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Sample records for 3d particle tracking

  1. 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.

  2. 3D imaging of particle tracks in Solid State Nuclear Track Detectors

    NASA Astrophysics Data System (ADS)

    Wertheim, D.; Gillmore, G.; Brown, L.; Petford, N.

    2009-04-01

    Inhalation of radon gas (222Rn) and associated ionizing decay products is known to cause lung cancer in human. In the U.K., it has been suggested that 3 to 5 % of total lung cancer deaths can be linked to elevated radon concentrations in the home and/or workplace. Radon monitoring in buildings is therefore routinely undertaken in areas of known risk. Indeed, some organisations such as the Radon Council in the UK and the Environmental Protection Agency in the USA, advocate a ‘to test is best' policy. Radon gas occurs naturally, emanating from the decay of 238U in rock and soils. Its concentration can be measured using CR?39 plastic detectors which conventionally are assessed by 2D image analysis of the surface; however there can be some variation in outcomes / readings even in closely spaced detectors. A number of radon measurement methods are currently in use (for examples, activated carbon and electrets) but the most widely used are CR?39 solid state nuclear track?etch detectors (SSNTDs). In this technique, heavily ionizing alpha particles leave tracks in the form of radiation damage (via interaction between alpha particles and the atoms making up the CR?39 polymer). 3D imaging of the tracks has the potential to provide information relating to angle and energy of alpha particles but this could be time consuming. Here we describe a new method for rapid high resolution 3D imaging of SSNTDs. A ‘LEXT' OLS3100 confocal laser scanning microscope was used in confocal mode to successfully obtain 3D image data on four CR?39 plastic detectors. 3D visualisation and image analysis enabled characterisation of track features. This method may provide a means of rapid and detailed 3D analysis of SSNTDs. Keywords: Radon; SSNTDs; confocal laser scanning microscope; 3D imaging; LEXT

  3. 3D measurement of the position of gold particles via evanescent digital holographic particle tracking velocimetry

    NASA Astrophysics Data System (ADS)

    Satake, Shin-ichi; Unno, Noriyuki; Nakata, Shuichiro; Taniguchi, Jun

    2016-08-01

    A new technique based on digital holography and evanescent waves was developed for 3D measurements of the position of gold nanoparticles in water. In this technique, an intensity profile is taken from a holographic image of a gold particle. To detect the position of the gold particle with high accuracy, its holographic image is recorded on a nanosized step made of MEXFLON, which has a refractive index close to that of water, and the position of the particle is reconstructed by means of digital holography. The height of the nanosized step was measured by using a profilometer and the digitally reconstructed height of the glass substrate had good agreement with the measured value. Furthermore, this method can be used to accurately track the 3D position of a gold particle in water.

  4. A 3D diamond detector for particle tracking

    NASA Astrophysics Data System (ADS)

    Artuso, M.; Bachmair, F.; Bäni, L.; Bartosik, M.; Beacham, J.; Bellini, V.; Belyaev, V.; Bentele, B.; Berdermann, E.; Bergonzo, P.; Bes, A.; Brom, J.-M.; Bruzzi, M.; Cerv, M.; Chau, C.; Chiodini, G.; Chren, D.; Cindro, V.; Claus, G.; Collot, J.; Costa, S.; Cumalat, J.; Dabrowski, A.; D`Alessandro, R.; de Boer, W.; Dehning, B.; Dobos, D.; Dünser, M.; Eremin, V.; Eusebi, R.; Forcolin, G.; Forneris, J.; Frais-Kölbl, H.; Gan, K. K.; Gastal, M.; Goffe, M.; Goldstein, J.; Golubev, A.; Gonella, L.; Gorišek, A.; Graber, L.; Grigoriev, E.; Grosse-Knetter, J.; Gui, B.; Guthoff, M.; Haughton, I.; Hidas, D.; Hits, D.; Hoeferkamp, M.; Hofmann, T.; Hosslet, J.; Hostachy, J.-Y.; Hügging, F.; Jansen, H.; Janssen, J.; Kagan, H.; Kanxheri, K.; Kasieczka, G.; Kass, R.; Kassel, F.; Kis, M.; Kramberger, G.; Kuleshov, S.; Lacoste, A.; Lagomarsino, S.; Lo Giudice, A.; Maazouzi, C.; Mandic, I.; Mathieu, C.; McFadden, N.; McGoldrick, G.; Menichelli, M.; Mikuž, M.; Morozzi, A.; Moss, J.; Mountain, R.; Murphy, S.; Oh, A.; Olivero, P.; Parrini, G.; Passeri, D.; Pauluzzi, M.; Pernegger, H.; Perrino, R.; Picollo, F.; Pomorski, M.; Potenza, R.; Quadt, A.; Re, A.; Riley, G.; Roe, S.; Sapinski, M.; Scaringella, M.; Schnetzer, S.; Schreiner, T.; Sciortino, S.; Scorzoni, A.; Seidel, S.; Servoli, L.; Sfyrla, A.; Shimchuk, G.; Smith, D. S.; Sopko, B.; Sopko, V.; Spagnolo, S.; Spanier, S.; Stenson, K.; Stone, R.; Sutera, C.; Taylor, A.; Traeger, M.; Tromson, D.; Trischuk, W.; Tuve, C.; Uplegger, L.; Velthuis, J.; Venturi, N.; Vittone, E.; Wagner, S.; Wallny, R.; Wang, J. C.; Weilhammer, P.; Weingarten, J.; Weiss, C.; Wengler, T.; Wermes, N.; Yamouni, M.; Zavrtanik, M.

    2016-07-01

    In the present study, results towards the development of a 3D diamond sensor are presented. Conductive channels are produced inside the sensor bulk using a femtosecond laser. This electrode geometry allows full charge collection even for low quality diamond sensors. Results from testbeam show that charge is collected by these electrodes. In order to understand the channel growth parameters, with the goal of producing low resistivity channels, the conductive channels produced with a different laser setup are evaluated by Raman spectroscopy.

  5. 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

  6. 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.

  7. 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.

  8. Particle Filters and Occlusion Handling for Rigid 2D-3D Pose Tracking.

    PubMed

    Lee, Jehoon; Sandhu, Romeil; Tannenbaum, Allen

    2013-08-01

    In this paper, we address the problem of 2D-3D pose estimation. Specifically, we propose an approach to jointly track a rigid object in a 2D image sequence and to estimate its pose (position and orientation) in 3D space. We revisit a joint 2D segmentation/3D pose estimation technique, and then extend the framework by incorporating a particle filter to robustly track the object in a challenging environment, and by developing an occlusion detection and handling scheme to continuously track the object in the presence of occlusions. In particular, we focus on partial occlusions that prevent the tracker from extracting an exact region properties of the object, which plays a pivotal role for region-based tracking methods in maintaining the track. To this end, a dynamical choice of how to invoke the objective functional is performed online based on the degree of dependencies between predictions and measurements of the system in accordance with the degree of occlusion and the variation of the object's pose. This scheme provides the robustness to deal with occlusions of an obstacle with different statistical properties from that of the object of interest. Experimental results demonstrate the practical applicability and robustness of the proposed method in several challenging scenarios. PMID:24058277

  9. 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.

  10. Fast parallel interferometric 3D tracking of numerous optically trapped particles and their hydrodynamic interaction.

    PubMed

    Ruh, Dominic; Tränkle, Benjamin; Rohrbach, Alexander

    2011-10-24

    Multi-dimensional, correlated particle tracking is a key technology to reveal dynamic processes in living and synthetic soft matter systems. In this paper we present a new method for tracking micron-sized beads in parallel and in all three dimensions - faster and more precise than existing techniques. Using an acousto-optic deflector and two quadrant-photo-diodes, we can track numerous optically trapped beads at up to tens of kHz with a precision of a few nanometers by back-focal plane interferometry. By time-multiplexing the laser focus, we can calibrate individually all traps and all tracking signals in a few seconds and in 3D. We show 3D histograms and calibration constants for nine beads in a quadratic arrangement, although trapping and tracking is easily possible for more beads also in arbitrary 2D arrangements. As an application, we investigate the hydrodynamic coupling and diffusion anomalies of spheres trapped in a 3 × 3 arrangement. PMID:22109012

  11. A 3D Vector/Scalar Visualization and Particle Tracking Package

    1999-08-19

    BOILERMAKER is an interactive visualization system consisting of three components: a visualization component, a particle tracking component, and a communication layer. The software, to date, has been used primarily in the visualization of vector and scalar fields associated with computational fluid dynamics (CFD) models of flue gas flows in industrial boilers and incinerators. Users can interactively request and toggle static vector fields, dynamic streamlines, and flowing vector fields. In addition, the user can interactively placemore » injector nozzles on boiler walls and visualize massed, evaporating sprays emanating from them. Some characteristics of the spray can be adjusted from within the visualization environment including spray shape and particle size. Also included with this release is software that supports 3D menu capabilities, scrollbars, communication and navigation.« less

  12. A 3D Vector/Scalar Visualization and Particle Tracking Package

    SciTech Connect

    Freitag, Lori; Disz, Terry; Papka, Mike; Heath, Daniel; Diachin, Darin; Herzog, Jim; Ryan, and Bob

    1999-08-19

    BOILERMAKER is an interactive visualization system consisting of three components: a visualization component, a particle tracking component, and a communication layer. The software, to date, has been used primarily in the visualization of vector and scalar fields associated with computational fluid dynamics (CFD) models of flue gas flows in industrial boilers and incinerators. Users can interactively request and toggle static vector fields, dynamic streamlines, and flowing vector fields. In addition, the user can interactively place injector nozzles on boiler walls and visualize massed, evaporating sprays emanating from them. Some characteristics of the spray can be adjusted from within the visualization environment including spray shape and particle size. Also included with this release is software that supports 3D menu capabilities, scrollbars, communication and navigation.

  13. Application of 3D hydrodynamic and particle tracking models for better environmental management of finfish culture

    NASA Astrophysics Data System (ADS)

    Moreno Navas, Juan; Telfer, Trevor C.; Ross, Lindsay G.

    2011-04-01

    Hydrographic conditions, and particularly current speeds, have a strong influence on the management of fish cage culture. These hydrodynamic conditions can be used to predict particle movement within the water column and the results used to optimise environmental conditions for effective site selection, setting of environmental quality standards, waste dispersion, and potential disease transfer. To this end, a 3D hydrodynamic model, MOHID, has been coupled to a particle tracking model to study the effects of mean current speed, quiescent water periods and bulk water circulation in Mulroy Bay, Co. Donegal Ireland, an Irish fjard (shallow fjordic system) important to the aquaculture industry. A Lagangrian method simulated the instantaneous release of "particles" emulating discharge from finfish cages to show the behaviour of waste in terms of water circulation and water exchange. The 3D spatial models were used to identify areas of mixed and stratified water using a version of the Simpson-Hunter criteria, and to use this in conjunction with models of current flow for appropriate site selection for salmon aquaculture. The modelled outcomes for stratification were in good agreement with the direct measurements of water column stratification based on observed density profiles. Calculations of the Simpson-Hunter tidal parameter indicated that most of Mulroy Bay was potentially stratified with a well mixed region over the shallow channels where the water is faster flowing. The fjard was characterised by areas of both very low and high mean current speeds, with some areas having long periods of quiescent water. The residual current and the particle tracking animations created through the models revealed an anticlockwise eddy that may influence waste dispersion and potential for disease transfer, among salmon cages and which ensures that the retention time of waste substances from cages is extended. The hydrodynamic model results were incorporated into the ArcView TM GIS

  14. Longitudinal Measurement of Extracellular Matrix Rigidity in 3D Tumor Models Using Particle-tracking Microrheology

    PubMed Central

    El-Hamidi, Hamid; Celli, Jonathan P.

    2014-01-01

    The mechanical microenvironment has been shown to act as a crucial regulator of tumor growth behavior and signaling, which is itself remodeled and modified as part of a set of complex, two-way mechanosensitive interactions. While the development of biologically-relevant 3D tumor models have facilitated mechanistic studies on the impact of matrix rheology on tumor growth, the inverse problem of mapping changes in the mechanical environment induced by tumors remains challenging. Here, we describe the implementation of particle-tracking microrheology (PTM) in conjunction with 3D models of pancreatic cancer as part of a robust and viable approach for longitudinally monitoring physical changes in the tumor microenvironment, in situ. The methodology described here integrates a system of preparing in vitro 3D models embedded in a model extracellular matrix (ECM) scaffold of Type I collagen with fluorescently labeled probes uniformly distributed for position- and time-dependent microrheology measurements throughout the specimen. In vitro tumors are plated and probed in parallel conditions using multiwell imaging plates. Drawing on established methods, videos of tracer probe movements are transformed via the Generalized Stokes Einstein Relation (GSER) to report the complex frequency-dependent viscoelastic shear modulus, G*(ω). Because this approach is imaging-based, mechanical characterization is also mapped onto large transmitted-light spatial fields to simultaneously report qualitative changes in 3D tumor size and phenotype. Representative results showing contrasting mechanical response in sub-regions associated with localized invasion-induced matrix degradation as well as system calibration, validation data are presented. Undesirable outcomes from common experimental errors and troubleshooting of these issues are also presented. The 96-well 3D culture plating format implemented in this protocol is conducive to correlation of microrheology measurements with therapeutic

  15. Mapping dynamic mechanical remodeling in 3D tumor models via particle tracking microrheology

    NASA Astrophysics Data System (ADS)

    Jones, Dustin P.; Hanna, William; Celli, Jonathan P.

    2015-03-01

    Particle tracking microrheology (PTM) has recently been employed as a non-destructive way to longitudinally track physical changes in 3D pancreatic tumor co-culture models concomitant with tumor growth and invasion into the extracellular matrix (ECM). While the primary goal of PTM is to quantify local viscoelasticity via the Generalized Stokes-Einstein Relation (GSER), a more simplified way of describing local tissue mechanics lies in the tabulation and subsequent visualization of the spread of probe displacements in a given field of view. Proper analysis of this largely untapped byproduct of standard PTM has the potential to yield valuable insight into the structure and integrity of the ECM. Here, we use clustering algorithms in R to analyze the trajectories of probes in 3D pancreatic tumor/fibroblast co-culture models in an attempt to differentiate between probes that are effectively constrained by the ECM and/or contractile traction forces, and those that exhibit uninhibited mobility in local water-filled pores. We also discuss the potential pitfalls of this method. Accurately and reproducibly quantifying the boundary between these two categories of probe behavior could result in an effective method for measuring the average pore size in a given region of ECM. Such a tool could prove useful for studying stromal depletion, physical impedance to drug delivery, and degradation due to cellular invasion.

  16. 3-D Particle Tracking Velocimetry: Development and Applications in Small Scale Flows

    NASA Astrophysics Data System (ADS)

    Tien, Wei-Hsin

    The thesis contains two parts of studies. In part I, a novel volumetric velocimetry technique is developed to measure the 3-D flow field of small-scale flows. The technique utilizes a color-coded pinhole plate with multiple light sources aligned to each pinhole to achieve high particle image density and large measurable depth on a single lens microscope system. A color separation algorithm and an improved particle identification algorithm are developed to identify individual particle images from each pinhole view. Furthermore, a calibration-based technique based on epi-polar line search method is developed to reconstruct the spatial coordinates of the particle, and a new two-frame tracking particle-tracking algorithm is developed to calculate the velocity field. The system was setup to achieve a magnification of 2.69, resulting in an imaging volume of 3.35 x 2.5 x 1.5 mm3 and showed satisfactory measurement accuracy. The technique was then further miniaturized to achieve a magnification of 10, resulting in a imaging volume of 600 x 600 x 600 microm3. The system was applied to a backward-facing step flow to test its ability to reconstruct the unsteady flow field with two-frame tracking. Finally, this technique was applied to a steady streaming flow field in a microfluidic device used to trap particles. The results revealed the three-dimensional flow structure that has not been observed in previous studies, and provided insights to the design of a more efficient trapping device. In part II, an in-vitro study was carried out to investigate the flow around a prosthetic venous valve. Using 2-D PIV, the dynamics of the valve motion was captured and the velocity fields were measured to investigate the effect of the sinus pocket and the coupling effect of a pair of valves. The PIV and hemodynamic results showed that the sinus pocket around the valve functioned as a flow regulator to smooth the entrained velocity profile and suppress the jet width. For current prosthetic

  17. Ultra-high-speed 3D astigmatic particle tracking velocimetry: application to particle-laden supersonic impinging jets

    NASA Astrophysics Data System (ADS)

    Buchmann, N. A.; Cierpka, C.; Kähler, C. J.; Soria, J.

    2014-11-01

    The paper demonstrates ultra-high-speed three-component, three-dimensional (3C3D) velocity measurements of micron-sized particles suspended in a supersonic impinging jet flow. Understanding the dynamics of individual particles in such flows is important for the design of particle impactors for drug delivery or cold gas dynamic spray processing. The underexpanded jet flow is produced via a converging nozzle, and micron-sized particles ( d p = 110 μm) are introduced into the gas flow. The supersonic jet impinges onto a flat surface, and the particle impact velocity and particle impact angle are studied for a range of flow conditions and impingement distances. The imaging system consists of an ultra-high-speed digital camera (Shimadzu HPV-1) capable of recording rates of up to 1 Mfps. Astigmatism particle tracking velocimetry (APTV) is used to measure the 3D particle position (Cierpka et al., Meas Sci Technol 21(045401):13, 2010) by coding the particle depth location in the 2D images by adding a cylindrical lens to the high-speed imaging system. Based on the reconstructed 3D particle positions, the particle trajectories are obtained via a higher-order tracking scheme that takes advantage of the high temporal resolution to increase robustness and accuracy of the measurement. It is shown that the particle velocity and impingement angle are affected by the gas flow in a manner depending on the nozzle pressure ratio and stand-off distance where higher pressure ratios and stand-off distances lead to higher impact velocities and larger impact angles.

  18. 3D positional tracking of ellipsoidal particles in a microtube flow using holographic microscopy

    NASA Astrophysics Data System (ADS)

    Byeon, Hyeok Jun; Seo, Kyung Won; Lee, Sang Joon

    2014-11-01

    Understanding of micro-scale flow phenomena is getting large attention under advances in micro-scale measurement technologies. Especially, the dynamics of particles suspended in a fluid is essential in both scientific and industrial fields. Moreover, most particles handled in research and industrial fields have non-spherical shapes rather than a simple spherical shape. Under various flow conditions, these non-spherical particles exhibit unique dynamic behaviors. To analyze these dynamic behaviors in a fluid flow, 3D positional information of the particles should be measured accurately. In this study, digital holographic microscopy (DHM) is employed to measure the 3D positional information of non-spherical particles, which are fabricated by stretching spherical polystyrene particles. 3D motions of those particles are obtained by interpreting the holograms captured from particles. Ellipsoidal particles with known size and shape are observed to verify the performance of the DHM technique. In addition, 3D positions of particles in a microtube flow are traced. This DHM technique exhibits promising potential in the analysis of dynamic behaviors of non-spherical particles suspended in micro-scale fluid flows.

  19. Digital In-Line Holography System for 3D-3C Particle Tracking Velocimetry

    NASA Astrophysics Data System (ADS)

    Malek, Mokrane; Lebrun, Denis; Allano, Daniel

    Digital in-line holography is a suitable method for measuring three dimensional (3D) velocity fields. Such a system records directly on a charge-coupled device (CCD) camera a couple of diffraction patterns produced by small particles illuminated by a modulated laser diode. The numerical reconstruction is based on the wavelet transformation method. A 3D particle field is reconstructed by computing the wavelet components for different scale parameters. The scale parameter is directly related to the axial distance between a given particle and the CCD camera. The particle images are identified and localized by analyzing the maximum of the wavelet transform modulus (WTMM) and the equivalent diameter of the particle image (Deq). Afterwards, a 3D point-matching (PM) algorithm is applied to the pair of sets containing the 3D particle locations. In the PM algorithm, the displacement of the particles is modeled by an affine transformation. This affine transformation is based on the use of the dual number quaternions. Afterwards, the velocity-field extraction is performed. This system is tested with simulated particle field displacements and the feasibility is checked with an experimental displacement.

  20. Particle tracking approach for transport in three-dimensional discrete fracture networks: Particle tracking in 3-D DFNs

    DOE PAGESBeta

    Makedonska, Nataliia; Painter, Scott L.; Bui, Quan M.; Gable, Carl W.; Karra, Satish

    2015-09-16

    The discrete fracture network (DFN) model is a method to mimic discrete pathways for fluid flow through a fractured low-permeable rock mass, and may be combined with particle tracking simulations to address solute transport. However, experience has shown that it is challenging to obtain accurate transport results in three-dimensional DFNs because of the high computational burden and difficulty in constructing a high-quality unstructured computational mesh on simulated fractures. We present a new particle tracking capability, which is adapted to control volume (Voronoi polygons) flow solutions on unstructured grids (Delaunay triangulations) on three-dimensional DFNs. The locally mass-conserving finite-volume approach eliminates massmore » balance-related problems during particle tracking. The scalar fluxes calculated for each control volume face by the flow solver are used to reconstruct a Darcy velocity at each control volume centroid. The groundwater velocities can then be continuously interpolated to any point in the domain of interest. The control volumes at fracture intersections are split into four pieces, and the velocity is reconstructed independently on each piece, which results in multiple groundwater velocities at the intersection, one for each fracture on each side of the intersection line. This technique enables detailed particle transport representation through a complex DFN structure. Verified for small DFNs, the new simulation capability enables numerical experiments on advective transport in large DFNs to be performed. As a result, we demonstrate this particle transport approach on a DFN model using parameters similar to those of crystalline rock at a proposed geologic repository for spent nuclear fuel in Forsmark, Sweden.« less

  1. Particle tracking approach for transport in three-dimensional discrete fracture networks: Particle tracking in 3-D DFNs

    SciTech Connect

    Makedonska, Nataliia; Painter, Scott L.; Bui, Quan M.; Gable, Carl W.; Karra, Satish

    2015-09-16

    The discrete fracture network (DFN) model is a method to mimic discrete pathways for fluid flow through a fractured low-permeable rock mass, and may be combined with particle tracking simulations to address solute transport. However, experience has shown that it is challenging to obtain accurate transport results in three-dimensional DFNs because of the high computational burden and difficulty in constructing a high-quality unstructured computational mesh on simulated fractures. We present a new particle tracking capability, which is adapted to control volume (Voronoi polygons) flow solutions on unstructured grids (Delaunay triangulations) on three-dimensional DFNs. The locally mass-conserving finite-volume approach eliminates mass balance-related problems during particle tracking. The scalar fluxes calculated for each control volume face by the flow solver are used to reconstruct a Darcy velocity at each control volume centroid. The groundwater velocities can then be continuously interpolated to any point in the domain of interest. The control volumes at fracture intersections are split into four pieces, and the velocity is reconstructed independently on each piece, which results in multiple groundwater velocities at the intersection, one for each fracture on each side of the intersection line. This technique enables detailed particle transport representation through a complex DFN structure. Verified for small DFNs, the new simulation capability enables numerical experiments on advective transport in large DFNs to be performed. As a result, we demonstrate this particle transport approach on a DFN model using parameters similar to those of crystalline rock at a proposed geologic repository for spent nuclear fuel in Forsmark, Sweden.

  2. A Framework for 3D Model-Based Visual Tracking Using a GPU-Accelerated Particle Filter.

    PubMed

    Brown, J A; Capson, D W

    2012-01-01

    A novel framework for acceleration of particle filtering approaches to 3D model-based, markerless visual tracking in monocular video is described. Specifically, we present a methodology for partitioning and mapping the computationally expensive weight-update stage of a particle filter to a graphics processing unit (GPU) to achieve particle- and pixel-level parallelism. Nvidia CUDA and Direct3D are employed to harness the massively parallel computational power of modern GPUs for simulation (3D model rendering) and evaluation (segmentation, feature extraction, and weight calculation) of hundreds of particles at high speeds. The proposed framework addresses the computational intensity that is intrinsic to all particle filter approaches, including those that have been modified to minimize the number of particles required for a particular task. Performance and tracking quality results for rigid object and articulated hand tracking experiments demonstrate markerless, model-based visual tracking on consumer-grade graphics hardware with pixel-level accuracy up to 95 percent at 60+ frames per second. The framework accelerates particle evaluation up to 49 times over a comparable CPU-only implementation, providing an increased particle count while maintaining real-time frame rates. PMID:21301027

  3. A novel 3D micron-scale DPTV (Defocused Particle Tracking Velocimetry) and its applications in microfluidic devices

    NASA Astrophysics Data System (ADS)

    Roberts, John

    2005-11-01

    The rapid advancements in micro/nano biotechnology demand quantitative tools for characterizing microfluidic flows in lab-on-a-chip applications, validation of computational results for fully 3D flows in complex micro-devices, and efficient observation of cellular dynamics in 3D. We present a novel 3D micron-scale DPTV (defocused particle tracking velocimetry) that is capable of mapping out 3D Lagrangian, as well as 3D Eulerian velocity flow fields at sub-micron resolution and with one camera. The main part of the imaging system is an epi-fluorescent microscope (Olympus IX 51), and the seeding particles are fluorescent particles with diameter range 300nm - 10um. A software package has been developed for identifying (x,y,z,t) coordinates of the particles using the defocused images. Using the imaging system, we successfully mapped the pressure driven flow fields in microfluidic channels. In particular, we measured the Laglangian flow fields in a microfluidic channel with a herring bone pattern at the bottom, the later is used to enhance fluid mixing in lateral directions. The 3D particle tracks revealed the flow structure that has only been seen in numerical computation. This work is supported by the National Science Foundation (CTS - 0514443), the Nanobiotechnology Center at Cornell, and The New York State Center for Life Science Enterprise.

  4. 3D silicon sensors with variable electrode depth for radiation hard high resolution particle tracking

    NASA Astrophysics Data System (ADS)

    Da Vià, C.; Borri, M.; Dalla Betta, G.; Haughton, I.; Hasi, J.; Kenney, C.; Povoli, M.; Mendicino, R.

    2015-04-01

    3D sensors, with electrodes micro-processed inside the silicon bulk using Micro-Electro-Mechanical System (MEMS) technology, were industrialized in 2012 and were installed in the first detector upgrade at the LHC, the ATLAS IBL in 2014. They are the radiation hardest sensors ever made. A new idea is now being explored to enhance the three-dimensional nature of 3D sensors by processing collecting electrodes at different depths inside the silicon bulk. This technique uses the electric field strength to suppress the charge collection effectiveness of the regions outside the p-n electrodes' overlap. Evidence of this property is supported by test beam data of irradiated and non-irradiated devices bump-bonded with pixel readout electronics and simulations. Applications include High-Luminosity Tracking in the high multiplicity LHC forward regions. This paper will describe the technical advantages of this idea and the tracking application rationale.

  5. Direct measurement of particle size and 3D velocity of a gas-solid pipe flow with digital holographic particle tracking velocimetry.

    PubMed

    Wu, Yingchun; Wu, Xuecheng; Yao, Longchao; Gréhan, Gérard; Cen, Kefa

    2015-03-20

    The 3D measurement of the particles in a gas-solid pipe flow is of great interest, but remains challenging due to curved pipe walls in various engineering applications. Because of the astigmatism induced by the pipe, concentric ellipse fringes in the hologram of spherical particles are observed in the experiments. With a theoretical analysis of the particle holography by an ABCD matrix, the in-focus particle image can be reconstructed by the modified convolution method and fractional Fourier transform. Thereafter, the particle size, 3D position, and velocity are simultaneously measured by digital holographic particle tracking velocimetry (DHPTV). The successful application of DHPTV to the particle size and 3D velocity measurement in a glass pipe's flow can facilitate its 3D diagnostics. PMID:25968543

  6. Real-time visual sensing system achieving high-speed 3D particle tracking with nanometer resolution.

    PubMed

    Cheng, Peng; Jhiang, Sissy M; Menq, Chia-Hsiang

    2013-11-01

    This paper presents a real-time visual sensing system, which is created to achieve high-speed three-dimensional (3D) motion tracking of microscopic spherical particles in aqueous solutions with nanometer resolution. The system comprises a complementary metal-oxide-semiconductor (CMOS) camera, a field programmable gate array (FPGA), and real-time image processing programs. The CMOS camera has high photosensitivity and superior SNR. It acquires images of 128×120 pixels at a frame rate of up to 10,000 frames per second (fps) under the white light illumination from a standard 100 W halogen lamp. The real-time image stream is downloaded from the camera directly to the FPGA, wherein a 3D particle-tracking algorithm is implemented to calculate the 3D positions of the target particle in real time. Two important objectives, i.e., real-time estimation of the 3D position matches the maximum frame rate of the camera and the timing of the output data stream of the system is precisely controlled, are achieved. Two sets of experiments were conducted to demonstrate the performance of the system. First, the visual sensing system was used to track the motion of a 2 μm polystyrene bead, whose motion was controlled by a three-axis piezo motion stage. The ability to track long-range motion with nanometer resolution in all three axes is demonstrated. Second, it was used to measure the Brownian motion of the 2 μm polystyrene bead, which was stabilized in aqueous solution by a laser trapping system. PMID:24216655

  7. Four-directional stereo-microscopy for 3D particle tracking with real-time error evaluation.

    PubMed

    Hay, R F; Gibson, G M; Lee, M P; Padgett, M J; Phillips, D B

    2014-07-28

    High-speed video stereo-microscopy relies on illumination from two distinct angles to create two views of a sample from different directions. The 3D trajectory of a microscopic object can then be reconstructed using parallax to combine 2D measurements of its position in each image. In this work, we evaluate the accuracy of 3D particle tracking using this technique, by extending the number of views from two to four directions. This allows us to record two independent sets of measurements of the 3D coordinates of tracked objects, and comparison of these enables measurement and minimisation of the tracking error in all dimensions. We demonstrate the method by tracking the motion of an optically trapped microsphere of 5 μm in diameter, and find an accuracy of 2-5 nm laterally, and 5-10 nm axially, representing a relative error of less than 2.5% of its range of motion in each dimension. PMID:25089484

  8. 3D Joint Speaker Position and Orientation Tracking with Particle Filters

    PubMed Central

    Segura, Carlos; Hernando, Javier

    2014-01-01

    This paper addresses the problem of three-dimensional speaker orientation estimation in a smart-room environment equipped with microphone arrays. A Bayesian approach is proposed to jointly track the location and orientation of an active speaker. The main motivation is that the knowledge of the speaker orientation may yield an increased localization performance and vice versa. Assuming that the sound produced by the speaker is originated from his mouth, the center of the head is deduced based on the estimated head orientation. Moreover, the elevation angle of the head of the speaker can be partly inferred from the fast vertical movements of the computed mouth location. In order to test the performance of the proposed algorithm, a new multimodal dataset has been recorded for this purpose, where the corresponding 3D orientation angles are acquired by an inertial measurement unit (IMU) provided by accelerometers, magnetometers and gyroscopes in the three-axes. The proposed joint algorithm outperforms a two-step approach in terms of localization and orientation angle precision assessing the superiority of the joint approach. PMID:24481230

  9. 3D joint speaker position and orientation tracking with particle filters.

    PubMed

    Segura, Carlos; Hernando, Javier

    2014-01-01

    This paper addresses the problem of three-dimensional speaker orientation estimation in a smart-room environment equipped with microphone arrays. A Bayesian approach is proposed to jointly track the location and orientation of an active speaker. The main motivation is that the knowledge of the speaker orientation may yield an increased localization performance and vice versa. Assuming that the sound produced by the speaker is originated from his mouth, the center of the head is deduced based on the estimated head orientation. Moreover, the elevation angle of the head of the speaker can be partly inferred from the fast vertical movements of the computed mouth location. In order to test the performance of the proposed algorithm, a new multimodal dataset has been recorded for this purpose, where the corresponding 3D orientation angles are acquired by an inertial measurement unit (IMU) provided by accelerometers, magnetometers and gyroscopes in the three-axes. The proposed joint algorithm outperforms a two-step approach in terms of localization and orientation angle precision assessing the superiority of the joint approach. PMID:24481230

  10. Lagrangian 3D particle tracking in high-speed flows: Shake-The-Box for multi-pulse systems

    NASA Astrophysics Data System (ADS)

    Novara, Matteo; Schanz, Daniel; Reuther, Nico; Kähler, Christian J.; Schröder, Andreas

    2016-08-01

    The Shake-The-Box (STB) particle tracking technique, recently introduced for time-resolved 3D particle image velocimetry (PIV) images, is applied here to data from a multi-pulse investigation of a turbulent boundary layer flow with adverse pressure gradient in air at 36 m/s ( Re τ = 10,650). The multi-pulse acquisition strategy allows for the recording of four-pulse long time-resolved sequences with a time separation of a few microseconds. The experimental setup consists of a dual-imaging system and a dual-double-cavity laser emitting orthogonal polarization directions to separate the four pulses. The STB particle triangulation and tracking strategy is adapted here to cope with the limited amount of realizations available along the time sequence and to take advantage of the ghost track reduction offered by the use of two independent imaging systems. Furthermore, a correction scheme to compensate for camera vibrations is discussed, together with a method to accurately identify the position of the wall within the measurement domain. Results show that approximately 80,000 tracks can be instantaneously reconstructed within the measurement volume, enabling the evaluation of both dense velocity fields, suitable for spatial gradients evaluation, and highly spatially resolved boundary layer profiles. Turbulent boundary layer profiles obtained from ensemble averaging of the STB tracks are compared to results from 2D-PIV and long-range micro particle tracking velocimetry; the comparison shows the capability of the STB approach in delivering accurate results across a wide range of scales.

  11. Robust and highly performant ring detection algorithm for 3d particle tracking using 2d microscope imaging.

    PubMed

    Afik, Eldad

    2015-01-01

    Three-dimensional particle tracking is an essential tool in studying dynamics under the microscope, namely, fluid dynamics in microfluidic devices, bacteria taxis, cellular trafficking. The 3d position can be determined using 2d imaging alone by measuring the diffraction rings generated by an out-of-focus fluorescent particle, imaged on a single camera. Here I present a ring detection algorithm exhibiting a high detection rate, which is robust to the challenges arising from ring occlusion, inclusions and overlaps, and allows resolving particles even when near to each other. It is capable of real time analysis thanks to its high performance and low memory footprint. The proposed algorithm, an offspring of the circle Hough transform, addresses the need to efficiently trace the trajectories of many particles concurrently, when their number in not necessarily fixed, by solving a classification problem, and overcomes the challenges of finding local maxima in the complex parameter space which results from ring clusters and noise. Several algorithmic concepts introduced here can be advantageous in other cases, particularly when dealing with noisy and sparse data. The implementation is based on open-source and cross-platform software packages only, making it easy to distribute and modify. It is implemented in a microfluidic experiment allowing real-time multi-particle tracking at 70 Hz, achieving a detection rate which exceeds 94% and only 1% false-detection. PMID:26329642

  12. Robust and highly performant ring detection algorithm for 3d particle tracking using 2d microscope imaging

    PubMed Central

    Afik, Eldad

    2015-01-01

    Three-dimensional particle tracking is an essential tool in studying dynamics under the microscope, namely, fluid dynamics in microfluidic devices, bacteria taxis, cellular trafficking. The 3d position can be determined using 2d imaging alone by measuring the diffraction rings generated by an out-of-focus fluorescent particle, imaged on a single camera. Here I present a ring detection algorithm exhibiting a high detection rate, which is robust to the challenges arising from ring occlusion, inclusions and overlaps, and allows resolving particles even when near to each other. It is capable of real time analysis thanks to its high performance and low memory footprint. The proposed algorithm, an offspring of the circle Hough transform, addresses the need to efficiently trace the trajectories of many particles concurrently, when their number in not necessarily fixed, by solving a classification problem, and overcomes the challenges of finding local maxima in the complex parameter space which results from ring clusters and noise. Several algorithmic concepts introduced here can be advantageous in other cases, particularly when dealing with noisy and sparse data. The implementation is based on open-source and cross-platform software packages only, making it easy to distribute and modify. It is implemented in a microfluidic experiment allowing real-time multi-particle tracking at 70 Hz, achieving a detection rate which exceeds 94% and only 1% false-detection. PMID:26329642

  13. Robust and highly performant ring detection algorithm for 3d particle tracking using 2d microscope imaging

    NASA Astrophysics Data System (ADS)

    Afik, Eldad

    2015-09-01

    Three-dimensional particle tracking is an essential tool in studying dynamics under the microscope, namely, fluid dynamics in microfluidic devices, bacteria taxis, cellular trafficking. The 3d position can be determined using 2d imaging alone by measuring the diffraction rings generated by an out-of-focus fluorescent particle, imaged on a single camera. Here I present a ring detection algorithm exhibiting a high detection rate, which is robust to the challenges arising from ring occlusion, inclusions and overlaps, and allows resolving particles even when near to each other. It is capable of real time analysis thanks to its high performance and low memory footprint. The proposed algorithm, an offspring of the circle Hough transform, addresses the need to efficiently trace the trajectories of many particles concurrently, when their number in not necessarily fixed, by solving a classification problem, and overcomes the challenges of finding local maxima in the complex parameter space which results from ring clusters and noise. Several algorithmic concepts introduced here can be advantageous in other cases, particularly when dealing with noisy and sparse data. The implementation is based on open-source and cross-platform software packages only, making it easy to distribute and modify. It is implemented in a microfluidic experiment allowing real-time multi-particle tracking at 70 Hz, achieving a detection rate which exceeds 94% and only 1% false-detection.

  14. Breakup of Finite-Size Colloidal Aggregates in Turbulent Flow Investigated by Three-Dimensional (3D) Particle Tracking Velocimetry.

    PubMed

    Saha, Debashish; Babler, Matthaus U; Holzner, Markus; Soos, Miroslav; Lüthi, Beat; Liberzon, Alex; Kinzelbach, Wolfgang

    2016-01-12

    Aggregates grown in mild shear flow are released, one at a time, into homogeneous isotropic turbulence, where their motion and intermittent breakup is recorded by three-dimensional particle tracking velocimetry (3D-PTV). The aggregates have an open structure with a fractal dimension of ∼2.2, and their size is 1.4 ± 0.4 mm, which is large, compared to the Kolmogorov length scale (η = 0.15 mm). 3D-PTV of flow tracers allows for the simultaneous measurement of aggregate trajectories and the full velocity gradient tensor along their pathlines, which enables us to access the Lagrangian stress history of individual breakup events. From this data, we found no consistent pattern that relates breakup to the local flow properties at the point of breakup. Also, the correlation between the aggregate size and both shear stress and normal stress at the location of breakage is found to be weaker, when compared with the correlation between size and drag stress. The analysis suggests that the aggregates are mostly broken due to the accumulation of the drag stress over a time lag on the order of the Kolmogorov time scale. This finding is explained by the fact that the aggregates are large, which gives their motion inertia and increases the time for stress propagation inside the aggregate. Furthermore, it is found that the scaling of the largest fragment and the accumulated stress at breakup follows an earlier established power law, i.e., dfrag ∼ σ(-0.6) obtained from laminar nozzle experiments. This indicates that, despite the large size and the different type of hydrodynamic stress, the microscopic mechanism causing breakup is consistent over a wide range of aggregate size and stress magnitude. PMID:26646289

  15. Applications of 3D hydrodynamic and particle tracking models in the San Francisco bay-delta estuary

    USGS Publications Warehouse

    Smith, P.E.; Donovan, J.M.; Wong, H.F.N.

    2005-01-01

    Three applications of three-dimensional hydrodynamic and particle-tracking models are currently underway by the United States Geological Survey in the San Francisco Bay-Delta Estuary. The first application is to the San Francisco Bay and a portion of the coastal ocean. The second application is to an important, gated control channel called the Delta Cross Channel, located within the northern portion of the Sacramento-San Joaquin River Delta. The third application is to a reach of the San Joaquin River near Stockton, California where a significant dissolved oxygen problem exists due, in part, to conditions associated with the deep-water ship channel for the Port of Stockton, California. This paper briefly discusses the hydrodynamic and particle tracking models being used and the three applications. Copyright ASCE 2005.

  16. Electrically tunable lens speeds up 3D orbital tracking

    PubMed Central

    Annibale, Paolo; Dvornikov, Alexander; Gratton, Enrico

    2015-01-01

    3D orbital particle tracking is a versatile and effective microscopy technique that allows following fast moving fluorescent objects within living cells and reconstructing complex 3D shapes using laser scanning microscopes. We demonstrated notable improvements in the range, speed and accuracy of 3D orbital particle tracking by replacing commonly used piezoelectric stages with Electrically Tunable Lens (ETL) that eliminates mechanical movement of objective lenses. This allowed tracking and reconstructing shape of structures extending 500 microns in the axial direction. Using the ETL, we tracked at high speed fluorescently labeled genomic loci within the nucleus of living cells with unprecedented temporal resolution of 8ms using a 1.42NA oil-immersion objective. The presented technology is cost effective and allows easy upgrade of scanning microscopes for fast 3D orbital tracking. PMID:26114037

  17. 3D camera tracking from disparity images

    NASA Astrophysics Data System (ADS)

    Kim, Kiyoung; Woo, Woontack

    2005-07-01

    In this paper, we propose a robust camera tracking method that uses disparity images computed from known parameters of 3D camera and multiple epipolar constraints. We assume that baselines between lenses in 3D camera and intrinsic parameters are known. The proposed method reduces camera motion uncertainty encountered during camera tracking. Specifically, we first obtain corresponding feature points between initial lenses using normalized correlation method. In conjunction with matching features, we get disparity images. When the camera moves, the corresponding feature points, obtained from each lens of 3D camera, are robustly tracked via Kanade-Lukas-Tomasi (KLT) tracking algorithm. Secondly, relative pose parameters of each lens are calculated via Essential matrices. Essential matrices are computed from Fundamental matrix calculated using normalized 8-point algorithm with RANSAC scheme. Then, we determine scale factor of translation matrix by d-motion. This is required because the camera motion obtained from Essential matrix is up to scale. Finally, we optimize camera motion using multiple epipolar constraints between lenses and d-motion constraints computed from disparity images. The proposed method can be widely adopted in Augmented Reality (AR) applications, 3D reconstruction using 3D camera, and fine surveillance systems which not only need depth information, but also camera motion parameters in real-time.

  18. Self consistent particles dynamics in/out of the cusp region by using back tracking technics; a global 3D PIC simulation approach

    NASA Astrophysics Data System (ADS)

    Esmaeili, A.; Cai, D.; Lembege, B.; Nishikawa, K.

    2013-12-01

    Large scale three dimensionbal PIC (particle in cell) simulations are presently used in order to analyze the global solar wind-terrestrial magnetosphere intreraction within a full self-consistent approach, and where both electrons and ions are treated as an assembly of individual particles. This 3D kinetic approach allows us to analyze in particular the dynamics and the fine structures of the cusp region when including self consistently not only its whole neighborhood (in the terrestrial magnetosphere) but also the impact of the solar wind and the interplanetary field (IMF) features. Herein, we focuss our attention on the cusp region and in particular on the acceleration and precipitation of particles (both ions and electrons) within the cusp. In present simulations, the IMF is chosen northward, (i.e. where the X -reconnection region is just above the cusp, in the meridian plane). Back-trackings of self-consistent particles are analyzed in details in order to determine (i) which particles (just above the cusp) are precipitated deeply into the cusp, (ii) which populations are injected from the cusp into the nearby tail, (iii) where the particles suffer the largest energisation along their self-consistent trajectories, (iv) where these populations accumulate, and (v) where the most energetic particles are originally coming from. This approach allows to make a traking of particles within the scenario "solar wind-magnetosheath- cusp -nearbytail"; moreover it strongly differs from the standard test particles technics and allows to provide informations not accessible when using full MHD approach. Keywords: Tracing Particles, Particle In Cell (PIC) simulation, double cusp, test particles method, IMF, Solar wind, Magnetosphere

  19. 3D imaging of neutron tracks using confocal microscopy

    NASA Astrophysics Data System (ADS)

    Gillmore, Gavin; Wertheim, David; Flowers, Alan

    2016-04-01

    Neutron detection and neutron flux assessment are important aspects in monitoring nuclear energy production. Neutron flux measurements can also provide information on potential biological damage from exposure. In addition to the applications for neutron measurement in nuclear energy, neutron detection has been proposed as a method of enhancing neutrino detectors and cosmic ray flux has also been assessed using ground-level neutron detectors. Solid State Nuclear Track Detectors (or SSNTDs) have been used extensively to examine cosmic rays, long-lived radioactive elements, radon concentrations in buildings and the age of geological samples. Passive SSNTDs consisting of a CR-39 plastic are commonly used to measure radon because they respond to incident charged particles such as alpha particles from radon gas in air. They have a large dynamic range and a linear flux response. We have previously applied confocal microscopy to obtain 3D images of alpha particle tracks in SSNTDs from radon track monitoring (1). As a charged particle traverses through the polymer it creates an ionisation trail along its path. The trail or track is normally enhanced by chemical etching to better expose radiation damage, as the damaged area is more sensitive to the etchant than the bulk material. Particle tracks in CR-39 are usually assessed using 2D optical microscopy. In this study 6 detectors were examined using an Olympus OLS4100 LEXT 3D laser scanning confocal microscope (Olympus Corporation, Japan). The detectors had been etched for 2 hours 50 minutes at 85 °C in 6.25M NaOH. Post etch the plastics had been treated with a 10 minute immersion in a 2% acetic acid stop bath, followed by rinsing in deionised water. The detectors examined had been irradiated with a 2mSv neutron dose from an Am(Be) neutron source (producing roughly 20 tracks per mm2). We were able to successfully acquire 3D images of neutron tracks in the detectors studied. The range of track diameter observed was between 4

  20. Particle Acceleration in 3D Magnetic Reconnection

    NASA Astrophysics Data System (ADS)

    Dahlin, J.; Drake, J. F.; Swisdak, M.

    2015-12-01

    Magnetic reconnection is an important driver of energetic particles in phenomena such as magnetospheric storms and solar flares. Using kinetic particle-in-cell (PIC) simulations, we show that the stochastic magnetic field structure which develops during 3D reconnection plays a vital role in particle acceleration and transport. In a 2D system, electrons are trapped in magnetic islands which limits their energy gain. In a 3D system, however, the stochastic magnetic field enables the energetic electrons to access volume-filling acceleration regions and therefore gain energy much more efficiently than in the 2D system. We also examine the relative roles of two important acceleration drivers: parallel electric fields and a Fermi mechanism associated with reflection of charged particles from contracting field lines. We find that parallel electric fields are most important for accelerating low energy particles, whereas Fermi reflection dominates energetic particle production. We also find that proton energization is reduced in the 3D system.

  1. 3D laser traking of a particle in 3DFM

    NASA Astrophysics Data System (ADS)

    Desai, Kalpit; Welch, Gregory; Bishop, Gary; Taylor, Russell; Superfine, Richard

    2003-11-01

    The principal goal of 3D tracking in our home-built 3D Magnetic Force Microscope is to monitor movement of the particle with respect to laser beam waist and keep the particle at the center of laser beam. The sensory element is a Quadrant Photo Diode (QPD) which captures scattering of light caused by particle motion with bandwidth up to 40 KHz. XYZ translation stage is the driver element which moves particle back in the center of the laser with accuracy of couple of nanometers and with bandwidth up to 300 Hz. Since our particles vary in size, composition and shape, instead of using a priori model we use standard system identification techniques to have optimal approximation to the relationship between particle motion and QPD response. We have developed position feedback control system software that is capable of 3-dimensional tracking of beads that are attached to cilia on living cells which are beating at up to 15Hz. We have also modeled the control system of instrument to simulate performance of 3D particle tracking for different experimental conditions. Given operational level of nanometers, noise poses a great challenge for the tracking system. We propose to use stochastic control theory approaches to increase robustness of tracking.

  2. 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

  3. 3D visualisation and analysis of single and coalescing tracks in Solid state Nuclear Track Detectors

    NASA Astrophysics Data System (ADS)

    Wertheim, David; Gillmore, Gavin; Brown, Louise; Petford, Nick

    2010-05-01

    Exposure to radon gas (222Rn) and associated ionising decay products can cause lung cancer in humans (1). Solid state Nuclear Track Detectors (SSNTDs) can be used to monitor radon concentrations (2). Radon particles form tracks in the detectors and these tracks can be etched in order to enable 2D surface image analysis. We have previously shown that confocal microscopy can be used for 3D visualisation of etched SSNTDs (3). The aim of the study was to further investigate track angles and patterns in SSNTDs. A 'LEXT' confocal laser scanning microscope (Olympus Corporation, Japan) was used to acquire 3D image datasets of five CR-39 plastic SSNTD's. The resultant 3D visualisations were analysed by eye and inclination angles assessed on selected tracks. From visual assessment, single isolated tracks as well as coalescing tracks were observed on the etched detectors. In addition varying track inclination angles were observed. Several different patterns of track formation were seen such as single isolated and double coalescing tracks. The observed track angles of inclination may help to assess the angle at which alpha particles hit the detector. Darby, S et al. Radon in homes and risk of lung cancer : collaborative analysis of individual data from 13 European case-control studies. British Medical Journal 2005; 330, 223-226. Phillips, P.S., Denman, A.R., Crockett, R.G.M., Gillmore, G., Groves-Kirkby, C.J., Woolridge, A., Comparative Analysis of Weekly vs. Three monthly radon measurements in dwellings. DEFRA Report No., DEFRA/RAS/03.006. (2004). Wertheim D, Gillmore G, Brown L, and Petford N. A new method of imaging particle tracks in Solid State Nuclear Track Detectors. Journal of Microscopy 2010; 237: 1-6.

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

    NASA Astrophysics Data System (ADS)

    Wieneke, Bernhard; Neal, Douglas

    2011-11-01

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

  5. 3D View of Mars Particle

    NASA Technical Reports Server (NTRS)

    2008-01-01

    This is a 3D representation of the pits seen in the first Atomic Force Microscope, or AFM, images sent back from NASA's Phoenix Mars Lander. Red represents the highest point and purple represents the lowest point.

    The particle in the upper left corner shown at the highest magnification ever seen from another world is a rounded particle about one micrometer, or one millionth of a meter, across. It is a particle of the dust that cloaks Mars. Such dust particles color the Martian sky pink, feed storms that regularly envelop the planet and produce Mars' distinctive red soil.

    The particle was part of a sample informally called 'Sorceress' delivered to the AFM on the 38th Martian day, or sol, of the mission (July 2, 2008). The AFM is part of Phoenix's microscopic station called MECA, or the Microscopy, Electrochemistry, and Conductivity Analyzer.

    The AFM was developed by a Swiss-led consortium, with Imperial College London producing the silicon substrate that holds sampled particles.

    The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by NASA's Jet Propulsion Laboratory, Pasadena, Calif. Spacecraft development is by Lockheed Martin Space Systems, Denver.

  6. Track and trap in 3D

    NASA Astrophysics Data System (ADS)

    Glückstad, Jesper; Rodrigo, Peter J.; Nielsen, Ivan P.; Alonzo, Carlo A.

    2007-04-01

    Three-dimensional light structures can be created by modulating the spatial phase and polarization properties of an an expanded laser beam. A particularly promising technique is the Generalized Phase Contrast (GPC) method invented and patented at Risø National Laboratory. Based on the combination of programmable spatial light modulator devices and an advanced graphical user-interface the GPC method enables real-time, interactive and arbitrary control over the dynamics and geometry of synthesized light patterns. Recent experiments have shown that GPC-driven micro-manipulation provides a unique technology platform for fully user-guided assembly of a plurality of particles in a plane, control of particle stacking along the beam axis, manipulation of multiple hollow beads, and the organization of living cells into three-dimensional colloidal structures. Here we present GPC-based optical micromanipulation in a microfluidic system where trapping experiments are computer-automated and thereby capable of running with only limited supervision. The system is able to dynamically detect living yeast cells using a computer-interfaced CCD camera, and respond to this by instantly creating traps at positions of the spotted cells streaming at flow velocities that would be difficult for a human operator to handle.

  7. 3-D rigid body tracking using vision and depth sensors.

    PubMed

    Gedik, O Serdar; Alatan, A Aydn

    2013-10-01

    In robotics and augmented reality applications, model-based 3-D tracking of rigid objects is generally required. With the help of accurate pose estimates, it is required to increase reliability and decrease jitter in total. Among many solutions of pose estimation in the literature, pure vision-based 3-D trackers require either manual initializations or offline training stages. On the other hand, trackers relying on pure depth sensors are not suitable for AR applications. An automated 3-D tracking algorithm, which is based on fusion of vision and depth sensors via extended Kalman filter, is proposed in this paper. A novel measurement-tracking scheme, which is based on estimation of optical flow using intensity and shape index map data of 3-D point cloud, increases 2-D, as well as 3-D, tracking performance significantly. The proposed method requires neither manual initialization of pose nor offline training, while enabling highly accurate 3-D tracking. The accuracy of the proposed method is tested against a number of conventional techniques, and a superior performance is clearly observed in terms of both objectively via error metrics and subjectively for the rendered scenes. PMID:23955795

  8. Automatic respiration tracking for radiotherapy using optical 3D camera

    NASA Astrophysics Data System (ADS)

    Li, Tuotuo; Geng, Jason; Li, Shidong

    2013-03-01

    Rapid optical three-dimensional (O3D) imaging systems provide accurate digitized 3D surface data in real-time, with no patient contact nor radiation. The accurate 3D surface images offer crucial information in image-guided radiation therapy (IGRT) treatments for accurate patient repositioning and respiration management. However, applications of O3D imaging techniques to image-guided radiotherapy have been clinically challenged by body deformation, pathological and anatomical variations among individual patients, extremely high dimensionality of the 3D surface data, and irregular respiration motion. In existing clinical radiation therapy (RT) procedures target displacements are caused by (1) inter-fractional anatomy changes due to weight, swell, food/water intake; (2) intra-fractional variations from anatomy changes within any treatment session due to voluntary/involuntary physiologic processes (e.g. respiration, muscle relaxation); (3) patient setup misalignment in daily reposition due to user errors; and (4) changes of marker or positioning device, etc. Presently, viable solution is lacking for in-vivo tracking of target motion and anatomy changes during the beam-on time without exposing patient with additional ionized radiation or high magnet field. Current O3D-guided radiotherapy systems relay on selected points or areas in the 3D surface to track surface motion. The configuration of the marks or areas may change with time that makes it inconsistent in quantifying and interpreting the respiration patterns. To meet the challenge of performing real-time respiration tracking using O3D imaging technology in IGRT, we propose a new approach to automatic respiration motion analysis based on linear dimensionality reduction technique based on PCA (principle component analysis). Optical 3D image sequence is decomposed with principle component analysis into a limited number of independent (orthogonal) motion patterns (a low dimension eigen-space span by eigen-vectors). New

  9. Ion track reconstruction in 3D using alumina-based fluorescent nuclear track detectors.

    PubMed

    Niklas, M; Bartz, J A; Akselrod, M S; Abollahi, A; Jäkel, O; Greilich, S

    2013-09-21

    Fluorescent nuclear track detectors (FNTDs) based on Al2O3: C, Mg single crystal combined with confocal microscopy provide 3D information on ion tracks with a resolution only limited by light diffraction. FNTDs are also ideal substrates to be coated with cells to engineer cell-fluorescent ion track hybrid detectors (Cell-Fit-HD). This radiobiological tool enables a novel platform linking cell responses to physical dose deposition on a sub-cellular level in proton and heavy ion therapies. To achieve spatial correlation between single ion hits in the cell coating and its biological response the ion traversals have to be reconstructed in 3D using the depth information gained by the FNTD read-out. FNTDs were coated with a confluent human lung adenocarcinoma epithelial (A549) cell layer. Carbon ion irradiation of the hybrid detector was performed perpendicular and angular to the detector surface. In situ imaging of the fluorescently labeled cell layer and the FNTD was performed in a sequential read-out. Making use of the trajectory information provided by the FNTD the accuracy of 3D track reconstruction of single particles traversing the hybrid detector was studied. The accuracy is strongly influenced by the irradiation angle and therefore by complexity of the FNTD signal. Perpendicular irradiation results in highest accuracy with error of smaller than 0.10°. The ability of FNTD technology to provide accurate 3D ion track reconstruction makes it a powerful tool for radiobiological investigations in clinical ion beams, either being used as a substrate to be coated with living tissue or being implanted in vivo. PMID:23965401

  10. Ion track reconstruction in 3D using alumina-based fluorescent nuclear track detectors

    NASA Astrophysics Data System (ADS)

    Niklas, M.; Bartz, J. A.; Akselrod, M. S.; Abollahi, A.; Jäkel, O.; Greilich, S.

    2013-09-01

    Fluorescent nuclear track detectors (FNTDs) based on Al2O3: C, Mg single crystal combined with confocal microscopy provide 3D information on ion tracks with a resolution only limited by light diffraction. FNTDs are also ideal substrates to be coated with cells to engineer cell-fluorescent ion track hybrid detectors (Cell-Fit-HD). This radiobiological tool enables a novel platform linking cell responses to physical dose deposition on a sub-cellular level in proton and heavy ion therapies. To achieve spatial correlation between single ion hits in the cell coating and its biological response the ion traversals have to be reconstructed in 3D using the depth information gained by the FNTD read-out. FNTDs were coated with a confluent human lung adenocarcinoma epithelial (A549) cell layer. Carbon ion irradiation of the hybrid detector was performed perpendicular and angular to the detector surface. In situ imaging of the fluorescently labeled cell layer and the FNTD was performed in a sequential read-out. Making use of the trajectory information provided by the FNTD the accuracy of 3D track reconstruction of single particles traversing the hybrid detector was studied. The accuracy is strongly influenced by the irradiation angle and therefore by complexity of the FNTD signal. Perpendicular irradiation results in highest accuracy with error of smaller than 0.10°. The ability of FNTD technology to provide accurate 3D ion track reconstruction makes it a powerful tool for radiobiological investigations in clinical ion beams, either being used as a substrate to be coated with living tissue or being implanted in vivo.

  11. 3D hand tracking using Kalman filter in depth space

    NASA Astrophysics Data System (ADS)

    Park, Sangheon; Yu, Sunjin; Kim, Joongrock; Kim, Sungjin; Lee, Sangyoun

    2012-12-01

    Hand gestures are an important type of natural language used in many research areas such as human-computer interaction and computer vision. Hand gestures recognition requires the prior determination of the hand position through detection and tracking. One of the most efficient strategies for hand tracking is to use 2D visual information such as color and shape. However, visual-sensor-based hand tracking methods are very sensitive when tracking is performed under variable light conditions. Also, as hand movements are made in 3D space, the recognition performance of hand gestures using 2D information is inherently limited. In this article, we propose a novel real-time 3D hand tracking method in depth space using a 3D depth sensor and employing Kalman filter. We detect hand candidates using motion clusters and predefined wave motion, and track hand locations using Kalman filter. To verify the effectiveness of the proposed method, we compare the performance of the proposed method with the visual-based method. Experimental results show that the performance of the proposed method out performs visual-based method.

  12. Computationally efficient storage of 3D particle intensity and position data for use in 3D PIV and 3D PTV

    NASA Astrophysics Data System (ADS)

    Atkinson, C.; Buchmann, N. A.; Soria, J.

    2013-11-01

    Three-dimensional (3D) volumetric velocity measurement techniques, such as tomographic or holographic particle image velocimetry (PIV), rely upon the computationally intensive formation, storage and localized interrogation of multiple 3D particle intensity fields. Calculation of a single velocity field typically requires the extraction of particle intensities into tens of thousands of 3D sub-volumes or discrete particle clusters, the processing of which can significantly affect the performance of 3D cross-correlation based PIV and 3D particle tracking velocimetry (PTV). In this paper, a series of popular and customized volumetric data formats are presented and investigated using synthetic particle volumes and experimental data arising from tomographic PIV measurements of a turbulent boundary layer. Results show that the use of a sub-grid ordered non-zero intensity format with a sub-grid size of 16 × 16 × 16 points provides the best performance for cross-correlation based PIV analysis, while a particle clustered non-zero intensity format provides the best format for PTV applications. In practical tomographic PIV measurements the sub-grid ordered non-zero intensity format offered a 29% improvement in reconstruction times, while providing a 93% reduction in volume data requirements and a 28% overall improvement in cross-correlation based velocity analysis and validation times.

  13. Monocular 3-D gait tracking in surveillance scenes.

    PubMed

    Rogez, Grégory; Rihan, Jonathan; Guerrero, Jose J; Orrite, Carlos

    2014-06-01

    Gait recognition can potentially provide a noninvasive and effective biometric authentication from a distance. However, the performance of gait recognition systems will suffer in real surveillance scenarios with multiple interacting individuals and where the camera is usually placed at a significant angle and distance from the floor. We present a methodology for view-invariant monocular 3-D human pose tracking in man-made environments in which we assume that observed people move on a known ground plane. First, we model 3-D body poses and camera viewpoints with a low dimensional manifold and learn a generative model of the silhouette from this manifold to a reduced set of training views. During the online stage, 3-D body poses are tracked using recursive Bayesian sampling conducted jointly over the scene's ground plane and the pose-viewpoint manifold. For each sample, the homography that relates the corresponding training plane to the image points is calculated using the dominant 3-D directions of the scene, the sampled location on the ground plane and the sampled camera view. Each regressed silhouette shape is projected using this homographic transformation and is matched in the image to estimate its likelihood. Our framework is able to track 3-D human walking poses in a 3-D environment exploring only a 4-D state space with success. In our experimental evaluation, we demonstrate the significant improvements of the homographic alignment over a commonly used similarity transformation and provide quantitative pose tracking results for the monocular sequences with a high perspective effect from the CAVIAR dataset. PMID:23955796

  14. A 3D feature point tracking method for ion radiation.

    PubMed

    Kouwenberg, Jasper J M; Ulrich, Leonie; Jäkel, Oliver; Greilich, Steffen

    2016-06-01

    A robust and computationally efficient algorithm for automated tracking of high densities of particles travelling in (semi-) straight lines is presented. It extends the implementation of (Sbalzarini and Koumoutsakos 2005) and is intended for use in the analysis of single ion track detectors. By including information of existing tracks in the exclusion criteria and a recursive cost minimization function, the algorithm is robust to variations on the measured particle tracks. A trajectory relinking algorithm was included to resolve the crossing of tracks in high particle density images. Validation of the algorithm was performed using fluorescent nuclear track detectors (FNTD) irradiated with high- and low (heavy) ion fluences and showed less than 1% faulty trajectories in the latter. PMID:27163162

  15. A 3D feature point tracking method for ion radiation

    NASA Astrophysics Data System (ADS)

    Kouwenberg, Jasper J. M.; Ulrich, Leonie; Jäkel, Oliver; Greilich, Steffen

    2016-06-01

    A robust and computationally efficient algorithm for automated tracking of high densities of particles travelling in (semi-) straight lines is presented. It extends the implementation of (Sbalzarini and Koumoutsakos 2005) and is intended for use in the analysis of single ion track detectors. By including information of existing tracks in the exclusion criteria and a recursive cost minimization function, the algorithm is robust to variations on the measured particle tracks. A trajectory relinking algorithm was included to resolve the crossing of tracks in high particle density images. Validation of the algorithm was performed using fluorescent nuclear track detectors (FNTD) irradiated with high- and low (heavy) ion fluences and showed less than 1% faulty trajectories in the latter.

  16. A new 3D tracking method exploiting the capabilities of digital holography in microscopy

    NASA Astrophysics Data System (ADS)

    Miccio, L.; Memmolo, P.; Merola, F.; Fusco, S.; Embrione, V.; Netti, P. A.; Ferraro, P.

    2013-04-01

    A method for 3D tracking has been developed exploiting Digital Holographic Microscopy (DHM) features. In the framework of self-consistent platform for manipulation and measurement of biological specimen we use DHM for quantitative and completely label free analysis of specimen with low amplitude contrast. Tracking capability extend the potentiality of DHM allowing to monitor the motion of appropriate probes and correlate it with sample properties. Complete 3D tracking has been obtained for the probes avoiding the issue of amplitude refocusing in traditional tracking processing. Our technique belongs to the video tracking methods that, conversely from Quadrant Photo-Diode method, opens the possibility to track multiples probes. All the common used video tracking algorithms are based on the numerical analysis of amplitude images in the focus plane and the shift of the maxima in the image plane are measured after the application of an appropriate threshold. Our approach for video tracking uses different theoretical basis. A set of interferograms is recorded and the complex wavefields are managed numerically to obtain three dimensional displacements of the probes. The procedure works properly on an higher number of probes and independently from their size. This method overcomes the traditional video tracking issues as the inability to measure the axial movement and the choice of suitable threshold mask. The novel configuration allows 3D tracking of micro-particles and simultaneously can furnish Quantitative Phase-contrast maps of tracked micro-objects by interference microscopy, without changing the configuration. In this paper, we show a new concept for a compact interferometric microscope that can ensure the multifunctionality, accomplishing accurate 3D tracking and quantitative phase-contrast analysis. Experimental results are presented and discussed for in vitro cells. Through a very simple and compact optical arrangement we show how two different functionalities

  17. 3D flare particle model for ShipIR/NTCS

    NASA Astrophysics Data System (ADS)

    Ramaswamy, Srinivasan; Vaitekunas, David A.

    2016-05-01

    A key component in any soft-kill response to an incoming guided missile is the flare /chaff decoy used to distract or seduce the seeker homing system away from the naval platform. This paper describes a new 3D flare particle model in the naval threat countermeasure simulator (NTCS) of the NATO-standard ship signature model (ShipIR), which provides independent control over the size and radial distribution of its signature. The 3D particles of each flare sub-munition are modelled stochastically and rendered using OpenGL z-buffering, 2D projection, and alpha-blending to produce a unique and time varying signature. A sensitivity analysis on each input parameter provides the data and methods needed to synthesize a model from an IR measurement of a decoy. The new model also eliminated artifacts and deficiencies in our previous model which prevented reliable tracks from the adaptive track gate algorithm already presented by Ramaswamy and Vaitekunas (2015). A sequence of scenarios are used to test and demonstrate the new flare model during a missile engagement.

  18. Light driven micro-robotics with holographic 3D tracking

    NASA Astrophysics Data System (ADS)

    Glückstad, Jesper

    2016-04-01

    We recently pioneered the concept of light-driven micro-robotics including the new and disruptive 3D-printed micro-tools coined Wave-guided Optical Waveguides that can be real-time optically trapped and "remote-controlled" in a volume with six-degrees-of-freedom. To be exploring the full potential of this new drone-like 3D light robotics approach in challenging microscopic geometries requires a versatile and real-time reconfigurable light coupling that can dynamically track a plurality of "light robots" in 3D to ensure continuous optimal light coupling on the fly. Our latest developments in this new and exciting area will be reviewed in this invited paper.

  19. Note: Time-gated 3D single quantum dot tracking with simultaneous spinning disk imaging

    NASA Astrophysics Data System (ADS)

    DeVore, M. S.; Stich, D. G.; Keller, A. M.; Cleyrat, C.; Phipps, M. E.; Hollingsworth, J. A.; Lidke, D. S.; Wilson, B. S.; Goodwin, P. M.; Werner, J. H.

    2015-12-01

    We describe recent upgrades to a 3D tracking microscope to include simultaneous Nipkow spinning disk imaging and time-gated single-particle tracking (SPT). Simultaneous 3D molecular tracking and spinning disk imaging enable the visualization of cellular structures and proteins around a given fluorescently labeled target molecule. The addition of photon time-gating to the SPT hardware improves signal to noise by discriminating against Raman scattering and short-lived fluorescence. In contrast to camera-based SPT, single-photon arrival times are recorded, enabling time-resolved spectroscopy (e.g., measurement of fluorescence lifetimes and photon correlations) to be performed during single molecule/particle tracking experiments.

  20. Rapid 3D Track Reconstruction with the BaBar Trigger Upgrade

    SciTech Connect

    Bailey, S

    2004-05-24

    As the PEP-II luminosity increases the BaBar trigger and dataflow systems must accommodate the increasing data rate. A significant source of background events at the first trigger level comes from beam particle interactions with the beampipe and synchrotron masks, which are separated from the interaction region by more than 20 cm. The BaBar trigger upgrade will provide 3D tracking capabilities at the first trigger level in order to remove background events by distinguishing the origin of particle tracks. Each new z{sub 0} p{sub T} Discriminator (ZPD) board processes over 1 gigabyte of data per second in order to reconstruct the tracks and make trigger decisions based upon the 3D track parameters.

  1. Note: Time-gated 3D single quantum dot tracking with simultaneous spinning disk imaging

    SciTech Connect

    DeVore, M. S.; Stich, D. G.; Keller, A. M.; Phipps, M. E.; Hollingsworth, J. A.; Goodwin, P. M.; Werner, J. H.; Cleyrat, C.; Lidke, D. S.; Wilson, B. S.

    2015-12-15

    We describe recent upgrades to a 3D tracking microscope to include simultaneous Nipkow spinning disk imaging and time-gated single-particle tracking (SPT). Simultaneous 3D molecular tracking and spinning disk imaging enable the visualization of cellular structures and proteins around a given fluorescently labeled target molecule. The addition of photon time-gating to the SPT hardware improves signal to noise by discriminating against Raman scattering and short-lived fluorescence. In contrast to camera-based SPT, single-photon arrival times are recorded, enabling time-resolved spectroscopy (e.g., measurement of fluorescence lifetimes and photon correlations) to be performed during single molecule/particle tracking experiments.

  2. Speeding up 3D speckle tracking using PatchMatch

    NASA Astrophysics Data System (ADS)

    Zontak, Maria; O'Donnell, Matthew

    2016-03-01

    Echocardiography provides valuable information to diagnose heart dysfunction. A typical exam records several minutes of real-time cardiac images. To enable complete analysis of 3D cardiac strains, 4-D (3-D+t) echocardiography is used. This results in a huge dataset and requires effective automated analysis. Ultrasound speckle tracking is an effective method for tissue motion analysis. It involves correlation of a 3D kernel (block) around a voxel with kernels in later frames. The search region is usually confined to a local neighborhood, due to biomechanical and computational constraints. For high strains and moderate frame-rates, however, this search region will remain large, leading to a considerable computational burden. Moreover, speckle decorrelation (due to high strains) leads to errors in tracking. To solve this, spatial motion coherency between adjacent voxels should be imposed, e.g., by averaging their correlation functions.1 This requires storing correlation functions for neighboring voxels, thus increasing memory demands. In this work, we propose an efficient search using PatchMatch, 2 a powerful method to find correspondences between images. Here we adopt PatchMatch for 3D volumes and radio-frequency signals. As opposed to an exact search, PatchMatch performs random sampling of the search region and propagates successive matches among neighboring voxels. We show that: 1) Inherently smooth offset propagation in PatchMatch contributes to spatial motion coherence without any additional processing or memory demand. 2) For typical scenarios, PatchMatch is at least 20 times faster than the exact search, while maintaining comparable tracking accuracy.

  3. 3D Finite Element Analysis of Particle-Reinforced Aluminum

    NASA Technical Reports Server (NTRS)

    Shen, H.; Lissenden, C. J.

    2002-01-01

    Deformation in particle-reinforced aluminum has been simulated using three distinct types of finite element model: a three-dimensional repeating unit cell, a three-dimensional multi-particle model, and two-dimensional multi-particle models. The repeating unit cell model represents a fictitious periodic cubic array of particles. The 3D multi-particle (3D-MP) model represents randomly placed and oriented particles. The 2D generalized plane strain multi-particle models were obtained from planar sections through the 3D-MP model. These models were used to study the tensile macroscopic stress-strain response and the associated stress and strain distributions in an elastoplastic matrix. The results indicate that the 2D model having a particle area fraction equal to the particle representative volume fraction of the 3D models predicted the same macroscopic stress-strain response as the 3D models. However, there are fluctuations in the particle area fraction in a representative volume element. As expected, predictions from 2D models having different particle area fractions do not agree with predictions from 3D models. More importantly, it was found that the microscopic stress and strain distributions from the 2D models do not agree with those from the 3D-MP model. Specifically, the plastic strain distribution predicted by the 2D model is banded along lines inclined at 45 deg from the loading axis while the 3D model prediction is not. Additionally, the triaxial stress and maximum principal stress distributions predicted by 2D and 3D models do not agree. Thus, it appears necessary to use a multi-particle 3D model to accurately predict material responses that depend on local effects, such as strain-to-failure, fracture toughness, and fatigue life.

  4. Tracking people and cars using 3D modeling and CCTV.

    PubMed

    Edelman, Gerda; Bijhold, Jurrien

    2010-10-10

    The aim of this study was to find a method for the reconstruction of movements of people and cars using CCTV footage and a 3D model of the environment. A procedure is proposed, in which video streams are synchronized and displayed in a 3D model, by using virtual cameras. People and cars are represented by cylinders and boxes, which are moved in the 3D model, according to their movements as shown in the video streams. The procedure was developed and tested in an experimental setup with test persons who logged their GPS coordinates as a recording of the ground truth. Results showed that it is possible to implement this procedure and to reconstruct movements of people and cars from video recordings. The procedure was also applied to a forensic case. In this work we experienced that more situational awareness was created by the 3D model, which made it easier to track people on multiple video streams. Based on all experiences from the experimental set up and the case, recommendations are formulated for use in practice. PMID:20439141

  5. Inertial Motion-Tracking Technology for Virtual 3-D

    NASA Technical Reports Server (NTRS)

    2005-01-01

    In the 1990s, NASA pioneered virtual reality research. The concept was present long before, but, prior to this, the technology did not exist to make a viable virtual reality system. Scientists had theories and ideas they knew that the concept had potential, but the computers of the 1970s and 1980s were not fast enough, sensors were heavy and cumbersome, and people had difficulty blending fluidly with the machines. Scientists at Ames Research Center built upon the research of previous decades and put the necessary technology behind them, making the theories of virtual reality a reality. Virtual reality systems depend on complex motion-tracking sensors to convey information between the user and the computer to give the user the feeling that he is operating in the real world. These motion-tracking sensors measure and report an object s position and orientation as it changes. A simple example of motion tracking would be the cursor on a computer screen moving in correspondence to the shifting of the mouse. Tracking in 3-D, necessary to create virtual reality, however, is much more complex. To be successful, the perspective of the virtual image seen on the computer must be an accurate representation of what is seen in the real world. As the user s head or camera moves, turns, or tilts, the computer-generated environment must change accordingly with no noticeable lag, jitter, or distortion. Historically, the lack of smooth and rapid tracking of the user s motion has thwarted the widespread use of immersive 3-D computer graphics. NASA uses virtual reality technology for a variety of purposes, mostly training of astronauts. The actual missions are costly and dangerous, so any opportunity the crews have to practice their maneuvering in accurate situations before the mission is valuable and instructive. For that purpose, NASA has funded a great deal of virtual reality research, and benefited from the results.

  6. 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

  7. 3D harmonic phase tracking with anatomical regularization.

    PubMed

    Zhou, Yitian; Bernard, Olivier; Saloux, Eric; Manrique, Alain; Allain, Pascal; Makram-Ebeid, Sherif; De Craene, Mathieu

    2015-12-01

    This paper presents a novel algorithm that extends HARP to handle 3D tagged MRI images. HARP results were regularized by an original regularization framework defined in an anatomical space of coordinates. In the meantime, myocardium incompressibility was integrated in order to correct the radial strain which is reported to be more challenging to recover. Both the tracking and regularization of LV displacements were done on a volumetric mesh to be computationally efficient. Also, a window-weighted regression method was extended to cardiac motion tracking which helps maintain a low complexity even at finer scales. On healthy volunteers, the tracking accuracy was found to be as accurate as the best candidates of a recent benchmark. Strain accuracy was evaluated on synthetic data, showing low bias and strain errors under 5% (excluding outliers) for longitudinal and circumferential strains, while the second and third quartiles of the radial strain errors are in the (-5%,5%) range. In clinical data, strain dispersion was shown to correlate with the extent of transmural fibrosis. Also, reduced deformation values were found inside infarcted segments. PMID:26363844

  8. 3-D tracking in a miniature time projection chamber

    NASA Astrophysics Data System (ADS)

    Vahsen, S. E.; Hedges, M. T.; Jaegle, I.; Ross, S. J.; Seong, I. S.; Thorpe, T. N.; Yamaoka, J.; Kadyk, J. A.; Garcia-Sciveres, M.

    2015-07-01

    The three-dimensional (3-D) detection of millimeter-scale ionization trails is of interest for detecting nuclear recoils in directional fast neutron detectors and in direction-sensitive searches for weakly interacting massive particles (WIMPs), which may constitute the Dark Matter of the universe. We report on performance characterization of a miniature gas target Time Projection Chamber (TPC) where the drift charge is avalanche-multiplied with Gas Electron Multipliers (GEMs) and detected with the ATLAS FE-I3 Pixel Application Specific Integrated Circuit (ASIC). We report on measurements of gain, gain resolution, point resolution, diffusion, angular resolution, and energy resolution with low-energy X-rays, cosmic rays, and alpha particles, using the gases Ar:CO2 (70:30) and He:CO2 (70:30) at atmospheric pressure. We discuss the implications for future, larger directional neutron and Dark Matter detectors. With an eye to designing and selecting components for these, we generalize our results into analytical expressions for detector performance whenever possible. We conclude by demonstrating the 3-D directional detection of a fast neutron source.

  9. Optofluidic fabrication for 3D-shaped particles.

    PubMed

    Paulsen, Kevin S; Di Carlo, Dino; Chung, Aram J

    2015-01-01

    Complex three-dimensional (3D)-shaped particles could play unique roles in biotechnology, structural mechanics and self-assembly. Current methods of fabricating 3D-shaped particles such as 3D printing, injection moulding or photolithography are limited because of low-resolution, low-throughput or complicated/expensive procedures. Here, we present a novel method called optofluidic fabrication for the generation of complex 3D-shaped polymer particles based on two coupled processes: inertial flow shaping and ultraviolet (UV) light polymerization. Pillars within fluidic platforms are used to deterministically deform photosensitive precursor fluid streams. The channels are then illuminated with patterned UV light to polymerize the photosensitive fluid, creating particles with multi-scale 3D geometries. The fundamental advantages of optofluidic fabrication include high-resolution, multi-scalability, dynamic tunability, simple operation and great potential for bulk fabrication with full automation. Through different combinations of pillar configurations, flow rates and UV light patterns, an infinite set of 3D-shaped particles is available, and a variety are demonstrated. PMID:25904062

  10. Optofluidic fabrication for 3D-shaped particles

    NASA Astrophysics Data System (ADS)

    Paulsen, Kevin S.; di Carlo, Dino; Chung, Aram J.

    2015-04-01

    Complex three-dimensional (3D)-shaped particles could play unique roles in biotechnology, structural mechanics and self-assembly. Current methods of fabricating 3D-shaped particles such as 3D printing, injection moulding or photolithography are limited because of low-resolution, low-throughput or complicated/expensive procedures. Here, we present a novel method called optofluidic fabrication for the generation of complex 3D-shaped polymer particles based on two coupled processes: inertial flow shaping and ultraviolet (UV) light polymerization. Pillars within fluidic platforms are used to deterministically deform photosensitive precursor fluid streams. The channels are then illuminated with patterned UV light to polymerize the photosensitive fluid, creating particles with multi-scale 3D geometries. The fundamental advantages of optofluidic fabrication include high-resolution, multi-scalability, dynamic tunability, simple operation and great potential for bulk fabrication with full automation. Through different combinations of pillar configurations, flow rates and UV light patterns, an infinite set of 3D-shaped particles is available, and a variety are demonstrated.

  11. Holographic microscopy for 3D tracking of bacteria

    NASA Astrophysics Data System (ADS)

    Nadeau, Jay; Cho, Yong Bin; El-Kholy, Marwan; Bedrossian, Manuel; Rider, Stephanie; Lindensmith, Christian; Wallace, J. Kent

    2016-03-01

    Understanding when, how, and if bacteria swim is key to understanding critical ecological and biological processes, from carbon cycling to infection. Imaging motility by traditional light microscopy is limited by focus depth, requiring cells to be constrained in z. Holographic microscopy offers an instantaneous 3D snapshot of a large sample volume, and is therefore ideal in principle for quantifying unconstrained bacterial motility. However, resolving and tracking individual cells is difficult due to the low amplitude and phase contrast of the cells; the index of refraction of typical bacteria differs from that of water only at the second decimal place. In this work we present a combination of optical and sample-handling approaches to facilitating bacterial tracking by holographic phase imaging. The first is the design of the microscope, which is an off-axis design with the optics along a common path, which minimizes alignment issues while providing all of the advantages of off-axis holography. Second, we use anti-reflective coated etalon glass in the design of sample chambers, which reduce internal reflections. Improvement seen with the antireflective coating is seen primarily in phase imaging, and its quantification is presented here. Finally, dyes may be used to increase phase contrast according to the Kramers-Kronig relations. Results using three test strains are presented, illustrating the different types of bacterial motility characterized by an enteric organism (Escherichia coli), an environmental organism (Bacillus subtilis), and a marine organism (Vibrio alginolyticus). Data processing steps to increase the quality of the phase images and facilitate tracking are also discussed.

  12. 3D model-based detection and tracking for space autonomous and uncooperative rendezvous

    NASA Astrophysics Data System (ADS)

    Shang, Yang; Zhang, Yueqiang; Liu, Haibo

    2015-10-01

    In order to fully navigate using a vision sensor, a 3D edge model based detection and tracking technique was developed. Firstly, we proposed a target detection strategy over a sequence of several images from the 3D model to initialize the tracking. The overall purpose of such approach is to robustly match each image with the model views of the target. Thus we designed a line segment detection and matching method based on the multi-scale space technology. Experiments on real images showed that our method is highly robust under various image changes. Secondly, we proposed a method based on 3D particle filter (PF) coupled with M-estimation to track and estimate the pose of the target efficiently. In the proposed approach, a similarity observation model was designed according to a new distance function of line segments. Then, based on the tracking results of PF, the pose was optimized using M-estimation. Experiments indicated that the proposed method can effectively track and accurately estimate the pose of freely moving target in unconstrained environment.

  13. 3D whiteboard: collaborative sketching with 3D-tracked smart phones

    NASA Astrophysics Data System (ADS)

    Lue, James; Schulze, Jürgen P.

    2014-02-01

    We present the results of our investigation of the feasibility of a new approach for collaborative drawing in 3D, based on Android smart phones. Our approach utilizes a number of fiduciary markers, placed in the working area where they can be seen by the smart phones' cameras, in order to estimate the pose of each phone in the room. Our prototype allows two users to draw 3D objects with their smart phones by moving their phones around in 3D space. For example, 3D lines are drawn by recording the path of the phone as it is moved around in 3D space, drawing line segments on the screen along the way. Each user can see the virtual drawing space on their smart phones' displays, as if the display was a window into this space. Besides lines, our prototype application also supports 3D geometry creation, geometry transformation operations, and it shows the location of the other user's phone.

  14. Preparation and 3D Tracking of Catalytic Swimming Devices.

    PubMed

    Campbell, Andrew; Archer, Richard; Ebbens, Stephen

    2016-01-01

    We report a method to prepare catalytically active Janus colloids that "swim" in fluids and describe how to determine their 3D motion using fluorescence microscopy. One commonly deployed method for catalytically active colloids to produce enhanced motion is via an asymmetrical distribution of catalyst. Here this is achieved by spin coating a dispersed layer of fluorescent polymeric colloids onto a flat planar substrate, and then using directional platinum vapor deposition to half coat the exposed colloid surface, making a two faced "Janus" structure. The Janus colloids are then re-suspended from the planar substrate into an aqueous solution containing hydrogen peroxide. Hydrogen peroxide serves as a fuel for the platinum catalyst, which is decomposed into water and oxygen, but only on one side of the colloid. The asymmetry results in gradients that produce enhanced motion, or "swimming". A fluorescence microscope, together with a video camera is used to record the motion of individual colloids. The center of the fluorescent emission is found using image analysis to provide an x and y coordinate for each frame of the video. While keeping the microscope focal position fixed, the fluorescence emission from the colloid produces a characteristic concentric ring pattern which is subject to image analysis to determine the particles relative z position. In this way 3D trajectories for the swimming colloid are obtained, allowing swimming velocity to be accurately measured, and physical phenomena such as gravitaxis, which may bias the colloids motion to be detected. PMID:27404327

  15. 3D track initiation in clutter using 2D measurements

    NASA Astrophysics Data System (ADS)

    Lin, Lin; Kirubarajan, Thiagalingam; Bar-Shalom, Yaakov

    2001-11-01

    In this paper we present an algorithm for initiating 3-D tracks using range and azimuth (bearing) measurements from a 2-D radar on a moving platform. The work is motivated by the need to track possibly low-flying targets, e.g., cruise missiles, using reports from an aircraft-based surveillance radar. Previous work on this problem considered simple linear motion in a flat earth coordinate frame. Our research extends this to a more realistic scenario where the earth"s curvature is also considered. The target is assumed to be moving along a great circle at a constant altitude. After the necessary coordinate transformations, the measurements are nonlinear functions of the target state and the observability of target altitude is severely limited. The observability, quantified by the Cramer-Rao Lower Bound (CRLB), is very sensitive to the sensor-to-target geometry. The paper presents a Maximum Likelihood (ML) estimator for estimating the target motion parameters in the Earth Centered Earth Fixed coordinate frame from 2-D range and angle measurements. In order to handle the possibility of false measurements and missed detections, which was not considered in, we use the Probabilistic Data Association (PDA) algorithm to weight the detections in a frame. The PDA-based modified global likelihood is optimized using a numerical search. The accuracies obtained by the resulting ML-PDA estimator are quantified using the CRLB for different sensor-target configurations. It is shown that the proposed estimator is efficient, that is, it meets the CRLB. Of particular interest is the achievable accuracy for estimating the target altitude, which is not observed directly by the 2-D radar, but can be only inferred from the range and bearing observations.

  16. Light Attenuation Method for 3D data acquisition (LAM3D) of bottom particle deposits

    NASA Astrophysics Data System (ADS)

    Er, Jenn Wei; Law, Adrian W. K.; Adams, E. Eric; Yang, Yang

    2015-11-01

    We have developed a novel experimental technique, Light Attenuation Method for 3D data acquisition (LAM3D), to acquire three-dimensional spatial characteristics and temporal development of bottom particle deposits. The new technique performs data acquisition with higher spatial and temporal resolution than existing approaches with laser and ultrasonic 3D profilers, and is therefore ideal for laboratory investigations with fast varying changes in the sediment bed, such as the developing deposition profile from sediment clouds commonly formed during dredging or land reclamation projects and the dynamic evolution in movable bed processes in rivers. The principle of the technique is based on the analysis of the light attenuation due to multiple light scattering through the particle deposits layer compared to the clear water column. With appropriate calibration, the particles size and distribution thickness can be quantified by the transmitted light spectrum. In the presentation, we will first show our measurement setup with a light panel for calibrated illumination and a system of DSLR cameras for the light capturing. Subsequently, we shall present the experimental results of fast evolving deposition profile of a barge-disposed sediment cloud upon its bottom impact on the sea bed.

  17. Ultrafine particle emissions from desktop 3D printers

    NASA Astrophysics Data System (ADS)

    Stephens, Brent; Azimi, Parham; El Orch, Zeineb; Ramos, Tiffanie

    2013-11-01

    The development of low-cost desktop versions of three-dimensional (3D) printers has made these devices widely accessible for rapid prototyping and small-scale manufacturing in home and office settings. Many desktop 3D printers rely on heated thermoplastic extrusion and deposition, which is a process that has been shown to have significant aerosol emissions in industrial environments. However, we are not aware of any data on particle emissions from commercially available desktop 3D printers. Therefore, we report on measurements of size-resolved and total ultrafine particle (UFP) concentrations resulting from the operation of two types of commercially available desktop 3D printers inside a commercial office space. We also estimate size-resolved (11.5 nm-116 nm) and total UFP (<100 nm) emission rates and compare them to emission rates from other desktop devices and indoor activities known to emit fine and ultrafine particles. Estimates of emission rates of total UFPs were large, ranging from ˜2.0 × 1010 # min-1 for a 3D printer utilizing a polylactic acid (PLA) feedstock to ˜1.9 × 1011 # min-1 for the same type of 3D printer utilizing a higher temperature acrylonitrile butadiene styrene (ABS) thermoplastic feedstock. Because most of these devices are currently sold as standalone devices without any exhaust ventilation or filtration accessories, results herein suggest caution should be used when operating in inadequately ventilated or unfiltered indoor environments. Additionally, these results suggest that more controlled experiments should be conducted to more fundamentally evaluate particle emissions from a wider arrange of desktop 3D printers.

  18. Light shaping along 3D curves and particle manipulation

    NASA Astrophysics Data System (ADS)

    Rodrigo, José A.; Alieva, Tatiana

    2015-03-01

    We present a non-iterative holographic technique for efficient and versatile laser beam shaping along arbitrary 3D curves. Light beams with intensity shaped for several 3D curves: Tilted ring, Viviani's curve, Archimedean spiral, and trefoil-knotted curve have been experimentally generated and applied for optical trapping of micrometer-sized dielectric particles. The high intensity gradients and independent phase control prescribed along the curve make this kind of laser trap attractive for multiple particle manipulation and allow for forward and backward motion to the light source. Indeed, different configurations of tractor beam traps are experimentally demonstrated. This technique can also be applied for laser micro-machining.

  19. Nondestructive 3D confocal laser imaging with deconvolution of seven whole stardust tracks with complementary XRF and quantitative analysis

    SciTech Connect

    Greenberg, M.; Ebel, D.S.

    2009-03-19

    We present a nondestructive 3D system for analysis of whole Stardust tracks, using a combination of Laser Confocal Scanning Microscopy and synchrotron XRF. 3D deconvolution is used for optical corrections, and results of quantitative analyses of several tracks are presented. The Stardust mission to comet Wild 2 trapped many cometary and ISM particles in aerogel, leaving behind 'tracks' of melted silica aerogel on both sides of the collector. Collected particles and their tracks range in size from submicron to millimeter scale. Interstellar dust collected on the obverse of the aerogel collector is thought to have an average track length of {approx}15 {micro}m. It has been our goal to perform a total non-destructive 3D textural and XRF chemical analysis on both types of tracks. To that end, we use a combination of Laser Confocal Scanning Microscopy (LCSM) and X Ray Florescence (XRF) spectrometry. Utilized properly, the combination of 3D optical data and chemical data provides total nondestructive characterization of full tracks, prior to flattening or other destructive analysis methods. Our LCSM techniques allow imaging at 0.075 {micro}m/pixel, without the use of oil-based lenses. A full textural analysis on track No.82 is presented here as well as analysis of 6 additional tracks contained within 3 keystones (No.128, No.129 and No.140). We present a method of removing the axial distortion inherent in LCSM images, by means of a computational 3D Deconvolution algorithm, and present some preliminary experiments with computed point spread functions. The combination of 3D LCSM data and XRF data provides invaluable information, while preserving the integrity of the samples for further analysis. It is imperative that these samples, the first extraterrestrial solids returned since the Apollo era, be fully mapped nondestructively in 3D, to preserve the maximum amount of information prior to other, destructive analysis.

  20. Fuzzy Logic Particle Tracking

    NASA Technical Reports Server (NTRS)

    2005-01-01

    A new all-electronic Particle Image Velocimetry technique that can efficiently map high speed gas flows has been developed in-house at the NASA Lewis Research Center. Particle Image Velocimetry is an optical technique for measuring the instantaneous two component velocity field across a planar region of a seeded flow field. A pulsed laser light sheet is used to illuminate the seed particles entrained in the flow field at two instances in time. One or more charged coupled device (CCD) cameras can be used to record the instantaneous positions of particles. Using the time between light sheet pulses and determining either the individual particle displacements or the average displacement of particles over a small subregion of the recorded image enables the calculation of the fluid velocity. Fuzzy logic minimizes the required operator intervention in identifying particles and computing velocity. Using two cameras that have the same view of the illumination plane yields two single exposure image frames. Two competing techniques that yield unambiguous velocity vector direction information have been widely used for reducing the single-exposure, multiple image frame data: (1) cross-correlation and (2) particle tracking. Correlation techniques yield averaged velocity estimates over subregions of the flow, whereas particle tracking techniques give individual particle velocity estimates. For the correlation technique, the correlation peak corresponding to the average displacement of particles across the subregion must be identified. Noise on the images and particle dropout result in misidentification of the true correlation peak. The subsequent velocity vector maps contain spurious vectors where the displacement peaks have been improperly identified. Typically these spurious vectors are replaced by a weighted average of the neighboring vectors, thereby decreasing the independence of the measurements. In this work, fuzzy logic techniques are used to determine the true

  1. General defocusing particle tracking.

    PubMed

    Barnkob, Rune; Kähler, Christian J; Rossi, Massimiliano

    2015-09-01

    A General Defocusing Particle Tracking (GDPT) method is proposed for tracking the three-dimensional motion of particles in Lab-on-a-chip systems based on a set of calibration images and the normalized cross-correlation function. In comparison with other single-camera defocusing particle-tracking techniques, GDPT possesses a series of key advantages: it is applicable to particle images of arbitrary shapes, it is intuitive and easy to use, it can be used without advanced knowledge of optics and velocimetry theory, it is robust against outliers and overlapping particle images, and it requires only equipment which is standard in microfluidic laboratories. We demonstrate the method by tracking the three-dimensional motion of 2 μm spherical particles in a microfluidic channel using three different optical arrangements. The position of the particles was measured with an estimated uncertainty of 0.1 μm in the in-plane direction and 2 μm in the depth direction for a measurement volume of 1510 × 1270 × 160 μm(3). A ready-to-use GUI implementation of the method can be acquired on . PMID:26201498

  2. Vertical Flow Lithography for Fabrication of 3D Anisotropic Particles.

    PubMed

    Habasaki, Shohei; Lee, Won Chul; Yoshida, Shotaro; Takeuchi, Shoji

    2015-12-22

    A microfluidics-based method for the 3D fabrication of anisotropic particles is reported. The method uses a vertical microchannel where tunable light patterns solidify photocurable resins for stacking multiple layers of the resins, thus enabling an application of stereolithography concepts to conventional flow lithography. Multilayered, tapered, and angular compartmental microparticles are demonstrated. PMID:26551590

  3. Automated 3D trajectory measuring of large numbers of moving particles.

    PubMed

    Wu, Hai Shan; Zhao, Qi; Zou, Danping; Chen, Yan Qiu

    2011-04-11

    Complex dynamics of natural particle systems, such as insect swarms, bird flocks, fish schools, has attracted great attention of scientists for years. Measuring 3D trajectory of each individual in a group is vital for quantitative study of their dynamic properties, yet such empirical data is rare mainly due to the challenges of maintaining the identities of large numbers of individuals with similar visual features and frequent occlusions. We here present an automatic and efficient algorithm to track 3D motion trajectories of large numbers of moving particles using two video cameras. Our method solves this problem by formulating it as three linear assignment problems (LAP). For each video sequence, the first LAP obtains 2D tracks of moving targets and is able to maintain target identities in the presence of occlusions; the second one matches the visually similar targets across two views via a novel technique named maximum epipolar co-motion length (MECL), which is not only able to effectively reduce matching ambiguity but also further diminish the influence of frequent occlusions; the last one links 3D track segments into complete trajectories via computing a globally optimal assignment based on temporal and kinematic cues. Experiment results on simulated particle swarms with various particle densities validated the accuracy and robustness of the proposed method. As real-world case, our method successfully acquired 3D flight paths of fruit fly (Drosophila melanogaster) group comprising hundreds of freely flying individuals. PMID:21503074

  4. Multiview 3-D Echocardiography Fusion with Breath-Hold Position Tracking Using an Optical Tracking System.

    PubMed

    Punithakumar, Kumaradevan; Hareendranathan, Abhilash R; McNulty, Alexander; Biamonte, Marina; He, Allen; Noga, Michelle; Boulanger, Pierre; Becher, Harald

    2016-08-01

    Recent advances in echocardiography allow real-time 3-D dynamic image acquisition of the heart. However, one of the major limitations of 3-D echocardiography is the limited field of view, which results in an acquisition insufficient to cover the whole geometry of the heart. This study proposes the novel approach of fusing multiple 3-D echocardiography images using an optical tracking system that incorporates breath-hold position tracking to infer that the heart remains at the same position during different acquisitions. In six healthy male volunteers, 18 pairs of apical/parasternal 3-D ultrasound data sets were acquired during a single breath-hold as well as in subsequent breath-holds. The proposed method yielded a field of view improvement of 35.4 ± 12.5%. To improve the quality of the fused image, a wavelet-based fusion algorithm was developed that computes pixelwise likelihood values for overlapping voxels from multiple image views. The proposed wavelet-based fusion approach yielded significant improvement in contrast (66.46 ± 21.68%), contrast-to-noise ratio (49.92 ± 28.71%), signal-to-noise ratio (57.59 ± 47.85%) and feature count (13.06 ± 7.44%) in comparison to individual views. PMID:27166019

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

    SciTech Connect

    Quadros, William Roshan

    2015-08-22

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

  6. 3-D reconstruction of pre-characterized lithium and tungsten dust particle trajectories in NSTX

    NASA Astrophysics Data System (ADS)

    Nichols, J.; Roquemore, A. L.; Davis, W.; Mansfield, D. K.; Skinner, C. H.; Feibush, E.; Boeglin, W.; Patel, R.; Abolafia, D.; Hartzfeld, K.; Maqueda, R.

    2011-08-01

    Calibrated amounts of 40 μm lithium dust and 10 μm tungsten powder have been dropped from above into the SOL of the National Spherical Torus Experiment (NSTX) to benchmark modeling of dust dynamics and transport. By combining the output from two visible-range fast cameras, 3-D trajectories are reliably obtained and have resulted in the generation of several hundred individual particle tracks. Particles are observed to undergo a variety of accelerations both parallel and perpendicular to the magnetic field, as well as abrupt large-angle changes in direction. All tracks obtained to date display particle motion that is constrained to within a few centimeters of the last closed flux surface. The 3-D trajectories are presented and compared to the location of the last closed flux surface as determined by EFIT.

  7. On particle track detectors

    NASA Technical Reports Server (NTRS)

    Benton, E. V.; Gruhn, T. A.; Andrus, C. H.

    1973-01-01

    Aqueous sodium hydroxide is widely used to develop charged particle tracks in polycarbonate film, particularly Lexan. The chemical nature of the etching process for this system has been determined. A method employing ultra-violet absorbance was developed for monitoring the concentration of the etch products in solution. Using this method it was possible to study the formation of the etching solution saturated in etch products. It was found that the system super-saturates to a significant extent before precipitation occurs. It was also learned that the system approaches its equilibrium state rather slowly. It is felt that both these phenomena may be due to the presence of surfactant in the solution. In light of these findings, suggestions are given regarding the preparation and maintenance of the saturated etch solution. Two additional research projects, involving automated techniques for particle track analysis and particle identification using AgCl crystals, are briefly summarized.

  8. 3D Fluorescent and Reflective Imaging of Whole Stardust Tracks in Aerogel

    SciTech Connect

    Greenberg, M.; Ebel, D.S.

    2011-11-07

    The NASA Stardust mission returned to earth in 2006 with the cometary collector having captured over 1,000 particles in an aerogel medium at a relative velocity of 6.1 km/s. Particles captured in aerogel were heated, disaggregated and dispersed along 'tracks' or cavities in aerogel, singular tracks representing a history of one capture event. It has been our focus to chemically and morphologically characterize whole tracks in 3-dimensions, utilizing solely non-destructive methods. To this end, we have used a variety of methods: 3D Laser Scanning Confocal Microscopy (LSCM), synchrotron X-ray fluorescence (SXRF), and synchrotron X-ray diffraction (SXRD). In the past months we have developed two new techniques to aid in data collection. (1) We have received a new confocal microscope which has enabled autofluorescent and spectral imaging of aerogel samples. (2) We have developed a stereo-SXRF technique to chemically identify large grains in SXRF maps in 3-space. The addition of both of these methods to our analytic abilities provides a greater understanding of the mechanisms and results of track formation.

  9. Development of a 3D particle treecode for plasma simulations

    NASA Astrophysics Data System (ADS)

    Ong, Benjamin; Christlieb, Andrew; Krasny, Robert

    2008-11-01

    In this work we present a fully 3-D Boundary Integral Treecode (BIT). We apply the method to several classic problems such as sheath formation and 3D simulations of a Penning trap. In addition, we investigate the ability of the solver to naturally capture Coloumb scattering. A key point in the investigation is to understand the effect of different types of regularizations, and how to appropriately incorporate the regularization in the BIT framework. This work builds on substantial efforts in 1- and 2-D. [1] R. Krasny and K. Lindsay, A particle method and adaptive treecode for vortex sheet motion in 3-D flow, JCP, Vol. 172, No. 2, 879-907 [2] K. Matyash, R. Schneider, R. Sydora, and F. Taccogna, Application of a Grid-Free Kinetic Model to the Collisionless Sheath, Contrib. Plasma Phys, Vol. 48, No. 1-3, 116-120 (2008) [3] K. Cartwright and A. Christlieb, Boundary Integral Corrected Particle in Cell, SIAM Journal on Sci. Comput., submitted [4] A. Christlieb, R. Krasny, B. Ong and J. Qiu, A Step Towards Addressing Temporal Multi-scale Problems in Plasma Physics, in prep.

  10. PARTICLE BEAM TRACKING CIRCUIT

    DOEpatents

    Anderson, O.A.

    1959-05-01

    >A particle-beam tracking and correcting circuit is described. Beam induction electrodes are placed on either side of the beam, and potentials induced by the beam are compared in a voltage comparator or discriminator. This comparison produces an error signal which modifies the fm curve at the voltage applied to the drift tube, thereby returning the orbit to the preferred position. The arrangement serves also to synchronize accelerating frequency and magnetic field growth. (T.R.H.)

  11. Real Time 3D Facial Movement Tracking Using a Monocular Camera.

    PubMed

    Dong, Yanchao; Wang, Yanming; Yue, Jiguang; Hu, Zhencheng

    2016-01-01

    The paper proposes a robust framework for 3D facial movement tracking in real time using a monocular camera. It is designed to estimate the 3D face pose and local facial animation such as eyelid movement and mouth movement. The framework firstly utilizes the Discriminative Shape Regression method to locate the facial feature points on the 2D image and fuses the 2D data with a 3D face model using Extended Kalman Filter to yield 3D facial movement information. An alternating optimizing strategy is adopted to fit to different persons automatically. Experiments show that the proposed framework could track the 3D facial movement across various poses and illumination conditions. Given the real face scale the framework could track the eyelid with an error of 1 mm and mouth with an error of 2 mm. The tracking result is reliable for expression analysis or mental state inference. PMID:27463714

  12. Flare Particle Escape in 3D Solar Eruptive Events

    NASA Astrophysics Data System (ADS)

    Antiochos, Spiro K.; Masson, Sophie; DeVore, C. R.

    2015-04-01

    Among the most important, but least understood forms of space weather are the so-called Impulsive Solar Energetic Particle (SEP) events, which can be especially hazardous to deep-space astronauts. These energetic particles are generally believed to be produced by the flare reconnection that is the primary driver of solar eruptive events (SEE). A key point is that in the standard model of SEEs, the particles should remain trapped in the coronal flare loops and in the ejected plasmoid, the CME. However, flare-accelerated particles frequently reach the Earth long before the CME does. In previous 2.5D calculations we showed how the external reconnection that is an essential element of the breakout model for CME initiation could lead to the escape of flare-accelerated particles. The problem, however, is that in 2.5D this reconnection also tends to destroy the plasmoid, which disagrees with the observation that SEP events are often associated with well-defined plasmoids at 1 AU known as “magnetic clouds”. Consequently, we have extended our model to a fully 3D topology that includes a multi-polar coronal field suitable for a breakout SEE near a coronal hole region. We performed high-resolution 3D MHD numerical simulations with the Adaptively Refined MHD Solver (ARMS). Our results demonstrate that the model allows for the effective escape of energetic particles from deep within an ejecting well-defined plasmoid. We show how the complex interactions between the flare and breakout reconnection reproduce all the main observational features of SEEs and SEPs. We discuss the implications of our calculations for the upcoming Solar Orbiter and Solar Probe Plus missions, which will measure SEEs and SEPs near the Sun, thereby, mitigating propagation effects.This research was supported, in part, by the NASA SR&T and TR&T Programs.

  13. Tracking single particle rotation: Probing dynamics in four dimensions

    DOE PAGESBeta

    Anthony, Stephen Michael; Yu, Yan

    2015-04-29

    Direct visualization and tracking of small particles at high spatial and temporal resolution provides a powerful approach to probing complex dynamics and interactions in chemical and biological processes. Analysis of the rotational dynamics of particles adds a new dimension of information that is otherwise impossible to obtain with conventional 3-D particle tracking. In this review, we survey recent advances in single-particle rotational tracking, with highlights on the rotational tracking of optically anisotropic Janus particles. Furthermore, strengths and weaknesses of the various particle tracking methods, and their applications are discussed.

  14. THE THOMSON SURFACE. III. TRACKING FEATURES IN 3D

    SciTech Connect

    Howard, T. A.; DeForest, C. E.; Tappin, S. J.; Odstrcil, D.

    2013-03-01

    In this, the final installment in a three-part series on the Thomson surface, we present simulated observations of coronal mass ejections (CMEs) observed by a hypothetical polarizing white light heliospheric imager. Thomson scattering yields a polarization signal that can be exploited to locate observed features in three dimensions relative to the Thomson surface. We consider how the appearance of the CME changes with the direction of trajectory, using simulations of a simple geometrical shape and also of a more realistic CME generated using the ENLIL model. We compare the appearance in both unpolarized B and polarized pB light, and show that there is a quantifiable difference in the measured brightness of a CME between unpolarized and polarized observations. We demonstrate a technique for using this difference to extract the three-dimensional (3D) trajectory of large objects such as CMEs. We conclude with a discussion on how a polarizing heliospheric imager could be used to extract 3D trajectory information about CMEs or other observed features.

  15. A non-disruptive technology for robust 3D tool tracking for ultrasound-guided interventions.

    PubMed

    Mung, Jay; Vignon, Francois; Jain, Ameet

    2011-01-01

    In the past decade ultrasound (US) has become the preferred modality for a number of interventional procedures, offering excellent soft tissue visualization. The main limitation however is limited visualization of surgical tools. A new method is proposed for robust 3D tracking and US image enhancement of surgical tools under US guidance. Small US sensors are mounted on existing surgical tools. As the imager emits acoustic energy, the electrical signal from the sensor is analyzed to reconstruct its 3D coordinates. These coordinates can then be used for 3D surgical navigation, similar to current day tracking systems. A system with real-time 3D tool tracking and image enhancement was implemented on a commercial ultrasound scanner and 3D probe. Extensive water tank experiments with a tracked 0.2mm sensor show robust performance in a wide range of imaging conditions and tool position/orientations. The 3D tracking accuracy was 0.36 +/- 0.16mm throughout the imaging volume of 55 degrees x 27 degrees x 150mm. Additionally, the tool was successfully tracked inside a beating heart phantom. This paper proposes an image enhancement and tool tracking technology with sub-mm accuracy for US-guided interventions. The technology is non-disruptive, both in terms of existing clinical workflow and commercial considerations, showing promise for large scale clinical impact. PMID:22003612

  16. Tracking 3-D body motion for docking and robot control

    NASA Technical Reports Server (NTRS)

    Donath, M.; Sorensen, B.; Yang, G. B.; Starr, R.

    1987-01-01

    An advanced method of tracking three-dimensional motion of bodies has been developed. This system has the potential to dynamically characterize machine and other structural motion, even in the presence of structural flexibility, thus facilitating closed loop structural motion control. The system's operation is based on the concept that the intersection of three planes defines a point. Three rotating planes of laser light, fixed and moving photovoltaic diode targets, and a pipe-lined architecture of analog and digital electronics are used to locate multiple targets whose number is only limited by available computer memory. Data collection rates are a function of the laser scan rotation speed and are currently selectable up to 480 Hz. The tested performance on a preliminary prototype designed for 0.1 in accuracy (for tracking human motion) at a 480 Hz data rate includes a worst case resolution of 0.8 mm (0.03 inches), a repeatability of plus or minus 0.635 mm (plus or minus 0.025 inches), and an absolute accuracy of plus or minus 2.0 mm (plus or minus 0.08 inches) within an eight cubic meter volume with all results applicable at the 95 percent level of confidence along each coordinate region. The full six degrees of freedom of a body can be computed by attaching three or more target detectors to the body of interest.

  17. Modeling cell migration on filamentous tracks in 3D

    NASA Astrophysics Data System (ADS)

    Schwarz, J. M.

    2014-03-01

    Cell motility is integral to a number of physiological processes ranging from wound healing to immune response to cancer metastasis. Many studies of cell migration, both experimental and theoretical, have addressed various aspects of it in two dimensions, including protrusion and retraction at the level of single cells. However, the in vivo environment for a crawling cell is typically a three-dimensional environment, consisting of the extracellular matrix (ECM) and surrounding cells. Recent experiments demonstrate that some cells crawling along fibers of the ECM mimic the geometry of the fibers to become long and thin, as opposed to fan-like in two dimensions, and can remodel the ECM. Inspired by these experiments, a model cell consisting of beads and springs that moves along a tense semiflexible filamentous track is constructed and studied, paying particular attention to the mechanical feedback between the model cell and the track, as mediated by the active myosin-driven contractility and the catch/slip bond behavior of the focal adhesions, as the model cell crawls. This simple construction can then be scaled up to a model cell moving along a three-dimensional filamentous network, with a prescribed microenvironment, in order to make predictions for proposed experiments.

  18. Track of Right-Wheel Drag (3-D)

    NASA Technical Reports Server (NTRS)

    2004-01-01

    [figure removed for brevity, see original site] Figure 1

    [figure removed for brevity, see original site] Figure 2

    This 360-degree stereo panorama combines several frames taken by the navigation camera on NASA's Mars Exploration Rover Spirit during the rover's 313th martian day (Nov. 19, 2004). The site, labeled Spirit site 93, is in the 'Columbia Hills' inside Gusev Crater. The rover tracks point westward. Spirit had driven eastward, in reverse and dragging its right front wheel, for about 30 meters (100 feet) on the day the picture was taken. Driving backwards while dragging that wheel is a precautionary strategy to extend the usefulness of the wheel for when it is most needed, because it has developed more friction than the other wheels. The right-hand track in this look backwards shows how the dragging disturbed the soil. This view is presented in a cylindrical-perspective projection with geometric seam correction.

    Figure 1 is the left-eye view of a stereo pair and Figure 2 is the right-eye view of a stereo pair.

  19. Ultra-Wideband Time-Difference-of-Arrival High Resolution 3D Proximity Tracking System

    NASA Technical Reports Server (NTRS)

    Ni, Jianjun; Arndt, Dickey; Ngo, Phong; Phan, Chau; Dekome, Kent; Dusl, John

    2010-01-01

    This paper describes a research and development effort for a prototype ultra-wideband (UWB) tracking system that is currently under development at NASA Johnson Space Center (JSC). The system is being studied for use in tracking of lunar./Mars rovers and astronauts during early exploration missions when satellite navigation systems are not available. U IATB impulse radio (UWB-IR) technology is exploited in the design and implementation of the prototype location and tracking system. A three-dimensional (3D) proximity tracking prototype design using commercially available UWB products is proposed to implement the Time-Difference- Of-Arrival (TDOA) tracking methodology in this research effort. The TDOA tracking algorithm is utilized for location estimation in the prototype system, not only to exploit the precise time resolution possible with UWB signals, but also to eliminate the need for synchronization between the transmitter and the receiver. Simulations show that the TDOA algorithm can achieve the fine tracking resolution with low noise TDOA estimates for close-in tracking. Field tests demonstrated that this prototype UWB TDOA High Resolution 3D Proximity Tracking System is feasible for providing positioning-awareness information in a 3D space to a robotic control system. This 3D tracking system is developed for a robotic control system in a facility called "Moonyard" at Honeywell Defense & System in Arizona under a Space Act Agreement.

  20. 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

  1. Optimizing Stellarators for Energetic Particle Confinement using BEAMS3D

    NASA Astrophysics Data System (ADS)

    Bolgert, Peter; Drevlak, Michael; Lazerson, Sam; Gates, David; White, Roscoe

    2015-11-01

    Energetic particle (EP) loss has been called the ``Achilles heel of stellarators,'' (Helander, Rep. Prog. Phys. 77 087001 (2014)) and there is a great need for magnetic configurations with improved EP confinement. In this study we utilize a newly developed capability of the stellarator optimization code STELLOPT: the ability to optimize EP confinement via an interface with guiding center code BEAMS3D (McMillan et al., Plasma Phys. Control. Fusion 56, 095019 (2014)). Using this new tool, optimizations of the W7-X experiment and ARIES-CS reactor are performed where the EP loss fraction is one of many target functions to be minimized. In W7-X, we simulate the experimental NBI system using realistic beam geometry and beam deposition physics. The goal is to find configurations with improved neutral beam deposition and energetic particle confinement. These calculations are compared to previous studies of W7-X NBI deposition. In ARIES-CS, we launch 3.5 MeV alpha particles from a near-axis flux surface using a uniform grid in toroidal and poloidal angle. As these particles are born from D-T reactions, we consider an isotropic distribution in velocity space. This research is supported by DoE Contract Number DE-AC02-09CH11466.

  2. LV motion tracking from 3D echocardiography using textural and structural information.

    PubMed

    Myronenko, Andriy; Song, Xubo; Sahn, David J

    2007-01-01

    Automated motion reconstruction of the left ventricle (LV) from 3D echocardiography provides insight into myocardium architecture and function. Low image quality and artifacts make 3D ultrasound image processing a challenging problem. We introduce a LV tracking method, which combines textural and structural information to overcome the image quality limitations. Our method automatically reconstructs the motion of the LV contour (endocardium and epicardium) from a sequence of 3D ultrasound images. PMID:18044597

  3. 3-D Particle Simulation of Current Sheet Instabilities

    NASA Astrophysics Data System (ADS)

    Wang, Zhenyu; Lin, Yu; Wang, Xueyi; Tummel, Kurt; Chen, Liu

    2015-11-01

    The electrostatic (ES) and electromagnetic (EM) instabilities of a Harris current sheet are investigated using a 3-D linearized (δf) gyrokinetic (GK) electron and fully kinetic (FK) ion (GeFi) particle simulation code. The equilibrium magnetic field consists of an asymptotic anti-parallel Bx 0 and a guide field BG. The ES simulations show the excitation of lower-hybrid drift instability (LHDI) at the current sheet edge. The growth rate of the 3-D LHDI is scanned through the (kx ,ky) space. The most unstable modes are found to be at k∥ = 0 for smaller ky. As ky increases, the growth rate shows two peaks at k∥ ≠ 0 , consistent with analytical GK theory. The eigenmode structure and growth rate of LHDI obtained from the GeFi simulation agree well with those obtained from the FK PIC simulation. Decreasing BG, the asymptotic βe 0, or background density can destabilize the LHDI. In the EM simulation, tearing mode instability is dominant in the cases with ky kx , there exist two unstable modes: a kink-like (LHDI) mode at the current sheet edge and a sausage-like mode at the sheet center. The results are compared with the GK eigenmode theory and the FK simulation.

  4. 3D deformable organ model based liver motion tracking in ultrasound videos

    NASA Astrophysics Data System (ADS)

    Kim, Jung-Bae; Hwang, Youngkyoo; Oh, Young-Taek; Bang, Won-Chul; Lee, Heesae; Kim, James D. K.; Kim, Chang Yeong

    2013-03-01

    This paper presents a novel method of using 2D ultrasound (US) cine images during image-guided therapy to accurately track the 3D position of a tumor even when the organ of interest is in motion due to patient respiration. Tracking is possible thanks to a 3D deformable organ model we have developed. The method consists of three processes in succession. The first process is organ modeling where we generate a personalized 3D organ model from high quality 3D CT or MR data sets captured during three different respiratory phases. The model includes the organ surface, vessel and tumor, which can all deform and move in accord with patient respiration. The second process is registration of the organ model to 3D US images. From 133 respiratory phase candidates generated from the deformable organ model, we resolve the candidate that best matches the 3D US images according to vessel centerline and surface. As a result, we can determine the position of the US probe. The final process is real-time tracking using 2D US cine images captured by the US probe. We determine the respiratory phase by tracking the diaphragm on the image. The 3D model is then deformed according to respiration phase and is fitted to the image by considering the positions of the vessels. The tumor's 3D positions are then inferred based on respiration phase. Testing our method on real patient data, we have found the accuracy of 3D position is within 3.79mm and processing time is 5.4ms during tracking.

  5. 3D model-based catheter tracking for motion compensation in EP procedures

    NASA Astrophysics Data System (ADS)

    Brost, Alexander; Liao, Rui; Hornegger, Joachim; Strobel, Norbert

    2010-02-01

    Atrial fibrillation is the most common sustained heart arrhythmia and a leading cause of stroke. Its treatment by radio-frequency catheter ablation, performed using fluoroscopic image guidance, is gaining increasingly more importance. Two-dimensional fluoroscopic navigation can take advantage of overlay images derived from pre-operative 3-D data to add anatomical details otherwise not visible under X-ray. Unfortunately, respiratory motion may impair the utility of these static overlay images for catheter navigation. We developed an approach for image-based 3-D motion compensation as a solution to this problem. A bi-plane C-arm system is used to take X-ray images of a special circumferential mapping catheter from two directions. In the first step of the method, a 3-D model of the device is reconstructed. Three-dimensional respiratory motion at the site of ablation is then estimated by tracking the reconstructed catheter model in 3-D. This step involves bi-plane fluoroscopy and 2-D/3-D registration. Phantom data and clinical data were used to assess our model-based catheter tracking method. Experiments involving a moving heart phantom yielded an average 2-D tracking error of 1.4 mm and an average 3-D tracking error of 1.1 mm. Our evaluation of clinical data sets comprised 469 bi-plane fluoroscopy frames (938 monoplane fluoroscopy frames). We observed an average 2-D tracking error of 1.0 mm +/- 0.4 mm and an average 3-D tracking error of 0.8 mm +/- 0.5 mm. These results demonstrate that model-based motion-compensation based on 2-D/3-D registration is both feasible and accurate.

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

    DOE PAGESBeta

    Quadros, William Roshan

    2015-08-22

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

  7. Improving z-tracking accuracy in the two-photon single-particle tracking microscope

    NASA Astrophysics Data System (ADS)

    Liu, C.; Liu, Y.-L.; Perillo, E. P.; Jiang, N.; Dunn, A. K.; Yeh, H.-C.

    2015-10-01

    Here, we present a method that can improve the z-tracking accuracy of the recently invented TSUNAMI (Tracking of Single particles Using Nonlinear And Multiplexed Illumination) microscope. This method utilizes a maximum likelihood estimator (MLE) to determine the particle's 3D position that maximizes the likelihood of the observed time-correlated photon count distribution. Our Monte Carlo simulations show that the MLE-based tracking scheme can improve the z-tracking accuracy of TSUNAMI microscope by 1.7 fold. In addition, MLE is also found to reduce the temporal correlation of the z-tracking error. Taking advantage of the smaller and less temporally correlated z-tracking error, we have precisely recovered the hybridization-melting kinetics of a DNA model system from thousands of short single-particle trajectories in silico. Our method can be generally applied to other 3D single-particle tracking techniques.

  8. Improving z-tracking accuracy in the two-photon single-particle tracking microscope

    SciTech Connect

    Liu, C.; Liu, Y.-L.; Perillo, E. P.; Jiang, N.; Dunn, A. K. E-mail: tim.yeh@austin.utexas.edu; Yeh, H.-C. E-mail: tim.yeh@austin.utexas.edu

    2015-10-12

    Here, we present a method that can improve the z-tracking accuracy of the recently invented TSUNAMI (Tracking of Single particles Using Nonlinear And Multiplexed Illumination) microscope. This method utilizes a maximum likelihood estimator (MLE) to determine the particle's 3D position that maximizes the likelihood of the observed time-correlated photon count distribution. Our Monte Carlo simulations show that the MLE-based tracking scheme can improve the z-tracking accuracy of TSUNAMI microscope by 1.7 fold. In addition, MLE is also found to reduce the temporal correlation of the z-tracking error. Taking advantage of the smaller and less temporally correlated z-tracking error, we have precisely recovered the hybridization-melting kinetics of a DNA model system from thousands of short single-particle trajectories in silico. Our method can be generally applied to other 3D single-particle tracking techniques.

  9. Sketch on dynamic gesture tracking and analysis exploiting vision-based 3D interface

    NASA Astrophysics Data System (ADS)

    Woo, Woontack; Kim, Namgyu; Wong, Karen; Tadenuma, Makoto

    2000-12-01

    In this paper, we propose a vision-based 3D interface exploiting invisible 3D boxes, arranged in the personal space (i.e. reachable space by the body without traveling), which allows robust yet simple dynamic gesture tracking and analysis, without exploiting complicated sensor-based motion tracking systems. Vision-based gesture tracking and analysis is still a challenging problem, even though we have witnessed rapid advances in computer vision over the last few decades. The proposed framework consists of three main parts, i.e. (1) object segmentation without bluescreen and 3D box initialization with depth information, (2) movement tracking by observing how the body passes through the 3D boxes in the personal space and (3) movement feature extraction based on Laban's Effort theory and movement analysis by mapping features to meaningful symbols using time-delay neural networks. Obviously, exploiting depth information using multiview images improves the performance of gesture analysis by reducing the errors introduced by simple 2D interfaces In addition, the proposed box-based 3D interface lessens the difficulties in both tracking movement in 3D space and in extracting low-level features of the movement. Furthermore, the time-delay neural networks lessens the difficulties in movement analysis by training. Due to its simplicity and robustness, the framework will provide interactive systems, such as ATR I-cubed Tangible Music System or ATR Interactive Dance system, with improved quality of the 3D interface. The proposed simple framework also can be extended to other applications requiring dynamic gesture tracking and analysis on the fly.

  10. Nearly automatic motion capture system for tracking octopus arm movements in 3D space.

    PubMed

    Zelman, Ido; Galun, Meirav; Akselrod-Ballin, Ayelet; Yekutieli, Yoram; Hochner, Binyamin; Flash, Tamar

    2009-08-30

    Tracking animal movements in 3D space is an essential part of many biomechanical studies. The most popular technique for human motion capture uses markers placed on the skin which are tracked by a dedicated system. However, this technique may be inadequate for tracking animal movements, especially when it is impossible to attach markers to the animal's body either because of its size or shape or because of the environment in which the animal performs its movements. Attaching markers to an animal's body may also alter its behavior. Here we present a nearly automatic markerless motion capture system that overcomes these problems and successfully tracks octopus arm movements in 3D space. The system is based on three successive tracking and processing stages. The first stage uses a recently presented segmentation algorithm to detect the movement in a pair of video sequences recorded by two calibrated cameras. In the second stage, the results of the first stage are processed to produce 2D skeletal representations of the moving arm. Finally, the 2D skeletons are used to reconstruct the octopus arm movement as a sequence of 3D curves varying in time. Motion tracking, segmentation and reconstruction are especially difficult problems in the case of octopus arm movements because of the deformable, non-rigid structure of the octopus arm and the underwater environment in which it moves. Our successful results suggest that the motion-tracking system presented here may be used for tracking other elongated objects. PMID:19505502

  11. Eulerian and Lagrangian methods for vortex tracking in 2D and 3D flows

    NASA Astrophysics Data System (ADS)

    Huang, Yangzi; Green, Melissa

    2014-11-01

    Coherent structures are a key component of unsteady flows in shear layers. Improvement of experimental techniques has led to larger amounts of data and requires of automated procedures for vortex tracking. Many vortex criteria are Eulerian, and identify the structures by an instantaneous local swirling motion in the field, which are indicated by closed or spiral streamlines or pathlines in a reference frame. Alternatively, a Lagrangian Coherent Structures (LCS) analysis is a Lagrangian method based on the quantities calculated along fluid particle trajectories. In the current work, vortex detection is demonstrated on data from the simulation of two cases: a 2D flow with a flat plate undergoing a 45 ° pitch-up maneuver and a 3D wall-bounded turbulence channel flow. Vortices are visualized and tracked by their centers and boundaries using Γ1, the Q criterion, and LCS saddle points. In the cases of 2D flow, saddle points trace showed a rapid acceleration of the structure which indicates the shedding from the plate. For channel flow, saddle points trace shows that average structure convection speed exhibits a similar trend as a function of wall-normal distance as the mean velocity profile, and leads to statistical quantities of vortex dynamics. Dr. Jeff Eldredge and his research group at UCLA are gratefully acknowledged for sharing the database of simulation for the current research. This work was supported by the Air Force Office of Scientific Research under AFOSR Award No. FA9550-14-1-0210.

  12. Computational Graph Model for 3D Cells Tracking in Zebra Fish Datasets

    NASA Astrophysics Data System (ADS)

    Zhang, Lelin; Xiong, Hongkai; Zhao, Yang; Zhang, Kai; Zhou, Xiaobo

    2007-11-01

    This paper leads to a novel technique for tracking and identification of zebra-fish cells in 3D image sequences, extending graph-based multi-objects tracking algorithm to 3D applications. As raised in previous work of 2D graph-based method, separated cells are modeled as vertices that connected by edges. Then the tracking work is simplified to that of vertices matching between graphs generated from consecutive frames. Graph-based tracking is composed of three steps: graph generation, initial source vertices selection and graph saturation. To satisfy demands in this work separated cell records are segmented from original datasets using 3D level-set algorithms. Besides, advancements are achieved in each of the step including graph regulations, multi restrictions on source vertices and enhanced flow quantifications. Those strategies make a good compensation for graph-based multi-objects tracking method in 2D space. Experiments are carried out in 3D datasets sampled from zebra fish, results of which shows that this enhanced method could be potentially applied to tracking of objects with diverse features.

  13. High-throughput 3D tracking of bacteria on a standard phase contrast microscope

    NASA Astrophysics Data System (ADS)

    Taute, K. M.; Gude, S.; Tans, S. J.; Shimizu, T. S.

    2015-11-01

    Bacteria employ diverse motility patterns in traversing complex three-dimensional (3D) natural habitats. 2D microscopy misses crucial features of 3D behaviour, but the applicability of existing 3D tracking techniques is constrained by their performance or ease of use. Here we present a simple, broadly applicable, high-throughput 3D bacterial tracking method for use in standard phase contrast microscopy. Bacteria are localized at micron-scale resolution over a range of 350 × 300 × 200 μm by maximizing image cross-correlations between their observed diffraction patterns and a reference library. We demonstrate the applicability of our technique to a range of bacterial species and exploit its high throughput to expose hidden contributions of bacterial individuality to population-level variability in motile behaviour. The simplicity of this powerful new tool for bacterial motility research renders 3D tracking accessible to a wider community and paves the way for investigations of bacterial motility in complex 3D environments.

  14. High-throughput 3D tracking of bacteria on a standard phase contrast microscope

    PubMed Central

    Taute, K.M.; Gude, S.; Tans, S.J.; Shimizu, T.S.

    2015-01-01

    Bacteria employ diverse motility patterns in traversing complex three-dimensional (3D) natural habitats. 2D microscopy misses crucial features of 3D behaviour, but the applicability of existing 3D tracking techniques is constrained by their performance or ease of use. Here we present a simple, broadly applicable, high-throughput 3D bacterial tracking method for use in standard phase contrast microscopy. Bacteria are localized at micron-scale resolution over a range of 350 × 300 × 200 μm by maximizing image cross-correlations between their observed diffraction patterns and a reference library. We demonstrate the applicability of our technique to a range of bacterial species and exploit its high throughput to expose hidden contributions of bacterial individuality to population-level variability in motile behaviour. The simplicity of this powerful new tool for bacterial motility research renders 3D tracking accessible to a wider community and paves the way for investigations of bacterial motility in complex 3D environments. PMID:26522289

  15. Tracking 3D Picometer-Scale Motions of Single Nanoparticles with High-Energy Electron Probes

    PubMed Central

    Ogawa, Naoki; Hoshisashi, Kentaro; Sekiguchi, Hiroshi; Ichiyanagi, Kouhei; Matsushita, Yufuku; Hirohata, Yasuhisa; Suzuki, Seiichi; Ishikawa, Akira; Sasaki, Yuji C.

    2013-01-01

    We observed the high-speed anisotropic motion of an individual gold nanoparticle in 3D at the picometer scale using a high-energy electron probe. Diffracted electron tracking (DET) using the electron back-scattered diffraction (EBSD) patterns of labeled nanoparticles under wet-SEM allowed us to super-accurately measure the time-resolved 3D motion of individual nanoparticles in aqueous conditions. The highly precise DET data corresponded to the 3D anisotropic log-normal Gaussian distributions over time at the millisecond scale. PMID:23868465

  16. Detailed Evaluation of Five 3D Speckle Tracking Algorithms Using Synthetic Echocardiographic Recordings.

    PubMed

    Alessandrini, Martino; Heyde, Brecht; Queiros, Sandro; Cygan, Szymon; Zontak, Maria; Somphone, Oudom; Bernard, Olivier; Sermesant, Maxime; Delingette, Herve; Barbosa, Daniel; De Craene, Mathieu; ODonnell, Matthew; Dhooge, Jan

    2016-08-01

    A plethora of techniques for cardiac deformation imaging with 3D ultrasound, typically referred to as 3D speckle tracking techniques, are available from academia and industry. Although the benefits of single methods over alternative ones have been reported in separate publications, the intrinsic differences in the data and definitions used makes it hard to compare the relative performance of different solutions. To address this issue, we have recently proposed a framework to simulate realistic 3D echocardiographic recordings and used it to generate a common set of ground-truth data for 3D speckle tracking algorithms, which was made available online. The aim of this study was therefore to use the newly developed database to contrast non-commercial speckle tracking solutions from research groups with leading expertise in the field. The five techniques involved cover the most representative families of existing approaches, namely block-matching, radio-frequency tracking, optical flow and elastic image registration. The techniques were contrasted in terms of tracking and strain accuracy. The feasibility of the obtained strain measurements to diagnose pathology was also tested for ischemia and dyssynchrony. PMID:26960220

  17. Vision-Based Long-Range 3D Tracking, applied to Underground Surveying Tasks

    NASA Astrophysics Data System (ADS)

    Mossel, Annette; Gerstweiler, Georg; Vonach, Emanuel; Kaufmann, Hannes; Chmelina, Klaus

    2014-04-01

    To address the need of highly automated positioning systems in underground construction, we present a long-range 3D tracking system based on infrared optical markers. It provides continuous 3D position estimation of static or kinematic targets with low latency over a tracking volume of 12 m x 8 m x 70 m (width x height x depth). Over the entire volume, relative 3D point accuracy with a maximal deviation ≤ 22 mm is ensured with possible target rotations of yaw, pitch = 0 - 45° and roll = 0 - 360°. No preliminary sighting of target(s) is necessary since the system automatically locks onto a target without user intervention and autonomously starts tracking as soon as a target is within the view of the system. The proposed system needs a minimal hardware setup, consisting of two machine vision cameras and a standard workstation for data processing. This allows for quick installation with minimal disturbance of construction work. The data processing pipeline ensures camera calibration and tracking during on-going underground activities. Tests in real underground scenarios prove the system's capabilities to act as 3D position measurement platform for multiple underground tasks that require long range, low latency and high accuracy. Those tasks include simultaneously tracking of personnel, machines or robots.

  18. 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.

  19. 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

  20. Design and Performance Evaluation on Ultra-Wideband Time-Of-Arrival 3D Tracking System

    NASA Technical Reports Server (NTRS)

    Ni, Jianjun; Arndt, Dickey; Ngo, Phong; Dusl, John

    2012-01-01

    A three-dimensional (3D) Ultra-Wideband (UWB) Time--of-Arrival (TOA) tracking system has been studied at NASA Johnson Space Center (JSC) to provide the tracking capability inside the International Space Station (ISS) modules for various applications. One of applications is to locate and report the location where crew experienced possible high level of carbon-dioxide and felt upset. In order to accurately locate those places in a multipath intensive environment like ISS modules, it requires a robust real-time location system (RTLS) which can provide the required accuracy and update rate. A 3D UWB TOA tracking system with two-way ranging has been proposed and studied. The designed system will be tested in the Wireless Habitat Testbed which simulates the ISS module environment. In this presentation, we discuss the 3D TOA tracking algorithm and the performance evaluation based on different tracking baseline configurations. The simulation results show that two configurations of the tracking baseline are feasible. With 100 picoseconds standard deviation (STD) of TOA estimates, the average tracking error 0.2392 feet (about 7 centimeters) can be achieved for configuration Twisted Rectangle while the average tracking error 0.9183 feet (about 28 centimeters) can be achieved for configuration Slightly-Twisted Top Rectangle . The tracking accuracy can be further improved with the improvement of the STD of TOA estimates. With 10 picoseconds STD of TOA estimates, the average tracking error 0.0239 feet (less than 1 centimeter) can be achieved for configuration "Twisted Rectangle".

  1. Particle Tracks in Aerogel

    NASA Technical Reports Server (NTRS)

    2005-01-01

    In an experiment using a special air gun, particles are shot into aerogel at high velocities. Closeup of particles that have been captured in aerogel are shown here. The particles leave a carrot-shaped trail in the aerogel. Aerogel was used on the Stardust spacecraft to capture comet particles from Comet Wild 2.

  2. Moving Human Path Tracking Based on Video Surveillance in 3d Indoor Scenarios

    NASA Astrophysics Data System (ADS)

    Zhou, Yan; Zlatanova, Sisi; Wang, Zhe; Zhang, Yeting; Liu, Liu

    2016-06-01

    Video surveillance systems are increasingly used for a variety of 3D indoor applications. We can analyse human behaviour, discover and avoid crowded areas, monitor human traffic and so forth. In this paper we concentrate on use of surveillance cameras to track and reconstruct the path a person has followed. For the purpose we integrated video surveillance data with a 3D indoor model of the building and develop a single human moving path tracking method. We process the surveillance videos to detected single human moving traces; then we match the depth information of 3D scenes to the constructed 3D indoor network model and define the human traces in the 3D indoor space. Finally, the single human traces extracted from multiple cameras are connected with the help of the connectivity provided by the 3D network model. Using this approach, we can reconstruct the entire walking path. The provided experiments with a single person have verified the effectiveness and robustness of the method.

  3. A full-parallax 3D display with restricted viewing zone tracking viewer's eye

    NASA Astrophysics Data System (ADS)

    Beppu, Naoto; Yendo, Tomohiro

    2015-03-01

    The Three-Dimensional (3D) vision became widely known as familiar imaging technique now. The 3D display has been put into practical use in various fields, such as entertainment and medical fields. Development of 3D display technology will play an important role in a wide range of fields. There are various ways to the method of displaying 3D image. There is one of the methods that showing 3D image method to use the ray reproduction and we focused on it. This method needs many viewpoint images when achieve a full-parallax because this method display different viewpoint image depending on the viewpoint. We proposed to reduce wasteful rays by limiting projector's ray emitted to around only viewer using a spinning mirror, and to increase effectiveness of display device to achieve a full-parallax 3D display. We propose a method by using a tracking viewer's eye, a high-speed projector, a rotating mirror that tracking viewer (a spinning mirror), a concave mirror array having the different vertical slope arranged circumferentially (a concave mirror array), a cylindrical mirror. About proposed method in simulation, we confirmed the scanning range and the locus of the movement in the horizontal direction of the ray. In addition, we confirmed the switching of the viewpoints and convergence performance in the vertical direction of rays. Therefore, we confirmed that it is possible to realize a full-parallax.

  4. The BaBar Level 1 Drift-Chamber Trigger Upgrade With 3D Tracking

    SciTech Connect

    Chai, X.D.; /Iowa U.

    2005-11-29

    At BABAR, the Level 1 Drift Chamber trigger is being upgraded to reduce increasing background rates while the PEP-II luminosity keeps improving. This upgrade uses the drift time information and stereo wires in the drift chamber to perform a 3D track reconstruction that effectively rejects background events spread out along the beam line.

  5. 3D single molecule tracking in thick cellular specimens using multifocal plane microscopy

    NASA Astrophysics Data System (ADS)

    Ram, Sripad; Ward, E. Sally; Ober, Raimund J.

    2011-03-01

    One of the major challenges in single molecule microscopy concerns 3D tracking of single molecules in cellular specimens. This has been a major impediment to study many fundamental cellular processes, such as protein transport across thick cellular specimens (e.g. a cell-monolayer). Here we show that multifocal plane microscopy (MUM), an imaging modality developed by our group, provides the much needed solution to this longstanding problem. While MUM was previously used for 3D single molecule tracking at shallow depths (~ 1 micron) in live-cells, the question arises if MUM can also live up to the significant challenge of tracking single molecules in thick samples. Here by substantially expanding the capabilities of MUM, we demonstrate 3D tracking of quantum-dot labeled molecules in a ~ 10 micron thick cell monolayer. In this way we have reconstructed the complete 3D intracellular trafficking itinerary of single molecules at high spatial and temporal precision in a thick cell-sample. Funding support: NIH and the National MS Society.

  6. Mesoscopic in vivo 3-D tracking of sparse cell populations using angular multiplexed optical projection tomography

    PubMed Central

    Chen, Lingling; Alexandrov, Yuriy; Kumar, Sunil; Andrews, Natalie; Dallman, Margaret J.; French, Paul M. W.; McGinty, James

    2015-01-01

    We describe an angular multiplexed imaging technique for 3-D in vivo cell tracking of sparse cell distributions and optical projection tomography (OPT) with superior time-lapse resolution and a significantly reduced light dose compared to volumetric time-lapse techniques. We demonstrate that using dual axis OPT, where two images are acquired simultaneously at different projection angles, can enable localization and tracking of features in 3-D with a time resolution equal to the camera frame rate. This is achieved with a 200x reduction in light dose compared to an equivalent volumetric time-lapse single camera OPT acquisition with 200 projection angles. We demonstrate the application of this technique to mapping the 3-D neutrophil migration pattern observed over ~25.5 minutes in a live 2 day post-fertilisation transgenic LysC:GFP zebrafish embryo following a tail wound. PMID:25909009

  7. Fuzzy logic particle tracking velocimetry

    NASA Technical Reports Server (NTRS)

    Wernet, Mark P.

    1993-01-01

    Fuzzy logic has proven to be a simple and robust method for process control. Instead of requiring a complex model of the system, a user defined rule base is used to control the process. In this paper the principles of fuzzy logic control are applied to Particle Tracking Velocimetry (PTV). Two frames of digitally recorded, single exposure particle imagery are used as input. The fuzzy processor uses the local particle displacement information to determine the correct particle tracks. Fuzzy PTV is an improvement over traditional PTV techniques which typically require a sequence (greater than 2) of image frames for accurately tracking particles. The fuzzy processor executes in software on a PC without the use of specialized array or fuzzy logic processors. A pair of sample input images with roughly 300 particle images each, results in more than 200 velocity vectors in under 8 seconds of processing time.

  8. Parameterization of real-time 3D speckle tracking framework for cardiac strain assessment.

    PubMed

    Lorsakul, Auranuch; Duan, Qi; Po, Ming Jack; Angelini, Elsa; Homma, Shunichi; Laine, Andrew F

    2011-01-01

    Cross-correlation based 3D speckle tracking algorithm can be used to automatically track myocardial motion on three dimensional real-time (RT3D) echocardiography. The goal of this study was to experimentally investigate the effects of different parameters associated with such algorithm to ensure accurate cardiac strain measurements. The investigation was performed on 10 chronic obstructive pulmonary disease RT3DE cardiac ultrasound images. The following two parameters were investigated: 1) the gradient threshold of the anisotropic diffusion pre-filtering and 2) the window size of the cross correlation template matching in the speckle tracking. Results suggest that the optimal gradient threshold of the anisotropic filter depends on the average gradient of the background speckle noise, and that an optimal pair of template size and search window size can be identified determines the cross-correlation level and computational cost. PMID:22254887

  9. Extracting, Tracking, and Visualizing Magnetic Flux Vortices in 3D Complex-Valued Superconductor Simulation Data.

    PubMed

    Guo, Hanqi; Phillips, Carolyn L; Peterka, Tom; Karpeyev, Dmitry; Glatz, Andreas

    2016-01-01

    We propose a method for the vortex extraction and tracking of superconducting magnetic flux vortices for both structured and unstructured mesh data. In the Ginzburg-Landau theory, magnetic flux vortices are well-defined features in a complex-valued order parameter field, and their dynamics determine electromagnetic properties in type-II superconductors. Our method represents each vortex line (a 1D curve embedded in 3D space) as a connected graph extracted from the discretized field in both space and time. For a time-varying discrete dataset, our vortex extraction and tracking method is as accurate as the data discretization. We then apply 3D visualization and 2D event diagrams to the extraction and tracking results to help scientists understand vortex dynamics and macroscale superconductor behavior in greater detail than previously possible. PMID:26529730

  10. Eye Tracking to Explore the Impacts of Photorealistic 3d Representations in Pedstrian Navigation Performance

    NASA Astrophysics Data System (ADS)

    Dong, Weihua; Liao, Hua

    2016-06-01

    Despite the now-ubiquitous two-dimensional (2D) maps, photorealistic three-dimensional (3D) representations of cities (e.g., Google Earth) have gained much attention by scientists and public users as another option. However, there is no consistent evidence on the influences of 3D photorealism on pedestrian navigation. Whether 3D photorealism can communicate cartographic information for navigation with higher effectiveness and efficiency and lower cognitive workload compared to the traditional symbolic 2D maps remains unknown. This study aims to explore whether the photorealistic 3D representation can facilitate processes of map reading and navigation in digital environments using a lab-based eye tracking approach. Here we show the differences of symbolic 2D maps versus photorealistic 3D representations depending on users' eye-movement and navigation behaviour data. We found that the participants using the 3D representation were less effective, less efficient and were required higher cognitive workload than using the 2D map for map reading. However, participants using the 3D representation performed more efficiently in self-localization and orientation at the complex decision points. The empirical results can be helpful to improve the usability of pedestrian navigation maps in future designs.

  11. Label free cell tracking in 3D tissue engineering constructs with high resolution imaging

    NASA Astrophysics Data System (ADS)

    Smith, W. A.; Lam, K.-P.; Dempsey, K. P.; Mazzocchi-Jones, D.; Richardson, J. B.; Yang, Y.

    2014-02-01

    Within the field of tissue engineering there is an emphasis on studying 3-D live tissue structures. Consequently, to investigate and identify cellular activities and phenotypes in a 3-D environment for all in vitro experiments, including shape, migration/proliferation and axon projection, it is necessary to adopt an optical imaging system that enables monitoring 3-D cellular activities and morphology through the thickness of the construct for an extended culture period without cell labeling. This paper describes a new 3-D tracking algorithm developed for Cell-IQ®, an automated cell imaging platform, which has been equipped with an environmental chamber optimized to enable capturing time-lapse sequences of live cell images over a long-term period without cell labeling. As an integral part of the algorithm, a novel auto-focusing procedure was developed for phase contrast microscopy equipped with 20x and 40x objectives, to provide a more accurate estimation of cell growth/trajectories by allowing 3-D voxels to be computed at high spatiotemporal resolution and cell density. A pilot study was carried out in a phantom system consisting of horizontally aligned nanofiber layers (with precise spacing between them), to mimic features well exemplified in cellular activities of neuronal growth in a 3-D environment. This was followed by detailed investigations concerning axonal projections and dendritic circuitry formation in a 3-D tissue engineering construct. Preliminary work on primary animal neuronal cells in response to chemoattractant and topographic cue within the scaffolds has produced encouraging results.

  12. Towards robust 3D visual tracking for motion compensation in beating heart surgery.

    PubMed

    Richa, Rogério; Bó, Antônio P L; Poignet, Philippe

    2011-06-01

    In the context of minimally invasive cardiac surgery, active vision-based motion compensation schemes have been proposed for mitigating problems related to physiological motion. However, robust and accurate visual tracking remains a difficult task. The purpose of this paper is to present a robust visual tracking method that estimates the 3D temporal and spatial deformation of the heart surface using stereo endoscopic images. The novelty is the combination of a visual tracking method based on a Thin-Plate Spline (TPS) model for representing the heart surface deformations with a temporal heart motion model based on a time-varying dual Fourier series for overcoming tracking disturbances or failures. The considerable improvements in tracking robustness facing specular reflections and occlusions are demonstrated through experiments using images of in vivo porcine and human beating hearts. PMID:21277821

  13. 3-D PARTICLE TRANSPORT WITHIN THE HUMAN UPPER RESPIRATORY TRACT

    EPA Science Inventory

    In this study trajectories of inhaled particulate matter (PM) were simulated within a three-dimensional (3-D) computer model of the human upper respiratory tract (URT). The airways were described by computer-reconstructed images of a silicone rubber cast of the human head, throat...

  14. Alignment of 3D Building Models and TIR Video Sequences with Line Tracking

    NASA Astrophysics Data System (ADS)

    Iwaszczuk, D.; Stilla, U.

    2014-11-01

    Thermal infrared imagery of urban areas became interesting for urban climate investigations and thermal building inspections. Using a flying platform such as UAV or a helicopter for the acquisition and combining the thermal data with the 3D building models via texturing delivers a valuable groundwork for large-area building inspections. However, such thermal textures are useful for further analysis if they are geometrically correctly extracted. This can be achieved with a good coregistrations between the 3D building models and thermal images, which cannot be achieved by direct georeferencing. Hence, this paper presents methodology for alignment of 3D building models and oblique TIR image sequences taken from a flying platform. In a single image line correspondences between model edges and image line segments are found using accumulator approach and based on these correspondences an optimal camera pose is calculated to ensure the best match between the projected model and the image structures. Among the sequence the linear features are tracked based on visibility prediction. The results of the proposed methodology are presented using a TIR image sequence taken from helicopter in a densely built-up urban area. The novelty of this work is given by employing the uncertainty of the 3D building models and by innovative tracking strategy based on a priori knowledge from the 3D building model and the visibility checking.

  15. 3D single-molecule tracking using one- and two-photon excitation microscopy

    NASA Astrophysics Data System (ADS)

    Liu, Cong; Perillo, Evan P.; Zhuang, Quincy; Huynh, Khang T.; Dunn, Andrew K.; Yeh, Hsin-Chih

    2014-03-01

    Three dimensional single-molecule tracking (3D-SMT) has revolutionized the way we study fundamental cellular processes. By analyzing the spatial trajectories of individual molecules (e.g. a receptor or a signaling molecule) in 3D space, one can discern the internalization or transport dynamics of these molecules, study the heterogeneity of subcellular structures, and elucidate the complex spatiotemporal regulation mechanisms. Sub-diffraction localization precision, sub-millisecond temporal resolution and tens-of-seconds observation period are the benchmarks of current 3D-SMT techniques. We have recently built two molecular tracking systems in our labs. The first system is a previously reported confocal tracking system, which we denote as the 1P-1E-4D (one-photon excitation, one excitation beam, and four fiber-coupled detectors) system. The second system is a whole new design that is based on two-photon excitation, which we denote as the 2P-4E-1D (two-photon excitation, four excitation beams, and only one detector) system. Here we compare these two systems based on Monte Carlo simulation of tracking a diffusing fluorescent molecule. Through our simulation, we have characterized the limitation of individual systems and optimized the system parameters such as magnification, z-plane separation, and feedback gains.

  16. 3D tracking and phase-contrast imaging by twin-beams digital holographic microscope in microfluidics

    NASA Astrophysics Data System (ADS)

    Miccio, L.; Memmolo, P.; Finizio, A.; Paturzo, M.; Merola, F.; Grilli, S.; Ferraro, P.

    2012-06-01

    A compact twin-beam interferometer that can be adopted as a flexible diagnostic tool in microfluidic platforms is presented. The devise has two functionalities, as explained in the follow, and can be easily integrated in microfluidic chip. The configuration allows 3D tracking of micro-particles and, at same time, furnishes Quantitative Phase-Contrast maps of tracked micro-objects by interference microscopy. Experimental demonstration of its effectiveness and compatibility with biological field is given on for in vitro cells in microfluidic environment. Nowadays, several microfluidic configuration exist and many of them are commercially available, their development is due to the possibility for manipulating droplets, handling micro and nano-objects, visualize and quantify processes occurring in small volumes and, clearly, for direct applications on lab-on-a chip devices. In microfluidic research field, optical/photonics approaches are the more suitable ones because they have various advantages as to be non-contact, full-field, non-invasive and can be packaged thanks to the development of integrable optics. Moreover, phase contrast approaches, adapted to a lab-on-a-chip configurations, give the possibility to get quantitative information with remarkable lateral and vertical resolution directly in situ without the need to dye and/or kill cells. Furthermore, numerical techniques for tracking of micro-objects needs to be developed for measuring velocity fields, trajectories patterns, motility of cancer cell and so on. Here, we present a compact holographic microscope that can ensure, by the same configuration and simultaneously, accurate 3D tracking and quantitative phase-contrast analysis. The system, simple and solid, is based on twin laser beams coming from a single laser source. Through a easy conceptual design, we show how these two different functionalities can be accomplished by the same optical setup. The working principle, the optical setup and the mathematical

  17. A new 3D tracking method for cell mechanics investigation exploiting the capabilities of digital holography in microscopy

    NASA Astrophysics Data System (ADS)

    Miccio, L.; Memmolo, P.; Merola, F.; Fusco, S.; Netti, P. A.; Ferraro, P.

    2014-03-01

    A method for 3D tracking has been developed exploiting Digital Holography features in Microscopy (DHM). In the framework of self-consistent platform for manipulation and measurement of biological specimen we use DHM for quantitative and completely label free analysis of samples with low amplitude contrast. Tracking capability extend the potentiality of DHM allowing to monitor the motion of appropriate probes and correlate it with sample properties. Complete 3D tracking has been obtained for the probes avoiding the amplitude refocusing in traditional tracking processes. Moreover, in biology and biomedical research fields one of the main topic is the understanding of morphology and mechanics of cells and microorganisms. Biological samples present low amplitude contrast that limits the information that can be retrieved through optical bright-field microscope measurements. The main effect on light propagating in such objects is in phase. This is known as phase-retardation or phase-shift. DHM is an innovative and alternative approach in microscopy, it's a good candidate for no-invasive and complete specimen analysis because its main characteristic is the possibility to discern between intensity and phase information performing quantitative mapping of the Optical Path Length. In this paper, the flexibility of DH is employed to analyze cell mechanics of unstained cells subjected to appropriate stimuli. DHM is used to measure all the parameters useful to understand the deformations induced by external and controlled stresses on in-vitro cells. Our configuration allows 3D tracking of micro-particles and, simultaneously, furnish quantitative phase-contrast maps. Experimental results are presented and discussed for in vitro cells.

  18. Drogue tracking using 3D flash lidar for autonomous aerial refueling

    NASA Astrophysics Data System (ADS)

    Chen, Chao-I.; Stettner, Roger

    2011-06-01

    Autonomous aerial refueling (AAR) is an important capability for an unmanned aerial vehicle (UAV) to increase its flying range and endurance without increasing its size. This paper presents a novel tracking method that utilizes both 2D intensity and 3D point-cloud data acquired with a 3D Flash LIDAR sensor to establish relative position and orientation between the receiver vehicle and drogue during an aerial refueling process. Unlike classic, vision-based sensors, a 3D Flash LIDAR sensor can provide 3D point-cloud data in real time without motion blur, in the day or night, and is capable of imaging through fog and clouds. The proposed method segments out the drogue through 2D analysis and estimates the center of the drogue from 3D point-cloud data for flight trajectory determination. A level-set front propagation routine is first employed to identify the target of interest and establish its silhouette information. Sufficient domain knowledge, such as the size of the drogue and the expected operable distance, is integrated into our approach to quickly eliminate unlikely target candidates. A statistical analysis along with a random sample consensus (RANSAC) is performed on the target to reduce noise and estimate the center of the drogue after all 3D points on the drogue are identified. The estimated center and drogue silhouette serve as the seed points to efficiently locate the target in the next frame.

  19. Particle Acceleration in the Low Corona Over Broad Longitudes: Coupling MHD and 3D Particle Simulations

    NASA Astrophysics Data System (ADS)

    Gorby, M.; Schwadron, N.; Torok, T.; Downs, C.; Lionello, R.; Linker, J.; Titov, V. S.; Mikic, Z.; Riley, P.; Desai, M. I.; Dayeh, M. A.

    2014-12-01

    Recent work on the coupling between the Energetic Particle Radiation Environment Module (EPREM, a 3D energetic particle model) and Magnetohydrodynamics Around a Sphere (MAS, an MHD code developed at Predictive Science, Inc.) has demonstrated the efficacy of compression regions around fast coronal mass ejections (CMEs) for particle acceleration low in the corona (˜ 3 - 6 solar radii). These couplings show rapid particle acceleration over a broad longitudinal extent (˜ 80 degrees) resulting from the pile-up of magnetic flux in the compression regions and their subsequent expansion. The challenge for forming large SEP events in such compression-acceleration scenarios is to have enhanced scattering within the acceleration region while also allowing for efficient escape of accelerated particles downstream (away from the Sun) from the compression region. We present here the most recent simulation results including energetic particle and CME plasma profiles, the subsequent flux and dosages at 1AU, and an analysis of the compressional regions as efficient accelerators.

  20. Measurement Matrix Optimization and Mismatch Problem Compensation for DLSLA 3-D SAR Cross-Track Reconstruction.

    PubMed

    Bao, Qian; Jiang, Chenglong; Lin, Yun; Tan, Weixian; Wang, Zhirui; Hong, Wen

    2016-01-01

    With a short linear array configured in the cross-track direction, downward looking sparse linear array three-dimensional synthetic aperture radar (DLSLA 3-D SAR) can obtain the 3-D image of an imaging scene. To improve the cross-track resolution, sparse recovery methods have been investigated in recent years. In the compressive sensing (CS) framework, the reconstruction performance depends on the property of measurement matrix. This paper concerns the technique to optimize the measurement matrix and deal with the mismatch problem of measurement matrix caused by the off-grid scatterers. In the model of cross-track reconstruction, the measurement matrix is mainly affected by the configuration of antenna phase centers (APC), thus, two mutual coherence based criteria are proposed to optimize the configuration of APCs. On the other hand, to compensate the mismatch problem of the measurement matrix, the sparse Bayesian inference based method is introduced into the cross-track reconstruction by jointly estimate the scatterers and the off-grid error. Experiments demonstrate the performance of the proposed APCs' configuration schemes and the proposed cross-track reconstruction method. PMID:27556471

  1. A 3D front tracking method on a CPU/GPU system

    SciTech Connect

    Bo, Wurigen; Grove, John

    2011-01-21

    We describe the method to port a sequential 3D interface tracking code to a GPU with CUDA. The interface is represented as a triangular mesh. Interface geometry properties and point propagation are performed on a GPU. Interface mesh adaptation is performed on a CPU. The convergence of the method is assessed from the test problems with given velocity fields. Performance results show overall speedups from 11 to 14 for the test problems under mesh refinement. We also briefly describe our ongoing work to couple the interface tracking method with a hydro solver.

  2. Vision-based endoscope tracking for 3D ultrasound image-guided surgical navigation.

    PubMed

    Yang, L; Wang, J; Ando, T; Kubota, A; Yamashita, H; Sakuma, I; Chiba, T; Kobayashi, E

    2015-03-01

    This work introduces a self-contained framework for endoscopic camera tracking by combining 3D ultrasonography with endoscopy. The approach can be readily incorporated into surgical workflows without installing external tracking devices. By fusing the ultrasound-constructed scene geometry with endoscopic vision, this integrated approach addresses issues related to initialization, scale ambiguity, and interest point inadequacy that may be faced by conventional vision-based approaches when applied to fetoscopic procedures. Vision-based pose estimations were demonstrated by phantom and ex vivo monkey placenta imaging. The potential contribution of this method may extend beyond fetoscopic procedures to include general augmented reality applications in minimally invasive procedures. PMID:25263644

  3. Error control in the set-up of stereo camera systems for 3d animal tracking

    NASA Astrophysics Data System (ADS)

    Cavagna, A.; Creato, C.; Del Castello, L.; Giardina, I.; Melillo, S.; Parisi, L.; Viale, M.

    2015-12-01

    Three-dimensional tracking of animal systems is the key to the comprehension of collective behavior. Experimental data collected via a stereo camera system allow the reconstruction of the 3d trajectories of each individual in the group. Trajectories can then be used to compute some quantities of interest to better understand collective motion, such as velocities, distances between individuals and correlation functions. The reliability of the retrieved trajectories is strictly related to the accuracy of the 3d reconstruction. In this paper, we perform a careful analysis of the most significant errors affecting 3d reconstruction, showing how the accuracy depends on the camera system set-up and on the precision of the calibration parameters.

  4. Rapid 3D Track Reconstruction with the BaBar Trigger Upgrade

    SciTech Connect

    Bailey, S

    2004-05-24

    A new hardware trigger system based on tracks detected by a stereo drift chamber has been developed for the BABAR experiment at the Stanford Linear Accelerator Center. The z{sub 0} p{sub T} Discriminator (ZPD) is capable of fast, 3-dimensional reconstruction of charged particle tracks and provides rejection of background events due to beam particles interacting with the beam pipe at the first-level trigger. Over 1 gigabyte of data is processed per second by each ZPD module. Rapid track reconstruction has been realized using Xilinx Virtex-II FPGAs.

  5. 3D Visualization of Monte-Carlo Simulation's of HZE Track Structure and Initial Chemical Species

    NASA Technical Reports Server (NTRS)

    Plante, Ianik; Cucinotta, Francis A.

    2009-01-01

    Heavy ions biophysics is important for space radiation risk assessment [1] and hadron-therapy [2]. The characteristic of heavy ions tracks include a very high energy deposition region close to the track (<20 nm) denoted as the track core, and an outer penumbra region consisting of individual secondary electrons (6-rays). A still open question is the radiobiological effects of 6- rays relative to the track core. Of importance is the induction of double-strand breaks (DSB) [3] and oxidative damage to the biomolecules and the tissue matrix, considered the most important lesions for acute and long term effects of radiation. In this work, we have simulated a 56Fe26+ ion track of 1 GeV/amu with our Monte-Carlo code RITRACKS [4]. The simulation results have been used to calculate the energy depiction and initial chemical species in a "voxelized" space, which is then visualized in 3D. Several voxels with dose >1000 Gy are found in the penumbra, some located 0.1 mm from the track core. In computational models, the DSB induction probability is calculated with radial dose [6], which may not take into account the higher RBE of electron track ends for DSB induction. Therefore, these simulations should help improve models of DSB induction and our understanding of heavy ions biophysics.

  6. Freestanding 3D supramolecular particle bridges: fabrication and mechanical behavior.

    PubMed

    Ling, Xing Yi; Phang, In Yee; Schönherr, Holger; Reinhoudt, David N; Vancso, G Julius; Huskens, Jurriaan

    2009-06-01

    Freestanding particle bridges with controlled composition and macroscopic robustness are demonstrated by the use of supramolecular nanoparticle assembly. Self-assembly of nanoparticles, templating, and supramolecular glue infiltration are combined to form stable and ordered three-dimensional polystyrene particle composites on a polydimethylsiloxane stamp. Freestanding hybrid polystyrene nanoparticle bridges are obtained by transfer printing of the hybrid structures onto topographically patterned substrates via host-guest interactions. The mechanical robustness and rigidity of the particle bridges can be controlled by manipulating the layer-by-layer cycles of supramolecular glues of gold nanoparticles and dendrimers. Atomic force microscopy-based microbending results, in particular the location and force-dependent deflection behavior, confirm that the particle bridge fulfills the classical supported-beam characteristics. As estimated from classical beam theory, the bending moduli of the particle bridges vary between 0.8 and 1.1 GPa, depending on the degree of filling by the supramolecular glues. Failure analysis on the particle structure indicates linear elastic behavior and a plastic deformation upon failure. PMID:19373830

  7. 3D motion tracking of the heart using Harmonic Phase (HARP) isosurfaces

    NASA Astrophysics Data System (ADS)

    Soliman, Abraam S.; Osman, Nael F.

    2010-03-01

    Tags are non-invasive features induced in the heart muscle that enable the tracking of heart motion. Each tag line, in fact, corresponds to a 3D tag surface that deforms with the heart muscle during the cardiac cycle. Tracking of tag surfaces deformation is useful for the analysis of left ventricular motion. Cardiac material markers (Kerwin et al, MIA, 1997) can be obtained from the intersections of orthogonal surfaces which can be reconstructed from short- and long-axis tagged images. The proposed method uses Harmonic Phase (HARP) method for tracking tag lines corresponding to a specific harmonic phase value and then the reconstruction of grid tag surfaces is achieved by a Delaunay triangulation-based interpolation for sparse tag points. Having three different tag orientations from short- and long-axis images, the proposed method showed the deformation of 3D tag surfaces during the cardiac cycle. Previous work on tag surface reconstruction was restricted for the "dark" tag lines; however, the use of HARP as proposed enables the reconstruction of isosurfaces based on their harmonic phase values. The use of HARP, also, provides a fast and accurate way for tag lines identification and tracking, and hence, generating the surfaces.

  8. Real-time tracking with a 3D-Flow processor array

    SciTech Connect

    Crosetto, D.

    1993-06-01

    The problem of real-time track-finding has been performed to date with CAM (Content Addressable Memories) or with fast coincidence logic, because the processing scheme was thought to have much slower performance. Advances in technology together with a new architectural approach make it feasible to also explore the computing technique for real-time track finding thus giving the advantages of implementing algorithms that can find more parameters such as calculate the sagitta, curvature, pt, etc., with respect to the CAM approach. The report describes real-time track finding using new computing approach technique based on the 3D-Flow array processor system. This system consists of a fixed interconnection architecture scheme, allowing flexible algorithm implementation on a scalable platform. The 3D-Flow parallel processing system for track finding is scalable in size and performance by either increasing the number of processors, or increasing the speed or else the number of pipelined stages. The present article describes the conceptual idea and the design stage of the project.

  9. Meanie3D - a mean-shift based, multivariate, multi-scale clustering and tracking algorithm

    NASA Astrophysics Data System (ADS)

    Simon, Jürgen-Lorenz; Malte, Diederich; Silke, Troemel

    2014-05-01

    Project OASE is the one of 5 work groups at the HErZ (Hans Ertel Centre for Weather Research), an ongoing effort by the German weather service (DWD) to further research at Universities concerning weather prediction. The goal of project OASE is to gain an object-based perspective on convective events by identifying them early in the onset of convective initiation and follow then through the entire lifecycle. The ability to follow objects in this fashion requires new ways of object definition and tracking, which incorporate all the available data sets of interest, such as Satellite imagery, weather Radar or lightning counts. The Meanie3D algorithm provides the necessary tool for this purpose. Core features of this new approach to clustering (object identification) and tracking are the ability to identify objects using the mean-shift algorithm applied to a multitude of variables (multivariate), as well as the ability to detect objects on various scales (multi-scale) using elements of Scale-Space theory. The algorithm works in 2D as well as 3D without modifications. It is an extension of a method well known from the field of computer vision and image processing, which has been tailored to serve the needs of the meteorological community. In spite of the special application to be demonstrated here (like convective initiation), the algorithm is easily tailored to provide clustering and tracking for a wide class of data sets and problems. In this talk, the demonstration is carried out on two of the OASE group's own composite sets. One is a 2D nationwide composite of Germany including C-Band Radar (2D) and Satellite information, the other a 3D local composite of the Bonn/Jülich area containing a high-resolution 3D X-Band Radar composite.

  10. High-throughput lensfree 3D tracking of human sperms reveals rare statistics of helical trajectories

    PubMed Central

    Su, Ting-Wei; Xue, Liang; Ozcan, Aydogan

    2012-01-01

    Dynamic tracking of human sperms across a large volume is a challenging task. To provide a high-throughput solution to this important need, here we describe a lensfree on-chip imaging technique that can track the three-dimensional (3D) trajectories of > 1,500 individual human sperms within an observation volume of approximately 8–17 mm3. This computational imaging platform relies on holographic lensfree shadows of sperms that are simultaneously acquired at two different wavelengths, emanating from two partially-coherent sources that are placed at 45° with respect to each other. This multiangle and multicolor illumination scheme permits us to dynamically track the 3D motion of human sperms across a field-of-view of > 17 mm2 and depth-of-field of approximately 0.5–1 mm with submicron positioning accuracy. The large statistics provided by this lensfree imaging platform revealed that only approximately 4–5% of the motile human sperms swim along well-defined helices and that this percentage can be significantly suppressed under seminal plasma. Furthermore, among these observed helical human sperms, a significant majority (approximately 90%) preferred right-handed helices over left-handed ones, with a helix radius of approximately 0.5–3 μm, a helical rotation speed of approximately 3–20 rotations/s and a linear speed of approximately 20–100 μm/s. This high-throughput 3D imaging platform could in general be quite valuable for observing the statistical swimming patterns of various other microorganisms, leading to new insights in their 3D motion and the underlying biophysics. PMID:22988076

  11. Current loop coalescence studied by 3-D electromagnetic particle code

    NASA Technical Reports Server (NTRS)

    Nishikawa, Ken-Ichi; Sakai, Jun-Ichi; Koide, Shinji; Buneman, O.; Neubert, T.

    1993-01-01

    Solar flare plasma data from the Yohkoh satellite is analyzed. The interactions of current loops were observed in the active regions on the Sun. This observation pointed out the importance of the idea that the solar flare is generated by the coalescence of current loops. The three dimensional electromagnetic particle simulations are to help in understanding the global interaction between two current loops including the evolution of the twist of loops due to instabilities. Associated rapid dynamics of current loop coalescence such as reconnection, shock waves and associated kinetic processes such as energy transfer, acceleration of particles, and electromagnetic emissions are to be studied by the code to complement analytical theories and magnetohydrodynamic simulations of the current loop coalescence. The simulation results show the strong interactions between two current loops, beam and whistler instabilities, and associated parallel and perpendicular particle heating.

  12. Online reconstruction of 3D magnetic particle imaging data

    NASA Astrophysics Data System (ADS)

    Knopp, T.; Hofmann, M.

    2016-06-01

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

  13. Online reconstruction of 3D magnetic particle imaging data.

    PubMed

    Knopp, T; Hofmann, M

    2016-06-01

    Magnetic particle imaging is a quantitative functional imaging technique that allows imaging of the spatial distribution of super-paramagnetic iron oxide particles at high temporal resolution. The raw data acquisition can be performed at frame rates of more than 40 volumes s(-1). However, to date image reconstruction is performed in an offline step and thus no direct feedback is available during the experiment. Considering potential interventional applications such direct feedback would be mandatory. In this work, an online reconstruction framework is implemented that allows direct visualization of the particle distribution on the screen of the acquisition computer with a latency of about 2 s. The reconstruction process is adaptive and performs block-averaging in order to optimize the signal quality for a given amount of reconstruction time. PMID:27182668

  14. Automated 3-D tracking of centrosomes in sequences of confocal image stacks.

    PubMed

    Kerekes, Ryan A; Gleason, Shaun S; Trivedi, Niraj; Solecki, David J

    2009-01-01

    In order to facilitate the study of neuron migration, we propose a method for 3-D detection and tracking of centrosomes in time-lapse confocal image stacks of live neuron cells. We combine Laplacian-based blob detection, adaptive thresholding, and the extraction of scale and roundness features to find centrosome-like objects in each frame. We link these detections using the joint probabilistic data association filter (JPDAF) tracking algorithm with a Newtonian state-space model tailored to the motion characteristics of centrosomes in live neurons. We apply our algorithm to image sequences containing multiple cells, some of which had been treated with motion-inhibiting drugs. We provide qualitative results and quantitative comparisons to manual segmentation and tracking results showing that our average motion estimates agree to within 13% of those computed manually by neurobiologists. PMID:19964725

  15. Sensor Spatial Distortion, Visual Latency, and Update Rate Effects on 3D Tracking in Virtual Environments

    NASA Technical Reports Server (NTRS)

    Ellis, S. R.; Adelstein, B. D.; Baumeler, S.; Jense, G. J.; Jacoby, R. H.; Trejo, Leonard (Technical Monitor)

    1998-01-01

    Several common defects that we have sought to minimize in immersing virtual environments are: static sensor spatial distortion, visual latency, and low update rates. Human performance within our environments during large amplitude 3D tracking was assessed by objective and subjective methods in the presence and absence of these defects. Results show that 1) removal of our relatively small spatial sensor distortion had minor effects on the tracking activity, 2) an Adapted Cooper-Harper controllability scale proved the most sensitive subjective indicator of the degradation of dynamic fidelity caused by increasing latency and decreasing frame rates, and 3) performance, as measured by normalized RMS tracking error or subjective impressions, was more markedly influenced by changing visual latency than by update rate.

  16. Stochastic Particle Tracking in Fractured Sedimentary Formations

    NASA Astrophysics Data System (ADS)

    Willmann, Matthias; Kinzelbach, Wolfgang

    2014-05-01

    depends only on the (hydraulic) fracture aperture and the matrix flux perpendicular to the fracture as well as a molecular diffusion component. A flux-weighted random choice at fracture intersection makes the method essentially stochastic. Finally, we apply the method to a fractured sedimentary formation in Northern Switzerland which is currently under investigation as a host rock formation for nuclear waste. It is a 3D data set with about 15 Mio. nodes and 3 stochastically distributed fracture systems. In our particle tracking analysis we find a markedly different transport behavior at the lower permeable parts of the formation than at the more permeable ones. Overall, we find this particle tracking method very useful to investigate fractured sedimentary formations.

  17. 3-D Spreadsheet Simulation of a Modern Particle Detector

    ERIC Educational Resources Information Center

    Scott, Alan J.

    2004-01-01

    A spreadsheet simulation of a modern particle detector has been developed and can be readily used as an instructional tool in the physics classroom. The spreadsheet creates a three-dimensional model that can be rotated and helical trajectories can be highlighted. An associated student worksheet is also presented.

  18. A brain-computer interface method combined with eye tracking for 3D interaction.

    PubMed

    Lee, Eui Chul; Woo, Jin Cheol; Kim, Jong Hwa; Whang, Mincheol; Park, Kang Ryoung

    2010-07-15

    With the recent increase in the number of three-dimensional (3D) applications, the need for interfaces to these applications has increased. Although the eye tracking method has been widely used as an interaction interface for hand-disabled persons, this approach cannot be used for depth directional navigation. To solve this problem, we propose a new brain computer interface (BCI) method in which the BCI and eye tracking are combined to analyze depth navigation, including selection and two-dimensional (2D) gaze direction, respectively. The proposed method is novel in the following five ways compared to previous works. First, a device to measure both the gaze direction and an electroencephalogram (EEG) pattern is proposed with the sensors needed to measure the EEG attached to a head-mounted eye tracking device. Second, the reliability of the BCI interface is verified by demonstrating that there is no difference between the real and the imaginary movements for the same work in terms of the EEG power spectrum. Third, depth control for the 3D interaction interface is implemented by an imaginary arm reaching movement. Fourth, a selection method is implemented by an imaginary hand grabbing movement. Finally, for the independent operation of gazing and the BCI, a mode selection method is proposed that measures a user's concentration by analyzing the pupil accommodation speed, which is not affected by the operation of gazing and the BCI. According to experimental results, we confirmed the feasibility of the proposed 3D interaction method using eye tracking and a BCI. PMID:20580646

  19. 3D Smoothed Particle Hydrodynamics Models of Betelgeuse's Bow Shock

    NASA Astrophysics Data System (ADS)

    Mohamed, S.; Mackey, J.; Langer, N.

    2013-05-01

    Betelgeuse, the bright red supergiant (RSG) in Orion, is a runaway star. Its supersonic motion through the interstellar medium has resulted in the formation of a bow shock, a cometary structure pointing in the direction of motion. We present the first 3D hydrodynamic simulations of the formation and evolution of Betelgeuse's bow shock. We show that the bow shock morphology depends substantially on the growth timescale for Rayleigh-Taylor versus Kelvin-Helmholtz instabilities. We discuss our models in light of the recent Herschel, GALEX and VLA observations. If the mass in the bow shock shell is low (~few × 10-3 M⊙), as seems to be implied by the AKARI and Herschel observations, then Betelgeuse's bow shock is very young and is unlikely to have reached a steady state. The circular, smooth bow shock shell is consistent with this conclusion. We further discuss the implications of our results, in particular, the possibility that Betelgeuse may have only recently entered the RSG phase.

  20. Single-camera, three-dimensional particle tracking velocimetry.

    PubMed

    Peterson, Kevin; Regaard, Boris; Heinemann, Stefan; Sick, Volker

    2012-04-01

    This paper introduces single-camera, three-dimensional particle tracking velocimetry (SC3D-PTV), an image-based, single-camera technique for measuring 3-component, volumetric velocity fields in environments with limited optical access, in particular, optically accessible internal combustion engines. The optical components used for SC3D-PTV are similar to those used for two-camera stereoscopic-µPIV, but are adapted to project two simultaneous images onto a single image sensor. A novel PTV algorithm relying on the similarity of the particle images corresponding to a single, physical particle produces 3-component, volumetric velocity fields, rather than the 3-component, planar results obtained with stereoscopic PIV, and without the reconstruction of an instantaneous 3D particle field. The hardware and software used for SC3D-PTV are described, and experimental results are presented. PMID:22513613

  1. Using the symmetries in 3D Smoothed Particle Hydrodynamics

    NASA Astrophysics Data System (ADS)

    Cruz-Pérez, Juan P.; González, José A.

    2011-10-01

    We apply the cartoon SPH technique to solve numerically the Newtonian Euler's equations in scenarios with spherical symmetry with the standard Smoothed Particle Hydrodynamics method, using the equations written in cartesian coordinates. This implementation allow us to increase the resolution of the simulations in order to obtain accurate results. We test it using the Shock tube and the isothermal collapse of a perfect fluid in spherical symmetry.

  2. Using natural versus artificial stimuli to perform calibration for 3D gaze tracking

    NASA Astrophysics Data System (ADS)

    Maggia, Christophe; Guyader, Nathalie; Guérin-Dugué, Anne

    2013-03-01

    The presented study tests which type of stereoscopic image, natural or artificial, is more adapted to perform efficient and reliable calibration in order to track the gaze of observers in 3D space using classical 2D eye tracker. We measured the horizontal disparities, i.e. the difference between the x coordinates of the two eyes obtained using a 2D eye tracker. This disparity was recorded for each observer and for several target positions he had to fixate. Target positions were equally distributed in the 3D space, some on the screen (with a null disparity), some behind the screen (uncrossed disparity) and others in front of the screen (crossed disparity). We tested different regression models (linear and non linear) to explain either the true disparity or the depth with the measured disparity. Models were tested and compared on their prediction error for new targets at new positions. First of all, we found that we obtained more reliable disparities measures when using natural stereoscopic images rather than artificial. Second, we found that overall a non-linear model was more efficient. Finally, we discuss the fact that our results were observer dependent, with variability's between the observer's behavior when looking at 3D stimuli. Because of this variability, we proposed to compute observer specific model to accurately predict their gaze position when exploring 3D stimuli.

  3. Microfabricated collagen tracks facilitate single cell metastatic invasion in 3D.

    PubMed

    Kraning-Rush, Casey M; Carey, Shawn P; Lampi, Marsha C; Reinhart-King, Cynthia A

    2013-03-01

    While the mechanisms employed by metastatic cancer cells to migrate remain poorly understood, it has been widely accepted that metastatic cancer cells can invade the tumor stroma by degrading the extracellular matrix (ECM) with matrix metalloproteinases (MMPs). Although MMP inhibitors showed early promise in preventing metastasis in animal models, they have largely failed clinically. Recently, studies have shown that some cancer cells can use proteolysis to mechanically rearrange their ECM to form tube-like "microtracks" which other cells can follow without using MMPs themselves. We speculate that this mode of migration in the secondary cells may be one example of migration which can occur without endogenous protease activity in the secondary cells. Here we present a technique to study this migration in a 3D, collagen-based environment which mimics the size and topography of the tracks produced by proteolytically active cancer cells. Using time-lapse phase-contrast microscopy, we find that these microtracks permit the rapid and persistent migration of noninvasive MCF10A mammary epithelial cells, which are unable to otherwise migrate in 3D collagen. Additionally, while highly metastatic MDAMB231 breast cancer cells are able to invade a 3D collagen matrix, seeding within the patterned microtracks induced significantly increased cell migration speed, which was not decreased by pharmacological MMP inhibition. Together, these data suggest that microtracks within a 3D ECM may facilitate the migration of cells in an MMP-independent fashion, and may reveal novel insight into the clinical challenges facing MMP inhibitors. PMID:23388698

  4. Particle Tracking of Fluorescent Microspheres

    NASA Astrophysics Data System (ADS)

    Kaminski, Zofia; Mueller, Joachim; Berk, Serkan

    2010-10-01

    In this research, the diffusion coefficients of the fluorescent microspheres and the relation of those coefficients to particle radius were investigated. An additional focus was to see how well the measured radius of the microspheres compared to the radius as reported by the manufacturer and to measure the distribution of radii in a sample. This study further developed the critical process of ensuring particle movement within the sample volume and made preliminary sample measurements.The methods developed for tracking microspheres will later be used to determine the radii of virus like particles (VLPs), which are a non-infectious model system of the HIV virus. Results from our measurements will be reported.

  5. Particle tracking around surface nanobubbles

    NASA Astrophysics Data System (ADS)

    Dietrich, Erik; Zandvliet, Harold J. W.; Lohse, Detlef; Seddon, James R. T.

    2013-05-01

    The exceptionally long lifetime of surface nanobubbles remains one of the biggest questions in the field. One of the proposed mechanisms for producing the stability is the dynamic equilibrium model, which describes a constant flux of gas in and out of the bubble. Here, we describe results from particle tracking experiments carried out to measure this flow. The results are analysed by measuring the Voronoï cell size distribution, the diffusion, and the speed of the tracer particles. We show that there is no detectable difference in the movement of particles above nanobubble-laden surfaces as compared to ones above nanobubble-free surfaces.

  6. Particle displacement tracking for PIV

    NASA Technical Reports Server (NTRS)

    Wernet, Mark P.

    1990-01-01

    A new Particle Imaging Velocimetry (PIV) data acquisition and analysis system, which is an order of magnitude faster than any previously proposed system has been constructed and tested. The new Particle Displacement Tracing (PDT) system is an all electronic technique employing a video camera and a large memory buffer frame-grabber board. Using a simple encoding scheme, a time sequence of single exposure images are time coded into a single image and then processed to track particle displacements and determine velocity vectors. Application of the PDT technique to a counter-rotating vortex flow produced over 1100 velocity vectors in 110 seconds when processed on an 80386 PC.

  7. Detection, 3-D positioning, and sizing of small pore defects using digital radiography and tracking

    NASA Astrophysics Data System (ADS)

    Lindgren, Erik

    2014-12-01

    This article presents an algorithm that handles the detection, positioning, and sizing of submillimeter-sized pores in welds using radiographic inspection and tracking. The possibility to detect, position, and size pores which have a low contrast-to-noise ratio increases the value of the nondestructive evaluation of welds by facilitating fatigue life predictions with lower uncertainty. In this article, a multiple hypothesis tracker with an extended Kalman filter is used to track an unknown number of pore indications in a sequence of radiographs as an object is rotated. Each pore is not required to be detected in all radiographs. In addition, in the tracking step, three-dimensional (3-D) positions of pore defects are calculated. To optimize, set up, and pre-evaluate the algorithm, the article explores a design of experimental approach in combination with synthetic radiographs of titanium laser welds containing pore defects. The pre-evaluation on synthetic radiographs at industrially reasonable contrast-to-noise ratios indicate less than 1% false detection rates at high detection rates and less than 0.1 mm of positioning errors for more than 90% of the pores. A comparison between experimental results of the presented algorithm and a computerized tomography reference measurement shows qualitatively good agreement in the 3-D positions of approximately 0.1-mm diameter pores in 5-mm-thick Ti-6242.

  8. METHODS FOR USING 3-D ULTRASOUND SPECKLE TRACKING IN BIAXIAL MECHANICAL TESTING OF BIOLOGICAL TISSUE SAMPLES

    PubMed Central

    Yap, Choon Hwai; Park, Dae Woo; Dutta, Debaditya; Simon, Marc; Kim, Kang

    2014-01-01

    Being multilayered and anisotropic, biological tissues such as cardiac and arterial walls are structurally complex, making full assessment and understanding of their mechanical behavior challenging. Current standard mechanical testing uses surface markers to track tissue deformations and does not provide deformation data below the surface. In the study described here, we found that combining mechanical testing with 3-D ultrasound speckle tracking could overcome this limitation. Rat myocardium was tested with a biaxial tester and was concurrently scanned with high-frequency ultrasound in three dimensions. The strain energy function was computed from stresses and strains using an iterative non-linear curve-fitting algorithm. Because the strain energy function consists of terms for the base matrix and for embedded fibers, spatially varying fiber orientation was also computed by curve fitting. Using finite-element simulations, we first validated the accuracy of the non-linear curve-fitting algorithm. Next, we compared experimentally measured rat myocardium strain energy function values with those in the literature and found a matching order of magnitude. Finally, we retained samples after the experiments for fiber orientation quantification using histology and found that the results satisfactorily matched those computed in the experiments. We conclude that 3-D ultrasound speckle tracking can be a useful addition to traditional mechanical testing of biological tissues and may provide the benefit of enabling fiber orientation computation. PMID:25616585

  9. Ultrasonic diaphragm tracking for cardiac interventional navigation on 3D motion compensated static roadmaps

    NASA Astrophysics Data System (ADS)

    Timinger, Holger; Kruger, Sascha; Dietmayer, Klaus; Borgert, Joern

    2005-04-01

    In this paper, a novel approach to cardiac interventional navigation on 3D motion-compensated static roadmaps is presented. Current coronary interventions, e.g. percutaneous transluminal coronary angioplasties, are performed using 2D X-ray fluoroscopy. This comes along with well-known drawbacks like radiation exposure, use of contrast agent, and limited visualization, e.g. overlap and foreshortening, due to projection imaging. In the presented approach, the interventional device, i.e. the catheter, is tracked using an electromagnetic tracking system (MTS). Therefore, the catheters position is mapped into a static 3D image of the volume of interest (VOI) by means of an affine registration. In order to compensate for respiratory motion of the catheter with respect to the static image, a parameterized affine motion model is used which is driven by a respiratory sensor signal. This signal is derived from ultrasonic diaphragm tracking. The motion compensation for the heartbeat is done using ECG-gating. The methods are validated using a heart- and diaphragm-phantom. The mean displacement of the catheter due to the simulated organ motion decreases from approximately 9 mm to 1.3 mm. This result indicates that the proposed method is able to reconstruct the catheter position within the VOI accurately and that it can help to overcome drawbacks of current interventional procedures.

  10. Oblique needle segmentation and tracking for 3D TRUS guided prostate brachytherapy

    SciTech Connect

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

    2005-09-15

    An algorithm was developed in order to segment and track brachytherapy needles inserted along oblique trajectories. Three-dimensional (3D) transrectal ultrasound (TRUS) images of the rigid rod simulating the needle inserted into the tissue-mimicking agar and chicken breast phantoms were obtained to test the accuracy of the algorithm under ideal conditions. Because the robot possesses high positioning and angulation accuracies, we used the robot as a ''gold standard,'' and compared the results of algorithm segmentation to the values measured by the robot. Our testing results showed that the accuracy of the needle segmentation algorithm depends on the needle insertion distance into the 3D TRUS image and the angulations with respect to the TRUS transducer, e.g., at a 10 deg. insertion anglulation in agar phantoms, the error of the algorithm in determining the needle tip position was less than 1 mm when the insertion distance was greater than 15 mm. Near real-time needle tracking was achieved by scanning a small volume containing the needle. Our tests also showed that, the segmentation time was less than 60 ms, and the scanning time was less than 1.2 s, when the insertion distance into the 3D TRUS image was less than 55 mm. In our needle tracking tests in chicken breast phantoms, the errors in determining the needle orientation were less than 2 deg. in robot yaw and 0.7 deg. in robot pitch orientations, for up to 20 deg. needle insertion angles with the TRUS transducer in the horizontal plane when the needle insertion distance was greater than 15 mm.

  11. An automated tool for 3D tracking of single molecules in living cells

    NASA Astrophysics Data System (ADS)

    Gardini, L.; Capitanio, M.; Pavone, F. S.

    2015-03-01

    Since the behaviour of proteins and biological molecules is tightly related to cell's environment, more and more microscopy techniques are moving from in vitro to in living cells experiments. Looking at both diffusion and active transportation processes inside a cell requires three-dimensional localization over a few microns range, high SNR images and high temporal resolution. Since protein dynamics inside a cell involve all three dimensions, we developed an automated routine for 3D tracking of single fluorescent molecules inside living cells with nanometer accuracy, by exploiting the properties of the point-spread-function of out-of-focus Quantum Dots bound to the protein of interest.

  12. Study of a viewer tracking system with multiview 3D display

    NASA Astrophysics Data System (ADS)

    Yang, Jinn-Cherng; Wu, Chang-Shuo; Hsiao, Chuan-Heng; Yang, Ming-Chieh; Liu, Wen-Chieh; Hung, Yi-Ping

    2008-02-01

    An autostereoscopic display provides users great enjoyment of stereo visualization without uncomfortable and inconvenient drawbacks of wearing stereo glasses. However, bandwidth constraints of current multi-view 3D display severely restrict the number of views that can be simultaneously displayed without degrading resolution or increasing display cost unacceptably. An alternative to multiple view presentation is that the position of observer can be measured by using viewer-tracking sensor. It is a very important module of the viewer-tracking component for fluently rendering and accurately projecting the stereo video. In order to render stereo content with respect to user's view points and to optically project the content onto the left and right eyes of the user accurately, the real-time viewer tracking technique that allows the user to move around freely when watching the autostereoscopic display is developed in this study. It comprises the face detection by using multiple eigenspaces of various lighting conditions, fast block matching for tracking four motion parameters of the user's face region. The Edge Orientation Histogram (EOH) on Real AdaBoost to improve the performance of original AdaBoost algorithm is also applied in this study. The AdaBoost algorithm using Haar feature in OpenCV library developed by Intel to detect human face and enhance the accuracy performance with rotating image. The frame rate of viewer tracking process can achieve up to 15 Hz. Since performance of the viewer tracking autostereoscopic display is still influenced under variant environmental conditions, the accuracy, robustness and efficiency of the viewer-tracking system are evaluated in this study.

  13. The effect of object speed and direction on the performance of 3D speckle tracking using a 3D swept-volume ultrasound probe

    NASA Astrophysics Data System (ADS)

    Harris, Emma J.; Miller, Naomi R.; Bamber, Jeffrey C.; Symonds-Tayler, J. Richard N.; Evans, Philip M.

    2011-11-01

    Three-dimensional (3D) soft tissue tracking using 3D ultrasound is of interest for monitoring organ motion during therapy. Previously we demonstrated feature tracking of respiration-induced liver motion in vivo using a 3D swept-volume ultrasound probe. The aim of this study was to investigate how object speed affects the accuracy of tracking ultrasonic speckle in the absence of any structural information, which mimics the situation in homogenous tissue for motion in the azimuthal and elevational directions. For object motion prograde and retrograde to the sweep direction of the transducer, the spatial sampling frequency increases or decreases with object speed, respectively. We examined the effect object motion direction of the transducer on tracking accuracy. We imaged a homogenous ultrasound speckle phantom whilst moving the probe with linear motion at a speed of 0-35 mm s-1. Tracking accuracy and precision were investigated as a function of speed, depth and direction of motion for fixed displacements of 2 and 4 mm. For the azimuthal direction, accuracy was better than 0.1 and 0.15 mm for displacements of 2 and 4 mm, respectively. For a 2 mm displacement in the elevational direction, accuracy was better than 0.5 mm for most speeds. For 4 mm elevational displacement with retrograde motion, accuracy and precision reduced with speed and tracking failure was observed at speeds of greater than 14 mm s-1. Tracking failure was attributed to speckle de-correlation as a result of decreasing spatial sampling frequency with increasing speed of retrograde motion. For prograde motion, tracking failure was not observed. For inter-volume displacements greater than 2 mm, only prograde motion should be tracked which will decrease temporal resolution by a factor of 2. Tracking errors of the order of 0.5 mm for prograde motion in the elevational direction indicates that using the swept probe technology speckle tracking accuracy is currently too poor to track homogenous tissue over

  14. An automated tool for 3D tracking of single molecules in living cells

    NASA Astrophysics Data System (ADS)

    Gardini, L.; Capitanio, M.; Pavone, F. S.

    2015-07-01

    Recently, tremendous improvements have been achieved in the precision of localization of single fluorescent molecules, allowing localization and tracking of biomolecules at the nm level. Since the behaviour of proteins and biological molecules is tightly influenced by the cell's environment, a growing number of microscopy techniques are moving from in vitro to live cell experiments. Looking at both diffusion and active transportation processes inside a cell requires three-dimensional localization over a few microns range, high SNR images and high temporal resolution (ms order of magnitude). To satisfy these requirements we developed an automated routine that allow 3D tracking of single fluorescent molecules in living cells with nanometer accuracy, by exploiting the properties of the point-spread-function of out-of-focus Quantum Dots bound to the protein of interest.

  15. The ESyS_Particle: A New 3-D Discrete Element Model with Single Particle Rotation

    NASA Astrophysics Data System (ADS)

    Wang, Yucang; Mora, Peter

    In this paper, the Discrete Element Model (DEM) is reviewed, and the ESyS_Particle, our new version of DEM, is introduced. We particularly highlight some of the major physical concerns about DEMs and major differences between our model and most current DEMs. In the new model, single particle rotation is introduced and represented by a unit quaternion. For each 3-D particle, six degrees of freedom are employed: three for translational motion, and three for orientation. Six kinds of relative motions are permitted between two neighboring particles, and six interactions are transferred, i.e., radial, two shearing forces, twisting and two bending torques. The relative rotation between two particles is decomposed into two sequence-independent rotations such that all interactions due to the relative motions between interactive rigid bodies can be uniquely determined. This algorithm can give more accurate results because physical principles are obeyed. A theoretical analysis about how to choose the model parameters is presented. Several numerical tests have been carried out, the results indicate that most laboratory tests can be well reproduced using our model.

  16. Quantifying the 3D Odorant Concentration Field Used by Actively Tracking Blue Crabs

    NASA Astrophysics Data System (ADS)

    Webster, D. R.; Dickman, B. D.; Jackson, J. L.; Weissburg, M. J.

    2007-11-01

    Blue crabs and other aquatic organisms locate food and mates by tracking turbulent odorant plumes. The odorant concentration fluctuates unpredictably due to turbulent transport, and many characteristics of the fluctuation pattern have been hypothesized as useful cues for orienting to the odorant source. To make a direct linkage between tracking behavior and the odorant concentration signal, we developed a measurement system based the laser induced fluorescence technique to quantify the instantaneous 3D concentration field surrounding actively tracking blue crabs. The data suggest a correlation between upstream walking speed and the concentration of the odorant signal arriving at the antennule chemosensors, which are located near the mouth region. More specifically, we note an increase in upstream walking speed when high concentration bursts arrive at the antennules location. We also test hypotheses regarding the ability of blue crabs to steer relative to the plume centerline based on the signal contrast between the chemosensors located on their leg appendages. These chemosensors are located much closer to the substrate compared to the antennules and are separated by the width of the blue crab. In this case, it appears that blue crabs use the bilateral signal comparison to track along the edge of the plume.

  17. A Software System for Filling Complex Holes in 3D Meshes by Flexible Interacting Particles

    NASA Astrophysics Data System (ADS)

    Yamazaki, Daisuke; Savchenko, Vladimir

    3D meshes generated by acquisition devices such as laser range scanners often contain holes due to occlusion, etc. In practice, these holes are extremely geometrically and topologically complex. We propose a heuristic hole filling technique using particle systems to fill complex holes with arbitrary topology in 3D meshes. Our approach includes the following steps: hole identification, base surface creation, particle distribution, triangulation, and mesh refinement. We demonstrate the functionality of the proposed surface retouching system on synthetic and real data.

  18. The birth of a dinosaur footprint: Subsurface 3D motion reconstruction and discrete element simulation reveal track ontogeny

    PubMed Central

    2014-01-01

    Locomotion over deformable substrates is a common occurrence in nature. Footprints represent sedimentary distortions that provide anatomical, functional, and behavioral insights into trackmaker biology. The interpretation of such evidence can be challenging, however, particularly for fossil tracks recovered at bedding planes below the originally exposed surface. Even in living animals, the complex dynamics that give rise to footprint morphology are obscured by both foot and sediment opacity, which conceals animal–substrate and substrate–substrate interactions. We used X-ray reconstruction of moving morphology (XROMM) to image and animate the hind limb skeleton of a chicken-like bird traversing a dry, granular material. Foot movement differed significantly from walking on solid ground; the longest toe penetrated to a depth of ∼5 cm, reaching an angle of 30° below horizontal before slipping backward on withdrawal. The 3D kinematic data were integrated into a validated substrate simulation using the discrete element method (DEM) to create a quantitative model of limb-induced substrate deformation. Simulation revealed that despite sediment collapse yielding poor quality tracks at the air–substrate interface, subsurface displacements maintain a high level of organization owing to grain–grain support. Splitting the substrate volume along “virtual bedding planes” exposed prints that more closely resembled the foot and could easily be mistaken for shallow tracks. DEM data elucidate how highly localized deformations associated with foot entry and exit generate specific features in the final tracks, a temporal sequence that we term “track ontogeny.” This combination of methodologies fosters a synthesis between the surface/layer-based perspective prevalent in paleontology and the particle/volume-based perspective essential for a mechanistic understanding of sediment redistribution during track formation. PMID:25489092

  19. Data acquisition electronics and reconstruction software for real time 3D track reconstruction within the MIMAC project

    NASA Astrophysics Data System (ADS)

    Bourrion, O.; Bosson, G.; Grignon, C.; Bouly, J. L.; Richer, J. P.; Guillaudin, O.; Mayet, F.; Billard, J.; Santos, D.

    2011-11-01

    Directional detection of non-baryonic Dark Matter requires 3D reconstruction of low energy nuclear recoils tracks. A gaseous micro-TPC matrix, filled with either 3He, CF4 or C4H10 has been developed within the MIMAC project. A dedicated acquisition electronics and a real time track reconstruction software have been developed to monitor a 512 channel prototype. This auto-triggered electronic uses embedded processing to reduce the data transfer to its useful part only, i.e. decoded coordinates of hit tracks and corresponding energy measurements. An acquisition software with on-line monitoring and 3D track reconstruction is also presented.

  20. Segmentation and Tracking of Adherens Junctions in 3D for the Analysis of Epithelial Tissue Morphogenesis

    PubMed Central

    Cilla, Rodrigo; Mechery, Vinodh; Hernandez de Madrid, Beatriz; Del Signore, Steven; Dotu, Ivan; Hatini, Victor

    2015-01-01

    Epithelial morphogenesis generates the shape of tissues, organs and embryos and is fundamental for their proper function. It is a dynamic process that occurs at multiple spatial scales from macromolecular dynamics, to cell deformations, mitosis and apoptosis, to coordinated cell rearrangements that lead to global changes of tissue shape. Using time lapse imaging, it is possible to observe these events at a system level. However, to investigate morphogenetic events it is necessary to develop computational tools to extract quantitative information from the time lapse data. Toward this goal, we developed an image-based computational pipeline to preprocess, segment and track epithelial cells in 4D confocal microscopy data. The computational pipeline we developed, for the first time, detects the adherens junctions of epithelial cells in 3D, without the need to first detect cell nuclei. We accentuate and detect cell outlines in a series of steps, symbolically describe the cells and their connectivity, and employ this information to track the cells. We validated the performance of the pipeline for its ability to detect vertices and cell-cell contacts, track cells, and identify mitosis and apoptosis in surface epithelia of Drosophila imaginal discs. We demonstrate the utility of the pipeline to extract key quantitative features of cell behavior with which to elucidate the dynamics and biomechanical control of epithelial tissue morphogenesis. We have made our methods and data available as an open-source multiplatform software tool called TTT (http://github.com/morganrcu/TTT) PMID:25884654

  1. 3D reconstruction and particle acceleration properties of Coronal Shock Waves During Powerful Solar Particle Events

    NASA Astrophysics Data System (ADS)

    Plotnikov, Illya; Vourlidas, Angelos; Tylka, Allan J.; Pinto, Rui; Rouillard, Alexis; Tirole, Margot

    2016-07-01

    Identifying the physical mechanisms that produce the most energetic particles is a long-standing observational and theoretical challenge in astrophysics. Strong pressure waves have been proposed as efficient accelerators both in the solar and astrophysical contexts via various mechanisms such as diffusive-shock/shock-drift acceleration and betatron effects. In diffusive-shock acceleration, the efficacy of the process relies on shock waves being super-critical or moving several times faster than the characteristic speed of the medium they propagate through (a high Alfven Mach number) and on the orientation of the magnetic field upstream of the shock front. High-cadence, multipoint imaging using the NASA STEREO, SOHO and SDO spacecrafts now permits the 3-D reconstruction of pressure waves formed during the eruption of coronal mass ejections. Using these unprecedented capabilities, some recent studies have provided new insights on the timing and longitudinal extent of solar energetic particles, including the first derivations of the time-dependent 3-dimensional distribution of the expansion speed and Mach numbers of coronal shock waves. We will review these recent developments by focusing on particle events that occurred between 2011 and 2015. These new techniques also provide the opportunity to investigate the enigmatic long-duration gamma ray events.

  2. Regional airflow and particle distribution in the lung with a 3D-1D coupled subject-specific boundary condition

    NASA Astrophysics Data System (ADS)

    Choi, Jiwoong; Yin, Youbing; Hoffman, Eric; Tawhai, Merryn; Lin, Ching-Long

    2010-11-01

    Correct prediction of regional distribution of inhaled aerosol particles is vital to improve pulmonary medicine. Physiologically consistent regional ventilations of airflow and aerosol particles are simulated with a 3D-1D coupled subject-specific boundary condition (BC). In 3D CT-resolved 7-generation airways, large eddy simulations are performed to capture detailed airflow characteristics and Lagrangian particle simulations are carried to track the particle transport and deposition. Results are compared with two traditional outlet BCs: uniform velocity and uniform pressure. Proposed BC is eligible for physiologically consistent airflow distribution in the lung, while the others are not. The regional ventilation and deposition of particles reflect the regional ventilation of airflow. In this study, two traditional BCs yield up to 98% (334%) over-prediction in lobar particle ventilation (deposition) fraction. Upper to lower particle ventilation ratios of both left and right lungs read ˜0.4 with the proposed BC, while those for the other two BCs vary with the error up to 73%.

  3. Neural network techniques for invariant recognition and motion tracking of 3-D objects

    SciTech Connect

    Hwang, J.N.; Tseng, Y.H.

    1995-12-31

    Invariant recognition and motion tracking of 3-D objects under partial object viewing are difficult tasks. In this paper, we introduce a new neural network solution that is robust to noise corruption and partial viewing of objects. This method directly utilizes the acquired range data and requires no feature extraction. In the proposed approach, the object is first parametrically represented by a continuous distance transformation neural network (CDTNN) which is trained by the surface points of the exemplar object. When later presented with the surface points of an unknown object, this parametric representation allows the mismatch information to back-propagate through the CDTNN to gradually determine the best similarity transformation (translation and rotation) of the unknown object. The mismatch can be directly measured in the reconstructed representation domain between the model and the unknown object.

  4. Imaging SPR combined with stereoscopic 3D tracking to study barnacle cyprid-surface interactions

    NASA Astrophysics Data System (ADS)

    Maleshlijski, S.; Sendra, G. H.; Aldred, N.; Clare, A. S.; Liedberg, B.; Grunze, M.; Ederth, T.; Rosenhahn, A.

    2016-01-01

    Barnacle larvae (cyprids) explore surfaces to identify suitable settlement sites. This process is selective, and cyprids respond to numerous surface cues. To better understand the settlement process, it is desirable to simultaneously monitor both the surface exploration behavior and any close interactions with the surface. Stereoscopic 3D tracking of the cyprids provides quantitative access to surface exploration and pre-settlement rituals. Imaging surface plasmon resonance (SPR) reveals any interactions with the surfaces, such as surface inspection during bipedal walking and deposition of temporary adhesives. We report on a combination of both techniques to bring together information on swimming behavior in the vicinity of the interface and physical interactions of the cyprid with the surface. The technical requirements are described, and we applied the setup to cyprids of Balanus amphitrite. Initial data shows the applicability of the combined instrument to correlate exploration and touchdown events on surfaces with different chemical termination.

  5. CISUS: an integrated 3D ultrasound system for IGT using a modular tracking API

    NASA Astrophysics Data System (ADS)

    Boctor, Emad M.; Viswanathan, Anand; Pieper, Steve; Choti, Michael A.; Taylor, Russell H.; Kikinis, Ron; Fichtinger, Gabor

    2004-05-01

    Ultrasound has become popular in clinical/surgical applications, both as the primary image guidance modality and also in conjunction with other modalities like CT or MRI. Three dimensional ultrasound (3DUS) systems have also demonstrated usefulness in image-guided therapy (IGT). At the same time, however, current lack of open-source and open-architecture multi-modal medical visualization systems prevents 3DUS from fulfilling its potential. Several stand-alone 3DUS systems, like Stradx or In-Vivo exist today. Although these systems have been found to be useful in real clinical setting, it is difficult to augment their functionality and integrate them in versatile IGT systems. To address these limitations, a robotic/freehand 3DUS open environment (CISUS) is being integrated into the 3D Slicer, an open-source research tool developed for medical image analysis and surgical planning. In addition, the system capitalizes on generic application programming interfaces (APIs) for tracking devices and robotic control. The resulting platform-independent open-source system may serve as a valuable tool to the image guided surgery community. Other researchers could straightforwardly integrate the generic CISUS system along with other functionalities (i.e. dual view visualization, registration, real-time tracking, segmentation, etc) to rapidly create their medical/surgical applications. Our current driving clinical application is robotically assisted and freehand 3DUS-guided liver ablation, which is fully being integrated under the CISUS-3D Slicer. Initial functionality and pre-clinical feasibility are demonstrated on phantom and ex-vivo animal models.

  6. Using an Automated 3D-tracking System to Record Individual and Shoals of Adult Zebrafish

    PubMed Central

    Maaswinkel, Hans; Zhu, Liqun; Weng, Wei

    2013-01-01

    Like many aquatic animals, zebrafish (Danio rerio) moves in a 3D space. It is thus preferable to use a 3D recording system to study its behavior. The presented automatic video tracking system accomplishes this by using a mirror system and a calibration procedure that corrects for the considerable error introduced by the transition of light from water to air. With this system it is possible to record both single and groups of adult zebrafish. Before use, the system has to be calibrated. The system consists of three modules: Recording, Path Reconstruction, and Data Processing. The step-by-step protocols for calibration and using the three modules are presented. Depending on the experimental setup, the system can be used for testing neophobia, white aversion, social cohesion, motor impairments, novel object exploration etc. It is especially promising as a first-step tool to study the effects of drugs or mutations on basic behavioral patterns. The system provides information about vertical and horizontal distribution of the zebrafish, about the xyz-components of kinematic parameters (such as locomotion, velocity, acceleration, and turning angle) and it provides the data necessary to calculate parameters for social cohesions when testing shoals. PMID:24336189

  7. A new method for automatic tracking of facial landmarks in 3D motion captured images (4D).

    PubMed

    Al-Anezi, T; Khambay, B; Peng, M J; O'Leary, E; Ju, X; Ayoub, A

    2013-01-01

    The aim of this study was to validate the automatic tracking of facial landmarks in 3D image sequences. 32 subjects (16 males and 16 females) aged 18-35 years were recruited. 23 anthropometric landmarks were marked on the face of each subject with non-permanent ink using a 0.5mm pen. The subjects were asked to perform three facial animations (maximal smile, lip purse and cheek puff) from rest position. Each animation was captured by the 3D imaging system. A single operator manually digitised the landmarks on the 3D facial models and their locations were compared with those of the automatically tracked ones. To investigate the accuracy of manual digitisation, the operator re-digitised the same set of 3D images of 10 subjects (5 male and 5 female) at 1 month interval. The discrepancies in x, y and z coordinates between the 3D position of the manual digitised landmarks and that of the automatic tracked facial landmarks were within 0.17mm. The mean distance between the manually digitised and the automatically tracked landmarks using the tracking software was within 0.55 mm. The automatic tracking of facial landmarks demonstrated satisfactory accuracy which would facilitate the analysis of the dynamic motion during facial animations. PMID:23218511

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

  9. Methods for Measuring the Orientation and Rotation Rate of 3D-printed Particles in Turbulence.

    PubMed

    Cole, Brendan C; Marcus, Guy G; Parsa, Shima; Kramel, Stefan; Ni, Rui; Voth, Greg A

    2016-01-01

    Experimental methods are presented for measuring the rotational and translational motion of anisotropic particles in turbulent fluid flows. 3D printing technology is used to fabricate particles with slender arms connected at a common center. Shapes explored are crosses (two perpendicular rods), jacks (three perpendicular rods), triads (three rods in triangular planar symmetry), and tetrads (four arms in tetrahedral symmetry). Methods for producing on the order of 10,000 fluorescently dyed particles are described. Time-resolved measurements of their orientation and solid-body rotation rate are obtained from four synchronized videos of their motion in a turbulent flow between oscillating grids with Rλ = 91. In this relatively low-Reynolds number flow, the advected particles are small enough that they approximate ellipsoidal tracer particles. We present results of time-resolved 3D trajectories of position and orientation of the particles as well as measurements of their rotation rates. PMID:27404898

  10. Development of a 3D Digital Particle Image Thermometry and Velocimetry (3DDPITV) System

    NASA Astrophysics Data System (ADS)

    Schmitt, David; Rixon, Greg; Dabiri, Dana

    2006-11-01

    A novel 3D Digital Particle Image Thermometry and Velocimetry (3DDPITV) system has been designed and fabricated. By combining 3D Digital Particle Image Velocimetry (3DDPIV) and Digital Particle Image Thermometry (DPIT) into one system, this technique provides simultaneous temperature and velocity data in a volume of ˜1x1x0.5 in^3 using temperature sensitive liquid crystal particles as flow sensors. Two high-intensity xenon flashlamps were used as illumination sources. The imaging system consists of six CCD cameras, three allocated for measuring velocity, based on particle motion, and three for measuring temperature, based on particle color. The cameras were optically aligned using a precision grid and high-resolution translation stages. Temperature calibration was then performed using a precision thermometer and a temperature-controlled bath. Results from proof-of-concept experiments will be presented and discussed.

  11. Automatic alignment of standard views in 3D echocardiograms using real-time tracking

    NASA Astrophysics Data System (ADS)

    Orderud, Fredrik; Torp, Hans; Rabben, Stein Inge

    2009-02-01

    In this paper, we present an automatic approach for alignment of standard apical and short-axis slices, and correcting them for out-of-plane motion in 3D echocardiography. This is enabled by using real-time Kalman tracking to perform automatic left ventricle segmentation using a coupled deformable model, consisting of a left ventricle model, as well as structures for the right ventricle and left ventricle outflow tract. Landmark points from the segmented model are then used to generate standard apical and short-axis slices. The slices are automatically updated after tracking in each frame to correct for out-of-plane motion caused by longitudinal shortening of the left ventricle. Results from a dataset of 35 recordings demonstrate the potential for automating apical slice initialization and dynamic short-axis slices. Apical 4-chamber, 2-chamber and long-axis slices are generated based on an assumption of fixed angle between the slices, and short-axis slices are generated so that they follow the same myocardial tissue over the entire cardiac cycle. The error compared to manual annotation was 8.4 +/- 3.5 mm for apex, 3.6 +/- 1.8 mm for mitral valve and 8.4 +/- 7.4 for apical 4-chamber view. The high computational efficiency and automatic behavior of the method enables it to operate in real-time, potentially during image acquisition.

  12. The systematic and random errors determination using realtime 3D surface tracking system in breast cancer

    NASA Astrophysics Data System (ADS)

    Kanphet, J.; Suriyapee, S.; Dumrongkijudom, N.; Sanghangthum, T.; Kumkhwao, J.; Wisetrintong, M.

    2016-03-01

    The purpose of this study to determine the patient setup uncertainties in deep inspiration breath-hold (DIBH) radiation therapy for left breast cancer patients using real-time 3D surface tracking system. The six breast cancer patients treated by 6 MV photon beams from TrueBeam linear accelerator were selected. The patient setup errors and motion during treatment were observed and calculated for interfraction and intrafraction motions. The systematic and random errors were calculated in vertical, longitudinal and lateral directions. From 180 images tracking before and during treatment, the maximum systematic error of interfraction and intrafraction motions were 0.56 mm and 0.23 mm, the maximum random error of interfraction and intrafraction motions were 1.18 mm and 0.53 mm, respectively. The interfraction was more pronounce than the intrafraction, while the systematic error was less impact than random error. In conclusion the intrafraction motion error from patient setup uncertainty is about half of interfraction motion error, which is less impact due to the stability in organ movement from DIBH. The systematic reproducibility is also half of random error because of the high efficiency of modern linac machine that can reduce the systematic uncertainty effectively, while the random errors is uncontrollable.

  13. Investigating particle phase velocity in a 3D spouted bed by a novel fiber high speed photography method

    NASA Astrophysics Data System (ADS)

    Qian, Long; Lu, Yong; Zhong, Wenqi; Chen, Xi; Ren, Bing; Jin, Baosheng

    2013-07-01

    A novel fiber high speed photography method has been developed to measure particle phase velocity in a dense gas-solid flow. The measurement system mainly includes a fiber-optic endoscope, a high speed video camera, a metal halide light source and a powerful computer with large memory. The endoscope which could be inserted into the reactors is used to form motion images of particles within the measurement window illuminated by the metal halide lamp. These images are captured by the high speed video camera and processed through a series of digital image processing algorithms, such as calibration, denoising, enhancement and binarization in order to improve the image quality. Then particles' instantaneous velocity is figured out by tracking each particle in consecutive frames. Particle phase velocity is statistically calculated according to the probability of particle velocity in each frame within a time period. This system has been applied to the investigation of particles fluidization characteristics in a 3D spouted bed. The experimental results indicate that the particle fluidization feature in the region investigated could be roughly classified into three sections by particle phase vertical velocity and the boundary between the first section and the second is the surface where particle phase velocity tends to be 0, which is in good agreement with the results published in other literature.

  14. M3D-K simulations of sawteeth and energetic particle transport in tokamak plasmas

    NASA Astrophysics Data System (ADS)

    Shen, Wei; Fu, G. Y.; Sheng, Zheng-Mao; Breslau, J. A.; Wang, Feng

    2014-09-01

    Nonlinear simulations of sawteeth and related energetic particle transport are carried out using the kinetic/magnetohydrodynamic (MHD) hybrid code M3D-K. MHD simulations show repeated sawtooth cycles for a model tokamak equilibrium. Furthermore, test particle simulations are carried out to study the energetic particle transport due to a sawtooth crash. The results show that energetic particles are redistributed radially in the plasma core, depending on pitch angle and energy. For trapped particles, the redistribution occurs for particle energy below a critical value in agreement with existing theories. For co-passing particles, the redistribution is strong with little dependence on particle energy. In contrast, the redistribution level of counter-passing particles decreases with increasing particle energy.

  15. M3D-K Simulations of Sawteeth and Energetic Particle Transport in Tokamak Plasmas

    NASA Astrophysics Data System (ADS)

    Shen, Wei; Fu, Guoyong; Sheng, Zhengmao; Breslau, Joshua; Wang, Feng

    2013-10-01

    Nonlinear simulations of Sawteeth and energetic particle transport are carried out using the kinetic/MHD hybrid code M3D-K. MHD simulations show repeated sawtooth cycles due to a resistive (1,1) internal kink mode for a model tokamak equilibrium. Furthermore, test particle simulations are carried out to study the energetic particle transport due to a sawtooth crash. The results show that energetic particles are redistributed radially in plasma core depending on pitch angle and energy. For trapped particles, the redistribution occurs for particle energy below a critical value in agreement with previous theory. For co-passing particles, the redistribution is strong with little dependence on particle energy. In contrast, the redistribution level of counter-passing particles decreases as particle energy becomes large.

  16. M3D-K simulations of sawteeth and energetic particle transport in tokamak plasmas

    SciTech Connect

    Shen, Wei; Sheng, Zheng-Mao; Fu, G. Y.; Breslau, J. A.; Wang, Feng

    2014-09-15

    Nonlinear simulations of sawteeth and related energetic particle transport are carried out using the kinetic/magnetohydrodynamic (MHD) hybrid code M3D-K. MHD simulations show repeated sawtooth cycles for a model tokamak equilibrium. Furthermore, test particle simulations are carried out to study the energetic particle transport due to a sawtooth crash. The results show that energetic particles are redistributed radially in the plasma core, depending on pitch angle and energy. For trapped particles, the redistribution occurs for particle energy below a critical value in agreement with existing theories. For co-passing particles, the redistribution is strong with little dependence on particle energy. In contrast, the redistribution level of counter-passing particles decreases with increasing particle energy.

  17. Effect of Model Scale and Particle Size Distribution on PFC3D Simulation Results

    NASA Astrophysics Data System (ADS)

    Ding, Xiaobin; Zhang, Lianyang; Zhu, Hehua; Zhang, Qi

    2014-11-01

    This paper investigates the effect of model scale and particle size distribution on the simulated macroscopic mechanical properties, unconfined compressive strength (UCS), Young's modulus and Poisson's ratio, using the three-dimensional particle flow code (PFC3D). Four different maximum to minimum particle size ( d max/ d min) ratios, all having a continuous uniform size distribution, were considered and seven model (specimen) diameter to median particle size ratios ( L/ d) were studied for each d max/ d min ratio. The results indicate that the coefficients of variation (COVs) of the simulated macroscopic mechanical properties using PFC3D decrease significantly as L/ d increases. The results also indicate that the simulated mechanical properties using PFC3D show much lower COVs than those in PFC2D at all model scales. The average simulated UCS and Young's modulus using the default PFC3D procedure keep increasing with larger L/ d, although the rate of increase decreases with larger L/ d. This is mainly caused by the decrease of model porosity with larger L/ d associated with the default PFC3D method and the better balanced contact force chains at larger L/ d. After the effect of model porosity is eliminated, the results on the net model scale effect indicate that the average simulated UCS still increases with larger L/ d but the rate is much smaller, the average simulated Young's modulus decreases with larger L/ d instead, and the average simulated Poisson's ratio versus L/ d relationship remains about the same. Particle size distribution also affects the simulated macroscopic mechanical properties, larger d max/ d min leading to greater average simulated UCS and Young's modulus and smaller average simulated Poisson's ratio, and the changing rates become smaller at larger d max/ d min. This study shows that it is important to properly consider the effect of model scale and particle size distribution in PFC3D simulations.

  18. Three-Dimensional Visualization of Particle Tracks.

    ERIC Educational Resources Information Center

    Julian, Glenn M.

    1993-01-01

    Suggests ways to bring home to the introductory physics student some of the excitement of recent discoveries in particle physics. Describes particle detectors and encourages the use of the Standard Model along with real images of particle tracks to determine three-dimensional views of tracks. (MVL)

  19. Particle-based optical pressure sensors for 3D pressure mapping.

    PubMed

    Banerjee, Niladri; Xie, Yan; Chalaseni, Sandeep; Mastrangelo, Carlos H

    2015-10-01

    This paper presents particle-based optical pressure sensors for in-flow pressure sensing, especially for microfluidic environments. Three generations of pressure sensitive particles have been developed- flat planar particles, particles with integrated retroreflectors and spherical microballoon particles. The first two versions suffer from pressure measurement dependence on particles orientation in 3D space and angle of interrogation. The third generation of microspherical particles with spherical symmetry solves these problems making particle-based manometry in microfluidic environment a viable and efficient methodology. Static and dynamic pressure measurements have been performed in liquid medium for long periods of time in a pressure range of atmospheric to 40 psi. Spherical particles with radius of 12 μm and balloon-wall thickness of 0.5 μm are effective for more than 5 h in this pressure range with an error of less than 5%. PMID:26342493

  20. 3D Structural Fluctuation of IgG1 Antibody Revealed by Individual Particle Electron Tomography

    PubMed Central

    Zhang, Xing; Zhang, Lei; Tong, Huimin; Peng, Bo; Rames, Matthew J.; Zhang, Shengli; Ren, Gang

    2015-01-01

    Commonly used methods for determining protein structure, including X-ray crystallography and single-particle reconstruction, often provide a single and unique three-dimensional (3D) structure. However, in these methods, the protein dynamics and flexibility/fluctuation remain mostly unknown. Here, we utilized advances in electron tomography (ET) to study the antibody flexibility and fluctuation through structural determination of individual antibody particles rather than averaging multiple antibody particles together. Through individual-particle electron tomography (IPET) 3D reconstruction from negatively-stained ET images, we obtained 120 ab-initio 3D density maps at an intermediate resolution (~1–3 nm) from 120 individual IgG1 antibody particles. Using these maps as a constraint, we derived 120 conformations of the antibody via structural flexible docking of the crystal structure to these maps by targeted molecular dynamics simulations. Statistical analysis of the various conformations disclosed the antibody 3D conformational flexibility through the distribution of its domain distances and orientations. This blueprint approach, if extended to other flexible proteins, may serve as a useful methodology towards understanding protein dynamics and functions. PMID:25940394

  1. 3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography

    SciTech Connect

    Zhang, Xing; Zhang, Lei; Tong, Huimin; Peng, Bo; Rames, Matthew J.; Zhang, Shengli; Ren, Gang

    2015-05-05

    Commonly used methods for determining protein structure, including X-ray crystallography and single-particle reconstruction, often provide a single and unique three-dimensional (3D) structure. However, in these methods, the protein dynamics and flexibility/fluctuation remain mostly unknown. Here, we utilized advances in electron tomography (ET) to study the antibody flexibility and fluctuation through structural determination of individual antibody particles rather than averaging multiple antibody particles together. Through individual-particle electron tomography (IPET) 3D reconstruction from negatively-stained ET images, we obtained 120 ab-initio 3D density maps at an intermediate resolution (~1–3 nm) from 120 individual IgG1 antibody particles. Using these maps as a constraint, we derived 120 conformations of the antibody via structural flexible docking of the crystal structure to these maps by targeted molecular dynamics simulations. Statistical analysis of the various conformations disclosed the antibody 3D conformational flexibility through the distribution of its domain distances and orientations. This blueprint approach, if extended to other flexible proteins, may serve as a useful methodology towards understanding protein dynamics and functions.

  2. 3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography

    DOE PAGESBeta

    Zhang, Xing; Zhang, Lei; Tong, Huimin; Peng, Bo; Rames, Matthew J.; Zhang, Shengli; Ren, Gang

    2015-05-05

    Commonly used methods for determining protein structure, including X-ray crystallography and single-particle reconstruction, often provide a single and unique three-dimensional (3D) structure. However, in these methods, the protein dynamics and flexibility/fluctuation remain mostly unknown. Here, we utilized advances in electron tomography (ET) to study the antibody flexibility and fluctuation through structural determination of individual antibody particles rather than averaging multiple antibody particles together. Through individual-particle electron tomography (IPET) 3D reconstruction from negatively-stained ET images, we obtained 120 ab-initio 3D density maps at an intermediate resolution (~1–3 nm) from 120 individual IgG1 antibody particles. Using these maps as a constraint, wemore » derived 120 conformations of the antibody via structural flexible docking of the crystal structure to these maps by targeted molecular dynamics simulations. Statistical analysis of the various conformations disclosed the antibody 3D conformational flexibility through the distribution of its domain distances and orientations. This blueprint approach, if extended to other flexible proteins, may serve as a useful methodology towards understanding protein dynamics and functions.« less

  3. Confocal fluorometer for diffusion tracking in 3D engineered tissue constructs

    NASA Astrophysics Data System (ADS)

    Daly, D.; Zilioli, A.; Tan, N.; Buttenschoen, K.; Chikkanna, B.; Reynolds, J.; Marsden, B.; Hughes, C.

    2016-03-01

    We present results of the development of a non-contacting instrument, called fScan, based on scanning confocal fluorometry for assessing the diffusion of materials through a tissue matrix. There are many areas in healthcare diagnostics and screening where it is now widely accepted that the need for new quantitative monitoring technologies is a major pinch point in patient diagnostics and in vitro testing. With the increasing need to interpret 3D responses this commonly involves the need to track the diffusion of compounds, pharma-active species and cells through a 3D matrix of tissue. Methods are available but to support the advances that are currently only promised, this monitoring needs to be real-time, non-invasive, and economical. At the moment commercial meters tend to be invasive and usually require a sample of the medium to be removed and processed prior to testing. This methodology clearly has a number of significant disadvantages. fScan combines a fiber based optical arrangement with a compact, free space optical front end that has been integrated so that the sample's diffusion can be measured without interference. This architecture is particularly important due to the "wet" nature of the samples. fScan is designed to measure constructs located within standard well plates and a 2-D motion stage locates the required sample with respect to the measurement system. Results are presented that show how the meter has been used to evaluate movements of samples through collagen constructs in situ without disturbing their kinetic characteristics. These kinetics were little understood prior to these measurements.

  4. Simulation of surface tension in 2D and 3D with smoothed particle hydrodynamics method

    NASA Astrophysics Data System (ADS)

    Zhang, Mingyu

    2010-09-01

    The methods for simulating surface tension with smoothed particle hydrodynamics (SPH) method in two dimensions and three dimensions are developed. In 2D surface tension model, the SPH particle on the boundary in 2D is detected dynamically according to the algorithm developed by Dilts [G.A. Dilts, Moving least-squares particle hydrodynamics II: conservation and boundaries, International Journal for Numerical Methods in Engineering 48 (2000) 1503-1524]. The boundary curve in 2D is reconstructed locally with Lagrangian interpolation polynomial. In 3D surface tension model, the SPH particle on the boundary in 3D is detected dynamically according to the algorithm developed by Haque and Dilts [A. Haque, G.A. Dilts, Three-dimensional boundary detection for particle methods, Journal of Computational Physics 226 (2007) 1710-1730]. The boundary surface in 3D is reconstructed locally with moving least squares (MLS) method. By transforming the coordinate system, it is guaranteed that the interface function is one-valued in the local coordinate system. The normal vector and curvature of the boundary surface are calculated according to the reconstructed boundary surface and then surface tension force can be calculated. Surface tension force acts only on the boundary particle. Density correction is applied to the boundary particle in order to remove the boundary inconsistency. The surface tension models in 2D and 3D have been applied to benchmark tests for surface tension. The ability of the current method applying to the simulation of surface tension in 2D and 3D is proved.

  5. Performance of ultrasound based measurement of 3D displacement using a curvilinear probe for organ motion tracking

    NASA Astrophysics Data System (ADS)

    Harris, Emma J.; Miller, Naomi R.; Bamber, Jeffrey C.; Evans, Phillip M.; Symonds-Tayler, J. Richard N.

    2007-09-01

    Three-dimensional (3D) soft tissue tracking is of interest for monitoring organ motion during therapy. Our goal is to assess the tracking performance of a curvilinear 3D ultrasound probe in terms of the accuracy and precision of measured displacements. The first aim was to examine the depth dependence of the tracking performance. This is of interest because the spatial resolution varies with distance from the elevational focus and because the curvilinear geometry of the transducer causes the spatial sampling frequency to decrease with depth. Our second aim was to assess tracking performance as a function of the spatial sampling setting (low, medium or high sampling). These settings are incorporated onto 3D ultrasound machines to allow the user to control the trade-off between spatial sampling and temporal resolution. Volume images of a speckle-producing phantom were acquired before and after the probe had been moved by a known displacement (1, 2 or 8 mm). This allowed us to assess the optimum performance of the tracking algorithm, in the absence of motion. 3D speckle tracking was performed using 3D cross-correlation and sub-voxel displacements were estimated. The tracking performance was found to be best for axial displacements and poorest for elevational displacements. In general, the performance decreased with depth, although the nature of the depth dependence was complex. Under certain conditions, the tracking performance was sufficient to be useful for monitoring organ motion. For example, at the highest sampling setting, for a 2 mm displacement, good accuracy and precision (an error and standard deviation of <0.4 mm) were observed at all depths and for all directions of displacement. The trade-off between spatial sampling, temporal resolution and size of the field of view (FOV) is discussed.

  6. Automated 3D Motion Tracking using Gabor Filter Bank, Robust Point Matching, and Deformable Models

    PubMed Central

    Wang, Xiaoxu; Chung, Sohae; Metaxas, Dimitris; Axel, Leon

    2013-01-01

    Tagged Magnetic Resonance Imaging (tagged MRI or tMRI) provides a means of directly and noninvasively displaying the internal motion of the myocardium. Reconstruction of the motion field is needed to quantify important clinical information, e.g., the myocardial strain, and detect regional heart functional loss. In this paper, we present a three-step method for this task. First, we use a Gabor filter bank to detect and locate tag intersections in the image frames, based on local phase analysis. Next, we use an improved version of the Robust Point Matching (RPM) method to sparsely track the motion of the myocardium, by establishing a transformation function and a one-to-one correspondence between grid tag intersections in different image frames. In particular, the RPM helps to minimize the impact on the motion tracking result of: 1) through-plane motion, and 2) relatively large deformation and/or relatively small tag spacing. In the final step, a meshless deformable model is initialized using the transformation function computed by RPM. The model refines the motion tracking and generates a dense displacement map, by deforming under the influence of image information, and is constrained by the displacement magnitude to retain its geometric structure. The 2D displacement maps in short and long axis image planes can be combined to drive a 3D deformable model, using the Moving Least Square method, constrained by the minimization of the residual error at tag intersections. The method has been tested on a numerical phantom, as well as on in vivo heart data from normal volunteers and heart disease patients. The experimental results show that the new method has a good performance on both synthetic and real data. Furthermore, the method has been used in an initial clinical study to assess the differences in myocardial strain distributions between heart disease (left ventricular hypertrophy) patients and the normal control group. The final results show that the proposed method

  7. GPU COMPUTING FOR PARTICLE TRACKING

    SciTech Connect

    Nishimura, Hiroshi; Song, Kai; Muriki, Krishna; Sun, Changchun; James, Susan; Qin, Yong

    2011-03-25

    This is a feasibility study of using a modern Graphics Processing Unit (GPU) to parallelize the accelerator particle tracking code. To demonstrate the massive parallelization features provided by GPU computing, a simplified TracyGPU program is developed for dynamic aperture calculation. Performances, issues, and challenges from introducing GPU are also discussed. General purpose Computation on Graphics Processing Units (GPGPU) bring massive parallel computing capabilities to numerical calculation. However, the unique architecture of GPU requires a comprehensive understanding of the hardware and programming model to be able to well optimize existing applications. In the field of accelerator physics, the dynamic aperture calculation of a storage ring, which is often the most time consuming part of the accelerator modeling and simulation, can benefit from GPU due to its embarrassingly parallel feature, which fits well with the GPU programming model. In this paper, we use the Tesla C2050 GPU which consists of 14 multi-processois (MP) with 32 cores on each MP, therefore a total of 448 cores, to host thousands ot threads dynamically. Thread is a logical execution unit of the program on GPU. In the GPU programming model, threads are grouped into a collection of blocks Within each block, multiple threads share the same code, and up to 48 KB of shared memory. Multiple thread blocks form a grid, which is executed as a GPU kernel. A simplified code that is a subset of Tracy++ [2] is developed to demonstrate the possibility of using GPU to speed up the dynamic aperture calculation by having each thread track a particle.

  8. Towards intraoperative monitoring of ablation using tracked 3D ultrasound elastography and internal palpation

    NASA Astrophysics Data System (ADS)

    Foroughi, Pezhman; Burgner, Jessica; Choti, Michael A.; Webster, Robert J., III; Hager, Gregory D.; Boctor, Emad M.

    2012-03-01

    B-mode ultrasound is widely used in liver ablation. However, the necrosis zone is typically not visible under b-mode ultrasound, since ablation does not necessarily change the acoustic properties of the tissue. In contrast, the change in tissue stiffness makes elastography ideal for monitoring ablation. Tissue palpation for elastography is typically applied at the imaging probe, by indenting it slightly into the tissue surface. However, in this paper we propose an alternate approach, where palpation is applied by a surgical instrument located inside the tissue. In our approach, the ablation needle is placed inside a steerable device called an active cannula and inserted into the tissue. A controlled motion is applied to the center of the ablation zone via the active cannula. Since the type and direction of motion is known, displacement can then be computed from two frames with the desired motion. The elastography results show the ablated region around the needle. While internal palpation provides excellent local contrast, freehand palpation from outside of the tissue via the transducer can provide a more global view of the region of the interest. For this purpose, we used a tracked 3D transducer to generate volumetric elastography images covering the ablated region. The tracking information is employed to improve the elastography results by selecting volume pairs suitable for elastography. This is an extension of our 2D frame selection technique which can cope with uncertainties associated with intra-operative elastography. In our experiments with phantom and ex-vivo tissue, we were able to generate high-quality images depicting the boundaries of the hard lesions.

  9. Adaptive optics enables three-dimensional single particle tracking at the sub-millisecond scale

    NASA Astrophysics Data System (ADS)

    Juette, Manuel F.; Rivera-Molina, Felix E.; Toomre, Derek K.; Bewersdorf, Joerg

    2013-04-01

    We present the integration of an adaptive optics element into a feedback-driven single particle tracking microscope. Our instrument captures three-dimensional (3D) trajectories with down to 130 μs temporal resolution for dynamic studies on the nanoscale. Our 3D beam steering approach tracks particles over an axial range of >6 μm with ˜2 ms mechanical response times and isolates the sample from any tracking motion. Tracking of transport vesicles containing Alexa488-labeled transferrin glycoprotein in living cells demonstrates the speed and sensitivity of our instrument.

  10. Aref's chaotic orbits tracked by a general ellipsoid using 3D numerical simulations

    NASA Astrophysics Data System (ADS)

    Shui, Pei; Popinet, Stéphane; Govindarajan, Rama; Valluri, Prashant

    2015-11-01

    The motion of an ellipsoidal solid in an ideal fluid has been shown to be chaotic (Aref, 1993) under the limit of non-integrability of Kirchhoff's equations (Kozlov & Oniscenko, 1982). On the other hand, the particle could stop moving when the damping viscous force is strong enough. We present numerical evidence using our in-house immersed solid solver for 3D chaotic motion of a general ellipsoidal solid and suggest criteria for triggering such motion. Our immersed solid solver functions under the framework of the Gerris flow package of Popinet et al. (2003). This solver, the Gerris Immersed Solid Solver (GISS), resolves 6 degree-of-freedom motion of immersed solids with arbitrary geometry and number. We validate our results against the solution of Kirchhoff's equations. The study also shows that the translational/ rotational energy ratio plays the key role on the motion pattern, while the particle geometry and density ratio between the solid and fluid also have some influence on the chaotic behaviour. Along with several other benchmark cases for viscous flows, we propose prediction of chaotic Aref's orbits as a key benchmark test case for immersed boundary/solid solvers.

  11. Continuous dielectrophoretic particle separation using a microfluidic device with 3D electrodes and vaulted obstacles.

    PubMed

    Jia, Yankai; Ren, Yukun; Jiang, Hongyuan

    2015-08-01

    This paper reports a microfluidic separation device combining 3D electrodes and vaulted obstacles to continuously separate particles experiencing strong positive dielectrophoresis (DEP) from particles experiencing weak positive DEP, or from particles experiencing negative DEP. The separation is achieved by first focusing the particle mixture into a narrow stream by a hydrodynamic focusing flow, and then deviating them into different outlets by AC DEP. The vaulted obstacles facilitate the separation by both increasing the non-uniformity of the electric field, and influencing the particles to move in regions strongly affected by DEP. The 3D electrodes give rise to a spatially non-uniform electric field and extend DEP effect to the channel height. Numerical simulations are performed to investigate the effects of the obstacles on electric field distribution and particle trajectories so as to optimize the obstacle height and compare with the experimental results. The performance of the device is assessed by separating 25 μm gold-coated particles from 10 μm particles in different flow rates by positive DEP and negative DEP, and also separating 25 μm gold-coated particles from yeast cells using only positive DEP. The experimental observation shows a reasonable agreement with numerical simulation results. PMID:25962351

  12. ORBXYZ: a 3D single-particle orbit code for following charged-particle trajectories in equilibrium magnetic fields

    SciTech Connect

    Anderson, D.V.; Cohen, R.H.; Ferguson, J.R.; Johnston, B.M.; Sharp, C.B.; Willmann, P.A.

    1981-06-30

    The single particle orbit code, TIBRO, has been modified extensively to improve the interpolation methods used and to allow use of vector potential fields in the simulation of charged particle orbits on a 3D domain. A 3D cubic B-spline algorithm is used to generate spline coefficients used in the interpolation. Smooth and accurate field representations are obtained. When vector potential fields are used, the 3D cubic spline interpolation formula analytically generates the magnetic field used to push the particles. This field has del.BETA = 0 to computer roundoff. When magnetic induction is used the interpolation allows del.BETA does not equal 0, which can lead to significant nonphysical results. Presently the code assumes quadrupole symmetry, but this is not an essential feature of the code and could be easily removed for other applications. Many details pertaining to this code are given on microfiche accompanying this report.

  13. Holographic particle velocimetry - A 3D measurement technique for vortex interactions, coherent structures and turbulence

    NASA Astrophysics Data System (ADS)

    Meng, Hui; Hussain, Fazle

    1991-10-01

    To understand the topology and dynamics of coherent structures (CS), the interactions of CS with fine-scale turbulence, and the effects of CS on entrainment, mixing and combustion, experimental tools are needed that can measure velocity (preferably vorticity) vector fields in both 3D space and time. While traditional measurement techniques are not able to serve this purpose, holographic particle velocimetry (HPV) appears to be promising. In a demonstration experiment, the instantaneous 3D velocity vector fields in some simple vortical flows have been obtained using the HPV technique. In this preliminary report, the principles of the HPV technique are illustrated and the key issues in its implementation are discussed.

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

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

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

  17. Fast, automatic, and accurate catheter reconstruction in HDR brachytherapy using an electromagnetic 3D tracking system

    SciTech Connect

    Poulin, Eric; Racine, Emmanuel; Beaulieu, Luc; Binnekamp, Dirk

    2015-03-15

    Purpose: In high dose rate brachytherapy (HDR-B), current catheter reconstruction protocols are relatively slow and error prone. The purpose of this technical note is to evaluate the accuracy and the robustness of an electromagnetic (EM) tracking system for automated and real-time catheter reconstruction. Methods: For this preclinical study, a total of ten catheters were inserted in gelatin phantoms with different trajectories. Catheters were reconstructed using a 18G biopsy needle, used as an EM stylet and equipped with a miniaturized sensor, and the second generation Aurora{sup ®} Planar Field Generator from Northern Digital Inc. The Aurora EM system provides position and orientation value with precisions of 0.7 mm and 0.2°, respectively. Phantoms were also scanned using a μCT (GE Healthcare) and Philips Big Bore clinical computed tomography (CT) system with a spatial resolution of 89 μm and 2 mm, respectively. Reconstructions using the EM stylet were compared to μCT and CT. To assess the robustness of the EM reconstruction, five catheters were reconstructed twice and compared. Results: Reconstruction time for one catheter was 10 s, leading to a total reconstruction time inferior to 3 min for a typical 17-catheter implant. When compared to the μCT, the mean EM tip identification error was 0.69 ± 0.29 mm while the CT error was 1.08 ± 0.67 mm. The mean 3D distance error was found to be 0.66 ± 0.33 mm and 1.08 ± 0.72 mm for the EM and CT, respectively. EM 3D catheter trajectories were found to be more accurate. A maximum difference of less than 0.6 mm was found between successive EM reconstructions. Conclusions: The EM reconstruction was found to be more accurate and precise than the conventional methods used for catheter reconstruction in HDR-B. This approach can be applied to any type of catheters and applicators.

  18. Mapping 3D Strains with Ultrasound Speckle Tracking: Method Validation and Initial Results in Porcine Scleral Inflation.

    PubMed

    Cruz Perez, Benjamin; Pavlatos, Elias; Morris, Hugh J; Chen, Hong; Pan, Xueliang; Hart, Richard T; Liu, Jun

    2016-07-01

    This study aimed to develop and validate a high frequency ultrasound method for measuring distributive, 3D strains in the sclera during elevations of intraocular pressure. A 3D cross-correlation based speckle-tracking algorithm was implemented to compute the 3D displacement vector and strain tensor at each tracking point. Simulated ultrasound radiofrequency data from a sclera-like structure at undeformed and deformed states with known strains were used to evaluate the accuracy and signal-to-noise ratio (SNR) of strain estimation. An experimental high frequency ultrasound (55 MHz) system was built to acquire 3D scans of porcine eyes inflated from 15 to 17 and then 19 mmHg. Simulations confirmed good strain estimation accuracy and SNR (e.g., the axial strains had less than 4.5% error with SNRs greater than 16.5 for strains from 0.005 to 0.05). Experimental data in porcine eyes showed increasing tensile, compressive, and shear strains in the posterior sclera during inflation, with a volume ratio close to one suggesting near-incompressibility. This study established the feasibility of using high frequency ultrasound speckle tracking for measuring 3D tissue strains and its potential to characterize physiological deformations in the posterior eye. PMID:26563101

  19. Exploring single-molecule interactions through 3D optical trapping and tracking: From thermal noise to protein refolding

    NASA Astrophysics Data System (ADS)

    Wong, Wesley Philip

    The focus of this thesis is the development and application of a novel technique for investigating the structure and dynamics of weak interactions between and within single-molecules. This approach is designed to explore unusual features in bi-directional transitions near equilibrium. The basic idea is to infer molecular events by observing changes in the three-dimensional Brownian fluctuations of a functionalized microsphere held weakly near a reactive substrate. Experimentally, I have developed a unique optical tweezers system that combines an interference technique for accurate 3D tracking (˜1 nm vertically, and ˜2-3 nm laterally) with a continuous autofocus system which stabilizes the trap height to within 1-2 mn over hours. A number of different physical and biological systems were investigated with this instrument. Data interpretation was assisted by a multi-scale Brownian Dynamics simulation that I have developed. I have explored the 3D signatures of different molecular tethers, distinguishing between single and multiple attachments, as well as between stiff and soft linkages. As well, I have developed a technique for measuring the force-dependent compliance of molecular tethers from thermal noise fluctuations and demonstrated this with a short ssDNA oligomer. Another practical approach that I have developed for extracting information from fluctuation measurements is Inverse Brownian Dynamics, which yields the underlying potential of mean force and position dependent diffusion coefficient from the Brownian motion of a particle. I have also developed a new force calibration method that takes into account video motion blur, and that uses this information to measure bead dynamics. Perhaps most significantly, I have trade the first direct observations of the refolding of spectrin repeats under mechanical force, and investigated the force-dependent kinetics of this transition.

  20. Measuring the orientation and rotation rate of 3D printed particles in turbulent flow

    NASA Astrophysics Data System (ADS)

    Voth, Greg; Marcus, Guy G.; Parsa, Shima; Kramel, Stefan; Ni, Rui; Cole, Brendan

    2014-11-01

    The orientation distribution and rotations of anisotropic particles plays a key role in many applications ranging from icy clouds to papermaking and drag reduction in pipe flow. Experimental access to time resolved orientations of anisotropic particles has not been easy to achieve. We have found that 3D printing technology can be used to fabricate a wide range of particle shapes with smallest dimension down to 300 μm. So far we have studied rods, crosses, jacks, tetrads, and helical shapes. We extract the particle orientations from stereoscopic video images using a method of least squares optimization in Euler angle space. We find that in turbulence the orientation and rotation rate of many particles can be understood using a simple picture of alignment of both the vorticity and a long axis of the particle with the Lagrangian stretching direction of the flow. This research is supported by NSF Grant DMR-1208990.

  1. Measuring the orientation and rotation rate of 3D printed particles in turbulent flow

    NASA Astrophysics Data System (ADS)

    Voth, Greg; Kramel, Stefan; Cole, Brendan

    2015-03-01

    The orientation distribution and rotations of anisotropic particles plays a key role in many applications ranging from icy clouds to papermaking and drag reduction in pipe flow. Experimental access to time resolved orientations of anisotropic particles has not been easy to achieve. We have found that 3D printing technology can be used to fabricate a wide range of particle shapes with smallest dimension down to 300 ?m. So far we have studied rods, crosses, jacks, tetrads, and helical shapes. We extract the particle orientations from stereoscopic video images using a method of least squares optimization in Euler angle space. We find that in turbulence the orientation and rotation rate of many particles can be understood using a simple picture of alignment of both the vorticity and a long axis of the particle with the Lagrangian stretching direction of the flow.

  2. 3D Plasma Clusters: Analysis of dynamical evolution and individual particle interaction

    SciTech Connect

    Antonova, T.; Thomas, H. M.; Morfill, G. E.; Annaratone, B. M.

    2008-09-07

    3D plasma clusters (up to 100 particles) have been built inside small (32 mm{sup 3}) plasma volume in gravity. It has been estimated that the external confinement has a negligible influence on the processes inside the clusters. At such conditions the analysis of dynamical evolution and individual particle interactions have shown that the binary interaction among particles in addition to the repelling Coulomb force exhibits also an attractive part. The tendency of the systems to approach the state with minimum energy by rearranging particles inside has been detected. The measured 63 particles' cluster vibrations are in close agreement with vibrations of a drop with surface tension. This indicates that even a 63 particle cluster already exhibits properties normally associated with the cooperative regime.

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

    NASA Astrophysics Data System (ADS)

    Benedetto, A.

    2012-04-01

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

  4. PDT - PARTICLE DISPLACEMENT TRACKING SOFTWARE

    NASA Technical Reports Server (NTRS)

    Wernet, M. P.

    1994-01-01

    Particle Imaging Velocimetry (PIV) is a quantitative velocity measurement technique for measuring instantaneous planar cross sections of a flow field. The technique offers very high precision (1%) directionally resolved velocity vector estimates, but its use has been limited by high equipment costs and complexity of operation. Particle Displacement Tracking (PDT) is an all-electronic PIV data acquisition and reduction procedure which is simple, fast, and easily implemented. The procedure uses a low power, continuous wave laser and a Charged Coupled Device (CCD) camera to electronically record the particle images. A frame grabber board in a PC is used for data acquisition and reduction processing. PDT eliminates the need for photographic processing, system costs are moderately low, and reduced data are available within seconds of acquisition. The technique results in velocity estimate accuracies on the order of 5%. The software is fully menu-driven from the acquisition to the reduction and analysis of the data. Options are available to acquire a single image or 5- or 25-field series of images separated in time by multiples of 1/60 second. The user may process each image, specifying its boundaries to remove unwanted glare from the periphery and adjusting its background level to clearly resolve the particle images. Data reduction routines determine the particle image centroids and create time history files. PDT then identifies the velocity vectors which describe the particle movement in the flow field. Graphical data analysis routines are included which allow the user to graph the time history files and display the velocity vector maps, interpolated velocity vector grids, iso-velocity vector contours, and flow streamlines. The PDT data processing software is written in FORTRAN 77 and the data acquisition routine is written in C-Language for 80386-based IBM PC compatibles running MS-DOS v3.0 or higher. Machine requirements include 4 MB RAM (3 MB Extended), a single or

  5. Transfer-printing and host-guest properties of 3D supramolecular particle structures.

    PubMed

    Ling, Xing Yi; Phang, In Yee; Reinhoudt, David N; Vancso, G Julius; Huskens, Jurriaan

    2009-04-01

    Mechanically robust and crystalline supramolecular particle structures have been constructed by decoupling nanoparticle assembly and supramolecular glue infiltration into a sequential process. First, beta-cyclodextrin (CD)-functionalized polystyrene particles (d approximately 500 nm) were assembled on a CD-functionalized surface via convective assembly to form highly ordered, but mechanically unstable, particle crystals. Subsequently, the crystals were infiltrated by a solution of adamantyl-functionalized dendrimers, functioning as a supramolecular glue to bind neighboring particles together and to couple the entire particle crystal to the CD surface, both in a noncovalent manner. The supramolecular particle crystals are highly robust, as witnessed by their ability to withstand agitation by ultrasonication. When assembled on a poly(dimethylsiloxane) (PDMS) stamp, the dendrimer-infiltrated particle crystals could be transfer-printed onto a CD-functionalized target surface. By variation of the geometry and size of the PDMS stamps, single particle lines, interconnected particle rings, and V-shaped particle assemblies were obtained. The particle structures served as 3D receptors for the binding of (multiple) complementary guest molecules, indicating that the supramolecular host functionalities of the particle crystals were retained throughout the fabrication process. PMID:20356024

  6. Rapid, High-Throughput Tracking of Bacterial Motility in 3D via Phase-Contrast Holographic Video Microscopy

    PubMed Central

    Cheong, Fook Chiong; Wong, Chui Ching; Gao, YunFeng; Nai, Mui Hoon; Cui, Yidan; Park, Sungsu; Kenney, Linda J.; Lim, Chwee Teck

    2015-01-01

    Tracking fast-swimming bacteria in three dimensions can be extremely challenging with current optical techniques and a microscopic approach that can rapidly acquire volumetric information is required. Here, we introduce phase-contrast holographic video microscopy as a solution for the simultaneous tracking of multiple fast moving cells in three dimensions. This technique uses interference patterns formed between the scattered and the incident field to infer the three-dimensional (3D) position and size of bacteria. Using this optical approach, motility dynamics of multiple bacteria in three dimensions, such as speed and turn angles, can be obtained within minutes. We demonstrated the feasibility of this method by effectively tracking multiple bacteria species, including Escherichia coli, Agrobacterium tumefaciens, and Pseudomonas aeruginosa. In addition, we combined our fast 3D imaging technique with a microfluidic device to present an example of a drug/chemical assay to study effects on bacterial motility. PMID:25762336

  7. Improvement of the size estimation of 3D tracked droplets using digital in-line holography with joint estimation reconstruction

    NASA Astrophysics Data System (ADS)

    Verrier, N.; Grosjean, N.; Dib, E.; Méès, L.; Fournier, C.; Marié, J.-L.

    2016-04-01

    Digital holography is a valuable tool for three-dimensional information extraction. Among existing configurations, the originally proposed set-up (i.e. Gabor, or in-line holography), is reasonably immune to variations in the experimental environment making it a method of choice for studies of fluid dynamics. Nevertheless, standard hologram reconstruction techniques, based on numerical light back-propagation are prone to artifacts such as twin images or aliases that limit both the quality and quantity of information extracted from the acquired holograms. To get round this issue, the hologram reconstruction as a parametric inverse problem has been shown to accurately estimate 3D positions and the size of seeding particles directly from the hologram. To push the bounds of accuracy on size estimation still further, we propose to fully exploit the information redundancy of a hologram video sequence using joint estimation reconstruction. Applying this approach in a bench-top experiment, we show that it led to a relative precision of 0.13% (for a 60 μm diameter droplet) for droplet size estimation, and a tracking precision of {σx}× {σy}× {σz}=0.15× 0.15× 1~\\text{pixels} .

  8. Novel Discrete Element Method for 3D non-spherical granular particles.

    NASA Astrophysics Data System (ADS)

    Seelen, Luuk; Padding, Johan; Kuipers, Hans

    2015-11-01

    Granular materials are common in many industries and nature. The different properties from solid behavior to fluid like behavior are well known but less well understood. The main aim of our work is to develop a discrete element method (DEM) to simulate non-spherical granular particles. The non-spherical shape of particles is important, as it controls the behavior of the granular materials in many situations, such as static systems of packed particles. In such systems the packing fraction is determined by the particle shape. We developed a novel 3D discrete element method that simulates the particle-particle interactions for a wide variety of shapes. The model can simulate quadratic shapes such as spheres, ellipsoids, cylinders. More importantly, any convex polyhedron can be used as a granular particle shape. These polyhedrons are very well suited to represent non-rounded sand particles. The main difficulty of any non-spherical DEM is the determination of particle-particle overlap. Our model uses two iterative geometric algorithms to determine the overlap. The algorithms are robust and can also determine multiple contact points which can occur for these shapes. With this method we are able to study different applications such as the discharging of a hopper or silo. Another application the creation of a random close packing, to determine the solid volume fraction as a function of the particle shape.

  9. Charged-particle Gun Design with 3D Finite-element Methods

    NASA Astrophysics Data System (ADS)

    Humphries, Stanley

    2002-04-01

    The DARHT second-axis injector poses a major challenge for computer simulation. The relativistic electrons are subject to strong beam-generated electric and magnetic forces. The beam and applied fields are fully three-dimensional. Furthermore, accurate field calculations at surfaces are critical to model Child-law emission. Although several 2D relativistic beam codes are available, there is presently no 3D tool that can address all important processes in the DARHT injector. As a result, we created the OmniTrak 3D finite-element code suite. This talk gives a basic tutorial on finite-element methods with emphasis on electron gun design via the ray-tracing technique. Four main areas are covered: 1) the mesh as a tool to organize space, 2) transformation of the Poisson equation through the minimum residual principle, 3) orbit tracking in a complex environment and 4) handling self-consistent beam-generated fields. The components of a volume mesh (elements, nodes and facets) are reviewed. We consider motivations for choosing a 3D mesh style: structured versus unstructured, tetrahedrons versus hexahedrons. We discuss methods for taking volume integrals over arbitrary hexahedrons through normal coordinates and shape functions, leading to the fundamental field equations. The special problems of 3D magnetic field solutions and the advantages of the reduced potential method are outlined. Accurate field interpolations for orbit calculations require fast identification of occupied elements. A method for fast element identification that also yields the orbit penetration point on the element surface is described. The final topics are the assignment of charge and current to meshes from calculated orbits and techniques for space-charge-limited emission from multiple arbitrary 3D surfaces.

  10. A 3d particle simulation code for heavy ion fusion accelerator studies

    SciTech Connect

    Friedman, A.; Bangerter, R.O.; Callahan, D.A.; Grote, D.P.; Langdon, A.B. ); Haber, I. )

    1990-06-08

    We describe WARP, a new particle-in-cell code being developed and optimized for ion beam studies in true geometry. We seek to model transport around bends, axial compression with strong focusing, multiple beamlet interaction, and other inherently 3d processes that affect emittance growth. Constraints imposed by memory and running time are severe. Thus, we employ only two 3d field arrays ({rho} and {phi}), and difference {phi} directly on each particle to get E, rather than interpolating E from three meshes; use of a single 3d array is feasible. A new method for PIC simulation of bent beams follows the beam particles in a family of rotated laboratory frames, thus straightening'' the bends. We are also incorporating an envelope calculation, an (r, z) model, and 1d (axial) model within WARP. The BASIS development and run-time system is used, providing a powerful interactive environment in which the user has access to all variables in the code database. 10 refs., 3 figs.

  11. Spacecraft charging analysis with the implicit particle-in-cell code iPic3D

    SciTech Connect

    Deca, J.; Lapenta, G.; Marchand, R.; Markidis, S.

    2013-10-15

    We present the first results on the analysis of spacecraft charging with the implicit particle-in-cell code iPic3D, designed for running on massively parallel supercomputers. The numerical algorithm is presented, highlighting the implementation of the electrostatic solver and the immersed boundary algorithm; the latter which creates the possibility to handle complex spacecraft geometries. As a first step in the verification process, a comparison is made between the floating potential obtained with iPic3D and with Orbital Motion Limited theory for a spherical particle in a uniform stationary plasma. Second, the numerical model is verified for a CubeSat benchmark by comparing simulation results with those of PTetra for space environment conditions with increasing levels of complexity. In particular, we consider spacecraft charging from plasma particle collection, photoelectron and secondary electron emission. The influence of a background magnetic field on the floating potential profile near the spacecraft is also considered. Although the numerical approaches in iPic3D and PTetra are rather different, good agreement is found between the two models, raising the level of confidence in both codes to predict and evaluate the complex plasma environment around spacecraft.

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

    NASA Astrophysics Data System (ADS)

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

    2010-12-01

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

  13. 3D Printing Meets Computational Astrophysics: Deciphering the Structure of Eta Carinae’s Colliding Winds Using 3D Prints of Smoothed Particle Hydrodynamics Simulations

    NASA Astrophysics Data System (ADS)

    Madura, Thomas; Gull, Theodore R.; Clementel, Nicola; Paardekooper, Jan-Pieter; Kruip, Chael; Corcoran, Michael F.; Hamaguchi, Kenji; Teodoro, Mairan

    2015-01-01

    We present the first 3D prints of output from a supercomputer simulation of a complex astrophysical system, the colliding stellar winds in the massive (>120 MSun), highly eccentric (e ~ 0.9) binary Eta Carinae. Using a consumer-grade 3D printer (Makerbot Replicator 2X), we successfully printed 3D smoothed particle hydrodynamics simulations of Eta Carinae's inner (r ~110 AU) wind-wind collision interface at multiple orbital phases. These 3D prints reveal important, previously unknown 'finger-like' structures at orbital phases shortly after periastron (φ ~1.045) that protrude radially outward from the spiral wind-wind collision region. We speculate that these fingers are related to instabilities (e.g. Rayleigh-Taylor) that arise at the interface between the radiatively-cooled layer of dense post-shock primary-star wind and the hot, adiabatic post-shock companion-star wind. The success of our work and easy identification of previously unknown physical features highlight the important role 3D printing can play in the visualization and understanding of complex 3D time-dependent numerical simulations of astrophysical phenomena.

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

    PubMed

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

    2015-09-01

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

  15. Fast and efficient particle reconstruction on a 3D grid using sparsity

    NASA Astrophysics Data System (ADS)

    Cornic, P.; Champagnat, F.; Cheminet, A.; Leclaire, B.; Le Besnerais, G.

    2015-03-01

    We propose an approach for efficient localization and intensity reconstruction of particles on a 3D grid based on sparsity principles. The computational complexity of the method is limited by using the particle volume reconstruction paradigm (Champagnat et al. in Meas Sci Technol 25, 2014) and a reduction in the problem dimension. Tests on synthetic and experimental data show that the proposed method leads to more efficient detections and to reconstructions of higher quality than classical tomoPIV approaches on a large range of seeding densities, up to ppp ≈ 0.12.

  16. LEWICE3D/GlennHT Particle Analysis of the Honeywell Al502 Low Pressure Compressor

    NASA Technical Reports Server (NTRS)

    Bidwell, Colin S.; Rigby, David L.

    2015-01-01

    A flow and ice particle trajectory analysis was performed for the booster of the Honeywell AL502 engine. The analysis focused on two closely related conditions one of which produced a rollback and another which did not rollback during testing in the Propulsion Systems Lab at NASA Glenn Research Center. The flow analysis was generated using the NASA Glenn GlennHT flow solver and the particle analysis was generated using the NASA Glenn LEWICE3D v3.56 ice accretion software. The flow and particle analysis used a 3D steady flow, mixing plane approach to model the transport of flow and particles through the engine. The inflow conditions for the rollback case were: airspeed, 145 ms; static pressure, 33,373 Pa; static temperature, 253.3 K. The inflow conditions for the non-roll-back case were: airspeed, 153 ms; static pressure, 34,252 Pa; static temperature, 260.1 K. Both cases were subjected to an ice particle cloud with a median volume diameter of 24 microns, an ice water content of 2.0 gm3 and a relative humidity of 100 percent. The most significant difference between the rollback and non-rollback conditions was the inflow static temperature which was 6.8 K higher for the non-rollback case.

  17. Model-based lasso catheter tracking in monoplane fluoroscopy for 3D breathing motion compensation during EP procedures

    NASA Astrophysics Data System (ADS)

    Liao, Rui

    2010-02-01

    Radio-frequency catheter ablation (RFCA) of the pulmonary veins (PVs) attached to the left atrium (LA) is usually carried out under fluoroscopy guidance. Overlay of detailed anatomical structures via 3-D CT and/or MR volumes onto the fluoroscopy helps visualization and navigation in electrophysiology procedures (EP). Unfortunately, respiratory motion may impair the utility of static overlay of the volume with fluoroscopy for catheter navigation. In this paper, we propose a B-spline based method for tracking the circumferential catheter (lasso catheter) in monoplane fluoroscopy. The tracked motion can be used for the estimation of the 3-D trajectory of breathing motion and for subsequent motion compensation. A lasso catheter is typically used during EP procedures and is pushed against the ostia of the PVs to be ablated. Hence this method does not require additional instruments, and achieves motion estimation right at the site of ablation. The performance of the proposed tracking algorithm was evaluated on 340 monoplane frames with an average error of 0.68 +/- 0.36 mms. Our contributions in this work are twofold. First and foremost, we show how to design an effective, practical, and workflow-friendly 3-D motion compensation scheme for EP procedures in a monoplane setup. In addition, we develop an efficient and accurate method for model-based tracking of the circumferential lasso catheter in the low-dose EP fluoroscopy.

  18. MetaTracker: integration and abstraction of 3D motion tracking data from multiple hardware systems

    NASA Astrophysics Data System (ADS)

    Kopecky, Ken; Winer, Eliot

    2014-06-01

    Motion tracking has long been one of the primary challenges in mixed reality (MR), augmented reality (AR), and virtual reality (VR). Military and defense training can provide particularly difficult challenges for motion tracking, such as in the case of Military Operations in Urban Terrain (MOUT) and other dismounted, close quarters simulations. These simulations can take place across multiple rooms, with many fast-moving objects that need to be tracked with a high degree of accuracy and low latency. Many tracking technologies exist, such as optical, inertial, ultrasonic, and magnetic. Some tracking systems even combine these technologies to complement each other. However, there are no systems that provide a high-resolution, flexible, wide-area solution that is resistant to occlusion. While frameworks exist that simplify the use of tracking systems and other input devices, none allow data from multiple tracking systems to be combined, as if from a single system. In this paper, we introduce a method for compensating for the weaknesses of individual tracking systems by combining data from multiple sources and presenting it as a single tracking system. Individual tracked objects are identified by name, and their data is provided to simulation applications through a server program. This allows tracked objects to transition seamlessly from the area of one tracking system to another. Furthermore, it abstracts away the individual drivers, APIs, and data formats for each system, providing a simplified API that can be used to receive data from any of the available tracking systems. Finally, when single-piece tracking systems are used, those systems can themselves be tracked, allowing for real-time adjustment of the trackable area. This allows simulation operators to leverage limited resources in more effective ways, improving the quality of training.

  19. 3-D Particl-in-Cell Simulations of Transport Driven Currents

    NASA Astrophysics Data System (ADS)

    Tsung, F. S.; Dawson, J. M.

    1997-11-01

    In the advanced tokamak regime, transport phenomena can account for a signficant fraction of the toroidal current, possibly over that driven directly by the ohmic heating electric fields. Although bootstrap theory accounts for contributions of the collisional modification of banana orbits on the toroidal currents, the corresponding transport theory does not accurately predict the transport of particles and heat in present-day tokamak experiments. Furthermore, in our previous simulations in 21/2-D, currents were spontaneously generated in both the cylindrical and the toroidal geometries, contrary to neoclassical predictions. In these calculations, it was believed that the driving mechanism is the preferential loss of particles whose initial velocity is opposite to that of the plasma current. Because the preferential loss mechanism assumes the conservation of toroidal angular momentum, we have extended these simulations to three dimensions to study the effects of toroidal assymetries. A parallel, 3-D electromagnetic PIC code running on the IBM SP, with a localized field-solver has been developed to investigate the effects of perturbations parallel to the field lines, and direct comparisons has been made between the 21/2-D and 3-D simulations, and we have found good agreements between the 2 1/2-D calculations and the 3-D results. We will present these results at the meeting.

  20. GPU accelerated simulations of 3D deterministic particle transport using discrete ordinates method

    NASA Astrophysics Data System (ADS)

    Gong, Chunye; Liu, Jie; Chi, Lihua; Huang, Haowei; Fang, Jingyue; Gong, Zhenghu

    2011-07-01

    Graphics Processing Unit (GPU), originally developed for real-time, high-definition 3D graphics in computer games, now provides great faculty in solving scientific applications. The basis of particle transport simulation is the time-dependent, multi-group, inhomogeneous Boltzmann transport equation. The numerical solution to the Boltzmann equation involves the discrete ordinates ( Sn) method and the procedure of source iteration. In this paper, we present a GPU accelerated simulation of one energy group time-independent deterministic discrete ordinates particle transport in 3D Cartesian geometry (Sweep3D). The performance of the GPU simulations are reported with the simulations of vacuum boundary condition. The discussion of the relative advantages and disadvantages of the GPU implementation, the simulation on multi GPUs, the programming effort and code portability are also reported. The results show that the overall performance speedup of one NVIDIA Tesla M2050 GPU ranges from 2.56 compared with one Intel Xeon X5670 chip to 8.14 compared with one Intel Core Q6600 chip for no flux fixup. The simulation with flux fixup on one M2050 is 1.23 times faster than on one X5670.

  1. GPU accelerated simulations of 3D deterministic particle transport using discrete ordinates method

    SciTech Connect

    Gong Chunye; Liu Jie; Chi Lihua; Huang Haowei; Fang Jingyue; Gong Zhenghu

    2011-07-01

    Graphics Processing Unit (GPU), originally developed for real-time, high-definition 3D graphics in computer games, now provides great faculty in solving scientific applications. The basis of particle transport simulation is the time-dependent, multi-group, inhomogeneous Boltzmann transport equation. The numerical solution to the Boltzmann equation involves the discrete ordinates (S{sub n}) method and the procedure of source iteration. In this paper, we present a GPU accelerated simulation of one energy group time-independent deterministic discrete ordinates particle transport in 3D Cartesian geometry (Sweep3D). The performance of the GPU simulations are reported with the simulations of vacuum boundary condition. The discussion of the relative advantages and disadvantages of the GPU implementation, the simulation on multi GPUs, the programming effort and code portability are also reported. The results show that the overall performance speedup of one NVIDIA Tesla M2050 GPU ranges from 2.56 compared with one Intel Xeon X5670 chip to 8.14 compared with one Intel Core Q6600 chip for no flux fixup. The simulation with flux fixup on one M2050 is 1.23 times faster than on one X5670.

  2. Development and Characterization of Embedded Sensory Particles Using Multi-Scale 3D Digital Image Correlation

    NASA Technical Reports Server (NTRS)

    Cornell, Stephen R.; Leser, William P.; Hochhalter, Jacob D.; Newman, John A.; Hartl, Darren J.

    2014-01-01

    A method for detecting fatigue cracks has been explored at NASA Langley Research Center. Microscopic NiTi shape memory alloy (sensory) particles were embedded in a 7050 aluminum alloy matrix to detect the presence of fatigue cracks. Cracks exhibit an elevated stress field near their tip inducing a martensitic phase transformation in nearby sensory particles. Detectable levels of acoustic energy are emitted upon particle phase transformation such that the existence and location of fatigue cracks can be detected. To test this concept, a fatigue crack was grown in a mode-I single-edge notch fatigue crack growth specimen containing sensory particles. As the crack approached the sensory particles, measurements of particle strain, matrix-particle debonding, and phase transformation behavior of the sensory particles were performed. Full-field deformation measurements were performed using a novel multi-scale optical 3D digital image correlation (DIC) system. This information will be used in a finite element-based study to determine optimal sensory material behavior and density.

  3. 3D printing enables separation of orthogonal functions within a hydrogel particle.

    PubMed

    Raman, Ritu; Clay, Nicholas E; Sen, Sanjeet; Melhem, Molly; Qin, Ellen; Kong, Hyunjoon; Bashir, Rashid

    2016-06-01

    Multifunctional particles with distinct physiochemical phases are required by a variety of applications in biomedical engineering, such as diagnostic imaging and targeted drug delivery. This motivates the development of a repeatable, efficient, and customizable approach to manufacturing particles with spatially segregated bioactive moieties. This study demonstrates a stereolithographic 3D printing approach for designing and fabricating large arrays of biphasic poly (ethylene glycol) diacrylate (PEGDA) gel particles. The fabrication parameters governing the physical and biochemical properties of multi-layered particles are thoroughly investigated, yielding a readily tunable approach to manufacturing customizable arrays of multifunctional particles. The advantage in spatially organizing functional epitopes is examined by loading superparamagnetic iron oxide nanoparticles (SPIONs) and bovine serum albumin (BSA) in separate layers of biphasic PEGDA gel particles and examining SPION-induced magnetic resonance (MR) contrast and BSA-release kinetics. Particles with spatial segregation of functional moieties have demonstrably higher MR contrast and BSA release. Overall, this study will contribute significant knowledge to the preparation of multifunctional particles for use as biomedical tools. PMID:27215416

  4. Angle only tracking with particle flow filters

    NASA Astrophysics Data System (ADS)

    Daum, Fred; Huang, Jim

    2011-09-01

    We show the results of numerical experiments for tracking ballistic missiles using only angle measurements. We compare the performance of an extended Kalman filter with a new nonlinear filter using particle flow to compute Bayes' rule. For certain difficult geometries, the particle flow filter is an order of magnitude more accurate than the EKF. Angle only tracking is of interest in several different sensors; for example, passive optics and radars in which range and Doppler data are spoiled by jamming.

  5. Uniformly spaced 3D modeling of human face from two images using parallel particle swarm optimization

    NASA Astrophysics Data System (ADS)

    Chang, Yau-Zen; Hou, Jung-Fu; Tsao, Yi Hsiang; Lee, Shih-Tseng

    2011-09-01

    This paper proposes a scheme for finding the correspondence between uniformly spaced locations on the images of human face captured from different viewpoints at the same instant. The correspondence is dedicated for 3D reconstruction to be used in the registration procedure for neurosurgery where the exposure to projectors must be seriously restricted. The approach utilizes structured light to enhance patterns on the images and is initialized with the scale-invariant feature transform (SIFT). Successive locations are found according to spatial order using a parallel version of the particle swarm optimization algorithm. Furthermore, false locations are singled out for correction by searching for outliers from fitted curves. Case studies show that the scheme is able to correctly generate 456 evenly spaced 3D coordinate points in 23 seconds from a single shot of projected human face using a PC with 2.66 GHz Intel Q9400 CPU and 4GB RAM.

  6. Atmospheric Motion Vectors from INSAT-3D: Initial quality assessment and its impact on track forecast of cyclonic storm NANAUK

    NASA Astrophysics Data System (ADS)

    Deb, S. K.; Kishtawal, C. M.; Kumar, Prashant; Kiran Kumar, A. S.; Pal, P. K.; Kaushik, Nitesh; Sangar, Ghansham

    2016-03-01

    The advanced Indian meteorological geostationary satellite INSAT-3D was launched on 26 July 2013 with an improved imager and an infrared sounder and is placed at 82°E over the Indian Ocean region. With the advancement in retrieval techniques of different atmospheric parameters and with improved imager data have enhanced the scope for better understanding of the different tropical atmospheric processes over this region. The retrieval techniques and accuracy of one such parameter, Atmospheric Motion Vectors (AMV) has improved significantly with the availability of improved spatial resolution data along with more options of spectral channels in the INSAT-3D imager. The present work is mainly focused on providing brief descriptions of INSAT-3D data and AMV derivation processes using these data. It also discussed the initial quality assessment of INSAT-3D AMVs for a period of six months starting from 01 February 2014 to 31 July 2014 with other independent observations: i) Meteosat-7 AMVs available over this region, ii) in-situ radiosonde wind measurements, iii) cloud tracked winds from Multi-angle Imaging Spectro-Radiometer (MISR) and iv) numerical model analysis. It is observed from this study that the qualities of newly derived INSAT-3D AMVs are comparable with existing two versions of Meteosat-7 AMVs over this region. To demonstrate its initial application, INSAT-3D AMVs are assimilated in the Weather Research and Forecasting (WRF) model and it is found that the assimilation of newly derived AMVs has helped in reduction of track forecast errors of the recent cyclonic storm NANAUK over the Arabian Sea. Though, the present study is limited to its application to one case study, however, it will provide some guidance to the operational agencies for implementation of this new AMV dataset for future applications in the Numerical Weather Prediction (NWP) over the south Asia region.

  7. Shape measurement by a multi-view methodology based on the remote tracking of a 3D optical scanner

    NASA Astrophysics Data System (ADS)

    Barone, Sandro; Paoli, Alessandro; Viviano Razionale, Armando

    2012-03-01

    Full field optical techniques can be reliably used for 3D measurements of complex shapes by multi-view processes, which require the computation of transformation parameters relating different views into a common reference system. Although, several multi-view approaches have been proposed, the alignment process is still the crucial step of a shape reconstruction. In this paper, a methodology to automatically align 3D views has been developed by integrating a stereo vision system and a full field optical scanner. In particular, the stereo vision system is used to remotely track the optical scanner within a working volume. The tracking system uses stereo images to detect the 3D coordinates of retro-reflective infrared markers rigidly connected to the scanner. Stereo correspondences are established by a robust methodology based on combining the epipolar geometry with an image spatial transformation constraint. The proposed methodology has been validated by experimental tests regarding both the evaluation of the measurement accuracy and the 3D reconstruction of an industrial shape.

  8. Multi-modality fusion of CT, 3D ultrasound, and tracked strain images for breast irradiation planning

    NASA Astrophysics Data System (ADS)

    Foroughi, Pezhman; Csoma, Csaba; Rivaz, Hassan; Fichtinger, Gabor; Zellars, Richard; Hager, Gregory; Boctor, Emad

    2009-02-01

    Breast irradiation significantly reduces the risk of recurrence of cancer. There is growing evidence suggesting that irradiation of only the involved area of the breast, partial breast irradiation (PBI), is as effective as whole breast irradiation. Benefits of PBI include shortened treatment time, and perhaps fewer side effects as less tissue is treated. However, these benefits cannot be realized without precise and accurate localization of the lumpectomy cavity. Several studies have shown that accurate delineation of the cavity in CT scans is very challenging and the delineated volumes differ dramatically over time and among users. In this paper, we propose utilizing 3D ultrasound (3D-US) and tracked strain images as complementary modalities to reduce uncertainties associated with current CT planning workflow. We present the early version of an integrated system that fuses 3D-US and real-time strain images. For the first time, we employ tracking information to reduce the noise in calculation of strain image by choosing the properly compressed frames and to position the strain image within the ultrasound volume. Using this system, we provide the tools to retrieve additional information from 3D-US and strain image alongside the CT scan. We have preliminarily evaluated our proposed system in a step-by-step fashion using a breast phantom and clinical experiments.

  9. 3D hybrid simulations with gyrokinetic particle ions and fluid electrons

    SciTech Connect

    Belova, E.V.; Park, W.; Fu, G.Y.; Strauss, H.R.; Sugiyama, L.E.

    1998-12-31

    The previous hybrid MHD/particle model (MH3D-K code) represented energetic ions as gyrokinetic (or drift-kinetic) particles coupled to MHD equations using the pressure or current coupling scheme. A small energetic to bulk ion density ratio was assumed, n{sub h}/n{sub b} {much_lt} 1, allowing the neglect of the energetic ion perpendicular inertia in the momentum equation and the use of MHD Ohm`s law E = {minus}v{sub b} {times} B. A generalization of this model in which all ions are treated as gyrokinetic/drift-kinetic particles and fluid description is used for the electron dynamics is considered in this paper.

  10. Effect of particle size in a colloidal hydrogel scaffold for 3D cell culture.

    PubMed

    Gu, Jianjun; Zhao, Yening; Guan, Ying; Zhang, Yongjun

    2015-12-01

    The in situ-forming colloidal hydrogels from the thermal gelation of poly(N-isopropylacrylamide) (PNIPAM) microgel dispersions have been exploited for 3D cell culture. The properties of the hydrogel scaffold need to be tuned to further improve its performance. In addition, cellular uptake of the microgel particles need to be reduced to avoid their potential undesired influence. For these purposes we systematically examined the effect of microgel particle size on the hydrogel scaffold. It was found that gel properties could be tuned via changing particle size. Increasing particle size reduces the gel strength and its syneresis degree, both of which are favorable for cell growth. Meanwhile increasing particle size could also reduce significantly the cellular uptake of the microgel particles. Microgel with a size of ~162 nm shows the highest cellular uptake, beyond which cellular uptake decreases with increasing particle size. Hydrogel scaffold from 300 nm microgel, with suitable physical properties and reduced cellular uptake, were successfully used for multicellular spheroid generation. PMID:26613865

  11. Numerical simulation of inhaled aerosol particle deposition within 3D realistic human upper respiratory tract

    NASA Astrophysics Data System (ADS)

    Lin, J.; Fan, J. R.; Zheng, Y. Q.; Hu, G. L.; Pan, D.

    2010-03-01

    Computational fluid dynamics (CFD) simulations of airflow and particle deposition in the upper respiratory tract (URT) were conducted in this paper. Based on the CT (Computerized Tomography) scanned images of a 19-years-old healthy boy, a realistic geometric model of URT from oral cavity to the upper six-generation bronchial is rebuilt. To investigate airflow and particle deposition in the obtained realistic human upper respiratory tract, RNG k-ɛ turbulence model was used to describe the primary flow and particle deposition under three breathing intensity such as 15 L/min, 30 L/min and 60 L/min. The particle is tracked and analyzed in the Lagrangian frame. The velocity fields of airflow under different airflow rates were computed and discussed. In order to study the characteristics of particles movement and the effect of particles diameter on the deposition pattern, eleven kinds of sphere particles with different diameters are selected as research object. The diameters of selected particles as follows: 0.1 μm, 0.5 μm, 1 μm, 2.5 μm, 3 μm, 3.5 μm, 4 μm, 4.5 μm, 5 μm, 6.5 μm and 8 μm. The variation of inhalable particles deposition in realistic human upper respiratory tract with respiratory intensity and particle size was researched and compared. Furthermore, the more real inhalable particles with Rosin-Rammler mass distribution are used to study the effect of particles size. The deposition rate of particles with the different diameter scope in the different part of upper respiratory tract was summarized. The geometrical model based images technology promises to provide more real results of airflow field and particle deposition in the URT.

  12. Simulation of the 3D viscoelastic free surface flow by a parallel corrected particle scheme

    NASA Astrophysics Data System (ADS)

    Jin-Lian, Ren; Tao, Jiang

    2016-02-01

    In this work, the behavior of the three-dimensional (3D) jet coiling based on the viscoelastic Oldroyd-B model is investigated by a corrected particle scheme, which is named the smoothed particle hydrodynamics with corrected symmetric kernel gradient and shifting particle technique (SPH_CS_SP) method. The accuracy and stability of SPH_CS_SP method is first tested by solving Poiseuille flow and Taylor-Green flow. Then the capacity for the SPH_CS_SP method to solve the viscoelastic fluid is verified by the polymer flow through a periodic array of cylinders. Moreover, the convergence of the SPH_CS_SP method is also investigated. Finally, the proposed method is further applied to the 3D viscoelastic jet coiling problem, and the influences of macroscopic parameters on the jet coiling are discussed. The numerical results show that the SPH_CS_SP method has higher accuracy and better stability than the traditional SPH method and other corrected SPH method, and can improve the tensile instability. Project supported by the Natural Science Foundation of Jiangsu Province, China (Grant Nos. BK20130436 and BK20150436) and the Natural Science Foundation of the Higher Education Institutions of Jiangsu Province, China (Grant No. 15KJB110025).

  13. Parallel 3-D particle-in-cell modelling of charged ultrarelativistic beam dynamics

    NASA Astrophysics Data System (ADS)

    Boronina, Marina A.; Vshivkov, Vitaly A.

    2015-12-01

    > ) in supercolliders. We use the 3-D set of Maxwell's equations for the electromagnetic fields, and the Vlasov equation for the distribution function of the beam particles. The model incorporates automatically the longitudinal effects, which can play a significant role in the cases of super-high densities. We present numerical results for the dynamics of two focused ultrarelativistic beams with a size ratio 10:1:100. The results demonstrate high efficiency of the proposed computational methods and algorithms, which are applicable to a variety of problems in relativistic plasma physics.

  14. Magnetic properties of 3D nanocomposites consisting of an opal matrix with embedded spinel ferrite particles

    NASA Astrophysics Data System (ADS)

    Rinkevich, A. B.; Korolev, A. V.; Samoylovich, M. I.; Kleshcheva, S. M.; Perov, D. V.

    2016-02-01

    The magnetic properties of 3D nanocomposites representing Mn-Zn, Ni-Zn, Co-Zn, La-Co-Zn, and Nd-Co-Zn spinel ferrite particles embedded in the interspherical spaces of opal matrices are studied. Experimental data are obtained in the temperature interval 2-300 K by measuring the magnetization at a static magnetic field strength of up to 50 kOe and the ac magnetic susceptibility at an alternating magnetic field amplitude of 4 kOe and a frequency of 80 Hz.

  15. 3D imaging of particle-scale rotational motion in cyclically driven granular flows

    NASA Astrophysics Data System (ADS)

    Harrington, Matt; Powers, Dylan; Cooper, Eric; Losert, Wolfgang

    Recent experimental advances have enabled three-dimensional (3D) imaging of motion, structure, and failure within granular systems. 3D imaging allows researchers to directly characterize bulk behaviors that arise from particle- and meso-scale features. For instance, segregation of a bidisperse system of spheres under cyclic shear can originate from microscopic irreversibilities and the development of convective secondary flows. Rotational motion and frictional rotational coupling, meanwhile, have been less explored in such experimental 3D systems, especially under cyclic forcing. In particular, relative amounts of sliding and/or rolling between pairs of contacting grains could influence the reversibility of both trajectories, in terms of both position and orientation. In this work, we apply the Refractive Index Matched Scanning technique to a granular system that is cyclically driven and measure both translational and rotational motion of individual grains. We relate measured rotational motion to resulting shear bands and convective flows, further indicating the degree to which pairs and neighborhoods of grains collectively rotate.

  16. Global gyrokinetic models for energetic particle driven Alfvén instabilities in 3D equilibria

    NASA Astrophysics Data System (ADS)

    Spong, Don; Holod, Ihor

    2015-11-01

    The GTC global gyrokinetic PIC model has been adapted to 3D VMEC equilibria and provides a new method for the analysis of Alfvénic instabilities in stellarators, 3D tokamaks, and helical RFP states. The gyrokinetic orderings (k||/k⊥ << 1, ω/Ωci << 1, ρEP/L << 1) are applicable to a range of energetic particle driven instabilities that have been observed in 3D configurations. Applications of this model to stellarators have indicated that a variety of different Alfvén instabilities can be excited, depending on the toroidal mode number, fast ion average energy and fast ion density profile. Both an LHD discharge where bursting n = 1 Alfvén activity in the TAE gap was observed and a W7-X case have been examined. TAE,/EAE/GAE modes have been found in the simulations, depending on the mode family and fast ion profiles used. The dynamical evolution of the instabilities shows the field period coupling between n and n + Nfp expected for a stellarator. The development of gyrofluid reduced models that can capture relevant physics aspects of the gyrokinetic models will also be discussed. Research sponsored by the U.S. Department of Energy under Contract DE-AC05-00OR22725 with UT-Battelle, LLC and the GSEP SciDAC Center.

  17. 3D Discrete Element Model with 1 Million Particles: an Example of Hydro-fracturing

    NASA Astrophysics Data System (ADS)

    Liu, C.; Pollard, D. D.

    2013-12-01

    The Discrete Element Method (DEM) permits large relative motion and breakage of elements, and does not require re-meshing, for example as would the Finite Element Method. DEM has a wide range of applications in the fields of solid-earth geophysics, geomechanics, mining engineering, and structural geology. However, due to the computational cost, particle numbers of discrete element models are generally less than a few tens of thousands, which limits the applications. A new 3D DEM system 'MatDEM' can complete dynamic simulations of one million particles. The conversion formulas between particle parameters and model mechanical properties were derived, and the conversion of energy in DEM can be simulated. In a recent paper (Liu et al., 2013, JGR), the analytical solutions of elastic properties and failure modes of a 2D close-packed discrete element model were proposed. Based on these theoretical results, it is easy to create materials using DEM, which have similar mechanical properties to rock. Given the mechanical properties and state of stress, geologists and engineers can investigate the characteristics of rock deformation and failure under different conditions. MatDEM provides an alternative way to study the micro-macro relationships of rock and soil, and the evolution of geologic structures. As an example, MatDEM was used to investigate the generation and development of fluid driven fractures around a micro pore. The simulation result of fractures of an anisotropic 3D model, which includes 1 million particles, is demonstrated. Via parallel computing technology, MatDEM may handle tens of millions of particles in near future. Left: Fluid pressure is applied in the pore to generate fractures. Right: Simulation results (black segments represent fractures).

  18. Olivines: revelation of tracks of charged particles.

    PubMed

    Krishnaswami, S; Lal, D; Prabhu, N; Tamhane, A S

    1971-10-15

    A one-step, three-component aqueous etchant was developed for revealing the tracks of charged particles in olivine. The etchant reveals tracks of small cone angle, which are equally well developed in all the crystallographic directions. The scope of fossil cosmic-ray track studies in extraterrestrial samples has thus been increased, because olivine is often an abundant constituent and because it has a higher threshold ionization for track registration and has lower uranium, thorium, and trace element concentrations as compared with pyroxenes and feldspars. The etchant does not attack any of the principal rock-forming minerals in normal etching time, which allows a nondestructive study of fossil tracks in thin-section mounts. The study of fossil cosmic-ray tracks in olivine is particularly valuable for investigations of very, very heavy cosmic-ray nuclei and for highly irradiated samples such as those found in the lunar regolith. PMID:17778062

  19. 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.

  20. Enhanced copper micro/nano-particle mixed paste sintered at low temperature for 3D interconnects

    NASA Astrophysics Data System (ADS)

    Dai, Y. Y.; Ng, M. Z.; Anantha, P.; Lin, Y. D.; Li, Z. G.; Gan, C. L.; Tan, C. S.

    2016-06-01

    An enhanced copper paste, formulated by copper micro- and nano-particles mixture, is reported to prevent paste cracking and obtain an improved packing density. The particle mixture of two different sizes enables reduction in porosity of the micro-paste and resolves the cracking issue in the nano-paste. In-situ temperature and resistance measurements indicate that the mixed paste has a lower densification temperature. Electrical study also shows a ˜12× lower sheet resistance of 0.27 Ω/sq. In addition, scanning electron microscope image analysis confirms a ˜50% lower porosity, which is consistent with the thermal and electrical results. The 3:1 (micro:nano, wt. %) mixed paste is found to have the strongest synergistic effect. This phenomenon is discussed further. Consequently, the mixed paste is a promising material for potential low temperature 3D interconnects fabrication.

  1. A Parallelized 3D Particle-In-Cell Method With Magnetostatic Field Solver And Its Applications

    NASA Astrophysics Data System (ADS)

    Hsu, Kuo-Hsien; Chen, Yen-Sen; Wu, Men-Zan Bill; Wu, Jong-Shinn

    2008-10-01

    A parallelized 3D self-consistent electrostatic particle-in-cell finite element (PIC-FEM) code using an unstructured tetrahedral mesh was developed. For simulating some applications with external permanent magnet set, the distribution of the magnetostatic field usually also need to be considered and determined accurately. In this paper, we will firstly present the development of a 3D magnetostatic field solver with an unstructured mesh for the flexibility of modeling objects with complex geometry. The vector Poisson equation for magnetostatic field is formulated using the Galerkin nodal finite element method and the resulting matrix is solved by parallel conjugate gradient method. A parallel adaptive mesh refinement module is coupled to this solver for better resolution. Completed solver is then verified by simulating a permanent magnet array with results comparable to previous experimental observations and simulations. By taking the advantage of the same unstructured grid format of this solver, the developed PIC-FEM code could directly and easily read the magnetostatic field for particle simulation. In the upcoming conference, magnetron is simulated and presented for demonstrating the capability of this code.

  2. Feasibility of low-dose single-view 3D fiducial tracking concurrent with external beam delivery

    SciTech Connect

    Speidel, Michael A.; Wilfley, Brian P.; Hsu, Annie; Hristov, Dimitre

    2012-04-15

    Purpose: In external-beam radiation therapy, existing on-board x-ray imaging chains orthogonal to the delivery beam cannot recover 3D target trajectories from a single view in real-time. This limits their utility for real-time motion management concurrent with beam delivery. To address this limitation, the authors propose a novel concept for on-board imaging based on the inverse-geometry Scanning-Beam Digital X-ray (SBDX) system and evaluate its feasibility for single-view 3D intradelivery fiducial tracking. Methods: A chest phantom comprising a posterior wall, a central lung volume, and an anterior wall was constructed. Two fiducials were placed along the mediastinal ridge between the lung cavities: a 1.5 mm diameter steel sphere superiorly and a gold cylinder (2.6 mm length x 0.9 mm diameter) inferiorly. The phantom was placed on a linear motion stage that moved sinusoidally. Fiducial motion was along the source-detector (z) axis of the SBDX system with {+-}10 mm amplitude and a programmed period of either 3.5 s or 5 s. The SBDX system was operated at 15 frames per second, 100 kVp, providing good apparent conspicuity of the fiducials. With the stage moving, detector data were acquired and subsequently reconstructed into 15 planes with a 12 mm plane-to-plane spacing using digital tomosynthesis. A tracking algorithm was applied to the image planes for each temporal frame to determine the position of each fiducial in (x,y,z)-space versus time. A 3D time-sinusoidal motion model was fit to the measured 3D coordinates and root mean square (RMS) deviations about the fitted trajectory were calculated. Results: Tracked motion was sinusoidal and primarily along the source-detector (z) axis. The RMS deviation of the tracked z-coordinate ranged from 0.53 to 0.71 mm. The motion amplitude derived from the model fit agreed with the programmed amplitude to within 0.28 mm for the steel sphere and within -0.77 mm for the gold seed. The model fit periods agreed with the programmed

  3. 3D shape tracking of minimally invasive medical instruments using optical frequency domain reflectometry

    NASA Astrophysics Data System (ADS)

    Parent, Francois; Kanti Mandal, Koushik; Loranger, Sebastien; Watanabe Fernandes, Eric Hideki; Kashyap, Raman; Kadoury, Samuel

    2016-03-01

    We propose here a new alternative to provide real-time device tracking during minimally invasive interventions using a truly-distributed strain sensor based on optical frequency domain reflectometry (OFDR) in optical fibers. The guidance of minimally invasive medical instruments such as needles or catheters (ex. by adding a piezoelectric coating) has been the focus of extensive research in the past decades. Real-time tracking of instruments in medical interventions facilitates image guidance and helps the user to reach a pre-localized target more precisely. Image-guided systems using ultrasound imaging and shape sensors based on fiber Bragg gratings (FBG)-embedded optical fibers can provide retroactive feedback to the user in order to reach the targeted areas with even more precision. However, ultrasound imaging with electro-magnetic tracking cannot be used in the magnetic resonance imaging (MRI) suite, while shape sensors based on FBG embedded in optical fibers provides discrete values of the instrument position, which requires approximations to be made to evaluate its global shape. This is why a truly-distributed strain sensor based on OFDR could enhance the tracking accuracy. In both cases, since the strain is proportional to the radius of curvature of the fiber, a strain sensor can provide the three-dimensional shape of medical instruments by simply inserting fibers inside the devices. To faithfully follow the shape of the needle in the tracking frame, 3 fibers glued in a specific geometry are used, providing 3 degrees of freedom along the fiber. Near real-time tracking of medical instruments is thus obtained offering clear advantages for clinical monitoring in remotely controlled catheter or needle guidance. We present results demonstrating the promising aspects of this approach as well the limitations of using the OFDR technique.

  4. 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.

  5. Measurements of the solid-body rotation of anisotropic particles in 3D turbulence

    NASA Astrophysics Data System (ADS)

    Marcus, Guy G.; Parsa, Shima; Kramel, Stefan; Ni, Rui; Voth, Greg A.

    2014-10-01

    We introduce a new method to measure Lagrangian vorticity and the rotational dynamics of anisotropic particles in a turbulent fluid flow. We use 3D printing technology to fabricate crosses (two perpendicular rods) and jacks (three mutually perpendicular rods). Time-resolved measurements of their orientation and solid-body rotation rate are obtained from four video images of their motion in a turbulent flow between oscillating grids with {{R}λ } = 91. The advected particles have a largest dimension of 6 times the Kolmogorov length, making them a good approximation to anisotropic tracer particles. Crosses rotate like disks and jacks rotate like spheres, so these measurements, combined with previous measurements of tracer rods, allow experimental study of axisymmetric ellipsoids across the full range of aspect ratios. The measured mean square tumbling rate, < {{\\dot{p}}i}{{\\dot{p}}i}> , confirms previous direct numerical simulations that indicate that disks tumble much more rapidly than rods. Measurements of the alignment of a unit vector defining the orientation of crosses with the direction of their solid-body rotation rate vector provide the first direct observation of the alignment of anisotropic particles by the velocity gradients in a turbulent flow.

  6. Some Progress in Large-Eddy Simulation using the 3-D Vortex Particle Method

    NASA Technical Reports Server (NTRS)

    Winckelmans, G. S.

    1995-01-01

    This two-month visit at CTR was devoted to investigating possibilities in LES modeling in the context of the 3-D vortex particle method (=vortex element method, VEM) for unbounded flows. A dedicated code was developed for that purpose. Although O(N(sup 2)) and thus slow, it offers the advantage that it can easily be modified to try out many ideas on problems involving up to N approx. 10(exp 4) particles. Energy spectrums (which require O(N(sup 2)) operations per wavenumber) are also computed. Progress was realized in the following areas: particle redistribution schemes, relaxation schemes to maintain the solenoidal condition on the particle vorticity field, simple LES models and their VEM extension, possible new avenues in LES. Model problems that involve strong interaction between vortex tubes were computed, together with diagnostics: total vorticity, linear and angular impulse, energy and energy spectrum, enstrophy. More work is needed, however, especially regarding relaxation schemes and further validation and development of LES models for VEM. Finally, what works well will eventually have to be incorporated into the fast parallel tree code.

  7. Tracking and imaging elementary particles

    SciTech Connect

    Breuker, H.; Drevermann, H.; Grab, C.; Rademakers, A.A.; Stone, H. )

    1991-08-01

    The Large Electron-Positron (LEP) Collider is one of the most powerful particle accelerators ever built. It smashes electrons into their antimatter counterparts, positrons, releasing as much as 100 billion electron volts of energy within each of four enormous detectors. Each burst of energy generates a spray of hundreds of elementary particles that are monitored by hundreds of thousands of sensors. In less than a second, an electronic system must sort through the data from some 50,000 electron-positron encounters, searching for just one or two head-on collisions that might lead to discoveries about the fundamental forces and the elementary particles of nature. When the electronic systems identify such a promising event, a picture of the data must be transmitted to the most ingenious image processor ever created. The device is the human brain. Computers cannot match the brain's capacity to recognize complicated patterns in the data collected by the LEP detectors. The work of understanding subnuclear events begins therefore through the visualization of objects that are trillions of times smaller than the eye can see and that move millions of times faster than the eye can follow. During the past decade, the authors and their colleagues at the European laboratory for particle physics (CERN) have attempted to design the perfect interface between the minds of physicists and the barrage of electronic signals from the LEP detectors. Using sophisticated computers, they translate raw data - 500,000 numbers from each event - into clear, meaningful images. With shapes, curves and colors, they represent the trajectories of particles, their type, their energy and many other properties.

  8. Prediction of 3D internal organ position from skin surface motion: results from electromagnetic tracking studies

    NASA Astrophysics Data System (ADS)

    Wong, Kenneth H.; Tang, Jonathan; Zhang, Hui J.; Varghese, Emmanuel; Cleary, Kevin R.

    2005-04-01

    An effective treatment method for organs that move with respiration (such as the lungs, pancreas, and liver) is a major goal of radiation medicine. In order to treat such tumors, we need (1) real-time knowledge of the current location of the tumor, and (2) the ability to adapt the radiation delivery system to follow this constantly changing location. In this study, we used electromagnetic tracking in a swine model to address the first challenge, and to determine if movement of a marker attached to the skin could accurately predict movement of an internal marker embedded in an organ. Under approved animal research protocols, an electromagnetically tracked needle was inserted into a swine liver and an electromagnetically tracked guidewire was taped to the abdominal skin of the animal. The Aurora (Northern Digital Inc., Waterloo, Canada) electromagnetic tracking system was then used to monitor the position of both of these sensors every 40 msec. Position readouts from the sensors were then tested to see if any of the movements showed correlation. The strongest correlations were observed between external anterior-posterior motion and internal inferior-superior motion, with many other axes exhibiting only weak correlation. We also used these data to build a predictive model of internal motion by taking segments from the data and using them to derive a general functional relationship between the internal needle and the external guidewire. For the axis with the strongest correlation, this model enabled us to predict internal organ motion to within 1 mm.

  9. Particle Acceleration in the Low Corona Over Broad Longitudes: Coupling Between 3D Magnetohydrodynamic and Energetic Particle Models

    NASA Astrophysics Data System (ADS)

    Gorby, M.; Schwadron, N.; Lee, M. A.; Booth, A. C.; Spence, H.; Torok, T.; Downs, C.; Lionello, R.; Linker, J.; Titov, V. S.; Mikic, Z.; Riley, P.; Desai, M. I.; Dayeh, M. A.; Kozarev, K. A.

    2013-12-01

    Recent work on the coupling between 3D energetic particle models (e.g., the Energetic Particle Radiation Environment Model, EPREM) and magnetohydrodynamic (MHD) models of Coronal Mass Ejections (CMEs, e.g., the PSI MAS model) has demonstrated the efficacy of compression regions in front of fast CMEs for particle acceleration from remarkably low in the corona (3-6 solar radii). Typically particle acceleration becomes rapid beyond 3Rs and often in regions where compression regions have not yet formed active shocks. The challenge for forming large SEP events in such compression-acceleration scenarios is to have enhanced scattering within the acceleration region while also allowing for efficient escape of accelerated particles downstream (away from the Sun) from the compression region. Simulations show rapid particle acceleration in the range of 3-8 Rs over a broad longitudinal region (80°) resulting from the pile-up of magnetic flux in the compression and the subsequent expansion of these fields. These results have important implications for multi-instrument observations that will allow Solar Probe Plus and Solar Orbiter to test the developing paradigm of SEP acceleration and transport from coronal compressions. We present here recent coupled simulations for SEP acceleration and transport, including energetic particle and CME plasma profiles. The broadness of the longitudinal profile from such events may be a key observational test of compression acceleration in the low corona.

  10. 3D Particle image velocimetry test of inner flow in a double blade pump impeller

    NASA Astrophysics Data System (ADS)

    Liu, Houlin; Wang, Kai; Yuan, Shouqi; Tan, Minggao; Wang, Yong; Ru, Weimin

    2012-05-01

    The double blade pump is widely used in sewage treatment industry, however, the research on the internal flow characteristics of the double blade pump with particle image velocimetry (PIV) technology is very little at present. To reveal inner flow characteristics in double blade pump impeller under off-design and design conditions, inner flows in a double blade pump impeller, whose specific speed is 111, are measured under the five off-design conditions and design condition by using 3D PIV test technology. In order to ensure the accuracy of the 3D PIV test, the external trigger synchronization system which makes use of fiber optic and equivalent calibration method are applied. The 3D PIV relative velocity synthesis procedure is compiled by using Visual C++ 2005. Then absolute velocity distribution and relative velocity distribution in the double blade pump impeller are obtained. Test results show that vortex exists in each condition, but the location, size and velocity of vortex core are different. Average absolute velocity value of impeller outlet increases at first, then decreases, and then increases again with increase of flow rate. Again average relative velocity values under 0.4, 0.8, and 1.2 design condition are higher than that under 1.0 design condition, while under 0.6 and 1.4 design condition it is lower. Under low flow rate conditions, radial vectors of absolute velocities at impeller outlet and blade inlet near the pump shaft decrease with increase of flow rate, while that of relative velocities at the suction side near the pump shaft decreases. Radial vectors of absolute velocities and relative velocities change slightly under the two large flow rate conditions. The research results can be applied to instruct the hydraulic optimization design of double blade pumps.

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

    PubMed

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

    2015-08-01

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

  12. Tracking particles by passing messages between images

    SciTech Connect

    Chertkov, Michael; Kroc, Lukas; Zdeborova, Lenka; Krakala, Florent; Vergassola, M

    2009-01-01

    Methods to extract information from the tracking of mobile objects/particles have broad interest in biological and physical sciences. Techniques based on the simple criterion of proximity in time-consecutive snapshots are useful to identify the trajectories of the particles. However, they become problematic as the motility and/or the density of the particles increases because of the uncertainties on the trajectories that particles have followed during the acquisition time of the images. Here, we report efficient methods for learning parameters of the dynamics of the particles from their positions in time-consecutive images. Our algorithm belongs to the class of message-passing algorithms, also known in computer science, information theory and statistical physics under the name of Belief Propagation (BP). The algorithm is distributed, thus allowing parallel implementation suitable for computations on multiple machines without significant inter-machine overhead. We test our method on the model example of particle tracking in turbulent flows, which is particularly challenging due to the strong transport that those flows produce. Our numerical experiments show that the BP algorithm compares in quality with exact Markov Chain Monte-Carlo algorithms, yet BP is far superior in speed. We also suggest and analyze a random-distance model that provides theoretical justification for BP accuracy. Methods developed here systematically formulate the problem of particle tracking and provide fast and reliable tools for its extensive range of applications.

  13. Earth's Magnetosphere 3D Simulation by Coupling Particle-In-Cell and Magnetohydrodynamics Models: Parametric Study

    NASA Astrophysics Data System (ADS)

    Baraka, S. M.; Ben-Jaffel, L. B.

    2014-12-01

    We use particle-in-cell PIC 3D Electromagnetic, relativistic global code to address large-scale problems in magnetosphere electrodynamics. Terrestrial bow shock is simulated as an example. 3D Magnetohydrodynamics model ,MHD GUMICS in CCMC project, have been used in parallel with PIC under same scaled Solar wind (SW) and IMF conditions. We report new results from the coupling between the two models. Further investigations are required for confirmations of these results. In both codes the Earth's bow shock position is found at ~14.8 RE along the Sun-Earth line, and ~29 RE on the dusk side which is consistent with past in situ observation. Both simulations reproduce the theoretical jump conditions at the shock. However, PIC code density and temperature distributions are inflated and slightly shifted sunward when compared to MHD results. Reflected ions upstream of the bow shock may cause this sunward shift for density and temperature. Distribution of reflected ions and electrons are shown in the foreshock region, within the transition of the shock and in the downstream. The current version of PIC code can be run under modest computing facilities and resources. Additionally, existing MHD simulations should be useful to calibrate scaled properties of plasma resulting from PIC simulations for comparison with observations. Similarities and drawbacks of the results obtained by the two models are listed. The ultimate goal of using these different models in a complimentary manner rather than competitive is to better understand the macrostructure of the magnetosphere

  14. Particle entry through "Sash" groove simulated by Global 3D Electromagnetic Particle code with duskward IMF By

    NASA Astrophysics Data System (ADS)

    Yan, X.; Cai, D.; Nishikawa, K.; Lembege, B.

    2004-12-01

    We made our efforts to parallelize the global 3D HPF Electromagnetic particle model (EMPM) for several years and have also reported our meaningful simulation results that revealed the essential physics involved in interaction of the solar wind with the Earth's magnetosphere using this EMPM (Nishikawa et al., 1995; Nishikawa, 1997, 1998a, b, 2001, 2002) in our PC cluster and supercomputer(D.S. Cai et al., 2001, 2003). Sash patterns and related phenomena have been observed and reported in some satellite observations (Fujumoto et al. 1997; Maynard, 2001), and have motivated 3D MHD simulations (White and al., 1998). We also investigated it with our global 3D parallelized HPF EMPM with dawnward IMF By (K.-I. Nishikawa, 1998) and recently new simulation with dusk-ward IMF By was accomplished in the new VPP5000 supercomputer. In the new simulations performed on the new VPP5000 supercomputer of Tsukuba University, we used larger domain size, 305×205×205, smaller grid size (Δ ), 0.5R E(the radium of the Earth), more total particle number, 220,000,000 (about 8 pairs per cell). At first, we run this code until we get the so-called quasi-stationary status; After the quasi-stationary status was established, we applied a northward IMF (B z=0.2), and then wait until the IMF arrives around the magnetopuase. After the arrival of IMF, we begin to change the IMF from northward to duskward (IMF B y=-0.2). The results revealed that the groove structure at the day-side magnetopause, that causes particle entry into inner magnetosphere and the cross structure or S-structure at near magneto-tail are formed. Moreover, in contrast with MHD simulations, kinetic characteristic of this event is also analyzed self-consistently with this simulation. The new simulation provides new and more detailed insights for the observed sash event.

  15. Laetoli's lost tracks: 3D generated mean shape and missing footprints.

    PubMed

    Bennett, M R; Reynolds, S C; Morse, S A; Budka, M

    2016-01-01

    The Laetoli site (Tanzania) contains the oldest known hominin footprints, and their interpretation remains open to debate, despite over 35 years of research. The two hominin trackways present are parallel to one another, one of which is a composite formed by at least two individuals walking in single file. Most researchers have focused on the single, clearly discernible G1 trackway while the G2/3 trackway has been largely dismissed due to its composite nature. Here we report the use of a new technique that allows us to decouple the G2 and G3 tracks for the first time. In so doing we are able to quantify the mean footprint topology of the G3 trackway and render it useable for subsequent data analyses. By restoring the effectively 'lost' G3 track, we have doubled the available data on some of the rarest traces directly associated with our Pliocene ancestors. PMID:26902912

  16. Laetoli’s lost tracks: 3D generated mean shape and missing footprints

    PubMed Central

    Bennett, M. R.; Reynolds, S. C.; Morse, S. A.; Budka, M.

    2016-01-01

    The Laetoli site (Tanzania) contains the oldest known hominin footprints, and their interpretation remains open to debate, despite over 35 years of research. The two hominin trackways present are parallel to one another, one of which is a composite formed by at least two individuals walking in single file. Most researchers have focused on the single, clearly discernible G1 trackway while the G2/3 trackway has been largely dismissed due to its composite nature. Here we report the use of a new technique that allows us to decouple the G2 and G3 tracks for the first time. In so doing we are able to quantify the mean footprint topology of the G3 trackway and render it useable for subsequent data analyses. By restoring the effectively ‘lost’ G3 track, we have doubled the available data on some of the rarest traces directly associated with our Pliocene ancestors. PMID:26902912

  17. 3D environment modeling and location tracking using off-the-shelf components

    NASA Astrophysics Data System (ADS)

    Luke, Robert H.

    2016-05-01

    The remarkable popularity of smartphones over the past decade has led to a technological race for dominance in market share. This has resulted in a flood of new processors and sensors that are inexpensive, low power and high performance. These sensors include accelerometers, gyroscope, barometers and most importantly cameras. This sensor suite, coupled with multicore processors, allows a new community of researchers to build small, high performance platforms for low cost. This paper describes a system using off-the-shelf components to perform position tracking as well as environment modeling. The system relies on tracking using stereo vision and inertial navigation to determine movement of the system as well as create a model of the environment sensed by the system.

  18. 3D cloud detection and tracking system for solar forecast using multiple sky imagers

    SciTech Connect

    Peng, Zhenzhou; Yu, Dantong; Huang, Dong; Heiser, John; Yoo, Shinjae; Kalb, Paul

    2015-06-23

    We propose a system for forecasting short-term solar irradiance based on multiple total sky imagers (TSIs). The system utilizes a novel method of identifying and tracking clouds in three-dimensional space and an innovative pipeline for forecasting surface solar irradiance based on the image features of clouds. First, we develop a supervised classifier to detect clouds at the pixel level and output cloud mask. In the next step, we design intelligent algorithms to estimate the block-wise base height and motion of each cloud layer based on images from multiple TSIs. Thus, this information is then applied to stitch images together into larger views, which are then used for solar forecasting. We examine the system’s ability to track clouds under various cloud conditions and investigate different irradiance forecast models at various sites. We confirm that this system can 1) robustly detect clouds and track layers, and 2) extract the significant global and local features for obtaining stable irradiance forecasts with short forecast horizons from the obtained images. Finally, we vet our forecasting system at the 32-megawatt Long Island Solar Farm (LISF). Compared with the persistent model, our system achieves at least a 26% improvement for all irradiance forecasts between one and fifteen minutes.

  19. 3D cloud detection and tracking system for solar forecast using multiple sky imagers

    DOE PAGESBeta

    Peng, Zhenzhou; Yu, Dantong; Huang, Dong; Heiser, John; Yoo, Shinjae; Kalb, Paul

    2015-06-23

    We propose a system for forecasting short-term solar irradiance based on multiple total sky imagers (TSIs). The system utilizes a novel method of identifying and tracking clouds in three-dimensional space and an innovative pipeline for forecasting surface solar irradiance based on the image features of clouds. First, we develop a supervised classifier to detect clouds at the pixel level and output cloud mask. In the next step, we design intelligent algorithms to estimate the block-wise base height and motion of each cloud layer based on images from multiple TSIs. Thus, this information is then applied to stitch images together intomore » larger views, which are then used for solar forecasting. We examine the system’s ability to track clouds under various cloud conditions and investigate different irradiance forecast models at various sites. We confirm that this system can 1) robustly detect clouds and track layers, and 2) extract the significant global and local features for obtaining stable irradiance forecasts with short forecast horizons from the obtained images. Finally, we vet our forecasting system at the 32-megawatt Long Island Solar Farm (LISF). Compared with the persistent model, our system achieves at least a 26% improvement for all irradiance forecasts between one and fifteen minutes.« less

  20. Polyribosomes Are Molecular 3D Nanoprinters That Orchestrate the Assembly of Vault Particles

    PubMed Central

    2014-01-01

    Ribosomes are molecular machines that function in polyribosome complexes to translate genetic information, guide the synthesis of polypeptides, and modulate the folding of nascent proteins. Here, we report a surprising function for polyribosomes as a result of a systematic examination of the assembly of a large ribonucleoprotein complex, the vault particle. Structural and functional evidence points to a model of vault assembly whereby the polyribosome acts like a 3D nanoprinter to direct the ordered translation and assembly of the multi-subunit vault homopolymer, a process which we refer to as polyribosome templating. Structure-based mutagenesis and cell-free in vitro expression studies further demonstrated the critical importance of the polyribosome in vault assembly. Polyribosome templating prevents chaos by ensuring efficiency and order in the production of large homopolymeric protein structures in the crowded cellular environment and might explain the origin of many polyribosome-associated molecular assemblies inside the cell. PMID:25354757

  1. Full-field drift Hamiltonian particle orbits in 3D geometry

    NASA Astrophysics Data System (ADS)

    Cooper, W. A.; Graves, J. P.; Brunner, S.; Isaev, M. Yu

    2011-02-01

    A Hamiltonian/Lagrangian theory to describe guiding centre orbit drift motion which is canonical in the Boozer coordinate frame has been extended to include full electromagnetic perturbed fields in anisotropic pressure 3D equilibria with nested magnetic flux surfaces. A redefinition of the guiding centre velocity to eliminate the motion due to finite equilibrium radial magnetic fields and the choice of a gauge condition that sets the radial component of the electromagnetic vector potential to zero are invoked to guarantee that the Boozer angular coordinates retain the canonical structure. The canonical momenta are identified and the guiding centre particle radial drift motion and parallel gyroradius evolution are derived. The particle coordinate position is linearly modified by wave-particle interactions. All the nonlinear wave-wave interactions appear explicitly only in the evolution of the parallel gyroradius. The radial variation of the electrostatic potential is related to the binormal component of the displacement vector for MHD-type perturbations. The electromagnetic vector potential projections can then be determined from the electrostatic potential and the radial component of the MHD displacement vector.

  2. Acoustical vortices on a Chip for 3D single particle manipulation and vorticity control

    NASA Astrophysics Data System (ADS)

    Riaud, Antoine; Thomas, Jean-Louis; Bou Matar, Olivier; Baudoin, Michael

    Surface acoustic waves offer most of the basic functions required for on-chip actuation of fluids at small scales: efficient flow mixing, integrated pumping, particles separation, droplet displacement, atomization, division and fusion. Nevertheless some more advanced functions such as 3D particles manipulation and vorticity control require the introduction of some specific kind of waves called acoustic vortices. These helical waves propagate spinning around a phase singularity called the dark core. On the one hand, the beam angular momentum can be transferred to the fluid and create point-wise vorticity for confined mixing, and on the other the dark core can trap individual particles in an acoustic well for single object manipulation. In this presentation, I will show how acoustical vortices on-a-chip can be synthesized with a programmable electronics and an array of transducers. I will then highlight how some of their specificities can be used for acoustical tweezing and twisting. This work is supported by ANR Project No. ANR-12-BS09-0021-01 and ANR-12- BS09-0021-02, and Rgion Nord Pas de Calais.

  3. 3D quantification of brain microvessels exposed to heavy particle radiation

    NASA Astrophysics Data System (ADS)

    Hintermüller, C.; Coats, J. S.; Obenaus, A.; Nelson, G.; Krucker, T.; Stampanoni, M.

    2009-09-01

    Space radiation with high energy particles and cosmic rays presents a significant hazard to spaceflight crews. Recent reviews of the health risk to astronauts from ionizing radiation concluded to establish a level of risk which may indicate the possible performance decrements and decreased latency of late dysfunction syndromes (LDS) of the brain. A hierarchical imaging approach developed at ETH Zürich and PSI, which relies on synchrotron based X-ray Tomographic Microscopy (SRXTM), was used to visualize and analyze 3D vascular structures down to the capillary level in their precise anatomical context. Various morphological parameters, such as overall vessel volume, vessel thickness and spacing, are extracted to characterize the vascular structure within a region of interest. For a first quantification of the effect of high energy particles on the vasculature we scanned a set of 6 animals, all of same age. The animals were irradiated with 1 Gy, 2 Gy and 4 Gy of 600MeV 56Fe heavy particles simulating the space radiation environment. We found that with increasing dose the diameter of vessels and the overall vessel volume are decreased whereas the vessel spacing is increased. As these parameters reflect blood flow in three-dimensional space they can be used as indicators for the degree of vascular efficiency which can have an impact on the function and development of lung tissue or tumors.

  4. Test-particle Orbit Simulations in Fields from a Realistic 3D MHD Simulation

    NASA Astrophysics Data System (ADS)

    Decker, R. B.; Opher, M.; Hill, M. E.

    2007-05-01

    Models designed to explore the global structure of the heliosphere have become increasing sophisticated. Incentives to increase and to further explore the predictive capabilities of such models include the entry of the Voyager spacecraft into the foreshock region of the termination shock (TS), Voyager 1 in mid-2002 and Voyager 2 in late 2004, and the crossing of the TS and passage into the heliosheath (HSH) of Voyager 1 in 2004 day 351. Using the electric and magnetic fields generated by a MHD model of a 3D, asymmetric heliosphere [Opher et al., Ap. J. L., 640, 2006], we have developed full-particle and adiabatic-orbit codes to simulate the motion of test particles in the solar wind, TS, and HSH environments. The full-particle orbits are necessary to investigate energetic ion (e.g., anomalous and galactic cosmic ray) motion at the TS and within the heliospheric current sheet that is included in the MHD model. Adiabatic orbits are used to study particle motion in the much larger volume of the HSH where the non-homogeneous model fields produce complex guiding center motions, including mirroring in local field compressions. We will present results from these orbit computations, which are intended to provide an initial, albeit simplified, look at the propagation of high-energy charged particles, in the scatter-free limit, in the best model of the TS/HSH field configurations currently available. We will also display drift paths of high-energy ions in the HSH fields using the guiding center drift equations that are applicable in the limit of diffusive propagation.

  5. Bi-planar 2D-to-3D registration in Fourier domain for stereoscopic x-ray motion tracking

    NASA Astrophysics Data System (ADS)

    Zosso, Dominique; Le Callennec, Benoît; Bach Cuadra, Meritxell; Aminian, Kamiar; Jolles, Brigitte M.; Thiran, Jean-Philippe

    2008-03-01

    In this paper we present a new method to track bone movements in stereoscopic X-ray image series of the knee joint. The method is based on two different X-ray image sets: a rotational series of acquisitions of the still subject knee that allows the tomographic reconstruction of the three-dimensional volume (model), and a stereoscopic image series of orthogonal projections as the subject performs movements. Tracking the movements of bones throughout the stereoscopic image series means to determine, for each frame, the best pose of every moving element (bone) previously identified in the 3D reconstructed model. The quality of a pose is reflected in the similarity between its theoretical projections and the actual radiographs. We use direct Fourier reconstruction to approximate the three-dimensional volume of the knee joint. Then, to avoid the expensive computation of digitally rendered radiographs (DRR) for pose recovery, we develop a corollary to the 3-dimensional central-slice theorem and reformulate the tracking problem in the Fourier domain. Under the hypothesis of parallel X-ray beams, the heavy 2D-to-3D registration of projections in the signal domain is replaced by efficient slice-to-volume registration in the Fourier domain. Focusing on rotational movements, the translation-relevant phase information can be discarded and we only consider scalar Fourier amplitudes. The core of our motion tracking algorithm can be implemented as a classical frame-wise slice-to-volume registration task. Results on both synthetic and real images confirm the validity of our approach.

  6. 3D Plasma Equilibrium and Stability with Hot Particle Anisotropic Pressure

    SciTech Connect

    Cooper, W. A.; Graves, J. P.; Hirshman, S. P.; Merkel, P.; Kisslinger, J.; Wobig, H. F. G.; Watanabe, K. Y.; Narushima, Y.

    2008-11-01

    The anisotropic pressure free-boundary three-dimsnsional (3D) equilibrium code ANI-MEC with nested magnetic flux surfaces has been developed as an extension of the VMEC2000 code. The preconditioning algorithm included is exploited to allow the computation of equilibrium states with radial force balance error improvements exceeding 4 orders of magnitude compared with the non-conditioned results. Large off-axis energetic particle deposition has been applied in a 2-field period quasiaxisymmetric stellarator reactor at <{beta}>{approx_equal}4.5% to test the limitations of the code. The hot particle pressures are roughly uniform around the flux surfaces when p{sub parallel}>p{sub perpendicular}. The fast particle perpendicular pressures localise in the region of deposition for p{sub perpendicular}>p{sub parallel}, while the energetic particle parallel pressures concentrate on the low-field side. Two anisotropic pressure models for global fluid stability implemented in the TERPSICHORE code have been applied to the LHD Heliotron for a sequence of equilibria with fixed <{beta}{sub dia}>{approx_equal}5%(<{beta}{sub th}>{approx_equal}3.5%) varying the fast particle temperature ratio T{sub parallel}/T{sub perpendicular}. Global magnetohydrodynamic modes are quasi-stable according to the model with rigid hot particle layers, while they become stabilised according to the fully interacting energetic particle model with increasing T{sub parallel}/T{sub perpendicular}. As T{sub parallel}/T{sub perpendicular} approaches 3, however, the n = 1 mode family becomes unstable. A transition from a nearly stable quasi-external ballooning-interchange structure to a weakly unstable internal kink mode takes place. The investigation of beam-driven fusion in a Heliotron system is broached. A background plasma with cold ions and warm electrons at <{beta}{sub ith}>{approx_equal}1% is examined with fixed T{sub parallel}/T{sub perpendicular} = 10 in which the hot particle contribution to <{beta

  7. Pulmonary CT image registration and warping for tracking tissue deformation during the respiratory cycle through 3D consistent image registration

    PubMed Central

    Li, Baojun; Christensen, Gary E.; Hoffman, Eric A.; McLennan, Geoffrey; Reinhardt, Joseph M.

    2008-01-01

    Tracking lung tissues during the respiratory cycle has been a challenging task for diagnostic CT and CT-guided radiotherapy. We propose an intensity- and landmark-based image registration algorithm to perform image registration and warping of 3D pulmonary CT image data sets, based on consistency constraints and matching corresponding airway branchpoints. In this paper, we demonstrate the effectivenss and accuracy of this algorithm in tracking lung tissues by both animal and human data sets. In the animal study, the result showed a tracking accuracy of 1.9 mm between 50% functional residual capacity (FRC) and 85% total lung capacity (TLC) for 12 metal seeds implanted in the lungs of a breathing sheep under precise volume control using a pulmonary ventilator. Visual inspection of the human subject results revealed the algorithm’s potential not only in matching the global shapes, but also in registering the internal structures (e.g., oblique lobe fissures, pulmonary artery branches, etc.). These results suggest that our algorithm has significant potential for warping and tracking lung tissue deformation with applications in diagnostic CT, CT-guided radiotherapy treatment planning, and therapeutic effect evaluation. PMID:19175115

  8. Visualizing and Tracking Evolving Features in 3D Unstructured and Adaptive Datasets

    SciTech Connect

    Silver, D.; Zabusky, N.

    2002-08-01

    The massive amounts of time-varying datasets being generated demand new visualization and quantification techniques. Visualization alone is not sufficient. Without proper measurement information/computations real science cannot be done. Our focus is this work was to combine visualization with quantification of the data to allow for advanced querying and searching. As part of this proposal, we have developed a feature extraction adn tracking methodology which allows researcher to identify features of interest and follow their evolution over time. The implementation is distributed and operates over data In-situ: where it is stored and when it was computed.

  9. Modeling the influence of particle morphology on the fracture behavior of silica sand using a 3D discrete element method

    NASA Astrophysics Data System (ADS)

    Cil, Mehmet B.; Alshibli, Khalid A.

    2015-02-01

    The constitutive behavior and deformation characteristics of uncemented granular materials are to a large extent derived from the fabric or geometry of the particle structure and the interparticle friction resulting from normal forces acting on particles or groups of particles. Granular materials consist of discrete particles with a fabric (microstructure) that changes under loading. Synchrotron micro-computed tomography (SMT) has emerged as a powerful non-destructive 3D scanning technique to study geomaterials. In this paper, SMT was used to acquire in situ scans of the oedometry test of a column of three silica sand particles. The sand is known as ASTM 20-30 Ottawa sand, and has a grain size between US sieves #20 (0.841 mm) and #30 (0.595 mm). The characteristics and evolution of particle fracture in sand were examined using SMT images, and a 3D discrete element method (DEM) was used to model the fracture behavior of sand particles. It adopts the bonded particle model to generate a crushable agglomerate that consists of a large number of small spherical sub-particles. The agglomerate shape matches the 3D physical shape of the tested sand particles by mapping the particle morphology from the SMT images. The paper investigates and discusses the influence of agglomerate packing (i.e., the number and size distribution of spherical sub-particles that constitute the agglomerate) and agglomerate shape on the fracture behavior of crushable particles.

  10. Optimal transcostal high-intensity focused ultrasound with combined real-time 3D movement tracking and correction

    NASA Astrophysics Data System (ADS)

    Marquet, F.; Aubry, J. F.; Pernot, M.; Fink, M.; Tanter, M.

    2011-11-01

    Recent studies have demonstrated the feasibility of transcostal high intensity focused ultrasound (HIFU) treatment in liver. However, two factors limit thermal necrosis of the liver through the ribs: the energy deposition at focus is decreased by the respiratory movement of the liver and the energy deposition on the skin is increased by the presence of highly absorbing bone structures. Ex vivo ablations were conducted to validate the feasibility of a transcostal real-time 3D movement tracking and correction mode. Experiments were conducted through a chest phantom made of three human ribs immersed in water and were placed in front of a 300 element array working at 1 MHz. A binarized apodization law introduced recently in order to spare the rib cage during treatment has been extended here with real-time electronic steering of the beam. Thermal simulations have been conducted to determine the steering limits. In vivo 3D-movement detection was performed on pigs using an ultrasonic sequence. The maximum error on the transcostal motion detection was measured to be 0.09 ± 0.097 mm on the anterior-posterior axis. Finally, a complete sequence was developed combining real-time 3D transcostal movement correction and spiral trajectory of the HIFU beam, allowing the system to treat larger areas with optimized efficiency. Lesions as large as 1 cm in diameter have been produced at focus in excised liver, whereas no necroses could be obtained with the same emitted power without correcting the movement of the tissue sample.

  11. 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

  12. A Detailed Study of FDIRC Prototype with Waveform Digitizing Electronics in Cosmic Ray Telescope Using 3D Tracks

    SciTech Connect

    Nishimura, K.; Dey, B.; Aston, D.; Leith, D.W.G.S.; Ratcliff, B.; Roberts, D.; Ruckman, L.; Shtol, D.; Varner, G.S.; Va'vra, J.; Vavra, Jerry; /SLAC

    2012-07-30

    We present a detailed study of a novel Cherenkov imaging detector called the Focusing DIRC (FDIRC) with waveform digitizing electronics. In this test study, the FDIRC prototype has been instrumented with seven Hamamatsu H-8500 MaPMTs. Waveforms from {approx}450 pixels are digitized with waveform sampling electronics based on the BLAB2 ASIC, operating at a sampling speed of {approx}2.5 GSa/s. The FDIRC prototype was tested in a large cosmic ray telescope (CRT) providing 3D muon tracks with {approx}1.5 mrad angular resolution and muon energy of E{sub muon} > 1.6 GeV. In this study we provide a detailed analysis of the tails in the Cherenkov angle distribution as a function of various variables, compare experimental results with simulation, and identify the major contributions to the tails. We demonstrate that to see the full impact of these tails on the Cherenkov angle resolution, it is crucial to use 3D tracks, and have a full understanding of the role of ambiguities. These issues could not be fully explored in previous FDIRC studies where the beam was perpendicular to the quartz radiator bars. This work is relevant for the final FDIRC prototype of the PID detector at SuperB, which will be tested this year in the CRT setup.

  13. A Detailed Study of FDIRC Prototype with Waveform Digitizing Electronics in Cosmic Ray Telescope Using 3D Tracks.

    SciTech Connect

    Nishimura, K

    2012-07-01

    We present a detailed study of a novel Cherenkov imaging detector called the Focusing DIRC (FDIRC) with waveform digitizing electronics. In this test study, the FDIRC prototype has been instrumented with seven Hamamatsu H-8500 MaPMTs. Waveforms from ~450 pixels are digitized with waveform sampling electronics based on the BLAB2 ASIC, operating at a sampling speed of ~2.5 GSa/s. The FDIRC prototype was tested in a large cosmic ray telescope (CRT) providing 3D muon tracks with ~1.5 mrad angular resolution and muon energy of Emuon greater than 1.6 GeV. In this study we provide a detailed analysis of the tails in the Cherenkov angle distribution as a function of various variables, compare experimental results with simulation, and identify the major contributions to the tails. We demonstrate that to see the full impact of these tails on the Cherenkov angle resolution, it is crucial to use 3D tracks, and have a full understanding of the role of ambiguities. These issues could not be fully explored in previous FDIRC studies where the beam was perpendicular to the quartz radiator bars. This work is relevant for the final FDIRC prototype of the PID detector at SuperB, which will be tested this year in the CRT setup.

  14. A smart homecage system with 3D tracking for long-term behavioral experiments.

    PubMed

    Byunghun Lee; Kiani, Mehdi; Ghovanloo, Maysam

    2014-01-01

    A wirelessly-powered homecage system, called the EnerCage-HC, that is equipped with multi-coil wireless power transfer, closed-loop power control, optical behavioral tracking, and a graphic user interface (GUI) is presented for long-term electrophysiology experiments. The EnerCage-HC system can wirelessly power a mobile unit attached to a small animal subject and also track its behavior in real-time as it is housed inside a standard homecage. The EnerCage-HC system is equipped with one central and four overlapping slanted wire-wound coils (WWCs) with optimal geometries to form 3-and 4-coil power transmission links while operating at 13.56 MHz. Utilizing multi-coil links increases the power transfer efficiency (PTE) compared to conventional 2-coil links and also reduces the number of power amplifiers (PAs) to only one, which significantly reduces the system complexity, cost, and dissipated heat. A Microsoft Kinect installed 90 cm above the homecage localizes the animal position and orientation with 1.6 cm accuracy. An in vivo experiment was conducted on a freely behaving rat by continuously delivering 24 mW to the mobile unit for > 7 hours inside a standard homecage. PMID:25570379

  15. A Smart Homecage System with 3D Tracking for Long-Term Behavioral Experiments

    PubMed Central

    Lee, Byunghun; Kiani, Mehdi; Ghovanloo, Maysam

    2015-01-01

    A wirelessly-powered homecage system, called the EnerCage-HC, that is equipped with multi-coil wireless power transfer, closed-loop power control, optical behavioral tracking, and a graphic user interface (GUI) is presented for long-term electrophysiology experiments. The EnerCage-HC system can wirelessly power a mobile unit attached to a small animal subject and also track its behavior in real-time as it is housed inside a standard homecage. The EnerCage-HC system is equipped with one central and four overlapping slanted wire-wound coils (WWCs) with optimal geometries to form 3- and 4-coil power transmission links while operating at 13.56 MHz. Utilizing multi-coil links increases the power transfer efficiency (PTE) compared to conventional 2-coil links and also reduces the number of power amplifiers (PAs) to only one, which significantly reduces the system complexity, cost, and dissipated heat. A Microsoft Kinect installed 90 cm above the homecage localizes the animal position and orientation with 1.6 cm accuracy. An in vivo experiment was conducted on a freely behaving rat by continuously delivering 24 mW to the mobile unit for > 7 hours inside a standard homecage. PMID:25570379

  16. Multisensor 3D tracking for counter small unmanned air vehicles (CSUAV)

    NASA Astrophysics Data System (ADS)

    Vasquez, Juan R.; Tarplee, Kyle M.; Case, Ellen E.; Zelnio, Anne M.; Rigling, Brian D.

    2008-04-01

    A variety of unmanned air vehicles (UAVs) have been developed for both military and civilian use. The typical large UAV is typically state owned, whereas small UAVs (SUAVs) may be in the form of remote controlled aircraft that are widely available. The potential threat of these SUAVs to both the military and civilian populace has led to research efforts to counter these assets via track, ID, and attack. Difficulties arise from the small size and low radar cross section when attempting to detect and track these targets with a single sensor such as radar or video cameras. In addition, clutter objects make accurate ID difficult without very high resolution data, leading to the use of an acoustic array to support this function. This paper presents a multi-sensor architecture that exploits sensor modes including EO/IR cameras, an acoustic array, and future inclusion of a radar. A sensor resource management concept is presented along with preliminary results from three of the sensors.

  17. Readily Accessible Multiplane Microscopy: 3D Tracking the HIV-1 Genome in Living Cells.

    PubMed

    Itano, Michelle S; Bleck, Marina; Johnson, Daniel S; Simon, Sanford M

    2016-02-01

    Human immunodeficiency virus (HIV)-1 infection and the associated disease AIDS are a major cause of human death worldwide with no vaccine or cure available. The trafficking of HIV-1 RNAs from sites of synthesis in the nucleus, through the cytoplasm, to sites of assembly at the plasma membrane are critical steps in HIV-1 viral replication, but are not well characterized. Here we present a broadly accessible microscopy method that captures multiple focal planes simultaneously, which allows us to image the trafficking of HIV-1 genomic RNAs with high precision. This method utilizes a customization of a commercial multichannel emission splitter that enables high-resolution 3D imaging with single-macromolecule sensitivity. We show with high temporal and spatial resolution that HIV-1 genomic RNAs are most mobile in the cytosol, and undergo confined mobility at sites along the nuclear envelope and in the nucleus and nucleolus. These provide important insights regarding the mechanism by which the HIV-1 RNA genome is transported to the sites of assembly of nascent virions. PMID:26567131

  18. Real-time estimation of FLE statistics for 3-D tracking with point-based registration.

    PubMed

    Wiles, Andrew D; Peters, Terry M

    2009-09-01

    Target registration error (TRE) has become a widely accepted error metric in point-based registration since the error metric was introduced in the 1990s. It is particularly prominent in image-guided surgery (IGS) applications where point-based registration is used in both image registration and optical tracking. In point-based registration, the TRE is a function of the fiducial marker geometry, location of the target and the fiducial localizer error (FLE). While the first two items are easily obtained, the FLE is usually estimated using an a priori technique and applied without any knowledge of real-time information. However, if the FLE can be estimated in real-time, particularly as it pertains to optical tracking, then the TRE can be estimated more robustly. In this paper, a method is presented where the FLE statistics are estimated from the latest measurement of the fiducial registration error (FRE) statistics. The solution is obtained by solving a linear system of equations of the form Ax=b for each marker at each time frame where x are the six independent FLE covariance parameters and b are the six independent estimated FRE covariance parameters. The A matrix is only a function of the tool geometry and hence the inverse of the matrix can be computed a priori and used at each instant in which the FLE estimation is required, hence minimizing the level of computation at each frame. When using a good estimate of the FRE statistics, Monte Carlo simulations demonstrate that the root mean square of the FLE can be computed within a range of 70-90 microm. Robust estimation of the TRE for an optically tracked tool, using a good estimate of the FLE, will provide two enhancements in IGS. First, better patient to image registration will be obtained by using the TRE of the optical tool as a weighting factor of point-based registration used to map the patient to image space. Second, the directionality of the TRE can be relayed back to the surgeon giving the surgeon the option

  19. 3D and r,z particle simulations of heavy ion fusion beams

    NASA Astrophysics Data System (ADS)

    Friedman, A.; Grote, D. P.; Callahan, D. A.; Langdon, A. B.; Haber, I.

    1992-08-01

    The space-charge-dominated beams in a heavy ion beam driven inertial fusion (HIF) accelerator must be focused onto small (few mm) spots at the fusion target, and so preservation of a small emittance is crucial. The nonlinear beam self-fields can lead to emittance growth; thus, a self-consistent field description is necessary. We have developed a multi-dimensional time-dependent discrete particle simulation code, WARP, and are using it to study the behavior of HIF beams. The code's 3d package combines features of an accelerator code and a particle-in-cell (PIC) plasma simulation. Novel techniques allow it to follow beams through many accelerator elements over long distances and around bends. We have used the code to understand the emittance growth observed in the MBE4 experiment at Lawrence Berkeley Laboratory (LBL) under conditions of aggressive drift-compression. We are currently applying it to LBL's planned ILSE experiments, and (most recently) to an ESQ injector option being evaluated for ILSE. The code's r, z package is being used to study the axial confinement afforded by the shaped ends of the accelerating pulses, and to study longitudinal instability induced by induction module impedance.

  20. Single Particle Cryo-electron Microscopy and 3-D Reconstruction of Viruses

    PubMed Central

    Guo, Fei; Jiang, Wen

    2014-01-01

    With fast progresses in instrumentation, image processing algorithms, and computational resources, single particle electron cryo-microscopy (cryo-EM) 3-D reconstruction of icosahedral viruses has now reached near-atomic resolutions (3–4 Å). With comparable resolutions and more predictable outcomes, cryo-EM is now considered a preferred method over X-ray crystallography for determination of atomic structure of icosahedral viruses. At near-atomic resolutions, all-atom models or backbone models can be reliably built that allow residue level understanding of viral assembly and conformational changes among different stages of viral life cycle. With the developments of asymmetric reconstruction, it is now possible to visualize the complete structure of a complex virus with not only its icosahedral shell but also its multiple non-icosahedral structural features. In this chapter, we will describe single particle cryo-EM experimental and computational procedures for both near-atomic resolution reconstruction of icosahedral viruses and asymmetric reconstruction of viruses with both icosahedral and non-icosahedral structure components. Procedures for rigorous validation of the reconstructions and resolution evaluations using truly independent de novo initial models and refinements are also introduced. PMID:24357374

  1. Ghost Particle Velocimetry: Accurate 3D Flow Visualization Using Standard Lab Equipment

    NASA Astrophysics Data System (ADS)

    Buzzaccaro, Stefano; Secchi, Eleonora; Piazza, Roberto

    2013-07-01

    We describe and test a new approach to particle velocimetry, based on imaging and cross correlating the scattering speckle pattern generated on a near-field plane by flowing tracers with a size far below the diffraction limit, which allows reconstructing the velocity pattern in microfluidic channels without perturbing the flow. As a matter of fact, adding tracers is not even strictly required, provided that the sample displays sufficiently refractive-index fluctuations. For instance, phase separation in liquid mixtures in the presence of shear is suitable to be directly investigated by this “ghost particle velocimetry” technique, which just requires a microscope with standard lamp illumination equipped with a low-cost digital camera. As a further bonus, the peculiar spatial coherence properties of the illuminating source, which displays a finite longitudinal coherence length, allows for a 3D reconstruction of the profile with a resolution of few tenths of microns and makes the technique suitable to investigate turbid samples with negligible multiple scattering effects.

  2. CAST: Effective and Efficient User Interaction for Context-Aware Selection in 3D Particle Clouds.

    PubMed

    Yu, Lingyun; Efstathiou, Konstantinos; Isenberg, Petra; Isenberg, Tobias

    2016-01-01

    We present a family of three interactive Context-Aware Selection Techniques (CAST) for the analysis of large 3D particle datasets. For these datasets, spatial selection is an essential prerequisite to many other analysis tasks. Traditionally, such interactive target selection has been particularly challenging when the data subsets of interest were implicitly defined in the form of complicated structures of thousands of particles. Our new techniques SpaceCast, TraceCast, and PointCast improve usability and speed of spatial selection in point clouds through novel context-aware algorithms. They are able to infer a user's subtle selection intention from gestural input, can deal with complex situations such as partially occluded point clusters or multiple cluster layers, and can all be fine-tuned after the selection interaction has been completed. Together, they provide an effective and efficient tool set for the fast exploratory analysis of large datasets. In addition to presenting Cast, we report on a formal user study that compares our new techniques not only to each other but also to existing state-of-the-art selection methods. Our results show that Cast family members are virtually always faster than existing methods without tradeoffs in accuracy. In addition, qualitative feedback shows that PointCast and TraceCast were strongly favored by our participants for intuitiveness and efficiency. PMID:26390474

  3. DLP technology application: 3D head tracking and motion correction in medical brain imaging

    NASA Astrophysics Data System (ADS)

    Olesen, Oline V.; Wilm, Jakob; Paulsen, Rasmus R.; Højgaard, Liselotte; Larsen, Rasmus

    2014-03-01

    In this paper we present a novel sensing system, robust Near-infrared Structured Light Scanning (NIRSL) for three-dimensional human model scanning application. Human model scanning due to its nature of various hair and dress appearance and body motion has long been a challenging task. Previous structured light scanning methods typically emitted visible coded light patterns onto static and opaque objects to establish correspondence between a projector and a camera for triangulation. In the success of these methods rely on scanning objects with proper reflective surface for visible light, such as plaster, light colored cloth. Whereas for human model scanning application, conventional methods suffer from low signal to noise ratio caused by low contrast of visible light over the human body. The proposed robust NIRSL, as implemented with the near infrared light, is capable of recovering those dark surfaces, such as hair, dark jeans and black shoes under visible illumination. Moreover, successful structured light scan relies on the assumption that the subject is static during scanning. Due to the nature of body motion, it is very time sensitive to keep this assumption in the case of human model scan. The proposed sensing system, by utilizing the new near-infrared capable high speed LightCrafter DLP projector, is robust to motion, provides accurate and high resolution three-dimensional point cloud, making our system more efficient and robust for human model reconstruction. Experimental results demonstrate that our system is effective and efficient to scan real human models with various dark hair, jeans and shoes, robust to human body motion and produces accurate and high resolution 3D point cloud.

  4. Particle tracking and mean residence time in barchan dunes

    NASA Astrophysics Data System (ADS)

    Zhang, Deguo; Narteau, Clement; Rozier, Olivier

    2013-04-01

    We analyze sediment particles motions in steady-state barchan dunes by tracking individual cells of a 3-D cellular automaton dune model. The overall sediment flux may be decomposed into advective and dispersive fluxes to estimate the relative contribution of the underlying physical processes to the barchan dune shape. The net lateral sediment transport from the center to the horns indicates that dispersion on the stoss slope is more efficient than avalanches on the lee slope. The combined effect of these two antagonistic dispersive processes restricts the lateral mixing of sediment particles in the central region of barchan dunes. Then, for different flow strength and dune size, we find that the mean residence time of sediment particles in barchan dunes is equal to the surface of the central longitudinal dune slices divided by the input sand flux. We infer that this central slice contains most of the relevant information about barchan dune morphodynamics. Finally, we initiate a discussion about sediment transport and memory in presence of bedforms using the advantages of the particle tracking technique.

  5. Track nanodosimetry of an alpha particle.

    PubMed

    De Nardo, L; Colautti, P; Baek, W Y; Grosswendt, B; Alkaa, A; Ségur, P; Tornielli, G

    2002-01-01

    Experimental measurements and calculations are described of ionisation distributions in propane wall-less gas cavities of about 20 nm simulated size, performed at different distances from a 244Cm alpha particle track. Ionisation events are detected one by one by collecting electrons from the sensitive volume and by separating them with a drift column. Experimental results and Monte Carlo calculations indicate that, in the delta ray cloud, conditional probability curves, average cluster size and the ratio of second moment above first moment of the cluster distribution are invariant with track distance. PMID:12194323

  6. Advanced 3D Poisson solvers and particle-in-cell methods for accelerator modeling

    NASA Astrophysics Data System (ADS)

    Serafini, David B.; McCorquodale, Peter; Colella, Phillip

    2005-01-01

    We seek to improve on the conventional FFT-based algorithms for solving the Poisson equation with infinite-domain (open) boundary conditions for large problems in accelerator modeling and related areas. In particular, improvements in both accuracy and performance are possible by combining several technologies: the method of local corrections (MLC); the James algorithm; and adaptive mesh refinement (AMR). The MLC enables the parallelization (by domain decomposition) of problems with large domains and many grid points. This improves on the FFT-based Poisson solvers typically used as it doesn't require the all-to-all communication pattern that parallel 3d FFT algorithms require, which tends to be a performance bottleneck on current (and foreseeable) parallel computers. In initial tests, good scalability up to 1000 processors has been demonstrated for our new MLC solver. An essential component of our approach is a new version of the James algorithm for infinite-domain boundary conditions for the case of three dimensions. By using a simplified version of the fast multipole method in the boundary-to-boundary potential calculation, we improve on the performance of the Hockney algorithm typically used by reducing the number of grid points by a factor of 8, and the CPU costs by a factor of 3. This is particularly important for large problems where computer memory limits are a consideration. The MLC allows for the use of adaptive mesh refinement, which reduces the number of grid points and increases the accuracy in the Poisson solution. This improves on the uniform grid methods typically used in PIC codes, particularly in beam problems where the halo is large. Also, the number of particles per cell can be controlled more closely with adaptivity than with a uniform grid. To use AMR with particles is more complicated than using uniform grids. It affects depositing particles on the non-uniform grid, reassigning particles when the adaptive grid changes and maintaining the load

  7. Radiation Quality Effects on Transcriptome Profiles in 3-d Cultures After Particle Irradiation

    NASA Technical Reports Server (NTRS)

    Patel, Z. S.; Kidane, Y. H.; Huff, J. L.

    2014-01-01

    In this work, we evaluate the differential effects of low- and high-LET radiation on 3-D organotypic cultures in order to investigate radiation quality impacts on gene expression and cellular responses. Reducing uncertainties in current risk models requires new knowledge on the fundamental differences in biological responses (the so-called radiation quality effects) triggered by heavy ion particle radiation versus low-LET radiation associated with Earth-based exposures. We are utilizing novel 3-D organotypic human tissue models that provide a format for study of human cells within a realistic tissue framework, thereby bridging the gap between 2-D monolayer culture and animal models for risk extrapolation to humans. To identify biological pathway signatures unique to heavy ion particle exposure, functional gene set enrichment analysis (GSEA) was used with whole transcriptome profiling. GSEA has been used extensively as a method to garner biological information in a variety of model systems but has not been commonly used to analyze radiation effects. It is a powerful approach for assessing the functional significance of radiation quality-dependent changes from datasets where the changes are subtle but broad, and where single gene based analysis using rankings of fold-change may not reveal important biological information. We identified 45 statistically significant gene sets at 0.05 q-value cutoff, including 14 gene sets common to gamma and titanium irradiation, 19 gene sets specific to gamma irradiation, and 12 titanium-specific gene sets. Common gene sets largely align with DNA damage, cell cycle, early immune response, and inflammatory cytokine pathway activation. The top gene set enriched for the gamma- and titanium-irradiated samples involved KRAS pathway activation and genes activated in TNF-treated cells, respectively. Another difference noted for the high-LET samples was an apparent enrichment in gene sets involved in cycle cycle/mitotic control. It is

  8. Method for dose-reduced 3D catheter tracking on a scanning-beam digital x-ray system using dynamic electronic collimation

    NASA Astrophysics Data System (ADS)

    Dunkerley, David A. P.; Funk, Tobias; Speidel, Michael A.

    2016-03-01

    Scanning-beam digital x-ray (SBDX) is an inverse geometry x-ray fluoroscopy system capable of tomosynthesis-based 3D catheter tracking. This work proposes a method of dose-reduced 3D tracking using dynamic electronic collimation (DEC) of the SBDX scanning x-ray tube. Positions in the 2D focal spot array are selectively activated to create a regionof- interest (ROI) x-ray field around the tracked catheter. The ROI position is updated for each frame based on a motion vector calculated from the two most recent 3D tracking results. The technique was evaluated with SBDX data acquired as a catheter tip inside a chest phantom was pulled along a 3D trajectory. DEC scans were retrospectively generated from the detector images stored for each focal spot position. DEC imaging of a catheter tip in a volume measuring 11.4 cm across at isocenter required 340 active focal spots per frame, versus 4473 spots in full-FOV mode. The dose-area-product (DAP) and peak skin dose (PSD) for DEC versus full field-of-view (FOV) scanning were calculated using an SBDX Monte Carlo simulation code. DAP was reduced to 7.4% to 8.4% of the full-FOV value, consistent with the relative number of active focal spots (7.6%). For image sequences with a moving catheter, PSD was 33.6% to 34.8% of the full-FOV value. The root-mean-squared-deviation between DEC-based 3D tracking coordinates and full-FOV 3D tracking coordinates was less than 0.1 mm. The 3D distance between the tracked tip and the sheath centerline averaged 0.75 mm. Dynamic electronic collimation can reduce dose with minimal change in tracking performance.

  9. Monitoring an eruption fissure in 3D: video recording, particle image velocimetry and dynamics

    NASA Astrophysics Data System (ADS)

    Witt, Tanja; Walter, Thomas R.

    2015-04-01

    The processes during an eruption are very complex. To get a better understanding several parameters are measured. One of the measured parameters is the velocity of particles and patterns, as ash and emitted magma, and of the volcano itself. The resulting velocity field provides insights into the dynamics of a vent. Here we test our algorithm for 3 dimensional velocity fields on videos of the second fissure eruption of Bárdarbunga 2014. There we acquired videos from lava fountains of the main fissure with 2 high speed cameras with small angles between the cameras. Additionally we test the algorithm on videos from the geyser Strokkur, where we had 3 cameras and larger angles between the cameras. The velocity is calculated by a correlation in the Fourier space of contiguous images. Considering that we only have the velocity field of the surface smaller angles result in a better resolution of the existing velocity field in the near field. For general movements also larger angles can be useful, e.g. to get the direction, height and velocity of eruption clouds. In summary, it can be stated that 3D velocimetry can be used for several application and with different setup due to the application.

  10. 3D Particle-In-Cell (PIC) simulations of plasma sheath formation above lunar craters

    NASA Astrophysics Data System (ADS)

    Likhanskii, A.; Poppe, A. R.; Piquette, M.; Amyx, K.; Messmer, P.; Horanyi, M.

    2010-12-01

    Comprehensive investigation of plasma sheath formation and consequent dust levitation on lunar surface is important for interpretation of results of future lunar missions (such as LADEE and ARTEMIS). Until recently, most of such studies were done in experimental laboratories at reduced scales. Due to the complexity and nonlinearity of the problem, only simplified theories, describing this effect, were developed. However, recent progress in high-performance kinetic plasma simulations allowed tackling the problem of plasma sheath formation numerically. In this poster we will present the simulation results of plasma sheath formation above the lunar craters in presence of solar wind and photoelectron emission. These results were obtained using 3D Particle-In-Cell (PIC) code VORPAL. In the simulations we considered plasma sheath formation for normal, 45 and 90 degree incidence solar wind. Sample distribution of electric field in plasma sheath is shown in Figure 1. In the second part of the poster, we will present results of simulations of the LASP (Laboratory for Atmospheric and Space Physics at University of Colorado) experiments on study of plasma sheath formation above hemispherical isolated dimple. Figure 1. Electric field distribution in the plasma sheath above the lunar crater

  11. Apparent subdiffusion inherent to single particle tracking.

    PubMed Central

    Martin, Douglas S; Forstner, Martin B; Käs, Josef A

    2002-01-01

    Subdiffusion and its causes in both in vivo and in vitro lipid membranes have become the focus of recent research. We report apparent subdiffusion, observed via single particle tracking (SPT), in a homogeneous system that only allows normal diffusion (a DMPC monolayer in the fluid state). The apparent subdiffusion arises from slight errors in finding the actual particle position due to noise inherent in all experimental SPT systems. A model is presented that corrects this artifact, and predicts the time scales after which the effect becomes negligible. The techniques and results presented in this paper should be of use in all SPT experiments studying normal and anomalous diffusion. PMID:12324428

  12. Apparent subdiffusion inherent to single particle tracking.

    PubMed

    Martin, Douglas S; Forstner, Martin B; Käs, Josef A

    2002-10-01

    Subdiffusion and its causes in both in vivo and in vitro lipid membranes have become the focus of recent research. We report apparent subdiffusion, observed via single particle tracking (SPT), in a homogeneous system that only allows normal diffusion (a DMPC monolayer in the fluid state). The apparent subdiffusion arises from slight errors in finding the actual particle position due to noise inherent in all experimental SPT systems. A model is presented that corrects this artifact, and predicts the time scales after which the effect becomes negligible. The techniques and results presented in this paper should be of use in all SPT experiments studying normal and anomalous diffusion. PMID:12324428

  13. Fast and accurate global multiphase arrival tracking: the irregular shortest-path method in a 3-D spherical earth model

    NASA Astrophysics Data System (ADS)

    Huang, Guo-Jiao; Bai, Chao-Ying; Greenhalgh, Stewart

    2013-09-01

    The traditional grid/cell-based wavefront expansion algorithms, such as the shortest path algorithm, can only find the first arrivals or multiply reflected (or mode converted) waves transmitted from subsurface interfaces, but cannot calculate the other later reflections/conversions having a minimax time path. In order to overcome the above limitations, we introduce the concept of a stationary minimax time path of Fermat's Principle into the multistage irregular shortest path method. Here we extend it from Cartesian coordinates for a flat earth model to global ray tracing of multiple phases in a 3-D complex spherical earth model. The ray tracing results for 49 different kinds of crustal, mantle and core phases show that the maximum absolute traveltime error is less than 0.12 s and the average absolute traveltime error is within 0.09 s when compared with the AK135 theoretical traveltime tables for a 1-D reference model. Numerical tests in terms of computational accuracy and CPU time consumption indicate that the new scheme is an accurate, efficient and a practical way to perform 3-D multiphase arrival tracking in regional or global traveltime tomography.

  14. Three-dimensional single-particle tracking in live cells: news from the third dimension

    NASA Astrophysics Data System (ADS)

    Dupont, A.; Gorelashvili, M.; Schüller, V.; Wehnekamp, F.; Arcizet, D.; Katayama, Y.; Lamb, D. C.; Heinrich, D.

    2013-07-01

    Single-particle tracking (SPT) is of growing importance in the biophysical community. It is used to investigate processes such as drug and gene delivery, viral uptake, intracellular trafficking or membrane-bound protein mobility. Traditionally, SPT is performed in two dimensions (2D) because of its technical simplicity. However, life occurs in three dimensions (3D) and many methods have been recently developed to track particles in 3D. Now, is the third dimension worth the effort? Here we investigate the differences between the 2D and 3D analyses of intracellular transport with the 3D development of a time-resolved mean square displacement (MSD) analysis introduced previously. The 3D trajectories, and the 2D projections, of fluorescent nanoparticles were obtained with an orbital tracking microscope in two different cell types: in Dictyostelium discoideum ameba and in adherent, more flattened HuH-7 human cells. As expected from the different 3D organization of both cells’ cytoskeletons, a third of the active transport was lost upon projection in the ameba whereas the identification of the active phases was barely affected in the HuH-7 cells. In both cell types, we found intracellular diffusion to be anisotropic and the diffusion coefficient values derived from the 2D analysis were therefore biased.

  15. Surface processes on the asteroid deduced from the external 3D shapes and surface features of Itokawa particles

    NASA Astrophysics Data System (ADS)

    Tsuchiyama, A.; Matsumoto, T.

    2015-10-01

    Particles on the surface of S-type Asteroid 25143 Itokawa were successfully recovered by the Hayabusa mission of JAXA (e.g., [1,2]). They are not only the first samples recovered from an asteroid, but also the second extraterrestrial regolith to have been sampled, the first being the Moon by Apollo and Luna missions. The analysis of tiny sample particles (20-200 μm) shows that the Itokawa surface material is consistent with LL chondrites suffered by space weathering as expected and brought an end to the origin of meteorites (e.g., [2-4]). In addition, the examination of Itokawa particles allow studies of surface processes on the asteroid because regolith particles can be regarded as an interface with the space environment, where the impacts of small objects and irradiation by the solar wind and galactic cosmic rays should have been recorded. External 3D shapes and surface features of Itokawa regolith particles were examined. Two kinds of surface modification, formation of space-weathering rims mainly by solar wind implantation and surface abrasion by grain migration, were recognized. Spectral change of the asteroid proceeded by formation of space-weathering rims and refreshment of the regolith surfaces. External 3D shapes and surface morphologies of the regolith particles can provide information about formation and evolution history of regolith particles in relation to asteroidal surface processes. 3D shapes of Itokawa regolith particles were obtained using microtomography [3]. The surface nanomiromorpholgy of Itokawa particles were also observed using FE-SEM [5]. However, the number of particles was limited and genial feature on the surface morphology has not been understood. In this study, the surface morphology of Itokawa regolith particles was systematically investigated together with their 3D structures.

  16. XEDS STEM Tomography For 3D Chemical Characterization Of Nanoscale Particles

    SciTech Connect

    Genc, Arda; Kovarik, Libor; Gu, Meng; Cheng, Huikai; Plachinda, Pavel; Pullan, Lee; Freitag, Bert; Wang, Chong M.

    2013-08-01

    We present a tomography technique which couples scanning transmission electron microscopy (STEM) and X-ray energy dispersive spectrometry (XEDS) to resolve 3D distribution of elements in nanoscale materials. STEM imaging when combined with a symmetrically arranged XEDS detector design around the specimen overcomes many of the obstacles in 3D spectroscopic tomography of nanoscale materials and successfully elucidate the 3D chemical information in a large field of view of the TEM sample. We employed this technique to investigate 3D distribution of Nickel (Ni), Manganese (Mn) and Oxygen (O) in Li(NiMn)O2 battery cathode material. For this purpose, 2D elemental maps were acquired for a range of tilt angles and reconstructed to obtain 3D elemental distribution in an isolated Li(NiMnO2) nanoparticle. The results highlight the strength of this technique in 3D chemical analysis of nanoscale materials by successfully resolving Ni, Mn and O elemental distributions in 3D and discovering the new phenomenon of Ni surface segregation in this material. Furthermore, the comparison of simultaneously acquired HAADF STEM and XEDS STEM tomography results show that XEDS STEM tomography provides additional 3D chemical information of the material especially when there is low atomic number (Z) contrast in the material of interest.

  17. A quantitative study of 3D-scanning frequency and Δd of tracking points on the tooth surface

    PubMed Central

    Li, Hong; Lyu, Peijun; Sun, Yuchun; Wang, Yong; Liang, Xiaoyue

    2015-01-01

    Micro-movement of human jaws in the resting state might influence the accuracy of direct three-dimensional (3D) measurement. Providing a reference for sampling frequency settings of intraoral scanning systems to overcome this influence is important. In this study, we measured micro-movement, or change in distance (∆d), as the change in position of a single tracking point from one sampling time point to another in five human subjects. ∆d of tracking points on incisors at 7 sampling frequencies was judged against the clinical accuracy requirement to select proper sampling frequency settings. The curve equation was then fit quantitatively between ∆d median and the sampling frequency to predict the trend of ∆d with increasing f. The difference of ∆d among the subjects and the difference between upper and lower incisor feature points of the same subject were analyzed by a non-parametric test (α = 0.05). Significant differences of incisor feature points were noted among different subjects and between upper and lower jaws of the same subject (P < 0.01). Overall, ∆d decreased with increasing frequency. When the frequency was 60 Hz, ∆d nearly reached the clinical accuracy requirement. Frequencies higher than 60 Hz did not significantly decrease Δd further. PMID:26400112

  18. Python algorithms in particle tracking microrheology

    PubMed Central

    2012-01-01

    Background Particle tracking passive microrheology relates recorded trajectories of microbeads, embedded in soft samples, to the local mechanical properties of the sample. The method requires intensive numerical data processing and tools allowing control of the calculation errors. Results We report the development of a software package collecting functions and scripts written in Python for automated and manual data processing, to extract viscoelastic information about the sample using recorded particle trajectories. The resulting program package analyzes the fundamental diffusion characteristics of particle trajectories and calculates the frequency dependent complex shear modulus using methods published in the literature. In order to increase conversion accuracy, segmentwise, double step, range-adaptive fitting and dynamic sampling algorithms are introduced to interpolate the data in a splinelike manner. Conclusions The presented set of algorithms allows for flexible data processing for particle tracking microrheology. The package presents improved algorithms for mean square displacement estimation, controlling effects of frame loss during recording, and a novel numerical conversion method using segmentwise interpolation, decreasing the conversion error from about 100% to the order of 1%. PMID:23186362

  19. Three-dimensional textural and compositional analysis of particle tracks and fragmentation history in aerogel

    SciTech Connect

    Ebel, Denton S.; Greenberg, Michael; Rivers, Mark L.; Newville, Matthew

    2010-05-04

    We report analyses of aerogel tracks using (1) synchrotron X-ray computed microtomography (XRCMT), (2) laser confocal scanning microscopy (LCSM), and (3) synchrotron radiation X-ray fluorescence (SRXRF) of particles and their paths resulting from simulated hypervelocity impacts (1-2), and a single {approx}1 mm aerogel track from the Stardust cometary sample collector (1-3). Large aerogel pieces can be imaged sequentially, resulting in high spatial resolution images spanning many tomographic fields of view ('lambda-tomography'). We report calculations of energy deposited, and tests on aromatic hydrocarbons showing no alteration in tomography experiments. Imaging at resolutions from -17 to -1 micron/pixel edge (XRCMT) and to <100 nm/pixel edge (LCSM) illustrates track geometry and interaction of particles with aerogel, including rifling, particle fragmentation, and final particle location. We present a 3-D deconvolution method using an estimated point-spread function for aerogel, allowing basic corrections of LCSM data for axial distortion. LCSM allows rapid, comprehensive, non-destructive, high information return analysis of tracks in aerogel keystones, prior to destructive grain extraction. SRXRF with LCSM allows spatial correlation of grain size, chemical, and mineralogical data. If optical methods are precluded in future aerogel capture missions, XRCMT is a viable 3D imaging technique. Combinations of these methods allow for complete, nondestructive, quantitative 3-D analysis of captured materials at high spatial resolution. This data is fundamental to understanding the hypervelocity particle-aerogel interaction histories of Stardust grains.

  20. Extending particle tracking capability with Delaunay triangulation.

    PubMed

    Chen, Kejia; Anthony, Stephen M; Granick, Steve

    2014-04-29

    Particle tracking, the analysis of individual moving elements in time series of microscopic images, enables burgeoning new applications, but there is need to better resolve conformation and dynamics. Here we describe the advantages of Delaunay triangulation to extend the capabilities of particle tracking in three areas: (1) discriminating irregularly shaped objects, which allows one to track items other than point features; (2) combining time and space to better connect missing frames in trajectories; and (3) identifying shape backbone. To demonstrate the method, specific examples are given, involving analyzing the time-dependent molecular conformations of actin filaments and λ-DNA. The main limitation of this method, shared by all other clustering techniques, is the difficulty to separate objects when they are very close. This can be mitigated by inspecting locally to remove edges that are longer than their neighbors and also edges that link two objects, using methods described here, so that the combination of Delaunay triangulation with edge removal can be robustly applied to processing large data sets. As common software packages, both commercial and open source, can construct Delaunay triangulation on command, the methods described in this paper are both computationally efficient and easy to implement. PMID:24734998

  1. 3-D turbulent particle dispersion submodel development. Quarterly progress report No. 1, 5 April--5 July 1991

    SciTech Connect

    Smith, P.J.

    1991-12-31

    The lack of a mathematical description of the interactions of fluid turbulence with other physics-chemical processes is a major obstacle in modeling many industrial program. Turbulent two-phase flow is a phenomenon that is of significant practical importance to coal combustion as well as other disciplines. The interactions of fluid turbulence with the particulate phase has yet to be accurately and efficiently modeled for these industrial applications. On 15 May 1991 work was initiated to cover four major tasks toward the development of a computational submodel for turbulent particle dispersion that would be applicable to coal combustion simulations. Those four tasks are: 1. A critical evaluation of the 2-D Lagrangian particle dispersion submodel, 2. Development of a 3-D submodel for turbulent particle dispersion, 3. Evaluation of the 3-D submodel for turbulent particle dispersion, 4.Exploration of extensions of the Lagrangian dispersion theory to other applications including chemistry-turbulence interactions.

  2. 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.

  3. Synthesis of micro-sized shell-isolated 3D plasmonic superstructures for in situ single-particle SERS monitoring.

    PubMed

    Zhang, Kun; Zhao, Jingjing; Ji, Ji; Liu, Baohong

    2016-04-21

    A single-particle SERS system enabling real-time and in situ observation of Au-catalyzed reactions has been developed. Both the catalytic activity and the SERS effect are coupled into a single bi-functional 3D superstructure comprising Au nanosatellites self-assembled onto a shell-insulated Ag microflower core, which eliminates the interference from photocatalysis. PMID:27044886

  4. Particle tracking by full-field complex wavefront subtraction in digital holography microscopy.

    PubMed

    Miccio, L; Memmolo, P; Merola, F; Fusco, S; Embrione, V; Paciello, A; Ventre, M; Netti, P A; Ferraro, P

    2014-03-21

    The 3D tracking of micro-objects, based on digital holography, is proposed through the analysis of the complex wavefront of the light scattered by the micro-samples. Exploiting the advantages of the off-axis full-field holographic interferometry, the tracking of multiple objects is achieved by a direct wavefront analysis at the focal plane overcoming the limitation of the conventional back focal plane interferometry in which only one object at a time can be tracked. Furthermore, the method proposed and demonstrated here is a step forward with respect to other holographic tracking tools. The approach is tested in two experiments, the first investigates the Brownian motion of particles trapped by holographic optical tweezers, while the second relates to the cell motility in a 3D collagen matrix, thus showing its usefulness for lab-on-chip systems in typical bioassay testing. PMID:24463986

  5. Prospective motion correction of 3D echo-planar imaging data for functional MRI using optical tracking

    PubMed Central

    Todd, Nick; Josephs, Oliver; Callaghan, Martina F.; Lutti, Antoine; Weiskopf, Nikolaus

    2015-01-01

    We evaluated the performance of an optical camera based prospective motion correction (PMC) system in improving the quality of 3D echo-planar imaging functional MRI data. An optical camera and external marker were used to dynamically track the head movement of subjects during fMRI scanning. PMC was performed by using the motion information to dynamically update the sequence's RF excitation and gradient waveforms such that the field-of-view was realigned to match the subject's head movement. Task-free fMRI experiments on five healthy volunteers followed a 2 × 2 × 3 factorial design with the following factors: PMC on or off; 3.0 mm or 1.5 mm isotropic resolution; and no, slow, or fast head movements. Visual and motor fMRI experiments were additionally performed on one of the volunteers at 1.5 mm resolution comparing PMC on vs PMC off for no and slow head movements. Metrics were developed to quantify the amount of motion as it occurred relative to k-space data acquisition. The motion quantification metric collapsed the very rich camera tracking data into one scalar value for each image volume that was strongly predictive of motion-induced artifacts. The PMC system did not introduce extraneous artifacts for the no motion conditions and improved the time series temporal signal-to-noise by 30% to 40% for all combinations of low/high resolution and slow/fast head movement relative to the standard acquisition with no prospective correction. The numbers of activated voxels (p < 0.001, uncorrected) in both task-based experiments were comparable for the no motion cases and increased by 78% and 330%, respectively, for PMC on versus PMC off in the slow motion cases. The PMC system is a robust solution to decrease the motion sensitivity of multi-shot 3D EPI sequences and thereby overcome one of the main roadblocks to their widespread use in fMRI studies. PMID:25783205

  6. Particle path tracking method in two- and three-dimensional continuously rotating detonation engines

    NASA Astrophysics Data System (ADS)

    Zhou, Rui; Wu, Dan; Liu, Yan; Wang, Jian-Ping

    2014-12-01

    The particle path tracking method is proposed and used in two-dimensional (2D) and three-dimensional (3D) numerical simulations of continuously rotating detonation engines (CRDEs). This method is used to analyze the combustion and expansion processes of the fresh particles, and the thermodynamic cycle process of CRDE. In a 3D CRDE flow field, as the radius of the annulus increases, the no-injection area proportion increases, the non-detonation proportion decreases, and the detonation height decreases. The flow field parameters on the 3D mid annulus are different from in the 2D flow field under the same chamber size. The non-detonation proportion in the 3D flow field is less than in the 2D flow field. In the 2D and 3D CRDE, the paths of the flow particles have only a small fluctuation in the circumferential direction. The numerical thermodynamic cycle processes are qualitatively consistent with the three ideal cycle models, and they are right in between the ideal F—J cycle and ideal ZND cycle. The net mechanical work and thermal efficiency are slightly smaller in the 2D simulation than in the 3D simulation. In the 3D CRDE, as the radius of the annulus increases, the net mechanical work is almost constant, and the thermal efficiency increases. The numerical thermal efficiencies are larger than F—J cycle, and much smaller than ZND cycle.

  7. Particle entry through sash in the magnetopause with a dawndard IMF as simulated by a 3-D EM particle code

    NASA Astrophysics Data System (ADS)

    Cai, D.; Yan, X.; Lembege, B.; Nishikawa, K.

    2003-12-01

    We report a new progress in the long-term effort to represent the global interaction of the solar wind with the Earth's magnetosphere using a three-dimensional electromagnetic particle code with the improved resolutions using the HPF Tristan code. After a quasi-steady state is established with an unmagnetized solar wind we gradually switch on a northward interplanetary magnetic field (IMF), which causes a magnetic reconnection at the nightside cusps and the magnetosphere to be depolarized. In the case that the northward IMF is switched gradually to dawnward, there is no signature of reconnection in the near-Earth magnetotail as in the case with the southward turning. On the contrary analysis of magnetic fields in the magnetopause confirms a signature of magnetic reconnection at both the dawnside and duskside. And the plasma sheet in the near-Earth magnetotail clearly thins as in the case of southward turning. Arrival of dawnward IMF to the magnetopause creates a reconnection groove which cause particle entry into the deep region of the magnetosphere via field lines that go near the magnetopause. This deep connection is more fully recognized tailward of Earth. The flank weak-field fan joins onto the plasma sheet and the current sheet to form a geometrical feature called the cross-tail S that structurally integrates the magnetopause and the tail interior. This structure contributes to direct plasma entry between the magnetosheath to the inner magnetosphere and plasma sheet, in which the entry process heats the magnetosheath plasma to plasma sheet temperatures. These phenomena have been found by Cluster observations. Further investigation with Cluster observations will provide new insights for unsolved problems such as hot flow anomalies (HFAs), substorms, and storm-substorm relationship. 3-D movies with sash structure will be presented at the meeting.

  8. Orbital single particle tracking on a commercial confocal microscope using piezoelectric stage feedback

    NASA Astrophysics Data System (ADS)

    Lanzanò, L.; Gratton, E.

    2014-06-01

    Single Particle Tracking (SPT) is a technique used to locate fluorescent particles with nanometer precision. In the orbital tracking method the position of a particle is obtained analyzing the distribution of intensity along a circular orbit scanned around the particle. In combination with an active feedback this method allows tracking of particles in 2D and 3D with millisecond temporal resolution. Here we describe a SPT setup based on a feedback approach implemented with minimal modification of a commercially available confocal laser scanning microscope, the Zeiss LSM 510, in combination with an external piezoelectric stage scanner. The commercial microscope offers the advantage of a user-friendly software interface and pre-calibrated hardware components. The use of an external piezo-scanner allows the addition of feedback into the system but also represents a limitation in terms of its mechanical response. We describe in detail this implementation of the orbital tracking method and discuss advantages and limitations. As an example of application to live cell experiments we perform the 3D tracking of acidic vesicles in live polarized epithelial cells.

  9. Objective comparison of particle tracking methods.

    PubMed

    Chenouard, Nicolas; Smal, Ihor; de Chaumont, Fabrice; Maška, Martin; Sbalzarini, Ivo F; Gong, Yuanhao; Cardinale, Janick; Carthel, Craig; Coraluppi, Stefano; Winter, Mark; Cohen, Andrew R; Godinez, William J; Rohr, Karl; Kalaidzidis, Yannis; Liang, Liang; Duncan, James; Shen, Hongying; Xu, Yingke; Magnusson, Klas E G; Jaldén, Joakim; Blau, Helen M; Paul-Gilloteaux, Perrine; Roudot, Philippe; Kervrann, Charles; Waharte, François; Tinevez, Jean-Yves; Shorte, Spencer L; Willemse, Joost; Celler, Katherine; van Wezel, Gilles P; Dan, Han-Wei; Tsai, Yuh-Show; Ortiz de Solórzano, Carlos; Olivo-Marin, Jean-Christophe; Meijering, Erik

    2014-03-01

    Particle tracking is of key importance for quantitative analysis of intracellular dynamic processes from time-lapse microscopy image data. Because manually detecting and following large numbers of individual particles is not feasible, automated computational methods have been developed for these tasks by many groups. Aiming to perform an objective comparison of methods, we gathered the community and organized an open competition in which participating teams applied their own methods independently to a commonly defined data set including diverse scenarios. Performance was assessed using commonly defined measures. Although no single method performed best across all scenarios, the results revealed clear differences between the various approaches, leading to notable practical conclusions for users and developers. PMID:24441936

  10. Collider ring particle loss tracking with SSCTRK

    SciTech Connect

    Garavaglia, T.; Kauffmann, S.K.; Stiening, R.

    1990-04-01

    The SSCTRK numerical simulation tracking code has been used to study the benefit of increasing the SSC dipole magnet aperture from 4 to 5 cm. This study has been carried out for both hypothetical highly corrected and plausibly corrected machines, the former having no systematic multipole errors and chromaticity identically zero. The choice of tune values, phase advance per cell, random multipole errors, systematic multipole errors and chromaticity (for the plausibly corrected machines), closed orbit error, the criterion for particle loss, etc. are set forth in detail. Runs of 10{sup 5} turns and 3 {times} 10{sup 6} turns are presented together with the approximate dynamic apertures they yield from their particle loss patterns.

  11. Objective comparison of particle tracking methods

    PubMed Central

    Chenouard, Nicolas; Smal, Ihor; de Chaumont, Fabrice; Maška, Martin; Sbalzarini, Ivo F.; Gong, Yuanhao; Cardinale, Janick; Carthel, Craig; Coraluppi, Stefano; Winter, Mark; Cohen, Andrew R.; Godinez, William J.; Rohr, Karl; Kalaidzidis, Yannis; Liang, Liang; Duncan, James; Shen, Hongying; Xu, Yingke; Magnusson, Klas E. G.; Jaldén, Joakim; Blau, Helen M.; Paul-Gilloteaux, Perrine; Roudot, Philippe; Kervrann, Charles; Waharte, François; Tinevez, Jean-Yves; Shorte, Spencer L.; Willemse, Joost; Celler, Katherine; van Wezel, Gilles P.; Dan, Han-Wei; Tsai, Yuh-Show; de Solórzano, Carlos Ortiz; Olivo-Marin, Jean-Christophe; Meijering, Erik

    2014-01-01

    Particle tracking is of key importance for quantitative analysis of intracellular dynamic processes from time-lapse microscopy image data. Since manually detecting and following large numbers of individual particles is not feasible, automated computational methods have been developed for these tasks by many groups. Aiming to perform an objective comparison of methods, we gathered the community and organized, for the first time, an open competition, in which participating teams applied their own methods independently to a commonly defined data set including diverse scenarios. Performance was assessed using commonly defined measures. Although no single method performed best across all scenarios, the results revealed clear differences between the various approaches, leading to important practical conclusions for users and developers. PMID:24441936

  12. Simultaneous tracking of 3D actin and microtubule strains in individual MLO-Y4 osteocytes under oscillatory flow.

    PubMed

    Baik, Andrew D; Qiu, Jun; Hillman, Elizabeth M C; Dong, Cheng; Guo, X Edward

    2013-02-22

    Osteocytes in vivo experience complex fluid shear flow patterns to activate mechanotransduction pathways. The actin and microtubule (MT) cytoskeletons have been shown to play an important role in the osteocyte's biochemical response to fluid shear loading. The dynamic nature of physiologically relevant fluid flow profiles (i.e., 1Hz oscillatory flow) impedes the ability to image and study both actin and MT cytoskeletons simultaneously in the same cell with high spatiotemporal resolution. To overcome these limitations, a multi-channel quasi-3D microscopy technique was developed to track the actin and MT networks simultaneously under steady and oscillatory flow. Cells displayed high intercellular variability and intracellular cytoskeletal variability in strain profiles. Shear Exz was the predominant strain in both steady and oscillatory flows in the form of viscoelastic creep and elastic oscillations, respectively. Dramatic differences were seen in oscillatory flow, however. The actin strains displayed an oscillatory strain profile more often than the MT networks in all the strains tested and had a higher peak-to-trough strain magnitude. Taken together, the actin networks are the more responsive cytoskeletal networks in osteocytes under oscillatory flow and may play a bigger role in mechanotransduction pathway activation and regulation. PMID:23352617

  13. Particle displacement tracking applied to air flows

    NASA Technical Reports Server (NTRS)

    Wernet, Mark P.

    1991-01-01

    Electronic Particle Image Velocimeter (PIV) techniques offer many advantages over conventional photographic PIV methods such as fast turn around times and simplified data reduction. A new all electronic PIV technique was developed which can measure high speed gas velocities. The Particle Displacement Tracking (PDT) technique employs a single cw laser, small seed particles (1 micron), and a single intensified, gated CCD array frame camera to provide a simple and fast method of obtaining two-dimensional velocity vector maps with unambiguous direction determination. Use of a single CCD camera eliminates registration difficulties encountered when multiple cameras are used to obtain velocity magnitude and direction information. An 80386 PC equipped with a large memory buffer frame-grabber board provides all of the data acquisition and data reduction operations. No array processors of other numerical processing hardware are required. Full video resolution (640x480 pixel) is maintained in the acquired images, providing high resolution video frames of the recorded particle images. The time between data acquisition to display of the velocity vector map is less than 40 sec. The new electronic PDT technique is demonstrated on an air nozzle flow with velocities less than 150 m/s.

  14. 3D image reconstruction algorithms for cryo-electron-microscopy images of virus particles

    NASA Astrophysics Data System (ADS)

    Doerschuk, Peter C.; Johnson, John E.

    2000-11-01

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

  15. 2.9 Å Resolution Cryo-EM 3D Reconstruction of Close-Packed Virus Particles.

    PubMed

    Liu, Zheng; Guo, Fei; Wang, Feng; Li, Tian-Cheng; Jiang, Wen

    2016-02-01

    Single-particle cryoelectron microscopy typically discards close-packed particle images as unusable data. Here, we report an image processing strategy and case study of obtaining near-atomic resolution 3D reconstructions from close-packed particles. Multiple independent de novo initial models were constructed to determine and cross-validate the particle parameters. The particles with consistent views were further refined including not only Euler angles and center positions but also defocus, astigmatism, beam tilt, and overall and anisotropic magnification. We demonstrated this strategy with a 2.9 Å resolution reconstruction of a 1.67 MDa virus-like particle of a circovirus, PCV2, recorded on 86 photographic films. The map resolution was further validated with a phase-randomization test and local resolution assessment, and the atomic model was validated with MolProbity and EMRinger. Close-packed virus particles were thus shown not only to be useful for high-resolution 3D reconstructions but also to allow data collection at significantly improved throughput for near-atomic resolution reconstructions. PMID:26777413

  16. Enabling Lorentz boosted frame particle-in-cell simulations of laser wakefield acceleration in quasi-3D geometry

    NASA Astrophysics Data System (ADS)

    Yu, Peicheng; Xu, Xinlu; Davidson, Asher; Tableman, Adam; Dalichaouch, Thamine; Li, Fei; Meyers, Michael D.; An, Weiming; Tsung, Frank S.; Decyk, Viktor K.; Fiuza, Frederico; Vieira, Jorge; Fonseca, Ricardo A.; Lu, Wei; Silva, Luis O.; Mori, Warren B.

    2016-07-01

    When modeling laser wakefield acceleration (LWFA) using the particle-in-cell (PIC) algorithm in a Lorentz boosted frame, the plasma is drifting relativistically at βb c towards the laser, which can lead to a computational speedup of ∼ γb2 = (1 - βb2)-1. Meanwhile, when LWFA is modeled in the quasi-3D geometry in which the electromagnetic fields and current are decomposed into a limited number of azimuthal harmonics, speedups are achieved by modeling three dimensional (3D) problems with the computational loads on the order of two dimensional r - z simulations. Here, we describe a method to combine the speedups from the Lorentz boosted frame and quasi-3D algorithms. The key to the combination is the use of a hybrid Yee-FFT solver in the quasi-3D geometry that significantly mitigates the Numerical Cerenkov Instability (NCI) which inevitably arises in a Lorentz boosted frame due to the unphysical coupling of Langmuir modes and EM modes of the relativistically drifting plasma in these simulations. In addition, based on the space-time distribution of the LWFA data in the lab and boosted frame, we propose to use a moving window to follow the drifting plasma, instead of following the laser driver as is done in the LWFA lab frame simulations, in order to further reduce the computational loads. We describe the details of how the NCI is mitigated for the quasi-3D geometry, the setups for simulations which combine the Lorentz boosted frame, quasi-3D geometry, and the use of a moving window, and compare the results from these simulations against their corresponding lab frame cases. Good agreement is obtained among these sample simulations, particularly when there is no self-trapping, which demonstrates it is possible to combine the Lorentz boosted frame and the quasi-3D algorithms when modeling LWFA. We also discuss the preliminary speedups achieved in these sample simulations.

  17. 3D flow visualization and tomographic particle image velocimetry for vortex breakdown over a non-slender delta wing

    NASA Astrophysics Data System (ADS)

    Wang, ChengYue; Gao, Qi; Wei, RunJie; Li, Tian; Wang, JinJun

    2016-06-01

    Volumetric measurement for the leading-edge vortex (LEV) breakdown of a delta wing has been conducted by three-dimensional (3D) flow visualization and tomographic particle image velocimetry (TPIV). The 3D flow visualization is employed to show the vortex structures, which was recorded by four cameras with high resolution. 3D dye streaklines of the visualization are reconstructed using a similar way of particle reconstruction in TPIV. Tomographic PIV is carried out at the same time using same cameras with the dye visualization. Q criterion is employed to identify the LEV. Results of tomographic PIV agree well with the reconstructed 3D dye streaklines, which proves the validity of the measurements. The time-averaged flow field based on TPIV is shown and described by sections of velocity and streamwise vorticity. Combining the two measurement methods sheds light on the complex structures of both bubble type and spiral type of breakdown. The breakdown position is recognized by investigating both the streaklines and TPIV velocity fields. Proper orthogonal decomposition is applied to extract a pair of conjugated helical instability modes from TPIV data. Therefore, the dominant frequency of the instability modes is obtained from the corresponding POD coefficients of the modes based on wavelet transform analysis.

  18. 3D Characterization of Transmitral Vortex using Defocusing Digital Particle Image Velocimetry

    NASA Astrophysics Data System (ADS)

    Falahatpisheh, Ahmad; Dueitt, Brandon; Pahlevan, Niema; Kheradvar, Arash

    2011-11-01

    In this study, we have experimentally characterized the 3D vortex passing through a physiologically relevant model of mitral valve using Defocusing Digital PIV (DDPIV). The valve model was made of soft silicone with diameter of 25 mm , similar to the adult mitral valve. The mitral model possesses a large anterior and a small posterior leaflet that results in asymmetric formation of transmitral vortex. A piston-cylinder mechanism drives the flow and travels to produce a range of L / D from 2 to 6. We have characterized the shape of the 3D vortex forming through the D-shaped orifice of a mitral valve using DDPIV technique. The evolution of the vortex has been illustrated for different stroke ratios.

  19. Synthesis of micro-sized shell-isolated 3D plasmonic superstructures for in situ single-particle SERS monitoring

    NASA Astrophysics Data System (ADS)

    Zhang, Kun; Zhao, Jingjing; Ji, Ji; Liu, Baohong

    2016-04-01

    A single-particle SERS system enabling real-time and in situ observation of Au-catalyzed reactions has been developed. Both the catalytic activity and the SERS effect are coupled into a single bi-functional 3D superstructure comprising Au nanosatellites self-assembled onto a shell-insulated Ag microflower core, which eliminates the interference from photocatalysis.A single-particle SERS system enabling real-time and in situ observation of Au-catalyzed reactions has been developed. Both the catalytic activity and the SERS effect are coupled into a single bi-functional 3D superstructure comprising Au nanosatellites self-assembled onto a shell-insulated Ag microflower core, which eliminates the interference from photocatalysis. Electronic supplementary information (ESI) available: Details of the synthesis and characterization of the Ag@SiO2@Au superstructures (SEM and TEM images, UV/vis and SERS spectra). See DOI: 10.1039/c6nr00278a

  20. Development of a 3D to 1D Particle Transport Model to Predict Deposition in the Lungs

    NASA Astrophysics Data System (ADS)

    Oakes, Jessica M.; Grandmont, Celine; Shadden, Shawn C.; Vignon-Clementel, Irene E.

    2014-11-01

    Aerosolized particles are commonly used for therapeutic drug delivery as they can be delivered to the body systemically or be used to treat lung diseases. Recent advances in computational resources have allowed for sophisticated pulmonary simulations, however it is currently impossible to solve for airflow and particle transport for all length and time scales of the lung. Instead, multi-scale methods must be used. In our recent work, where computational methods were employed to solve for airflow and particle transport in the rat airways (Oakes et al. (2014), Annals of Biomedical Engineering 42, 899), the number of particles to exit downstream of the 3D domain was determined. In this current work, the time-dependent Lagrangian description of particles was used to numerically solve a 1D convection-diffusion model (trumpet model, Taulbee and Yu (1975), Journal of Applied Physiology, 38, 77) parameterized specifically for the lung. The expansion of the airway dimensions was determined based on data collected from our aerosol exposure experiments (Oakes et al. (2014), Journal of Applied Physiology, 116, 1561). This 3D-1D framework enables us to predict the fate of particles in the whole lung. This work was supported by the Whitaker Foundation at the IIE, a INRIA Associated Team Postdoc Grant, and a UC Presidential Fellowship.

  1. 3D real-time visualization of blood flow in cerebral aneurysms by light field particle image velocimetry

    NASA Astrophysics Data System (ADS)

    Carlsohn, Matthias F.; Kemmling, André; Petersen, Arne; Wietzke, Lennart

    2016-04-01

    Cerebral aneurysms require endovascular treatment to eliminate potentially lethal hemorrhagic rupture by hemostasis of blood flow within the aneurysm. Devices (e.g. coils and flow diverters) promote homeostasis, however, measurement of blood flow within an aneurysm or cerebral vessel before and after device placement on a microscopic level has not been possible so far. This would allow better individualized treatment planning and improve manufacture design of devices. For experimental analysis, direct measurement of real-time microscopic cerebrovascular flow in micro-structures may be an alternative to computed flow simulations. An application of microscopic aneurysm flow measurement on a regular basis to empirically assess a high number of different anatomic shapes and the corresponding effect of different devices would require a fast and reliable method at low cost with high throughout assessment. Transparent three dimensional 3D models of brain vessels and aneurysms may be used for microscopic flow measurements by particle image velocimetry (PIV), however, up to now the size of structures has set the limits for conventional 3D-imaging camera set-ups. On line flow assessment requires additional computational power to cope with the processing large amounts of data generated by sequences of multi-view stereo images, e.g. generated by a light field camera capturing the 3D information by plenoptic imaging of complex flow processes. Recently, a fast and low cost workflow for producing patient specific three dimensional models of cerebral arteries has been established by stereo-lithographic (SLA) 3D printing. These 3D arterial models are transparent an exhibit a replication precision within a submillimeter range required for accurate flow measurements under physiological conditions. We therefore test the feasibility of microscopic flow measurements by PIV analysis using a plenoptic camera system capturing light field image sequences. Averaging across a sequence of

  2. Hybrid MV-kV 3D respiratory motion tracking during radiation therapy with low imaging dose

    NASA Astrophysics Data System (ADS)

    Yan, Huagang; Li, Haiyun; Liu, Zhixiang; Nath, Ravinder; Liu, Wu

    2012-12-01

    A novel real-time adaptive MV-kV imaging framework for image-guided radiation therapy is developed to reduce the thoracic and abdominal tumor targeting uncertainty caused by respiration-induced intrafraction motion with ultra-low patient imaging dose. In our method, continuous stereoscopic MV-kV imaging is used at the beginning of a radiation therapy delivery for several seconds to measure the implanted marker positions. After this stereoscopic imaging period, the kV imager is switched off except for the times when no fiducial marker is detected in the cine-MV images. The 3D time-varying marker positions are estimated by combining the MV 2D projection data and the motion correlations between directional components of marker motion established from the stereoscopic imaging period and updated afterwards; in particular, the most likely position is assumed to be the position on the projection line that has the shortest distance to the first principal component line segment constructed from previous trajectory points. An adaptive windowed auto-regressive prediction is utilized to predict the marker position a short time later (310 ms and 460 ms in this study) to allow for tracking system latency. To demonstrate the feasibility and evaluate the accuracy of the proposed method, computer simulations were performed for both arc and fixed-gantry deliveries using 66 h of retrospective tumor motion data from 42 patients treated for thoracic or abdominal cancers. The simulations reveal that using our hybrid approach, a smaller than 1.2 mm or 1.5 mm root-mean-square tracking error can be achieved at a system latency of 310 ms or 460 ms, respectively. Because the kV imaging is only used for a short period of time in our method, extra patient imaging dose can be reduced by an order of magnitude compared to continuous MV-kV imaging, while the clinical tumor targeting accuracy for thoracic or abdominal cancers is maintained. Furthermore, no additional hardware is required with the

  3. DNA fragmentation by charged particle tracks

    NASA Astrophysics Data System (ADS)

    Stenerlöw, B.; Höglund, E.; Carlsson, J.

    High-LET (linear energy transfer) charged particles induce DNA double-strand breaks (DSB) in a non-random fashion in mammalian cells. The clustering of DSB, probably determined by track structure as well as chromatin conformation, results in an excess of small- and intermediate-sized DNA fragments. DNA fragmentation in normal human fibroblasts (GM5758) was analyzed by pulsed-field gel electrophoresis after irradiation with photons ( 60Co) or 125 keV/μm nitrogen ions. Compared to conventional DSB analysis, i.e. assays only measuring the fraction of DNA smaller than a single threshold, the relative biological effectiveness (RBE) for DSB induction increased with 100%. Further, the size distribution of DNA fragments showed a significant dependence on radiation quality, with an excess of fragments up to 1 Mbp. Irradiation of naked genomic DNA without histone proteins increased the DSB yields 25 and 13 times for photons and nitrogen ions, respectively. The results suggest possible roles of both track structure and chromatin organization in the distribution of DNA double-strand breaks along the chromosome.

  4. Recent improvements to the ASTRA particle tracking code

    SciTech Connect

    Flottmann, Klaus; Lidia, Steven; Piot, Philippe

    2003-05-19

    The Astra simulation code has been successfully used in the design of linac and rf photoinjector systems utilizing beams with azimuthal symmetry. We present recently implemented changes to Astra that allow tracking of beams in beamlines without the assumption of any symmetry. The changes especially include a 3D mesh space charge algorithm and the possibility to import 3D electromagnetic fieldmaps from eigensolver programs.

  5. 3D Unsteady Multiphase Simulation of Uranium Tetrafluoride Particle Fluorination in Fluidized Bed Pilot

    NASA Astrophysics Data System (ADS)

    Konan, N. A.; Neau, H.; Simonin, O.; Dupoizat, M.; Le Geaziou, T.

    This paper investigates Eulerian simulation approach of uranium hexafluoride production in fluidized bed pilot. Mass transfer is modeled by using the shrinking particle model. The model successfully predicts expected amount of uranium hexafluoride. As heat transfers with wall are neglected, temperature increases within the reactor and there is no gradient in wall-normal direction of reactor. External diffusion model of reactive gas around particle is developed. Effect of fluorine diffusion within nitrogen is found to be negligible under the simulation conditions. Moreover, inter-particle radiative heat transfer between particles of dense phase in the bed is investigated in the frame of Rosseland approximation.

  6. Dual-wavelength digital holography for 3D particle image velocimetry: experimental validation.

    PubMed

    Grare, S; Allano, D; Coëtmellec, S; Perret, G; Corbin, F; Brunel, M; Gréhan, G; Lebrun, D

    2016-01-20

    A multi-exposure digital in-line hologram of a particle field is recorded by two successive pulses of different wavelengths. During the reconstruction step, each recording can be independently analyzed by selecting a given wavelength. This procedure enables avoiding the superimposition of particle images that may be close to each other. PMID:26835957

  7. Fully 3D Particle-in-Cell Simulation of Double Post-Hole Convolute on PTS Facility

    NASA Astrophysics Data System (ADS)

    Zhao, Hailong; Dong, Ye; Zhou, Haijing; Zou, Wenkang; Institute of Fluid Physics Collaboration; Institute of Applied Physics; Computational Mathematics Collaboration

    2015-11-01

    In order to get better understand of energy transforming and converging process during High Energy Density Physics (HEDP) experiments, fully 3D particle-in-cell (PIC) simulation code NEPTUNE3D was used to provide numerical approach towards parameters which could hardly be acquired through diagnostics. Cubic region (34cm × 34cm × 18cm) including the double post-hole convolute (DPHC) on the primary test stand (PTS) facility was chosen to perform a series of fully 3D PIC simulations, calculating ability of codes were tested and preliminary simulation results about DPHC on PTS facility were discussed. Taking advantages of 3D simulation codes and large-scale parallel computation, massive data (~ 250GB) could be acquired in less than 5 hours and clear process of current transforming and electron emission in DPHC were demonstrated with the help of visualization tools. Cold-chamber tests were performed during which only cathode electron emission was considered without temperature rise or ion emission, current loss efficiency was estimated to be 0.46% ~ 0.48% by comparisons between output magnetic field profiles with or without electron emission. Project supported by the National Natural Science Foundation of China (Grant No. 11205145, 11305015, 11475155).

  8. A novel clustering approach to positron emission particle tracking

    NASA Astrophysics Data System (ADS)

    Wiggins, Cody; Santos, Roque; Ruggles, Arthur

    2016-03-01

    A novel approach to positron emission particle tracking is presented based on determining regions of space with high density of line of response crossing via clustering. The method is shown to be able to accurately track multiple particles in systems where the number of particles is unknown and in which particles can enter and leave the field of view of the scanning system. This method is explored in various environments and its parametric dependence is studied.

  9. On the comparison of visual discomfort generated by S3D and 2D content based on eye-tracking features

    NASA Astrophysics Data System (ADS)

    Iatsun, Iana; Larabi, Mohamed-Chaker; Fernandez-Maloigne, Christine

    2014-03-01

    The changing of TV systems from 2D to 3D mode is the next expected step in the telecommunication world. Some works have already been done to perform this progress technically, but interaction of the third dimension with humans is not yet clear. Previously, it was found that any increased load of visual system can create visual fatigue, like prolonged TV watching, computer work or video gaming. But watching S3D can cause another nature of visual fatigue, since all S3D technologies creates illusion of the third dimension based on characteristics of binocular vision. In this work we propose to evaluate and compare the visual fatigue from watching 2D and S3D content. This work shows the difference in accumulation of visual fatigue and its assessment for two types of content. In order to perform this comparison eye-tracking experiments using six commercially available movies were conducted. Healthy naive participants took part into the test and gave their answers feeling the subjective evaluation. It was found that watching stereo 3D content induce stronger feeling of visual fatigue than conventional 2D, and the nature of video has an important effect on its increase. Visual characteristics obtained by using eye-tracking were investigated regarding their relation with visual fatigue.

  10. Fabrication of a three dimensional particle focusing microfluidic device using a 3D printer, PDMS, and glass

    NASA Astrophysics Data System (ADS)

    Collette, Robyn; Rosen, Daniel; Shirk, Kathryn

    Microfluidic devices have high importance in fields such as bioanalysis because they can manipulate volumes of fluid in the range of microliters to picoliters. Small samples can be quickly and easily tested using complex microfluidic devices. Typically, these devices are created through lithography techniques, which can be costly and time consuming. It has been shown that inexpensive microfluidic devices can be produced quickly using a 3D printer and PDMS. However, a size limitation prohibits the fabrication of precisely controlled microchannels. By using shrinking materials in combination with 3D printing of flow-focusing geometries, this limitation can be overcome. This research seeks to employ these techniques to quickly fabricate an inexpensive, working device with three dimensional particle focusing capabilities. By modifying the channel geometry, colloidal particles in a solution will be focused into a single beam when passed through this device. The ability to focus particles is necessary for a variety of biological applications which requires precise detection and characterization of particles in a sample. We would like to thank the Shippensburg University Undergraduate Research Grant Program for their generous funding.

  11. Design of a 3D Digital Liquid Crystal Particle Thermometry and Velocimetry (3DDLCPT/V) System

    NASA Astrophysics Data System (ADS)

    Grothe, Rob; Rixon, Greg; Dabiri, Dana

    2007-11-01

    A novel 3D Digital Liquid Crystal Particle Thermometry and Velocimetry (3DDLCPT/V) system has been designed and fabricated. By combining 3D Defocusing Particle Image Velocimetry (3DDPIV) and Digital Particle Image Thermometry (DPIT) into one system, this technique provides simultaneous temperature and velocity data using temperature-sensitive liquid crystal particles (LCP) as flow sensors. A custom water-filled prism corrects for astigmatism caused by off-axis imaging. New optics equations are derived to account for multi-surface refractions. This redesign also maximizes the use of the CCD area to more efficiently image the volume of interest. Six CCD cameras comprise the imaging system, with three allocated for velocity measurements and three for temperature measurements. The cameras are optically aligned to sub-pixel accuracy using a precision grid and high-resolution translation stages. Two high-intensity custom-designed xenon flashlamps provide illumination. Temperature calibration of the LCP is then performed. These results and proof-of-concept experiments will be discussed in detail.

  12. Holographic particle image velocimetry: a comparison of digital shearing and 3D correlation analysis methods

    NASA Astrophysics Data System (ADS)

    Yang, Hui; Alcock, Rob D.; Halliwell, Neil A.; Coupland, Jeremy M.

    2003-11-01

    In the past, the use of optical and digital three-dimensional correlation methods have been demonstrated to extract velocity data from the complex amplitude distribution of particle images in holographic particle image velocimetry (HPIV). Recently we have proposed a digital shearing method to extract three-component particle displacement data throughout a complete image field. In contrast to full three-dimensional correlation, it has been shown that all three components of particle image displacement can be retrieved using just four two-dimensional fast Fourier transform (FFT) operations and appropriate coordinate transformations. In this paper we describe three-dimensional correlation and digital shearing methods and compare their performance in terms of computational efficiency and measurement accuracy. The simulated results show that the digital shearing method has comparable accuracy to three-dimensional correlation but is significantly faster.

  13. On the calibration of astigmatism particle tracking velocimetry for microflows

    NASA Astrophysics Data System (ADS)

    Cierpka, C.; Rossi, M.; Segura, R.; Kähler, C. J.

    2011-01-01

    Astigmatism particle tracking velocimetry (APTV) is a method to determine three components (3C) of the velocity field in a volume (3D) using a single camera. The depth position of the particles is coded by optical distortions caused by a cylindrical lens in the optical setup. This technique is particularly suited for microfluidic applications as measurement errors due to spatial averaging and depth of correlation, typically encountered with μPIV approaches, are eliminated so that the measurement precision is enhanced. Unfortunately, the current state of the technique is limited by the small measurement region achievable with the current calibration procedures as well as by higher order image aberrations (Cierpka et al 2010 Meas. Sci. Technol. 21 045401). In order to extend the size of the measurement volume and to account for all image aberrations, a new intrinsic calibration procedure, based on the imaging function of the particles, is proposed in the paper at hand. It provides an extended measurement depth, taking into account all image aberrations. In this work, the calibration procedure was applied to a μPIV arrangement but could also be implemented on macroscopic experimental setups. The calibration procedure is qualified with synthetic data as well as Poiseuille flow in a straight rectangular micro-channel with a cross-sectional area of 200 × 500 µm2. The three-dimensional velocity distribution of the whole channel was resolved via APTV with uncertainties of 0.9% and 3.7% of the centerline velocity, uc, for the in-plane and out-of-plane components, respectively. Further investigations using different cylindrical-lens focal lengths, magnifications and particle sizes provide information about achievable measurement depths and help to design and adapt the optimal system for the desired experiment.

  14. Gravity driven deterministic lateral displacement for suspended particles in a 3D obstacle array

    PubMed Central

    Du, Siqi; Drazer, German

    2016-01-01

    We present a simple modification to enhance the separation ability of deterministic lateral displacement (DLD) systems by expanding the two-dimensional nature of these devices and driving the particles into size-dependent, fully three-dimensional trajectories. Specifically, we drive the particles through an array of long cylindrical posts, such that they not only move parallel to the basal plane of the posts as in traditional two-dimensional DLD systems (in-plane motion), but also along the axial direction of the solid posts (out-of-plane motion). We show that the (projected) in-plane motion of the particles is completely analogous to that observed in 2D-DLD systems. In fact, a theoretical model originally developed for force-driven, two-dimensional DLD systems accurately describes the experimental results. More importantly, we analyze the particles out-of-plane motion and observe, for certain orientations of the driving force, significant differences in the out-of-plane displacement depending on particle size. Therefore, taking advantage of both the in-plane and out-of-plane motion of the particles, it is possible to achieve the simultaneous fractionation of a polydisperse suspension into multiple streams. PMID:27526935

  15. Gravity driven deterministic lateral displacement for suspended particles in a 3D obstacle array.

    PubMed

    Du, Siqi; Drazer, German

    2016-01-01

    We present a simple modification to enhance the separation ability of deterministic lateral displacement (DLD) systems by expanding the two-dimensional nature of these devices and driving the particles into size-dependent, fully three-dimensional trajectories. Specifically, we drive the particles through an array of long cylindrical posts, such that they not only move parallel to the basal plane of the posts as in traditional two-dimensional DLD systems (in-plane motion), but also along the axial direction of the solid posts (out-of-plane motion). We show that the (projected) in-plane motion of the particles is completely analogous to that observed in 2D-DLD systems. In fact, a theoretical model originally developed for force-driven, two-dimensional DLD systems accurately describes the experimental results. More importantly, we analyze the particles out-of-plane motion and observe, for certain orientations of the driving force, significant differences in the out-of-plane displacement depending on particle size. Therefore, taking advantage of both the in-plane and out-of-plane motion of the particles, it is possible to achieve the simultaneous fractionation of a polydisperse suspension into multiple streams. PMID:27526935

  16. On charged particle tracks in cellulose nitrate and Lexan

    NASA Technical Reports Server (NTRS)

    Benton, E. V.; Henke, R. P.

    1972-01-01

    Investigations were performed aimed at developing plastic nuclear track detectors into quantitative tools for recording and measuring multicharged, heavy particles. Accurate track etch rate measurements as a function of LET were performed for cellulose nitrate and Lexan plastic detectors. This was done using a variety of incident charged particle types and energies. The effect of aging of latent tracks in Lexan in different gaseous atmospheres was investigated. Range distributions of high energy N-14 particle bevatron beams in nuclear emulsion were measured. Investigation of charge resolution and Bragg peak measurements were carried out using plastic nuclear track detectors.

  17. Soot particle size modelling in 3D simulations of diesel engine combustion

    NASA Astrophysics Data System (ADS)

    Fraioli, V.; Beatrice, C.; Lazzaro, M.

    2011-12-01

    The present work is focused on multi-dimensional simulations of combustion in diesel engines. The primary objective was to test, in a diesel engine framework, a soot particle size model to represent the carbon particle formation and calculate the corresponding size distribution function. Simulations are performed by means of a parallel version of the KIVA3V numerical code, modified to adopt detailed kinetics reaction mechanisms. A skeletal reaction scheme for n-heptane autoignition has been extended, to include PAH kinetics and carbonaceous particle formation and consumption rates: the full reaction set is made up of 82 gas species and 50 species accounting for the particles, thus the complete reaction scheme comprises 132 species and 2206 reaction steps. Four different engine operative conditions, varying engine speed and load, are taken into account and experimentally tested on a single cylinder diesel engine fuelling pure n-heptane. Computed particle size distribution functions are compared with corresponding measurements at the exhaust, performed by a differential mobility spectrometer. A satisfying agreement between computed and measured combustion profiles is obtained in all the conditions. A reasonable aerosol evolution can be obtained, yet in all the cases the model exhibits the tendency to overestimate the number of particles within the range 5-160 nm. Moreover calculations predict a nucleation mode not detected by the available instrument. According to the simulations, the total number and size of the nascent particles would not depend on the operative conditions, while the features of the larger aggregates distinctly vary with the engine functioning.

  18. Confocal (micro)-XRF for 3D anlaysis of elements distribution in hot environmental particles

    SciTech Connect

    Bielewski, M; Eriksson, M; Himbert, J; Simon, R; Betti, M; Hamilton, T F

    2007-11-27

    Studies on the fate and transport of radioactive contaminates in the environment are often constrained by a lack of knowledge on the elemental distribution and general behavior of particulate bound radionuclides contained in hot particles. A number of hot particles were previously isolated from soil samples collected at former U.S. nuclear test sites in the Marshall Islands and characterized using non-destructive techniques [1]. The present investigation at HASYLAB is a part of larger research program at ITU regarding the characterization of environmental radioactive particles different locations and source-terms. Radioactive particles in the environment are formed under a number of different release scenarios and, as such, their physicochemical properties may provide a basis for identifying source-term specific contamination regimes. Consequently, studies on hot particles are not only important in terms of studying the elemental composition and geochemical behavior of hot particles but may also lead to advances in assessing the long-term impacts of radioactive contamination on the environment. Six particles isolated from soil samples collected at the Marshall Islands were studied. The element distribution in the particles was determined by confocal {micro}-XRF analysis using the ANKA FLUO beam line. The CRL (compound refractive lens) was used to focus the exciting beam and the polycapillary half lens to collimate the detector. The dimensions of confocal spot were measured by 'knife edge scanning' method with thin gold structure placed at Si wafer. The values of 3.1 x 1.4 x 18.4 {micro}m were achieved if defined as FWHMs of measured L?intensity profiles and when the19.1 keV exciting radiation was used. The collected XRF spectra were analyzed offline with AXIL [2] software to obtain net intensities of element characteristic lines.Further data processing and reconstruction of element distribution was done with the software 'R' [3] dedicated for statistical

  19. Measuring Single Particle Microrheology of Human Mucus Using the 3D Force Microscope

    NASA Astrophysics Data System (ADS)

    Cribb, Jeremy; Hill, D. B.; Taylor, R.; O'Brien, E. T.; Davis, C. W.; Matsui, H.; Vicci, L.; Matthews, G.; Fisher, J.; Desai, K. V.; Wilde, B.; Superfine, R.

    2003-11-01

    In many patients with Cystic Fibrosis, the viscosity of mucus is higher than that found in normal patients, contributing to the failure of cilia to sweep mucus away from the lungs effectively. Microrheological measurements of biologically relevant fluids, such as mucus, are important to understand the physical environment in which cilia operate. The complex viscoelastic moduli and apparent viscosity of several mucus concentrations were determined by tracking 1 micron beads undergoing Brownian motion. Further, the apparent viscosity of each mucus solution was determined from the Stokes' drag on a superparamagnetic bead driven by the 3-dimensional force microscope (3DFM).

  20. HSA: integrating multi-track Hi-C data for genome-scale reconstruction of 3D chromatin structure.

    PubMed

    Zou, Chenchen; Zhang, Yuping; Ouyang, Zhengqing

    2016-01-01

    Genome-wide 3C technologies (Hi-C) are being increasingly employed to study three-dimensional (3D) genome conformations. Existing computational approaches are unable to integrate accumulating data to facilitate studying 3D chromatin structure and function. We present HSA ( http://ouyanglab.jax.org/hsa/ ), a flexible tool that jointly analyzes multiple contact maps to infer 3D chromatin structure at the genome scale. HSA globally searches the latent structure underlying different cleavage footprints. Its robustness and accuracy outperform or rival existing tools on extensive simulations and orthogonal experiment validations. Applying HSA to recent in situ Hi-C data, we found the 3D chromatin structures are highly conserved across various human cell types. PMID:26936376

  1. 3-D RPIC simulations of relativistic jets: Particle acceleration, magnetic field generation, and emission

    NASA Technical Reports Server (NTRS)

    Nishikawa, K.-I.

    2006-01-01

    Nonthermal radiation observed from astrophysical systems containing (relativistic) jets and shocks, e.g., supernova remnants, active galactic nuclei (AGNs), gamma-ray bursts (GRBs), and Galactic microquasar systems usually have power-law emission spectra. Fermi acceleration is the mechanism usually assumed for the acceleration of particles in astrophysical environments. Recent PIC simulations using injected relativistic electron-ion (electro-positron) jets show that acceleration occurs within the downstream jet, rather than by the scattering of particles back and forth across the shock as in Fermi acceleration. Shock acceleration is a ubiquitous phenomenon in astrophysical plasmas. Plasma waves and their associated instabilities (e.g., the Buneman instability, other two-streaming instability, and the Weibel instability) created in the .shocks are responsible for particle (electron, positron, and ion) acceleration. The simulation results show that the Weibel instability is responsible for generating and amplifying highly nonuniform, small-scale magnetic fields. These magnetic fields contribute to the electron's transverse deflection behind the jet head. The "jitter" radiation from deflected electrons has different properties than synchrotron radiation which is calculated in a uniform magnetic field. This jitter radiation may be important to understanding the complex time evolution and/or spectral structure in gamma-ray bursts, relativistic jets, and supernova remnants. We will review recent PIC simulations which show particle acceleration in jets.

  2. Advanced 3D electromagnetic and particle-in-cell modeling on structured/unstructured hybrid grids

    SciTech Connect

    Seidel, D.B.; Pasik, M.F.; Kiefer, M.L.; Riley, D.J.; Turner, C.D.

    1998-01-01

    New techniques have been recently developed that allow unstructured, free meshes to be embedded into standard 3-dimensional, rectilinear, finite-difference time-domain grids. The resulting hybrid-grid modeling capability allows the higher resolution and fidelity of modeling afforded by free meshes to be combined with the simplicity and efficiency of rectilinear techniques. Integration of these new methods into the full-featured, general-purpose QUICKSILVER electromagnetic, Particle-In-Cell (PIC) code provides new modeling capability for a wide variety of electromagnetic and plasma physics problems. To completely exploit the integration of this technology into QUICKSILVER for applications requiring the self-consistent treatment of charged particles, this project has extended existing PIC methods for operation on these hybrid unstructured/rectilinear meshes. Several technical issues had to be addressed in order to accomplish this goal, including the location of particles on the unstructured mesh, adequate conservation of charge, and the proper handling of particles in the transition region between structured and unstructured portions of the hybrid grid.

  3. Energy loss of a heavy particle near 3D charged rotating hairy black hole

    NASA Astrophysics Data System (ADS)

    Naji, Jalil

    2014-01-01

    In this paper we consider a charged rotating black hole in three dimensions with a scalar charge and discuss the energy loss of a heavy particle moving near the black-hole horizon. We also study quasi-normal modes and find the dispersion relations. We find that the effect of scalar charge and electric charge increases the energy loss.

  4. Cosmic Ray and Solar Energetic Particle Observations In The 3-d Heliosphere Near Solar Maximum

    NASA Astrophysics Data System (ADS)

    McKibben, R. B.; Connell, J. J.; Lopate, C.

    Observations from the COSPIN High Energy Telescope during Ulysses recent fast lat- itude scan have provided the first latitudinal survey of intensities of cosmic rays and solar energetic particles near solar maximum. During the previous fast latitude scan near solar minimum, no significant solar energetic particle events were observed, but the galactic and anomalous component cosmic ray intensities showed small positive latitudinal gradients organized around a southwardly displaced heliospheric current sheet. The small size of the gradients, together with observation near the poles of 26-day intensity variations impressed by near-equatorial CIR-structures, led to the conclusion that latitudinal transport across the mean Parker spiral magnetic fields was much easier than had been expected prior to Ulysses observations. During the recently completed fast latitude scan near solar maximum, galactic cosmic rays could be ob- served only occasionally in the quiet times between frequent solar energetic particle events. When cosmic ray intensities could be observed, no measurable latitude gradi- ents were found, implying that modulation became much more spherically symmetric near solar maximum. From observations of the solar energetic particle intensities, we found that almost all large gradual events produced intensity increases both at Ulysses and at IMP-8 near Earth, regardless of the latitude or longitude of the spacecrafts relative to the initiating event in the corona. Most often the intensities at Ulysses and IMP-8 became comparable a few days after the onset of the event and remained nearly equal for the rest of the decay, which in some cases lasted as much as a full solar rota- tion. Both the cosmic ray and the solar energetic particle observations imply efficient latitudinal and cross-field transport of energetic particles even in the complex inter- planetary magnetic fields of solar maximum. Recent observations suggest that the solar polar coronal holes have

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

    NASA Astrophysics Data System (ADS)

    Hu, X.; Zhang, Y.

    2007-05-01

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

  6. 3D Electromagnetic Particle-in-Cell simulations of the solar wind interaction with lunar magnetic anomalies

    NASA Astrophysics Data System (ADS)

    Deca, J.; Lapenta, G.; Divin, A. V.; Lembege, B.; Markidis, S.

    2013-12-01

    Unlike the Earth and Mercury, our Moon has no global magnetic field and is therefore not shielded from the impinging solar wind by a magnetosphere. However, lunar magnetic field measurements made by the Apollo missions provided direct evidence that the Moon has regions of small-scale crustal magnetic fields, ranging up to a few 100km in scale size with surface magnetic field strengths up to hundreds of nanoTeslas. More recently, the Lunar Prospector spacecraft has provided high-resolution observations allowing to construct magnetic field maps of the entire Moon, confirming the earlier results from Apollo, but also showing that the lunar plasma environment is much richer than earlier believed. Typically the small-scale magnetic fields are non-dipolar and rather tiny compared to the lunar radius and mainly clustered on the far side of the moon. Using iPic3D we present the first 3D fully kinetic and electromagnetic Particle-in-Cell simulations of the solar wind interaction with lunar magnetic anomalies. We study the behaviour of a dipole model with variable surface magnetic field strength under changing solar wind conditions and confirm that lunar crustal magnetic fields may indeed be strong enough to stand off the solar wind and form a mini-magnetosphere, as suggested by MHD and hybrid simulations and spacecraft observations. 3D-PIC simulations reveal to be very helpful to analyze the diversion/braking of the particle flux and the characteristics of the resulting particles accumulation. The particle flux to the surface is significantly reduced at the magnetic anomaly, surrounded by a region of enhanced density due to the magnetic mirror effect. Second, the ability of iPic3D to resolve all plasma components (heavy ions, protons and electrons) allows to discuss in detail the electron physics leading to the highly non-adiabatic interactions expected as well as the implications for solar wind shielding of the lunar surface, depending on the scale size (solar wind protons

  7. Particle sedimentation in curved tubes: A 3D simulation and optimization for treatment of vestibular vertigo

    NASA Astrophysics Data System (ADS)

    White, Brian; Squires, Todd M.; Hain, Timothy C.; Stone, Howard A.

    2003-11-01

    Benign paroxysmal positional vertigo (BPPV) is a mechanical disorder of the vestibular system where micron-size crystals abnormally drift into the semicircular canals of the inner ear that sense angular motion of the head. Sedimentation of these crystals causes sensation of motion after true head motion has stopped: vertigo results. The usual clinical treatment is through a series of head maneuvers designed to move the particles into a less sensitive region of the canal system. We present a three-dimensional model to simulate treatment of BPPV by determining the complete hydrodynamic motion of the particles through the course of a therapeutic maneuver while using a realistic representation of the actual geometry. Analyses of clinical maneuvers show the parameter range for which they are effective, and indicate inefficiencies in current practice. In addition, an optimization process determines the most effective head maneuver, which significantly differs from those currently in practice.

  8. 3-D RPIC Simulations of Relativistic Jets: Particle Acceleration, Magnetic Field Generation, and Emission

    NASA Technical Reports Server (NTRS)

    Nishikawa, K.-I.; Mizuno, Y.; Hardee, P.; Hededal, C. B.; Fishman, G. J.

    2006-01-01

    Recent PIC simulations using injected relativistic electron-ion (electro-positron) jets into ambient plasmas show that acceleration occurs in relativistic shocks. The Weibel instability created in shocks is responsible for particle acceleration, and generation and amplification of highly inhomogeneous, small-scale magnetic fields. These magnetic fields contribute to the electron's transverse deflection in relativistic jets. The "jitter" radiation from deflected electrons has different properties than the synchrotron radiation which is calculated in a uniform magnetic field. This jitter radiation may be important to understand the complex time evolution and spectral structure in relativistic jets and gamma-ray bursts. We will present recent PIC simulations which show particle acceleration and magnetic field generation. We will also calculate associated self-consistent emission from relativistic shocks.

  9. 3D particle simulation of beams using the WARP code: Transport around bends

    SciTech Connect

    Friedman, A.; Grote, D.P.; Callahan, D.A.; Langdon, A.B. ); Haber, I. )

    1990-11-30

    WARP is a discrete-particle simulation program which was developed for studies of space charge dominated ion beams. It combines features of an accelerator code and a particle-in-cell plasma simulation. The code architecture, and techniques employed to enhance efficiency, are briefly described. Current applications are reviewed. In this paper we emphasize the physics of transport of three-dimensional beams around bends. We present a simple bent-beam PIC algorithm. Using this model, we have followed a long, thin beam around a bend in a simple racetrack system (assuming straight-pipe self-fields). Results on beam dynamics are presented; no transverse emittance growth (at mid-pulse) is observed. 11 refs., 5 figs.

  10. Unstructured grids in 3D and 4D for a time-dependent interface in front tracking with improved accuracy

    SciTech Connect

    Glimm, J.; Grove, J. W.; Li, X. L.; Li, Y.; Xu, Z.

    2002-01-01

    Front tracking traces the dynamic evolution of an interface separating differnt materials or fluid components. In this paper, they describe three types of the grid generation methods used in the front tracking method. One is the unstructured surface grid. The second is a structured grid-based reconstruction method. The third is a time-space grid, also grid based, for a conservative tracking algorithm with improved accuracy.

  11. 3D rotating wall vessel and 2D cell culture of four veterinary virus pathogens: A comparison of virus yields, portions of infectious particles and virus growth curves.

    PubMed

    Malenovská, Hana

    2016-02-01

    Only very few comparative studies have been performed that evaluate general trends of virus growth under 3D in comparison with 2D cell culture conditions. The aim of this study was to investigate differences when four animal viruses are cultured in 2D and 3D. Suid herpesvirus 1 (SuHV-1), Vesicular stomatitis virus (VSIV), Bovine adenovirus (BAdV) and Bovine parainfluenza 3 virus (BPIV-3) were cultivated in 3D rotating wall vessels (RWVs) and conventional 2D cultures. The production of virus particles, the portion of infectious particles, and the infectious growth curves were compared. For all viruses, the production of virus particles (related to cell density), including the non-infectious ones, was lower in 3D than in 2D culture. The production of only infectious particles was significantly lower in BAdV and BPIV-3 in 3D cultures in relation to cell density. The two cultivation approaches resulted in significantly different virus particle-to-TCID50 ratios in three of the four viruses: lower in SuHV-1 and BPIV-3 and higher in BAdV in 3D culture. The infectious virus growth rates were not significantly different in all viruses. Although 3D RWV culture resulted in lower production of virus particles compared to 2D systems, the portion of infectious particles was higher for some viruses. PMID:26562056

  12. Particle tracking during Ostwald ripening using time-resolved laboratory X-ray microtomography

    SciTech Connect

    Werz, T.; Baumann, M.; Wolfram, U.; Krill, C.E.

    2014-04-01

    Laboratory X-ray microtomography is investigated as a method for obtaining time-resolved images of microstructural coarsening of the semisolid state of Al–5 wt.% Cu samples during Ostwald ripening. Owing to the 3D imaging capability of tomography, this technique uniquely provides access to the growth rates of individual particles, thereby not only allowing a statistical characterization of coarsening—as has long been possible by conventional metallography—but also enabling quantification of the influence of local environment on particle boundary migration. The latter information is crucial to understanding growth kinetics during Ostwald ripening at high volume fractions of the coarsening phase. Automated image processing and segmentation routines were developed to close gaps in the network of particle boundaries and to track individual particles from one annealing step to the next. The particle tracking success rate places an upper bound of only a few percent on the likelihood of segmentation errors for any given particle. The accuracy of particle size trajectories extracted from the time-resolved tomographic reconstructions is correspondingly high. Statistically averaged coarsening data and individual particle growth rates are in excellent agreement with the results of prior experimental studies and with computer simulations of Ostwald ripening. - Highlights: • Ostwald ripening in Al–5 wt.% Cu measured by laboratory X-ray microtomography • Time-resolved measurement of individual particle growth • Automated segmentation routines developed to close gaps in particle boundary network • Particle growth/shrinkage rates deviate from LSW model prediction.

  13. Color-Coded Three-Dimensional Particle Tracking Velocimetry for Micro-Flow Applications

    NASA Astrophysics Data System (ADS)

    Tien, Wei-Hsin; Dabiri, Dana; Hove, Jay

    2011-11-01

    A color-coded three-dimensional particle image velocimetry is successfully adapted into a microscope setup using a 10X magnification lens. 3 high-power LED with different wavelengths are used as light sources for each color-coded pinhole, and a color separation algorithm based on decorrelation stretch is developed to account for the multiple exposure problem caused by the color filters. Overlapped particle images are then identified with a cascade correlation method, and the triplets are matched to reconstruct the 3D particle locations with a calibration-based epi-polar line search method. The velocity field is reconstructed by a vision-based particle tracking algorithm. With the ability to tack particles in higher particle densities, the experimental setup is used to image an 800 x 800 x 500 micrometer volume of an accelerating backward-facing step micro-channel flow. This work is supported by the National Institute of Health (NIH).

  14. 3D Boltzmann Simulation of the Io's Plasma Environment with Adaptive Mesh and Particle Refinement

    NASA Astrophysics Data System (ADS)

    Lipatov, A. S.; Combi, M. R.

    2002-12-01

    The global dynamics of the ionized and neutral components in the environment of Io plays an important role in the interaction of Jupiter's corotating magnetospheric plasma with Io [Combi et al., 2002; 1998; Kabin et al., 2001]. The stationary simulation of this problem was done in the MHD [Combi et al., 1998; Linker et al, 1998; Kabin et al., 2001] and the electrodynamic [Saur et al., 1999] approaches. In this report, we develop a method of kinetic ion-neutral simulation, which is based on a multiscale adaptive mesh, particle and algorithm refinement. This method employs the fluid description for electrons whereas for ions the drift-kinetic and particle approaches are used. This method takes into account charge-exchange and photoionization processes. The first results of such simulation of the dynamics of ions in the Io's environment are discussed in this report. ~ M R Combi et al., J. Geophys. Res., 103, 9071, 1998. M R Combi, T I Gombosi, K Kabin, Atmospheres in the Solar System: Comparative\\ Aeronomy. Geophys. Monograph Series, 130, 151, 2002. K Kabin et al., Planetary and Space Sci., 49, 337, 2001. J A Linker et al., J. Geophys. Res., 103(E9), 19867, 1998. J Saur et al., J. Geophys. Res., 104, 25105, 1999.

  15. Solar Energetic Particle Observations and Propagation in the 3-D Heliosphere in December 2006

    NASA Astrophysics Data System (ADS)

    Malandraki, Olga E.; Marsden, Richard G.; Lario, David; Tranquille, Cecil; Heber, Bernd; Mewaldt, Richard A.; Cohen, Christina M. S.; Lanzerotti, Louis J.; Forsyth, Robert B.; Elliott, Heather A.

    2010-05-01

    Ulysses is the first spacecraft to fly over the poles of the Sun. Although the Sun was again close to its activity minimum during the recently completed third polar orbit of Ulysses, solar activity has been more prevalent during the declining phase of solar cycle 23 than was the case in the declining phase of the 22nd solar cycle, when the first polar passes occurred (1994-1995). In December 2006, an unexpected rise of solar activity occurred. Active Region 10930 produced a series of major solar flares with the strongest one (X9.0) recorded on December 5, after it rotated into view on the east limb of the Sun. In this work, we present in detail energetic particle observations obtained by various instruments onboard Ulysses, located at > 70 degrees south heliographic latitude during this period and discuss their implications for particle propagation to solar polar regions. The observed events are also compared with high latitudes measurements obtained previously by Ulysses close to solar maximum. Furthermore, comparisons with data acquired by the STEREO and ACE spacecraft near the ecliptic plane are discussed.

  16. Multiple states and joint objects particle filter for eye tracking

    NASA Astrophysics Data System (ADS)

    Xiong, Jin; Jiang, Zhaohui; Liu, Junwei; Feng, Huanqing

    2007-11-01

    Recent works have proven that the particle filter is a powerful tracking technique for non-linear and non-Gaussian estimation problem. This paper presents an extension algorithm based on the color-based particle filter framework, which is applicable for complex eye tracking because of two main innovations. Firstly, an employment of an extra discrete-value variable and its associated transition probability matrix (TPM) makes it feasible in tracking multiple states of the eye during blinking. Secondly, the joint-object thought used in state vector eliminates the distraction from eyes to each other. The experimental results illustrate that the proposed algorithm is efficient for eye tracking.

  17. Fluctuations in closed-loop fluorescent particle tracking

    NASA Astrophysics Data System (ADS)

    Berglund, Andrew J.; McHale, Kevin; Mabuchi, Hideo

    2007-06-01

    We present a comprehensive theory of closed-loop particle tracking for calculating the statistics of a diffusing fluorescent particle’s motion relative to the tracking lock point. A detailed comparison is made between the theory and experimental results, with excellent quantitative agreement found in all cases. A generalization of the theory of (open-loop) fluorescence correlation spectroscopy is developed, and the relationship to previous results is discussed. Two applications of the statistical techniques are given: a method for determining a tracked particle’s localization and an algorithm for rapid particle classification based on real-time analysis of the tracking control signal.

  18. 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.

  19. Using 3D Printing and Stereoscopic Imaging to Measure the Alignment and Rotation of Anisotropic Particles in Turbulence

    NASA Astrophysics Data System (ADS)

    Marcus, Guy

    2014-03-01

    We have developed a general methodology to experimentally measure the time-resolved Lagrangian orientation and solid body rotation rate of anisotropic particles with arbitrary aspect ratio from standard stereoscopic video image data. We apply these techniques to particles advected in a Rλ ~ 110 fluid flow, where turbulence is generated by two grids oscillating in phase. We use 3D printing technology to design and fabricate neutrally buoyant rods, crosses (two perpendicular rods), and jacks (three mutually perpendicular rods) with a largest dimension of 7 times the Kolmogorov length scale, which makes them good approximations to tracer particles. We have measured the mean square rotation rate, p˙ip˙i , of particles spanning the full range of aspect ratios and obtained results that agree with direct numerical simulations. Our measurements of the full solid-body rotation of jacks, in particular, are of broad experimental relevance because they demonstrate a new and extensible way to directly probe the Lagrangian vorticity of a fluid. Lastly, we will present our direct measurements of the alignment of crosses with the direction of their solid body rotation rate vector, demonstrating how turbulence aligns particles along their longest dimension. This work was completed while at Wesleyan University.

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

    NASA Astrophysics Data System (ADS)

    Zharkova, V. V.; Siversky, T.

    2015-09-01

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

  1. 3D Wind Reconstruction and Turbulence Estimation in the Boundary Layer from Doppler Lidar Measurements using Particle Method

    NASA Astrophysics Data System (ADS)

    Rottner, L.; Baehr, C.

    2014-12-01

    Turbulent phenomena in the atmospheric boundary layer (ABL) are characterized by small spatial and temporal scales which make them difficult to observe and to model.New remote sensing instruments, like Doppler Lidar, give access to fine and high-frequency observations of wind in the ABL. This study suggests to use a method of nonlinear estimation based on these observations to reconstruct 3D wind in a hemispheric volume, and to estimate atmospheric turbulent parameters. The wind observations are associated to particle systems which are driven by a local turbulence model. The particles have both fluid and stochastic properties. Therefore, spatial averages and covariances may be deduced from the particles. Among the innovative aspects, we point out the absence of the common hypothesis of stationary-ergodic turbulence and the non-use of particle model closure hypothesis. Every time observations are available, 3D wind is reconstructed and turbulent parameters such as turbulent kinectic energy, dissipation rate, and Turbulent Intensity (TI) are provided. This study presents some results obtained using real wind measurements provided by a five lines of sight Lidar. Compared with classical methods (e.g. eddy covariance) our technic renders equivalent long time results. Moreover it provides finer and real time turbulence estimations. To assess this new method, we suggest computing independently TI using different observation types. First anemometer data are used to have TI reference.Then raw and filtered Lidar observations have also been compared. The TI obtained from raw data is significantly higher than the reference one, whereas the TI estimated with the new algorithm has the same order.In this study we have presented a new class of algorithm to reconstruct local random media. It offers a new way to understand turbulence in the ABL, in both stable or convective conditions. Later, it could be used to refine turbulence parametrization in meteorological meso-scale models.

  2. Validation of 3D motion tracking of pulmonary lesions using CT fluoroscopy images for robotically assisted lung biopsy

    NASA Astrophysics Data System (ADS)

    Xu, Sheng; Fichtinger, Gabor; Taylor, Russell H.; Cleary, Kevin R.

    2005-04-01

    As recently proposed in our previous work, the two-dimensional CT fluoroscopy image series can be used to track the three-dimensional motion of a pulmonary lesion. The assumption is that the lung tissue is locally rigid, so that the real-time CT fluoroscopy image can be combined with a preoperative CT volume to infer the position of the lesion when the lesion is not in the CT fluoroscopy imaging plane. In this paper, we validate the basic properties of our tracking algorithm using a synthetic four-dimensional lung dataset. The motion tracking result is compared to the ground truth of the four-dimensional dataset. The optimal parameter configurations of the algorithm are discussed. The robustness and accuracy of the tracking algorithm are presented. The error analysis shows that the local rigidity error is the principle component of the tracking error. The error increases as the lesion moves away from the image region being registered. Using the synthetic four-dimensional lung data, the average tracking error over a complete respiratory cycle is 0.8 mm for target lesions inside the lung. As a result, the motion tracking algorithm can potentially alleviate the effect of respiratory motion in CT fluoroscopy-guided lung biopsy.

  3. Space Charge Models for Particle Tracking on Long Time Scales

    SciTech Connect

    Holmes, Jeffrey A; Cousineau, Sarah M; Shishlo, Andrei P; Potts III, Robert E

    2013-01-01

    In order to efficiently track charged particles over long times, most tracking codes use either analytic charge distributions or particle-in-cell (PIC) methods based on fast Fourier transforms (FFTs). While useful for theoretical studies, analytic distribution models do not allow accurate simulation of real machines. PIC calculations can utilize realistic space charge distributions, but these methods suffer from the presence of discretization errors. We examine the situation for particle tracking with space charge over long times, and consider possible ideas to improve the accuracy of such calculations.

  4. PLOT3D/AMES, APOLLO UNIX VERSION USING GMR3D (WITH TURB3D)

    NASA Technical Reports Server (NTRS)

    Buning, P.

    1994-01-01

    PLOT3D is an interactive graphics program designed to help scientists visualize computational fluid dynamics (CFD) grids and solutions. Today, supercomputers and CFD algorithms can provide scientists with simulations of such highly complex phenomena that obtaining an understanding of the simulations has become a major problem. Tools which help the scientist visualize the simulations can be of tremendous aid. PLOT3D/AMES offers more functions and features, and has been adapted for more types of computers than any other CFD graphics program. Version 3.6b+ is supported for five computers and graphic libraries. Using PLOT3D, CFD physicists can view their computational models from any angle, observing the physics of problems and the quality of solutions. As an aid in designing aircraft, for example, PLOT3D's interactive computer graphics can show vortices, temperature, reverse flow, pressure, and dozens of other characteristics of air flow during flight. As critical areas become obvious, they can easily be studied more closely using a finer grid. PLOT3D is part of a computational fluid dynamics software cycle. First, a program such as 3DGRAPE (ARC-12620) helps the scientist generate computational grids to model an object and its surrounding space. Once the grids have been designed and parameters such as the angle of attack, Mach number, and Reynolds number have been specified, a "flow-solver" program such as INS3D (ARC-11794 or COS-10019) solves the system of equations governing fluid flow, usually on a supercomputer. Grids sometimes have as many as two million points, and the "flow-solver" produces a solution file which contains density, x- y- and z-momentum, and stagnation energy for each grid point. With such a solution file and a grid file containing up to 50 grids as input, PLOT3D can calculate and graphically display any one of 74 functions, including shock waves, surface pressure, velocity vectors, and particle traces. PLOT3D's 74 functions are organized into

  5. PLOT3D/AMES, APOLLO UNIX VERSION USING GMR3D (WITHOUT TURB3D)

    NASA Technical Reports Server (NTRS)

    Buning, P.

    1994-01-01

    PLOT3D is an interactive graphics program designed to help scientists visualize computational fluid dynamics (CFD) grids and solutions. Today, supercomputers and CFD algorithms can provide scientists with simulations of such highly complex phenomena that obtaining an understanding of the simulations has become a major problem. Tools which help the scientist visualize the simulations can be of tremendous aid. PLOT3D/AMES offers more functions and features, and has been adapted for more types of computers than any other CFD graphics program. Version 3.6b+ is supported for five computers and graphic libraries. Using PLOT3D, CFD physicists can view their computational models from any angle, observing the physics of problems and the quality of solutions. As an aid in designing aircraft, for example, PLOT3D's interactive computer graphics can show vortices, temperature, reverse flow, pressure, and dozens of other characteristics of air flow during flight. As critical areas become obvious, they can easily be studied more closely using a finer grid. PLOT3D is part of a computational fluid dynamics software cycle. First, a program such as 3DGRAPE (ARC-12620) helps the scientist generate computational grids to model an object and its surrounding space. Once the grids have been designed and parameters such as the angle of attack, Mach number, and Reynolds number have been specified, a "flow-solver" program such as INS3D (ARC-11794 or COS-10019) solves the system of equations governing fluid flow, usually on a supercomputer. Grids sometimes have as many as two million points, and the "flow-solver" produces a solution file which contains density, x- y- and z-momentum, and stagnation energy for each grid point. With such a solution file and a grid file containing up to 50 grids as input, PLOT3D can calculate and graphically display any one of 74 functions, including shock waves, surface pressure, velocity vectors, and particle traces. PLOT3D's 74 functions are organized into

  6. Accuracy and precision of a custom camera-based system for 2D and 3D motion tracking during speech and nonspeech motor tasks

    PubMed Central

    Feng, Yongqiang; Max, Ludo

    2014-01-01

    Purpose Studying normal or disordered motor control requires accurate motion tracking of the effectors (e.g., orofacial structures). The cost of electromagnetic, optoelectronic, and ultrasound systems is prohibitive for many laboratories, and limits clinical applications. For external movements (lips, jaw), video-based systems may be a viable alternative, provided that they offer high temporal resolution and sub-millimeter accuracy. Method We examined the accuracy and precision of 2D and 3D data recorded with a system that combines consumer-grade digital cameras capturing 60, 120, or 240 frames per second (fps), retro-reflective markers, commercially-available computer software (APAS, Ariel Dynamics), and a custom calibration device. Results Overall mean error (RMSE) across tests was 0.15 mm for static tracking and 0.26 mm for dynamic tracking, with corresponding precision (SD) values of 0.11 and 0.19 mm, respectively. The effect of frame rate varied across conditions, but, generally, accuracy was reduced at 240 fps. The effect of marker size (3 vs. 6 mm diameter) was negligible at all frame rates for both 2D and 3D data. Conclusion Motion tracking with consumer-grade digital cameras and the APAS software can achieve sub-millimeter accuracy at frame rates that are appropriate for kinematic analyses of lip/jaw movements for both research and clinical purposes. PMID:24686484

  7. Accuracy and precision of a custom camera-based system for 2-d and 3-d motion tracking during speech and nonspeech motor tasks.

    PubMed

    Feng, Yongqiang; Max, Ludo

    2014-04-01

    PURPOSE Studying normal or disordered motor control requires accurate motion tracking of the effectors (e.g., orofacial structures). The cost of electromagnetic, optoelectronic, and ultrasound systems is prohibitive for many laboratories and limits clinical applications. For external movements (lips, jaw), video-based systems may be a viable alternative, provided that they offer high temporal resolution and submillimeter accuracy. METHOD The authors examined the accuracy and precision of 2-D and 3-D data recorded with a system that combines consumer-grade digital cameras capturing 60, 120, or 240 frames per second (fps), retro-reflective markers, commercially available computer software (APAS, Ariel Dynamics), and a custom calibration device. RESULTS Overall root-mean-square error (RMSE) across tests was 0.15 mm for static tracking and 0.26 mm for dynamic tracking, with corresponding precision (SD) values of 0.11 and 0.19 mm, respectively. The effect of frame rate varied across conditions, but, generally, accuracy was reduced at 240 fps. The effect of marker size (3- vs. 6-mm diameter) was negligible at all frame rates for both 2-D and 3-D data. CONCLUSION Motion tracking with consumer-grade digital cameras and the APAS software can achieve submillimeter accuracy at frame rates that are appropriate for kinematic analyses of lip/jaw movements for both research and clinical purposes. PMID:24686484

  8. Position tracking of moving liver lesion based on real-time registration between 2D ultrasound and 3D preoperative images

    SciTech Connect

    Weon, Chijun; Hyun Nam, Woo; Lee, Duhgoon; Ra, Jong Beom; Lee, Jae Young

    2015-01-15

    Purpose: Registration between 2D ultrasound (US) and 3D preoperative magnetic resonance (MR) (or computed tomography, CT) images has been studied recently for US-guided intervention. However, the existing techniques have some limits, either in the registration speed or the performance. The purpose of this work is to develop a real-time and fully automatic registration system between two intermodal images of the liver, and subsequently an indirect lesion positioning/tracking algorithm based on the registration result, for image-guided interventions. Methods: The proposed position tracking system consists of three stages. In the preoperative stage, the authors acquire several 3D preoperative MR (or CT) images at different respiratory phases. Based on the transformations obtained from nonrigid registration of the acquired 3D images, they then generate a 4D preoperative image along the respiratory phase. In the intraoperative preparatory stage, they properly attach a 3D US transducer to the patient’s body and fix its pose using a holding mechanism. They then acquire a couple of respiratory-controlled 3D US images. Via the rigid registration of these US images to the 3D preoperative images in the 4D image, the pose information of the fixed-pose 3D US transducer is determined with respect to the preoperative image coordinates. As feature(s) to use for the rigid registration, they may choose either internal liver vessels or the inferior vena cava. Since the latter is especially useful in patients with a diffuse liver disease, the authors newly propose using it. In the intraoperative real-time stage, they acquire 2D US images in real-time from the fixed-pose transducer. For each US image, they select candidates for its corresponding 2D preoperative slice from the 4D preoperative MR (or CT) image, based on the predetermined pose information of the transducer. The correct corresponding image is then found among those candidates via real-time 2D registration based on a

  9. Guiding-centre and full-Lorentz orbit solving in 3D magnetic coordinates for fast particle simulations

    NASA Astrophysics Data System (ADS)

    Cooper, Wilfred A.; Pfefferle, David; Graves, Jonathan P.

    2014-10-01

    Designed to accurately solve the motion of energetic particles in the presence of 3D magnetic fields, the VENUS-LEVIS code leans on a non-canonical general coordinate Lagrangian formulation of the equations of motion. It switches between full-orbit particle following and guiding-centre tracing by verifying the perpendicular variation of magnetic vector field, not only including gradients and curvature terms but also the shearing of field-lines. The criteria is particularly relevant for the study of fast ion redistribution in the kinked core of hybrid plasmas, where the compression of flux-surfaces against the axisymmetric outer mantle creates strongly varying magnetic field-lines and large parallel currents. Slowing-down simulations of NBI fast ions show that co-passing particles helically align in the opposite side of the plasma deformation whereas counter-passing particles are barely affected by the kinked structure. Results are compared with experimental neutron camera traces and FIDA measurements during long-lived modes (LLM).

  10. Particle track simulation by N2 laser radiation

    NASA Astrophysics Data System (ADS)

    Gushchin, E.; Lebedev, A. N.; Somov, S. V.

    1984-07-01

    The use of N2 high-power pulsed lasers to simulate particle tracks is discussed. In gas-filled detectors, the tracks are attributed to either direct photoionization of the surface of dust particles or to two-photon ionization of unidentified molecular impurities with an ionization potential less than 2 hnu. Two-photon ionization of various saturated organic vapors is investigated and it is found that the addition of these substances to the working gas makes it possible to decrease the laser power and obtain laser tracks with virtually any electron density. It is also shown that the electron density is proportional to the square of the light power. Laser track simulation has applications in spatial and energy calibration of positive-sensitive detectors, the measurement of the drift of particle tracks in streamer, spark, and bubble chambers, and photoionization molecular spectroscopy.

  11. Optical tracking of nanoscale particles in microscale environments

    PubMed Central

    Mathai, P. P.; Liddle, J. A.; Stavis, S. M.

    2016-01-01

    The trajectories of nanoscale particles through microscale environments record useful information about both the particles and the environments. Optical microscopes provide efficient access to this information through measurements of light in the far field from nanoparticles. Such measurements necessarily involve trade-offs in tracking capabilities. This article presents a measurement framework, based on information theory, that facilitates a more systematic understanding of such trade-offs to rationally design tracking systems for diverse applications. This framework includes the degrees of freedom of optical microscopes, which determine the limitations of tracking measurements in theory. In the laboratory, tracking systems are assemblies of sources and sensors, optics and stages, and nanoparticle emitters. The combined characteristics of such systems determine the limitations of tracking measurements in practice. This article reviews this tracking hardware with a focus on the essential functions of nanoparticles as optical emitters and microenvironmental probes. Within these theoretical and practical limitations, experimentalists have implemented a variety of tracking systems with different capabilities. This article reviews a selection of apparatuses and techniques for tracking multiple and single particles by tuning illumination and detection, and by using feedback and confinement to improve the measurements. Prior information is also useful in many tracking systems and measurements, which apply across a broad spectrum of science and technology. In the context of the framework and review of apparatuses and techniques, this article reviews a selection of applications, with particle diffusion serving as a prelude to tracking measurements in biological, fluid, and material systems, fabrication and assembly processes, and engineered devices. In so doing, this review identifies trends and gaps in particle tracking that might influence future research. PMID:27213022

  12. Optical tracking of nanoscale particles in microscale environments

    NASA Astrophysics Data System (ADS)

    Mathai, P. P.; Liddle, J. A.; Stavis, S. M.

    2016-03-01

    The trajectories of nanoscale particles through microscale environments record useful information about both the particles and the environments. Optical microscopes provide efficient access to this information through measurements of light in the far field from nanoparticles. Such measurements necessarily involve trade-offs in tracking capabilities. This article presents a measurement framework, based on information theory, that facilitates a more systematic understanding of such trade-offs to rationally design tracking systems for diverse applications. This framework includes the degrees of freedom of optical microscopes, which determine the limitations of tracking measurements in theory. In the laboratory, tracking systems are assemblies of sources and sensors, optics and stages, and nanoparticle emitters. The combined characteristics of such systems determine the limitations of tracking measurements in practice. This article reviews this tracking hardware with a focus on the essential functions of nanoparticles as optical emitters and microenvironmental probes. Within these theoretical and practical limitations, experimentalists have implemented a variety of tracking systems with different capabilities. This article reviews a selection of apparatuses and techniques for tracking multiple and single particles by tuning illumination and detection, and by using feedback and confinement to improve the measurements. Prior information is also useful in many tracking systems and measurements, which apply across a broad spectrum of science and technology. In the context of the framework and review of apparatuses and techniques, this article reviews a selection of applications, with particle diffusion serving as a prelude to tracking measurements in biological, fluid, and material systems, fabrication and assembly processes, and engineered devices. In so doing, this review identifies trends and gaps in particle tracking that might influence future research.

  13. Creation of 3D digital anthropomorphic phantoms which model actual patient non-rigid body motion as determined from MRI and position tracking studies of volunteers

    NASA Astrophysics Data System (ADS)

    Connolly, C. M.; Konik, A.; Dasari, P. K. R.; Segars, P.; Zheng, S.; Johnson, K. L.; Dey, J.; King, M. A.

    2011-03-01

    Patient motion can cause artifacts, which can lead to difficulty in interpretation. The purpose of this study is to create 3D digital anthropomorphic phantoms which model the location of the structures of the chest and upper abdomen of human volunteers undergoing a series of clinically relevant motions. The 3D anatomy is modeled using the XCAT phantom and based on MRI studies. The NURBS surfaces of the XCAT are interactively adapted to fit the MRI studies. A detailed XCAT phantom is first developed from an EKG triggered Navigator acquisition composed of sagittal slices with a 3 x 3 x 3 mm voxel dimension. Rigid body motion states are then acquired at breath-hold as sagittal slices partially covering the thorax, centered on the heart, with 9 mm gaps between them. For non-rigid body motion requiring greater sampling, modified Navigator sequences covering the entire thorax with 3 mm gaps between slices are obtained. The structures of the initial XCAT are then adapted to fit these different motion states. Simultaneous to MRI imaging the positions of multiple reflective markers on stretchy bands about the volunteer's chest and abdomen are optically tracked in 3D via stereo imaging. These phantoms with combined position tracking will be used to investigate both imaging-data-driven and motion-tracking strategies to estimate and correct for patient motion. Our initial application will be to cardiacperfusion SPECT imaging where the XCAT phantoms will be used to create patient activity and attenuation distributions for each volunteer with corresponding motion tracking data from the markers on the body-surface. Monte Carlo methods will then be used to simulate SPECT acquisitions, which will be used to evaluate various motion estimation and correction strategies.

  14. Experimental evaluations of the accuracy of 3D and 4D planning in robotic tracking stereotactic body radiotherapy for lung cancers

    SciTech Connect

    Chan, Mark K. H.; Kwong, Dora L. W.; Ng, Sherry C. Y.; Tong, Anthony S. M.; Tam, Eric K. W.

    2013-04-15

    Purpose: Due to the complexity of 4D target tracking radiotherapy, the accuracy of this treatment strategy should be experimentally validated against established standard 3D technique. This work compared the accuracy of 3D and 4D dose calculations in respiration tracking stereotactic body radiotherapy (SBRT). Methods: Using the 4D planning module of the CyberKnife treatment planning system, treatment plans for a moving target and a static off-target cord structure were created on different four-dimensional computed tomography (4D-CT) datasets of a thorax phantom moving in different ranges. The 4D planning system used B-splines deformable image registrations (DIR) to accumulate dose distributions calculated on different breathing geometries, each corresponding to a static 3D-CT image of the 4D-CT dataset, onto a reference image to compose a 4D dose distribution. For each motion, 4D optimization was performed to generate a 4D treatment plan of the moving target. For comparison with standard 3D planning, each 4D plan was copied to the reference end-exhale images and a standard 3D dose calculation was followed. Treatment plans of the off-target structure were first obtained by standard 3D optimization on the end-exhale images. Subsequently, they were applied to recalculate the 4D dose distributions using DIRs. All dose distributions that were initially obtained using the ray-tracing algorithm with equivalent path-length heterogeneity correction (3D{sub EPL} and 4D{sub EPL}) were recalculated by a Monte Carlo algorithm (3D{sub MC} and 4D{sub MC}) to further investigate the effects of dose calculation algorithms. The calculated 3D{sub EPL}, 3D{sub MC}, 4D{sub EPL}, and 4D{sub MC} dose distributions were compared to measurements by Gafchromic EBT2 films in the axial and coronal planes of the moving target object, and the coronal plane for the static off-target object based on the {gamma} metric at 5%/3mm criteria ({gamma}{sub 5%/3mm}). Treatment plans were considered

  15. Using virtual reality technology and hand tracking technology to create software for training surgical skills in 3D game

    NASA Astrophysics Data System (ADS)

    Zakirova, A. A.; Ganiev, B. A.; Mullin, R. I.

    2015-11-01

    The lack of visible and approachable ways of training surgical skills is one of the main problems in medical education. Existing simulation training devices are not designed to teach students, and are not available due to the high cost of the equipment. Using modern technologies such as virtual reality and hands movements fixation technology we want to create innovative method of learning the technics of conducting operations in 3D game format, which can make education process interesting and effective. Creating of 3D format virtual simulator will allow to solve several conceptual problems at once: opportunity of practical skills improvement unlimited by the time without the risk for patient, high realism of environment in operational and anatomic body structures, using of game mechanics for information perception relief and memorization of methods acceleration, accessibility of this program.

  16. Characteristics of divertor heat and particle deposition with intrinsic and applied 3-D fields in NSTX H-mode plasmas

    SciTech Connect

    Ahn, J.W.; Canik, John; Maingi, Rajesh; Gray, Travis K; Lore, Jeremy D; McLean, Adam G; Park, J.-K.; Roquemore, A. L.; Soukhanovskii, V. A.

    2011-01-01

    Divertor heat and particle flux profiles are modified by externally imposed non-axisymmetric magnetic perturbations in the National Spherical Torus Experiment. The applied 3-D field causes strike point splitting that is represented as local peaks and valleys in the divertor profiles. The plasma response in an ideal perturbed equilibrium approach was included in the field line tracing by taking account of the B-field generated by the plasma current up to a certain fraction of normalized flux inside the separatrix and being superposed to the vacuum field. The inclusion of this type of plasma response does not significantly affect the location and spacing of the split strike points at the divertor surface. A modest level of divertor profile modification is found to occur even without the application of 3-D fields in certain high triangularity (delta = 0.65-0.8) discharges, with the location of local peaks and valleys same before and after the application. The intrinsic error field from the non-circularity of PF5 coil is known to have primarily n = 3 component in NSTX and was modeled to be included in the vacuum field line tracing. The produced puncture plot of the field line along with the connection length profile shows that the radial location of local peaks agrees well with the measurement, identifying intrinsic error field as a possible source of intrinsic strike point splitting. The radial location of local peaks in the profiles during the triggered ELM by the applied n = 3 field is the same before and after the 3-D field application. This shows that the heat flux from the triggered ELMs appears to follow the imposed n = 3 field structure.

  17. Longitudinal, label-free, quantitative tracking of cell death and viability in a 3D tumor model with OCT.

    PubMed

    Jung, Yookyung; Klein, Oliver J; Wang, Hequn; Evans, Conor L

    2016-01-01

    Three-dimensional in vitro tumor models are highly useful tools for studying tumor growth and treatment response of malignancies such as ovarian cancer. Existing viability and treatment assessment assays, however, face shortcomings when applied to these large, complex, and heterogeneous culture systems. Optical coherence tomography (OCT) is a noninvasive, label-free, optical imaging technique that can visualize live cells and tissues over time with subcellular resolution and millimeters of optical penetration depth. Here, we show that OCT is capable of carrying out high-content, longitudinal assays of 3D culture treatment response. We demonstrate the usage and capability of OCT for the dynamic monitoring of individual and combination therapeutic regimens in vitro, including both chemotherapy drugs and photodynamic therapy (PDT) for ovarian cancer. OCT was validated against the standard LIVE/DEAD Viability/Cytotoxicity Assay in small tumor spheroid cultures, showing excellent correlation with existing standards. Importantly, OCT was shown to be capable of evaluating 3D spheroid treatment response even when traditional viability assays failed. OCT 3D viability imaging revealed synergy between PDT and the standard-of-care chemotherapeutic carboplatin that evolved over time. We believe the efficacy and accuracy of OCT in vitro drug screening will greatly contribute to the field of cancer treatment and therapy evaluation. PMID:27248849

  18. Longitudinal, label-free, quantitative tracking of cell death and viability in a 3D tumor model with OCT

    PubMed Central

    Jung, Yookyung; Klein, Oliver J.; Wang, Hequn; Evans, Conor L.

    2016-01-01

    Three-dimensional in vitro tumor models are highly useful tools for studying tumor growth and treatment response of malignancies such as ovarian cancer. Existing viability and treatment assessment assays, however, face shortcomings when applied to these large, complex, and heterogeneous culture systems. Optical coherence tomography (OCT) is a noninvasive, label-free, optical imaging technique that can visualize live cells and tissues over time with subcellular resolution and millimeters of optical penetration depth. Here, we show that OCT is capable of carrying out high-content, longitudinal assays of 3D culture treatment response. We demonstrate the usage and capability of OCT for the dynamic monitoring of individual and combination therapeutic regimens in vitro, including both chemotherapy drugs and photodynamic therapy (PDT) for ovarian cancer. OCT was validated against the standard LIVE/DEAD Viability/Cytotoxicity Assay in small tumor spheroid cultures, showing excellent correlation with existing standards. Importantly, OCT was shown to be capable of evaluating 3D spheroid treatment response even when traditional viability assays failed. OCT 3D viability imaging revealed synergy between PDT and the standard-of-care chemotherapeutic carboplatin that evolved over time. We believe the efficacy and accuracy of OCT in vitro drug screening will greatly contribute to the field of cancer treatment and therapy evaluation. PMID:27248849

  19. Longitudinal, label-free, quantitative tracking of cell death and viability in a 3D tumor model with OCT

    NASA Astrophysics Data System (ADS)

    Jung, Yookyung; Klein, Oliver J.; Wang, Hequn; Evans, Conor L.

    2016-06-01

    Three-dimensional in vitro tumor models are highly useful tools for studying tumor growth and treatment response of malignancies such as ovarian cancer. Existing viability and treatment assessment assays, however, face shortcomings when applied to these large, complex, and heterogeneous culture systems. Optical coherence tomography (OCT) is a noninvasive, label-free, optical imaging technique that can visualize live cells and tissues over time with subcellular resolution and millimeters of optical penetration depth. Here, we show that OCT is capable of carrying out high-content, longitudinal assays of 3D culture treatment response. We demonstrate the usage and capability of OCT for the dynamic monitoring of individual and combination therapeutic regimens in vitro, including both chemotherapy drugs and photodynamic therapy (PDT) for ovarian cancer. OCT was validated against the standard LIVE/DEAD Viability/Cytotoxicity Assay in small tumor spheroid cultures, showing excellent correlation with existing standards. Importantly, OCT was shown to be capable of evaluating 3D spheroid treatment response even when traditional viability assays failed. OCT 3D viability imaging revealed synergy between PDT and the standard-of-care chemotherapeutic carboplatin that evolved over time. We believe the efficacy and accuracy of OCT in vitro drug screening will greatly contribute to the field of cancer treatment and therapy evaluation.

  20. Evaluation of Baltic Sea transport properties using particle tracking

    NASA Astrophysics Data System (ADS)

    Dargahi, Bijan; Cvetkovic, Vladimir

    2014-05-01

    Particle tracking model (PTM) is an effective tool for quantifying transport properties of large water bodies such as the Baltic Sea. We have applied PTM to our fully calibrated and validated Baltic Sea 3D hydrodynamic model for a 10-years period (2000-9). One hundred particles were released at a constant rate during an initial 10-days period from all the Baltic Sea sub-basins, the major rivers, and the open boundary in the Arkona Basin. In each basin, the particles were released at two different depths corresponding to the deep water and middle water layers. The objectives of the PTM simulations were to analyse the intra-exchange processes between the Baltic Sea basins and to estimate the arrival times and the paths of particles released from the rivers. The novel contribution of this study is determining the paths and arrival times of deeper water masses rather than the surface masses. Advective and diffusive transport processes in the Bornholm and Arkona basins are both driven by the interacting flows of the northern basins of the Baltic Sea and the North Sea. Particles released from Arkona basin flows northwards along the Stople Channel. The Gotland basins are the major contributors to the exchange process in the Baltic Sea. We find high values of the advection ratio, indicative of a forced advective transport process. The Bay of Gdansk is probably the most vulnerable region in the Baltic Sea. This is despite the fact that the main exchanging basins are the Bornholm Sea and the Easter Gotland Basin. The main reason is the intensive supply of the particles from the northern basins that normally take about 3000 days to reach the Bay of Gdansk. The process maintains a high level of particle concentration (90%) along its coastlines even after the 10-years period. Comparing the particle paths in the Western and Eastern Gotland basins two interesting features were found. Particles travelled in all four directions in the former basin and the middle layer particles

  1. Use of MV and kV imager correlation for maintaining continuous real-time 3D internal marker tracking during beam interruptions

    NASA Astrophysics Data System (ADS)

    Wiersma, R. D.; Riaz, N.; Dieterich, Sonja; Suh, Yelin; Xing, L.

    2009-01-01

    The integration of onboard kV imaging together with a MV electronic portal imaging device (EPID) on linear accelerators (LINAC) can provide an easy to implement real-time 3D organ position monitoring solution for treatment delivery. Currently, real-time MV-kV tracking has only been demonstrated by simultaneous imagining by both MV and kV imaging devices. However, modalities such as step-and-shoot IMRT (SS-IMRT), which inherently contain MV beam interruptions, can lead to loss of target information necessary for 3D localization. Additionally, continuous kV imaging throughout the treatment delivery can lead to high levels of imaging dose to the patient. This work demonstrates for the first time how full 3D target tracking can be maintained even in the presence of such beam interruption, or MV/kV beam interleave, by use of a relatively simple correlation model together with MV-kV tracking. A moving correlation model was constructed using both present and prior positions of the marker in the available MV or kV image to compute the position of the marker on the interrupted imager. A commercially available radiotherapy system, equipped with both MV and kV imaging devices, was used to deliver typical SS-IMRT lung treatment plans to a 4D phantom containing internally embedded metallic markers. To simulate actual lung tumor motion, previous recorded 4D lung patient motion data were used. Lung tumor motion data of five separate patients were inputted into the 4D phantom, and typical SS-IMRT lung plans were delivered to simulate actual clinical deliveries. Application of the correlation model to SS-IMRT lung treatment deliveries was found to be an effective solution for maintaining continuous 3D tracking during 'step' beam interruptions. For deliveries involving five or more gantry angles with 50 or more fields per plan, the positional errors were found to have <=1 mm root mean squared error (RMSE) in all three spatial directions. In addition to increasing the robustness of

  2. Performance and suitability assessment of a real-time 3D electromagnetic needle tracking system for interstitial brachytherapy

    PubMed Central

    Boutaleb, Samir; Fillion, Olivier; Bonillas, Antonio; Hautvast, Gilion; Binnekamp, Dirk; Beaulieu, Luc

    2015-01-01

    Purpose Accurate insertion and overall needle positioning are key requirements for effective brachytherapy treatments. This work aims at demonstrating the accuracy performance and the suitability of the Aurora® V1 Planar Field Generator (PFG) electromagnetic tracking system (EMTS) for real-time treatment assistance in interstitial brachytherapy procedures. Material and methods The system's performance was characterized in two distinct studies. First, in an environment free of EM disturbance, the boundaries of the detection volume of the EMTS were characterized and a tracking error analysis was performed. Secondly, a distortion analysis was conducted as a means of assessing the tracking accuracy performance of the system in the presence of potential EM disturbance generated by the proximity of standard brachytherapy components. Results The tracking accuracy experiments showed that positional errors were typically 2 ± 1 mm in a zone restricted to the first 30 cm of the detection volume. However, at the edges of the detection volume, sensor position errors of up to 16 mm were recorded. On the other hand, orientation errors remained low at ± 2° for most of the measurements. The EM distortion analysis showed that the presence of typical brachytherapy components in vicinity of the EMTS had little influence on tracking accuracy. Position errors of less than 1 mm were recorded with all components except with a metallic arm support, which induced a mean absolute error of approximately 1.4 mm when located 10 cm away from the needle sensor. Conclusions The Aurora® V1 PFG EMTS possesses a great potential for real-time treatment assistance in general interstitial brachytherapy. In view of our experimental results, we however recommend that the needle axis remains as parallel as possible to the generator surface during treatment and that the tracking zone be restricted to the first 30 cm from the generator surface. PMID:26622231

  3. MHD-Epic: Embedded Particle-in-Cell Simulations of Reconnection in Global 3D Extended MHD Simulations

    NASA Astrophysics Data System (ADS)

    Daldorff, L. K. S.; Toth, G.; Borovikov, D.; Gombosi, T. I.; Lapenta, G.

    2014-12-01

    With the new modeling capability in the Space Weather Modeling Framework (SWMF) of embedding an implicit Particle-in-Cell (PIC) model iPIC3D into the BATS-R-US magnetohydrodynamics model (Daldorff et al. 2014, JCP, 268, 236) we are ready to locally handle the full physics of the reconnection and its implications on the full system where globally, away from the reconnection region, a magnetohydrodynamic description is satisfactory. As magnetic reconnection is one of the main drivers in magnetospheric and heliospheric plasma dynamics, the self-consistent description of the electron dynamics in the coupled MHD-EPIC model is well suited for investigating the nature of these systems. We will compare the new embedded MHD-EPIC model with pure MHD and Hall MHD simulations of the Earth's magnetosphere.

  4. Particle-vortex duality of 2d Dirac fermion from electric-magnetic duality of 3d topological insulators

    NASA Astrophysics Data System (ADS)

    Metlitski, Max; Vishwanath, Ashvin

    Particle-vortex duality is a powerful theoretical tool that has been used to study systems of bosons. In arXiv:1505.05142, we propose an analogous duality for Dirac fermions in 2+1 dimensions. The physics of a single Dirac cone is proposed to be described by a dual theory, QED3 with a dual Dirac fermion coupled to a u(1) gauge field. This duality is established by considering two alternate descriptions of the 3d topological insulator (TI) surface. The first description is the usual Dirac cone surface state. The second description is accessed via an electric-magnetic duality of the bulk TI coupled to a gauge field, which maps it to a gauged topological superconductor. This alternate description ultimately leads to a new surface theory - dual QED3. The dual theory provides an explicit derivation of the T-Pfaffian state, a proposed surface topological order of the TI, which is simply the paired superfluid state of the dual fermions. The roles of time reversal and particle-hole symmetry are exchanged by the duality, which connects some of our results to a recent conjecture by Son on particle-hole symmetric quantum Hall states at ν = 1 / 2 .

  5. Grid dependent noise and entropy growth in anisotropic 3d particle-in-cell simulation of high intensity beams

    NASA Astrophysics Data System (ADS)

    Hofmann, I.; Boine-Frankenheim, O.

    2014-12-01

    The numerical noise inherent to particle-in-cell (PIC) simulation of 3d anisotropic high intensity bunched beams in periodic focusing is compared with the analytical model by Struckmeier [Part. Accel. 45, 229 (1994)]. The latter assumes that entropy growth can be related to Markov type stochastic processes due to temperature anisotropy and the artificial "collisions" caused by using macro-particles and calculating the space charge effect. The PIC simulations are carried out with the tracewin code widely used for high intensity beam simulation. The resulting noise can lead to growth of the six-dimensional rms emittance. The logarithm of the latter is shown to qualify as rms-based entropy. We confirm the dependence of this growth on the bunch temperature anisotropy as predicted by Struckmeier. However, we also find a grid and focusing dependent component of noise not predicted by Struckmeier. Although commonalities exist with well-established models for collision effects in PIC-simulation of extended plasmas, a distinctive feature is the presence of a periodic focusing potential, wherein the beam one-component plasma extends only over relatively few Debye lengths. Our findings are applied in particular to noise in high current linac beam simulation, where they help for optimization of the balance between the number of simulation particles and the grid resolution.

  6. Nonlinear Evolution of a 3D Inertial Alfvén Wave and Its Implication in Particle Acceleration

    NASA Astrophysics Data System (ADS)

    Sharma, Prachi; Yadav, Nitin; Sharma, R. P.

    2016-03-01

    A simulation based on a pseudo-spectral method has been performed in order to study particle acceleration. A model for the acceleration of charged particles by field localization is developed for the low-β plasma. For this purpose, a fractional diffusion approach has been employed. The nonlinear interaction between a 3D inertial Alfvén wave and a slow magnetosonic wave has been examined, and the dynamical equations of these two waves in the presence of ponderomotive nonlinearity have been solved numerically. The nonlinear evolution of the inertial Alfvén wave in the presence of slow magnetosonic wave undergoes a filamentation instability and results in field intensity localization. The results obtained show the localization and power spectrum of inertial Alfvén wave due to nonlinear coupling. The scaling obtained after the first break point of the magnetic power spectrum has been used to calculate the formation of the thermal tail of energetic particles in the solar corona.

  7. Tightly Coupled Low Cost 3D RISS/GPS Integration Using a Mixture Particle Filter for Vehicular Navigation

    PubMed Central

    Georgy, Jacques; Noureldin, Aboelmagd

    2011-01-01

    Satellite navigation systems such as the global positioning system (GPS) are currently the most common technique used for land vehicle positioning. However, in GPS-denied environments, there is an interruption in the positioning information. Low-cost micro-electro mechanical system (MEMS)-based inertial sensors can be integrated with GPS and enhance the performance in denied GPS environments. The traditional technique for this integration problem is Kalman filtering (KF). Due to the inherent errors of low-cost MEMS inertial sensors and their large stochastic drifts, KF, with its linearized models, has limited capabilities in providing accurate positioning. Particle filtering (PF) was recently suggested as a nonlinear filtering technique to accommodate for arbitrary inertial sensor characteristics, motion dynamics and noise distributions. An enhanced version of PF called the Mixture PF is utilized in this study to perform tightly coupled integration of a three dimensional (3D) reduced inertial sensors system (RISS) with GPS. In this work, the RISS consists of one single-axis gyroscope and a two-axis accelerometer used together with the vehicle’s odometer to obtain 3D navigation states. These sensors are then integrated with GPS in a tightly coupled scheme. In loosely-coupled integration, at least four satellites are needed to provide acceptable GPS position and velocity updates for the integration filter. The advantage of the tightly-coupled integration is that it can provide GPS measurement update(s) even when the number of visible satellites is three or lower, thereby improving the operation of the navigation system in environments with partial blockages by providing continuous aiding to the inertial sensors even during limited GPS satellite availability. To effectively exploit the capabilities of PF, advanced modeling for the stochastic drift of the vertically aligned gyroscope is used. In order to benefit from measurement updates for such drift, which are

  8. Tightly coupled low cost 3D RISS/GPS integration using a mixture particle filter for vehicular navigation.

    PubMed

    Georgy, Jacques; Noureldin, Aboelmagd

    2011-01-01

    Satellite navigation systems such as the global positioning system (GPS) are currently the most common technique used for land vehicle positioning. However, in GPS-denied environments, there is an interruption in the positioning information. Low-cost micro-electro mechanical system (MEMS)-based inertial sensors can be integrated with GPS and enhance the performance in denied GPS environments. The traditional technique for this integration problem is Kalman filtering (KF). Due to the inherent errors of low-cost MEMS inertial sensors and their large stochastic drifts, KF, with its linearized models, has limited capabilities in providing accurate positioning. Particle filtering (PF) was recently suggested as a nonlinear filtering technique to accommodate for arbitrary inertial sensor characteristics, motion dynamics and noise distributions. An enhanced version of PF called the Mixture PF is utilized in this study to perform tightly coupled integration of a three dimensional (3D) reduced inertial sensors system (RISS) with GPS. In this work, the RISS consists of one single-axis gyroscope and a two-axis accelerometer used together with the vehicle's odometer to obtain 3D navigation states. These sensors are then integrated with GPS in a tightly coupled scheme. In loosely-coupled integration, at least four satellites are needed to provide acceptable GPS position and velocity updates for the integration filter. The advantage of the tightly-coupled integration is that it can provide GPS measurement update(s) even when the number of visible satellites is three or lower, thereby improving the operation of the navigation system in environments with partial blockages by providing continuous aiding to the inertial sensors even during limited GPS satellite availability. To effectively exploit the capabilities of PF, advanced modeling for the stochastic drift of the vertically aligned gyroscope is used. In order to benefit from measurement updates for such drift, which are

  9. SU-E-T-380: Particle Microdosimetry Study Based On 3D-Cylindrical Silicon Radiaton Detectors

    SciTech Connect

    Guardiola, C; Carabe-Fernandez, A; Gomez, F; Pellegrini, G; Fleta, C; Quirion, D; Lozano, M

    2014-06-01

    Purpose: A new design of a solid-state-microdetector based on silicon 3D microfabrication and its performance to characterise Lineal energy, Specific Energy, dose, LET and other microdosimetric variables required for modelling particle relative biological effectiveness (RBE) is presented. Methods: A microdosimeter formed by a matrix of independent sensors with well-defined micrometric cylindrical shape and with a volume similar to those of cellular dimensions is used to measure microdosimetric variables. Each sensor measures the radiation deposited energy which, divided by the mean cord length of the sensors, provides us with the Linear Energy (y) of the radiation as well as its energy distribution, and frequencymean. Starting from the these distributions in different points of a proton beam, we generate biophysical data (e.g. Linear Energy Transfer (LET), Specific Energy (z), etc…) needed for relative biological effectiveness (RBE) calculations radiation effect models used in particle radiotherapy treatment planning. In addition, a Tissue Equivalent Proportional Counter (TEPC) will be used as baseline to calibrate the “y” magnitude of the microdosimeter unit-cells. Results: The experimental measurements will soon be carried out at the Perelman Center for Advanced Medicine (University of Pennsylvania), which provides proton beam for clinical research proposals. The results of distributions measured of the microdosimetric variables from the first tests developed in the proton facility will be presented and compared with Monte Carlo simulations using the Geant4 code. Conclusion: The use of 3D microdosimeters such as the one presented here will enhance the accuracy of RBE calculations normally affected by the inherent uncertainty of monte carlo simulations due to the approximation of material composition and energy dependent physical laws involved in such calculations. The effect of such approximations will be quatified by comparison with absolute measurement of

  10. Digital-Particle-Image-Velocimetry (DPIV) in a scanning light-sheet: 3D starting flow around a short cylinder

    NASA Astrophysics Data System (ADS)

    Brücker, Ch.

    1995-08-01

    Scanning-Particle-Image-Velocimetry Technique (SPIV), introduced by Brücker (1992) and Brücker and Althaus (1992), offers the quantitative investigation of three-dimensional vortical structures in unsteady flows. On principle, this technique combines classical Particle-Image-Velocimetry (PIV) with volume scanning using a scanning light-sheet. In our previous studies, single scans obtained from photographic frame series were evaluated to show the instantaneous vortical structure of the respective flow phenomena. Here, continuous video recordings are processed to capture also the temporal information for the study of the set-up of 3D effects in the cylinder wake. The flow is continuously sampled in depth by the scanning light-sheet and in each of the parallel planes frame-to-frame cross-correlation of the video images (DPIV) is applied to obtain the 2D velocity field. Because the scanning frequency and repetition rate is high in comparison with the characteristic time-scale of the flow, the evaluation provides a complete time-record of the 3D flow during the starting process. With use of the continuity concept as described by Robinson and Rockwell (1993), we obtained in addition the out-of-plane component of the velocity in spanwise direction. This in view, the described technique enabled the reconstruction of the three-dimensional time-dependent velocity and vorticity field. The visualization of the dynamical behaviour of these quantities as, e.g. by video, gave a good impression of the spanwise flow showing the “tornado-like” suction effect of the starting vortices.

  11. Tracking time interval changes of pulmonary nodules on follow-up 3D CT images via image-based risk score of lung cancer

    NASA Astrophysics Data System (ADS)

    Kawata, Y.; Niki, N.; Ohmatsu, H.; Kusumoto, M.; Tsuchida, T.; Eguchi, K.; Kaneko, M.; Moriyama, N.

    2013-03-01

    In this paper, we present a computer-aided follow-up (CAF) scheme to support physicians to track interval changes of pulmonary nodules on three dimensional (3D) CT images and to decide the treatment strategies without making any under or over treatment. Our scheme involves analyzing CT histograms to evaluate the volumetric distribution of CT values within pulmonary nodules. A variational Bayesian mixture modeling framework translates the image-derived features into an image-based risk score for predicting the patient recurrence-free survival. Through applying our scheme to follow-up 3D CT images of pulmonary nodules, we demonstrate the potential usefulness of the CAF scheme which can provide the trajectories that can characterize time interval changes of pulmonary nodules.

  12. An optimization-based parallel particle filter for multitarget tracking

    NASA Astrophysics Data System (ADS)

    Sutharsan, S.; Sinha, A.; Kirubarajan, T.; Farooq, M.

    2005-09-01

    Particle filter based estimation is becoming more popular because it has the capability to effectively solve nonlinear and non-Gaussian estimation problems. However, the particle filter has high computational requirements and the problem becomes even more challenging in the case of multitarget tracking. In order to perform data association and estimation jointly, typically an augmented state vector of target dynamics is used. As the number of targets increases, the computation required for each particle increases exponentially. Thus, parallelization is a possibility in order to achieve the real time feasibility in large-scale multitarget tracking applications. In this paper, we present a real-time feasible scheduling algorithm that minimizes the total computation time for the bus connected heterogeneous primary-secondary architecture. This scheduler is capable of selecting the optimal number of processors from a large pool of secondary processors and mapping the particles among the selected processors. Furthermore, we propose a less communication intensive parallel implementation of the particle filter without sacrificing tracking accuracy using an efficient load balancing technique, in which optimal particle migration is ensured. In this paper, we present the mathematical formulations for scheduling the particles as well as for particle migration via load balancing. Simulation results show the tracking performance of our parallel particle filter and the speedup achieved using parallelization.

  13. Simultaneous Eye Tracking and Blink Detection with Interactive Particle Filters

    NASA Astrophysics Data System (ADS)

    Wu, Junwen; Trivedi, Mohan M.

    2007-12-01

    We present a system that simultaneously tracks eyes and detects eye blinks. Two interactive particle filters are used for this purpose, one for the closed eyes and the other one for the open eyes. Each particle filter is used to track the eye locations as well as the scales of the eye subjects. The set of particles that gives higher confidence is defined as the primary set and the other one is defined as the secondary set. The eye location is estimated by the primary particle filter, and whether the eye status is open or closed is also decided by the label of the primary particle filter. When a new frame comes, the secondary particle filter is reinitialized according to the estimates from the primary particle filter. We use autoregression models for describing the state transition and a classification-based model for measuring the observation. Tensor subspace analysis is used for feature extraction which is followed by a logistic regression model to give the posterior estimation. The performance is carefully evaluated from two aspects: the blink detection rate and the tracking accuracy. The blink detection rate is evaluated using videos from varying scenarios, and the tracking accuracy is given by comparing with the benchmark data obtained using the Vicon motion capturing system. The setup for obtaining benchmark data for tracking accuracy evaluation is presented and experimental results are shown. Extensive experimental evaluations validate the capability of the algorithm.

  14. Particle Trajectory and Icing Analysis of the E(sup 3) Turbofan Engine Using LEWICE3D Version 3

    NASA Technical Reports Server (NTRS)

    Bidwell, Colin S.

    2011-01-01

    Particle trajectory and ice shape calculations were made for the Energy Efficient Engine (E(sup 3)) using the LEWICE3D Version 3 software. The particle trajectory and icing computations were performed using the new "block-to-block" collection efficiency method which has been incorporated into the LEWICE3D Version 3 software. The E(sup 3) was developed by NASA and GE in the early 1980 s as a technology demonstrator and is representative of a modern high bypass turbofan engine. The E(sup 3) flow field was calculated using the NASA Glenn ADPAC turbomachinery flow solver. Computations were performed for the low pressure compressor of the E(sup 3) for a Mach 0.8 cruise condition at 11,887 m assuming a standard warm day for three drop sizes and two drop distributions typically used in aircraft design and certification. Particle trajectory computations were made for water drop sizes of 5, 20, and 100 microns. Particle trajectory and ice shape predictions were made for a 20 micron Langmuir-D distribution and for a 92 mm Super-cooled Large Droplet (SLD) distribution with and without splashing effects for a Liquid Water Content (LWC) of 0.3 g/cu m and an icing time of 30 min. The E3 fan and spinner combination proved to be an effective ice removal mechanism as they removed greater than 36 percent of the mass entering the inlet for the icing cases. The maximum free stream catch fraction for the fan and spinner combination was 0.60 while that on the elements downstream of the fan was 0.03. The non-splashing trajectory and collection efficiency results showed that as drop size increased impingement rates increased on the spinner and fan leaving less mass to impinge on downstream components. The SLD splashing case yielded more mass downstream of the fan than the SLD non-splashing case due to mass being splashed from the upstream inlet lip, spinner and fan components. The ice shapes generated downstream of the fan were either small or nonexistent due to the small available mass

  15. 3-D Full-kinetic Simulations of the Solar Wind Interaction with Lunar Magnetic Anomalies: Particle Behaviour

    NASA Astrophysics Data System (ADS)

    Deca, J.; Divin, A. V.; Wang, X.; Lembege, B.; Markidis, S.; Lapenta, G.; Horanyi, M.

    2015-12-01

    We present three-dimensional full-kinetic electromagnetic simulations of the solar wind interaction with lunar crustal magnetic anomalies (LMAs). Using the implicit particle-in-cell code iPic3D, we confirm that LMAs may indeed be strong enough to stand off the solar wind from directly impacting the lunar surface forming a mini-magnetosphere, as suggested by spacecraft observations and theory. In contrast to earlier MHD and hybrid simulations, the full-kinetic nature of iPic3D allows to self-consistently investigate space charge effects, and in particular the electron dynamics dominating the near-surface lunar plasma environment. We describe the general mechanism of the interaction of both a horizontal and vertical dipole model embedded just below the lunar surface focussing on the ion and electron kinetic behaviour of the system. It is shown that the configurations are largely dominated by electron motion, because the LMA scale size is small with respect to the gyro-radius of the solar wind ions. The formation of mini-magnetospheres is an electrostatic effect. Additionally, we discuss typical particle trajectories as well as complete particle distribution functions covering thermal and suprathermal energies, within the interaction region and on viable spacecraft altitudes. Our work opens new frontiers of research toward a deeper understanding of LMAs and is ideally suited to be compared with field or particle observations from spacecraft such as Kaguya (SELENE), Lunar Prospector or ARTEMIS. The ability to evaluate the implications for future lunar exploration as well as lunar science in general hinges on a better understanding of LMAs.This research has received funding from the European Commission's FP7 Program with the grant agreement EHEROES (project 284461, www.eheroes.eu). The simulations were conducted on the computational resources provided by the PRACE Tier-0 project 2013091928 (SuperMUC). This research was supported by the Swedish National Space Board

  16. Tracking naturally occurring indoor features in 2-D and 3-D with lidar range/amplitude data

    SciTech Connect

    Adams, M.D.; Kerstens, A.

    1998-09-01

    Sensor-data processing for the interpretation of a mobile robot`s indoor environment, and the manipulation of this data for reliable localization, are still some of the most important issues in robotics. This article presents algorithms that determine the true position of a mobile robot, based on real 2-D and 3-D optical range and intensity data. The authors start with the physics of the particular type of sensor used, so that the extraction of reliable and repeatable information (namely, edge coordinates) can be determined, taking into account the noise associated with each range sample and the possibility of optical multiple-path effects. Again, applying the physical model of the sensor, the estimated positions of the mobile robot and the uncertainty in these positions are determined. They demonstrate real experiments using 2-D and 3-D scan data taken in indoor environments. To update the robot`s position reliably, the authors address the problem of matching the information recorded in a scan to, first, an a priori map, and second, to information recorded in previous scans, eliminating the need for an a priori map.

  17. Development of multi-spectral three-dimensional micro particle tracking velocimetry

    NASA Astrophysics Data System (ADS)

    Tien, Wei-Hsin

    2016-08-01

    The color-coded 3D micro particle tracking velocimetry system (CC3DμPTV) is a volumetric velocimetry technique that uses the defocusing digital particle image velocimetry (DDPIV) approach to reconstruct the 3D location of the particle. It is suited for microscopic flow visualization because of the single camera configuration. However, several factors limit the performance of the system. In this study, the limitation of the CC3DμPTV is discussed in detail and a new concept of a multi-camera 3D μ-PTV system is proposed to improve the performance of the original CC3DμPTV system. The system utilizes two dichroic beam splitters to separate the incoming light into 3 spectral ranges, and image with three monochrome image sensors. The use of a color-matched light source, off-center individual pinhole and monochrome image sensors allow the system to achieve better sensitivity and optical resolution. The use of coherent lasers light sources with high-speed cameras improves the velocity measurement dynamic range. The performance of the proposed multi-spectral system is first evaluated with a simulation model based on the finite element method (FEM). The performance is also compared numerically with the CC3DμPTV system. The test results show significant improvements on the signal to noise ratio and optical resolution. Originally presented in 11th International Symposium on Particle Image Velocimetry, Santa Barbara, California, September 14–16, 2015.

  18. Unsteady Analysis of Particle Transport and Deposition in the Human Lung: A Hybrid 3D/0D Model

    NASA Astrophysics Data System (ADS)

    Haworth, Daniel C.; Kunz, Robert F.; Leemhuis, Laura S.; Banks, Syreeta S.; Kriete, Andres

    2003-11-01

    Three-dimensional CFD meshes including up the sixteenth generation of branching in a human tracheo-bronchial tree have been generated from surface data extracted using novel high-resolution bio-medical imaging and rendering methods. A zero-dimensional model for the deeper generations has been coupled with the three-dimensional model at each of the truncated branches. The 0D model imposes a time-varying volume to simulate realistic breathing cycles; it also includes a simple model for particle deposition. The resulting hybrid 3D/0D model has been exercised to compute the transport and deposition rates of particles of different sizes through full breathing cycles. Results are compared to earlier steady-flow CFD results, to results obtained using one-dimensional functional models of the human lung, and to experimental and modeling results for idealized branching-duct configurations. The aim of the research is to develop a virtual human respiratory system that can be used to address issues in pulmonary health in

  19. Synthesis of crystalline and amorphous, particle-agglomerated 3-D nanostructures of Al and Si oxides by femtosecond laser and the prediction of these particle sizes

    PubMed Central

    2012-01-01

    We report a single step technique of synthesizing particle-agglomerated, amorphous 3-D nanostructures of Al and Si oxides on powder-fused aluminosilicate ceramic plates and a simple novel method of wafer-foil ablation to fabricate crystalline nanostructures of Al and Si oxides at ambient conditions. We also propose a particle size prediction mechanism to regulate the size of vapor-condensed agglomerated nanoparticles in these structures. Size characterization studies performed on the agglomerated nanoparticles of fabricated 3-D structures showed that the size distributions vary with the fluence-to-threshold ratio. The variation in laser parameters leads to varying plume temperature, pressure, amount of supersaturation, nucleation rate, and the growth rate of particles in the plume. The novel wafer-foil ablation technique could promote the possibilities of fabricating oxide nanostructures with varying Al/Si ratio, and the crystallinity of these structures enhances possible applications. The fabricated nanostructures of Al and Si oxides could have great potentials to be used in the fabrication of low power-consuming complementary metal-oxide-semiconductor circuits and in Mn catalysts to enhance the efficiency of oxidation on ethylbenzene to acetophenone in the super-critical carbon dioxide. PMID:23140103

  20. Nuclear Track Detectors for Particle Searches

    NASA Astrophysics Data System (ADS)

    Manzoor, S.; Balestra, S.; Cozzi, M.; Errico, M.; Giacomelli, G.; Giorgini, M.; Kumar, A.; Margiotta, A.; Medinaceli, E.; Patrizii, L.; Popa, V.; Qureshi, I. E.; Togo, V.

    2007-10-01

    In this paper we report a search for intermediate mass magnetic monopoles and nuclearites using CR39 and Makrofol Nuclear Track Detectors (NTDs) of the SLIM large area experiment, 440 m 2 exposed at the high altitude laboratory of Chacaltaya (Bolivia) and about 100 m 2 at Koksil, Himalaya (Pakistan). We discuss the new chemical etching and improved analysis of the SLIM CR39 sheets. Preliminary limits are based on 316 m 2 of CR39 NTDs exposed for 3.9 y.

  1. Propagation of numerical noise in particle-in-cell tracking

    NASA Astrophysics Data System (ADS)

    Kesting, Frederik; Franchetti, Giuliano

    2015-11-01

    Particle-in-cell (PIC) is the most used algorithm to perform self-consistent tracking of intense charged particle beams. It is based on depositing macroparticles on a grid, and subsequently solving on it the Poisson equation. It is well known that PIC algorithms occupy intrinsic limitations as they introduce numerical noise. Although not significant for short-term tracking, this becomes important in simulations for circular machines over millions of turns as it may induce artificial diffusion of the beam. In this work, we present a modeling of numerical noise induced by PIC algorithms, and discuss its influence on particle dynamics. The combined effect of particle tracking and noise created by PIC algorithms leads to correlated or decorrelated numerical noise. For decorrelated numerical noise we derive a scaling law for the simulation parameters, allowing an estimate of artificial emittance growth. Lastly, the effect of correlated numerical noise is discussed, and a mitigation strategy is proposed.

  2. Ballistic target tracking algorithm based on improved particle filtering

    NASA Astrophysics Data System (ADS)

    Ning, Xiao-lei; Chen, Zhan-qi; Li, Xiao-yang

    2015-10-01

    Tracking ballistic re-entry target is a typical nonlinear filtering problem. In order to track the ballistic re-entry target in the nonlinear and non-Gaussian complex environment, a novel chaos map particle filter (CMPF) is used to estimate the target state. CMPF has better performance in application to estimate the state and parameter of nonlinear and non-Gassuian system. The Monte Carlo simulation results show that, this method can effectively solve particle degeneracy and particle impoverishment problem by improving the efficiency of particle sampling to obtain the better particles to part in estimation. Meanwhile CMPF can improve the state estimation precision and convergence velocity compared with EKF, UKF and the ordinary particle filter.

  3. A particle-tracking approach for accurate material derivative measurements with tomographic PIV

    NASA Astrophysics Data System (ADS)

    Novara, Matteo; Scarano, Fulvio

    2013-08-01

    The evaluation of the instantaneous 3D pressure field from tomographic PIV data relies on the accurate estimate of the fluid velocity material derivative, i.e., the velocity time rate of change following a given fluid element. To date, techniques that reconstruct the fluid parcel trajectory from a time sequence of 3D velocity fields obtained with Tomo-PIV have already been introduced. However, an accurate evaluation of the fluid element acceleration requires trajectory reconstruction over a relatively long observation time, which reduces random errors. On the other hand, simple integration and finite difference techniques suffer from increasing truncation errors when complex trajectories need to be reconstructed over a long time interval. In principle, particle-tracking velocimetry techniques (3D-PTV) enable the accurate reconstruction of single particle trajectories over a long observation time. Nevertheless, PTV can be reliably performed only at limited particle image number density due to errors caused by overlapping particles. The particle image density can be substantially increased by use of tomographic PIV. In the present study, a technique to combine the higher information density of tomographic PIV and the accurate trajectory reconstruction of PTV is proposed (Tomo-3D-PTV). The particle-tracking algorithm is applied to the tracers detected in the 3D domain obtained by tomographic reconstruction. The 3D particle information is highly sparse and intersection of trajectories is virtually impossible. As a result, ambiguities in the particle path identification over subsequent recordings are easily avoided. Polynomial fitting functions are introduced that describe the particle position in time with sequences based on several recordings, leading to the reduction in truncation errors for complex trajectories. Moreover, the polynomial regression approach provides a reduction in the random errors due to the particle position measurement. Finally, the acceleration

  4. 3D tracking of single nanoparticles and quantum dots in living cells by out-of-focus imaging with diffraction pattern recognition

    NASA Astrophysics Data System (ADS)

    Gardini, Lucia; Capitanio, Marco; Pavone, Francesco S.

    2015-11-01

    Live cells are three-dimensional environments where biological molecules move to find their targets and accomplish their functions. However, up to now, most single molecule investigations have been limited to bi-dimensional studies owing to the complexity of 3d-tracking techniques. Here, we present a novel method for three-dimensional localization of single nano-emitters based on automatic recognition of out-of-focus diffraction patterns. Our technique can be applied to track the movements of single molecules in living cells using a conventional epifluorescence microscope. We first demonstrate three-dimensional localization of fluorescent nanobeads over 4 microns depth with accuracy below 2 nm in vitro. Remarkably, we also establish three-dimensional tracking of Quantum Dots, overcoming their anisotropic emission, by adopting a ligation strategy that allows rotational freedom of the emitter combined with proper pattern recognition. We localize commercially available Quantum Dots in living cells with accuracy better than 7 nm over 2 microns depth. We validate our technique by tracking the three-dimensional movements of single protein-conjugated Quantum Dots in living cell. Moreover, we find that important localization errors can occur in off-focus imaging when improperly calibrated and we give indications to avoid them. Finally, we share a Matlab script that allows readily application of our technique by other laboratories.

  5. 3D tracking of single nanoparticles and quantum dots in living cells by out-of-focus imaging with diffraction pattern recognition

    PubMed Central

    Gardini, Lucia; Capitanio, Marco; Pavone, Francesco S.

    2015-01-01

    Live cells are three-dimensional environments where biological molecules move to find their targets and accomplish their functions. However, up to now, most single molecule investigations have been limited to bi-dimensional studies owing to the complexity of 3d-tracking techniques. Here, we present a novel method for three-dimensional localization of single nano-emitters based on automatic recognition of out-of-focus diffraction patterns. Our technique can be applied to track the movements of single molecules in living cells using a conventional epifluorescence microscope. We first demonstrate three-dimensional localization of fluorescent nanobeads over 4 microns depth with accuracy below 2 nm in vitro. Remarkably, we also establish three-dimensional tracking of Quantum Dots, overcoming their anisotropic emission, by adopting a ligation strategy that allows rotational freedom of the emitter combined with proper pattern recognition. We localize commercially available Quantum Dots in living cells with accuracy better than 7 nm over 2 microns depth. We validate our technique by tracking the three-dimensional movements of single protein-conjugated Quantum Dots in living cell. Moreover, we find that important localization errors can occur in off-focus imaging when improperly calibrated and we give indications to avoid them. Finally, we share a Matlab script that allows readily application of our technique by other laboratories. PMID:26526410

  6. 3D tracking of single nanoparticles and quantum dots in living cells by out-of-focus imaging with diffraction pattern recognition.

    PubMed

    Gardini, Lucia; Capitanio, Marco; Pavone, Francesco S

    2015-01-01

    Live cells are three-dimensional environments where biological molecules move to find their targets and accomplish their functions. However, up to now, most single molecule investigations have been limited to bi-dimensional studies owing to the complexity of 3d-tracking techniques. Here, we present a novel method for three-dimensional localization of single nano-emitters based on automatic recognition of out-of-focus diffraction patterns. Our technique can be applied to track the movements of single molecules in living cells using a conventional epifluorescence microscope. We first demonstrate three-dimensional localization of fluorescent nanobeads over 4 microns depth with accuracy below 2 nm in vitro. Remarkably, we also establish three-dimensional tracking of Quantum Dots, overcoming their anisotropic emission, by adopting a ligation strategy that allows rotational freedom of the emitter combined with proper pattern recognition. We localize commercially available Quantum Dots in living cells with accuracy better than 7 nm over 2 microns depth. We validate our technique by tracking the three-dimensional movements of single protein-conjugated Quantum Dots in living cell. Moreover, we find that important localization errors can occur in off-focus imaging when improperly calibrated and we give indications to avoid them. Finally, we share a Matlab script that allows readily application of our technique by other laboratories. PMID:26526410

  7. Ion-counting nanodosemeter with particle tracking capabilities.

    PubMed

    Bashkirov, V; Schulte, R; Breskin, A; Chechik, R; Schemelinin, S; Garty, G; Wroe, A; Sadrozinski, H; Grosswendt, B

    2006-01-01

    An ion-counting nanodosemeter (ND) yielding the distribution of radiation-induced ions in a low-pressure gas within a millimetric, wall-less sensitive volume (SV) was equipped with a silicon microstrip telescope that tracks the primary particles, allowing correlation of nanodosimetric data with particle position relative to the SV. The performance of this tracking ND was tested with a broad 250 MeV proton beam at Loma Linda University Medical Center. The high-resolution tracking capability made it possible to map the ion registration efficiency distribution within the SV, for which only calculated data were available before. It was shown that tracking information combined with nanodosimetric data can map the ionisation pattern of track segments within 150 nm-equivalent long SVs with a longitudinal resolution of approximately 5 tissue-equivalent nanometers. Data acquired in this work were compared with results of Monte Carlo track structure simulations. The good agreement between 'tracking nanodosimetry' data acquired with the new system and simulated data supports the application of ion-counting nanodosimetry in experimental track-structure studies. PMID:17283009

  8. Boosting target tracking using particle filter with flow control

    NASA Astrophysics Data System (ADS)

    Moshtagh, Nima; Chan, Moses W.

    2013-05-01

    Target detection and tracking with passive infrared (IR) sensors can be challenging due to significant degradation and corruption of target signature by atmospheric transmission and clutter effects. This paper summarizes our efforts in phenomenology modeling of boosting targets with IR sensors, and developing algorithms for tracking targets in the presence of background clutter. On the phenomenology modeling side, the clutter images are generated using a high fidelity end-to-end simulation testbed. It models atmospheric transmission, structured clutter and solar reflections to create realistic background images. The dynamics and intensity of a boosting target are modeled and injected onto the background scene. Pixel level images are then generated with respect to the sensor characteristics. On the tracking analysis side, a particle filter for tracking targets in a sequence of clutter images is developed. The particle filter is augmented with a mechanism to control particle flow. Specifically, velocity feedback is used to constrain and control the particles. The performance of the developed "adaptive" particle filter is verified with tracking of a boosting target in the presence of clutter and occlusion.

  9. Live imaging and quantitative analysis of gastrulation in mouse embryos using light-sheet microscopy and 3D tracking tools.

    PubMed

    Ichikawa, Takehiko; Nakazato, Kenichi; Keller, Philipp J; Kajiura-Kobayashi, Hiroko; Stelzer, Ernst H K; Mochizuki, Atsushi; Nonaka, Shigenori

    2014-03-01

    This protocol describes how to observe gastrulation in living mouse embryos by using light-sheet microscopy and computational tools to analyze the resulting image data at the single-cell level. We describe a series of techniques needed to image the embryos under physiological conditions, including how to hold mouse embryos without agarose embedding, how to transfer embryos without air exposure and how to construct environmental chambers for live imaging by digital scanned light-sheet microscopy (DSLM). Computational tools include manual and semiautomatic tracking programs that are developed for analyzing the large 4D data sets acquired with this system. Note that this protocol does not include details of how to build the light-sheet microscope itself. Time-lapse imaging ends within 12 h, with subsequent tracking analysis requiring 3-6 d. Other than some mouse-handling skills, this protocol requires no advanced skills or knowledge. Light-sheet microscopes are becoming more widely available, and thus the techniques outlined in this paper should be helpful for investigating mouse embryogenesis. PMID:24525751

  10. Terrestrial laser scanning point clouds time series for the monitoring of slope movements: displacement measurement using image correlation and 3D feature tracking

    NASA Astrophysics Data System (ADS)

    Bornemann, Pierrick; Jean-Philippe, Malet; André, Stumpf; Anne, Puissant; Julien, Travelletti

    2016-04-01

    Dense multi-temporal point clouds acquired with terrestrial laser scanning (TLS) have proved useful for the study of structure and kinematics of slope movements. Most of the existing deformation analysis methods rely on the use of interpolated data. Approaches that use multiscale image correlation provide a precise and robust estimation of the observed movements; however, for non-rigid motion patterns, these methods tend to underestimate all the components of the movement. Further, for rugged surface topography, interpolated data introduce a bias and a loss of information in some local places where the point cloud information is not sufficiently dense. Those limits can be overcome by using deformation analysis exploiting directly the original 3D point clouds assuming some hypotheses on the deformation (e.g. the classic ICP algorithm requires an initial guess by the user of the expected displacement patterns). The objective of this work is therefore to propose a deformation analysis method applied to a series of 20 3D point clouds covering the period October 2007 - October 2015 at the Super-Sauze landslide (South East French Alps). The dense point clouds have been acquired with a terrestrial long-range Optech ILRIS-3D laser scanning device from the same base station. The time series are analyzed using two approaches: 1) a method of correlation of gradient images, and 2) a method of feature tracking in the raw 3D point clouds. The estimated surface displacements are then compared with GNSS surveys on reference targets. Preliminary results tend to show that the image correlation method provides a good estimation of the displacement fields at first order, but shows limitations such as the inability to track some deformation patterns, and the use of a perspective projection that does not maintain original angles and distances in the correlated images. Results obtained with 3D point clouds comparison algorithms (C2C, ICP, M3C2) bring additional information on the

  11. Tracking low SNR targets using particle filter with flow control

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

    In this work we study the problem of detecting and tracking challenging targets that exhibit low signal-to-noise ratios (SNR). We have developed a particle filter-based track-before-detect (TBD) algorithm for tracking such dim targets. The approach incorporates the most recent state estimates to control the particle flow accounting for target dynamics. The flow control enables accumulation of signal information over time to compensate for target motion. The performance of this approach is evaluated using a sensitivity analysis based on varying target speed and SNR values. This analysis was conducted using high-fidelity sensor and target modeling in realistic scenarios. Our results show that the proposed TBD algorithm is capable of tracking targets in cluttered images with SNR values much less than one.

  12. Scintillator-fiber charged particle track-imaging detector

    NASA Technical Reports Server (NTRS)

    Binns, W. R.; Israel, M. H.; Klarmann, J.

    1983-01-01

    A scintillator-fiber charged-particle track-imaging detector was developed using a bundle of square cross section plastic scintillator fiber optics, proximity focused onto an image intensified charge injection device (CID) camera. The tracks of charged particle penetrating into the scintillator fiber bundle are projected onto the CID camera and the imaging information is read out in video format. The detector was exposed to beams of 15 MeV protons and relativistic Neon, Manganese, and Gold nuclei and images of their tracks were obtained. Details of the detector technique, properties of the tracks obtained, and preliminary range measurements of 15 MeV protons stopping in the fiber bundle are presented.

  13. Three-dimensional tracking of acoustophoretic particle trajectories in a Poiseuille flow

    NASA Astrophysics Data System (ADS)

    Barnkob, Rune; Rossi, Massimiliano; Marin, Alvaro G.; Kähler, Christian J.

    2013-11-01

    Acoustics in microfluidics has proved as an excellent technique for particle separation. The technique is often based on advecting the particles by a Poiseuille flow, while acoustic forces push the particles transversely across the flow according to particle size, density, and compressibility. In this work we study such particle trajectories in a microchannel containing a dilute particle suspension. The microchannel is excited in its transverse ultrasound half-wave resonance, while a Poiseuille flow is imposed along the channel. In addition to the viscous drag force from the imposed flow, the particles are subject to forces from acoustic radiation as well as viscous drag from acoustic streaming (Muller et al., PRE, in press, 2013). In the microchannel cross-section, the acoustic streaming is two-dimensional, while the acoustic radiation force is one-dimensional. However, the actual particle velocity induced by the acoustic radiation force has a two-dimensional character due to wall-enhancement of the viscous Stokes drag. In the experiments, we use a 3D astigmatic particle tracking technique (APTV, Cierpka et al., Meas Sci Technol 22, 2011) to determine the particle trajectories, which we compare to theoretical predictions for future optimization of acoustic separation systems. DFG, grant no. KA 1808/16-1.

  14. Determining the 3D orientation of optically trapped upconverting nanorods by in situ single-particle polarized spectroscopy

    NASA Astrophysics Data System (ADS)

    Rodríguez-Sevilla, Paloma; Labrador-Páez, Lucía; Wawrzyńczyk, Dominika; Nyk, Marcin; Samoć, Marek; Kar, Ajoy Kumar; MacKenzie, Mark D.; Paterson, Lynn; Jaque, Daniel; Haro-González, Patricia

    2015-12-01

    An approach to unequivocally determine the three-dimensional orientation of optically manipulated NaYF4:Er3+,Yb3+ upconverting nanorods (UCNRs) is demonstrated. Long-term immobilization of individual UCNRs inside single and multiple resonant optical traps allow for stable single UCNR spectroscopy studies. Based on the strong polarization dependent upconverted luminescence of UCNRs it is possible to unequivocally determine, in real time, their three-dimensional orientation when optically trapped. In single-beam traps, polarized single particle spectroscopy has concluded that UCNRs orientate parallel to the propagation axis of the trapping beam. On the other hand, when multiple-beam optical tweezers are used, single particle polarization spectroscopy demonstrated how full spatial control over UCNR orientation can be achieved by changing the trap-to-trap distance as well as the relative orientation between optical traps. All these results show the possibility of real time three-dimensional manipulation and tracking of anisotropic nanoparticles with wide potential application in modern nanobiophotonics.An approach to unequivocally determine the three-dimensional orientation of optically manipulated NaYF4:Er3+,Yb3+ upconverting nanorods (UCNRs) is demonstrated. Long-term immobilization of individual UCNRs inside single and multiple resonant optical traps allow for stable single UCNR spectroscopy studies. Based on the strong polarization dependent upconverted luminescence of UCNRs it is possible to unequivocally determine, in real time, their three-dimensional orientation when optically trapped. In single-beam traps, polarized single particle spectroscopy has concluded that UCNRs orientate parallel to the propagation axis of the trapping beam. On the other hand, when multiple-beam optical tweezers are used, single particle polarization spectroscopy demonstrated how full spatial control over UCNR orientation can be achieved by changing the trap-to-trap distance as well as

  15. 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.

  16. Development of the 3-D Track Imager for Medium and High-Energy Gamma-Ray Telescopes

    NASA Technical Reports Server (NTRS)

    Hunter, Stanley D.

    2006-01-01

    The Advanced Compton Telescope (ACT) and Advanced Pair Telescope (APT) are envisioned as the next medium (0.3 ^ 50 MeV) and high-energy (30 MeV - greater than 100 GeV) gamma-ray missions. These missions will address many research focus areas of the Structure and Evolution of the Universe Roadmap. These areas include: element formation, matter, energy, & magnetic field interactions in galaxies, AGN & GRB emission, and behavior of matter in extreme environments of black holes & pulsars. Achieving these science goals requires a substantial increases in telescope sensitivity and angular resolution. This talk will discuss how these goals can be met with the three-dimensional track imager (3-DTI), a large volume, low density, time projection chamber with two-dimensional micro-well detector readout and report on our development of a 10 cm x 10 cm x 30 prototype instrument.

  17. Modeling oceanic multiphase flow by using Lagrangian particle tracking

    NASA Astrophysics Data System (ADS)

    Matsumura, Y.

    2014-12-01

    While the density of seawater is basically determined by its temperature, salinity and pressure, the effective density becomes higher when the water mass contains suspended sediment. On the other hands, effective density declines when water mass contains fine scale materials of lower density such as bubbles and ice crystals. Such density anomaly induced by small scale materials suspended in water masses sometimes plays important roles in the sub-mesoscale ocean physics. To simulate these small scale oceanic multiphase flow, a new modeling framework using an online Lagrangian particle tracking method is developed. A Lagrangian particle tracking method has substantial advantages such as an explicit treatment of buoyancy force acting on each individual particle, no numerical diffusion and dissipation, high dynamic range and an ability to track the history and each individual particle. However, its numerical cost causes difficulty when we try to simulate a large number of particles. In the present study we implement a numerically efficient particle tracking scheme using linked-list data structure, which is coupled with a nonhydrostatic dynamical core. This newly developed model successfully reproduces characteristics of some interesting small scale multiphase processes, for example hyperpycnal flow (a sediment-rich river water plume trapped at ocean floor) and grease ice cover (a slurry mixture of frazil ice crystals and seawater).

  18. Luminescent Sensors for Tracking Spatial Particle Distribution in an Explosion

    NASA Astrophysics Data System (ADS)

    Eilers, Hergen; Gunawidjaja, Ray; Diez-Y-Riega, Helena; Svingala, Forrest; Daniels, Amber; Lightstone, James; Washington State University Collaboration; Nswc Iheodtd Collaboration

    2015-06-01

    We previously developed and tested thermally sensitive particles that, when seeded into an explosive event, flow with the expanding post-detonation fireball and provide ex-situ measurements of this thermal environment. This current work presents the development and testing of tracking particles that are used in concert with the thermally sensitive particles to encode the initial positions of materials recovered for ex-situ analysis. These tracking sensors consist of fully-crystallized (c) rare-earth-doped yttria particles such as c-Dy:Y2O3, c-Sm:Y2O3, and c-Er,Yb:Y2O3. The temperature sensors consist of mixtures of precursor (p) and fully crystallized materials such as p-Eu:Y2O3/c-Tb:Y2O3 orp-Eu:ZrO2/c-Tb:Y2O3. Three mixtures containing one of the tracking sensors and one of the temperature sensing mixtures are placed at different locations within the chamber. Post-detonation, the tracking particles in the debris are excited by 365 nm light, resulting in different color luminescence, and allowing for potential visual inspection of the particle distribution originating from the different locations. Meanwhile, the temperature is determined from spectral changes of the precursor sensor materials or by comparison of the precursor sensor materials with the Tb:Y2O3 intensity reference. Defense Threat Reduction Agency, HDTRA1-10-1-0005.

  19. Scintillator-fiber charged-particle track-imaging detector

    NASA Technical Reports Server (NTRS)

    Binns, W. R.; Israel, M. H.; Klarmann, J.

    1983-01-01

    A scintillator-fiber charged-particle track-imaging detector has been developed using a bundle of square cross-section plastic scintillator fiber optics, proximity focused onto an image intensified Charge Injection Device (CID) camera. Detector to beams of 15 MeV protons and relativistic Neon, Manganese, and Gold nuclei have been exposed and images of their tracks are obtained. This paper presents details of the detector technique, properties of the tracks obtained, and range measurements of 15 MeV protons stopping in the fiber bundle.

  20. Collective Bacterial Dynamics Revealed Using a Three-Dimensional Population-Scale Defocused Particle Tracking Technique

    PubMed Central

    Wu, Mingming; Roberts, John W.; Kim, Sue; Koch, Donald L.; DeLisa, Matthew P.

    2006-01-01

    An ability to monitor bacterial locomotion and collective dynamics is crucial to our understanding of a number of well-characterized phenotypes including biofilm formation, chemotaxis, and virulence. Here, we report the tracking of multiple swimming Escherichia coli cells in three spatial dimensions and at single-cell resolution using a novel three-dimensional (3D) defocused particle tracking (DPT) method. The 3D trajectories were generated for wild-type Escherichia coli strain RP437 as well as for isogenic derivatives that display smooth swimming due to a cheA deletion (strain RP9535) or incessant tumbling behavior due to a cheZ deletion (strain RP1616). The 3D DPT method successfully differentiated these three modes of locomotion and allowed direct calculation of the diffusion coefficient for each strain. As expected, we found that the smooth swimmer diffused more readily than the wild type, and both the smooth swimmer and the wild-type cells exhibited diffusion coefficients that were at least two orders of magnitude larger than that of the tumbler. Finally, we found that the diffusion coefficient increased with increasing cell density, a phenomenon that can be attributed to the hydrodynamic disturbances caused by neighboring bacteria. PMID:16820497

  1. Determining the 3D orientation of optically trapped upconverting nanorods by in situ single-particle polarized spectroscopy.

    PubMed

    Rodríguez-Sevilla, Paloma; Labrador-Páez, Lucía; Wawrzyńczyk, Dominika; Nyk, Marcin; Samoć, Marek; Kar, Ajoy Kumar; Mackenzie, Mark D; Paterson, Lynn; Jaque, Daniel; Haro-González, Patricia

    2016-01-01

    An approach to unequivocally determine the three-dimensional orientation of optically manipulated NaYF4:Er(3+),Yb(3+) upconverting nanorods (UCNRs) is demonstrated. Long-term immobilization of individual UCNRs inside single and multiple resonant optical traps allow for stable single UCNR spectroscopy studies. Based on the strong polarization dependent upconverted luminescence of UCNRs it is possible to unequivocally determine, in real time, their three-dimensional orientation when optically trapped. In single-beam traps, polarized single particle spectroscopy has concluded that UCNRs orientate parallel to the propagation axis of the trapping beam. On the other hand, when multiple-beam optical tweezers are used, single particle polarization spectroscopy demonstrated how full spatial control over UCNR orientation can be achieved by changing the trap-to-trap distance as well as the relative orientation between optical traps. All these results show the possibility of real time three-dimensional manipulation and tracking of anisotropic nanoparticles with wide potential application in modern nanobiophotonics. PMID:26607763

  2. Improved image guidance technique for minimally invasive mitral valve repair using real-time tracked 3D ultrasound

    NASA Astrophysics Data System (ADS)

    Rankin, Adam; Moore, John; Bainbridge, Daniel; Peters, Terry

    2016-03-01

    In the past ten years, numerous new surgical and interventional techniques have been developed for treating heart valve disease without the need for cardiopulmonary bypass. Heart valve repair is now being performed in a blood-filled environment, reinforcing the need for accurate and intuitive imaging techniques. Previous work has demonstrated how augmenting ultrasound with virtual representations of specific anatomical landmarks can greatly simplify interventional navigation challenges and increase patient safety. These techniques often complicate interventions by requiring additional steps taken to manually define and initialize virtual models. Furthermore, overlaying virtual elements into real-time image data can also obstruct the view of salient image information. To address these limitations, a system was developed that uses real-time volumetric ultrasound alongside magnetically tracked tools presented in an augmented virtuality environment to provide a streamlined navigation guidance platform. In phantom studies simulating a beating-heart navigation task, procedure duration and tool path metrics have achieved comparable performance to previous work in augmented virtuality techniques, and considerable improvement over standard of care ultrasound guidance.

  3. Inference in particle tracking experiments by passing messages between images.

    PubMed

    Chertkov, M; Kroc, L; Krzakala, F; Vergassola, M; Zdeborová, L

    2010-04-27

    Methods to extract information from the tracking of mobile objects/particles have broad interest in biological and physical sciences. Techniques based on simple criteria of proximity in time-consecutive snapshots are useful to identify the trajectories of the particles. However, they become problematic as the motility and/or the density of the particles increases due to uncertainties on the trajectories that particles followed during the images' acquisition time. Here, we report an efficient method for learning parameters of the dynamics of the particles from their positions in time-consecutive images. Our algorithm belongs to the class of message-passing algorithms, known in computer science, information theory, and statistical physics as belief propagation (BP). The algorithm is distributed, thus allowing parallel implementation suitable for computations on multiple machines without significant intermachine overhead. We test our method on the model example of particle tracking in turbulent flows, which is particularly challenging due to the strong transport that those flows produce. Our numerical experiments show that the BP algorithm compares in quality with exact Markov Chain Monte Carlo algorithms, yet BP is far superior in speed. We also suggest and analyze a random distance model that provides theoretical justification for BP accuracy. Methods developed here systematically formulate the problem of particle tracking and provide fast and reliable tools for the model's extensive range of applications. PMID:20368454

  4. Exploring dynamics in living cells by tracking single particles.

    PubMed

    Levi, Valeria; Gratton, Enrico

    2007-01-01

    In the last years, significant advances in microscopy techniques and the introduction of a novel technology to label living cells with genetically encoded fluorescent proteins revolutionized the field of Cell Biology. Our understanding on cell dynamics built from snapshots on fixed specimens has evolved thanks to our actual capability to monitor in real time the evolution of processes in living cells. Among these new tools, single particle tracking techniques were developed to observe and follow individual particles. Hence, we are starting to unravel the mechanisms driving the motion of a wide variety of cellular components ranging from organelles to protein molecules by following their way through the cell. In this review, we introduce the single particle tracking technology to new users. We briefly describe the instrumentation and explain some of the algorithms commonly used to locate and track particles. Also, we present some common tools used to analyze trajectories and illustrate with some examples the applications of single particle tracking to study dynamics in living cells. PMID:17703064

  5. Tracking-FCS: Fluorescence correlation spectroscopy of individual particles

    NASA Astrophysics Data System (ADS)

    Berglund, Andrew J.; Mabuchi, Hideo

    2005-10-01

    We exploit recent advances in single-particle tracking to perform fluorescence correlation spectroscopy on individual fluorescent particles, in contrast to traditional methods that build up statistics over a sequence of many measurements. By rapidly scanning the focus of an excitation laser in a circular pattern, demodulating the measured fluorescence, and feeding these results back to a piezoelectric translation stage, we track the Brownian motion of fluorescent polymer microspheres in aqueous solution in the plane transverse to the laser axis. We discuss the estimation of particle diffusion statistics from closed-loop position measurements, and we present a generalized theory of fluorescence correlation spectroscopy for the case that the motion of a single fluorescent particle is actively tracked by a time-dependent laser intensity. We model the motion of a tracked particle using Ornstein-Uhlenbeck statistics, using a general theory that contains a umber of existing results as specific cases. We find good agreement between our theory and experimental results, and discuss possible future applications of these techniques to passive, single-shot, single-molecule fluorescence measurements with many orders of magnitude in time resolution.

  6. SimTrack: A compact c++ code for particle orbit and spin tracking in accelerators

    SciTech Connect

    Luo, Yun

    2015-08-29

    SimTrack is a compact c++ code of 6-d symplectic element-by-element particle tracking in accelerators originally designed for head-on beam–beam compensation simulation studies in the Relativistic Heavy Ion Collider (RHIC) at Brookhaven National Laboratory. It provides a 6-d symplectic orbit tracking with the 4th order symplectic integration for magnet elements and the 6-d symplectic synchro-beam map for beam–beam interaction. Since its inception in 2009, SimTrack has been intensively used for dynamic aperture calculations with beam–beam interaction for RHIC. Recently, proton spin tracking and electron energy loss due to synchrotron radiation were added. In this article, I will present the code architecture, physics models, and some selected examples of its applications to RHIC and a future electron-ion collider design eRHIC.

  7. SimTrack: A compact c++ library for particle orbit and spin tracking in accelerators

    SciTech Connect

    Luo, Yun

    2015-06-24

    SimTrack is a compact c++ library of 6-d symplectic element-by-element particle tracking in accelerators originally designed for head-on beam-beam compensation simulation studies in the Relativistic Heavy Ion Collider (RHIC) at Brookhaven National Laboratory. It provides a 6-d symplectic orbit tracking with the 4th order symplectic integration for magnet elements and the 6-d symplectic synchro-beam map for beam-beam interaction. Since its inception in 2009, SimTrack has been intensively used for dynamic aperture calculations with beam-beam interaction for RHIC. Recently, proton spin tracking and electron energy loss due to synchrotron radiation were added. In this article, I will present the code architecture, physics models, and some selected examples of its applications to RHIC and a future electron-ion collider design eRHIC.

  8. SimTrack: A compact c++ code for particle orbit and spin tracking in accelerators

    DOE PAGESBeta

    Luo, Yun

    2015-08-29

    SimTrack is a compact c++ code of 6-d symplectic element-by-element particle tracking in accelerators originally designed for head-on beam–beam compensation simulation studies in the Relativistic Heavy Ion Collider (RHIC) at Brookhaven National Laboratory. It provides a 6-d symplectic orbit tracking with the 4th order symplectic integration for magnet elements and the 6-d symplectic synchro-beam map for beam–beam interaction. Since its inception in 2009, SimTrack has been intensively used for dynamic aperture calculations with beam–beam interaction for RHIC. Recently, proton spin tracking and electron energy loss due to synchrotron radiation were added. In this article, I will present the code architecture,more » physics models, and some selected examples of its applications to RHIC and a future electron-ion collider design eRHIC.« less

  9. Flow above and within granular media composed of spherical and non-spherical particles - using a 3D numerical model

    NASA Astrophysics Data System (ADS)

    Bartzke, Gerhard; Kuhlmann, Jannis; Huhn, Katrin

    2016-04-01

    The entrainment of single grains and, hence, their erosion characteristics are dependent on fluid forcing, grain size and density, but also shape variations. To quantitatively describe and capture the hydrodynamic conditions around individual grains, researchers commonly use empirical approaches such as laboratory flume tanks. Nonetheless, it is difficult with such physical experiments to measure the flow velocities in the direct vicinity or within the pore spaces of sediments, at a sufficient resolution and in a non-invasive way. As a result, the hydrodynamic conditions in the water column, at the fluid-porous interface and within pore spaces of a granular medium of various grain shapes is not yet fully understood. For that reason, there is a strong need for numerical models, since these are capable of quantifying fluid speeds within a granular medium. A 3D-SPH (Smooth Particle Hydrodynamics) numerical wave tank model was set up to provide quantitative evidence on the flow velocities in the direct vicinity and in the interior of granular beds composed of two shapes as a complementary method to the difficult task of in situ measurement. On the basis of previous successful numerical wave tank models with SPH, the model geometry was chosen in dimensions of X=2.68 [m], Y=0.48 [m], and Z=0.8 [m]. Three suites of experiments were designed with a range of particle shape models: (1) ellipsoids with the long axis oriented in the across-stream direction, (2) ellipsoids with the long axis oriented in the along-stream direction, and (3) spheres. Particle diameters ranged from 0.04 [m] to 0.08 [m]. A wave was introduced by a vertical paddle that accelerated to 0.8 [m/s] perpendicular to the granular bed. Flow measurements showed that the flow velocity values into the beds were highest when the grains were oriented across the stream direction and lowest in case when the grains were oriented parallel to the stream, indicating that the model was capable to simulate simultaneously

  10. Three‐Dimensional Echocardiography and 2D‐3D Speckle‐Tracking Imaging in Chronic Pulmonary Hypertension: Diagnostic Accuracy in Detecting Hemodynamic Signs of Right Ventricular (RV) Failure

    PubMed Central

    Vitarelli, Antonio; Mangieri, Enrico; Terzano, Claudio; Gaudio, Carlo; Salsano, Felice; Rosato, Edoardo; Capotosto, Lidia; D'Orazio, Simona; Azzano, Alessia; Truscelli, Giovanni; Cocco, Nino; Ashurov, Rasul

    2015-01-01

    Background Our aim was to compare three‐dimensional (3D) and 2D and 3D speckle‐tracking (2D‐STE, 3D‐STE) echocardiographic parameters with conventional right ventricular (RV) indexes in patients with chronic pulmonary hypertension (PH), and investigate whether these techniques could result in better correlation with hemodynamic variables indicative of heart failure. Methods and Results Seventy‐three adult patients (mean age, 53±13 years; 44% male) with chronic PH of different etiologies were studied by echocardiography and cardiac catheterization (25 precapillary PH from pulmonary arterial hypertension, 23 obstructive pulmonary heart disease, and 23 postcapillary PH from mitral regurgitation). Thirty healthy subjects (mean age, 54±15 years; 43% male) served as controls. Standard 2D measurements (RV–fractional area change–tricuspid annular plane systolic excursion) and mitral and tricuspid tissue Doppler annular velocities were obtained. RV 3D volumes and global and regional ejection fraction (3D‐RVEF) were determined. RV strains were calculated by 2D‐STE and 3D‐STE. RV 3D global‐free‐wall longitudinal strain (3DGFW‐RVLS), 2D global‐free‐wall longitudinal strain (GFW‐RVLS), apical‐free‐wall longitudinal strain, basal‐free‐wall longitudinal strain, and 3D‐RVEF were lower in patients with precapillary PH (P<0.0001) and postcapillary PH (P<0.01) compared to controls. 3DGFW‐RVLS (hazard ratio 4.6, 95% CI 2.79 to 8.38, P=0.004) and 3D‐RVEF (hazard ratio 5.3, 95% CI 2.85 to 9.89, P=0.002) were independent predictors of mortality. Receiver operating characteristic curves showed that the thresholds offering an adequate compromise between sensitivity and specificity for detecting hemodynamic signs of RV failure were 39% for 3D‐RVEF (AUC 0.89), −17% for 3DGFW‐RVLS (AUC 0.88), −18% for GFW‐RVLS (AUC 0.88), −16% for apical‐free‐wall longitudinal strain (AUC 0.85), 16 mm for tricuspid annular plane systolic

  11. In Situ Particle Tracking around kW Sized Wind Turbines

    NASA Astrophysics Data System (ADS)

    Brownstein, Ian; Dabiri, John

    2015-11-01

    Laboratory studies of model wind turbines are typically unable to match both the Reynolds number (Re) and tip speed ratio (TSR) of full-scale wind turbines. In order to match both relevant parameters, a quantitative flow visualization method was developed to take in situ measurements of the flow around full-scale wind turbines. The apparatus constructed was able to seed an approximately 9mx9mx5m volume in the wake of the turbine using artificial snow. Quantitative results were obtained by tracking the evolution of the snow using particle tracking algorithms. As a step toward full 3D-PTV measurements, results will be presented in which a 2D measurement is taken with a single camera positioned at the base of the turbine looking upward. The resulting tracking is therefore integrated in the span-wise direction. This method is demonstrated through a comparative study of a five-bladed VAWT producing power in different wind conditions at the Field Laboratory for Optimized Wind Energy (FLOWE) in Lancaster, CA. Future work to expand this method to 3D-PTV is also discussed.

  12. Nuclear particle detection using a track-recording solid

    NASA Technical Reports Server (NTRS)

    Weber, M.; Weber, D.

    1984-01-01

    The design of the nuclear particle detector located in Purdue University's Get Away Special package which was flown aboard STS-7 is detailed. The experiment consisted of a stack of particle-detecting polymer sheets. The sheets show positive results of tracks throughout the block. A slide of each sheet was made for further analysis. Recommendations for similar experiments performed in the future are discussed.

  13. Three-dimensional Particle Tracking Velocimetry for Turbulence Applications: Case of a Jet Flow.

    PubMed

    Kim, Jin-Tae; Kim, David; Liberzon, Alex; Chamorro, Leonardo P

    2016-01-01

    3D-PTV is a quantitative flow measurement technique that aims to track the Lagrangian paths of a set of particles in three dimensions using stereoscopic recording of image sequences. The basic components, features, constraints and optimization tips of a 3D-PTV topology consisting of a high-speed camera with a four-view splitter are described and discussed in this article. The technique is applied to the intermediate flow field (5 particles as well as curvature of the flow path, which are obtained from the Frenet-Serret equation. Estimation of the 3D velocity and turbulence fields around the jet core axis at a cross-plane located at ten diameters downstream of the jet is compared with literature, and the power spectrum of the large-scale streamwise velocity motions is obtained at various radial distances from the jet core. PMID:26967544

  14. A new GUI based toolbox to compare particle tracking approaches

    NASA Astrophysics Data System (ADS)

    Payne, Matthew; Münch, Gerald; Vallotton, Pascal

    2013-10-01

    A plethora of powerful particle tracking algorithms is available to the quantitative biologist to follow targets such as vesicles, single proteins, or cells. The question of which technique to use for particular applications has become an important topic in the discipline. We have developed a friendly graphical user interface, which generates synthetic data sets corresponding to fields of moving point-like targets. Thus, the ground truth is available and algorithms may be compared on relevant dynamics. We present this framework by applying it to four different particle tracking software and use Icy to compare the ground truth with the results produced by these algorithms. Our tool will be useful to those researchers interested to evaluate the performance of tracking algorithms in circumstances that are more general than random motion, or more general than mere translational motion perturbed by noise.

  15. Optimal diffusion coefficient estimation in single-particle tracking

    PubMed Central

    Michalet, Xavier; Berglund, Andrew J.

    2016-01-01

    Single-particle tracking is increasingly used to extract quantitative parameters on single molecules and their environment, while advances in spatial and temporal resolution of tracking techniques inspire new questions and avenues of investigation. Correspondingly, sophisticated analytical methods are constantly developed to obtain more refined information from measured trajectories. Here we point out some fundamental limitations of these approaches due to the finite length of trajectories, the presence of localization error, and motion blur, focusing on the simplest motion regime of free diffusion in an isotropic medium (Brownian motion). We show that two recently proposed algorithms approach the theoretical limit of diffusion coefficient uncertainty. We discuss the practical performance of the algorithms as well as some important implications of these results for single-particle tracking. PMID:23005136

  16. Physical Models for Particle Tracking Simulations in the RF Gap

    SciTech Connect

    Shishlo, Andrei P.; Holmes, Jeffrey A.

    2015-06-01

    This document describes the algorithms that are used in the PyORBIT code to track the particles accelerated in the Radio-Frequency cavities. It gives the mathematical description of the algorithms and the assumptions made in each case. The derived formulas have been implemented in the PyORBIT code. The necessary data for each algorithm are described in detail.

  17. Single Particle Orientation and Rotational Tracking (SPORT) in biopysical studies

    SciTech Connect

    Gu, Yan; Ha, Ji Won; Augspurger, Ashley E.; Chen, Kuangcai; Zhu, Shaobin; Fang, Ning

    2013-08-02

    The single particle orientation and rotational tracking (SPORT) techniques have seen rapid development in the past 5 years. Recent technical advances have greatly expanded the applicability of SPORT in biophysical studies. In this feature article, we survey the current development of SPORT and discuss its potential applications in biophysics, including cellular membrane processes and intracellular transport.

  18. In situ 3-D mapping of pore structures and hollow grains of interplanetary dust particles with phase contrast X-ray nanotomography

    NASA Astrophysics Data System (ADS)

    Hu, Z. W.; Winarski, R. P.

    2016-06-01

    Unlocking the 3-D structure and properties of intact chondritic porous interplanetary dust particles (IDPs) in nanoscale detail is challenging, which is also complicated by atmospheric entry heating, but is important for advancing our understanding of the formation and origins of IDPs and planetary bodies as well as dust and ice agglomeration in the outer protoplanetary disk. Here, we show that indigenous pores, pristine grains, and thermal alteration products throughout intact particles can be noninvasively visualized and distinguished morphologically and microstructurally in 3-D detail down to ~10 nm by exploiting phase contrast X-ray nanotomography. We have uncovered the surprisingly intricate, submicron, and nanoscale pore structures of a ~10-μm-long porous IDP, consisting of two types of voids that are interconnected in 3-D space. One is morphologically primitive and mostly submicron-sized intergranular voids that are ubiquitous; the other is morphologically advanced and well-defined intragranular nanoholes that run through the approximate centers of ~0.3 μm or lower submicron hollow grains. The distinct hollow grains exhibit complex 3-D morphologies but in 2-D projections resemble typical organic hollow globules observed by transmission electron microscopy. The particle, with its outer region characterized by rough vesicular structures due to thermal alteration, has turned out to be an inherently fragile and intricately submicron- and nanoporous aggregate of the sub-μm grains or grain clumps that are delicately bound together frequently with little grain-to-grain contact in 3-D space.

  19. In situ 3-D mapping of pore structures and hollow grains of interplanetary dust particles with phase contrast X-ray nanotomography

    NASA Astrophysics Data System (ADS)

    Hu, Z. W.; Winarski, R. P.

    2016-09-01

    Unlocking the 3-D structure and properties of intact chondritic porous interplanetary dust particles (IDPs) in nanoscale detail is challenging, which is also complicated by atmospheric entry heating, but is important for advancing our understanding of the formation and origins of IDPs and planetary bodies as well as dust and ice agglomeration in the outer protoplanetary disk. Here, we show that indigenous pores, pristine grains, and thermal alteration products throughout intact particles can be noninvasively visualized and distinguished morphologically and microstructurally in 3-D detail down to ~10 nm by exploiting phase contrast X-ray nanotomography. We have uncovered the surprisingly intricate, submicron, and nanoscale pore structures of a ~10-μm-long porous IDP, consisting of two types of voids that are interconnected in 3-D space. One is morphologically primitive and mostly submicron-sized intergranular voids that are ubiquitous; the other is morphologically advanced and well-defined intragranular nanoholes that run through the approximate centers of ~0.3 μm or lower submicron hollow grains. The distinct hollow grains exhibit complex 3-D morphologies but in 2-D projections resemble typical organic hollow globules observed by transmission electron microscopy. The particle, with its outer region characterized by rough vesicular structures due to thermal alteration, has turned out to be an inherently fragile and intricately submicron- and nanoporous aggregate of the sub-μm grains or grain clumps that are delicately bound together frequently with little grain-to-grain contact in 3-D space.

  20. Bearings-Only Tracking of Manoeuvring Targets Using Particle Filters

    NASA Astrophysics Data System (ADS)

    Arulampalam, M. Sanjeev; Ristic, B.; Gordon, N.; Mansell, T.

    2004-12-01

    We investigate the problem of bearings-only tracking of manoeuvring targets using particle filters (PFs). Three different (PFs) are proposed for this problem which is formulated as a multiple model tracking problem in a jump Markov system (JMS) framework. The proposed filters are (i) multiple model PF (MMPF), (ii) auxiliary MMPF (AUX-MMPF), and (iii) jump Markov system PF (JMS-PF). The performance of these filters is compared with that of standard interacting multiple model (IMM)-based trackers such as IMM-EKF and IMM-UKF for three separate cases: (i) single-sensor case, (ii) multisensor case, and (iii) tracking with hard constraints. A conservative CRLB applicable for this problem is also derived and compared with the RMS error performance of the filters. The results confirm the superiority of the PFs for this difficult nonlinear tracking problem.

  1. Comparison of three-dimensional particle tracking and sizing using plenoptic imaging and digital in-line holography.

    PubMed

    Hall, Elise M; Thurow, Brian S; Guildenbecher, Daniel R

    2016-08-10

    Digital in-line holography (DIH) and plenoptic photography are two techniques for single-shot, volumetric measurement of 3D particle fields. Here we present a comparison of the two methods by applying plenoptic imaging to experimental configurations that have been previously investigated with DIH. These experiments include the tracking of secondary droplets from the impact of a water drop on a thin film of water and tracking of pellets from a shotgun. Both plenoptic imaging and DIH successfully quantify the 3D nature of these particle fields. This includes measurement of the 3D particle position, individual particle sizes, and three-component velocity vectors. For the initial processing methods presented here, both techniques give out-of-plane positional accuracy of approximately 1-2 particle diameters. For a fixed image sensor, digital holography achieves higher effective in-plane spatial resolutions. However, collimated and coherent illumination makes holography susceptible to image distortion through index of refraction gradients, as demonstrated in the shotgun experiments. In contrast, plenoptic imaging allows for a simpler experimental configuration and, due to the use of diffuse, white-light illumination, plenoptic imaging is less susceptible to image distortion in the shotgun experiments. PMID:27534487

  2. Positron emission tracking of individual particles in particle-laden rimming flow

    SciTech Connect

    Denissenko, P. Thomas, P. J.; Guyez, E.; Parker, D. J.; Seville, J. P. K.

    2014-05-15

    The motion of a single tracer particle in particle-laden rimming flows is investigated experimentally by means of Positron Emission Particle Tracking (PEPT). Semi-dilute suspensions, with a volume fraction of 8% of heavy particles are considered. The trajectory of the tracer particle is monitored for several thousand cylinder revolutions and related to the optically recorded drift of the large-scale granular segregation bands developing in the cylinder. Results of the data analysis provide first insights into the relation between behaviour of individual particles and the spatiotemporal dynamics displayed by the macroscopic particle-segregation patterns.

  3. The constant displacement scheme for tracking particles in heterogeneous aquifers

    SciTech Connect

    Wen, X.H.; Gomez-Hernandez, J.J.

    1996-01-01

    Simulation of mass transport by particle tracking or random walk in highly heterogeneous media may be inefficient from a computational point of view if the traditional constant time step scheme is used. A new scheme which adjusts automatically the time step for each particle according to the local pore velocity, so that each particle always travels a constant distance, is shown to be computationally faster for the same degree of accuracy than the constant time step method. Using the constant displacement scheme, transport calculations in a 2-D aquifer model, with nature log-transmissivity variance of 4, can be 8.6 times faster than using the constant time step scheme.

  4. Large Silver Halide Single Crystals as Charged Particle Track Detectors

    NASA Technical Reports Server (NTRS)

    Kusmiss, J. H.

    1972-01-01

    The trajectory of the particle is made visible under a microscope by the accumulation of metallic silver at regions of the lattice damaged by the particle. This decoration of the particle track is accomplished by exposure of the crystal to light. The decoration of normally present lattice imperfections such as dislocations can be suppressed by the addition to the crystal of less than ten parts per million of a suitable polyvalent metal impurity. An account of some preliminary attempts to grow thin single crystals of AgCl is given also, and suggestions for a more refined technique are offered.

  5. Three-Dimensional Rotation, Twist and Torsion Analyses Using Real-Time 3D Speckle Tracking Imaging: Feasibility, Reproducibility, and Normal Ranges in Pediatric Population

    PubMed Central

    Han, Wei; Gao, Jun; He, Lin; Yang, Yali; Yin, Ping; Xie, Mingxing; Ge, Shuping

    2016-01-01

    Background and Objective The specific aim of this study was to evaluate the feasibility, reproducibility and maturational changes of LV rotation, twist and torsion variables by real-time 3D speckle-tracking echocardiography (RT3DSTE) in children. Methods A prospective study was conducted in 347 consecutive healthy subjects (181 males/156 females, mean age 7.12 ± 5.3 years, and range from birth to 18-years) using RT 3D echocardiography (3DE). The LV rotation, twist and torsion measurements were made off-line using TomTec software. Manual landmark selection and endocardial border editing were performed in 3 planes (apical “2”-, “4”-, and “3”- chamber views) and semi-automated tracking yielded LV rotation, twist and torsion measurements. LV rotation, twist and torsion analysis by RT 3DSTE were feasible in 307 out of 347 subjects (88.5%). Results There was no correlation between rotation or twist and age, height, weight, BSA or heart rate, respectively. However, there was statistically significant, but very modest correlation between LV torsion and age (R2 = 0.036, P< 0.001). The normal ranges were defined for rotation and twist in this cohort, and for torsion for each age group. The intra-observer and inter-observer variabilities for apical and basal rotation, twist and torsion ranged from 7.3% ± 3.8% to 12.3% ± 8.8% and from 8.8% ± 4.6% to 15.7% ± 10.1%, respectively. Conclusions We conclude that analysis of LV rotation, twist and torsion by this new RT3D STE is feasible and reproducible in pediatric population. There is no maturational change in rotation and twist, but torsion decreases with age in this cohort. Further refinement is warranted to validate the utility of this new methodology in more sensitive and quantitative evaluation of congenital and acquired heart diseases in children. PMID:27427968

  6. The use of particle tracks in problem analysis

    SciTech Connect

    Van Riper, K.A.; McKinney, G.W.; Urbatsch, T.

    1995-06-01

    The visualization of the microscopic phenomena in a Monte Carlo simulation can improve the understanding of the problem and provide an important check on the model definition and execution. The paths, or tracks, of a sample of the Monte Carlo particles show how fission source neutrons migrate from one generation to another. The location of fission source neutrons and interactions can be shown by event markers. This new visualization is available for the Monte Carlo n-particle code MCNP due to the addition of fission source neutrons, tagged by cycle number, to the particle track (PTRAC) data. We report here on the use of this and similar information for the analysis and illustration of criticality calculations.

  7. Optimizing experimental parameters for tracking of diffusing particles

    NASA Astrophysics Data System (ADS)

    Vestergaard, Christian L.

    2016-08-01

    We describe how a single-particle tracking experiment should be designed in order for its recorded trajectories to contain the most information about a tracked particle's diffusion coefficient. The precision of estimators for the diffusion coefficient is affected by motion blur, limited photon statistics, and the length of recorded time series. We demonstrate for a particle undergoing free diffusion that precision is negligibly affected by motion blur in typical experiments, while optimizing photon counts and the number of recorded frames is the key to precision. Building on these results, we describe for a wide range of experimental scenarios how to choose experimental parameters in order to optimize the precision. Generally, one should choose quantity over quality: experiments should be designed to maximize the number of frames recorded in a time series, even if this means lower information content in individual frames.

  8. Fish tracking by combining motion based segmentation and particle filtering

    NASA Astrophysics Data System (ADS)

    Bichot, E.; Mascarilla, L.; Courtellemont, P.

    2006-01-01

    In this paper, we suggest a new importance sampling scheme to improve a particle filtering based tracking process. This scheme relies on exploitation of motion segmentation. More precisely, we propagate hypotheses from particle filtering to blobs of similar motion to target. Hence, search is driven toward regions of interest in the state space and prediction is more accurate. We also propose to exploit segmentation to update target model. Once the moving target has been identified, a representative model is learnt from its spatial support. We refer to this model in the correction step of the tracking process. The importance sampling scheme and the strategy to update target model improve the performance of particle filtering in complex situations of occlusions compared to a simple Bootstrap approach as shown by our experiments on real fish tank sequences.

  9. Particle tracking from image sequences of complex plasma crystals

    SciTech Connect

    Hadziavdic, Vedad; Melandsoe, Frank; Hanssen, Alfred

    2006-05-15

    In order to gather information about the physics of the complex plasma crystals from the experimental data, particles have to be tracked through a sequence of images. An application of the Kalman filter for that purpose is presented, using a one-dimensional approximation of the particle dynamics as a model for the filter. It is shown that Kalman filter is capable of tracking dust particles even with high levels of measurement noise. An inherent part of the Kalman filter, the innovation process, can be used to estimate values of the physical system parameters from the experimental data. The method is shown to be able to estimate the characteristic oscillation frequency from noisy data.

  10. Evolution of 3-D subduction-induced mantle flow around lateral slab edges in analogue models of free subduction analysed by stereoscopic particle image velocimetry technique

    NASA Astrophysics Data System (ADS)

    Strak, Vincent; Schellart, Wouter P.

    2014-10-01

    We present analogue models of free subduction in which we investigate the three-dimensional (3-D) subduction-induced mantle flow focusing around the slab edges. We use a stereoscopic Particle Image Velocimetry (sPIV) technique to map the 3-D mantle flow on 4 vertical cross-sections for one experiment and on 3 horizontal depth-sections for another experiment. On each section the in-plane components are mapped as well as the out-of-plane component for several experimental times. The results indicate that four types of maximum upwelling are produced by the subduction-induced mantle flow. The first two are associated with the poloidal circulation occurring in the mantle wedge and in the sub-slab domain. A third type is produced by horizontal motion and deformation of the frontal part of the slab lying on the 660 km discontinuity. The fourth type results from quasi-toroidal return flow around the lateral slab edges, which produces a maximum upwelling located slightly laterally away from the sub-slab domain and can have another maximum upwelling located laterally away from the mantle wedge. These upwellings occur during the whole subduction process. In contrast, the poloidal circulation in the mantle wedge produces a zone of upwelling that is vigorous during the free falling phase of the slab sinking but that decreases in intensity when reaching the steady-state phase. The position of the maximum upward component and horizontal components of the mantle flow velocity field has been tracked through time. Their time-evolving magnitude is well correlated to the trench retreat rate. The maximum upwelling velocity located laterally away from the subducting plate is ∼18-24% of the trench retreat rate during the steady-state subduction phase. It is observed in the mid upper mantle but upwellings are produced throughout the whole upper mantle thickness, potentially promoting decompression melting. It could thereby provide a source for intraplate volcanism, such as Mount Etna in

  11. MRI - 3D Ultrasound - X-ray Image Fusion with Electromagnetic Tracking for Transendocardial Therapeutic Injections: In-vitro Validation and In-vivo Feasibility

    PubMed Central

    Hatt, Charles R.; Jain, Ameet K.; Parthasarathy, Vijay; Lang, Andrew; Raval, Amish N.

    2014-01-01

    Myocardial infarction (MI) is one of the leading causes of death in the world. Small animal studies have shown that stem-cell therapy offers dramatic functional improvement post-MI. An endomyocardial catheter injection approach to therapeutic agent delivery has been proposed to improve efficacy through increased cell retention. Accurate targeting is critical for reaching areas of greatest therapeutic potential while avoiding a life-threatening myocardial perforation. Multimodal image fusion has been proposed as a way to improve these procedures by augmenting traditional intra-operative imaging modalities with high resolution pre-procedural images. Previous approaches have suffered from a lack of real-time tissue imaging and dependence on X-ray imaging to track devices, leading to increased ionizing radiation dose. In this paper, we present a new image fusion system for catheter-based targeted delivery of therapeutic agents. The system registers real-time 3D echocardiography, magnetic resonance, X-ray, and electromagnetic sensor tracking within a single flexible framework. All system calibrations and registrations were validated and found to have target registration errors less than 5 mm in the worst case. Injection accuracy was validated in a motion enabled cardiac injection phantom, where targeting accuracy ranged from 0.57 to 3.81 mm. Clinical feasibility was demonstrated with in-vivo swine experiments, where injections were successfully made into targeted regions of the heart. PMID:23561056

  12. Tracking single p