensional numerical simulations of mantle convection incorporating this formalism using the finite volume code StagYY [Tackley (2008)]. First, we detail how the model is numerically implemented. Pressure and velocity fields are solved on a staggered grid using a SIMPLER-like method. Multigrid W-cycles and extra coarse-grid relaxations are employed to enhance the convergence of Stokes and continuity equations. The grain size is stored on a large number of tracers advected through the computational domain, which prevent numerical diffusion and allows a high resolution in the shear zones developing in the lithosphere. We also describe the physical formalism itself and propose the set of free parameters of the model. Normal growth, dynamic recrystallization and phase transitions all have a strong effect on the average grain size. We use a visco-plastic rheology in which the viscous strain rate is obtained by summation of dislocation, diffusion and grain boundary sliding creep. Second, we describe the 3D grain size distribution in the mantle and in the lithosphere. We characterize in which conditions plate margins can form, mainly investigating grain growth, recrystallization and rheology related parameters

  9. Automatic localization of vertebral levels in x-ray fluoroscopy using 3D-2D registration: a tool to reduce wrong-site surgery

    NASA Astrophysics Data System (ADS)

    Otake, Y.; Schafer, S.; Stayman, J. W.; Zbijewski, W.; Kleinszig, G.; Graumann, R.; Khanna, A. J.; Siewerdsen, J. H.

    2012-09-01

    Surgical targeting of the incorrect vertebral level (wrong-level surgery) is among the more common wrong-site surgical errors, attributed primarily to the lack of uniquely identifiable radiographic landmarks in the mid-thoracic spine. The conventional localization method involves manual counting of vertebral bodies under fluoroscopy, is prone to human error and carries additional time and dose. We propose an image registration and visualization system (referred to as LevelCheck), for decision support in spine surgery by automatically labeling vertebral levels in fluoroscopy using a GPU-accelerated, intensity-based 3D-2D (namely CT-to-fluoroscopy) registration. A gradient information (GI) similarity metric and a CMA-ES optimizer were chosen due to their robustness and inherent suitability for parallelization. Simulation studies involved ten patient CT datasets from which 50 000 simulated fluoroscopic images were generated from C-arm poses selected to approximate the C-arm operator and positioning variability. Physical experiments used an anthropomorphic chest phantom imaged under real fluoroscopy. The registration accuracy was evaluated as the mean projection distance (mPD) between the estimated and true center of vertebral levels. Trials were defined as successful if the estimated position was within the projection of the vertebral body (namely mPD <5 mm). Simulation studies showed a success rate of 99.998% (1 failure in 50 000 trials) and computation time of 4.7 s on a midrange GPU. Analysis of failure modes identified cases of false local optima in the search space arising from longitudinal periodicity in vertebral structures. Physical experiments demonstrated the robustness of the algorithm against quantum noise and x-ray scatter. The ability to automatically localize target anatomy in fluoroscopy in near-real-time could be valuable in reducing the occurrence of wrong-site surgery while helping to reduce radiation exposure. The method is applicable beyond

  10. Image guidance: treatment target localization systems.

    PubMed

    Sharpe, Michael B; Craig, Tim; Moseley, Douglas J

    2007-01-01

    Highly conformal radiation therapy tailors treatment to match the target shape and position, minimizing normal tissue damage to a greater extent than previously possible. Technological advances such as intensity-modulated radiation therapy, introduced a decade ago, have yielded significant gains in tumor control and reduced toxicity. Continuing advances have focused on the characterization and control of patient movement, organ motion, and anatomical deformation, which all introduce geometric uncertainty. These sources of uncertainty limit the effectiveness of high-precision treatment. Target localization, performed using appropriate technologies and frequency, is a critical component of treatment quality assurance. Until recently, the target position with respect to the beams has been inferred from surface marks on the patient's skin or through an immobilization device, and verified using megavoltage radiographs of the treatment portal. Advances in imaging technologies have made it possible to image soft tissue volumes in the treatment setting. Real-time tracking is also possible using a variety of technologies, including fluoroscopic imaging and radiopaque markers implanted in or near the tumor. The capacity to acquire volumetric soft tissue images in the treatment setting can also be used to assess anatomical changes over a course of treatment. Enhancing localization practices reduces treatment errors, and gives the capacity to monitor anatomical changes and reduce uncertainties that could influence clinical outcomes. This review presents the technologies available for target localization, and discusses some of the considerations that should be addressed in the implementation of many new clinical processes in radiation oncology. PMID:17641503

  11. Accuracy of x-ray image-based 3D localization from two C-arm views: a comparison between an ideal system and a real device

    NASA Astrophysics Data System (ADS)

    Brost, Alexander; Strobel, Norbert; Yatziv, Liron; Gilson, Wesley; Meyer, Bernhard; Hornegger, Joachim; Lewin, Jonathan; Wacker, Frank

    2009-02-01

    arm X-ray imaging devices are commonly used for minimally invasive cardiovascular or other interventional procedures. Calibrated state-of-the-art systems can, however, not only be used for 2D imaging but also for three-dimensional reconstruction either using tomographic techniques or even stereotactic approaches. To evaluate the accuracy of X-ray object localization from two views, a simulation study assuming an ideal imaging geometry was carried out first. This was backed up with a phantom experiment involving a real C-arm angiography system. Both studies were based on a phantom comprising five point objects. These point objects were projected onto a flat-panel detector under different C-arm view positions. The resulting 2D positions were perturbed by adding Gaussian noise to simulate 2D point localization errors. In the next step, 3D point positions were triangulated from two views. A 3D error was computed by taking differences between the reconstructed 3D positions using the perturbed 2D positions and the initial 3D positions of the five points. This experiment was repeated for various C-arm angulations involving angular differences ranging from 15° to 165°. The smallest 3D reconstruction error was achieved, as expected, by views that were 90° degrees apart. In this case, the simulation study yielded a 3D error of 0.82 mm +/- 0.24 mm (mean +/- standard deviation) for 2D noise with a standard deviation of 1.232 mm (4 detector pixels). The experimental result for this view configuration obtained on an AXIOM Artis C-arm (Siemens AG, Healthcare Sector, Forchheim, Germany) system was 0.98 mm +/- 0.29 mm, respectively. These results show that state-of-the-art C-arm systems can localize instruments with millimeter accuracy, and that they can accomplish this almost as well as an idealized theoretical counterpart. High stereotactic localization accuracy, good patient access, and CT-like 3D imaging capabilities render state-of-the-art C-arm systems ideal devices for X

  12. Artemisinin activity-based probes identify multiple molecular targets within the asexual stage of the malaria parasites Plasmodium falciparum 3D7

    PubMed Central

    Ismail, Hanafy M.; Barton, Victoria; Phanchana, Matthew; Charoensutthivarakul, Sitthivut; Wong, Michael H. L.; Hemingway, Janet; Biagini, Giancarlo A.; O’Neill, Paul M.; Ward, Stephen A.

    2016-01-01

    The artemisinin (ART)-based antimalarials have contributed significantly to reducing global malaria deaths over the past decade, but we still do not know how they kill parasites. To gain greater insight into the potential mechanisms of ART drug action, we developed a suite of ART activity-based protein profiling probes to identify parasite protein drug targets in situ. Probes were designed to retain biological activity and alkylate the molecular target(s) of Plasmodium falciparum 3D7 parasites in situ. Proteins tagged with the ART probe can then be isolated using click chemistry before identification by liquid chromatography–MS/MS. Using these probes, we define an ART proteome that shows alkylated targets in the glycolytic, hemoglobin degradation, antioxidant defense, and protein synthesis pathways, processes essential for parasite survival. This work reveals the pleiotropic nature of the biological functions targeted by this important class of antimalarial drugs. PMID:26858419

  13. Artemisinin activity-based probes identify multiple molecular targets within the asexual stage of the malaria parasites Plasmodium falciparum 3D7.

    PubMed

    Ismail, Hanafy M; Barton, Victoria; Phanchana, Matthew; Charoensutthivarakul, Sitthivut; Wong, Michael H L; Hemingway, Janet; Biagini, Giancarlo A; O'Neill, Paul M; Ward, Stephen A

    2016-02-23

    The artemisinin (ART)-based antimalarials have contributed significantly to reducing global malaria deaths over the past decade, but we still do not know how they kill parasites. To gain greater insight into the potential mechanisms of ART drug action, we developed a suite of ART activity-based protein profiling probes to identify parasite protein drug targets in situ. Probes were designed to retain biological activity and alkylate the molecular target(s) of Plasmodium falciparum 3D7 parasites in situ. Proteins tagged with the ART probe can then be isolated using click chemistry before identification by liquid chromatography-MS/MS. Using these probes, we define an ART proteome that shows alkylated targets in the glycolytic, hemoglobin degradation, antioxidant defense, and protein synthesis pathways, processes essential for parasite survival. This work reveals the pleiotropic nature of the biological functions targeted by this important class of antimalarial drugs. PMID:26858419

  14. Real-time motion- and B0-correction for LASER-localized spiral-accelerated 3D-MRSI of the brain at 3T

    PubMed Central

    Bogner, Wolfgang; Hess, Aaron T; Gagoski, Borjan; Tisdall, M. Dylan; van der Kouwe, Andre J.W.; Trattnig, Siegfried; Rosen, Bruce; Andronesi, Ovidiu C

    2013-01-01

    The full potential of magnetic resonance spectroscopic imaging (MRSI) is often limited by localization artifacts, motion-related artifacts, scanner instabilities, and long measurement times. Localized adiabatic selective refocusing (LASER) provides accurate B1-insensitive spatial excitation even at high magnetic fields. Spiral encoding accelerates MRSI acquisition, and thus, enables 3D-coverage without compromising spatial resolution. Real-time position-and shim/frequency-tracking using MR navigators correct motion- and scanner instability-related artifacts. Each of these three advanced MRI techniques provides superior MRSI data compared to commonly used methods. In this work, we integrated in a single pulse sequence these three promising approaches. Real-time correction of motion, shim, and frequency-drifts using volumetric dual-contrast echo planar imaging-based navigators were implemented in an MRSI sequence that uses low-power gradient modulated short-echo time LASER localization and time efficient spiral readouts, in order to provide fast and robust 3D-MRSI in the human brain at 3T. The proposed sequence was demonstrated to be insensitive to motion- and scanner drift-related degradations of MRSI data in both phantoms and volunteers. Motion and scanner drift artifacts were eliminated and excellent spectral quality was recovered in the presence of strong movement. Our results confirm the expected benefits of combining a spiral 3D-LASER-MRSI sequence with real-time correction. The new sequence provides accurate, fast, and robust 3D metabolic imaging of the human brain at 3T. This will further facilitate the use of 3D-MRSI for neuroscience and clinical applications. PMID:24201013

  15. Dual anode contact geometries for x-ray and gamma-ray spectroscopy and 3D localization

    NASA Astrophysics Data System (ADS)

    Martin, J. W.; Garson, A. B., III; Li, Q.; Lee, K.; Groza, M.; Buliga, V.; Burger, A.; Krawczynski, H.

    2009-08-01

    We report on the continued development and testing of unique types of Cadmium Zinc Telluride (CZT) detectors. Using large volume (10×20×20 mm3) CZT crystals, we contact various "dual anode" detector designs. We incorporate a segmented cathode with five regions so that the charge on all seven contacts can be used to determine the energy and the 3-D interaction location of detected X-ray and gamma-ray photons. We describe the status of the detector development program, emphasize strengths and weaknesses of the different contact configurations, and discuss possible applications of Dual Anode Detectors in radiation detection applications.

  16. Target localization and real-time tracking using the Calypso 4D localization system in patients with localized prostate cancer

    SciTech Connect

    Willoughby, Twyla R.; Kupelian, Patrick A. . E-mail: patrick.kupelian@orhs.org; Pouliot, Jean; Shinohara, Katsuto; Aubin, Michelle; Roach, Mack; Skrumeda, Lisa L.; Balter, James M.; Litzenberg, Dale W.; Hadley, Scott W.; Wei, John T.; Sandler, Howard M.

    2006-06-01

    Purpose: The Calypso 4D Localization System is being developed to provide accurate, precise, objective, and continuous target localization during radiotherapy. This study involves the first human use of the system, to evaluate the localization accuracy of this technique compared with radiographic localization and to assess its ability to obtain real-time prostate-motion information. Methods and Materials: Three transponders were implanted in each of 20 patients. Eleven eligible patients of the 20 patients participated in a study arm that compared radiographic triangulated transponder locations to electromagnetically recorded transponder locations. Transponders were tracked for 8-min periods. Results: The implantations were all successful, with no major complications. Intertransponder distances were largely stable. Comparison of the patient localization on the basis of transponder locations as per the Calypso system with the radiographic transponder localization showed an average ({+-}SD) 3D difference of 1.5 {+-} 0.9 mm. Upon tracking during 8 min, 2 of the 11 patients showed significant organ motion (>1 cm), with some motion lasting longer that 1 min. Conclusion: Calypso transponders can be used as magnetic intraprostatic fiducials. Clinical evaluation of this novel 4D nonionizing electromagnetic localization system with transponders indicates a comparable localization accuracy to isocenter (within 2 mm) compared with X-ray localiza0010ti.

  17. Lapse-time dependent coda-wave depth sensitivity to local velocity perturbations in 3-D heterogeneous elastic media

    NASA Astrophysics Data System (ADS)

    Obermann, Anne; Planès, Thomas; Hadziioannou, Céline; Campillo, Michel

    2016-07-01

    In the context of seismic monitoring, recent studies made successful use of seismic coda waves to locate medium changes on the horizontal plane. Locating the depth of the changes, however, remains a challenge. In this paper, we use 3-D wavefield simulations to address two problems: firstly, we evaluate the contribution of surface and body wave sensitivity to a change at depth. We introduce a thin layer with a perturbed velocity at different depths and measure the apparent relative velocity changes due to this layer at different times in the coda and for different degrees of heterogeneity of the model. We show that the depth sensitivity can be modelled as a linear combination of body- and surface-wave sensitivity. The lapse-time dependent sensitivity ratio of body waves and surface waves can be used to build 3-D sensitivity kernels for imaging purposes. Secondly, we compare the lapse-time behavior in the presence of a perturbation in horizontal and vertical slabs to address, for instance, the origin of the velocity changes detected after large earthquakes.

  18. A comparison of needle tip localization accuracy using 2D and 3D trans-rectal ultrasound for high-dose-rate prostate cancer brachytherapy treatment planning

    NASA Astrophysics Data System (ADS)

    Hrinivich, W. Thomas; Hoover, Douglas A.; Surry, Kathleen; Edirisinghe, Chandima; Montreuil, Jacques; D'Souza, David; Fenster, Aaron; Wong, Eugene

    2016-03-01

    Background: High-dose-rate brachytherapy (HDR-BT) is a prostate cancer treatment option involving the insertion of hollow needles into the gland through the perineum to deliver a radioactive source. Conventional needle imaging involves indexing a trans-rectal ultrasound (TRUS) probe in the superior/inferior (S/I) direction, using the axial transducer to produce an image set for organ segmentation. These images have limited resolution in the needle insertion direction (S/I), so the sagittal transducer is used to identify needle tips, requiring a manual registration with the axial view. This registration introduces a source of uncertainty in the final segmentations and subsequent treatment plan. Our lab has developed a device enabling 3D-TRUS guided insertions with high S/I spatial resolution, eliminating the need to align axial and sagittal views. Purpose: To compare HDR-BT needle tip localization accuracy between 2D and 3D-TRUS. Methods: 5 prostate cancer patients underwent conventional 2D TRUS guided HDR-BT, during which 3D images were also acquired for post-operative registration and segmentation. Needle end-length measurements were taken, providing a gold standard for insertion depths. Results: 73 needles were analyzed from all 5 patients. Needle tip position differences between imaging techniques was found to be largest in the S/I direction with mean+/-SD of -2.5+/-4.0 mm. End-length measurements indicated that 3D TRUS provided statistically significantly lower mean+/-SD insertion depth error of -0.2+/-3.4 mm versus 2.3+/-3.7 mm with 2D guidance (p < .001). Conclusions: 3D TRUS may provide more accurate HDR-BT needle localization than conventional 2D TRUS guidance for the majority of HDR-BT needles.

  19. Non-local effects by homogenization or 3D-1D dimension reduction in elastic materials reinforced by stiff fibers

    NASA Astrophysics Data System (ADS)

    Paroni, Roberto; Sili, Ali

    2016-02-01

    We first consider an elastic thin heterogeneous cylinder of radius of order ε: the interior of the cylinder is occupied by a stiff material (fiber) that is surrounded by a soft material (matrix). By assuming that the elasticity tensor of the fiber does not scale with ε and that of the matrix scales with ε2, we prove that the one dimensional model is a nonlocal system. We then consider a reference configuration domain filled out by periodically distributed rods similar to those described above. We prove that the homogenized model is a second order nonlocal problem. In particular, we show that the homogenization problem is directly connected to the 3D-1D dimensional reduction problem.

  20. Development of transferrin targeted NCL-240 micelles and their evaluation using in-vitro 3D cancer cell culture (spheroid) models

    NASA Astrophysics Data System (ADS)

    Nagelli, Srikar Goud

    The main objective of this project was to develop targeted micellar delivery systems of a novel cytotoxic drug (NCL-240; a second generation DM-PIT-1 analog) and to evaluate their efficacy using optimized 3D cell culture spheroid models. Spheroids were optimized for several cancer cell lines using a range of techniques such as non-adhesive liquid overlay method, hanging drop method, and co-culturing. Transferrin (Tf)-conjugated NCL-240 micelles were prepared with varying Tf amounts and their cytotoxicities were evaluated using the optimized spheroid models. The uptake and penetration of the formulations were also studied using confocal microscopy. The results indicated that the concentration of NCL-240 micelles required to achieve the same cytotoxicity was relatively higher in spheroids compared to the monolayers. Also, In NCI-ADR-RES, Tf-targeted NCL-240 micelles were shown to have a significant increase in cytotoxicity compared to untargeted NCL-240 micelles. Even the penetration and uptake studies indicated that targeting improves the uptake and penetration of formulations. However, in U87-MG spheroids, there was a significant difference in cell viability among micelles compared to free drug but no significant benefit due to targeting was observed. The same formulations penetrated lesser in U87-MG spheroids compared to NCI-ADR-RES spheroids. This study thereby emphasizes the importance of drug screening in spheroid models as the penetration dynamics are varying from cell line to cell line because of the 3D structure.

  1. Highly-accelerated quantitative 2D and 3D localized spectroscopy with linear algebraic modeling (SLAM) and sensitivity encoding

    NASA Astrophysics Data System (ADS)

    Zhang, Yi; Gabr, Refaat E.; Zhou, Jinyuan; Weiss, Robert G.; Bottomley, Paul A.

    2013-12-01

    Noninvasive magnetic resonance spectroscopy (MRS) with chemical shift imaging (CSI) provides valuable metabolic information for research and clinical studies, but is often limited by long scan times. Recently, spectroscopy with linear algebraic modeling (SLAM) was shown to provide compartment-averaged spectra resolved in one spatial dimension with many-fold reductions in scan-time. This was achieved using a small subset of the CSI phase-encoding steps from central image k-space that maximized the signal-to-noise ratio. Here, SLAM is extended to two- and three-dimensions (2D, 3D). In addition, SLAM is combined with sensitivity-encoded (SENSE) parallel imaging techniques, enabling the replacement of even more CSI phase-encoding steps to further accelerate scan-speed. A modified SLAM reconstruction algorithm is introduced that significantly reduces the effects of signal nonuniformity within compartments. Finally, main-field inhomogeneity corrections are provided, analogous to CSI. These methods are all tested on brain proton MRS data from a total of 24 patients with brain tumors, and in a human cardiac phosphorus 3D SLAM study at 3T. Acceleration factors of up to 120-fold versus CSI are demonstrated, including speed-up factors of 5-fold relative to already-accelerated SENSE CSI. Brain metabolites are quantified in SLAM and SENSE SLAM spectra and found to be indistinguishable from CSI measures from the same compartments. The modified reconstruction algorithm demonstrated immunity to maladjusted segmentation and errors from signal heterogeneity in brain data. In conclusion, SLAM demonstrates the potential to supplant CSI in studies requiring compartment-average spectra or large volume coverage, by dramatically reducing scan-time while providing essentially the same quantitative results.

  2. Highly-accelerated quantitative 2D and 3D localized spectroscopy with linear algebraic modeling (SLAM) and sensitivity encoding

    PubMed Central

    Zhang, Yi; Gabr, Refaat E.; Zhou, Jinyuan; Weiss, Robert G.; Bottomley, Paul A.

    2013-01-01

    Noninvasive magnetic resonance spectroscopy (MRS) with chemical shift imaging (CSI) provides valuable metabolic information for research and clinical studies, but is often limited by long scan times. Recently, spectroscopy with linear algebraic modeling (SLAM) was shown to provide compartment-averaged spectra resolved in one spatial dimension with many-fold reductions in scan-time. This was achieved using a small subset of the CSI phase-encoding steps from central image k-space that maximized the signal-to-noise ratio. Here, SLAM is extended to two- and three-dimensions (2D, 3D). In addition, SLAM is combined with sensitivity-encoded (SENSE) parallel imaging techniques, enabling the replacement of even more CSI phase-encoding steps to further accelerate scan-speed. A modified SLAM reconstruction algorithm is introduced that significantly reduces the effects of signal nonuniformity within compartments. Finally, main-field inhomogeneity corrections are provided, analogous to CSI. These methods are all tested on brain proton MRS data from a total of 24 patients with brain tumors, and in a human cardiac phosphorus 3D SLAM study at 3T. Acceleration factors of up to 120-fold versus CSI are demonstrated, including speed-up factors of 5-fold relative to already-accelerated SENSE CSI. Brain metabolites are quantified in SLAM and SENSE SLAM spectra and found to be indistinguishable from CSI measures from the same compartments. The modified reconstruction algorithm demonstrated immunity to maladjusted segmentation and errors from signal heterogeneity in brain data. In conclusion, SLAM demonstrates the potential to supplant CSI in studies requiring compartment-average spectra or large volume coverage, by dramatically reducing scan-time while providing essentially the same quantitative results. PMID:24188921

  3. 3D Porous Chitosan-Alginate Scaffolds as an In Vitro Model for Evaluating Nanoparticle-Mediated Tumor Targeting and Gene Delivery to Prostate Cancer.

    PubMed

    Wang, Kui; Kievit, Forrest M; Florczyk, Stephen J; Stephen, Zachary R; Zhang, Miqin

    2015-10-12

    Cationic nanoparticles (NPs) for targeted gene delivery are conventionally evaluated using 2D in vitro cultures. However, this does not translate well to corresponding in vivo studies because of the marked difference in NP behavior in the presence of the tumor microenvironment. In this study, we investigated whether prostate cancer (PCa) cells cultured in three-dimensional (3D) chitosan-alginate (CA) porous scaffolds could model cationic NP-mediated gene targeted delivery to tumors in vitro. We assessed in vitro tumor cell proliferation, formation of tumor spheroids, and expression of marker genes that promote tumor malignancy in CA scaffolds. The efficacy of NP-targeted gene delivery was evaluated in PCa cells in 2D cultures, PCa tumor spheroids grown in CA scaffolds, and PCa tumors in a mouse TRAMP-C2 flank tumor model. PCa cells cultured in CA scaffolds grew into tumor spheroids and displayed characteristics of higher malignancy as compared to those in 2D cultures. Significantly, targeted gene delivery was only observed in cells cultured in CA scaffolds, whereas cells cultured on 2D plates showed no difference in gene delivery between targeted and nontarget control NPs. In vivo NP evaluation confirmed targeted gene delivery, indicating that only CA scaffolds correctly modeled NP-mediated targeted delivery in vivo. These findings suggest that CA scaffolds serve as a better in vitro platform than 2D cultures for evaluation of NP-mediated targeted gene delivery to PCa. PMID:26347946

  4. 3-D ADI-FDTD modeling of GPR backscatter from complex targets for the training of artificial neural networks

    NASA Astrophysics Data System (ADS)

    Sassen, D. S.; Everett, M. E.

    2007-12-01

    Artificial neural networks can provide approximate solutions to ground-penetrating radar (GPR) problems in cases where real time performance is needed. Examples include discrimination of landmines or UXO's, and in circumstances that require a high number of successive forward problems, for example inversion or imaging. The training of neural networks to work within even a limited range of targets and electromagnetic properties requires a large set of successive examples generated from numerical methods such as finite difference time domain (FDTD). The traditional FDTD technique suffers from numerical dispersion unless time steps are kept below the Courant stability limit. The accurate modeling of electromagnetic scattering by complex targets require a refined grid, subgrids, or conformal grids that can significantly increase computation time, making neural network training inefficient. A relatively recent FDTD technique, ADI-FDTD, uses implicit equations that help to cancel numerical dispersion and allow for unconditionally stable modeling of EM propagation and therefore is not bound by the Courant stability limit. The technique is especially efficient for the accurate modeling of complex targets. Our ADI-FDTD code includes the ability to refine the model grid and to implement a conformal gridding to improve model accuracy without effecting the overall computation time. We will explore the tradeoff in computation time and accuracy in modeling the GPR backscatter of various targets using both the ADI-FDTD technique and the traditional FDTD technique for the purpose of neural network training.

  5. Novel Vertical 3D Structure of TaOx-based RRAM with Self-localized Switching Region by Sidewall Electrode Oxidation

    NASA Astrophysics Data System (ADS)

    Yu, Muxi; Cai, Yimao; Wang, Zongwei; Fang, Yichen; Liu, Yefan; Yu, Zhizhen; Pan, Yue; Zhang, Zhenxing; Tan, Jing; Yang, Xue; Li, Ming; Huang, Ru

    2016-02-01

    A novel vertical 3D RRAM structure with greatly improved reliability behavior is proposed and experimentally demonstrated through basically compatible process featuring self-localized switching region by sidewall electrode oxidation. Compared with the conventional structure, due to the effective confinement of the switching region, the newly-proposed structure shows about two orders higher endurance (>108 without verification operation) and better retention (>180h@150 °C), as well as high uniformity. Corresponding model is put forward, on the base of which thorough theoretical analysis and calculations are conducted as well, demonstrating that, resulting from the physically-isolated switching from neighboring cells, the proposed structure exhibits dramatically improved reliability due to effective suppression of thermal effects and oxygen vacancies diffusion interference, indicating that this novel structure is very promising for future high density 3D RRAM application.

  6. Novel Vertical 3D Structure of TaOx-based RRAM with Self-localized Switching Region by Sidewall Electrode Oxidation

    PubMed Central

    Yu, Muxi; Cai, Yimao; Wang, Zongwei; Fang, Yichen; Liu, Yefan; Yu, Zhizhen; Pan, Yue; Zhang, Zhenxing; Tan, Jing; Yang, Xue; Li, Ming; Huang, Ru

    2016-01-01

    A novel vertical 3D RRAM structure with greatly improved reliability behavior is proposed and experimentally demonstrated through basically compatible process featuring self-localized switching region by sidewall electrode oxidation. Compared with the conventional structure, due to the effective confinement of the switching region, the newly-proposed structure shows about two orders higher endurance (>108 without verification operation) and better retention (>180h@150 °C), as well as high uniformity. Corresponding model is put forward, on the base of which thorough theoretical analysis and calculations are conducted as well, demonstrating that, resulting from the physically-isolated switching from neighboring cells, the proposed structure exhibits dramatically improved reliability due to effective suppression of thermal effects and oxygen vacancies diffusion interference, indicating that this novel structure is very promising for future high density 3D RRAM application. PMID:26884054

  7. A new method for detecting colonic polyps based on local intensity structure analysis from 3D abdominal CT images

    NASA Astrophysics Data System (ADS)

    Oda, Masahiro; Nakada, Yuichi; Kitasaka, Takayuki; Mori, Kensaku; Suenaga, Yasuhito; Takayama, Tetsuji; Takabatake, Hirotsugu; Mori, Masaki; Natori, Hiroshi; Nawano, Shigeru

    2007-03-01

    This paper presents a new method for detecting colonic polyps from abdominal CT images based on Hessian matrix analysis. Recently, virtual colonoscopy (VC) has widely received attention as a new and less-invasive colon diagnostic method. A physician diagnoses the inside of the colon using a virtual colonoscopy system. However, since the colon has many haustra and its shape is long and convoluted, a physician has to change viewpoints and viewing directions of the virtual camera many times while diagnosing. Lesions behind haustra may be overlooked. Thus this paper proposes an automated colonic polyp detection method from 3D abdominal CT images. Colonic polyps are located on the colonic wall, and their CT values are higher than colonic lumen regions. In addition, CT values inside polyps tend to gradually increase from outward to inward (blob-like structure). We employ a blob structure enhancement filter based on the eigenvalues of a Hessian matrix to detect polyps with the above blob-shaped characteristics. For reducing FPs, we eliminate polyp candidate regions in which the maximum output value of the blob structure enhancement filter is smaller than given threshold values. Also small regions are removed from candidates. We applied the proposed method to 23 cases of abdominal CT images. Overall, 74.4% of the polyps were detected with 3.8 FPs per case.

  8. Comparison of 3-D Multi-Lag Cross-Correlation and Speckle Brightness Aberration Correction Algorithms on Static and Moving Targets

    PubMed Central

    Ivancevich, Nikolas M.; Dahl, Jeremy J.; Smith, Stephen W.

    2010-01-01

    Phase correction has the potential to increase the image quality of 3-D ultrasound, especially transcranial ultrasound. We implemented and compared 2 algorithms for aberration correction, multi-lag cross-correlation and speckle brightness, using static and moving targets. We corrected three 75-ns rms electronic aberrators with full-width at half-maximum (FWHM) auto-correlation lengths of 1.35, 2.7, and 5.4 mm. Cross-correlation proved the better algorithm at 2.7 and 5.4 mm correlation lengths (P < 0.05). Static cross-correlation performed better than moving-target cross-correlation at the 2.7 mm correlation length (P < 0.05). Finally, we compared the static and moving-target cross-correlation on a flow phantom with a skull casting aberrator. Using signal from static targets, the correction resulted in an average contrast increase of 22.2%, compared with 13.2% using signal from moving targets. The contrast-to-noise ratio (CNR) increased by 20.5% and 12.8% using static and moving targets, respectively. Doppler signal strength increased by 5.6% and 4.9% for the static and moving-targets methods, respectively. PMID:19942503

  9. High-Resolution Imaged-Based 3D Reconstruction Combined with X-Ray CT Data Enables Comprehensive Non-Destructive Documentation and Targeted Research of Astromaterials

    NASA Technical Reports Server (NTRS)

    Blumenfeld, E. H.; Evans, C. A.; Oshel, E. R.; Liddle, D. A.; Beaulieu, K.; Zeigler, R. A.; Righter, K.; Hanna, R. D.; Ketcham, R. A.

    2014-01-01

    Providing web-based data of complex and sensitive astromaterials (including meteorites and lunar samples) in novel formats enhances existing preliminary examination data on these samples and supports targeted sample requests and analyses. We have developed and tested a rigorous protocol for collecting highly detailed imagery of meteorites and complex lunar samples in non-contaminating environments. These data are reduced to create interactive 3D models of the samples. We intend to provide these data as they are acquired on NASA's Astromaterials Acquisition and Curation website at http://curator.jsc.nasa.gov/.

  10. Reorienting in Virtual 3D Environments: Do Adult Humans Use Principal Axes, Medial Axes or Local Geometry?

    PubMed Central

    Ambosta, Althea H.; Reichert, James F.; Kelly, Debbie M.

    2013-01-01

    Studies have shown that animals, including humans, use the geometric properties of environments to orient. It has been proposed that orientation is accomplished primarily by encoding the principal axes (i.e., global geometry) of an environment. However, recent research has shown that animals use local information such as wall length and corner angles as well as local shape parameters (i.e., medial axes) to orient. The goal of the current study was to determine whether adult humans reorient according to global geometry based on principal axes or whether reliance is on local geometry such as wall length and sense information or medial axes. Using a virtual environment task, participants were trained to select a response box located at one of two geometrically identical corners within a featureless rectangular-shaped environment. Participants were subsequently tested in a transformed L-shaped environment that allowed for a dissociation of strategies based on principal axes, medial axes and local geometry. Results showed that participants relied primarily on a medial axes strategy to reorient in the L-shaped test environment. Importantly, the search behaviour of participants could not be explained by a principal axes-based strategy. PMID:24223869

  11. A time series generalized functional model based method for vibration-based damage precise localization in structures consisting of 1D, 2D, and 3D elements

    NASA Astrophysics Data System (ADS)

    Sakaris, C. S.; Sakellariou, J. S.; Fassois, S. D.

    2016-06-01

    This study focuses on the problem of vibration-based damage precise localization via data-based, time series type, methods for structures consisting of 1D, 2D, or 3D elements. A Generalized Functional Model Based method is postulated based on an expanded Vector-dependent Functionally Pooled ARX (VFP-ARX) model form, capable of accounting for an arbitrary structural topology. The FP model's operating parameter vector elements are properly constrained to reflect any given topology. Damage localization is based on operating parameter vector estimation within the specified topology, so that the location estimate and its uncertainty bounds are statistically optimal. The method's effectiveness is experimentally demonstrated through damage precise localization on a laboratory spatial truss structure using various damage scenarios and a single pair of random excitation - vibration response signals in a low and limited frequency bandwidth.

  12. A new 3D parallel high resolution electromagnetic nonlinear inversion based on new global magnetic integral and local differential decomposition (GILD)

    SciTech Connect

    Xie, G.; Li, J.

    1997-05-01

    A new 3D electromagnetic modeling and nonlinear inversion algorithm is presented based on global integral and local differential equations decomposition (GILD). The GILD parallel nonlinear inversion algorithm consists of five parts: (1) the domain is decomposed into subdomain SI and subdomain SII; (2) a new global magnetic integral equation in SI and the local magnetic differential equations IN SII will be used together to obtain the magnetic field in the modeling step; (3) the new global magnetic integral Jacobian equation in SI and the local magnetic differential Jacobian equations in SII will be used together to update the electric conductivity and permittivity from the magnetic field data in the inversion step; (4) the subdomain SII can naturally and uniformly be decomposed into 2{sup n} smaller sub-cubic-domains; the sparse matrix in each sub-cubic-domain can be eliminated separately, in parallel; (5) a new parallel multiple hierarchy substructure algorithm will be used to solve the smaller full matrices in SI, in parallel. The applications of the new 3D parallel GILD EM modeling and nonlinear inversion algorithm and software are: (1) to create high resolution controlled-source electric conductivity and permittivity imaging for interpreting electromagnetic field data acquired from cross hole, surface to borehole, surface to surface, single hole, and multiple holes; (2) to create the magnetotelluric high resolution imaging from the surface impedance and field data. The new GILD parallel nonlinear inversion will be a 3D/2.5D powerful imaging tool for the oil geophysical exploration and environmental remediation and monitoring.

  13. On the numerical simulation of the ablative Rayleigh-Taylor instability in laser-driven ICF targets using the FastRad3D code

    NASA Astrophysics Data System (ADS)

    Bates, Jason; Schmitt, Andrew; Zalesak, Steve

    2015-11-01

    The ablative Rayleigh-Taylor (RT) instability is a key factor in the performance of directly-drive inertial-confinement-fusion (ICF) targets. Although this subject has been studied for quite some time, the accurate simulation of the ablative RT instability has proven to be a challenging task for many radiation hydrodynamics codes, particularly when it comes to capturing the ablatively-stabilized region of the linear dispersion spectrum and modeling ab initio perturbations. In this poster, we present results from recent two-dimensional numerical simulations of the ablative RT instability that were performed using the Eulerian code FastRad3D at the U.S. Naval Research Laboratory. We consider both planar and spherical geometries, low and moderate-Z target materials, different laser wavelengths and where possible, compare our findings with experiment data, linearized theory and/or results from other radiation hydrodynamics codes. Overall, we find that FastRad3D is capable of simulating the ablative RT instability quite accurately, although some uncertainties/discrepancies persist. We discuss these issues, as well as some of the numerical challenges associated with modeling this class of problems. Work supported by U.S. DOE/NNSA.

  14. An asynchronous modulation/demodulation technique for robust identification of a target for 3-D pose determination

    SciTech Connect

    Ferrell, R.K.; Jatko, W.B.; Sitter, D.N. Jr.

    1996-03-01

    Engineers at Oak Ridge National Laboratory have been investigating the feasibility of computer-controlled docking in resupply missions, sponsored by the US Army. The goal of this program is to autonomously dock an articulating robotic boom with a special receiving port. A video camera mounted on the boom provides video images of the docking port to an image processing computer that calculates the position and orientation (pose) of the target relative to the camera. The control system can then move the boom into docking position. This paper describes a method of uniquely identifying and segmenting the receiving port from its background in a sequence of video images. An array of light-emitting diodes was installed to mark the vertices of the port. The markers have a fixed geometric pattern and are modulated at a fixed frequency. An asynchronous demodulation technique to segment flashing markers from an image of the port was developed and tested under laboratory conditions. The technique acquires a sequence of images and digitally processes them in the time domain to suppress all image features except the flashing markers. Pixels that vary at frequencies within the filter bandwidth are passed unattenuated, while variations outside the passband are suppressed. The image coordinates of the segmented markers are computed and then used to calculate the pose of the receiving port. The technique has been robust and reliable in a laboratory demonstration of autodocking.

  15. Toroidal mode number estimation of the edge-localized modes using the KSTAR 3-D electron cyclotron emission imaging system

    SciTech Connect

    Lee, J.; Yun, G. S. Lee, J. E.; Kim, M.; Choi, M. J.; Lee, W.; Park, H. K.; Domier, C. W.; Luhmann, N. C.; Sabbagh, S. A.; Park, Y. S.; Lee, S. G.; Bak, J. G.

    2014-06-15

    A new and more accurate technique is presented for determining the toroidal mode number n of edge-localized modes (ELMs) using two independent electron cyclotron emission imaging (ECEI) systems in the Korea Superconducting Tokamak Advanced Research (KSTAR) device. The technique involves the measurement of the poloidal spacing between adjacent ELM filaments, and of the pitch angle α{sub *} of filaments at the plasma outboard midplane. Equilibrium reconstruction verifies that α{sub *} is nearly constant and thus well-defined at the midplane edge. Estimates of n obtained using two ECEI systems agree well with n measured by the conventional technique employing an array of Mirnov coils.

  16. Toroidal mode number estimation of the edge-localized modes using the KSTAR 3-D electron cyclotron emission imaging system.

    PubMed

    Lee, J; Yun, G S; Lee, J E; Kim, M; Choi, M J; Lee, W; Park, H K; Domier, C W; Luhmann, N C; Sabbagh, S A; Park, Y S; Lee, S G; Bak, J G

    2014-06-01

    A new and more accurate technique is presented for determining the toroidal mode number n of edge-localized modes (ELMs) using two independent electron cyclotron emission imaging (ECEI) systems in the Korea Superconducting Tokamak Advanced Research (KSTAR) device. The technique involves the measurement of the poloidal spacing between adjacent ELM filaments, and of the pitch angle α* of filaments at the plasma outboard midplane. Equilibrium reconstruction verifies that α* is nearly constant and thus well-defined at the midplane edge. Estimates of n obtained using two ECEI systems agree well with n measured by the conventional technique employing an array of Mirnov coils. PMID:24985817

  17. 3D He-3 diffusion MRI as a local in vivo morphometric tool to evaluate emphysematous rat lungs

    SciTech Connect

    Jacob, Rick E.; Minard, Kevin R.; Laicher, Gernot J.; Timchalk, Charles

    2008-08-21

    In this work, we validate 3He magnetic resonance imaging as a non-invasive morphometric tool to assess emphysematous disease state on a local level. Emphysema was induced intratracheally in rats with 25U/100g body weight of porcine pancreatic elastase dissolved in 200 μL saline. Rats were then paired with saline-dosed controls. Nine three-dimensional 3He diffusion-weighted images were acquired at one-, two-, or three-weeks post-dose, after which the lungs were harvested and prepared for histological analysis. Recently introduced indices sensitive to the heterogeneity of the airspace size distribution were calculated. These indices, D1 and D2, were derived from the moments of the mean equivalent airway diameters. Averaged over the entire lung, it is shown that the 3He diffusivity (Dave) and anisotropy (Dan) both correlate with histology (R = 0.85, p < 0.0001 and R = 0.88, p < 0.0001, respectively). By matching small (0.046 cm2) regions in 3He images with corresponding regions in histological slices, Dave and Dan each correlate significantly with both D1 and D2 (R = 0.93, p < 0.0001). It is concluded that 3He MRI is a viable non-invasive morphometric tool for localized in vivo emphysema assessment.

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

    NASA Technical Reports Server (NTRS)

    Walitt, L.

    1982-01-01

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

  19. A comparison study of atlas-based 3D cardiac MRI segmentation: global versus global and local transformations

    NASA Astrophysics Data System (ADS)

    Daryanani, Aditya; Dangi, Shusil; Ben-Zikri, Yehuda Kfir; Linte, Cristian A.

    2016-03-01

    Magnetic Resonance Imaging (MRI) is a standard-of-care imaging modality for cardiac function assessment and guidance of cardiac interventions thanks to its high image quality and lack of exposure to ionizing radiation. Cardiac health parameters such as left ventricular volume, ejection fraction, myocardial mass, thickness, and strain can be assessed by segmenting the heart from cardiac MRI images. Furthermore, the segmented pre-operative anatomical heart models can be used to precisely identify regions of interest to be treated during minimally invasive therapy. Hence, the use of accurate and computationally efficient segmentation techniques is critical, especially for intra-procedural guidance applications that rely on the peri-operative segmentation of subject-specific datasets without delaying the procedure workflow. Atlas-based segmentation incorporates prior knowledge of the anatomy of interest from expertly annotated image datasets. Typically, the ground truth atlas label is propagated to a test image using a combination of global and local registration. The high computational cost of non-rigid registration motivated us to obtain an initial segmentation using global transformations based on an atlas of the left ventricle from a population of patient MRI images and refine it using well developed technique based on graph cuts. Here we quantitatively compare the segmentations obtained from the global and global plus local atlases and refined using graph cut-based techniques with the expert segmentations according to several similarity metrics, including Dice correlation coefficient, Jaccard coefficient, Hausdorff distance, and Mean absolute distance error.

  20. 3D-localization microscopy and tracking of FoF1-ATP synthases in living bacteria

    NASA Astrophysics Data System (ADS)

    Renz, Anja; Renz, Marc; Klütsch, Diana; Deckers-Hebestreit, Gabriele; Börsch, Michael

    2015-03-01

    FoF1-ATP synthases are membrane-embedded protein machines that catalyze the synthesis of adenosine triphosphate. Using photoactivation-based localization microscopy (PALM) in TIR-illumination as well as structured illumination microscopy (SIM), we explore the spatial distribution and track single FoF1-ATP synthases in living E. coli cells under physiological conditions at different temperatures. For quantitative diffusion analysis by mean-squared-displacement measurements, the limited size of the observation area in the membrane with its significant membrane curvature has to be considered. Therefore, we applied a 'sliding observation window' approach (M. Renz et al., Proc. SPIE 8225, 2012) and obtained the one-dimensional diffusion coefficient of FoF1-ATP synthase diffusing on the long axis in living E. coli cells.

  1. Results and DVH analysis of late rectal bleeding in patients treated with 3D-CRT or IMRT for localized prostate cancer

    PubMed Central

    Someya, Masanori; Hori, Masakazu; Tateoka, Kunihiko; Nakata, Kensei; Takagi, Masaru; Saito, Masato; Hirokawa, Naoki; Hareyama, Masato; Sakata, Koh-ichi

    2015-01-01

    In patients undergoing radiotherapy for localized prostate cancer, dose–volume histograms and clinical variables were examined to search for correlations between radiation treatment planning parameters and late rectal bleeding. We analyzed 129 patients with localized prostate cancer who were managed from 2002 to 2010 at our institution. They were treated with 3D conformal radiation therapy (3D-CRT, 70 Gy/35 fractions, 55 patients) or intensity-modulated radiation therapy (IMRT, 76 Gy/38 fractions, 74 patients). All radiation treatment plans were retrospectively reconstructed, dose–volume histograms of the rectum were generated, and the doses delivered to the rectum were calculated. Time to rectal bleeding ranged from 9–53 months, with a median of 18.7 months. Of the 129 patients, 33 patients had Grade 1 bleeding and were treated with steroid suppositories, while 25 patients with Grade 2 bleeding received argon plasma laser coagulation therapy (APC). Three patients with Grade 3 bleeding required both APC and blood transfusion. The 5-year incidence rate of Grade 2 or 3 rectal bleeding was 21.8% for the 3D-CRT group and 21.6% for the IMRT group. Univariate analysis showed significant differences in the average values from V65 to V10 between Grades 0–1 and Grades 2–3. Multivariate analysis demonstrated that patients with V65 ≥ 17% had a significantly increased risk (P = 0.032) of Grade 2 or 3 rectal bleeding. Of the 28 patients of Grade 2 or 3 rectal bleeding, 17 patients (60.7%) were cured by a single session of APC, while the other 11 patients required two sessions. Thus, none of the patients had any further rectal bleeding after the second APC session. PMID:25212601

  2. The double-helix point spread function enables precise and accurate measurement of 3D single-molecule localization and orientation

    PubMed Central

    Backlund, Mikael P.; Lew, Matthew D.; Backer, Adam S.; Sahl, Steffen J.; Grover, Ginni; Agrawal, Anurag; Piestun, Rafael; Moerner, W. E.

    2014-01-01

    Single-molecule-based super-resolution fluorescence microscopy has recently been developed to surpass the diffraction limit by roughly an order of magnitude. These methods depend on the ability to precisely and accurately measure the position of a single-molecule emitter, typically by fitting its emission pattern to a symmetric estimator (e.g. centroid or 2D Gaussian). However, single-molecule emission patterns are not isotropic, and depend highly on the orientation of the molecule’s transition dipole moment, as well as its z-position. Failure to account for this fact can result in localization errors on the order of tens of nm for in-focus images, and ~50–200 nm for molecules at modest defocus. The latter range becomes especially important for three-dimensional (3D) single-molecule super-resolution techniques, which typically employ depths-of-field of up to ~2 μm. To address this issue we report the simultaneous measurement of precise and accurate 3D single-molecule position and 3D dipole orientation using the Double-Helix Point Spread Function (DH-PSF) microscope. We are thus able to significantly improve dipole-induced position errors, reducing standard deviations in lateral localization from ~2x worse than photon-limited precision (48 nm vs. 25 nm) to within 5 nm of photon-limited precision. Furthermore, by averaging many estimations of orientation we are able to improve from a lateral standard deviation of 116 nm (~4x worse than the precision, 28 nm) to 34 nm (within 6 nm). PMID:24817798

  3. Accurate and Fully Automatic Hippocampus Segmentation Using Subject-Specific 3D Optimal Local Maps Into a Hybrid Active Contour Model

    PubMed Central

    Gkontra, Polyxeni; Daras, Petros; Maglaveras, Nicos

    2014-01-01

    Assessing the structural integrity of the hippocampus (HC) is an essential step toward prevention, diagnosis, and follow-up of various brain disorders due to the implication of the structural changes of the HC in those disorders. In this respect, the development of automatic segmentation methods that can accurately, reliably, and reproducibly segment the HC has attracted considerable attention over the past decades. This paper presents an innovative 3-D fully automatic method to be used on top of the multiatlas concept for the HC segmentation. The method is based on a subject-specific set of 3-D optimal local maps (OLMs) that locally control the influence of each energy term of a hybrid active contour model (ACM). The complete set of the OLMs for a set of training images is defined simultaneously via an optimization scheme. At the same time, the optimal ACM parameters are also calculated. Therefore, heuristic parameter fine-tuning is not required. Training OLMs are subsequently combined, by applying an extended multiatlas concept, to produce the OLMs that are anatomically more suitable to the test image. The proposed algorithm was tested on three different and publicly available data sets. Its accuracy was compared with that of state-of-the-art methods demonstrating the efficacy and robustness of the proposed method. PMID:27170866

  4. Accurate and Fully Automatic Hippocampus Segmentation Using Subject-Specific 3D Optimal Local Maps Into a Hybrid Active Contour Model.

    PubMed

    Zarpalas, Dimitrios; Gkontra, Polyxeni; Daras, Petros; Maglaveras, Nicos

    2014-01-01

    Assessing the structural integrity of the hippocampus (HC) is an essential step toward prevention, diagnosis, and follow-up of various brain disorders due to the implication of the structural changes of the HC in those disorders. In this respect, the development of automatic segmentation methods that can accurately, reliably, and reproducibly segment the HC has attracted considerable attention over the past decades. This paper presents an innovative 3-D fully automatic method to be used on top of the multiatlas concept for the HC segmentation. The method is based on a subject-specific set of 3-D optimal local maps (OLMs) that locally control the influence of each energy term of a hybrid active contour model (ACM). The complete set of the OLMs for a set of training images is defined simultaneously via an optimization scheme. At the same time, the optimal ACM parameters are also calculated. Therefore, heuristic parameter fine-tuning is not required. Training OLMs are subsequently combined, by applying an extended multiatlas concept, to produce the OLMs that are anatomically more suitable to the test image. The proposed algorithm was tested on three different and publicly available data sets. Its accuracy was compared with that of state-of-the-art methods demonstrating the efficacy and robustness of the proposed method. PMID:27170866

  5. Localization of Metal Electrodes in the Intact Rat Brain Using Registration of 3D Microcomputed Tomography Images to a Magnetic Resonance Histology Atlas1,2,3

    PubMed Central

    Borg, Jana Schaich; Vu, Mai-Anh; Badea, Cristian; Badea, Alexandra; Johnson, G. Allan

    2015-01-01

    Abstract Simultaneous neural recordings taken from multiple areas of the rodent brain are garnering growing interest because of the insight they can provide about spatially distributed neural circuitry. The promise of such recordings has inspired great progress in methods for surgically implanting large numbers of metal electrodes into intact rodent brains. However, methods for localizing the precise location of these electrodes have remained severely lacking. Traditional histological techniques that require slicing and staining of physical brain tissue are cumbersome and become increasingly impractical as the number of implanted electrodes increases. Here we solve these problems by describing a method that registers 3D computed tomography (CT) images of intact rat brains implanted with metal electrode bundles to a magnetic resonance imaging histology (MRH) atlas. Our method allows accurate visualization of each electrode bundle’s trajectory and location without removing the electrodes from the brain or surgically implanting external markers. In addition, unlike physical brain slices, once the 3D images of the electrode bundles and the MRH atlas are registered, it is possible to verify electrode placements from many angles by “reslicing” the images along different planes of view. Furthermore, our method can be fully automated and easily scaled to applications with large numbers of specimens. Our digital imaging approach to efficiently localizing metal electrodes offers a substantial addition to currently available methods, which, in turn, may help accelerate the rate at which insights are gleaned from rodent network neuroscience. PMID:26322331

  6. Automatic abdominal lymph node detection method based on local intensity structure analysis from 3D x-ray CT images

    NASA Astrophysics Data System (ADS)

    Nakamura, Yoshihiko; Nimura, Yukitaka; Kitasaka, Takayuki; Mizuno, Shinji; Furukawa, Kazuhiro; Goto, Hidemi; Fujiwara, Michitaka; Misawa, Kazunari; Ito, Masaaki; Nawano, Shigeru; Mori, Kensaku

    2013-03-01

    This paper presents an automated method of abdominal lymph node detection to aid the preoperative diagnosis of abdominal cancer surgery. In abdominal cancer surgery, surgeons must resect not only tumors and metastases but also lymph nodes that might have a metastasis. This procedure is called lymphadenectomy or lymph node dissection. Insufficient lymphadenectomy carries a high risk for relapse. However, excessive resection decreases a patient's quality of life. Therefore, it is important to identify the location and the structure of lymph nodes to make a suitable surgical plan. The proposed method consists of candidate lymph node detection and false positive reduction. Candidate lymph nodes are detected using a multi-scale blob-like enhancement filter based on local intensity structure analysis. To reduce false positives, the proposed method uses a classifier based on support vector machine with the texture and shape information. The experimental results reveal that it detects 70.5% of the lymph nodes with 13.0 false positives per case.

  7. Towards 3D charge localization by a method derived from atomic force microscopy: the electrostatic force distance curve

    NASA Astrophysics Data System (ADS)

    Villeneuve-Faure, C.; Boudou, L.; Makasheva, K.; Teyssedre, G.

    2014-11-01

    Charges injection and accumulation in the dielectric remains a critical issue, mainly because these phenomena are involved in a great number of failure mechanisms in cables or electronic components. Achieving a better understanding of the mechanisms leading to charge injection, transport and trapping under electrical stress and of the relevant interface phenomena is a high priority. The classical methods used for space charge density profile measurements have a limited spatial resolution, which prevents them being used for investigating thin dielectric layers or interface processes. Thus, techniques derived from atomic force microscopy (AFM) have been investigated more and more for this kind of application, but so far they have been limited by their lack of in-depth sensitivity. In this paper a new method for space charge probing is described, the electrostatic force distance curve (EFDC), which is based on electrostatic force measurements using AFM. A comparison with the results obtained using kelvin force microscopy (KFM) allowed us to highlight the fact that EFDC is sensitive to charges localized in the third-dimension.

  8. Nanostructured exchange coupled hard/soft composites: From the local magnetization profile to an extended 3d simple model

    NASA Astrophysics Data System (ADS)

    Russier, V.; Younsi, K.; Bessais, L.

    2012-03-01

    In nanocomposite magnetic materials the exchange coupling between phases plays a central role in the determination of the extrinsic magnetic properties of the material: coercive field,remanence magnetization. Exchange coupling is therefore of crucial importance in composite systems made of magnetically hard and soft grains or in partially crystallized media including nanosized crystallites in a soft matrix. It has been shown also to be a key point in the control of stratified hard/soft media coercive field in the research for optimized recording media. A signature of the exchange coupling due to the nanostructure is generally obtained on the magnetization curve M(H) with a plateau characteristic of the domain wall compression at the hard/soft interface ending at the depinning of the wall inside the hard phase. This compression/depinning behavior is clearly evidenced through one dimensional description of the interface, which is rigorously possible only in stratified media. Starting from a local description of the hard/soft interface in a model for nanocomposite system we show that one can extend this kind of behavior for system of hard crystallites embedded in a soft matrix.

  9. Local D3/D7 μ-SPLIT SUSY, 125 GeV Higgs and Large Volume Ricci-Flat Swiss-Cheese Metrics:. a Brief Review

    NASA Astrophysics Data System (ADS)

    Misra, Aalok

    In this paper, we review briefly recent progress made in realizing local(ized around a mobile spacetime filling D3-brane in) D3/D7 μ-split Supersymmetry in (the large volume limit of Type IIB) String Theory (compactified on Swiss-Cheese Calabi-Yau orientifolds) as well as obtaining a 125 GeV (light) Higgs in the same setup. We also discuss obtaining the geometric Kähler potential (and hence the Ricci-flat metric) for the Swiss-Cheese Calabi-Yau in the large volume limit using the Donaldson's algorithm and intuition from GLSM-based calculations — we present new results for Swiss-Cheese Calabi-Yau (used in the setup) metrics at points finitely away from the "big" divisor.

  10. Density structure and geometry of the Costa Rican subduction zone from 3-D gravity modeling and local earthquake data

    NASA Astrophysics Data System (ADS)

    Lücke, O. H.; Arroyo, I. G.

    2015-07-01

    The eastern part of the oceanic Cocos Plate presents a heterogeneous crustal structure due to diverse origins and ages as well as plate-hot spot interactions which originated the Cocos Ridge, a structure that converges with the Caribbean Plate in southeastern Costa Rica. The complex structure of the oceanic plate directly influences the dynamics and geometry of the subduction zone along the Middle American Trench. In this paper an integrated interpretation of the slab geometry is presented based on three-dimensional density modeling of combined satellite and surface gravity data, constrained by available geophysical and geological data and seismological information obtained from local networks. The results show the continuation of steep subduction geometry from the Nicaraguan margin into Northwestern Costa Rica, followed by a moderate dipping slab under the Central Cordillera toward the end of the Central American Volcanic Arc. To the southeast end of the volcanic arc, our preferred model shows a steep, coherent slab that extends up to the landward projection of the Panama Fracture Zone. Overall, a gradual change in the depth of the intraplate seismicity is observed, reaching 220 km in the northwestern part, and becoming progressively shallower toward the southeast, where it reaches a terminal depth of 75 km. The changes in the terminal depth of the observed seismicity correlate with the increased density in the modeled slab. The absence of intermediate depth intraplate seismicity in the southeastern section and the higher densities for the subducted slab in this area, support a model in which dehydration reactions in the subducted slab cease at a shallower depth, originating an anhydrous and thus aseismic slab.

  11. FEM analysis of deformation localization mechanisms in a 3-D fractured medium under rotating compressive stress orientations

    NASA Astrophysics Data System (ADS)

    Strijker, Geertje; Beekman, Fred; Bertotti, Giovanni; Luthi, Stefan M.

    2013-05-01

    Stress distributions and deformation patterns in a medium with a pre-existing fracture set are analyzed as a function of the remote compressive stress orientation (σH) using finite element models with increasingly complex fracture configurations. Slip along the fractures causes deformation localization at the tips as wing cracks or shear zones. The deformation intensity is proportional to the amount of slip, attaining a peak value for α = 45° (α: angle between the fracture strike and σH) and slip is linearly proportional with fracture length. Wing cracks develop for high deformation intensities for 30° < α < 60°, whereas primary plastic shear zones develop for low deformation intensities. Additionally, two types of secondary shear zones develop for α < 30° and α > 60°, with constant angles of 135° and - 60° with σH, respectively. Mechanical interaction between fractures in a fracture zone, quantified as change in slip compared to an isolated fracture, decreases with increasing fracture separation. Fracture underlap elongates the fracture length and therefore increases the amount of slip, while fracture overlap exhibits the opposite effect. Fracture slip decreases with an increasing amount of directly adjacent fractures. Mechanical interaction becomes negligible for fracture configurations with spacing-to-length and spacing-to-overlap ratios exceeding 0.5 and that in this case fractures are decoupled. Independent of the pre-existing fracture configuration, the development of a secondary systematic fracture set driven by a remote stress rotation is dominated by σH; development of wing cracks or shear zones is restricted to the fracture tips. Blocks with tapered geometries are present in models with a variable fracture strike, where the maximum principal stress (σ1, applying the geological convention that compressive stresses are positive) trajectories consistently deviate from σH; the presence of two systematic σ1 trajectory orientations suggests

  12. Validation of hip joint center localization methods during gait analysis using 3D EOS imaging in typically developing and cerebral palsy children.

    PubMed

    Assi, Ayman; Sauret, Christophe; Massaad, Abir; Bakouny, Ziad; Pillet, Hélène; Skalli, Wafa; Ghanem, Ismat

    2016-07-01

    Localization of the hip joint center (HJC) is essential in computation of gait data. EOS low dose biplanar X-rays have been shown to be a good reference in evaluating various methods of HJC localization in adults. The aim is to evaluate predictive and functional techniques for HJC localization in typically developing (TD) and cerebral palsy (CP) children, using EOS as an image based reference. Eleven TD and 17 CP children underwent 3D gait analysis. Six HJC localization methods were evaluated in each group bilaterally: 3 predictive (Plug in Gait, Bell and Harrington) and 3 functional methods based on the star arc technique (symmetrical center of rotation estimate, center transformation technique and geometrical sphere fitting). All children then underwent EOS low dose biplanar radiographs. Pelvis, lower limbs and their corresponding external markers were reconstructed in 3D. The center of the femoral head was considered as the reference (HJCEOS). Euclidean distances between HJCs estimated by each of the 6 methods and the HJCEOS were calculated; distances were shown to be lower in predictive compared to functional methods (p<0.0001). Contrarily to findings in adults, functional methods were shown to be less accurate than predictive methods in TD and CP children, which could be mainly due to the shorter thigh segment in children. Harrington method was shown to be the most accurate in the prediction of HJC (mean error≈18mm, SD=9mm) and quasi-equivalent to the Bell method. The bias for each method was quantified, allowing its correction for an improved HJC estimation. PMID:27477704

  13. 6-Substituted Pyrrolo[2,3-d]pyrimidine Thienoyl Regioisomers as Targeted Antifolates for Folate Receptor α and the Proton-Coupled Folate Transporter in Human Tumors

    PubMed Central

    Wang, Lei; Wallace, Adrianne; Raghavan, Sudhir; Deis, Siobhan M.; Wilson, Mike R.; Yang, Si; Polin, Lisa; White, Kathryn; Kushner, Juiwanna; Orr, Steven; George, Christina; O’Connor, Carrie; Hou, Zhanjun; Mitchell-Ryan, Shermaine; Dann, Charles E.; Matherly, Larry H.; Gangjee, Aleem

    2016-01-01

    2-Amino-4-oxo-6-substituted-pyrrolo[2,3-d]-pyrimidine antifolate thiophene regioisomers of AGF94 (4) with a thienoyl side chain and three-carbon bridge lengths [AGF150 (5) and AGF154 (7)] were synthesized as potential antitumor agents. These analogues inhibited proliferation of Chinese hamster ovary (CHO) sublines expressing folate receptors (FRs) α or β (IC50s < 1 nM) or the proton-coupled folate transporter (PCFT) (IC50 < 7 nM). Compounds 5 and 7 inhibited KB, IGROV1, and SKOV3 human tumor cells at subnanomolar concentrations, reflecting both FRα and PCFT uptake. AGF152 (6) and AGF163 (8), 2,4-diamino-5-substituted-furo[2,3-d]pyrimidine thiophene regioisomers, also inhibited growth of FR-expressing CHO and KB cells. All four analogues inhibited glycinamide ribonucleotide formyltransferase (GARFTase). Crystal structures of human GARFTase complexed with 5 and 7 were reported. In severe combined immunodeficient mice bearing SKOV3 tumors, 7 was efficacious. The selectivity of these compounds for PCFT and for FRα and β over the ubiquitously expressed reduced folate carrier is a paradigm for selective tumor targeting. PMID:26317331

  14. Template CoMFA Generates Single 3D-QSAR Models that, for Twelve of Twelve Biological Targets, Predict All ChEMBL-Tabulated Affinities

    PubMed Central

    Cramer, Richard D.

    2015-01-01

    The possible applicability of the new template CoMFA methodology to the prediction of unknown biological affinities was explored. For twelve selected targets, all ChEMBL binding affinities were used as training and/or prediction sets, making these 3D-QSAR models the most structurally diverse and among the largest ever. For six of the targets, X-ray crystallographic structures provided the aligned templates required as input (BACE, cdk1, chk2, carbonic anhydrase-II, factor Xa, PTP1B). For all targets including the other six (hERG, cyp3A4 binding, endocrine receptor, COX2, D2, and GABAa), six modeling protocols applied to only three familiar ligands provided six alternate sets of aligned templates. The statistical qualities of the six or seven models thus resulting for each individual target were remarkably similar. Also, perhaps unexpectedly, the standard deviations of the errors of cross-validation predictions accompanying model derivations were indistinguishable from the standard deviations of the errors of truly prospective predictions. These standard deviations of prediction ranged from 0.70 to 1.14 log units and averaged 0.89 (8x in concentration units) over the twelve targets, representing an average reduction of almost 50% in uncertainty, compared to the null hypothesis of “predicting” an unknown affinity to be the average of known affinities. These errors of prediction are similar to those from Tanimoto coefficients of fragment occurrence frequencies, the predominant approach to side effect prediction, which template CoMFA can augment by identifying additional active structural classes, by improving Tanimoto-only predictions, by yielding quantitative predictions of potency, and by providing interpretable guidance for avoiding or enhancing any specific target response. PMID:26065424

  15. In Situ Investigation of the 3D Mechanical Microstructure at Nanoscale: Nano-CT Imaging Method of Local Small Region in Large Scale Sample

    PubMed Central

    Xu, Feng; Hu, Xiao-fang; Qu, Hong-yan; Kang, Dan; Xiao, Ti-qiao

    2014-01-01

    To investigate the local micro-/nanoscale region in a large scale sample, an image reconstruction method for nanometer computed tomography (nano-CT) was proposed in this paper. In the algorithm, wavelets were used to localize the filtered-backprojection (FBP) algorithm because of its space-frequency localization property. After the implementation of the algorithm, two simulation local reconstruction experiments were performed to confirm its effectiveness. Three evaluation criteria were used in the experiments to judge the quality of the reconstructed images. The experimental results showed that the algorithm proposed in this paper performed best because (1) the quality of its results had improved 20%–30% compared to the results of FBP and 10%–30% compared to the results of another wavelet algorithm; (2) the new algorithm was stable under different circumstances. Besides, an actual reconstruction experiment was performed using real projection data that had been collected in a CT experiment. Two-dimensional (2D) and three-dimensional (3D) images of the sample were reconstructed. The microstructure of the sample could be clearly observed in the reconstructed images. Since much attention has been directed towards the nano-CT technique to investigate the microstructure of materials, this new wavelet-based local tomography algorithm could be considered as a meaningful effort. PMID:24723829

  16. In situ investigation of the 3D mechanical microstructure at nanoscale: nano-CT imaging method of local small region in large scale sample.

    PubMed

    Dong, Bo; Xu, Feng; Hu, Xiao-fang; Qu, Hong-yan; Kang, Dan; Xiao, Ti-qiao

    2014-01-01

    To investigate the local micro-/nanoscale region in a large scale sample, an image reconstruction method for nanometer computed tomography (nano-CT) was proposed in this paper. In the algorithm, wavelets were used to localize the filtered-backprojection (FBP) algorithm because of its space-frequency localization property. After the implementation of the algorithm, two simulation local reconstruction experiments were performed to confirm its effectiveness. Three evaluation criteria were used in the experiments to judge the quality of the reconstructed images. The experimental results showed that the algorithm proposed in this paper performed best because (1) the quality of its results had improved 20%-30% compared to the results of FBP and 10%-30% compared to the results of another wavelet algorithm; (2) the new algorithm was stable under different circumstances. Besides, an actual reconstruction experiment was performed using real projection data that had been collected in a CT experiment. Two-dimensional (2D) and three-dimensional (3D) images of the sample were reconstructed. The microstructure of the sample could be clearly observed in the reconstructed images. Since much attention has been directed towards the nano-CT technique to investigate the microstructure of materials, this new wavelet-based local tomography algorithm could be considered as a meaningful effort. PMID:24723829

  17. TOUGH2Viewer: A post-processing tool for interactive 3D visualization of locally refined unstructured grids for TOUGH2

    NASA Astrophysics Data System (ADS)

    Bonduá, S.; Berry, P.; Bortolotti, V.; Cormio, C.

    2012-09-01

    Within the MAC-GEO research project, funded by Regione Toscana and addressed to the exploitation of high enthalpy geothermal systems, the authors worked on the utilization and customization of the open source numerical simulator TOUGH2, as implemented in the code dedicated to model calibration iTOUGH2. TOUGH2 is one of the most used numerical simulation software for non-isothermal flow of multicomponent, multiphase fluids in one, two and three-dimensional porous and fractured media. Lacking an official Graphical User Interface tool for post-processing operations, several commercial and academic software have been developed to manage and display TOUGH2 input and output data files. Almost all of these tools seem to have limits to visualizing parameter values of the numerical model, work only with a predefined binary version of TOUGH2, and only a few of them can manage locally refined unstructured grids (i.e. Voronoi grids). To overcome these limitations, the authors have developed and tested a dedicated software application (called TOUGH2Viewer) for reading and managing TOUGH2 output files, written in Java and able to provide an interactive 3D view of the numerical model. Several functionalities have been implemented for block query and searching, contour mapping and 3D surface mapping of TOUGH2 primary variables (i.e. pressure, temperature, etc.). TOUGH2Viewer is also able to display 2D and 3D views of mass and heat flow between blocks, for each time step in which the simulation proceeds. The application described in this paper is under development to improve its functionalities; nevertheless the current software release is a valid support tool for post-processing that significantly improves the possibility to inspect the simulated data coming from TOUGH2.

  18. 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

  19. A 3D Localized Surface Plasmon Resonance Biosensor for the Study of Trivalent Arsenic Binding to the ArsA ATPase

    PubMed Central

    Liu, Chang; Balsamo, Vittoria; Sun, Dali; Naja, Melodie; Wang, Xuemei; Rosen, Barry; Li, Chen-Zhong

    2012-01-01

    A self-assembled 3D hydrogel-nanoparticle composite integrated surface plasmon resonance (SPR) sensor is reported here. The novel assembled substrate was developed by means of a surface mediated radical co-polymerization process to obtain a highly sensitive hydrogel-based thin film that possesses specific binding sites for target analytes. Initially, amino group modified gold nanoparticles (AuNPs) were covalently linked to acrylic acid monomer. Following this, N-isopropylacrylamide (NIPAAm) and AuNPs linked acrylic acid (AAc) monomers were randomly co-polymerized by the “grafting from” method in the presence of initiator and crosslinker onto the sensing surface. Surface charecterization techniques were utilized to evaluate the thickness and composition of the hydrogel-nanoparticle film. The sensing platform was employed to study the binding kinetics and conformational changes of the ArsA ATPase as a consequence of binding trivalent arsenicals under a variety of conditions. ArsA, the catalytic subunit of the ArsAB arsenite (As(III)) translocating ATPase, is one of the five proteins encoded by the arsenical resistance (ars) operon of plasmid R773 in cells of Escherichia coli, that confers resistance to trivalent and pentavalent salts of the metalloid arsenic. SPR measurements indicate that the 3D hydrogel-nanoparticle coated sensors exhibited a higher sensitivity than that of the 2D AuNPs decorated sensors. Binding of As(III) to ArsA is greatly facilitated by the presence of magnesium ion and ATP. PMID:22658909

  20. Local ISM 3D distribution and soft X-ray background. Inferences on nearby hot gas and the North Polar Spur

    NASA Astrophysics Data System (ADS)

    Puspitarini, L.; Lallement, R.; Vergely, J.-L.; Snowden, S. L.

    2014-06-01

    Three-dimensional (3D) interstellar medium (ISM) maps can be used to locate not only interstellar (IS) clouds, but also IS bubbles between the clouds that are blown by stellar winds and supernovae, and that are filled by hot gas. To demonstrate this and to derive a clearer picture of the local ISM, we compare our recent 3D maps of the IS dust distribution to the ROSAT diffuse X-ray background maps after removing heliospheric emission. In the Galactic plane, there is a good correspondence between the locations and extents of the mapped nearby cavities and the soft (0.25 keV) background emission distribution, showing that most of these nearby cavities contribute to this soft X-ray emission. Assuming a constant dust-to-gas ratio and homogeneous 106 K hot gas filling the cavities, we modeled the 0.25 keV surface brightness in a simple way along the Galactic plane as seen from the Sun, taking the absorption by the mapped clouds into account. The data-model comparison favors the existence of hot gas in the solar neighborhood, the so-called Local Bubble (LB). The inferred average mean pressure in the local cavities is found to be on the order of 10 000 cm-3 K, in agreement with previous studies, providing a validation test for the method. On the other hand, the model overestimates the emission from the huge cavities located in the third quadrant. Using CaII absorption data, we show that the dust-to-CaII ratio is very low in this region, implying there is a large quantity of lower temperature (non-X-ray emitting) ionized gas and, as a consequence, a reduction in the volume filled by hot gas, explaining at least part of the discrepancy. In the meridian plane, the main two brightness enhancements coincide well with the LB's most elongated parts and chimneys connecting the LB to the halo, but no particular nearby cavity is found towards the enhancement in the direction of the bright North Polar Spur (NPS) at high latitude. We searched in the 3D maps for the source regions of

  1. Two-way regulation between cells and aligned collagen fibrils: local 3D matrix formation and accelerated neural differentiation of human decidua parietalis placental stem cells.

    PubMed

    Li, Wen; Zhu, Bofan; Strakova, Zuzana; Wang, Rong

    2014-08-01

    It has been well established that an aligned matrix provides structural and signaling cues to guide cell polarization and cell fate decision. However, the modulation role of cells in matrix remodeling and the feedforward effect on stem cell differentiation have not been studied extensively. In this study, we report on the concerted changes of human decidua parietalis placental stem cells (hdpPSCs) and the highly ordered collagen fibril matrix in response to cell-matrix interaction. With high-resolution imaging, we found the hdpPSCs interacted with the matrix by deforming the cell shape, harvesting the nearby collagen fibrils, and reorganizing the fibrils around the cell body to transform a 2D matrix to a localized 3D matrix. Such a unique 3D matrix prompted high expression of β-1 integrin around the cell body that mediates and facilitates the stem cell differentiation toward neural cells. The study offers insights into the coordinated, dynamic changes at the cell-matrix interface and elucidates cell modulation of its matrix to establish structural and biochemical cues for effective cell growth and differentiation. PMID:25003322

  2. Development of drug loaded nanoparticles for tumor targeting. Part 2: Enhancement of tumor penetration through receptor mediated transcytosis in 3D tumor models

    NASA Astrophysics Data System (ADS)

    El-Dakdouki, Mohammad H.; Puré, Ellen; Huang, Xuefei

    2013-04-01

    We report that receptor mediated transcytosis can be utilized to facilitate tumor penetration by drug loaded nanoparticles (NPs). We synthesized hyaluronan (HA) coated silica nanoparticles (SNPs) containing a highly fluorescent core to target CD44 expressed on the cancer cell surface. Although prior studies have primarily focused on CD44 mediated endocytosis to facilitate cellular uptake of HA-NPs by cancer cells, we discovered that, once internalized, the HA-SNPs could be transported out of the cells with their cargo. The exported NPs could be taken up by neighboring cells. This enabled the HA-SNPs to penetrate deeper inside tumors and reach a much greater number of tumor cells in 3D tumor models, presumably through tandem cycles of CD44 mediated endocytosis and exocytosis. When doxorubicin (DOX) was loaded onto the NPs, better penetration of multilayered tumor cells was observed with much improved cytotoxicities against both drug sensitive and drug resistant cancer spheroids compared to the free drug. Thus, targeting receptors such as CD44 that can readily undergo recycling between the cell surface and interior of the cells can become a useful strategy to enhance the tumor penetration potential of NPs and the efficiency of drug delivery through receptor mediated transcytosis.We report that receptor mediated transcytosis can be utilized to facilitate tumor penetration by drug loaded nanoparticles (NPs). We synthesized hyaluronan (HA) coated silica nanoparticles (SNPs) containing a highly fluorescent core to target CD44 expressed on the cancer cell surface. Although prior studies have primarily focused on CD44 mediated endocytosis to facilitate cellular uptake of HA-NPs by cancer cells, we discovered that, once internalized, the HA-SNPs could be transported out of the cells with their cargo. The exported NPs could be taken up by neighboring cells. This enabled the HA-SNPs to penetrate deeper inside tumors and reach a much greater number of tumor cells in 3D tumor

  3. A novel vector potential formulation of 3D Navier-Stokes equations with through-flow boundaries by a local meshless method

    NASA Astrophysics Data System (ADS)

    Young, D. L.; Tsai, C. H.; Wu, C. S.

    2015-11-01

    An alternative vector potential formulation is used to solve the Navier-Stokes (N-S) equations in 3D incompressible viscous flow problems with and without through-flow boundaries. Difficulties of the vector potential formulation include the implementation of boundary conditions for through-flow boundaries and the numerical treatment of fourth-order partial differential equations. The advantages on the other hand are the automatic satisfaction of the continuity equation; and pressure is decoupled from the velocity. The objective of this paper is to introduce the appropriate gauge and boundary conditions on the vector potential formulation by a localized meshless method. To handle the divergence-free property, a Coulomb gauge condition is enforced on the vector potential to ensure its existence and uniqueness mathematically. We further improve the algorithm to through-flow problems for the boundary conditions of vector potential by introducing the concept of Stokes' theorem. Based on this innovation, there is no need to include an additional variable to tackle the through-flow fields. This process will greatly simplify the imposition of boundary conditions by the vector potential approach. Under certain conditions, the coupled fourth-order partial differential equations can be easily solved by using this meshless local differential quadrature (LDQ) method. Due to the LDQ capability to deal with the high order differential equations, this algorithm is very attractive to solve this fourth-order vector potential formulation for the N-S equations as comparing to the conventional numerical schemes such as finite element or finite difference methods. The proposed vector potential formulation is simpler and has improved accuracy and efficiency compared to other pressure-free or pressure-coupled algorithms. This investigation can be regarded as the first complete study to obtain the N-S solutions by vector potential formulation through a LDQ method. Two classic 3D benchmark

  4. New weather depiction technology for night vision goggle (NVG) training: 3D virtual/augmented reality scene-weather-atmosphere-target simulation

    NASA Astrophysics Data System (ADS)

    Folaron, Michelle; Deacutis, Martin; Hegarty, Jennifer; Vollmerhausen, Richard; Schroeder, John; Colby, Frank P.

    2007-04-01

    US Navy and Marine Corps pilots receive Night Vision Goggle (NVG) training as part of their overall training to maintain the superiority of our forces. This training must incorporate realistic targets; backgrounds; and representative atmospheric and weather effects they may encounter under operational conditions. An approach for pilot NVG training is to use the Night Imaging and Threat Evaluation Laboratory (NITE Lab) concept. The NITE Labs utilize a 10' by 10' static terrain model equipped with both natural and cultural lighting that are used to demonstrate various illumination conditions, and visual phenomena which might be experienced when utilizing night vision goggles. With this technology, the military can safely, systematically, and reliably expose pilots to the large number of potentially dangerous environmental conditions that will be experienced in their NVG training flights. A previous SPIE presentation described our work for NAVAIR to add realistic atmospheric and weather effects to the NVG NITE Lab training facility using the NVG - WDT(Weather Depiction Technology) system (Colby, et al.). NVG -WDT consist of a high end multiprocessor server with weather simulation software, and several fixed and goggle mounted Heads Up Displays (HUDs). Atmospheric and weather effects are simulated using state-of-the-art computer codes such as the WRF (Weather Research μ Forecasting) model; and the US Air Force Research Laboratory MODTRAN radiative transport model. Imagery for a variety of natural and man-made obscurations (e.g. rain, clouds, snow, dust, smoke, chemical releases) are being calculated and injected into the scene observed through the NVG via the fixed and goggle mounted HUDs. This paper expands on the work described in the previous presentation and will describe the 3D Virtual/Augmented Reality Scene - Weather - Atmosphere - Target Simulation part of the NVG - WDT. The 3D virtual reality software is a complete simulation system to generate realistic

  5. Heterodyne 3D ghost imaging

    NASA Astrophysics Data System (ADS)

    Yang, Xu; Zhang, Yong; Yang, Chenghua; Xu, Lu; Wang, Qiang; Zhao, Yuan

    2016-06-01

    Conventional three dimensional (3D) ghost imaging measures range of target based on pulse fight time measurement method. Due to the limit of data acquisition system sampling rate, range resolution of the conventional 3D ghost imaging is usually low. In order to take off the effect of sampling rate to range resolution of 3D ghost imaging, a heterodyne 3D ghost imaging (HGI) system is presented in this study. The source of HGI is a continuous wave laser instead of pulse laser. Temporal correlation and spatial correlation of light are both utilized to obtain the range image of target. Through theory analysis and numerical simulations, it is demonstrated that HGI can obtain high range resolution image with low sampling rate.

  6. 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

  7. Correlation and Characterization of 3D Morphological Dependent Localized Surface Plasmon Resonance Spectra of Single Silver Nanoparticles Using Dark-field Optical Microscopy and Spectroscopy and AFM

    PubMed Central

    Song, Yujun; Nallathamby, Prakash D.; Huang, Tao; Elsayed-Ali, Hani E.; Xu, Xiao-Hong Nancy

    2009-01-01

    We have developed a new and effective methodology to correlate optical and AFM images of single Ag nanoparticles (NPs), allowing us to study 3D-morphological dependent localized surface plasmon resonance (LSPR) spectra of individual Ag NPs. We fabricated arrays of distinctive microwindows on glass coverslips using photo-lithography method, and created well-isolated individual Ag NPs with a wide variety of shapes and morphologies on the glass coverslips using a modified nanosphere lithography method (NSL). Using distinctive geometries of microwindows, we located individual Ag NPs of interest in their optical and AFM images, enabling us to correlate and characterize the LSPR spectra and 3D morphologies of the same single NPs using dark-field optical microscopy and spectroscopy (DFOMS) and AFM, respectively. We found that LSPR spectra of single Ag NPs, with nearly equal volume [(8.6 ± 0.4) × 103 nm3], cross-section [(2.2 ± 0.2) × 102 nm3], and height (39.6 ± 3.6 nm), highly depend on their shapes, showing the red shift of peak wavelength to 629 nm (quasi trapezoidal cylindrical NP) from that of 506 nm (quasi circular cylindrical NP). LSPR spectra of single Ag NPs simulated using discrete dipole approximation (DDA) agree well with those measured experimentally when their shapes and morphologies can be accuractely described in both methods, but differ when they are not. Furthermore, we found location-dependent LSPR spectra on and around a single NP, offering a unique opportunity to characterize multi-mode plasmonic NPs at nanometer resolution for better understanding their plasmonic optical properties and for rational design of single NP optics. PMID:20190865

  8. Adaptive-optics SLO imaging combined with widefield OCT and SLO enables precise 3D localization of fluorescent cells in the mouse retina

    PubMed Central

    Zawadzki, Robert J.; Zhang, Pengfei; Zam, Azhar; Miller, Eric B.; Goswami, Mayank; Wang, Xinlei; Jonnal, Ravi S.; Lee, Sang-Hyuck; Kim, Dae Yu; Flannery, John G.; Werner, John S.; Burns, Marie E.; Pugh, Edward N.

    2015-01-01

    Adaptive optics scanning laser ophthalmoscopy (AO-SLO) has recently been used to achieve exquisite subcellular resolution imaging of the mouse retina. Wavefront sensing-based AO typically restricts the field of view to a few degrees of visual angle. As a consequence the relationship between AO-SLO data and larger scale retinal structures and cellular patterns can be difficult to assess. The retinal vasculature affords a large-scale 3D map on which cells and structures can be located during in vivo imaging. Phase-variance OCT (pv-OCT) can efficiently image the vasculature with near-infrared light in a label-free manner, allowing 3D vascular reconstruction with high precision. We combined widefield pv-OCT and SLO imaging with AO-SLO reflection and fluorescence imaging to localize two types of fluorescent cells within the retinal layers: GFP-expressing microglia, the resident macrophages of the retina, and GFP-expressing cone photoreceptor cells. We describe in detail a reflective afocal AO-SLO retinal imaging system designed for high resolution retinal imaging in mice. The optical performance of this instrument is compared to other state-of-the-art AO-based mouse retinal imaging systems. The spatial and temporal resolution of the new AO instrumentation was characterized with angiography of retinal capillaries, including blood-flow velocity analysis. Depth-resolved AO-SLO fluorescent images of microglia and cone photoreceptors are visualized in parallel with 469 nm and 663 nm reflectance images of the microvasculature and other structures. Additional applications of the new instrumentation are discussed. PMID:26114038

  9. 3-D P-wave velocity structure and seismicity in Central Costa Rica from Local Earthquake Tomography using an amphibic network

    NASA Astrophysics Data System (ADS)

    Arroyo, I.; Husen, S.; Flueh, E.; Alvarado, G. E.

    2008-12-01

    The Central Pacific sector of the erosional margin in Costa Rica shows a high seismicity rate, coincident with the subduction of rough-relief ocean floor, and generates earthquakes up to Mw 7. Precise earthquake locations and detailed knowledge of the 3-D velocity structure provide key insights into the dynamics of subduction zones. To this end, we performed a 3-D Local Earthquake Tomography using P-wave traveltimes from 595 selected events recorded by a seismological network of off- and onshore stations, deployed for 6 months in the area. The results reflect the complexity associated to subduction of bathymetric highs and the transition from normal to thickened oceanic crust (Cocos Ridge). The slab is imaged as a high-velocity anomaly with a band of low velocities (LVB) on top enclosing the intraslab events deeper than ~30 km. Below the margin slope, the LVB is locally thickened by at least two seamounts. We observe an abrupt, eastward widening of the LVB, preceded by a low-velocity anomaly under the continental shelf, which we interpret as a big seamount. The thickening coincides with an inverted basin at the inner forearc and a low-velocity anomaly under it. The latter appears in a sector where blocks of inner forearc are uplifted, possibly by underplating of eroded material against the base of the crust. The anomaly promotes seismicity by high-friction with the upper plate, and could be linked to a Mw 6.4 earthquake in 2004. In the west part of the area, the interplate seismicity forms a cluster beneath the continental shelf. Its updip limit coincides with the 150° C isotherm and an increase in Vp along the plate boundary. This further supports a proposed model in which the seismicity onset along the plate interface is mainly due to a decrease in the abundance of the fluids released by subducted sediments. Higher seismicity rates locally concur with seamounts present at the seismogenic zone, while seamounts under the margin slope may shallow the onset of

  10. 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.

  11. Pharmacophore model prediction, 3D-QSAR and molecular docking studies on vinyl sulfones targeting Nrf2-mediated gene transcription intended for anti-Parkinson drug design.

    PubMed

    Athar, Mohd; Lone, Mohsin Yousuf; Khedkar, Vijay M; Jha, Prakash Chandra

    2016-06-01

    Despite intense research efforts towards clinical and molecular causes of Parkinson disease (PD), the etiology of disease still remains unclear. However, recent studies have provided ample evidences that the oxidative stress is the key player that contributes a lot to dopaminergic (DAergic) neurodegeneration in brain. It is due to the discrepancy of antioxidant defence system of which nuclear factor erythroid 2-related factor 2 (Nrf2) signalling is of central contour. In the current study, potent heme oxygenase-1 agonists (Nrf2 signalling regulator), vinyl sulfones, were selected and an optimal pharmacophore model was brought forth which was examined using a decoy set by atom-based 3D-QSAR. The best four-feature model consists of two hydrogen bond acceptors and two aromatic rings, which has the highest correlation coefficient, R(2) = .71 and [Formula: see text] = .73 in QSAR. These ligands were further studied for molecular docking with Nrf2-keap protein to gain insight into the major binding motifs followed by analysing pharmacokinetic properties to evaluate their bioavailability dominance. From this study, it is concluded that vinyl sulfones could be ideal compounds for targeting Nrf2 pathway which in turn halt the PD progression. Hence, these can be considered as potential leads for drug development against the same. PMID:26222438

  12. Impact of Increasing Margin Around the Lumpectomy Cavity to Define the Planning Target Volume for 3D Conformal External Beam Accelerated Partial Breast Irradiation

    SciTech Connect

    Cox, Brett W.; Horst, Kathleen C. Thornton, Sherri; Dirbas, Frederick M.

    2007-01-01

    The purpose of this study was to evaluate the dose to normal tissues as a function of increasing margins around the lumpectomy cavity in accelerated partial breast irradiation (APBI) using 3D-conformal radiotherapy (3DCRT). Eight patients with Stage 0-I breast cancer underwent treatment planning for 3DCRT APBI. The clinical target volume (CTV) was defined as a 15-mm expansion around the cavity limited by the chest wall and skin. Three planning target volumes (PTV1, PTV2, PTV3) were generated for each patient using a 0, 5-, and 10-mm expansion around the CTV, for a total margin of 15, 20, and 25 mm. Three treatment plans were generated for every patient using the 3 PTVs, and dose-volume analysis was performed for each plan. For each 5-mm increase in margin, the mean PTV:total breast volume ratio increased 10% and the relative increase in the mean ipsilateral breast dose was 15%. The mean volume of ipsilateral breast tissue receiving 75%, 50%, and 25% of the prescribed dose increased 6% to 7% for every 5 mm increase in PTV margin. Compared to lesions located in the upper outer quadrant, plans for medially located tumors revealed higher mean ipsilateral breast doses and 20% to 22% more ipsilateral breast tissue encompassed by the 25% IDL. The use of 3DCRT for APBI delivers higher doses to normal breast tissue as the PTV increases around the lumpectomy cavity. Efforts should be made to minimize the overall PTV when this technique is used. Ongoing studies will be necessary to determine the clinical relevance of these findings.

  13. Decoding 3D reach and grasp from hybrid signals in motor and premotor cortices: spikes, multiunit activity, and local field potentials

    PubMed Central

    Truccolo, Wilson; Vargas-Irwin, Carlos E.; Donoghue, John P.

    2012-01-01

    Neural activity in motor cortex during reach and grasp movements shows modulations in a broad range of signals from single-neuron spiking activity (SA) to various frequency bands in broadband local field potentials (LFPs). In particular, spatiotemporal patterns in multiband LFPs are thought to reflect dendritic integration of local and interareal synaptic inputs, attentional and preparatory processes, and multiunit activity (MUA) related to movement representation in the local motor area. Nevertheless, the relationship between multiband LFPs and SA, and their relationship to movement parameters and their relative value as brain-computer interface (BCI) control signals, remain poorly understood. Also, although this broad range of signals may provide complementary information channels in primary (MI) and ventral premotor (PMv) areas, areal differences in information have not been systematically examined. Here, for the first time, the amount of information in SA and multiband LFPs was compared for MI and PMv by recording from dual 96-multielectrode arrays while monkeys made naturalistic reach and grasp actions. Information was assessed as decoding accuracy for 3D arm end point and grip aperture kinematics based on SA or LFPs in MI and PMv, or combinations of signal types across areas. In contrast with previous studies with ≤16 simultaneous electrodes, here ensembles of >16 units (on average) carried more information than multiband, multichannel LFPs. Furthermore, reach and grasp information added by various LFP frequency bands was not independent from that in SA ensembles but rather typically less than and primarily contained within the latter. Notably, MI and PMv did not show a particular bias toward reach or grasp for this task or for a broad range of signal types. For BCIs, our results indicate that neuronal ensemble spiking is the preferred signal for decoding, while LFPs and combined signals from PMv and MI can add robustness to BCI control. PMID:22157115

  14. PLOT3D/AMES, APOLLO UNIX VERSION USING GMR3D (WITH TURB3D)

    NASA Technical Reports Server (NTRS)

    Buning, P.

    1994-01-01

    five groups: 1) Grid Functions for grids, grid-checking, etc.; 2) Scalar Functions for contour or carpet plots of density, pressure, temperature, Mach number, vorticity magnitude, helicity, etc.; 3) Vector Functions for vector plots of velocity, vorticity, momentum, and density gradient, etc.; 4) Particle Trace Functions for rake-like plots of particle flow or vortex lines; and 5) Shock locations based on pressure gradient. TURB3D is a modification of PLOT3D which is used for viewing CFD simulations of incompressible turbulent flow. Input flow data consists of pressure, velocity and vorticity. Typical quantities to plot include local fluctuations in flow quantities and turbulent production terms, plotted in physical or wall units. PLOT3D/TURB3D includes both TURB3D and PLOT3D because the operation of TURB3D is identical to PLOT3D, and there is no additional sample data or printed documentation for TURB3D. Graphical capabilities of PLOT3D version 3.6b+ vary among the implementations available through COSMIC. Customers are encouraged to purchase and carefully review the PLOT3D manual before ordering the program for a specific computer and graphics library. There is only one manual for use with all implementations of PLOT3D, and although this manual generally assumes that the Silicon Graphics Iris implementation is being used, informative comments concerning other implementations appear throughout the text. With all implementations, the visual representation of the object and flow field created by PLOT3D consists of points, lines, and polygons. Points can be represented with dots or symbols, color can be used to denote data values, and perspective is used to show depth. Differences among implementations impact the program's ability to use graphical features that are based on 3D polygons, the user's ability to manipulate the graphical displays, and the user's ability to obtain alternate forms of output. The Apollo implementation of PLOT3D uses some of the capabilities of

  15. PLOT3D/AMES, APOLLO UNIX VERSION USING GMR3D (WITHOUT TURB3D)

    NASA Technical Reports Server (NTRS)

    Buning, P.

    1994-01-01

    five groups: 1) Grid Functions for grids, grid-checking, etc.; 2) Scalar Functions for contour or carpet plots of density, pressure, temperature, Mach number, vorticity magnitude, helicity, etc.; 3) Vector Functions for vector plots of velocity, vorticity, momentum, and density gradient, etc.; 4) Particle Trace Functions for rake-like plots of particle flow or vortex lines; and 5) Shock locations based on pressure gradient. TURB3D is a modification of PLOT3D which is used for viewing CFD simulations of incompressible turbulent flow. Input flow data consists of pressure, velocity and vorticity. Typical quantities to plot include local fluctuations in flow quantities and turbulent production terms, plotted in physical or wall units. PLOT3D/TURB3D includes both TURB3D and PLOT3D because the operation of TURB3D is identical to PLOT3D, and there is no additional sample data or printed documentation for TURB3D. Graphical capabilities of PLOT3D version 3.6b+ vary among the implementations available through COSMIC. Customers are encouraged to purchase and carefully review the PLOT3D manual before ordering the program for a specific computer and graphics library. There is only one manual for use with all implementations of PLOT3D, and although this manual generally assumes that the Silicon Graphics Iris implementation is being used, informative comments concerning other implementations appear throughout the text. With all implementations, the visual representation of the object and flow field created by PLOT3D consists of points, lines, and polygons. Points can be represented with dots or symbols, color can be used to denote data values, and perspective is used to show depth. Differences among implementations impact the program's ability to use graphical features that are based on 3D polygons, the user's ability to manipulate the graphical displays, and the user's ability to obtain alternate forms of output. The Apollo implementation of PLOT3D uses some of the capabilities of

  16. The ATLAS3D project - XXI. Correlations between gradients of local escape velocity and stellar populations in early-type galaxies

    NASA Astrophysics Data System (ADS)

    Scott, Nicholas; Cappellari, Michele; Davies, Roger L.; Kleijn, Gijs Verdoes; Bois, Maxime; Alatalo, Katherine; Blitz, Leo; Bournaud, Frédéric; Bureau, Martin; Crocker, Alison; Davis, Timothy A.; de Zeeuw, P. T.; Duc, Pierre-Alain; Emsellem, Eric; Khochfar, Sadegh; Krajnović, Davor; Kuntschner, Harald; McDermid, Richard M.; Morganti, Raffaella; Naab, Thorsten; Oosterloo, Tom; Sarzi, Marc; Serra, Paolo; Weijmans, Anne-Marie; Young, Lisa M.

    2013-07-01

    We explore the connection between the local escape velocity, Vesc, and the stellar population properties in the ATLAS3D survey, a complete, volume-limited sample of nearby early-type galaxies. We make use of ugriz photometry to construct Multi-Gaussian Expansion models of the surface brightnesses of our galaxies. We are able to fit the full range of surface brightness profiles found in our sample, and in addition we reproduce the results of state-of-the-art photometry in the literature with residuals of 0.04 mag. We utilize these photometric models and SAURON integral-field spectroscopy, combined with Jeans dynamical modelling, to determine the local Vesc derived from the surface brightness. We find that the local Vesc is tightly correlated with the Mg b and Fe5015 line strengths and optical colours, and anti-correlated with the Hβ line strength. In the case of the Mg b and colour-Vesc relations we find that the relation within individual galaxies follows the global relation between different galaxies. We intentionally ignored any uncertain contribution due to dark matter since we are seeking an empirical description of stellar population gradients in early-type galaxies that is ideal for quantitative comparison with model predictions. We also make use of single stellar population (SSP) modelling to transform our line strength index measurements into the SSP-equivalent parameters age (t), metallicity ([Z/H]) and α-enhancement [α/Fe]. The residuals from the relation are correlated with age, [α/Fe], molecular gas mass and local environmental density. We identify a population of galaxies that occur only at low Vesc that exhibit negative gradients in the Mg b- and Colour-Vesc relations. These galaxies typically have young central stellar populations and contain significant amounts of molecular gas and dust. Combining these results with N-body simulations of binary mergers we use the Mg b-Vesc relation to constrain the possible number of dry mergers experienced by

  17. 3D multiplexed immunoplasmonics microscopy

    NASA Astrophysics Data System (ADS)

    Bergeron, Éric; Patskovsky, Sergiy; Rioux, David; Meunier, Michel

    2016-07-01

    Selective labelling, identification and spatial distribution of cell surface biomarkers can provide important clinical information, such as distinction between healthy and diseased cells, evolution of a disease and selection of the optimal patient-specific treatment. Immunofluorescence is the gold standard for efficient detection of biomarkers expressed by cells. However, antibodies (Abs) conjugated to fluorescent dyes remain limited by their photobleaching, high sensitivity to the environment, low light intensity, and wide absorption and emission spectra. Immunoplasmonics is a novel microscopy method based on the visualization of Abs-functionalized plasmonic nanoparticles (fNPs) targeting cell surface biomarkers. Tunable fNPs should provide higher multiplexing capacity than immunofluorescence since NPs are photostable over time, strongly scatter light at their plasmon peak wavelengths and can be easily functionalized. In this article, we experimentally demonstrate accurate multiplexed detection based on the immunoplasmonics approach. First, we achieve the selective labelling of three targeted cell surface biomarkers (cluster of differentiation 44 (CD44), epidermal growth factor receptor (EGFR) and voltage-gated K+ channel subunit KV1.1) on human cancer CD44+ EGFR+ KV1.1+ MDA-MB-231 cells and reference CD44- EGFR- KV1.1+ 661W cells. The labelling efficiency with three stable specific immunoplasmonics labels (functionalized silver nanospheres (CD44-AgNSs), gold (Au) NSs (EGFR-AuNSs) and Au nanorods (KV1.1-AuNRs)) detected by reflected light microscopy (RLM) is similar to the one with immunofluorescence. Second, we introduce an improved method for 3D localization and spectral identification of fNPs based on fast z-scanning by RLM with three spectral filters corresponding to the plasmon peak wavelengths of the immunoplasmonics labels in the cellular environment (500 nm for 80 nm AgNSs, 580 nm for 100 nm AuNSs and 700 nm for 40 nm × 92 nm AuNRs). Third, the developed

  18. 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.

  19. Enhancing Macrophage Drug Delivery Efficiency via Co-Localization of Cells and Drug-Loaded Microcarriers in 3D Resonant Ultrasound Field

    PubMed Central

    Lee, Yu-Hsiang; Wu, Zhen-Yu

    2015-01-01

    In this study, a novel synthetic 3D molecular transfer system which involved the use of model drug calcein-AM-encapsulated poly(lactic-co-glycolic acid) microspheres (CAPMs) and resonant ultrasound field (RUF) with frequency of 1 MHz and output intensity of 0.5 W/cm2 for macrophage drug delivery was explored. We hypothesized that the efficiency of CAPMs-mediated drug delivery aided by RUF can be promoted by increasing the contact opportunities between cells and the micrometer-sized drug carriers due to effects of acoustic radiation forces generated by RUF. Through the fluoromicroscopic and flow cytometric analyses, our results showed that both DH82 macrophages and CAPMs can be quickly brought to acoustic pressure nodes within 20 sec under RUF exposure, and were consequently aggregated throughout the time course. The efficacy of cellular uptake of CAPMs was enhanced with increased RUF exposure time where a 3-fold augmentation (P < 0.05) was obtained after 15 min of RUF exposure. We further demonstrated that the enhanced CAPM delivery efficiency was mainly contributed by the co-localization of cells and CAPMs resulting from the application of the RUF, rather than from sonoporation. In summary, the developed molecular delivery approach provides a feasible means for macrophage drug delivery. PMID:26267789

  20. Evaluation of local electric fields generated by transcranial direct current stimulation with an extracephalic reference electrode based on realistic 3D body modeling

    NASA Astrophysics Data System (ADS)

    Im, Chang-Hwan; Park, Ji-Hye; Shim, Miseon; Chang, Won Hyuk; Kim, Yun-Hee

    2012-04-01

    In this study, local electric field distributions generated by transcranial direct current stimulation (tDCS) with an extracephalic reference electrode were evaluated to address extracephalic tDCS safety issues. To this aim, we generated a numerical model of an adult male human upper body and applied the 3D finite element method to electric current conduction analysis. In our simulations, the active electrode was placed over the left primary motor cortex (M1) and the reference electrode was placed at six different locations: over the right temporal lobe, on the right supraorbital region, on the right deltoid, on the left deltoid, under the chin, and on the right buccinator muscle. The maximum current density and electric field intensity values in the brainstem generated by the extracephalic reference electrodes were comparable to, or even less than, those generated by the cephalic reference electrodes. These results suggest that extracephalic reference electrodes do not lead to unwanted modulation of the brainstem cardio-respiratory and autonomic centers, as indicated by recent experimental studies. The volume energy density was concentrated at the neck area by the use of deltoid reference electrodes, but was still smaller than that around the active electrode locations. In addition, the distributions of elicited cortical electric fields demonstrated that the use of extracephalic reference electrodes might allow for the robust prediction of cortical modulations with little dependence on the reference electrode locations.

  1. Fibroblast adhesion on ECM-derived peptide modified poly(2-hydroxyethyl methacrylate) brushes: ligand co-presentation and 3D-localization.

    PubMed

    Desseaux, Solenne; Klok, Harm-Anton

    2015-03-01

    Polymer brushes prepared via surface-initiated polymerization of 2-hydroxyethyl methacrylate are powerful platforms for the fabrication of model biointerfaces to study cell-substrate interactions. In this manuscript, the versatility of surface-initiated polymerization and the poly(2-hydroxyethyl methacrylate) (PHEMA) polymer brush platform are used to address two fundamental questions, viz. the effects of ligand co-presentation and of the 3D localization of biochemical cues on cell behavior. Using a series of PHEMA brushes that present RGD and PHSRN ligands in various relative surface concentrations, the present study unequivocally demonstrates that: (i) co-presentation of PHSRN cues on an RGD functionalized substrate enhances cell adhesion and (ii) this synergetic effect is highest when the two ligands are presented at equal surface concentrations. In the second part of this study, adhesion of 3T3 fibroblasts on a series of PHEMA brushes that present the RGD ligand at a distance of 12, 23 or 42 nm away from the cell substrate interface is investigated. While cells were found to adhere to surfaces that presented the cell adhesive peptides at distances up to 23 nm from the interface, polymer brushes that contained the RGD ligands 42 nm away from the interface did not support cell adhesion. PMID:25617123

  2. Quantum evolution: The case of weak localization for a 3D alloy-type Anderson model and application to Hamiltonian based quantum computation

    NASA Astrophysics Data System (ADS)

    Cao, Zhenwei

    Over the years, people have found Quantum Mechanics to be extremely useful in explaining various physical phenomena from a microscopic point of view. Anderson localization, named after physicist P. W. Anderson, states that disorder in a crystal can cause non-spreading of wave packets, which is one possible mechanism (at single electron level) to explain metal-insulator transitions. The theory of quantum computation promises to bring greater computational power over classical computers by making use of some special features of Quantum Mechanics. The first part of this dissertation considers a 3D alloy-type model, where the Hamiltonian is the sum of the finite difference Laplacian corresponding to free motion of an electron and a random potential generated by a sign-indefinite single-site potential. The result shows that localization occurs in the weak disorder regime, i.e., when the coupling parameter lambda is very small, for energies E ≤ --Clambda 2. The second part of this dissertation considers adiabatic quantum computing (AQC) algorithms for the unstructured search problem to the case when the number of marked items is unknown. In an ideal situation, an explicit quantum algorithm together with a counting subroutine are given that achieve the optimal Grover speedup over classical algorithms, i.e., roughly speaking, reduce O(2n) to O(2n/2), where n is the size of the problem. However, if one considers more realistic settings, the result shows this quantum speedup is achievable only under a very rigid control precision requirement (e.g., exponentially small control error).

  3. 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?

  4. Polycaprolactone-Coated 3D Printed Tricalcium Phosphate Scaffolds for Bone Tissue Engineering: In Vitro Alendronate Release Behavior and Local Delivery Effect on In Vivo Osteogenesis

    PubMed Central

    2015-01-01

    The aim of this work was to evaluate the effect of in vitro alendronate (AD) release behavior through polycaprolactone (PCL) coating on in vivo bone formation using PCL-coated 3D printed interconnected porous tricalcium phosphate (TCP) scaffolds. Higher AD and Ca2+ ion release was observed at lower pH (5.0) than that at higher pH (7.4). AD and Ca2+ release, surface morphology, and phase analysis after release indicated a matrix degradation dominated AD release caused by TCP dissolution. PCL coating showed its effectiveness for controlled and sustained AD release. Six different scaffold compositions, namely, (i) TCP (bare TCP), (ii) TCP + AD (AD-coated TCP), (iii) TCP + PCL (PCL-coated TCP), (iv) TCP + PCL + AD, (v) TCP + AD + PCL, and (vi) TCP + AD + PCL + AD were tested in the distal femoral defect of Sprague–Dawley rats for 6 and 10 weeks. An excellent bone formation inside the micro and macro pores of the scaffolds was observed from histomorphology. Histomorphometric analysis revealed maximum new bone formation in TCP + AD + PCL scaffolds after 6 weeks. No adverse effect of PCL on bioactivity of TCP and in vivo bone formation was observed. All scaffolds with AD showed higher bone formation and reduced TRAP (tartrate resistant acid phosphatase) positive cells activity compared to bare TCP and TCP coated with only PCL. Bare TCP scaffolds showed the highest TRAP positive cells activity followed by TCP + PCL scaffolds, whereas TCP + AD scaffolds showed the lowest TRAP activity. A higher TRAP positive cells activity was observed in TCP + AD + PCL compared to TCP + AD scaffolds after 6 weeks. Our results show that in vivo local AD delivery from PCL-coated 3DP TCP scaffolds could further induce increased early bone formation. PMID:24826838

  5. Presentation of a High Resolution Time Lapse 3D Groundwater Model of Metsähovi for Calculating the Gravity Effect of Groundwater in Local Scale

    NASA Astrophysics Data System (ADS)

    Hokkanen, T. M.; Hartikainen, A.; Raja-Halli, A.; Virtanen, H.; Makinen, J.

    2015-12-01

    INTRODUCTION The aim of this study is to construct a fine resolution time lapse groundwater (GW) model of Metsähovi (MH). GW, geological, and soil moisture (SM) data were collected for several years to achieve the goal. The knowledge of the behavior of the GW at local scale is essential for superconductive gravimeter (SG) investigations performing in MH. DESCRIPTION OF THE DATA Almost 50 sensors have been recorded SM data some 6 years with 1 to 5 minutes sampling frequency. The GW table has been monitored, both in bedrock and in soil, in many stages with all together 15 piezometers. Two geological sampling campaigns were conducted to get the knowledge of hydrological properties of soil in the study area of 200×200 m2 around SG station in MH. PRINCIPLE OF TIME LAPSE 3D HYDROGEOLOGICAL MODEL The model of study site consists of the surfaces of ground and bedrock gridded with 2×2 m2 resolution. The height of GW table was interpolated to 2×2×0.1 m3 grid between GW and SM monitoring points. Close to the outline of the study site and areas lacking of sensors GW table was defined by extrapolation and considering the geological information of the area. The bedrock porosity is 2% and soil porosity determined by geological information and SM recordings is from 5 to 35%. Only fully saturated media is considered in the time lapse model excluding unsaturated one. BENEFICIERS With a new model the fluctuation of GW table can be followed with ranging time lapses from 1 minute to 1 month. The gravity effect caused by the variation of GW table can be calculated more accurate than before in MH. Moreover, the new model can be validated and refined by measured gravity, i.e. hydrological model can be improved by SG recordings (Figure 1).

  6. 3D multiplexed immunoplasmonics microscopy.

    PubMed

    Bergeron, Éric; Patskovsky, Sergiy; Rioux, David; Meunier, Michel

    2016-07-21

    Selective labelling, identification and spatial distribution of cell surface biomarkers can provide important clinical information, such as distinction between healthy and diseased cells, evolution of a disease and selection of the optimal patient-specific treatment. Immunofluorescence is the gold standard for efficient detection of biomarkers expressed by cells. However, antibodies (Abs) conjugated to fluorescent dyes remain limited by their photobleaching, high sensitivity to the environment, low light intensity, and wide absorption and emission spectra. Immunoplasmonics is a novel microscopy method based on the visualization of Abs-functionalized plasmonic nanoparticles (fNPs) targeting cell surface biomarkers. Tunable fNPs should provide higher multiplexing capacity than immunofluorescence since NPs are photostable over time, strongly scatter light at their plasmon peak wavelengths and can be easily functionalized. In this article, we experimentally demonstrate accurate multiplexed detection based on the immunoplasmonics approach. First, we achieve the selective labelling of three targeted cell surface biomarkers (cluster of differentiation 44 (CD44), epidermal growth factor receptor (EGFR) and voltage-gated K(+) channel subunit KV1.1) on human cancer CD44(+) EGFR(+) KV1.1(+) MDA-MB-231 cells and reference CD44(-) EGFR(-) KV1.1(+) 661W cells. The labelling efficiency with three stable specific immunoplasmonics labels (functionalized silver nanospheres (CD44-AgNSs), gold (Au) NSs (EGFR-AuNSs) and Au nanorods (KV1.1-AuNRs)) detected by reflected light microscopy (RLM) is similar to the one with immunofluorescence. Second, we introduce an improved method for 3D localization and spectral identification of fNPs based on fast z-scanning by RLM with three spectral filters corresponding to the plasmon peak wavelengths of the immunoplasmonics labels in the cellular environment (500 nm for 80 nm AgNSs, 580 nm for 100 nm AuNSs and 700 nm for 40 nm × 92 nm AuNRs). Third

  7. Clinical Applications of 3-D Conformal Radiotherapy

    NASA Astrophysics Data System (ADS)

    Miralbell, Raymond

    Although a significant improvement in cancer cure (i.e. 20% increment) has been obtained in the last 2-3 decades, 30-40% of patients still fail locally after curative radiotherapy. In order to improve local tumor control rates with radiotherapy high doses to the tumor volume are frequently necessary. Three-dimensional conformal radiation therapy (3-D CRT) is used to denote a spectrum of radiation planning and delivery techniques that rely on three-dimensional imaging to define the target (tumor) and to distinguish it from normal tissues. Modern, high-precision radiotherapy (RT) techniques are needed in order to implement the goal of optimal tumor destruction delivering minimal dose to the non-target normal tissues. A better target definition is nowadays possible with contemporary imaging (computerized tomography, magnetic resonance imaging, and positron emission tomography) and image registration technology. A highly precise dose distributions can be obtained with optimal 3-D CRT treatment delivery techniques such as stereotactic RT, intensity modulated RT (IMRT), or protontherapy (the latter allowing for in-depth conformation). Patient daily set-up repositioning and internal organ immobilization systems are necessary before considering to undertake any of the above mentioned high-precision treatment approaches. Prostate cancer, brain tumors, and base of skull malignancies are among the sites most benefitting of dose escalation approaches. Nevertheless, a significant dose reduction to the normal tissues in the vicinity of the irradiated tumor also achievable with optimal 3-D CRT may also be a major issue in the treatment of pediatric tumors in order to preserve growth, normal development, and to reduce the risk of developing radiation induced diseases such as cancer or endocrinologic disorders.

  8. '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.

  9. 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)

  10. MRI-Guided 3D Optimization Significantly Improves DVH Parameters of Pulsed-Dose-Rate Brachytherapy in Locally Advanced Cervical Cancer

    SciTech Connect

    Lindegaard, Jacob C. Tanderup, Kari; Nielsen, Soren Kynde; Haack, Soren; Gelineck, John

    2008-07-01

    Purpose: To compare dose-volume histogram parameters of standard Point A and magnetic resonance imaging-based three-dimensional optimized dose plans in 21 consecutive patients who underwent pulsed-dose-rate brachytherapy (PDR-BT) for locally advanced cervical cancer. Methods and Materials: All patients received external beam radiotherapy (elective target dose, 45 Gy in 25-30 fractions; tumor target dose, 50-60 Gy in 25-30 fractions). PDR-BT was applied with a tandem-ring applicator. Additional ring-guided titanium needles were used in 4 patients and a multichannel vaginal cylinder in 2 patients. Dose planning was done using 1.5 Tesla T{sub 1}-weighted and T{sub 2}-weighted paratransversal magnetic resonance imaging scans. T{sub 1}-weighted visible oil-containing tubes were used for applicator reconstruction. The prescribed standard dose for PDR-BT was 10 Gy (1 Gy/pulse, 1 pulse/h) for two to three fractions to reach a physical dose of 80 Gy to Point A. The total dose (external beam radiotherapy plus brachytherapy) was normalized to an equivalent dose in 2-Gy fractions using {alpha}/{beta} = 10 Gy for tumor, {alpha}/{beta} = 3 Gy for normal tissue, and a repair half-time of 1.5 h. The goal of optimization was dose received by 90% of the target volume (D{sub 90}) of {>=}85 Gy{sub {alpha}}{sub /{beta}}{sub 10} in the high-risk clinical target volume (cervix and remaining tumor at brachytherapy), but keeping the minimal dose to 2 cm{sup 3} of the bladder and rectum/sigmoid at <90 and <75 Gy{sub {alpha}}{sub /{beta}}{sub 3}, respectively. Results: Using three-dimensional optimization, all dose-volume histogram constraints were met in 16 of 21 patients compared with 3 of 21 patients with two-dimensional library plans (p < 0.001). Optimization increased the minimal target dose (D{sub 100}) of the high-risk clinical target volume (p < 0.007) and decreased the minimal dose to 2 cm{sup 3} for the sigmoid significantly (p = 0.03). For the high-risk clinical target volume, D

  11. Virtual local target method for avoiding local minimum in potential field based robot navigation.

    PubMed

    Zou, Xi-Yong; Zhu, Jing

    2003-01-01

    A novel robot navigation algorithm with global path generation capability is presented. Local minimum is a most intractable but is an encountered frequently problem in potential field based robot navigation. Through appointing appropriately some virtual local targets on the journey, it can be solved effectively. The key concept employed in this algorithm are the rules that govern when and how to appoint these virtual local targets. When the robot finds itself in danger of local minimum, a virtual local target is appointed to replace the global goal temporarily according to the rules. After the virtual target is reached, the robot continues on its journey by heading towards the global goal. The algorithm prevents the robot from running into local minima anymore. Simulation results showed that it is very effective in complex obstacle environments. PMID:12765277

  12. Intensity-Modulated and 3D-Conformal Radiotherapy for Whole-Ventricular Irradiation as Compared With Conventional Whole-Brain Irradiation in the Management of Localized Central Nervous System Germ Cell Tumors

    SciTech Connect

    Chen, Michael Jenwei; Silva Santos, Adriana da; Sakuraba, Roberto Kenji; Lopes, Cleverson Perceu; Goncalves, Vinicius Demanboro; Weltman, Eduardo; Ferrigno, Robson; Cruz, Jose Carlos

    2010-02-01

    Purpose: To compare the sparing potential of cerebral hemispheres with intensity-modulated radiotherapy (IMRT) and three-dimensional conformal radiotherapy (3D-CRT) for whole-ventricular irradiation (WVI) and conventional whole-brain irradiation (WBI) in the management of localized central nervous system germ cell tumors (CNSGCTs). Methods and Materials: Ten cases of patients with localized CNSGCTs and submitted to WVI by use of IMRT with or without a 'boost' to the primary lesion were selected. For comparison purposes, similar treatment plans were produced by use of 3D-CRT (WVI with or without boost) and WBI (opposed lateral fields with or without boost), and cerebral hemisphere sparing was evaluated at dose levels ranging from 2 Gy to 40 Gy. Results: The median prescription dose for WVI was 30.6 Gy (range, 25.2-37.5 Gy), and that for the boost was 16.5 Gy (range, 0-23.4 Gy). Mean irradiated cerebral hemisphere volumes were lower for WVI with IMRT than for 3D-CRT and were lower for WVI with 3D-CRT than for WBI. Intensity-modulated radiotherapy was associated with the lowest irradiated volumes, with reductions of 7.5%, 12.2%, and 9.0% at dose levels of 20, 30, and 40 Gy, respectively, compared with 3D-CRT. Intensity-modulated radiotherapy provided statistically significant reductions of median irradiated volumes at all dose levels (p = 0.002 or less). However, estimated radiation doses to peripheral areas of the body were 1.9 times higher with IMRT than with 3D-CRT. Conclusions: Although IMRT is associated with increased radiation doses to peripheral areas of the body, its use can spare a significant amount of normal central nervous system tissue compared with 3D-CRT or WBI in the setting of CNSGCT treatment.

  13. 3D multiplexed immunoplasmonics microscopy

    NASA Astrophysics Data System (ADS)

    Bergeron, Éric; Patskovsky, Sergiy; Rioux, David; Meunier, Michel

    2016-07-01

    Selective labelling, identification and spatial distribution of cell surface biomarkers can provide important clinical information, such as distinction between healthy and diseased cells, evolution of a disease and selection of the optimal patient-specific treatment. Immunofluorescence is the gold standard for efficient detection of biomarkers expressed by cells. However, antibodies (Abs) conjugated to fluorescent dyes remain limited by their photobleaching, high sensitivity to the environment, low light intensity, and wide absorption and emission spectra. Immunoplasmonics is a novel microscopy method based on the visualization of Abs-functionalized plasmonic nanoparticles (fNPs) targeting cell surface biomarkers. Tunable fNPs should provide higher multiplexing capacity than immunofluorescence since NPs are photostable over time, strongly scatter light at their plasmon peak wavelengths and can be easily functionalized. In this article, we experimentally demonstrate accurate multiplexed detection based on the immunoplasmonics approach. First, we achieve the selective labelling of three targeted cell surface biomarkers (cluster of differentiation 44 (CD44), epidermal growth factor receptor (EGFR) and voltage-gated K+ channel subunit KV1.1) on human cancer CD44+ EGFR+ KV1.1+ MDA-MB-231 cells and reference CD44- EGFR- KV1.1+ 661W cells. The labelling efficiency with three stable specific immunoplasmonics labels (functionalized silver nanospheres (CD44-AgNSs), gold (Au) NSs (EGFR-AuNSs) and Au nanorods (KV1.1-AuNRs)) detected by reflected light microscopy (RLM) is similar to the one with immunofluorescence. Second, we introduce an improved method for 3D localization and spectral identification of fNPs based on fast z-scanning by RLM with three spectral filters corresponding to the plasmon peak wavelengths of the immunoplasmonics labels in the cellular environment (500 nm for 80 nm AgNSs, 580 nm for 100 nm AuNSs and 700 nm for 40 nm × 92 nm AuNRs). Third, the developed

  14. 3D statistical shape models incorporating 3D random forest regression voting for robust CT liver segmentation

    NASA Astrophysics Data System (ADS)

    Norajitra, Tobias; Meinzer, Hans-Peter; Maier-Hein, Klaus H.

    2015-03-01

    During image segmentation, 3D Statistical Shape Models (SSM) usually conduct a limited search for target landmarks within one-dimensional search profiles perpendicular to the model surface. In addition, landmark appearance is modeled only locally based on linear profiles and weak learners, altogether leading to segmentation errors from landmark ambiguities and limited search coverage. We present a new method for 3D SSM segmentation based on 3D Random Forest Regression Voting. For each surface landmark, a Random Regression Forest is trained that learns a 3D spatial displacement function between the according reference landmark and a set of surrounding sample points, based on an infinite set of non-local randomized 3D Haar-like features. Landmark search is then conducted omni-directionally within 3D search spaces, where voxelwise forest predictions on landmark position contribute to a common voting map which reflects the overall position estimate. Segmentation experiments were conducted on a set of 45 CT volumes of the human liver, of which 40 images were randomly chosen for training and 5 for testing. Without parameter optimization, using a simple candidate selection and a single resolution approach, excellent results were achieved, while faster convergence and better concavity segmentation were observed, altogether underlining the potential of our approach in terms of increased robustness from distinct landmark detection and from better search coverage.

  15. 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.

  16. 3D Molecular Modelling Study of the H7N9 RNA-Dependent RNA Polymerase as an Emerging Pharmacological Target

    PubMed Central

    Vlachakis, Dimitrios

    2013-01-01

    Currently not much is known about the H7N9 strain, and this is the major drawback for a scientific strategy to tackle this virus. Herein, the 3D complex structure of the H7N9 RNA-dependent RNA polymerase has been established using a repertoire of molecular modelling techniques including homology modelling, molecular docking, and molecular dynamics simulations. Strikingly, it was found that the oligonucleotide cleft and tunnel in the H7N9 RNA-dependent RNA polymerase are structurally very similar to the corresponding region on the hepatitis C virus RNA-dependent RNA polymerase crystal structure. A direct comparison and a 3D postdynamics analysis of the 3D complex of the H7N9 RNA-dependent RNA polymerase provide invaluable clues and insight regarding the role and mode of action of a series of interacting residues on the latter enzyme. Our study provides a novel and efficiently intergraded platform with structural insights for the H7N9 RNA-dependent RNA Polymerase. We propose that future use and exploitation of these insights may prove invaluable in the fight against this lethal, ongoing epidemic. PMID:24187616

  17. 3D hybrid wound devices for spatiotemporally controlled release kinetics.

    PubMed

    Ozbolat, Ibrahim T; Koc, Bahattin

    2012-12-01

    This paper presents localized and temporal control of release kinetics over 3-dimensional (3D) hybrid wound devices to improve wound-healing process. Imaging study is performed to extract wound bed geometry in 3D. Non-Uniform Rational B-Splines (NURBS) based surface lofting is applied to generate functionally graded regions. Diffusion-based release kinetics model is developed to predict time-based release of loaded modifiers for functionally graded regions. Multi-chamber single nozzle solid freeform dispensing system is used to fabricate wound devices with controlled dispensing concentration. Spatiotemporal control of biological modifiers thus enables a way to achieve target delivery to improve wound healing. PMID:22672934

  18. Electrostatic Steering Accelerates C3d:CR2 Association.

    PubMed

    Mohan, Rohith R; Huber, Gary A; Morikis, Dimitrios

    2016-08-25

    Electrostatic effects are ubiquitous in protein interactions and are found to be pervasive in the complement system as well. The interaction between complement fragment C3d and complement receptor 2 (CR2) has evolved to become a link between innate and adaptive immunity. Electrostatic interactions have been suggested to be the driving factor for the association of the C3d:CR2 complex. In this study, we investigate the effects of ionic strength and mutagenesis on the association of C3d:CR2 through Brownian dynamics simulations. We demonstrate that the formation of the C3d:CR2 complex is ionic strength-dependent, suggesting the presence of long-range electrostatic steering that accelerates the complex formation. Electrostatic steering occurs through the interaction of an acidic surface patch in C3d and the positively charged CR2 and is supported by the effects of mutations within the acidic patch of C3d that slow or diminish association. Our data are in agreement with previous experimental mutagenesis and binding studies and computational studies. Although the C3d acidic patch may be locally destabilizing because of unfavorable Coulombic interactions of like charges, it contributes to the acceleration of association. Therefore, acceleration of function through electrostatic steering takes precedence to stability. The site of interaction between C3d and CR2 has been the target for delivery of CR2-bound nanoparticle, antibody, and small molecule biomarkers, as well as potential therapeutics. A detailed knowledge of the physicochemical basis of C3d:CR2 association may be necessary to accelerate biomarker and drug discovery efforts. PMID:27092816

  19. Integrated modelling of toroidal rotation with the 3D non-local drift-kinetic code and boundary models for JT-60U analyses and predictive simulations

    NASA Astrophysics Data System (ADS)

    Honda, M.; Satake, S.; Suzuki, Y.; Yoshida, M.; Hayashi, N.; Kamiya, K.; Matsuyama, A.; Shinohara, K.; Matsunaga, G.; Nakata, M.; Ide, S.; Urano, H.

    2015-07-01

    The integrated simulation framework for toroidal momentum transport is developed, which self-consistently calculates the neoclassical toroidal viscosity (NTV), the radial electric field {{E}r} and the resultant toroidal rotation {{V}φ} together with the scrape-off-layer (SOL) physics-based boundary model. The coupling of three codes, the 1.5D transport code TOPICS, the three-dimensional (3D) equilibrium code VMEC and the 3D δ f drift-kinetic equation solver FORTEC-3D, makes it possible to calculate the NTV due to the non-axisymmetric perturbed magnetic field caused by toroidal field coils. Analyses reveal that the NTV significantly influences {{V}φ} in JT-60U and {{E}r} holds the key to determine the NTV profile. The sensitivity of the {{V}φ} profile to the boundary rotation necessitates a boundary condition modelling for toroidal momentum. Owing to the high-resolution measurement system in JT-60U, the {{E}r} gradient is found to be virtually zero at the separatrix regardless of toroidal rotation velocities. Focusing on {{E}r} , the boundary model of toroidal momentum is developed in conjunction with the SOL/divertor plasma code D5PM. This modelling realizes self-consistent predictive simulations for operation scenario development in ITER.

  20. 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.

  1. The effect of co-delivery of paclitaxel and curcumin by transferrin-targeted PEG-PE-based mixed micelles on resistant ovarian cancer in 3-D spheroids and in vivo tumors

    PubMed Central

    Sarisozen, Can; Abouzeid, Abraham H.; Torchilin, Vladimir P.

    2014-01-01

    Multicellular 3D cancer cell culture (spheroids) resemble to in vivo tumors in terms of shape, cell morphology, growth kinetics, gene expression and drug response. However, these characteristics cause very limited drug penetration into deeper parts of the spheroids. In this study, we used multi drug resistant (MDR) ovarian cancer cell spheroid and in vivo tumor models to evaluate the co-delivery of paclitaxel (PCL) and a potent NF-κB inhibitor curcumin (CUR). PCL and CUR were co-loaded into the polyethylene glycol-phosphatidyl ethanolamine (PEG-PE) based polymeric micelles modified with Transferrin (TF) as the targeting ligand. Cytotoxicity, cellular association and accumulation into the deeper layers were investigated in the spheroids and compared with the monolayer cell culture. Comparing to non-targeted micelles, flow cytometry and confocal imaging proved significantly deeper and higher micelle penetration into the spheroids with TF-targeting. Both in monolayers and spheroids, PCL cytotoxicity was significantly increased when co-delivered with CUR in non-targeted micelles or as single agent in TF-targeted micelles, whereas TF-modification of co-loaded micelles did not further enhance the cytotoxicity. In vivo tumor inhibition studies showed good correlation with the 3D cell culture experiments, which suggests the current spheroid model can be used as an intermediate model for evaluation of co-delivery of anticancer compounds in targeted micelles. PMID:25016976

  2. 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.

  3. 360-degree 3D profilometry

    NASA Astrophysics Data System (ADS)

    Song, Yuanhe; Zhao, Hong; Chen, Wenyi; Tan, Yushan

    1997-12-01

    A new method of 360 degree turning 3D shape measurement in which light sectioning and phase shifting techniques are both used is presented in this paper. A sine light field is applied in the projected light stripe, meanwhile phase shifting technique is used to calculate phases of the light slit. Thereafter wrapped phase distribution of the slit is formed and the unwrapping process is made by means of the height information based on the light sectioning method. Therefore phase measuring results with better precision can be obtained. At last the target 3D shape data can be produced according to geometric relationships between phases and the object heights. The principles of this method are discussed in detail and experimental results are shown in this paper.

  4. Targeting Nonsquamous Nonsmall Cell Lung Cancer via the Proton-Coupled Folate Transporter with 6-Substituted Pyrrolo[2,3-d]Pyrimidine Thienoyl Antifolates.

    PubMed

    Wilson, Mike R; Hou, Zhanjun; Yang, Si; Polin, Lisa; Kushner, Juiwanna; White, Kathryn; Huang, Jenny; Ratnam, Manohar; Gangjee, Aleem; Matherly, Larry H

    2016-04-01

    Pemetrexed (PMX) is a 5-substituted pyrrolo[2,3-d]pyrimidine antifolate used for therapy of nonsquamous nonsmall cell lung cancer (NS-NSCLC). PMX is transported by the reduced folate carrier (RFC) and proton-coupled folate transporter (PCFT). Unlike RFC, PCFT is active at acidic pH levels characterizing the tumor microenvironment. By real-time reverse-transcription polymerase chain reaction (RT-PCR) and immunohistochemistry, PCFT transcripts and proteins were detected in primary NS-NSCLC specimens. In six NS-NSCLC cell lines (A549, H1437, H460, H1299, H1650, and H2030), PCFT transcripts and proteins were detected by real-time RT-PCR and western blots, respectively. 6-Substituted pyrrolo[2,3-d]pyrimidine thienoyl antifolates related to PMX [compound 1 (C1) and compound 2 (C2), respectively] are selective substrates for PCFT over RFC. In the NS-NSCLC cell lines, both [(3)H]PMX and [(3)H]C2 were transported by PCFT. C1 and C2 inhibited proliferation of the NS-NSCLC cell lines; A549, H460, and H2030 cells were more sensitive to C1 than to PMX. C1 and C2 inhibited glycinamide ribonucleotide formyltransferase in de novo purine nucleotide biosynthesis. When treated at pH 6.8, which favors PCFT uptake, C1 and C2 inhibited clonogenicity of H460 cells greater than PMX; PMX inhibited clonogenicity more than C1 or C2 at pH 7.2, which favors RFC transport over PCFT. Knockdown of PCFT in H460 cells resulted in decreased [(3)H]PMX and [(3)H]C2 transport and decreased growth inhibition by C1 and C2, and to a lesser extent by PMX. In vivo efficacy of C1 was seen toward H460 tumor xenografts in severe-combined immunodeficient mice. Our results suggest that 6-substituted pyrrolo[2,3-d]pyrimidine thienoyl antifolates offer significant promise for treating NS-NSCLC by selective uptake by PCFT. PMID:26837243

  5. Optimizing visual comfort for stereoscopic 3D display based on color-plus-depth signals.

    PubMed

    Shao, Feng; Jiang, Qiuping; Fu, Randi; Yu, Mei; Jiang, Gangyi

    2016-05-30

    Visual comfort is a long-facing problem in stereoscopic 3D (S3D) display. In this paper, targeting to produce S3D content based on color-plus-depth signals, a general framework for depth mapping to optimize visual comfort for S3D display is proposed. The main motivation of this work is to remap the depth range of color-plus-depth signals to a new depth range that is suitable to comfortable S3D display. Towards this end, we first remap the depth range globally based on the adjusted zero disparity plane, and then present a two-stage global and local depth optimization solution to solve the visual comfort problem. The remapped depth map is used to generate the S3D output. We demonstrate the power of our approach on perceptually uncomfortable and comfortable stereoscopic images. PMID:27410090

  6. Docking and 3D-QSAR (quantitative structure activity relationship) studies of flavones, the potent inhibitors of p-glycoprotein targeting the nucleotide binding domain.

    PubMed

    Kothandan, Gugan; Gadhe, Changdev G; Madhavan, Thirumurthy; Choi, Cheol Hee; Cho, Seung Joo

    2011-09-01

    In order to explore the interactions between flavones and P-gp, in silico methodologies such as docking and 3D-QSAR were performed. CoMFA and CoMSIA analyses were done using ligand based and receptor guided alignment schemes. Validation statistics include leave-one-out cross-validated R(2) (q(2)), internal prediction parameter by progressive scrambling (Q(*2)), external prediction with test set. They show that models derived from this study are quite robust. Ligand based CoMFA (q(2) = 0.747, Q(*2) = 0.639, r(pred)(2)=0.802) and CoMSIA model (q(2) = 0.810, Q(*2) = 0.676, r(pred)(2)=0.785) were developed using atom by atom matching. Receptor guided CoMFA (q(2) = 0.712, Q(*2) = 0.497, r(pred)(2) = 0.841) and for CoMSIA (q(2) = 0.805, Q(*2) = 0.589, r(pred)(2) = 0.937) models were developed by docking of highly active flavone into the proposed NBD (nucleotide binding domain) of P-gp. The 3D-QSAR models generated here predicted that hydrophobic and steric parameters are important for activity toward P-gp. Our studies indicate the important amino acid in NBD crucial for binding in accordance with the previous results. This site forms a hydrophobic site. Since flavonoids have potential without toxicity, we propose to inspect this hydrophobic site including Asn1043 and Asp1049 should be considered for future inhibitor design. PMID:21723648

  7. GPU-Accelerated Denoising in 3D (GD3D)

    2013-10-01

    The raw computational power GPU Accelerators enables fast denoising of 3D MR images using bilateral filtering, anisotropic diffusion, and non-local means. This software addresses two facets of this promising application: what tuning is necessary to achieve optimal performance on a modern GPU? And what parameters yield the best denoising results in practice? To answer the first question, the software performs an autotuning step to empirically determine optimal memory blocking on the GPU. To answer themore » second, it performs a sweep of algorithm parameters to determine the combination that best reduces the mean squared error relative to a noiseless reference image.« less

  8. 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.

  9. Design, synthesis, anti-tumor activity, and molecular modeling of quinazoline and pyrido[2,3-d]pyrimidine derivatives targeting epidermal growth factor receptor.

    PubMed

    Hou, Ju; Wan, Shanhe; Wang, Guangfa; Zhang, Tingting; Li, Zhonghuang; Tian, Yuanxin; Yu, Yonghuan; Wu, Xiaoyun; Zhang, Jiajie

    2016-08-01

    Three series of novel quinazoline and pyrido[2,3-d]pyrimidine derivatives were designed, synthesized and evaluated for their ability to inhibit EGFR tyrosine kinase and a panel of five human cancer cell lines (MCF-7, A549, BT-474, SK-BR-3, and MDA-MB-231). Bioassay results indicated that five of these prepared compounds (12c-12e and 13c-13d) exhibited remarkably higher inhibitory activities against EGFR and SK-BR-3 cell line. Compounds 12c and 12e displayed the most potent EGFR inhibitory activity (IC50 = 2.97 nM and 3.58 nM, respectively) and good anti-proliferative effect against SK-BR-3 cell with the IC50 values of 3.10 μM and 5.87 μM, respectively. Furthermore, molecular docking and molecular dynamics simulation studies verified that compound 12c and 12e shared similar binding pattern with gefitinib in the binding pocket of EGFR. MM-GBSA binding free energy revealed that the compound 12c and 12e have almost the same inhibitory activity against EGFR as gefitinib, and that the dominating effect of van der Waals interactions drives the binding process. PMID:27132165

  10. Targeting Fat: Mechanisms of Protein Localization to Lipid Droplets.

    PubMed

    Kory, Nora; Farese, Robert V; Walther, Tobias C

    2016-07-01

    How proteins specifically localize to the phospholipid monolayer surface of lipid droplets (LDs) is being unraveled. We review here the major known pathways of protein targeting to LDs and suggest a classification framework based on the localization origin for the protein. Class I proteins often have a membrane-embedded, hydrophobic 'hairpin' motif, and access LDs from the endoplasmic reticulum (ER) either during LD formation or after formation via ER-LD membrane bridges. Class II proteins access the LD surface from the cytosol and bind through amphipathic helices or other hydrophobic domains. Other proteins require lipid modifications or protein-protein interactions to bind to LDs. We summarize knowledge for targeting and removal of the different classes, and highlight areas needing investigation. PMID:26995697

  11. Targeted Broadband UVB Phototherapy forthe Treatment of Localized Vitiligo

    PubMed Central

    Kim, Jeong Eun

    2008-01-01

    Background Several new treatments appear to have higher success rates than previous therapies for the treatment of vitiligo, and targeted phototherapy is an alternative that may prove to be time-efficient and an effective therapeutic option for the management of this condition. Objective The aim of this study was to evaluate the efficacy of targeted broadband UVB phototherapy for the treatment of localized vitiligo. Methods Fifty-three vitiliginous patches on thirty-five patients (16 males, 19 females) were treated using a targeted broadband UVB phototherapy device. Treatment was started at 70% of the minimal erythema dose, and then gradually increased. Lesions were treated twice a week for a maximum of 60 treatment sessions. Results Subjects tolerated treatment well. Forty-one of the fifty-three patches (77.4%) achieved repigmentation on ≤75% of the treated areas. Best results were obtained on the face and neck; 20 of the 24 patches (83.3%) concerned achieved ≤75% repigmentation. The least response was on the hands and feet; 3 of 6 patches (50%) showed ≤75% repigmentation. The results were better for focal type than segmental type vitiligo. Conclusion Targeted broadband UVB phototherapy appears to be highly effective at restoring pigmentation in patients with localized vitiligo. PMID:27303172

  12. Late Cretaceous Localized Crustal Thickening as a Primary Control on the 3-D Architecture and Exhumation Histories of Cordilleran Metamorphic Core Complexes

    NASA Astrophysics Data System (ADS)

    Gans, P. B.; Wong, M.

    2014-12-01

    The juxtaposition of mylonitic mid-crustal rocks and faulted supracrustal rocks in metamorphic core complexes (MMCs) is usually portrayed in 2 dimensions and attributed to a single event of large-scale slip ± isostatic doming along a low-angle "detachment fault"/ shear zone. This paradigm does not explain dramatic along strike (3-D) variations in slip magnitude, footwall architecture, and burial / exhumation histories of most MMCs. A fundamental question posed by MMCs is how did their earlier thickening and exhumation histories influence the geometric evolution and 3-D slip distribution on the subsequent detachment faults? New geologic mapping and 40Ar/39Ar thermochronology from the Snake Range-Kern Mts-Deep Creek Mts (SKDC) complex in eastern Nevada offer important insights into this question. Crustal shortening and thickening by large-scale non-cylindrical recumbent folds and associated thrust faults during the late Cretaceous (90-80 Ma) resulted in deep burial (650°C, 20-25 km) of the central part of the footwall, but metamorphic grade decreases dramatically to the N and S in concert with decreasing amplitude on the shortening structures. Subsequent Paleogene extensional exhumation by normal faulting and ESE-directed mylonitic shearing is greatest in areas of maximum earlier thickening and brought highest grade rocks back to depths of~10-12 km. After ≥15 Ma of quiescence, rapid E-directed slip initiated along the brittle Miocene Snake Range detachment at 20 Ma and reactivated the Eocene shear zone. The ≥200°C gradient across the footwall at this time implies that the Miocene slip surface originated as a moderately E-dipping normal fault. This Miocene slip surface can be tracked for more than 100 km along strike, but the greatest amount of Miocene slip also coincides with parts of the footwall that were most deeply buried in the Cretaceous. These relations indicate that not only is the SKDC MMC a composite feature, but that the crustal welt created by

  13. TH-C-12A-11: Target Correlation of a 3D Surface Surrogate for Left Breast Irradiation Using the Respiratory-Gated Deep-Inspiration Breath-Hold Technique

    SciTech Connect

    Rong, Y; Walston, S

    2014-06-15

    Purpose: To evaluate the use of 3D optical surface imaging as a new surrogate for respiratory motion gated deep-inspiration breath-hold (DIBH) technique for left breast cancer patients. Methods: Patients with left-sided breast cancer after lumpectomy or mastectomy were selected as candidates for DIBH technique for their external beam radiation therapy. Treatment plans were created on both free breathing (FB) and DIBH CTs to determine whether DIBH was beneficial in reducing heart doses. The Real-time Position Management (RPM) system was used to acquire patient's breathing trace during DIBH CT acquisition and treatment delivery. The reference 3D surface models from FB and DIBH CTs were generated and transferred to the “AlignRT” system for patient positioning and real-time treatment monitoring. MV Cine images were acquired for each beam as quality assurance for intra-fractional position verification. The chest wall excursions measured on these images were used to define the actual target position during treatment, and to investigate the accuracy and reproducibility of RPM and AlignRT. Results: Reduction in heart dose can be achieved for left-sided breast patients using DIBH. Results showed that RPM has poor correlation with target position, as determined by the MV Cine imaging. This indicates that RPM may not be an adequate surrogate in defining the breath-hold level when used alone. Alternatively, the AlignRT surface imaging demonstrated a better correlation with the actual CW excursion during DIBH. Both the vertical and magnitude real-time deltas (RTDs) reported by AlignRT can be used as the gating parameter, with a recommend threshold of ±3 mm and 5 mm, respectively. Conclusion: 3D optical surface imaging serves as a superior target surrogate for the left breast treatment when compared to RPM. Working together with the realtime MV Cine imaging, they ensure accurate patient setup and dose delivery, while minimizing the imaging dose to patients.

  14. Measurement of 3-D Vibrational Motion by Dynamic Photogrammetry Using Least-Square Image Matching for Sub-Pixel Targeting to Improve Accuracy

    PubMed Central

    Lee, Hyoseong; Rhee, Huinam; Oh, Jae Hong; Park, Jin Ho

    2016-01-01

    This paper deals with an improved methodology to measure three-dimensional dynamic displacements of a structure by digital close-range photogrammetry. A series of stereo images of a vibrating structure installed with targets are taken at specified intervals by using two daily-use cameras. A new methodology is proposed to accurately trace the spatial displacement of each target in three-dimensional space. This method combines the correlation and the least-square image matching so that the sub-pixel targeting can be obtained to increase the measurement accuracy. Collinearity and space resection theory are used to determine the interior and exterior orientation parameters. To verify the proposed method, experiments have been performed to measure displacements of a cantilevered beam excited by an electrodynamic shaker, which is vibrating in a complex configuration with mixed bending and torsional motions simultaneously with multiple frequencies. The results by the present method showed good agreement with the measurement by two laser displacement sensors. The proposed methodology only requires inexpensive daily-use cameras, and can remotely detect the dynamic displacement of a structure vibrating in a complex three-dimensional defection shape up to sub-pixel accuracy. It has abundant potential applications to various fields, e.g., remote vibration monitoring of an inaccessible or dangerous facility. PMID:26978366

  15. Measurement of 3-D Vibrational Motion by Dynamic Photogrammetry Using Least-Square Image Matching for Sub-Pixel Targeting to Improve Accuracy.

    PubMed

    Lee, Hyoseong; Rhee, Huinam; Oh, Jae Hong; Park, Jin Ho

    2016-01-01

    This paper deals with an improved methodology to measure three-dimensional dynamic displacements of a structure by digital close-range photogrammetry. A series of stereo images of a vibrating structure installed with targets are taken at specified intervals by using two daily-use cameras. A new methodology is proposed to accurately trace the spatial displacement of each target in three-dimensional space. This method combines the correlation and the least-square image matching so that the sub-pixel targeting can be obtained to increase the measurement accuracy. Collinearity and space resection theory are used to determine the interior and exterior orientation parameters. To verify the proposed method, experiments have been performed to measure displacements of a cantilevered beam excited by an electrodynamic shaker, which is vibrating in a complex configuration with mixed bending and torsional motions simultaneously with multiple frequencies. The results by the present method showed good agreement with the measurement by two laser displacement sensors. The proposed methodology only requires inexpensive daily-use cameras, and can remotely detect the dynamic displacement of a structure vibrating in a complex three-dimensional defection shape up to sub-pixel accuracy. It has abundant potential applications to various fields, e.g., remote vibration monitoring of an inaccessible or dangerous facility. PMID:26978366

  16. 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.

  17. 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.

  18. Clinical applications of 3-D dosimeters

    NASA Astrophysics Data System (ADS)

    Wuu, Cheng-Shie

    2015-01-01

    Both 3-D gels and radiochromic plastic dosimeters, in conjunction with dose image readout systems (MRI or optical-CT), have been employed to measure 3-D dose distributions in many clinical applications. The 3-D dose maps obtained from these systems can provide a useful tool for clinical dose verification for complex treatment techniques such as IMRT, SRS/SBRT, brachytherapy, and proton beam therapy. These complex treatments present high dose gradient regions in the boundaries between the target and surrounding critical organs. Dose accuracy in these areas can be critical, and may affect treatment outcome. In this review, applications of 3-D gels and PRESAGE dosimeter are reviewed and evaluated in terms of their performance in providing information on clinical dose verification as well as commissioning of various treatment modalities. Future interests and clinical needs on studies of 3-D dosimetry are also discussed.

  19. 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

  20. Localization of Transcranial Targets for Photoacoustic-Guided Endonasal Surgeries

    PubMed Central

    Lediju Bell, Muyinatu A.; Ostrowski, Anastasia K.; Li, Ke; Kazanzides, Peter; Boctor, Emad M.

    2015-01-01

    Neurosurgeries to remove pituitary tumors using the endonasal, transsphenoidal approach often incur the risk of patient death caused by injury to the carotid arteries hidden by surrounding sphenoid bone. To avoid this risk, we propose intraoperative photoacoustic vessel visualization with an optical fiber attached to the surgical tool and an external ultrasound transducer placed on the temple. Vessel detection accuracy is limited by acoustic propagation properties, which were investigated with k-Wave simulations. In a two-layer model of temporal bone (3200 m/s sound speed, 1-4 mm thickness) and surrounding tissues, the localization error was ≤2 mm in the tranducer's axial dimension, while temporal bone curvature further degraded target localization. Phantom experiments revealed that multiple image targets (e.g. sphenoid bone and vessels) can be visualized, particularly with coherence-based beamforming, to determine tool-to-vessel proximity despite expected localization errors. In addition, the potential flexibility of the fiber position relative to the transducer and vessel was elucidated. PMID:26236644

  1. Localization of Transcranial Targets for Photoacoustic-Guided Endonasal Surgeries.

    PubMed

    Lediju Bell, Muyinatu A; Ostrowski, Anastasia K; Li, Ke; Kazanzides, Peter; Boctor, Emad M

    2015-06-01

    Neurosurgeries to remove pituitary tumors using the endonasal, transsphenoidal approach often incur the risk of patient death caused by injury to the carotid arteries hidden by surrounding sphenoid bone. To avoid this risk, we propose intraoperative photoacoustic vessel visualization with an optical fiber attached to the surgical tool and an external ultrasound transducer placed on the temple. Vessel detection accuracy is limited by acoustic propagation properties, which were investigated with k-Wave simulations. In a two-layer model of temporal bone (3200 m/s sound speed, 1-4 mm thickness) and surrounding tissues, the localization error was ≤2 mm in the tranducer's axial dimension, while temporal bone curvature further degraded target localization. Phantom experiments revealed that multiple image targets (e.g. sphenoid bone and vessels) can be visualized, particularly with coherence-based beamforming, to determine tool-to-vessel proximity despite expected localization errors. In addition, the potential flexibility of the fiber position relative to the transducer and vessel was elucidated. PMID:26236644

  2. Intensity-Modulated Radiation Therapy Versus 3D Conformal Radiotherapy for Postoperative Gynecologic Cancer: Are They Covering the Same Planning Target Volume?

    PubMed Central

    Patil, Nikhilesh; D'souza, David; Millman, Barbara; Yaremko, Brian P; Leung, Eric; Whiston, Frances; Hajdok, George; Wong, Eugene

    2016-01-01

    Background and Purpose: This study compares dosimetric parameters of planning target volume (PTV) coverage and organs at risk (OAR) sparing when postoperative radiotherapy for gynecologic cancers is delivered using volumetric modulated arc therapy (VMAT) versus a four-field (4FLD) box technique. Material and Methods: From July to December 2012, women requiring postoperative radiation for gynecologic cancers were treated with a standardized VMAT protocol. Two sets of optimized 4FLD plans were retrospectively generated: one based on standard anatomical borders (4FLD) and one based on the clinical target volume (CTV) created for VMAT with a 2 cm expansion guiding field border placement (4FLD+2). Ninety-five percent isodose curves were generated to evaluate PTV coverage. Results: VMAT significantly improved dose conformity compared with 4FLD and 4FLD+2 plans (p < 0.001) and provided additional coverage of the PTV posteriorly and superiorly, corresponding to coverage of the presacral and proximal iliac vessels. There was a significant reduction in dose to all OARs with VMAT, including a 58% reduction in the volume of the small bowel receiving more than 45 Gy (p=0.005). Conclusions: Despite treating a larger volume, radiotherapy using a 4FLD technique is less homogenous and provides inferior coverage of the PTV compared with VMAT. With meticulous treatment planning and delivery, VMAT effectively encompasses the PTV and minimizes dose to OARs. PMID:26973802

  3. Stereotactic mammography imaging combined with 3D US imaging for image guided breast biopsy

    SciTech Connect

    Surry, K. J. M.; Mills, G. R.; Bevan, K.; Downey, D. B.; Fenster, A.

    2007-11-15

    Stereotactic X-ray mammography (SM) and ultrasound (US) guidance are both commonly used for breast biopsy. While SM provides three-dimensional (3D) targeting information and US provides real-time guidance, both have limitations. SM is a long and uncomfortable procedure and the US guided procedure is inherently two dimensional (2D), requiring a skilled physician for both safety and accuracy. The authors developed a 3D US-guided biopsy system to be integrated with, and to supplement SM imaging. Their goal is to be able to biopsy a larger percentage of suspicious masses using US, by clarifying ambiguous structures with SM imaging. Features from SM and US guided biopsy were combined, including breast stabilization, a confined needle trajectory, and dual modality imaging. The 3D US guided biopsy system uses a 7.5 MHz breast probe and is mounted on an upright SM machine for preprocedural imaging. Intraprocedural targeting and guidance was achieved with real-time 2D and near real-time 3D US imaging. Postbiopsy 3D US imaging allowed for confirmation that the needle was penetrating the target. The authors evaluated 3D US-guided biopsy accuracy of their system using test phantoms. To use mammographic imaging information, they registered the SM and 3D US coordinate systems. The 3D positions of targets identified in the SM images were determined with a target localization error (TLE) of 0.49 mm. The z component (x-ray tube to image) of the TLE dominated with a TLE{sub z} of 0.47 mm. The SM system was then registered to 3D US, with a fiducial registration error (FRE) and target registration error (TRE) of 0.82 and 0.92 mm, respectively. Analysis of the FRE and TRE components showed that these errors were dominated by inaccuracies in the z component with a FRE{sub z} of 0.76 mm and a TRE{sub z} of 0.85 mm. A stereotactic mammography and 3D US guided breast biopsy system should include breast compression for stability and safety and dual modality imaging for target localization

  4. The impact of non-local buoyancy flux on the convective boundary layer development as simulated by a 3-D TKE-based subgrid mixing scheme in a mesoscale model

    NASA Astrophysics Data System (ADS)

    Zhang, Xu; Bao, Jian-Wen; Chen, Baode

    2016-04-01

    This presentation highlights a study in which a series of dry convective boundary layer (CBL) simulations are carried out using a generalized 3-dimensional (3-D) TKE-based parameterization scheme of sub-grid turbulent mixing in the Weather Research and Forecasting (WRF) model. The simulated characteristics of dry CBL are analyzed for the purpose of evaluating this scheme in comparison with a commonly-used scheme for sub-grid turbulent mixing in NWP models (i.e., the Mellor-Yamada 1.5-order TKE scheme). The same surface layer scheme is used in all the simulations so that only the sensitivity of the WRF model to different parameterizations of the sub-grid turbulent mixing above the surface layer is examined. The effect of horizontal grid resolution on the simulated CBL is also examined by running the model with grid sizes of 200, 400 m, 600 m, 1 km and 3 km. We will first compare the characteristics of the simulated CBL using the two schemes with the WRF LES dataset. We will then illustrate the importance of including the non-local component in the vertical buoyancy specification in the 3-D TKE-based scheme. Finally, comparing the results from the simulations against coarse-grained WRF LES dataset, we will show the feasibility and advantage of replacing conventional planetary boundary layer parameterization schemes with a scale-aware 3-D TKE-based scheme in the WRF model.

  5. Local site-effects for the city of Thessaloniki (N. Greece) using a 3-D finite-difference method: a case of complex dependence on source and model parameters

    NASA Astrophysics Data System (ADS)

    Skarlatoudis, A. A.; Papazachos, C. B.; Theodoulidis, N.; Kristek, J.; Moczo, P.

    2010-07-01

    The site effects of seismic motion in the metropolitan area of the city of Thessaloniki (Northern Greece) are investigated using a 3-D finite-difference modelling approach. Three different seismic scenarios are assumed with two different focal mechanisms for each one. Standard spectral ratios (SSR) are calculated from 3-D synthetics and compared with the ratios from the recorded motion, as well as ratios obtained from 1-D and 2-D modelling by other researchers. The average SSR curves from the six scenarios are in good agreement with the empirical ones, whereas the SSR results from 3-D modelling are different from those from 1-D modelling, exhibiting higher fundamental frequencies and larger amplification amplitudes, in much better agreement with observed SSR ratios. Comparisons of Fourier amplitude spectra obtained for various scenarios for the broader area of Thessaloniki show considerable dependence of the site effects on the source properties (position, depth and fault-plane solution), as well as on the local structure.

  6. Problem-dependent 3-d Inversion of P-wave Arrivals From Local Events Recorded During The Svekalapko Deep Seismic Experiment In Finland

    NASA Astrophysics Data System (ADS)

    Kozlovskaya, E.; Hjelt, S.-E.; Yliniemi, J.; Korhonen, J.; Elo, S.; Svekalapko Seismic Tomography Working Group

    The SVEKALAPKO temporary seismic array was originally designed for studying the lithospheric structure beneath the southern Finland by means of teleseismic events. In addition, the high quality recordings of local seismic events (earthquakes and quarry blasts) registered by the SVEKALAPKO array contain a lot of information about the structure of the upper lithosphere beneath the southern Finland. However, the traditional local event tomography of SVEKALAPKO data cannot result in the ve- locity model valid for proper geological interpretation. The main reasons for this is the lack of the space resolution, which results in strong non-uniqueness of the to- mographic inversion. This problem can be treated by introducing various kinds of a-priori information into the inversion algorithm. The a-priori information available for the SVEKALAPKO study area includes not only the information from previous control source seismic experiments, but also potential fields data and petrophysical data. Usage of such a non-homogeneous a-priori information required a problem- dependent algorithm of seismic data inversion, which was developed on the base of non-probabilistic uncertainty measures. An example of this algorithm application to SVEKALAPKO local seismic event data is presented.

  7. Infrared target recognition based on improved joint local ternary pattern

    NASA Astrophysics Data System (ADS)

    Sun, Junding; Wu, Xiaosheng

    2016-05-01

    This paper presents a simple, efficient, yet robust approach, named joint orthogonal combination of local ternary pattern, for automatic forward-looking infrared target recognition. It gives more advantages to describe the macroscopic textures and microscopic textures by fusing variety of scales than the traditional LBP-based methods. In addition, it can effectively reduce the feature dimensionality. Further, the rotation invariant and uniform scheme, the robust LTP, and soft concave-convex partition are introduced to enhance its discriminative power. Experimental results demonstrate that the proposed method can achieve competitive results compared with the state-of-the-art methods.

  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. Multiple-input multiple-output 3D imaging laser radar

    NASA Astrophysics Data System (ADS)

    Liu, Chunbo; Wu, Chao; Han, Xiang'e.

    2015-10-01

    A 3D (angle-angle-range) imaging laser radar (LADAR) based on multiple-input multiple-output structure is proposed. In the LADAR, multiple coherent beams are randomly phased to form the structured light field and an APD array detector is utilized to receive the echoes from target. The sampled signals from each element of APD are correlated with the referenced light to reconstruct the local 3D images of target. The 3D panorama of target can be obtained by stitching the local images of all the elements. The system composition is described first, then the operation principle is presented and numerical simulations are provided to show the validity of the proposed scheme.

  12. Charge-compensation in 3d-transition-metal-oxide intercalation cathodes through the generation of localized electron holes on oxygen.

    PubMed

    Luo, Kun; Roberts, Matthew R; Hao, Rong; Guerrini, Niccoló; Pickup, David M; Liu, Yi-Sheng; Edström, Kristina; Guo, Jinghua; Chadwick, Alan V; Duda, Laurent C; Bruce, Peter G

    2016-07-01

    During the charging and discharging of lithium-ion-battery cathodes through the de- and reintercalation of lithium ions, electroneutrality is maintained by transition-metal redox chemistry, which limits the charge that can be stored. However, for some transition-metal oxides this limit can be broken and oxygen loss and/or oxygen redox reactions have been proposed to explain the phenomenon. We present operando mass spectrometry of (18)O-labelled Li1.2[Ni0.13(2+)Co0.13(3+)Mn0.54(4+)]O2, which demonstrates that oxygen is extracted from the lattice on charging a Li1.2[Ni0.13(2+)Co0.13(3+)Mn0.54(4+)]O2 cathode, although we detected no O2 evolution. Combined soft X-ray absorption spectroscopy, resonant inelastic X-ray scattering spectroscopy, X-ray absorption near edge structure spectroscopy and Raman spectroscopy demonstrates that, in addition to oxygen loss, Li(+) removal is charge compensated by the formation of localized electron holes on O atoms coordinated by Mn(4+) and Li(+) ions, which serve to promote the localization, and not the formation, of true O2(2-) (peroxide, O-O ~1.45 Å) species. The quantity of charge compensated by oxygen removal and by the formation of electron holes on the O atoms is estimated, and for the case described here the latter dominates. PMID:27325095

  13. Monte-Carlo Simulation of Heavy Ion Track Structure Calculation of Local Dose and 3D Time Evolution of Radiolytic Species

    NASA Technical Reports Server (NTRS)

    Plante, Ianik; Cucinotta, Francis A.

    2010-01-01

    Heavy ions have gained considerable importance in radiotherapy due to their advantageous dose distribution profile and high Relative Biological Effectiveness (RBE). Heavy ions are difficult to produce on Earth, but they are present in space and it is impossible at this moment to completely shield astronauts from them. The risk of these radiations is poorly understood, which is a concern for a 3-years Mars mission. The effects of radiation are mainly due to DNA damage such as DNA double-strand breaks (DSBs), although non-targeted effects are also very important. DNA can be damaged by the direct interaction of radiation and by reactions with chemical species produced by the radiolysis of water. The energy deposition is of crucial importance to understand biological effects of radiation. Therefore, much effort has been done recently to improve models of radiation tracks.

  14. Measurements of Polarization Transfers in Real Compton Scattering by a proton target at JLAB. A new source of information on the 3D shape of the nucleon

    SciTech Connect

    Fanelli, Cristiano V.

    2015-03-01

    In this thesis work, results of the analysis of the polarization transfers measured in real Compton scattering (RCS) by the Collaboration E07-002 at the Je fferson Lab Hall-C are presented. The data were collected at large scattering angle (theta_cm = 70deg) and with a polarized incident photon beam at an average energy of 3.8 GeV. Such a kind of experiments allows one to understand more deeply the reaction mechanism, that involves a real photon, by extracting both Compton form factors and Generalized Parton Distributions (GPDs) (also relevant for possibly shedding light on the total angular momentum of the nucleon). The obtained results for the longitudinal and transverse polarization transfers K_LL and K_LT, are of crucial importance, since they confirm unambiguously the disagreement between experimental data and pQCD prediction, as it was found in E99-114 experiment, and favor the Handbag mechanism. The E99-114 and E07-002 results can contribute to attract new interest on the great yield of the Compton scattering by a nucleon target, as demonstrated by the recent approval of an experimental proposal submitted to the Jefferson Lab PAC 42 for a Wide-angle Compton Scattering experiment, at 8 and 10 GeV Photon Energies. The new experiments approved to run with the updated 12 GeV electron beam at JLab, are characterized by much higher luminosities, and a new GEM tracker is under development to tackle the challenging backgrounds. Within this context, we present a new multistep tracking algorithm, based on (i) a Neural Network (NN) designed for a fast and efficient association of the hits measured by the GEM detector which allows the track identification, and (ii) the application of both a Kalman filter and Rauch-Tung-Striebel smoother to further improve the track reconstruction. The full procedure, i.e. NN and filtering, appears very promising, with high performances in terms of both association effciency and reconstruction accuracy, and these preliminary results will

  15. Angular description for 3D scattering centers

    NASA Astrophysics Data System (ADS)

    Bhalla, Rajan; Raynal, Ann Marie; Ling, Hao; Moore, John; Velten, Vincent J.

    2006-05-01

    The electromagnetic scattered field from an electrically large target can often be well modeled as if it is emanating from a discrete set of scattering centers (see Fig. 1). In the scattering center extraction tool we developed previously based on the shooting and bouncing ray technique, no correspondence is maintained amongst the 3D scattering center extracted at adjacent angles. In this paper we present a multi-dimensional clustering algorithm to track the angular and spatial behaviors of 3D scattering centers and group them into features. The extracted features for the Slicy and backhoe targets are presented. We also describe two metrics for measuring the angular persistence and spatial mobility of the 3D scattering centers that make up these features in order to gather insights into target physics and feature stability. We find that features that are most persistent are also the most mobile and discuss implications for optimal SAR imaging.

  16. 3D acoustic atmospheric tomography

    NASA Astrophysics Data System (ADS)

    Rogers, Kevin; Finn, Anthony

    2014-10-01

    This paper presents a method for tomographically reconstructing spatially varying 3D atmospheric temperature profiles and wind velocity fields based. Measurements of the acoustic signature measured onboard a small Unmanned Aerial Vehicle (UAV) are compared to ground-based observations of the same signals. The frequency-shifted signal variations are then used to estimate the acoustic propagation delay between the UAV and the ground microphones, which are also affected by atmospheric temperature and wind speed vectors along each sound ray path. The wind and temperature profiles are modelled as the weighted sum of Radial Basis Functions (RBFs), which also allow local meteorological measurements made at the UAV and ground receivers to supplement any acoustic observations. Tomography is used to provide a full 3D reconstruction/visualisation of the observed atmosphere. The technique offers observational mobility under direct user control and the capacity to monitor hazardous atmospheric environments, otherwise not justifiable on the basis of cost or risk. This paper summarises the tomographic technique and reports on the results of simulations and initial field trials. The technique has practical applications for atmospheric research, sound propagation studies, boundary layer meteorology, air pollution measurements, analysis of wind shear, and wind farm surveys.

  17. Automatic needle segmentation in 3D ultrasound images using 3D Hough transform

    NASA Astrophysics Data System (ADS)

    Zhou, Hua; Qiu, Wu; Ding, Mingyue; Zhang, Songgeng

    2007-12-01

    3D ultrasound (US) is a new technology that can be used for a variety of diagnostic applications, such as obstetrical, vascular, and urological imaging, and has been explored greatly potential in the applications of image-guided surgery and therapy. Uterine adenoma and uterine bleeding are the two most prevalent diseases in Chinese woman, and a minimally invasive ablation system using an RF button electrode which is needle-like is being used to destroy tumor cells or stop bleeding currently. Now a 3D US guidance system has been developed to avoid accidents or death of the patient by inaccurate localizations of the electrode and the tumor position during treatment. In this paper, we described two automated techniques, the 3D Hough Transform (3DHT) and the 3D Randomized Hough Transform (3DRHT), which is potentially fast, accurate, and robust to provide needle segmentation in 3D US image for use of 3D US imaging guidance. Based on the representation (Φ , θ , ρ , α ) of straight lines in 3D space, we used the 3DHT algorithm to segment needles successfully assumed that the approximate needle position and orientation are known in priori. The 3DRHT algorithm was developed to detect needles quickly without any information of the 3D US images. The needle segmentation techniques were evaluated using the 3D US images acquired by scanning water phantoms. The experiments demonstrated the feasibility of two 3D needle segmentation algorithms described in this paper.

  18. SU-C-213-07: Fabrication and Testing of a 3D-Printed Small Animal Rectal Cooling Device to Evaluate Local Hypothermia as a Radioprotector During Prostate SBRT

    SciTech Connect

    Hrycushko, B; Chopra, R; Futch, C; Bing, C; Wodzak, M; Stojadinovic, S; Jiang, S; Medin, P

    2015-06-15

    Purpose: The protective effects of induced or even accidental hypothermia on the human body are widespread with several medical uses currently under active research. In vitro experiments using human cell lines have shown hypothermia provides a radioprotective effect that becomes more pronounced at large, single-fraction doses common to SBRT treatments. Relevant to prostate SBRT, this work details the fabrication and testing of a 3D-printed cooling device to facilitate the investigation of the radioprotective effect of local hypothermia on the rat rectum. Methods: A 3cm long, two-channel rectal cooling device was designed in SOLIDWORKS CAD for 3D printing. The water intake nozzle is connected to a 1mm diameter brass pipe from which water flows and circulates back around to the exit nozzle. Both nozzles are connected by plastic tubing to a water chiller pump. Following leak-proof testing, fiber optic temperature probes were used to evaluate the temperature over time when placed adjacent to the cooling device within a rat rectum. MRI thermometry characterized the relative temperature distribution in concentric ROIs surrounding the probe. CBCT images from a small-animal irradiator were evaluated for imaging artifacts which could affect Monte Carlo dose calculations during treatment planning. Results: The rectal temperature adjacent to the cooling device decreased from body temperature (37°C) to 15°C in 10–20 minutes from device insertion. Rectal temperature was maintained at 15±3°C during active cooling. MRI thermometry tests revealed a steep temperature gradient with increasing distance from the cooling device, with the desired temperature range maintained within the surrounding few millimeters. Conclusion: A 3D printed rectal cooling device was fabricated for the purpose of inducing local hypothermia in rat rectums. Rectal cooling capabilities were characterized in-vivo to facilitate an investigation of the radioprotective effect of hypothermia for late rectal

  19. 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

  20. The role of the vestibular system in manual target localization

    NASA Technical Reports Server (NTRS)

    Barry, Susan R.; Mueller, S. Alyssa

    1995-01-01

    Astronauts experience perceptual and sensory-motor disturbances during spaceflight and immediately after return to the 1-g environment of Earth. During spaceflight, sensory information from the eyes, limbs and vestibular organs is reinterpreted by the central nervous system so that astronauts can produce appropriate body movements in microgravity. Alterations in sensory-motor function may affect eye-head-hand coordination and, thus, the crewmember's ability to manually locate objects in extrapersonal space. Previous reports have demonstrated that crewmembers have difficulty in estimating joint and limb position and in pointing to memorized target positions on orbit and immediately postflight. One set of internal cues that may assist in the manual localization of objects is information from the vestibular system. This system contributes to our sense of the body's position in space by providing information on head position and movement and the orientation of the body with respect to gravity. Research on the vestibular system has concentrated on its role in oculo-motor control. Little is known about the role that vestibular information plays in manual motor control, such as reaching and pointing movements. Since central interpretation of vestibular information is altered in microgravity, it is important to determine its role in this process. This summer, we determined the importance of vestibular information in a subject's ability to point accurately toward a target in extrapersonal space. Subjects were passively rotated across the earth-vertical axis and then asked to point back to a previously-seen target. In the first paradigm, the subjects used both visual and vestibular cues for the pointing response, while, in the second paradigm, subjects used only vestibular information. Subjects were able to point with 85 percent accuracy to a target using vestibular information alone. We infer from this result that vestibular input plays a role in the spatial programming of

  1. 3D local structure around copper site of rabbit prion-related protein: Quantitative determination by XANES spectroscopy combined with multiple-scattering calculations

    NASA Astrophysics Data System (ADS)

    Cui, P. X.; Lian, F. L.; Wang, Y.; Wen, Yi; Chu, W. S.; Zhao, H. F.; Zhang, S.; Li, J.; Lin, D. H.; Wu, Z. Y.

    2014-02-01

    Prion-related protein (PrP), a cell-surface copper-binding glycoprotein, is considered to be responsible for a number of transmissible spongiform encephalopathies (TSEs). The structural conversion of PrP from the normal cellular isoform (PrPC) to the post-translationally modified form (PrPSc) is thought to be relevant to Cu2+ binding to histidine residues. Rabbits are one of the few mammalian species that appear to be resistant to TSEs, because of the structural characteristics of the rabbit prion protein (RaPrPC) itself. Here we determined the three-dimensional local structure around the C-terminal high-affinity copper-binding sites using X-ray absorption near-edge structure combined with ab initio calculations in the framework of the multiple-scattering (MS) theory. Result shows that two amino acid resides, Gln97 and Met108, and two histidine residues, His95 and His110, are involved in binding this copper(II) ion. It might help us understand the roles of copper in prion conformation conversions, and the molecular mechanisms of prion-involved diseases.

  2. 3-D transient analysis of pebble-bed HTGR by TORT-TD/ATTICA3D

    SciTech Connect

    Seubert, A.; Sureda, A.; Lapins, J.; Buck, M.; Bader, J.; Laurien, E.

    2012-07-01

    As most of the acceptance criteria are local core parameters, application of transient 3-D fine mesh neutron transport and thermal hydraulics coupled codes is mandatory for best estimate evaluations of safety margins. This also applies to high-temperature gas cooled reactors (HTGR). Application of 3-D fine-mesh transient transport codes using few energy groups coupled with 3-D thermal hydraulics codes becomes feasible in view of increasing computing power. This paper describes the discrete ordinates based coupled code system TORT-TD/ATTICA3D that has recently been extended by a fine-mesh diffusion solver. Based on transient analyses for the PBMR-400 design, the transport/diffusion capabilities are demonstrated and 3-D local flux and power redistribution effects during a partial control rod withdrawal are shown. (authors)

  3. 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

  4. Transition from a localized to wide deformation along Eastern branch of Central East African Rift: Insights from 3D numerical models

    NASA Astrophysics Data System (ADS)

    Leroy, S. D.; Koptev, A.; Burov, E. B.; Calais, E.; Gerya, T.

    2015-12-01

    The Central East African Rift (CEAR) bifurcates in two branches (eastern, magma-rich and western, magma-poor) surrounding strong Tanzanian craton. Intensive magmatism and continental flood basalts are largely present in many of the eastern rift segments, but other segments, first of all the western branch, exhibit very small volcanic activity. The Eastern rift is characterized by southward progression of the onset of volcanism, the extensional features and topographic expression of the rift vary significantly north-southward: in northern Kenya the deformation is very wide (some 150-250 km in E-W direction), to the south the rift narrows to 60-70 km, yet further to the south the deformation widens again in the so-called Tanzania divergence zone. Widening of the Eastern branch within its southern part is associated with the impingement of the southward-propagating rift on the strong Masai block situated to east of the Tanzanian craton. To understand the mechanisms behind this complex deformation distribution, we implemented a 3Dl ultra-high resolution visco-plastic thermo-mechanical numerical model accounting for thermo-rheological structure of the lithosphere and hence captures essential features of the CEAR. The preferred model has a plume seeded slightly to the northeast of the craton center, consistent with seismic tomography, and produces surface strain distribution that is in good agreement with observed variation of deformation zone width along eastern side of Tanzanian craton: localized above bulk of mantle material deflected by cratonic keel narrow high strain zone (Kenia Rift) is replaced by wide distributed deformations within areas situated to north (northern Kenya, Turkana Rift) and to south (Tanzania divergence, Masai block) of it. These results demonstrate significant differences in the impact of the rheological profile on rifting style in case of dominant active rifting compared to dominant passive rifting. Narrow rifting, conventionally attributed to

  5. Non-Invasive Targeted Peripheral Nerve Ablation Using 3D MR Neurography and MRI-Guided High-Intensity Focused Ultrasound (MR-HIFU): Pilot Study in a Swine Model

    PubMed Central

    Huisman, Merel; Staruch, Robert M.; Ladouceur-Wodzak, Michelle; van den Bosch, Maurice A.; Burns, Dennis K.; Chhabra, Avneesh; Chopra, Rajiv

    2015-01-01

    Purpose Ultrasound (US)-guided high intensity focused ultrasound (HIFU) has been proposed for noninvasive treatment of neuropathic pain and has been investigated in in-vivo studies. However, ultrasound has important limitations regarding treatment guidance and temperature monitoring. Magnetic resonance (MR)-imaging guidance may overcome these limitations and MR-guided HIFU (MR-HIFU) has been used successfully for other clinical indications. The primary purpose of this study was to evaluate the feasibility of utilizing 3D MR neurography to identify and guide ablation of peripheral nerves using a clinical MR-HIFU system. Methods Volumetric MR-HIFU was used to induce lesions in the peripheral nerves of the lower limbs in three pigs. Diffusion-prep MR neurography and T1-weighted images were utilized to identify the target, plan treatment and immediate post-treatment evaluation. For each treatment, one 8 or 12 mm diameter treatment cell was used (sonication duration 20 s and 36 s, power 160–300 W). Peripheral nerves were extracted < 3 hours after treatment. Ablation dimensions were calculated from thermal maps, post-contrast MRI and macroscopy. Histological analysis included standard H&E staining, Masson’s trichrome and toluidine blue staining. Results All targeted peripheral nerves were identifiable on MR neurography and T1-weighted images and could be accurately ablated with a single exposure of focused ultrasound, with peak temperatures of 60.3 to 85.7°C. The lesion dimensions as measured on MR neurography were similar to the lesion dimensions as measured on CE-T1, thermal dose maps, and macroscopy. Histology indicated major hyperacute peripheral nerve damage, mostly confined to the location targeted for ablation. Conclusion Our preliminary results indicate that targeted peripheral nerve ablation is feasible with MR-HIFU. Diffusion-prep 3D MR neurography has potential for guiding therapy procedures where either nerve targeting or avoidance is desired, and may

  6. The Design and Discovery of Water Soluble 4-Substituted-2,6-dimethylfuro[2,3-d]pyrimidines as Multitargeted Receptor Tyrosine Kinase Inhibitors and Microtubule Targeting Antitumor Agents

    PubMed Central

    Zhang, Xin; Raghavan, Sudhir; Ihnat, Michael; Thorpe, Jessica E.; Disch, Bryan C.; Bastian, Anja; Bailey-Downs, Lora C.; Dybdal-Hargreaves, Nicholas F.; Rohena, Cristina C.; Hamel, Ernest; Mooberry, Susan L.; Gangjee, Aleem

    2014-01-01

    The design, synthesis and biological evaluations of fourteen 4-substituted 2,6-dimethylfuro[2,3-d]pyrimidines are reported. Four compounds (11–13, 15) inhibit vascular endothelial growth factor receptor-2 (VEGFR-2), platelet-derived growth factor receptor β (PDGFR-β), and target tubulin leading to cytotoxicity. Compound 11 has nanomolar potency, comparable to sunitinib and semaxinib, against tumor cell lines overexpressing VEGFR-2 and PDGFR-β. Further, 11 binds at the colchicine site on tubulin, depolymerizes cellular microtubules and inhibits purified tubulin assembly and overcomes both βIII-tubulin and P-glycoprotein-mediated drug resistance, and initiates mitotic arrest leading to apoptosis. In vivo, its HCl salt, 21, reduced tumor size and vascularity in xenograft and allograft murine models and was superior to docetaxel and sunitinib, without overt toxicity. Thus 21 affords potential combination chemotherapy in a single agent. PMID:24890652

  7. Additively Manufactured 3D Porous Ti-6Al-4V Constructs Mimic Trabecular Bone Structure and Regulate Osteoblast Proliferation, Differentiation and Local Factor Production in a Porosity and Surface Roughness Dependent Manner

    PubMed Central

    Cheng, Alice; Humayun, Aiza; Cohen, David J.; Boyan, Barbara D.; Schwartz, Zvi

    2014-01-01

    Additive manufacturing by laser sintering is able to produce high resolution metal constructs for orthopaedic and dental implants. In this study, we used a human trabecular bone template to design and manufacture Ti-6Al-4V constructs with varying porosity via laser sintering. Characterization of constructs revealed interconnected porosities ranging from 15–70% with compressive moduli of 2063–2954 MPa. These constructs with macro porosity were further surface-treated to create a desirable multi-scale micro-/nano-roughness, which has been shown to enhance the osseointegration process. Osteoblasts (MG63 cells) exhibited high viability when grown on the constructs. Proliferation (DNA) and alkaline phosphatase specific activity (ALP), an early differentiation marker, decreased as porosity increased, while osteocalcin (OCN), a late differentiation marker, as well as osteoprotegerin (OPG), vascular endothelial growth factor (VEGF) and bone morphogenetic proteins 2 and 4 (BMP2, BMP4) increased with increasing porosity. 3D constructs with the highest porosity and surface modification supported the greatest osteoblast differentiation and local factor production. These results indicate that additively manufactured 3D porous constructs mimicking human trabecular bone and produced with additional surface treatment can be customized for increased osteoblast response. Increased factors for osteoblast maturation and differentiation on high porosity constructs suggest the enhanced performance of these surfaces for increasing osseointegration in vivo. PMID:25287305

  8. 3D Printing Multi-Functionality: Embedded RF Antennas and Components

    NASA Technical Reports Server (NTRS)

    Shemelya, C. M.; Zemba, M.; Liang, M.; Espalin, D.; Kief, C.; Xin, H.; Wicker, R. B.; MacDonald, E. W.

    2015-01-01

    Significant research and press has recently focused on the fabrication freedom of Additive Manufacturing (AM) to create both conceptual models and final end-use products. This flexibility allows design modifications to be immediately reflected in 3D printed structures, creating new paradigms within the manufacturing process. 3D printed products will inevitably be fabricated locally, with unit-level customization, optimized to unique mission requirements. However, for the technology to be universally adopted, the processes must be enhanced to incorporate additional technologies; such as electronics, actuation, and electromagnetics. Recently, a novel 3D printing platform, Multi3D manufacturing, was funded by the presidential initiative for revitalizing manufacturing in the USA using 3D printing (America Makes - also known as the National Additive Manufacturing Innovation Institute). The Multi3D system specifically targets 3D printed electronics in arbitrary form; and building upon the potential of this system, this paper describes RF antennas and components fabricated through the integration of material extrusion 3D printing with embedded wire, mesh, and RF elements.

  9. Assessing 3d Photogrammetry Techniques in Craniometrics

    NASA Astrophysics Data System (ADS)

    Moshobane, M. C.; de Bruyn, P. J. N.; Bester, M. N.

    2016-06-01

    Morphometrics (the measurement of morphological features) has been revolutionized by the creation of new techniques to study how organismal shape co-varies with several factors such as ecophenotypy. Ecophenotypy refers to the divergence of phenotypes due to developmental changes induced by local environmental conditions, producing distinct ecophenotypes. None of the techniques hitherto utilized could explicitly address organismal shape in a complete biological form, i.e. three-dimensionally. This study investigates the use of the commercial software, Photomodeler Scanner® (PMSc®) three-dimensional (3D) modelling software to produce accurate and high-resolution 3D models. Henceforth, the modelling of Subantarctic fur seal (Arctocephalus tropicalis) and Antarctic fur seal (Arctocephalus gazella) skulls which could allow for 3D measurements. Using this method, sixteen accurate 3D skull models were produced and five metrics were determined. The 3D linear measurements were compared to measurements taken manually with a digital caliper. In addition, repetitive measurements were recorded by varying researchers to determine repeatability. To allow for comparison straight line measurements were taken with the software, assuming that close accord with all manually measured features would illustrate the model's accurate replication of reality. Measurements were not significantly different demonstrating that realistic 3D skull models can be successfully produced to provide a consistent basis for craniometrics, with the additional benefit of allowing non-linear measurements if required.

  10. 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.

  11. 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.  

  12. The role of visual context in manual target localization

    NASA Technical Reports Server (NTRS)

    Barry, Susan R.

    1993-01-01

    During space flight and immediately after return to the 1-g environment of earth, astronauts experience perceptual and sensory-motor disturbances. These changes result from adaptation of the astronaut to the microgravity environment of space. During space flight, sensory information from the eyes, limbs, and vestibular organs is reinterpreted by the central nervous system in order to produce appropriate body movements in the microgravity. This adaptation takes several days to develop. Upon return to earth, the changes in the sensory-motor system are no longer appropriate to a 1-g environment. Over several days, the astronaut must re-adapt to the terrestrial environment. Alterations in sensory-motor function may affect eye-head-hand coordination and, thus, the crewmember's ability to manually locate objects in extrapersonal space. Previous reports have demonstrated that crewmembers have difficulty in estimating joint and limb position and in pointing to memorized target positions on orbit and immediately postflight. The ability to point at or reach toward an object or perform other manual tasks is essential for safe Shuttle operation and may be compromised particularly during re-entry and landing sequences and during possible emergency egress from the Shuttle. An understanding of eye-head-hand coordination and the changes produced during space flight is necessary to develop effective countermeasures. This summer's project formed part of the study of the sensory cues use in the manual localization of objects.

  13. Analysis of laser-produces jets from locally heated targets

    NASA Astrophysics Data System (ADS)

    Schmitz, Holger; Robinson, Alex

    2015-11-01

    Recent simulations showed that it might be possible to produce a jet by locally heating a foil target with a high intensity laser, so as to produce a single blast wave which then drives jet formation. In contrast to many earlier experimental setups, the jets in this configuration are formed by a two stage process similar to that thought to be responsible for jets from young stellar objects. As the blast wave expands into the ambient medium it creates an inverse conical density structure. This inverse cone focuses the flow into a conically converging flow which then turns into a narrow jet. The realisation of this two step process in an experiment could make it possible to study the formation of stellar jets in the laboratory. We present new results investigating the criteria that lead to the creation of the inverse conical structure and the subsequent jet formation. The localised heating necessary for driving the jet is achieved by guiding the electrons in self generated magnetic fields at resistivity gradients. We present simulations demonstrating the geometries that lead to the localised heating suitable for jet formation. This work is funded by the European Research Council, grant STRUCMAGFAST (ERC-StG-2012).

  14. Local Recurrence in Rectal Cancer: Anatomic Localization and Effect on Radiation Target

    SciTech Connect

    Syk, Erik Torkzad, Michael R.; Blomqvist, Lennart; Nilsson, Per J.; Glimelius, Bengt

    2008-11-01

    Purpose: To determine the sites of local recurrence after total mesorectal excision for rectal cancer in an effort to optimize the radiation target. Methods and Materials: A total of 155 patients with recurrence after abdominal resection for rectal cancer were identified from a population-based consecutive cohort of 2,315 patients who had undergone surgery by surgeons trained in the total mesorectal excision procedure. A total of 99 cross-sectional imaging studies were retrieved and re-examined by one radiologist. The clinical records were examined for the remaining patients. Results: Evidence of residual mesorectal fat was identified in 50 of the 99 patients. In 83 patients, local recurrence was identified on the imaging studies. All recurrences were within the irradiated volume if the patients had undergone preoperative radiotherapy or within the same volume if they had not. The site of recurrence was in the lower 75% of the pelvis, anatomically below the S1-S2 interspace for all patients. Only 5 of the 44 recurrences in patients with primary tumors >5 cm from the anal verge were in the lowest 20% of the pelvis. Six recurrences involved the lateral lymph nodes. Conclusion: These data suggest that a lowering of the upper limit of the clinical target volume could be introduced. The anal sphincter complex with surrounding tissue could also be excluded in patients with primary tumors >5 cm from the anal verge.

  15. Advancements in 3D Structural Analysis of Geothermal Systems

    SciTech Connect

    Siler, Drew L; Faulds, James E; Mayhew, Brett; McNamara, David

    2013-06-23

    Robust geothermal activity in the Great Basin, USA is a product of both anomalously high regional heat flow and active fault-controlled extension. Elevated permeability associated with some fault systems provides pathways for circulation of geothermal fluids. Constraining the local-scale 3D geometry of these structures and their roles as fluid flow conduits is crucial in order to mitigate both the costs and risks of geothermal exploration and to identify blind (no surface expression) geothermal resources. Ongoing studies have indicated that much of the robust geothermal activity in the Great Basin is associated with high density faulting at structurally complex fault intersection/interaction areas, such as accommodation/transfer zones between discrete fault systems, step-overs or relay ramps in fault systems, intersection zones between faults with different strikes or different senses of slip, and horse-tailing fault terminations. These conceptualized models are crucial for locating and characterizing geothermal systems in a regional context. At the local scale, however, pinpointing drilling targets and characterizing resource potential within known or probable geothermal areas requires precise 3D characterization of the system. Employing a variety of surface and subsurface data sets, we have conducted detailed 3D geologic analyses of two Great Basin geothermal systems. Using EarthVision (Dynamic Graphics Inc., Alameda, CA) we constructed 3D geologic models of both the actively producing Brady’s geothermal system and a ‘greenfield’ geothermal prospect at Astor Pass, NV. These 3D models allow spatial comparison of disparate data sets in 3D and are the basis for quantitative structural analyses that can aid geothermal resource assessment and be used to pinpoint discrete drilling targets. The relatively abundant data set at Brady’s, ~80 km NE of Reno, NV, includes 24 wells with lithologies interpreted from careful analysis of cuttings and core, a 1

  16. 3D ladar ATR based on recognition by parts

    NASA Astrophysics Data System (ADS)

    Sobel, Erik; Douglas, Joel; Ettinger, Gil

    2003-09-01

    LADAR imaging is unique in its potential to accurately measure the 3D surface geometry of targets. We exploit this 3D geometry to perform automatic target recognition on targets in the domain of military and civilian ground vehicles. Here we present a robust model based 3D LADAR ATR system which efficiently searches through target hypothesis space by reasoning hierarchically from vehicle parts up to identification of a whole vehicle with specific pose and articulation state. The LADAR data consists of one or more 3D point clouds generated by laser returns from ground vehicles viewed from multiple sensor locations. The key to this approach is an automated 3D registration process to precisely align and match multiple data views to model based predictions of observed LADAR data. We accomplish this registration using robust 3D surface alignment techniques which we have also used successfully in 3D medical image analysis applications. The registration routine seeks to minimize a robust 3D surface distance metric to recover the best six-degree-of-freedom pose and fit. We process the observed LADAR data by first extracting salient parts, matching these parts to model based predictions and hierarchically constructing and testing increasingly detailed hypotheses about the identity of the observed target. This cycle of prediction, extraction, and matching efficiently partitions the target hypothesis space based on the distinctive anatomy of the target models and achieves effective recognition by progressing logically from a target's constituent parts up to its complete pose and articulation state.

  17. Fusion of multisensor passive and active 3D imagery

    NASA Astrophysics Data System (ADS)

    Fay, David A.; Verly, Jacques G.; Braun, Michael I.; Frost, Carl E.; Racamato, Joseph P.; Waxman, Allen M.

    2001-08-01

    We have extended our previous capabilities for fusion of multiple passive imaging sensors to now include 3D imagery obtained from a prototype flash ladar. Real-time fusion of low-light visible + uncooled LWIR + 3D LADAR, and SWIR + LWIR + 3D LADAR is demonstrated. Fused visualization is achieved by opponent-color neural networks for passive image fusion, which is then textured upon segmented object surfaces derived from the 3D data. An interactive viewer, coded in Java3D, is used to examine the 3D fused scene in stereo. Interactive designation, learning, recognition and search for targets, based on fused passive + 3D signatures, is achieved using Fuzzy ARTMAP neural networks with a Java-coded GUI. A client-server web-based architecture enables remote users to interact with fused 3D imagery via a wireless palmtop computer.

  18. 2D/3D Image Registration using Regression Learning

    PubMed Central

    Chou, Chen-Rui; Frederick, Brandon; Mageras, Gig; Chang, Sha; Pizer, Stephen

    2013-01-01

    In computer vision and image analysis, image registration between 2D projections and a 3D image that achieves high accuracy and near real-time computation is challenging. In this paper, we propose a novel method that can rapidly detect an object’s 3D rigid motion or deformation from a 2D projection image or a small set thereof. The method is called CLARET (Correction via Limited-Angle Residues in External Beam Therapy) and consists of two stages: registration preceded by shape space and regression learning. In the registration stage, linear operators are used to iteratively estimate the motion/deformation parameters based on the current intensity residue between the target projec-tion(s) and the digitally reconstructed radiograph(s) (DRRs) of the estimated 3D image. The method determines the linear operators via a two-step learning process. First, it builds a low-order parametric model of the image region’s motion/deformation shape space from its prior 3D images. Second, using learning-time samples produced from the 3D images, it formulates the relationships between the model parameters and the co-varying 2D projection intensity residues by multi-scale linear regressions. The calculated multi-scale regression matrices yield the coarse-to-fine linear operators used in estimating the model parameters from the 2D projection intensity residues in the registration. The method’s application to Image-guided Radiation Therapy (IGRT) requires only a few seconds and yields good results in localizing a tumor under rigid motion in the head and neck and under respiratory deformation in the lung, using one treatment-time imaging 2D projection or a small set thereof. PMID:24058278

  19. Vector quantization of 3-D point clouds

    NASA Astrophysics Data System (ADS)

    Sim, Jae-Young; Kim, Chang-Su; Lee, Sang-Uk

    2005-10-01

    A geometry compression algorithm for 3-D QSplat data using vector quantization (VQ) is proposed in this work. The positions of child spheres are transformed to the local coordinate system, which is determined by the parent children relationship. The coordinate transform makes child positions more compactly distributed in 3-D space, facilitating effective quantization. Moreover, we develop a constrained encoding method for sphere radii, which guarantees hole-free surface rendering at the decoder side. Simulation results show that the proposed algorithm provides a faithful rendering quality even at low bitrates.

  20. Infrared moving point target detection based on spatial-temporal local contrast filter

    NASA Astrophysics Data System (ADS)

    Deng, Lizhen; Zhu, Hu; Tao, Chao; Wei, Yantao

    2016-05-01

    Infrared moving point target detection is a challenging task. In this paper, we define a novel spatial local contrast (SLC) and a novel temporal local contrast (TLC) to enhance the target's contrast. Based on the defined spatial local contrast and temporal local contrast, we propose a simple but powerful spatial-temporal local contrast filter (STLCF) to detect moving point target from infrared image sequences. In order to verify the performance of spatial-temporal local contrast filter on detecting moving point target, different detection methods are used to detect the target from several infrared image sequences for comparison. The experimental results show that the proposed spatial-temporal local contrast filter has great superiority in moving point target detection.

  1. Modular 3-D Transport model

    EPA Science Inventory

    MT3D was first developed by Chunmiao Zheng in 1990 at S.S. Papadopulos & Associates, Inc. with partial support from the U.S. Environmental Protection Agency (USEPA). Starting in 1990, MT3D was released as a pubic domain code from the USEPA. Commercial versions with enhanced capab...

  2. Market study: 3-D eyetracker

    NASA Technical Reports Server (NTRS)

    1977-01-01

    A market study of a proposed version of a 3-D eyetracker for initial use at NASA's Ames Research Center was made. The commercialization potential of a simplified, less expensive 3-D eyetracker was ascertained. Primary focus on present and potential users of eyetrackers, as well as present and potential manufacturers has provided an effective means of analyzing the prospects for commercialization.

  3. LLNL-Earth3D

    2013-10-01

    Earth3D is a computer code designed to allow fast calculation of seismic rays and travel times through a 3D model of the Earth. LLNL is using this for earthquake location and global tomography efforts and such codes are of great interest to the Earth Science community.

  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. 3D World Building System

    SciTech Connect

    2013-10-30

    This video provides an overview of the Sandia National Laboratories developed 3-D World Model Building capability that provides users with an immersive, texture rich 3-D model of their environment in minutes using a laptop and color and depth camera.

  6. 3D World Building System

    ScienceCinema

    None

    2014-02-26

    This video provides an overview of the Sandia National Laboratories developed 3-D World Model Building capability that provides users with an immersive, texture rich 3-D model of their environment in minutes using a laptop and color and depth camera.

  7. Multi-view and 3D deformable part models.

    PubMed

    Pepik, Bojan; Stark, Michael; Gehler, Peter; Schiele, Bernt

    2015-11-01

    As objects are inherently 3D, they have been modeled in 3D in the early days of computer vision. Due to the ambiguities arising from mapping 2D features to 3D models, 3D object representations have been neglected and 2D feature-based models are the predominant paradigm in object detection nowadays. While such models have achieved outstanding bounding box detection performance, they come with limited expressiveness, as they are clearly limited in their capability of reasoning about 3D shape or viewpoints. In this work, we bring the worlds of 3D and 2D object representations closer, by building an object detector which leverages the expressive power of 3D object representations while at the same time can be robustly matched to image evidence. To that end, we gradually extend the successful deformable part model [1] to include viewpoint information and part-level 3D geometry information, resulting in several different models with different level of expressiveness. We end up with a 3D object model, consisting of multiple object parts represented in 3D and a continuous appearance model. We experimentally verify that our models, while providing richer object hypotheses than the 2D object models, provide consistently better joint object localization and viewpoint estimation than the state-of-the-art multi-view and 3D object detectors on various benchmarks (KITTI [2] , 3D object classes [3] , Pascal3D+ [4] , Pascal VOC 2007 [5] , EPFL multi-view cars[6] ). PMID:26440264

  8. Euro3D Science Conference

    NASA Astrophysics Data System (ADS)

    Walsh, J. R.

    2004-02-01

    The Euro3D RTN is an EU funded Research Training Network to foster the exploitation of 3D spectroscopy in Europe. 3D spectroscopy is a general term for spectroscopy of an area of the sky and derives its name from its two spatial + one spectral dimensions. There are an increasing number of instruments which use integral field devices to achieve spectroscopy of an area of the sky, either using lens arrays, optical fibres or image slicers, to pack spectra of multiple pixels on the sky (``spaxels'') onto a 2D detector. On account of the large volume of data and the special methods required to reduce and analyse 3D data, there are only a few centres of expertise and these are mostly involved with instrument developments. There is a perceived lack of expertise in 3D spectroscopy spread though the astronomical community and its use in the armoury of the observational astronomer is viewed as being highly specialised. For precisely this reason the Euro3D RTN was proposed to train young researchers in this area and develop user tools to widen the experience with this particular type of data in Europe. The Euro3D RTN is coordinated by Martin M. Roth (Astrophysikalisches Institut Potsdam) and has been running since July 2002. The first Euro3D science conference was held in Cambridge, UK from 22 to 23 May 2003. The main emphasis of the conference was, in keeping with the RTN, to expose the work of the young post-docs who are funded by the RTN. In addition the team members from the eleven European institutes involved in Euro3D also presented instrumental and observational developments. The conference was organized by Andy Bunker and held at the Institute of Astronomy. There were over thirty participants and 26 talks covered the whole range of application of 3D techniques. The science ranged from Galactic planetary nebulae and globular clusters to kinematics of nearby galaxies out to objects at high redshift. Several talks were devoted to reporting recent observations with newly

  9. PLOT3D user's manual

    NASA Technical Reports Server (NTRS)

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

    1990-01-01

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

  10. 3D printing in dentistry.

    PubMed

    Dawood, A; Marti Marti, B; Sauret-Jackson, V; Darwood, A

    2015-12-01

    3D printing has been hailed as a disruptive technology which will change manufacturing. Used in aerospace, defence, art and design, 3D printing is becoming a subject of great interest in surgery. The technology has a particular resonance with dentistry, and with advances in 3D imaging and modelling technologies such as cone beam computed tomography and intraoral scanning, and with the relatively long history of the use of CAD CAM technologies in dentistry, it will become of increasing importance. Uses of 3D printing include the production of drill guides for dental implants, the production of physical models for prosthodontics, orthodontics and surgery, the manufacture of dental, craniomaxillofacial and orthopaedic implants, and the fabrication of copings and frameworks for implant and dental restorations. This paper reviews the types of 3D printing technologies available and their various applications in dentistry and in maxillofacial surgery. PMID:26657435

  11. Scalable Multi-Platform Distribution of Spatial 3d Contents

    NASA Astrophysics Data System (ADS)

    Klimke, J.; Hagedorn, B.; Döllner, J.

    2013-09-01

    Virtual 3D city models provide powerful user interfaces for communication of 2D and 3D geoinformation. Providing high quality visualization of massive 3D geoinformation in a scalable, fast, and cost efficient manner is still a challenging task. Especially for mobile and web-based system environments, software and hardware configurations of target systems differ significantly. This makes it hard to provide fast, visually appealing renderings of 3D data throughout a variety of platforms and devices. Current mobile or web-based solutions for 3D visualization usually require raw 3D scene data such as triangle meshes together with textures delivered from server to client, what makes them strongly limited in terms of size and complexity of the models they can handle. In this paper, we introduce a new approach for provisioning of massive, virtual 3D city models on different platforms namely web browsers, smartphones or tablets, by means of an interactive map assembled from artificial oblique image tiles. The key concept is to synthesize such images of a virtual 3D city model by a 3D rendering service in a preprocessing step. This service encapsulates model handling and 3D rendering techniques for high quality visualization of massive 3D models. By generating image tiles using this service, the 3D rendering process is shifted from the client side, which provides major advantages: (a) The complexity of the 3D city model data is decoupled from data transfer complexity (b) the implementation of client applications is simplified significantly as 3D rendering is encapsulated on server side (c) 3D city models can be easily deployed for and used by a large number of concurrent users, leading to a high degree of scalability of the overall approach. All core 3D rendering techniques are performed on a dedicated 3D rendering server, and thin-client applications can be compactly implemented for various devices and platforms.

  12. Crashworthiness simulations with DYNA3D

    SciTech Connect

    Schauer, D.A.; Hoover, C.G.; Kay, G.J.; Lee, A.S.; De Groot, A.J.

    1996-04-01

    Current progress in parallel algorithm research and applications in vehicle crash simulation is described for the explicit, finite element algorithms in DYNA3D. Problem partitioning methods and parallel algorithms for contact at material interfaces are the two challenging algorithm research problems that are addressed. Two prototype parallel contact algorithms have been developed for treating the cases of local and arbitrary contact. Demonstration problems for local contact are crashworthiness simulations with 222 locally defined contact surfaces and a vehicle/barrier collision modeled with arbitrary contact. A simulation of crash tests conducted for a vehicle impacting a U-channel small sign post embedded in soil has been run on both the serial and parallel versions of DYNA3D. A significant reduction in computational time has been observed when running these problems on the parallel version. However, to achieve maximum efficiency, complex problems must be appropriately partitioned, especially when contact dominates the computation.

  13. Miniaturized 3D microscope imaging system

    NASA Astrophysics Data System (ADS)

    Lan, Yung-Sung; Chang, Chir-Weei; Sung, Hsin-Yueh; Wang, Yen-Chang; Chang, Cheng-Yi

    2015-05-01

    We designed and assembled a portable 3-D miniature microscopic image system with the size of 35x35x105 mm3 . By integrating a microlens array (MLA) into the optical train of a handheld microscope, the biological specimen's image will be captured for ease of use in a single shot. With the light field raw data and program, the focal plane can be changed digitally and the 3-D image can be reconstructed after the image was taken. To localize an object in a 3-D volume, an automated data analysis algorithm to precisely distinguish profundity position is needed. The ability to create focal stacks from a single image allows moving or specimens to be recorded. Applying light field microscope algorithm to these focal stacks, a set of cross sections will be produced, which can be visualized using 3-D rendering. Furthermore, we have developed a series of design rules in order to enhance the pixel using efficiency and reduce the crosstalk between each microlens for obtain good image quality. In this paper, we demonstrate a handheld light field microscope (HLFM) to distinguish two different color fluorescence particles separated by a cover glass in a 600um range, show its focal stacks, and 3-D position.

  14. The Indoor Localization and Tracking Estimation Method of Mobile Targets in Three-Dimensional Wireless Sensor Networks.

    PubMed

    Jia, Zixi; Wu, Chengdong; Li, Zhao; Zhang, Yunzhou; Guan, Bo

    2015-01-01

    Indoor localization is a significant research area in wireless sensor networks (WSNs). Generally, the nodes of WSNs are deployed in the same plane, i.e., the floor, as the target to be positioned, which causes the sensing signal to be influenced or even blocked by unpredictable obstacles, like furniture. However, a 3D system, like Cricket, can reduce the negative impact of obstacles to the maximum extent and guarantee the sensing signal transmission by using the line of sight (LOS). However, most of the traditional localization methods are not available for the new deployment mode. In this paper, we propose the self-localization of beacons method based on the Cayley-Menger determinant, which can determine the positions of beacons stuck in the ceiling; and differential sensitivity analysis (DSA) is also applied to eliminate measurement errors in measurement data fusion. Then, the calibration of beacons scheme is proposed to further refine the locations of beacons by the mobile robot. According to the robot's motion model based on dead reckoning, which is the process of determining one's current position, we employ the H∞ filter and the strong tracking filter (STF) to calibrate the rough locations, respectively. Lastly, the optimal node selection scheme based on geometric dilution precision (GDOP) is presented here, which is able to pick the group of beacons with the minimum GDOP from all of the beacons. Then, we propose the GDOP-based weighting estimation method (GWEM) to associate redundant information with the position of the target. To verify the proposed methods in the paper, we design and conduct a simulation and an experiment in an indoor setting. Compared to EKF and the H∞ filter, the adopted STF method can more effectively calibrate the locations of beacons; GWEM can provide centimeter-level precision in 3D environments by using the combination of beacons that minimizes GDOP. PMID:26610518

  15. The Indoor Localization and Tracking Estimation Method of Mobile Targets in Three-Dimensional Wireless Sensor Networks

    PubMed Central

    Jia, Zixi; Wu, Chengdong; Li, Zhao; Zhang, Yunzhou; Guan, Bo

    2015-01-01

    Indoor localization is a significant research area in wireless sensor networks (WSNs). Generally, the nodes of WSNs are deployed in the same plane, i.e., the floor, as the target to be positioned, which causes the sensing signal to be influenced or even blocked by unpredictable obstacles, like furniture. However, a 3D system, like Cricket, can reduce the negative impact of obstacles to the maximum extent and guarantee the sensing signal transmission by using the line of sight (LOS). However, most of the traditional localization methods are not available for the new deployment mode. In this paper, we propose the self-localization of beacons method based on the Cayley–Menger determinant, which can determine the positions of beacons stuck in the ceiling; and differential sensitivity analysis (DSA) is also applied to eliminate measurement errors in measurement data fusion. Then, the calibration of beacons scheme is proposed to further refine the locations of beacons by the mobile robot. According to the robot’s motion model based on dead reckoning, which is the process of determining one’s current position, we employ the H∞ filter and the strong tracking filter (STF) to calibrate the rough locations, respectively. Lastly, the optimal node selection scheme based on geometric dilution precision (GDOP) is presented here, which is able to pick the group of beacons with the minimum GDOP from all of the beacons. Then, we propose the GDOP-based weighting estimation method (GWEM) to associate redundant information with the position of the target. To verify the proposed methods in the paper, we design and conduct a simulation and an experiment in an indoor setting. Compared to EKF and the H∞ filter, the adopted STF method can more effectively calibrate the locations of beacons; GWEM can provide centimeter-level precision in 3D environments by using the combination of beacons that minimizes GDOP. PMID:26610518

  16. Evaluation of three types of reference image data for external beam radiotherapy target localization using digital tomosynthesis (DTS)

    SciTech Connect

    Godfrey, Devon J.; Ren Lei; Yan Hui; Wu, Q.; Yoo Sua; Oldham, M.; Yin Fangfang

    2007-08-15

    Digital tomosynthesis (DTS) is a fast, low-dose three-dimensional (3D) imaging approach which yields slice images with excellent in-plane resolution, though low plane-to-plane resolution. A stack of DTS slices can be reconstructed from a single limited-angle scan, with typical scan angles ranging from 10 deg. to 40 deg. and acquisition times of less than 10 s. The resulting DTS slices show soft tissue contrast approaching that of full cone-beam CT. External beam radiotherapy target localization using DTS requires the registration of on-board DTS images with corresponding reference image data. This study evaluates three types of reference volume: original reference CT, exact reference DTS (RDTS), and a more computationally efficient approximate reference DTS (RDTS{sub approx}), as well as three different DTS scan angles (22 deg., 44 deg., and 65 deg.) for the DTS target localization task. Three-dimensional mutual information (MI) shared between reference and on-board DTS volumes was computed in a region surrounding the spine of a chest phantom, as translations spanning {+-}5 mm and rotations spanning {+-}5 deg. were simulated along each dimension in the reference volumes. The locations of the MI maxima were used as surrogates for registration accuracy, and the width of the MI peaks were used to characterize the registration robustness. The results show that conventional treatment planning CT volumes are inadequate reference volumes for direct registration with on-board DTS data. The efficient RDTS{sub approx} method also appears insufficient for MI-based registration without further refinement of the technique, though it may be suitable for manual registration performed by a human observer. The exact RDTS volumes, on the other hand, delivered a 3D DTS localization accuracy of 0.5 mm and 0.5 deg. along each axis, using only a single 44 deg. coronal on-board DTS scan of the chest phantom.

  17. Bioprinting of 3D hydrogels.

    PubMed

    Stanton, M M; Samitier, J; Sánchez, S

    2015-08-01

    Three-dimensional (3D) bioprinting has recently emerged as an extension of 3D material printing, by using biocompatible or cellular components to build structures in an additive, layer-by-layer methodology for encapsulation and culture of cells. These 3D systems allow for cell culture in a suspension for formation of highly organized tissue or controlled spatial orientation of cell environments. The in vitro 3D cellular environments simulate the complexity of an in vivo environment and natural extracellular matrices (ECM). This paper will focus on bioprinting utilizing hydrogels as 3D scaffolds. Hydrogels are advantageous for cell culture as they are highly permeable to cell culture media, nutrients, and waste products generated during metabolic cell processes. They have the ability to be fabricated in customized shapes with various material properties with dimensions at the micron scale. 3D hydrogels are a reliable method for biocompatible 3D printing and have applications in tissue engineering, drug screening, and organ on a chip models. PMID:26066320

  18. Unassisted 3D camera calibration

    NASA Astrophysics Data System (ADS)

    Atanassov, Kalin; Ramachandra, Vikas; Nash, James; Goma, Sergio R.

    2012-03-01

    With the rapid growth of 3D technology, 3D image capture has become a critical part of the 3D feature set on mobile phones. 3D image quality is affected by the scene geometry as well as on-the-device processing. An automatic 3D system usually assumes known camera poses accomplished by factory calibration using a special chart. In real life settings, pose parameters estimated by factory calibration can be negatively impacted by movements of the lens barrel due to shaking, focusing, or camera drop. If any of these factors displaces the optical axes of either or both cameras, vertical disparity might exceed the maximum tolerable margin and the 3D user may experience eye strain or headaches. To make 3D capture more practical, one needs to consider unassisted (on arbitrary scenes) calibration. In this paper, we propose an algorithm that relies on detection and matching of keypoints between left and right images. Frames containing erroneous matches, along with frames with insufficiently rich keypoint constellations, are detected and discarded. Roll, pitch yaw , and scale differences between left and right frames are then estimated. The algorithm performance is evaluated in terms of the remaining vertical disparity as compared to the maximum tolerable vertical disparity.

  19. Arena3D: visualization of biological networks in 3D

    PubMed Central

    Pavlopoulos, Georgios A; O'Donoghue, Seán I; Satagopam, Venkata P; Soldatos, Theodoros G; Pafilis, Evangelos; Schneider, Reinhard

    2008-01-01

    Background Complexity is a key problem when visualizing biological networks; as the number of entities increases, most graphical views become incomprehensible. Our goal is to enable many thousands of entities to be visualized meaningfully and with high performance. Results We present a new visualization tool, Arena3D, which introduces a new concept of staggered layers in 3D space. Related data – such as proteins, chemicals, or pathways – can be grouped onto separate layers and arranged via layout algorithms, such as Fruchterman-Reingold, distance geometry, and a novel hierarchical layout. Data on a layer can be clustered via k-means, affinity propagation, Markov clustering, neighbor joining, tree clustering, or UPGMA ('unweighted pair-group method with arithmetic mean'). A simple input format defines the name and URL for each node, and defines connections or similarity scores between pairs of nodes. The use of Arena3D is illustrated with datasets related to Huntington's disease. Conclusion Arena3D is a user friendly visualization tool that is able to visualize biological or any other network in 3D space. It is free for academic use and runs on any platform. It can be downloaded or lunched directly from . Java3D library and Java 1.5 need to be pre-installed for the software to run. PMID:19040715

  20. bioWeb3D: an online webGL 3D data visualisation tool

    PubMed Central

    2013-01-01

    Background Data visualization is critical for interpreting biological data. However, in practice it can prove to be a bottleneck for non trained researchers; this is especially true for three dimensional (3D) data representation. Whilst existing software can provide all necessary functionalities to represent and manipulate biological 3D datasets, very few are easily accessible (browser based), cross platform and accessible to non-expert users. Results An online HTML5/WebGL based 3D visualisation tool has been developed to allow biologists to quickly and easily view interactive and customizable three dimensional representations of their data along with multiple layers of information. Using the WebGL library Three.js written in Javascript, bioWeb3D allows the simultaneous visualisation of multiple large datasets inputted via a simple JSON, XML or CSV file, which can be read and analysed locally thanks to HTML5 capabilities. Conclusions Using basic 3D representation techniques in a technologically innovative context, we provide a program that is not intended to compete with professional 3D representation software, but that instead enables a quick and intuitive representation of reasonably large 3D datasets. PMID:23758781

  1. Automatic needle segmentation in 3D ultrasound images using 3D improved Hough transform

    NASA Astrophysics Data System (ADS)

    Zhou, Hua; Qiu, Wu; Ding, Mingyue; Zhang, Songgen

    2008-03-01

    3D ultrasound (US) is a new technology that can be used for a variety of diagnostic applications, such as obstetrical, vascular, and urological imaging, and has been explored greatly potential in the applications of image-guided surgery and therapy. Uterine adenoma and uterine bleeding are the two most prevalent diseases in Chinese woman, and a minimally invasive ablation system using a needle-like RF button electrode is widely used to destroy tumor cells or stop bleeding. To avoid accidents or death of the patient by inaccurate localizations of the electrode and the tumor position during treatment, 3D US guidance system was developed. In this paper, a new automated technique, the 3D Improved Hough Transform (3DIHT) algorithm, which is potentially fast, accurate, and robust to provide needle segmentation in 3D US image for use of 3D US imaging guidance, was presented. Based on the coarse-fine search strategy and a four parameter representation of lines in 3D space, 3DIHT algorithm can segment needles quickly, accurately and robustly. The technique was evaluated using the 3D US images acquired by scanning a water phantom. The segmentation position deviation of the line was less than 2mm and angular deviation was much less than 2°. The average computational time measured on a Pentium IV 2.80GHz PC computer with a 381×381×250 image was less than 2s.

  2. Generation of 3D characterization databases in vector format

    NASA Astrophysics Data System (ADS)

    Wilkosz, Aaron; Williams, Bryan L.; Motz, Steve

    2001-09-01

    We discuss the methodology and techniques employed in transforming our 3D characterization databases and 3D target models from our internal 3D format to a more universal 3D format. Currently our 3D characterization databases and target models are encoded in an internal custom file format that targets specific simulators set up to receive out data. In order to make our databases available to a wider audience within the modeling and simulation community, we have developed techniques to transform our databases into the more common Open Flight file format. We outline the steps taken to accomplish this. We discuss the methodology and show examples of backgrounds, object discretes, and target models. The developed characterization databases are used in digital simulations by various customers within the US Army Aviation and Missile Command (AMCOM). These databases are used in closed loop dynamic simulations to evaluate the performance of various missile systems.

  3. Fdf in US3D

    NASA Astrophysics Data System (ADS)

    Otis, Collin; Ferrero, Pietro; Candler, Graham; Givi, Peyman

    2013-11-01

    The scalar filtered mass density function (SFMDF) methodology is implemented into the computer code US3D. This is an unstructured Eulerian finite volume hydrodynamic solver and has proven very effective for simulation of compressible turbulent flows. The resulting SFMDF-US3D code is employed for large eddy simulation (LES) on unstructured meshes. Simulations are conducted of subsonic and supersonic flows under non-reacting and reacting conditions. The consistency and the accuracy of the simulated results are assessed along with appraisal of the overall performance of the methodology. The SFMDF-US3D is now capable of simulating high speed flows in complex configurations.

  4. Phase unwrapping in the dynamic 3D measurement

    NASA Astrophysics Data System (ADS)

    Su, Xianyu; Zhang, Qican

    2010-04-01

    In the dynamic 3D shape measurement phase distribution has 3D character, in which phase changes along x and y directions in space and also along t direction in time. 3D phase unwrapping plays a very important role in the dynamic 3D shape measurement. In the dynamic 3D shape measurement methods based on the structured illumination, Fourier transformation profilometry (FTP) is particularly fit for dynamic 3D measurement, because of only one fringe pattern needed and full field analysis. In this paper some 3D phase unwrapping techniques for dynamic 3D shape measurement mainly in our Lab. are presented and reviewed. The basic methods and algorithm design are introduced. The basic methods include direct 3D phase unwrapping, 3D diamond phase unwrapping, 3D phase unwrapping based on reliability ordering, 3D phase unwrapping based on marked fringe tracing. The advantage of the phase unwrapping based on reliability ordering is that the path of phase unwrapping is always along the direction from the pixel with higher reliability parameter value to the pixel with low reliability parameter value. Therefore, in the worse case the error is limited, if there is any, to local minimum areas.

  5. Wavefront construction in 3-D

    SciTech Connect

    Chilcoat, S.R. Hildebrand, S.T.

    1995-12-31

    Travel time computation in inhomogeneous media is essential for pre-stack Kirchhoff imaging in areas such as the sub-salt province in the Gulf of Mexico. The 2D algorithm published by Vinje, et al, has been extended to 3D to compute wavefronts in complicated inhomogeneous media. The 3D wavefront construction algorithm provides many advantages over conventional ray tracing and other methods of computing travel times in 3D. The algorithm dynamically maintains a reasonably consistent ray density without making a priori guesses at the number of rays to shoot. The determination of caustics in 3D is a straight forward geometric procedure. The wavefront algorithm also enables the computation of multi-valued travel time surfaces.

  6. Combinatorial 3D Mechanical Metamaterials

    NASA Astrophysics Data System (ADS)

    Coulais, Corentin; Teomy, Eial; de Reus, Koen; Shokef, Yair; van Hecke, Martin

    2015-03-01

    We present a class of elastic structures which exhibit 3D-folding motion. Our structures consist of cubic lattices of anisotropic unit cells that can be tiled in a complex combinatorial fashion. We design and 3d-print this complex ordered mechanism, in which we combine elastic hinges and defects to tailor the mechanics of the material. Finally, we use this large design space to encode smart functionalities such as surface patterning and multistability.

  7. Timing matters: sonar call groups facilitate target localization in bats

    PubMed Central

    Kothari, Ninad B.; Wohlgemuth, Melville J.; Hulgard, Katrine; Surlykke, Annemarie; Moss, Cynthia F.

    2014-01-01

    To successfully negotiate a cluttered environment, an echolocating bat must control the timing of motor behaviors in response to dynamic sensory information. Here we detail the big brown bat's adaptive temporal control over sonar call production for tracking prey, moving predictably or unpredictably, under different experimental conditions. We studied the adaptive control of vocal-motor behaviors in free-flying big brown bats, Eptesicus fuscus, as they captured tethered and free-flying insects, in open and cluttered environments. We also studied adaptive sonar behavior in bats trained to track moving targets from a resting position. In each of these experiments, bats adjusted the features of their calls to separate target and clutter. Under many task conditions, flying bats produced prominent sonar sound groups identified as clusters of echolocation pulses with relatively stable intervals, surrounded by longer pulse intervals. In experiments where bats tracked approaching targets from a resting position, bats also produced sonar sound groups, and the prevalence of these sonar sound groups increased when motion of the target was unpredictable. We hypothesize that sonar sound groups produced during flight, and the sonar call doublets produced by a bat tracking a target from a resting position, help the animal resolve dynamic target location and represent the echo scene in greater detail. Collectively, our data reveal adaptive temporal control over sonar call production that allows the bat to negotiate a complex and dynamic environment. PMID:24860509

  8. Towards 3D ultrasound image based soft tissue tracking: a transrectal ultrasound prostate image alignment system.

    PubMed

    Baumann, Michael; Mozer, Pierre; Daanen, Vincent; Troccaz, Jocelyne

    2007-01-01

    The emergence of real-time 3D ultrasound (US) makes it possible to consider image-based tracking of subcutaneous soft tissue targets for computer guided diagnosis and therapy. We propose a 3D transrectal US based tracking system for precise prostate biopsy sample localisation. The aim is to improve sample distribution, to enable targeting of unsampled regions for repeated biopsies, and to make post-interventional quality controls possible. Since the patient is not immobilized, since the prostate is mobile and due to the fact that probe movements are only constrained by the rectum during biopsy acquisition, the tracking system must be able to estimate rigid transformations that are beyond the capture range of common image similarity measures. We propose a fast and robust multi-resolution attribute-vector registration approach that combines global and local optimization methods to solve this problem. Global optimization is performed on a probe movement model that reduces the dimensionality of the search space and thus renders optimization efficient. The method was tested on 237 prostate volumes acquired from 14 different patients for 3D to 3D and 3D to orthogonal 2D slices registration. The 3D-3D version of the algorithm converged correctly in 96.7% of all cases in 6.5s with an accuracy of 1.41mm (r.m.s.) and 3.84mm (max). The 3D to slices method yielded a success rate of 88.9% in 2.3s with an accuracy of 1.37mm (r.m.s.) and 4.3mm (max). PMID:18044549

  9. Thermomechanical properties of 3d transition metals

    SciTech Connect

    Karaoglu, B.; Rahman, S.M.M. . Dept. of Physics)

    1994-05-15

    The authors have investigated the density variation of the Einstein temperatures and elastic constants of the 3d transition metals. In this respect they have employed the transition metal (TM) pair potentials involving the sp contribution with an appropriate exchange and correlation function, the d-band broadening contribution and the d-band hybridization term. These calculations are aimed at testing the TM pair potentials in generating the quasilocal and local thermomechanical properties.

  10. From 3D view to 3D print

    NASA Astrophysics Data System (ADS)

    Dima, M.; Farisato, G.; Bergomi, M.; Viotto, V.; Magrin, D.; Greggio, D.; Farinato, J.; Marafatto, L.; Ragazzoni, R.; Piazza, D.

    2014-08-01

    In the last few years 3D printing is getting more and more popular and used in many fields going from manufacturing to industrial design, architecture, medical support and aerospace. 3D printing is an evolution of bi-dimensional printing, which allows to obtain a solid object from a 3D model, realized with a 3D modelling software. The final product is obtained using an additive process, in which successive layers of material are laid down one over the other. A 3D printer allows to realize, in a simple way, very complex shapes, which would be quite difficult to be produced with dedicated conventional facilities. Thanks to the fact that the 3D printing is obtained superposing one layer to the others, it doesn't need any particular work flow and it is sufficient to simply draw the model and send it to print. Many different kinds of 3D printers exist based on the technology and material used for layer deposition. A common material used by the toner is ABS plastics, which is a light and rigid thermoplastic polymer, whose peculiar mechanical properties make it diffusely used in several fields, like pipes production and cars interiors manufacturing. I used this technology to create a 1:1 scale model of the telescope which is the hardware core of the space small mission CHEOPS (CHaracterising ExOPlanets Satellite) by ESA, which aims to characterize EXOplanets via transits observations. The telescope has a Ritchey-Chrétien configuration with a 30cm aperture and the launch is foreseen in 2017. In this paper, I present the different phases for the realization of such a model, focusing onto pros and cons of this kind of technology. For example, because of the finite printable volume (10×10×12 inches in the x, y and z directions respectively), it has been necessary to split the largest parts of the instrument in smaller components to be then reassembled and post-processed. A further issue is the resolution of the printed material, which is expressed in terms of layers

  11. Geodiversity: Exploration of 3D geological model space

    NASA Astrophysics Data System (ADS)

    Lindsay, M. D.; Jessell, M. W.; Ailleres, L.; Perrouty, S.; de Kemp, E.; Betts, P. G.

    2013-05-01

    The process of building a 3D model necessitates the reconciliation of field observations, geophysical interpretation, geological data uncertainty and the prevailing tectonic evolution hypotheses and interpretations. Uncertainty is compounded when clustered data points collected at local scales are statistically upscaled to one or two points for use in regional models. Interpretation is required to interpolate between sparse field data points using ambiguous geophysical data in covered terranes. It becomes clear that multiple interpretations are possible during model construction. The various interpretations are considered as potential natural representatives, but pragmatism typically dictates that just a single interpretation is offered by the modelling process. Uncertainties are introduced into the 3D model during construction from a variety of sources and through data set optimisation that produces a single model. Practices such as these are likely to result in a model that does not adequately represent the target geology. A set of geometrical ‘geodiversity’ metrics are used to analyse a 3D model of the Gippsland Basin, southeastern Australia after perturbing geological input data via uncertainty simulation. The resulting sets of perturbed geological observations are used to calculate a suite of geological 3D models that display a range of geological architectures. The concept of biodiversity has been adapted for the geosciences to quantify geometric variability, or geodiversity, between models in order to understand the effect uncertainty has models geometry. Various geometrical relationships (depth, volume, contact surface area, curvature and geological complexity) are used to describe the range of possibilities exhibited throughout the model suite. End-member models geodiversity metrics are classified in a similar manner to taxonomic descriptions. Further analysis of the model suite is performed using principal component analysis (PCA) to determine

  12. Rubber Impact on 3D Textile Composites

    NASA Astrophysics Data System (ADS)

    Heimbs, Sebastian; Van Den Broucke, Björn; Duplessis Kergomard, Yann; Dau, Frederic; Malherbe, Benoit

    2012-06-01

    A low velocity impact study of aircraft tire rubber on 3D textile-reinforced composite plates was performed experimentally and numerically. In contrast to regular unidirectional composite laminates, no delaminations occur in such a 3D textile composite. Yarn decohesions, matrix cracks and yarn ruptures have been identified as the major damage mechanisms under impact load. An increase in the number of 3D warp yarns is proposed to improve the impact damage resistance. The characteristic of a rubber impact is the high amount of elastic energy stored in the impactor during impact, which was more than 90% of the initial kinetic energy. This large geometrical deformation of the rubber during impact leads to a less localised loading of the target structure and poses great challenges for the numerical modelling. A hyperelastic Mooney-Rivlin constitutive law was used in Abaqus/Explicit based on a step-by-step validation with static rubber compression tests and low velocity impact tests on aluminium plates. Simulation models of the textile weave were developed on the meso- and macro-scale. The final correlation between impact simulation results on 3D textile-reinforced composite plates and impact test data was promising, highlighting the potential of such numerical simulation tools.

  13. Spacecraft 3D Augmented Reality Mobile App

    NASA Technical Reports Server (NTRS)

    Hussey, Kevin J.; Doronila, Paul R.; Kumanchik, Brian E.; Chan, Evan G.; Ellison, Douglas J.; Boeck, Andrea; Moore, Justin M.

    2013-01-01

    The Spacecraft 3D application allows users to learn about and interact with iconic NASA missions in a new and immersive way using common mobile devices. Using Augmented Reality (AR) techniques to project 3D renditions of the mission spacecraft into real-world surroundings, users can interact with and learn about Curiosity, GRAIL, Cassini, and Voyager. Additional updates on future missions, animations, and information will be ongoing. Using a printed AR Target and camera on a mobile device, users can get up close with these robotic explorers, see how some move, and learn about these engineering feats, which are used to expand knowledge and understanding about space. The software receives input from the mobile device's camera to recognize the presence of an AR marker in the camera's field of view. It then displays a 3D rendition of the selected spacecraft in the user's physical surroundings, on the mobile device's screen, while it tracks the device's movement in relation to the physical position of the spacecraft's 3D image on the AR marker.

  14. YouDash3D: exploring stereoscopic 3D gaming for 3D movie theaters

    NASA Astrophysics Data System (ADS)

    Schild, Jonas; Seele, Sven; Masuch, Maic

    2012-03-01

    Along with the success of the digitally revived stereoscopic cinema, events beyond 3D movies become attractive for movie theater operators, i.e. interactive 3D games. In this paper, we present a case that explores possible challenges and solutions for interactive 3D games to be played by a movie theater audience. We analyze the setting and showcase current issues related to lighting and interaction. Our second focus is to provide gameplay mechanics that make special use of stereoscopy, especially depth-based game design. Based on these results, we present YouDash3D, a game prototype that explores public stereoscopic gameplay in a reduced kiosk setup. It features live 3D HD video stream of a professional stereo camera rig rendered in a real-time game scene. We use the effect to place the stereoscopic effigies of players into the digital game. The game showcases how stereoscopic vision can provide for a novel depth-based game mechanic. Projected trigger zones and distributed clusters of the audience video allow for easy adaptation to larger audiences and 3D movie theater gaming.

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

    NASA Technical Reports Server (NTRS)

    Buning, P.

    1994-01-01

    five groups: 1) Grid Functions for grids, grid-checking, etc.; 2) Scalar Functions for contour or carpet plots of density, pressure, temperature, Mach number, vorticity magnitude, helicity, etc.; 3) Vector Functions for vector plots of velocity, vorticity, momentum, and density gradient, etc.; 4) Particle Trace Functions for rake-like plots of particle flow or vortex lines; and 5) Shock locations based on pressure gradient. TURB3D is a modification of PLOT3D which is used for viewing CFD simulations of incompressible turbulent flow. Input flow data consists of pressure, velocity and vorticity. Typical quantities to plot include local fluctuations in flow quantities and turbulent production terms, plotted in physical or wall units. PLOT3D/TURB3D includes both TURB3D and PLOT3D because the operation of TURB3D is identical to PLOT3D, and there is no additional sample data or printed documentation for TURB3D. Graphical capabilities of PLOT3D version 3.6b+ vary among the implementations available through COSMIC. Customers are encouraged to purchase and carefully review the PLOT3D manual before ordering the program for a specific computer and graphics library. There is only one manual for use with all implementations of PLOT3D, and although this manual generally assumes that the Silicon Graphics Iris implementation is being used, informative comments concerning other implementations appear throughout the text. With all implementations, the visual representation of the object and flow field created by PLOT3D consists of points, lines, and polygons. Points can be represented with dots or symbols, color can be used to denote data values, and perspective is used to show depth. Differences among implementations impact the program's ability to use graphical features that are based on 3D polygons, the user's ability to manipulate the graphical displays, and the user's ability to obtain alternate forms of output. The VAX/VMS/DISSPLA implementation of PLOT3D supports 2-D polygons as

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

    NASA Technical Reports Server (NTRS)

    Buning, P. G.

    1994-01-01

    five groups: 1) Grid Functions for grids, grid-checking, etc.; 2) Scalar Functions for contour or carpet plots of density, pressure, temperature, Mach number, vorticity magnitude, helicity, etc.; 3) Vector Functions for vector plots of velocity, vorticity, momentum, and density gradient, etc.; 4) Particle Trace Functions for rake-like plots of particle flow or vortex lines; and 5) Shock locations based on pressure gradient. TURB3D is a modification of PLOT3D which is used for viewing CFD simulations of incompressible turbulent flow. Input flow data consists of pressure, velocity and vorticity. Typical quantities to plot include local fluctuations in flow quantities and turbulent production terms, plotted in physical or wall units. PLOT3D/TURB3D includes both TURB3D and PLOT3D because the operation of TURB3D is identical to PLOT3D, and there is no additional sample data or printed documentation for TURB3D. Graphical capabilities of PLOT3D version 3.6b+ vary among the implementations available through COSMIC. Customers are encouraged to purchase and carefully review the PLOT3D manual before ordering the program for a specific computer and graphics library. There is only one manual for use with all implementations of PLOT3D, and although this manual generally assumes that the Silicon Graphics Iris implementation is being used, informative comments concerning other implementations appear throughout the text. With all implementations, the visual representation of the object and flow field created by PLOT3D consists of points, lines, and polygons. Points can be represented with dots or symbols, color can be used to denote data values, and perspective is used to show depth. Differences among implementations impact the program's ability to use graphical features that are based on 3D polygons, the user's ability to manipulate the graphical displays, and the user's ability to obtain alternate forms of output. The VAX/VMS/DISSPLA implementation of PLOT3D supports 2-D polygons as

  17. Remote 3D Medical Consultation

    NASA Astrophysics Data System (ADS)

    Welch, Greg; Sonnenwald, Diane H.; Fuchs, Henry; Cairns, Bruce; Mayer-Patel, Ketan; Yang, Ruigang; State, Andrei; Towles, Herman; Ilie, Adrian; Krishnan, Srinivas; Söderholm, Hanna M.

    Two-dimensional (2D) video-based telemedical consultation has been explored widely in the past 15-20 years. Two issues that seem to arise in most relevant case studies are the difficulty associated with obtaining the desired 2D camera views, and poor depth perception. To address these problems we are exploring the use of a small array of cameras to synthesize a spatially continuous range of dynamic three-dimensional (3D) views of a remote environment and events. The 3D views can be sent across wired or wireless networks to remote viewers with fixed displays or mobile devices such as a personal digital assistant (PDA). The viewpoints could be specified manually or automatically via user head or PDA tracking, giving the remote viewer virtual head- or hand-slaved (PDA-based) remote cameras for mono or stereo viewing. We call this idea remote 3D medical consultation (3DMC). In this article we motivate and explain the vision for 3D medical consultation; we describe the relevant computer vision/graphics, display, and networking research; we present a proof-of-concept prototype system; and we present some early experimental results supporting the general hypothesis that 3D remote medical consultation could offer benefits over conventional 2D televideo.

  18. 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.

  19. 3D imaging of Sox2 enhancer clusters in embryonic stem cells

    PubMed Central

    Liu, Zhe; Legant, Wesley R; Chen, Bi-Chang; Li, Li; Grimm, Jonathan B; Lavis, Luke D; Betzig, Eric; Tjian, Robert

    2014-01-01

    Combinatorial cis-regulatory networks encoded in animal genomes represent the foundational gene expression mechanism for directing cell-fate commitment and maintenance of cell identity by transcription factors (TFs). However, the 3D spatial organization of cis-elements and how such sub-nuclear structures influence TF activity remain poorly understood. Here, we combine lattice light-sheet imaging, single-molecule tracking, numerical simulations, and ChIP-exo mapping to localize and functionally probe Sox2 enhancer-organization in living embryonic stem cells. Sox2 enhancers form 3D-clusters that are segregated from heterochromatin but overlap with a subset of Pol II enriched regions. Sox2 searches for specific binding targets via a 3D-diffusion dominant mode when shuttling long-distances between clusters while chromatin-bound states predominate within individual clusters. Thus, enhancer clustering may reduce global search efficiency but enables rapid local fine-tuning of TF search parameters. Our results suggest an integrated model linking cis-element 3D spatial distribution to local-versus-global target search modalities essential for regulating eukaryotic gene transcription. DOI: http://dx.doi.org/10.7554/eLife.04236.001 PMID:25537195

  20. 3D gesture recognition from serial range image

    NASA Astrophysics Data System (ADS)

    Matsui, Yasuyuki; Miyasaka, Takeo; Hirose, Makoto; Araki, Kazuo

    2001-10-01

    In this research, the recognition of gesture in 3D space is examined by using serial range images obtained by a real-time 3D measurement system developed in our laboratory. Using this system, it is possible to obtain time sequences of range, intensity and color data for a moving object in real-time without assigning markers to the targets. At first, gestures are tracked in 2D space by calculating 2D flow vectors at each points using an ordinal optical flow estimation method, based on time sequences of the intensity data. Then, location of each point after 2D movement is detected on the x-y plane using thus obtained 2D flow vectors. Depth information of each point after movement is then obtained from the range data and 3D flow vectors are assigned to each point. Time sequences of thus obtained 3D flow vectors allow us to track the 3D movement of the target. So, based on time sequences of 3D flow vectors of the targets, it is possible to classify the movement of the targets using continuous DP matching technique. This tracking of 3D movement using time sequences of 3D flow vectors may be applicable for a robust gesture recognition system.

  1. The effect of visual context on manual localization of remembered targets

    NASA Technical Reports Server (NTRS)

    Barry, S. R.; Bloomberg, J. J.; Huebner, W. P.

    1997-01-01

    This paper examines the contribution of egocentric cues and visual context to manual localization of remembered targets. Subjects pointed in the dark to the remembered position of a target previously viewed without or within a structured visual scene. Without a remembered visual context, subjects pointed to within 2 degrees of the target. The presence of a visual context with cues of straight ahead enhanced pointing performance to the remembered location of central but not off-center targets. Thus, visual context provides strong visual cues of target position and the relationship of body position to target location. Without a visual context, egocentric cues provide sufficient input for accurate pointing to remembered targets.

  2. PLOT3D/AMES, GENERIC UNIX VERSION USING DISSPLA (WITHOUT TURB3D)

    NASA Technical Reports Server (NTRS)

    Buning, P.

    1994-01-01

    five groups: 1) Grid Functions for grids, grid-checking, etc.; 2) Scalar Functions for contour or carpet plots of density, pressure, temperature, Mach number, vorticity magnitude, helicity, etc.; 3) Vector Functions for vector plots of velocity, vorticity, momentum, and density gradient, etc.; 4) Particle Trace Functions for rake-like plots of particle flow or vortex lines; and 5) Shock locations based on pressure gradient. TURB3D is a modification of PLOT3D which is used for viewing CFD simulations of incompressible turbulent flow. Input flow data consists of pressure, velocity and vorticity. Typical quantities to plot include local fluctuations in flow quantities and turbulent production terms, plotted in physical or wall units. PLOT3D/TURB3D includes both TURB3D and PLOT3D because the operation of TURB3D is identical to PLOT3D, and there is no additional sample data or printed documentation for TURB3D. Graphical capabilities of PLOT3D version 3.6b+ vary among the implementations available through COSMIC. Customers are encouraged to purchase and carefully review the PLOT3D manual before ordering the program for a specific computer and graphics library. There is only one manual for use with all implementations of PLOT3D, and although this manual generally assumes that the Silicon Graphics Iris implementation is being used, informative comments concerning other implementations appear throughout the text. With all implementations, the visual representation of the object and flow field created by PLOT3D consists of points, lines, and polygons. Points can be represented with dots or symbols, color can be used to denote data values, and perspective is used to show depth. Differences among implementations impact the program's ability to use graphical features that are based on 3D polygons, the user's ability to manipulate the graphical displays, and the user's ability to obtain alternate forms of output. The UNIX/DISSPLA implementation of PLOT3D supports 2-D polygons as

  3. PLOT3D/AMES, GENERIC UNIX VERSION USING DISSPLA (WITH TURB3D)

    NASA Technical Reports Server (NTRS)

    Buning, P.

    1994-01-01

    five groups: 1) Grid Functions for grids, grid-checking, etc.; 2) Scalar Functions for contour or carpet plots of density, pressure, temperature, Mach number, vorticity magnitude, helicity, etc.; 3) Vector Functions for vector plots of velocity, vorticity, momentum, and density gradient, etc.; 4) Particle Trace Functions for rake-like plots of particle flow or vortex lines; and 5) Shock locations based on pressure gradient. TURB3D is a modification of PLOT3D which is used for viewing CFD simulations of incompressible turbulent flow. Input flow data consists of pressure, velocity and vorticity. Typical quantities to plot include local fluctuations in flow quantities and turbulent production terms, plotted in physical or wall units. PLOT3D/TURB3D includes both TURB3D and PLOT3D because the operation of TURB3D is identical to PLOT3D, and there is no additional sample data or printed documentation for TURB3D. Graphical capabilities of PLOT3D version 3.6b+ vary among the implementations available through COSMIC. Customers are encouraged to purchase and carefully review the PLOT3D manual before ordering the program for a specific computer and graphics library. There is only one manual for use with all implementations of PLOT3D, and although this manual generally assumes that the Silicon Graphics Iris implementation is being used, informative comments concerning other implementations appear throughout the text. With all implementations, the visual representation of the object and flow field created by PLOT3D consists of points, lines, and polygons. Points can be represented with dots or symbols, color can be used to denote data values, and perspective is used to show depth. Differences among implementations impact the program's ability to use graphical features that are based on 3D polygons, the user's ability to manipulate the graphical displays, and the user's ability to obtain alternate forms of output. The UNIX/DISSPLA implementation of PLOT3D supports 2-D polygons as

  4. A 2D driven 3D vessel segmentation algorithm for 3D digital subtraction angiography data.

    PubMed

    Spiegel, M; Redel, T; Struffert, T; Hornegger, J; Doerfler, A

    2011-10-01

    Cerebrovascular disease is among the leading causes of death in western industrial nations. 3D rotational angiography delivers indispensable information on vessel morphology and pathology. Physicians make use of this to analyze vessel geometry in detail, i.e. vessel diameters, location and size of aneurysms, to come up with a clinical decision. 3D segmentation is a crucial step in this pipeline. Although a lot of different methods are available nowadays, all of them lack a method to validate the results for the individual patient. Therefore, we propose a novel 2D digital subtraction angiography (DSA)-driven 3D vessel segmentation and validation framework. 2D DSA projections are clinically considered as gold standard when it comes to measurements of vessel diameter or the neck size of aneurysms. An ellipsoid vessel model is applied to deliver the initial 3D segmentation. To assess the accuracy of the 3D vessel segmentation, its forward projections are iteratively overlaid with the corresponding 2D DSA projections. Local vessel discrepancies are modeled by a global 2D/3D optimization function to adjust the 3D vessel segmentation toward the 2D vessel contours. Our framework has been evaluated on phantom data as well as on ten patient datasets. Three 2D DSA projections from varying viewing angles have been used for each dataset. The novel 2D driven 3D vessel segmentation approach shows superior results against state-of-the-art segmentations like region growing, i.e. an improvement of 7.2% points in precision and 5.8% points for the Dice coefficient. This method opens up future clinical applications requiring the greatest vessel accuracy, e.g. computational fluid dynamic modeling. PMID:21908904

  5. A 2D driven 3D vessel segmentation algorithm for 3D digital subtraction angiography data

    NASA Astrophysics Data System (ADS)

    Spiegel, M.; Redel, T.; Struffert, T.; Hornegger, J.; Doerfler, A.

    2011-10-01

    Cerebrovascular disease is among the leading causes of death in western industrial nations. 3D rotational angiography delivers indispensable information on vessel morphology and pathology. Physicians make use of this to analyze vessel geometry in detail, i.e. vessel diameters, location and size of aneurysms, to come up with a clinical decision. 3D segmentation is a crucial step in this pipeline. Although a lot of different methods are available nowadays, all of them lack a method to validate the results for the individual patient. Therefore, we propose a novel 2D digital subtraction angiography (DSA)-driven 3D vessel segmentation and validation framework. 2D DSA projections are clinically considered as gold standard when it comes to measurements of vessel diameter or the neck size of aneurysms. An ellipsoid vessel model is applied to deliver the initial 3D segmentation. To assess the accuracy of the 3D vessel segmentation, its forward projections are iteratively overlaid with the corresponding 2D DSA projections. Local vessel discrepancies are modeled by a global 2D/3D optimization function to adjust the 3D vessel segmentation toward the 2D vessel contours. Our framework has been evaluated on phantom data as well as on ten patient datasets. Three 2D DSA projections from varying viewing angles have been used for each dataset. The novel 2D driven 3D vessel segmentation approach shows superior results against state-of-the-art segmentations like region growing, i.e. an improvement of 7.2% points in precision and 5.8% points for the Dice coefficient. This method opens up future clinical applications requiring the greatest vessel accuracy, e.g. computational fluid dynamic modeling.

  6. 3D-Printed Microfluidics.

    PubMed

    Au, Anthony K; Huynh, Wilson; Horowitz, Lisa F; Folch, Albert

    2016-03-14

    The advent of soft lithography allowed for an unprecedented expansion in the field of microfluidics. However, the vast majority of PDMS microfluidic devices are still made with extensive manual labor, are tethered to bulky control systems, and have cumbersome user interfaces, which all render commercialization difficult. On the other hand, 3D printing has begun to embrace the range of sizes and materials that appeal to the developers of microfluidic devices. Prior to fabrication, a design is digitally built as a detailed 3D CAD file. The design can be assembled in modules by remotely collaborating teams, and its mechanical and fluidic behavior can be simulated using finite-element modeling. As structures are created by adding materials without the need for etching or dissolution, processing is environmentally friendly and economically efficient. We predict that in the next few years, 3D printing will replace most PDMS and plastic molding techniques in academia. PMID:26854878

  7. 3D Imaging with Structured Illumination for Advanced Security Applications

    SciTech Connect

    Birch, Gabriel Carisle; Dagel, Amber Lynn; Kast, Brian A.; Smith, Collin S.

    2015-09-01

    Three-dimensional (3D) information in a physical security system is a highly useful dis- criminator. The two-dimensional data from an imaging systems fails to provide target dis- tance and three-dimensional motion vector, which can be used to reduce nuisance alarm rates and increase system effectiveness. However, 3D imaging devices designed primarily for use in physical security systems are uncommon. This report discusses an architecture favorable to physical security systems; an inexpensive snapshot 3D imaging system utilizing a simple illumination system. The method of acquiring 3D data, tests to understand illumination de- sign, and software modifications possible to maximize information gathering capability are discussed.

  8. 3D Computations and Experiments

    SciTech Connect

    Couch, R; Faux, D; Goto, D; Nikkel, D

    2004-04-05

    This project consists of two activities. Task A, Simulations and Measurements, combines all the material model development and associated numerical work with the materials-oriented experimental activities. The goal of this effort is to provide an improved understanding of dynamic material properties and to provide accurate numerical representations of those properties for use in analysis codes. Task B, ALE3D Development, involves general development activities in the ALE3D code with the focus of improving simulation capabilities for problems of mutual interest to DoD and DOE. Emphasis is on problems involving multi-phase flow, blast loading of structures and system safety/vulnerability studies.

  9. 3D Computations and Experiments

    SciTech Connect

    Couch, R; Faux, D; Goto, D; Nikkel, D

    2003-05-12

    This project is in its first full year after the combining of two previously funded projects: ''3D Code Development'' and ''Dynamic Material Properties''. The motivation behind this move was to emphasize and strengthen the ties between the experimental work and the computational model development in the materials area. The next year's activities will indicate the merging of the two efforts. The current activity is structured in two tasks. Task A, ''Simulations and Measurements'', combines all the material model development and associated numerical work with the materials-oriented experimental activities. Task B, ''ALE3D Development'', is a continuation of the non-materials related activities from the previous project.

  10. Infants' Visual Localization of Visual and Auditory Targets.

    ERIC Educational Resources Information Center

    Bechtold, A. Gordon; And Others

    This study is an investigation of 2-month-old infants' abilities to visually localize visual and auditory peripheral stimuli. Each subject (N=40) was presented with 50 trials; 25 of these visual and 25 auditory. The infant was placed in a semi-upright infant seat positioned 122 cm from the center speaker of an arc formed by five loudspeakers. At…

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

    PubMed Central

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

    2016-01-01

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

  12. Memory and visual search in naturalistic 2D and 3D environments

    PubMed Central

    Li, Chia-Ling; Aivar, M. Pilar; Kit, Dmitry M.; Tong, Matthew H.; Hayhoe, Mary M.

    2016-01-01

    The role of memory in guiding attention allocation in daily behaviors is not well understood. In experiments with two-dimensional (2D) images, there is mixed evidence about the importance of memory. Because the stimulus context in laboratory experiments and daily behaviors differs extensively, we investigated the role of memory in visual search, in both two-dimensional (2D) and three-dimensional (3D) environments. A 3D immersive virtual apartment composed of two rooms was created, and a parallel 2D visual search experiment composed of snapshots from the 3D environment was developed. Eye movements were tracked in both experiments. Repeated searches for geometric objects were performed to assess the role of spatial memory. Subsequently, subjects searched for realistic context objects to test for incidental learning. Our results show that subjects learned the room-target associations in 3D but less so in 2D. Gaze was increasingly restricted to relevant regions of the room with experience in both settings. Search for local contextual objects, however, was not facilitated by early experience. Incidental fixations to context objects do not necessarily benefit search performance. Together, these results demonstrate that memory for global aspects of the environment guides search by restricting allocation of attention to likely regions, whereas task relevance determines what is learned from the active search experience. Behaviors in 2D and 3D environments are comparable, although there is greater use of memory in 3D. PMID:27299769

  13. Memory and visual search in naturalistic 2D and 3D environments.

    PubMed

    Li, Chia-Ling; Aivar, M Pilar; Kit, Dmitry M; Tong, Matthew H; Hayhoe, Mary M

    2016-06-01

    The role of memory in guiding attention allocation in daily behaviors is not well understood. In experiments with two-dimensional (2D) images, there is mixed evidence about the importance of memory. Because the stimulus context in laboratory experiments and daily behaviors differs extensively, we investigated the role of memory in visual search, in both two-dimensional (2D) and three-dimensional (3D) environments. A 3D immersive virtual apartment composed of two rooms was created, and a parallel 2D visual search experiment composed of snapshots from the 3D environment was developed. Eye movements were tracked in both experiments. Repeated searches for geometric objects were performed to assess the role of spatial memory. Subsequently, subjects searched for realistic context objects to test for incidental learning. Our results show that subjects learned the room-target associations in 3D but less so in 2D. Gaze was increasingly restricted to relevant regions of the room with experience in both settings. Search for local contextual objects, however, was not facilitated by early experience. Incidental fixations to context objects do not necessarily benefit search performance. Together, these results demonstrate that memory for global aspects of the environment guides search by restricting allocation of attention to likely regions, whereas task relevance determines what is learned from the active search experience. Behaviors in 2D and 3D environments are comparable, although there is greater use of memory in 3D. PMID:27299769

  14. Localizing moving targets and organs using motion-managed CTs

    SciTech Connect

    Brandner, Edward D. . E-mail: brandnere@upmc.edu; Heron, Dwight; Wu, Andrew; Huq, M. Saiful; Yue, Ning J.; Chen, Hungcheng M.S.

    2006-07-01

    Respiration-induced target and organ motion impacts the radiotherapy strategies of some cancers. Various methods and techniques have been used to investigate motion-related radiotherapy issues, including retrospective 4-dimensional (4D) computed tomography (CT), prospective gated CT, and breath-hold CT scans. This paper reviews these methods and, particularly, the method using retrospective 4D CT scans, which has been developed at our institution. Some motion studies based on retrospective 4D CT images of patients are also examined. These studies have led to reduced planning target volume (PTV) margins for a number of patients, because the respiratory motion was observed to be minimal or gated radiotherapy was used. Respiratory motion managed CTs and, particularly, retrospective 4D CTs are proving to be useful for measuring soft tissue motion, identifying patients who could benefit from gated radiotherapy, and evaluating the effects of respiratory motion during radiotherapy.

  15. Sustained Attention to Local and Global Target Features Is Different: Performance and Tympanic Membrane Temperature

    ERIC Educational Resources Information Center

    Helton, William S.; Hayrynen, Lauren; Schaeffer, David

    2009-01-01

    Vision researchers have investigated the differences between global and local feature perception. No one has, however, examined the role of global and local feature discrimination in sustained attention tasks. In this experiment participants performed a sustained attention task requiring either global or local letter target discriminations or…

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

    PubMed Central

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

    2015-01-01

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

  17. 3D multifocus astigmatism and compressed sensing (3D MACS) based superresolution reconstruction.

    PubMed

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

    2015-03-01

    Single molecule based superresolution techniques (STORM/PALM) achieve nanometer spatial resolution by integrating the temporal information of the switching dynamics of fluorophores (emitters). When emitter density is low for each frame, they are located to the nanometer resolution. However, when the emitter density rises, causing significant overlapping, it becomes increasingly difficult to accurately locate individual emitters. This is particularly apparent in three dimensional (3D) localization because of the large effective volume of the 3D point spread function (PSF). The inability to precisely locate the emitters at a high density causes poor temporal resolution of localization-based superresolution technique and significantly limits its application in 3D live cell imaging. To address this problem, we developed a 3D high-density superresolution imaging platform that allows us to precisely locate the positions of emitters, even when they are significantly overlapped in three dimensional space. Our platform involves a multi-focus system in combination with astigmatic optics and an ℓ 1-Homotopy optimization procedure. To reduce the intrinsic bias introduced by the discrete formulation of compressed sensing, we introduced a debiasing step followed by a 3D weighted centroid procedure, which not only increases the localization accuracy, but also increases the computation speed of image reconstruction. We implemented our algorithms on a graphic processing unit (GPU), which speeds up processing 10 times compared with central processing unit (CPU) implementation. We tested our method with both simulated data and experimental data of fluorescently labeled microtubules and were able to reconstruct a 3D microtubule image with 1000 frames (512×512) acquired within 20 seconds. PMID:25798314

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

    NASA Technical Reports Server (NTRS)

    Buning, P.

    1994-01-01

    five groups: 1) Grid Functions for grids, grid-checking, etc.; 2) Scalar Functions for contour or carpet plots of density, pressure, temperature, Mach number, vorticity magnitude, helicity, etc.; 3) Vector Functions for vector plots of velocity, vorticity, momentum, and density gradient, etc.; 4) Particle Trace Functions for rake-like plo