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Sample records for atomic resolution 3d

  1. Atomic resolution 3D electron diffraction microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Miao, Jianwei; Ohsuna, Tetsu; Terasaki, Osamu; O' Keefe, Michael A.

    2002-03-01

    Electron lens aberration is the major barrier limiting the resolution of electron microscopy. Here we describe a novel form of electron microscopy to overcome electron lens aberration. By combining coherent electron diffraction with the oversampling phasing method, we show that the 3D structure of a 2 x 2 x 2 unit cell nano-crystal (framework of LTA [Al12Si12O48]8) can be ab initio determined at the resolution of 1 Angstrom from a series of simulated noisy diffraction pattern projections with rotation angles ranging from -70 degrees to +70 degrees in 5 degrees increments along a single rotation axis. This form of microscopy (which we call 3D electron diffraction microscopy) does not require any reference waves, and can image the 3D structure of nanocrystals, as well as non-crystalline biological and materials science samples, with the resolution limited only by the quality of sample diffraction.

  2. When fast atom diffraction turns 3D

    Energy Technology Data Exchange (ETDEWEB)

    Zugarramurdi, Asier; Borisov, Andrei G., E-mail: andrei.borissov@u-psud.fr

    2013-12-15

    Fast atom diffraction at surfaces (FAD) in grazing incidence geometry is characterized by the slow motion in the direction perpendicular to the surface and fast motion parallel to the surface plane along a low index direction. It is established experimentally that for the typical surfaces the FAD reveals the 2D diffraction patterns associated with exchange of the reciprocal lattice vector perpendicular to the direction of fast motion. The reciprocal lattice vector exchange along the direction of fast motion is negligible. The usual approximation made in the description of the experimental data is then to assume that the effective potential leading to the diffraction results from the averaging of the 3D surface potential along the atomic strings forming the axial channel. In this work we use full quantum wave packet propagation calculations to study theoretically the possibility to observe the 3D diffraction in FAD experiments. We show that for the surfaces with large unit cell, such as can be the case for reconstructed or vicinal surfaces, the 3D diffraction can be observed. The reciprocal lattice vector exchange along the direction of fast motion leads to several Laue circles in the diffraction pattern.

  3. Multi-resolution optical 3D sensor

    Science.gov (United States)

    Kühmstedt, Peter; Heinze, Matthias; Schmidt, Ingo; Breitbarth, Martin; Notni, Gunther

    2007-06-01

    A new multi resolution self calibrating optical 3D measurement system using fringe projection technique named "kolibri FLEX multi" will be presented. It can be utilised to acquire the all around shape of small to medium objects, simultaneously. The basic measurement principle is the phasogrammetric approach /1,2,3/ in combination with the method of virtual landmarks for the merging of the 3D single views. The system consists in minimum of two fringe projection sensors. The sensors are mounted on a rotation stage illuminating the object from different directions. The measurement fields of the sensors can be chosen different, here as an example 40mm and 180mm in diameter. In the measurement the object can be scanned at the same time with these two resolutions. Using the method of virtual landmarks both point clouds are calculated within the same world coordinate system resulting in a common 3D-point cloud. The final point cloud includes the overview of the object with low point density (wide field) and a region with high point density (focussed view) at the same time. The advantage of the new method is the possibility to measure with different resolutions at the same object region without any mechanical changes in the system or data post processing. Typical parameters of the system are: the measurement time is 2min for 12 images and the measurement accuracy is below 3μm up to 10 μm. The flexibility makes the measurement system useful for a wide range of applications such as quality control, rapid prototyping, design and CAD/CAM which will be shown in the paper.

  4. High resolution 3D nonlinear integrated inversion

    Institute of Scientific and Technical Information of China (English)

    Li Yong; Wang Xuben; Li Zhirong; Li Qiong; Li Zhengwen

    2009-01-01

    The high resolution 3D nonlinear integrated inversion method is based on nonlinear theory. Under layer control, the log data from several wells (or all wells) in the study area and seismic trace data adjacent to the wells are input to a network with multiple inputs and outputs and are integratedly trained to obtain an adaptive weight function of the entire study area. Integrated nonlinear mapping relationships are built and updated by the lateral and vertical geologic variations of the reservoirs. Therefore, the inversion process and its inversion results can be constrained and controlled and a stable seismic inversion section with high resolution with velocity inversion, impedance inversion, and density inversion sections, can be gained. Good geologic effects have been obtained in model computation tests and real data processing, which verified that this method has high precision, good practicality, and can be used for quantitative reservoir analysis.

  5. High resolution 3-D wavelength diversity imaging

    Science.gov (United States)

    Farhat, N. H.

    1981-09-01

    A physical optics, vector formulation of microwave imaging of perfectly conducting objects by wavelength and polarization diversity is presented. The results provide the theoretical basis for optimal data acquisition and three-dimensional tomographic image retrieval procedures. These include: (a) the selection of highly thinned (sparse) receiving array arrangements capable of collecting large amounts of information about remote scattering objects in a cost effective manner and (b) techniques for 3-D tomographic image reconstruction and display in which polarization diversity data is fully accounted for. Data acquisition employing a highly attractive AMTDR (Amplitude Modulated Target Derived Reference) technique is discussed and demonstrated by computer simulation. Equipment configuration for the implementation of the AMTDR technique is also given together with a measurement configuration for the implementation of wavelength diversity imaging in a roof experiment aimed at imaging a passing aircraft. Extension of the theory presented to 3-D tomographic imaging of passive noise emitting objects by spectrally selective far field cross-correlation measurements is also given. Finally several refinements made in our anechoic-chamber measurement system are shown to yield drastic improvement in performance and retrieved image quality.

  6. Serum induced degradation of 3D DNA box origami observed by high speed atomic force microscope

    DEFF Research Database (Denmark)

    Jiang, Zaixing; Zhang, Shuai; Yang, Chuanxu;

    2015-01-01

    3D DNA origami holds tremendous potential to encapsulate and selectively release therapeutic drugs. Observations of real-time performance of 3D DNA origami structures in physiological environment will contribute much to its further applications. Here, we investigate the degradation kinetics of 3D...... DNA box origami in serum using high-speed atomic force microscope optimized for imaging 3D DNA origami in real time. The time resolution allows characterizing the stages of serum effects on individual 3D DNA box origami with nanometer resolution. Our results indicate that the whole digest process...... is a combination of a rapid collapse phase and a slow degradation phase. The damages of box origami mainly happen in the collapse phase. Thus, the structure stability of 3D DNA box origami should be further improved, especially in the collapse phase, before clinical applications...

  7. 3D mapping from high resolution satellite images

    Science.gov (United States)

    Goulas, D.; Georgopoulos, A.; Sarakenos, A.; Paraschou, Ch.

    2013-08-01

    In recent years 3D information has become more easily available. Users' needs are constantly increasing, adapting to this reality and 3D maps are in more demand. 3D models of the terrain in CAD or other environments have already been common practice; however one is bound by the computer screen. This is why contemporary digital methods have been developed in order to produce portable and, hence, handier 3D maps of various forms. This paper deals with the implementation of the necessary procedures to produce holographic 3D maps and three dimensionally printed maps. The main objective is the production of three dimensional maps from high resolution aerial and/or satellite imagery with the use of holography and but also 3D printing methods. As study area the island of Antiparos was chosen, as there were readily available suitable data. These data were two stereo pairs of Geoeye-1 and a high resolution DTM of the island. Firstly the theoretical bases of holography and 3D printing are described, and the two methods are analyzed and there implementation is explained. In practice a x-axis parallax holographic map of the Antiparos Island is created and a full parallax (x-axis and y-axis) holographic map is created and printed, using the holographic method. Moreover a three dimensional printed map of the study area has been created using 3dp (3d printing) method. The results are evaluated for their usefulness and efficiency.

  8. Directing Matter: Toward Atomic-Scale 3D Nanofabrication.

    Science.gov (United States)

    Jesse, Stephen; Borisevich, Albina Y; Fowlkes, Jason D; Lupini, Andrew R; Rack, Philip D; Unocic, Raymond R; Sumpter, Bobby G; Kalinin, Sergei V; Belianinov, Alex; Ovchinnikova, Olga S

    2016-06-28

    Enabling memristive, neuromorphic, and quantum-based computing as well as efficient mainstream energy storage and conversion technologies requires the next generation of materials customized at the atomic scale. This requires full control of atomic arrangement and bonding in three dimensions. The last two decades witnessed substantial industrial, academic, and government research efforts directed toward this goal through various lithographies and scanning-probe-based methods. These technologies emphasize 2D surface structures, with some limited 3D capability. Recently, a range of focused electron- and ion-based methods have demonstrated compelling alternative pathways to achieving atomically precise manufacturing of 3D structures in solids, liquids, and at interfaces. Electron and ion microscopies offer a platform that can simultaneously observe dynamic and static structures at the nano- and atomic scales and also induce structural rearrangements and chemical transformation. The addition of predictive modeling or rapid image analytics and feedback enables guiding these in a controlled manner. Here, we review the recent results that used focused electron and ion beams to create free-standing nanoscale 3D structures, radiolysis, and the fabrication potential with liquid precursors, epitaxial crystallization of amorphous oxides with atomic layer precision, as well as visualization and control of individual dopant motion within a 3D crystal lattice. These works lay the foundation for approaches to directing nanoscale level architectures and offer a potential roadmap to full 3D atomic control in materials. In this paper, we lay out the gaps that currently constrain the processing range of these platforms, reflect on indirect requirements, such as the integration of large-scale data analysis with theory, and discuss future prospects of these technologies.

  9. Reconstruction of High Resolution 3D Objects from Incomplete Images and 3D Information

    Directory of Open Access Journals (Sweden)

    Alexander Pacheco

    2014-05-01

    Full Text Available To this day, digital object reconstruction is a quite complex area that requires many techniques and novel approaches, in which high-resolution 3D objects present one of the biggest challenges. There are mainly two different methods that can be used to reconstruct high resolution objects and images: passive methods and active methods. This methods depend on the type of information available as input for modeling 3D objects. The passive methods use information contained in the images and the active methods make use of controlled light sources, such as lasers. The reconstruction of 3D objects is quite complex and there is no unique solution- The use of specific methodologies for the reconstruction of certain objects it’s also very common, such as human faces, molecular structures, etc. This paper proposes a novel hybrid methodology, composed by 10 phases that combine active and passive methods, using images and a laser in order to supplement the missing information and obtain better results in the 3D object reconstruction. Finally, the proposed methodology proved its efficiency in two complex topological complex objects.

  10. Topological Quantum Information in a 3D Neutral Atom Array

    Science.gov (United States)

    2015-01-02

    v Prescribed by ANSI Std. Z39.18 12-23-2014 Final 12-01-2008-9-30-2014 ( DARPA ) TOPOLOGICAL QUANTUM INFORMATION IN A 3D NEUTRAL ATOM ARRAY FA9550-09...1-0041 David Weiss Penn State UP76XR0 AFOSR DARPA Approved for public release Work was performed to build core elements of a quantum computer...Hamiltonian within our trapped neutral atoms architecture. quantum computing, ultracold atoms David Weiss 814-861-3578 1 DARPA Final Report Grant

  11. Progress in sorting individual atoms in 3D

    Science.gov (United States)

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

    2016-05-01

    An exactly unity filled optical lattice is a desirable initial state for a neutral atom quantum computer. We have previously proposed an efficient way to compact a partially filled lattice into a perfectly filled one, by combining site-resolved imaging, site-selective qubit rotations and state-selective motion steps. We have previously demonstrated site-resolved imaging and site-selective rotations in our system of cesium atoms in a 40% filled 5x5x5 3D lattice. We have now demonstrated the final element, state-selective motion steps in 3D produced by rotating the polarizations of one of the lattice beams in each pair. We will present our progress in putting all the elements together to reach perfect unity filling. Supported by NSF.

  12. 3D super-resolution microscopy of bacterial division machinery

    Science.gov (United States)

    Vedyaykin, A. D.; Sabantsev, A. V.; Vishnyakov, I. E.; Morozova, N. E.; Polinovskaya, V. S.; Khodorkovskii, M. A.

    2016-08-01

    Super-resolution microscopy is a promising tool for the field of microbiology, as bacteria sizes are comparable to the resolution limit of light microscopy. Bacterial division machinery and FtsZ protein in particular attract much attention of scientists who use different super-resolution microscopy techniques, but most of the available data on FtsZ structures was obtained using two-dimensional (2D) super-resolution microscopy. Using 3D single-molecule localization microscopy (SMLM, namely dSTORM) to visualize FtsZ, we demonstrate that this approach allows more accurate interpretation of super-resolution images and provides new opportunities for the study of complex structures like bacterial divisome.

  13. SiC/SiO2界面的原子分辨率三维重构%Atomic resolution 3 D reconstruction of SiC/SiO2 interface

    Institute of Scientific and Technical Information of China (English)

    刘培植; 许并社; 郭俊杰

    2015-01-01

    Silicon carbide ( SiC) is widely used in high power electronics as a substitute of silicon. The key problem of SiC based metal⁃oxide⁃semiconductor field effect transistors ( MOSFET) is the relatively low channel electron mobility, and the transition layer of SiC/SiO2 interface is considered to be the main cause for the reduced electron mobility. However, the atomic structure of the transition layer is still unclear. In this paper, the transition layer was investigated with a 5th order spherical aberration corrected scanning transmission electron microscope. Depth sectioning images of SiC/SiO2 interface were obtained with the through⁃focal series technique, and an atomic resolution 3D structure of the interface was reconstructed with the through⁃focal series images. The clear 3D interface structure suggests that tshe interface has an atomic scale roughness, and the transition layer is a contrast of the roughness. The kinks, steps and microfacets increase the scattering probability of channel electrons, resulting in reducing the channel mobility of the MOSFET devices.%碳化硅( SiC)作为一种新型材料被广泛应用于高功率半导体器件中。目前的SiC基金属氧化物半导体场效应晶体管器件存在的主要问题是沟道电子迁移率低。 SiC/SiO2界面处的过渡层被认为是造成沟道电子迁移率低的主要原因,但是该过渡层的原子结构尚不清楚。本文利用球差矫正扫描透射电子显微镜深入研究了SiC/SiO2的界面。以变聚焦序列技术得到了界面过渡层不同深度的原子分辨率断层扫描图像,用变聚焦序列图像重构了界面的原子分辨率三维结构。精确的界面原子结构表明SiC/SiO2界面处的过渡区是由于邻晶界面上台阶突起和微刻面构成的。它是界面原子尺度的粗糙度的反映。邻晶界面上的台阶突起和微刻面增加了电子在界面传输过程中的散射几率,造成了沟道电子迁移率过低。

  14. Calibration of a High Resolution Airborne 3-D SAR

    DEFF Research Database (Denmark)

    Dall, Jørgen; Grinder-Pedersen, Jan; Madsen, S.N.

    1997-01-01

    (EMI). In order to achieve a high geodetic fidelity when using such systems operationally, calibration procedures must be applied. Inaccurate navigation data and system parameters as well as system imperfections must be accounted for. This paper presents theoretical models describing the impact of key......The potential of across-track interferometric (XTI) synthetic aperture radar (SAR) for producing high resolution 3D imagery has been demonstrated by several airborne systems including EMISAR, the dual frequency, polarimetric, and interferometric SAR developed at the Dept. of Electromagnetic Systems...

  15. Reading PDB: perception of molecules from 3D atomic coordinates.

    Science.gov (United States)

    Urbaczek, Sascha; Kolodzik, Adrian; Groth, Inken; Heuser, Stefan; Rarey, Matthias

    2013-01-28

    The analysis of small molecule crystal structures is a common way to gather valuable information for drug development. The necessary structural data is usually provided in specific file formats containing only element identities and three-dimensional atomic coordinates as reliable chemical information. Consequently, the automated perception of molecular structures from atomic coordinates has become a standard task in cheminformatics. The molecules generated by such methods must be both chemically valid and reasonable to provide a reliable basis for subsequent calculations. This can be a difficult task since the provided coordinates may deviate from ideal molecular geometries due to experimental uncertainties or low resolution. Additionally, the quality of the input data often differs significantly thus making it difficult to distinguish between actual structural features and mere geometric distortions. We present a method for the generation of molecular structures from atomic coordinates based on the recently published NAOMI model. By making use of this consistent chemical description, our method is able to generate reliable results even with input data of low quality. Molecules from 363 Protein Data Bank (PDB) entries could be perceived with a success rate of 98%, a result which could not be achieved with previously described methods. The robustness of our approach has been assessed by processing all small molecules from the PDB and comparing them to reference structures. The complete data set can be processed in less than 3 min, thus showing that our approach is suitable for large scale applications.

  16. High Resolution 3D Radar Imaging of Comet Interiors

    Science.gov (United States)

    Asphaug, E. I.; Gim, Y.; Belton, M.; Brophy, J.; Weissman, P. R.; Heggy, E.

    2012-12-01

    Knowing the interiors of comets and other primitive bodies is fundamental to our understanding of how planets formed. We have developed a Discovery-class mission formulation, Comet Radar Explorer (CORE), based on the use of previously flown planetary radar sounding techniques, with the goal of obtaining high resolution 3D images of the interior of a small primitive body. We focus on the Jupiter-Family Comets (JFCs) as these are among the most primitive bodies reachable by spacecraft. Scattered in from far beyond Neptune, they are ultimate targets of a cryogenic sample return mission according to the Decadal Survey. Other suitable targets include primitive NEOs, Main Belt Comets, and Jupiter Trojans. The approach is optimal for small icy bodies ~3-20 km diameter with spin periods faster than about 12 hours, since (a) navigation is relatively easy, (b) radar penetration is global for decameter wavelengths, and (c) repeated overlapping ground tracks are obtained. The science mission can be as short as ~1 month for a fast-rotating JFC. Bodies smaller than ~1 km can be globally imaged, but the navigation solutions are less accurate and the relative resolution is coarse. Larger comets are more interesting, but radar signal is unlikely to be reflected from depths greater than ~10 km. So, JFCs are excellent targets for a variety of reasons. We furthermore focus on the use of Solar Electric Propulsion (SEP) to rendezvous shortly after the comet's perihelion. This approach leaves us with ample power for science operations under dormant conditions beyond ~2-3 AU. This leads to a natural mission approach of distant observation, followed by closer inspection, terminated by a dedicated radar mapping orbit. Radar reflections are obtained from a polar orbit about the icy nucleus, which spins underneath. Echoes are obtained from a sounder operating at dual frequencies 5 and 15 MHz, with 1 and 10 MHz bandwidths respectively. The dense network of echoes is used to obtain global 3D

  17. 3D Flash LIDAR EDL Resolution Improvement Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Advanced Scientific Concepts, Inc. (ASC) is a small business that has developed 3D Flash LIDAR systems for space and terrestrial applications. 3D Flash LIDAR is...

  18. High resolution 3D imaging of synchrotron generated microbeams

    Energy Technology Data Exchange (ETDEWEB)

    Gagliardi, Frank M., E-mail: frank.gagliardi@wbrc.org.au [Alfred Health Radiation Oncology, The Alfred, Melbourne, Victoria 3004, Australia and School of Medical Sciences, RMIT University, Bundoora, Victoria 3083 (Australia); Cornelius, Iwan [Imaging and Medical Beamline, Australian Synchrotron, Clayton, Victoria 3168, Australia and Centre for Medical Radiation Physics, University of Wollongong, Wollongong, New South Wales 2500 (Australia); Blencowe, Anton [Division of Health Sciences, School of Pharmacy and Medical Sciences, The University of South Australia, Adelaide, South Australia 5000, Australia and Division of Information Technology, Engineering and the Environment, Mawson Institute, University of South Australia, Mawson Lakes, South Australia 5095 (Australia); Franich, Rick D. [School of Applied Sciences and Health Innovations Research Institute, RMIT University, Melbourne, Victoria 3000 (Australia); Geso, Moshi [School of Medical Sciences, RMIT University, Bundoora, Victoria 3083 (Australia)

    2015-12-15

    Purpose: Microbeam radiation therapy (MRT) techniques are under investigation at synchrotrons worldwide. Favourable outcomes from animal and cell culture studies have proven the efficacy of MRT. The aim of MRT researchers currently is to progress to human clinical trials in the near future. The purpose of this study was to demonstrate the high resolution and 3D imaging of synchrotron generated microbeams in PRESAGE® dosimeters using laser fluorescence confocal microscopy. Methods: Water equivalent PRESAGE® dosimeters were fabricated and irradiated with microbeams on the Imaging and Medical Beamline at the Australian Synchrotron. Microbeam arrays comprised of microbeams 25–50 μm wide with 200 or 400 μm peak-to-peak spacing were delivered as single, cross-fire, multidirectional, and interspersed arrays. Imaging of the dosimeters was performed using a NIKON A1 laser fluorescence confocal microscope. Results: The spatial fractionation of the MRT beams was clearly visible in 2D and up to 9 mm in depth. Individual microbeams were easily resolved with the full width at half maximum of microbeams measured on images with resolutions of as low as 0.09 μm/pixel. Profiles obtained demonstrated the change of the peak-to-valley dose ratio for interspersed MRT microbeam arrays and subtle variations in the sample positioning by the sample stage goniometer were measured. Conclusions: Laser fluorescence confocal microscopy of MRT irradiated PRESAGE® dosimeters has been validated in this study as a high resolution imaging tool for the independent spatial and geometrical verification of MRT beam delivery.

  19. CsI calorimeter with 3-D position resolution

    CERN Document Server

    Schopper, Herwig Franz; Shaw, H; Nefzger, C; Zoglauer, A; Schönfelder, V; Kanbach, G

    2000-01-01

    New gamma-ray calorimeter have been developed for the MEGA Compton camera. They consist of arrays of small CsI(Tl) scintillator bars read out by Silicon PIN-diodes and low noise, self-triggering frontend electronics. The length of the bars (the thickness of the calorimeter) can be varied for different applications to fit the stopping power needed and the light loss tolerable. In this paper we present calibration results from 2 cm long bars with diodes on one side, and 8 cm long bars with diodes on two opposite sides. Double-sided readout gives 3-D information of interactions which will be used to overcome the limited position resolution in Anger-cameras at high energies. Simpler detection devices like Anger-cameras might finally resolve only the centre of gravity. As events from gamma-rays with energies of MeV do extend over several cm, it is a prerequisite for an imaging device to resolve the interaction structure in detail. Combining CsI(Tl) scintillators, Silicon PIN-photodiodes and frontend electronics in...

  20. Achieving atomic resolution

    Directory of Open Access Journals (Sweden)

    John Spence

    2002-04-01

    Full Text Available The discovery of the nanotube in 19915 by high resolution electron microscopy (HREM, following closely on the discovery of fullerenes, has initiated a new field of science known as nanoscience. (In fact the fullerene buckyball itself was first observed in 1980, by HREM1. While nanoscience now spans many disciplines, from molecular biology to quantum computing, for all of them, the HREM technique has become the indispensable tool for analyzing the atomic structure of individual bulk nanostructural elements. However this method has long been the technique of choice whenever questions of microstructural characterization arise in materials science.

  1. Serum-induced degradation of 3D DNA box origami observed with high-speed atomic force microscopy

    Institute of Scientific and Technical Information of China (English)

    Zaixing Jiang[1,2,3; Shuai Zhang[2,3; Chuanxu Yang[2; Jorgen Kjems[2; Yudong Huang[1; Flemming Besenbacher[2; Mingdong Dong[2

    2015-01-01

    3D DNA origami holds tremendous potential for the encapsulation and selective release of therapeutic drugs. Observations of the real-time performance of these structures in physiological environments will contribute to the development of future applications. We investigated the degradation kinetics of 3D DNA box origami in serum by using high-speed atomic force microscope optimized for imaging 3D DNA origami in real time. The time resolution allowed to characterize the stages of serum effects on individual 3D DNA boxes origami with nanometer resolution. Our results indicate that the digestion process is a combination of rapid collapse and slow degradation phases. Damage to box origami occurs mainly in the collapse phase. Thus, the structural stability of 3D DNA box origami should be improved, especially in the collapse phase, before these structures are used in clinical applications.

  2. 3D Flash LIDAR EDL Resolution Improvement Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Advanced Scientific Concepts, Inc. (ASC) is a small business, which has developed a compact, eye-safe 3D Flash LIDARTM Camera (FLC) well suited for real-time...

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

    Science.gov (United States)

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

    2014-12-01

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

  4. Gradient-echo 3D imaging of Rb polarization in fiber-coupled atomic magnetometer.

    Science.gov (United States)

    Savukov, I

    2015-07-01

    The analogy between atomic and nuclear spins is exploited to implement 3D imaging of polarization inside the cell of an atomic magnetometer. The resolution of 0.8mm×1.2mm×1.4mm has been demonstrated with the gradient-echo imaging method. The imaging can be used in many applications. One such an application is the evaluation of active volume of an atomic magnetometer for sensitivity analysis and optimization. It has been found that imaging resolution is limited due to de-phasing from spin-exchange collisions and diffusion in the presence of gradients, and for a given magnetometer operational parameters, the imaging sequence has been optimized. Diffusion decay of the signal in the presence of gradients has been modeled numerically and analytically, and the analytical results, which agreed with numerical simulations, have been used to fit the spin-echo gradient measurements to extract the diffusion coefficient. The diffusion coefficient was found in agreement with previous measurements.

  5. 3D super-resolution imaging by localization microscopy.

    Science.gov (United States)

    Magenau, Astrid; Gaus, Katharina

    2015-01-01

    Fluorescence microscopy is an important tool in all fields of biology to visualize structures and monitor dynamic processes and distributions. Contrary to conventional microscopy techniques such as confocal microscopy, which are limited by their spatial resolution, super-resolution techniques such as photoactivated localization microscopy (PALM) and stochastic optical reconstruction microscopy (STORM) have made it possible to observe and quantify structure and processes on the single molecule level. Here, we describe a method to image and quantify the molecular distribution of membrane-associated proteins in two and three dimensions with nanometer resolution.

  6. Mesh Resolution Effect on 3D RANS Turbomachinery Flow Simulations

    CERN Document Server

    Yershov, Sergiy

    2016-01-01

    The paper presents the study of the effect of a mesh refinement on numerical results of 3D RANS computations of turbomachinery flows. The CFD solver F, which based on the second-order accurate ENO scheme, is used in this study. The simplified multigrid algorithm and local time stepping permit decreasing computational time. The flow computations are performed for a number of turbine and compressor cascades and stages. In all flow cases, the successively refined meshes of H-type with an approximate orthogonalization near the solid walls were generated. The results obtained are compared in order to estimate their both mesh convergence and ability to resolve the transonic flow pattern. It is concluded that for thorough studying the fine phenomena of the 3D turbomachinery flows, it makes sense to use the computational meshes with the number of cells from several millions up to several hundred millions per a single turbomachinery blade channel, while for industrial computations, a mesh of about or less than one mil...

  7. Electron crystallography of ultrathin 3D protein crystals: atomic model with charges.

    Science.gov (United States)

    Yonekura, Koji; Kato, Kazuyuki; Ogasawara, Mitsuo; Tomita, Masahiro; Toyoshima, Chikashi

    2015-03-17

    Membrane proteins and macromolecular complexes often yield crystals too small or too thin for even the modern synchrotron X-ray beam. Electron crystallography could provide a powerful means for structure determination with such undersized crystals, as protein atoms diffract electrons four to five orders of magnitude more strongly than they do X-rays. Furthermore, as electron crystallography yields Coulomb potential maps rather than electron density maps, it could provide a unique method to visualize the charged states of amino acid residues and metals. Here we describe an attempt to develop a methodology for electron crystallography of ultrathin (only a few layers thick) 3D protein crystals and present the Coulomb potential maps at 3.4-Å and 3.2-Å resolution, respectively, obtained from Ca(2+)-ATPase and catalase crystals. These maps demonstrate that it is indeed possible to build atomic models from such crystals and even to determine the charged states of amino acid residues in the Ca(2+)-binding sites of Ca(2+)-ATPase and that of the iron atom in the heme in catalase.

  8. High resolution 3D gas-jet characterization.

    Science.gov (United States)

    Landgraf, Björn; Schnell, Michael; Sävert, Alexander; Kaluza, Malte C; Spielmann, Christian

    2011-08-01

    We present a tomographic characterization of gas jets employed for high-intensity laser-plasma interaction experiments where the shape can be non-symmetrically. With a Mach-Zehnder interferometer we measured the phase shift for different directions through the neutral density distribution of the gas jet. From the recorded interferograms it is possible to retrieve 3-dimensional neutral density distributions by tomographic reconstruction based on the filtered back projections. We report on criteria for the smallest number of recorded interferograms as well as a comparison with the widely used phase retrieval based on an Abel inversion. As an example for the performance of our approach, we present the characterization of nozzles with rectangular openings or gas jets with shock waves. With our setup we obtained a spatial resolution of less than 60 μm for an Argon density as low as 2 × 10(17) cm(-3).

  9. Tuning the electronic and magnetic properties of borophene by 3d transition-metal atom adsorption

    Science.gov (United States)

    Li, J. Y.; Lv, H. Y.; Lu, W. J.; Shao, D. F.; Xiao, R. C.; Sun, Y. P.

    2016-12-01

    The electronic and magnetic properties of borophene functionalized by 3d transition metal (TM) atom adsorption are investigated by using first-principles calculations. The results show that the 3d TM atoms can be adsorbed on borophene with high binding energies ranging between 5.9 and 8.3 eV. Interestingly, the originally nonmagnetic borophene tends to be ferromagnetic when Ti, V, Cr, Mn, and Fe atoms are adsorbed, and the magnetic moments are dominated by the TM atoms. The origin of the ferromagnetism is discussed based on the Stoner criterion. Our results indicate that the magnetic properties of borophene can be effectively tuned through the adsorption of 3d TM atoms, which could have promising applications in spintronics and nanoelectronics.

  10. Repumping of ultracold strontium atoms using the ^3P2 - ^3D2 transition

    Science.gov (United States)

    Mickelson, P. G.; Martinez de Escobar, Y. N.; Traverso, A. J.; Killian, T. C.

    2008-05-01

    We discuss recent experiments involving ultracold strontium. Using a commercially-available 3 micron laser, we repump atoms out of the ^3P2 level via the ^3D2 state and gain almost a factor of 10 in the number of atoms in our system. This increase in the signal-to-noise ratio enables improved spectroscopy of strontium in our optical trap.

  11. Fluorescence in situ hybridization applications for super-resolution 3D structured illumination microscopy.

    Science.gov (United States)

    Markaki, Yolanda; Smeets, Daniel; Cremer, Marion; Schermelleh, Lothar

    2013-01-01

    Fluorescence in situ hybridization on three-dimensionally preserved cells (3D-FISH) is an efficient tool to analyze the subcellular localization and spatial arrangement of targeted DNA sequences and RNA transcripts at the single cell level. 3D reconstructions from serial optical sections obtained by confocal laser scanning microscopy (CLSM) have long been considered the gold standard for 3D-FISH analyses. Recent super-resolution techniques circumvent the diffraction-limit of optical resolution and have defined a new state-of-the-art in bioimaging. Three-dimensional structured illumination microscopy (3D-SIM) represents one of these technologies. Notably, 3D-SIM renders an eightfold improved volumetric resolution over conventional imaging, and allows the simultaneous visualization of differently labeled target structures. These features make this approach highly attractive for the analysis of spatial relations and substructures of nuclear targets that escape detection by conventional light microscopy. Here, we focus on the application of 3D-SIM for the visualization of subnuclear 3D-FISH preparations. In comparison with conventional fluorescence microscopy, the quality of 3D-SIM data is dependent to a much greater extent on the optimal sample preparation, labeling and acquisition conditions. We describe typical problems encountered with super-resolution imaging of in situ hybridizations in mammalian tissue culture cells and provide optimized DNA-/(RNA)-FISH protocols including combinations with immunofluorescence staining (Immuno-FISH) and DNA replication labeling using click chemistry.

  12. Ultra-compact, High Resolution, LADAR system for 3D Imaging Project

    Data.gov (United States)

    National Aeronautics and Space Administration — SiWave proposes to develop an innovative, ultra-compact, high resolution, long range LADAR system to produce a 3D map of the exterior of any object in space such as...

  13. Methodology of High Accuracy and Resolution 3D Geological Model Generation and Application

    Institute of Scientific and Technical Information of China (English)

    吴键; 曹代勇; 邓爱居; 李东津; 蒋涛; 翟光华

    2004-01-01

    By generating a high accuracy and high resolution geological model in Liuchu oil field, the technique of geological modeling is expanded and involved in primary geological study, making the sand bodies and reservoir be easily described in detail. The 3D visualization and 3D interactive editing of geological structure model are the key for modeling procedure. And a high accuracy and resolution geological model has been well applied in optimizing the production scheme.

  14. A novel time-multiplexed autostereoscopic multiview full resolution 3D display

    Science.gov (United States)

    Liou, Jian-Chiun; Chen, Fu-Hao

    2012-03-01

    Many people believe that in the future, autostereoscopic 3D displays will become a mainstream display type. Achievement of higher quality 3D images requires both higher panel resolution and more viewing zones. Consequently, the transmission bandwidth of the 3D display systems involves enormous amounts of data transfer. We propose and experimentally demonstrate a novel time-multiplexed autostereoscopic multi-view full resolution 3D display based on the lenticular lens array in association with the control of the active dynamic LED backlight. The lenticular lenses of the lens array optical system receive the light and deflect the light into each viewing zone in a time sequence. The crosstalk under different observation scanning angles is showed, including the cases of 4-views field scanning. The crosstalk of any view zones is about 5% respectively; the results are better than other 3D type.

  15. AFM's path to atomic resolution

    OpenAIRE

    2005-01-01

    We review progress in improving the spatial resolution of atomic force microscopy (AFM) under vacuum. After an introduction to the basic imaging principle and a conceptual comparison to scanning tunneling microscopy (STM), we outline the main challenges of AFM as well as the solutions that have evolved in the first 20 years of its existence. Some crucial steps along AFM's path toward higher resolution are discussed, followed by an outlook on current and future applications.

  16. Oxygen lines in solar granulation. I. Testing 3D models against new observations with high spatial and spectral resolution

    CERN Document Server

    Pereira, Tiago M D; Asplund, Martin

    2009-01-01

    Aims: we seek to provide additional tests of the line formation of theoretical 3D solar photosphere models. In particular, we set out to test the spatially-resolved line formation at several viewing angles, from the solar disk-centre to the limb and focusing on atomic oxygen lines. The purpose of these tests is to provide additional information on whether the 3D model is suitable to derive the solar oxygen abundance. We also aim to empirically constrain the NLTE recipes for neutral hydrogen collisions, using the spatially-resolved observations of the OI 777 nm lines. Methods: using the Swedish 1-m Solar Telescope we obtained high-spatial-resolution observations of five atomic oxygen lines (along with lines for other species) for five positions on the solar disk. These observations have a high spatial and spectral resolution, and a continuum intensity contrast up to 9% at 615 nm. The theoretical line profiles were computed using the 3D model, with a full 3D NLTE treatment for oxygen and LTE for the other lines...

  17. Spatial resolution of the HRRT PET scanner using 3D-OSEM PSF reconstruction

    DEFF Research Database (Denmark)

    Olesen, Oline Vinter; Sibomana, Merence; Keller, Sune Høgild;

    2009-01-01

    The spatial resolution of the Siemens High Resolution Research Tomograph (HRRT) dedicated brain PET scanner installed at Copenhagen University Hospital (Rigshospitalet) was measured using a point-source phantom with high statistics. Further, it was demonstrated how the newly developed 3D-OSEM PSF...

  18. High-resolution 3D T2-weighted fast spin echo: new applications in the orbit

    Energy Technology Data Exchange (ETDEWEB)

    Simon, Erin M. [Department of Radiology, University of California San Francisco, San Francisco, CA (United States); Department of Radiology, Children' s Hospital of Philadelphia, 34th Street and Civic Center Boulevard, Philadelphia, PA 19104-4399 (United States); McCaffery, Sharon; O' Brien, Joan M. [Department of Ophthalmology, University of California San Francisco, San Francisco, CA (United States); Rowley, Howard A. [Department of Radiology, University of California San Francisco, San Francisco, CA (United States); University of Wisconsin Medical School, Madison, WI (United States); Fischbein, Nancy J. [Department of Radiology, University of California San Francisco, San Francisco, CA (United States); Shimikawa, Ann [General Electric Medical Systems, Milwaukee, WI (United States)

    2003-07-01

    Recent developments have made available for ophthalmologic MR imaging a very high-resolution 3D fast spin echo T2 (3D FSE T2) sequence, which runs in a standard head coil. A modification of this technique, 3D FSEz T2, uses a zero-filled slice interpolation method during post-processing to further improve spatial resolution. We describe the technique and share our early clinical observations in patients with ocular masses. Briefly, the additional information from the 3D FSEz T2 resulted in a change in diagnosis from the conventional imaging series in 11 of (41%) 27 studies, usually through the identification of previously treated retinoblastoma lesions. The new sequence significantly increased diagnostic confidence in six (38%) of the remaining 16 cases, usually through better anatomical detail and lesion conspicuity, and did not change interpretation in 10 cases. Such an approach improves diagnostic confidence and may eliminate the need for a dedicated surface coil examination. (orig.)

  19. Application of multi-resolution 3D techniques in crime scene documentation with bloodstain pattern analysis.

    Science.gov (United States)

    Hołowko, Elwira; Januszkiewicz, Kamil; Bolewicki, Paweł; Sitnik, Robert; Michoński, Jakub

    2016-10-01

    In forensic documentation with bloodstain pattern analysis (BPA) it is highly desirable to obtain non-invasively overall documentation of a crime scene, but also register in high resolution single evidence objects, like bloodstains. In this study, we propose a hierarchical 3D scanning platform designed according to the top-down approach known from the traditional forensic photography. The overall 3D model of a scene is obtained via integration of laser scans registered from different positions. Some parts of a scene being particularly interesting are documented using midrange scanner, and the smallest details are added in the highest resolution as close-up scans. The scanning devices are controlled using developed software equipped with advanced algorithms for point cloud processing. To verify the feasibility and effectiveness of multi-resolution 3D scanning in crime scene documentation, our platform was applied to document a murder scene simulated by the BPA experts from the Central Forensic Laboratory of the Police R&D, Warsaw, Poland. Applying the 3D scanning platform proved beneficial in the documentation of a crime scene combined with BPA. The multi-resolution 3D model enables virtual exploration of a scene in a three-dimensional environment, distance measurement, and gives a more realistic preservation of the evidences together with their surroundings. Moreover, high-resolution close-up scans aligned in a 3D model can be used to analyze bloodstains revealed at the crime scene. The result of BPA such as trajectories, and the area of origin are visualized and analyzed in an accurate model of a scene. At this stage, a simplified approach considering the trajectory of blood drop as a straight line is applied. Although the 3D scanning platform offers a new quality of crime scene documentation with BPA, some of the limitations of the technique are also mentioned.

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

    Science.gov (United States)

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

    2014-09-01

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

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

    Science.gov (United States)

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

    2016-05-01

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

  2. Designing and building a permanent magnet Zeeman slower for calcium atoms using a 3D printer

    Science.gov (United States)

    Parsagian, Alexandria; Kleinert, Michaela

    2015-10-01

    We present the design of a Zeeman slower for calcium atoms using permanent magnets instead of more traditional electromagnets and the novel technique of 3D printing to create a very robust and flexible structure for these magnets. Zeeman slowers are ideal tools to slow atoms from several hundreds of meters per second to just a few tens of meters per second. These slower atoms can then easily be trapped in a magneto-optical trap, making Zeeman slowers a very valuable tool in many cold atom labs. The use of permanent magnets and 3D printing results in a highly stable and robust slower that is suitable for undergraduate laboratories. In our design, we arranged 28 magnet pairs, 2.0 cm apart along the axis of the slower and at varying radial distances from the axis. We determined the radial position of the magnets by simulating the combined field of all magnet pairs using Mathematica and comparing it to the ideal theoretical field for a Zeeman slower. Finally, we designed a stable, robust, compact, and easy-to-align mounting structure for the magnets in Google Sketchup, which we then printed using a commercially available 3D printer by Solidoodle. The resulting magnetic field is well suited to slow calcium atoms from the 770 m/s rms velocity at a temperature of 950 K, down to the capture velocity of the magneto-optical trap.

  3. Atomically thin layered NiFe double hydroxides assembled 3D microspheres with promoted electrochemical performances

    Science.gov (United States)

    Li, Xiaomin; Zai, Jiantao; Liu, Yuanyuan; He, Xiaobo; Xiang, Shijie; Ma, Zifeng; Qian, Xuefeng

    2016-09-01

    LDHs in atomic thickness (mono-/bi-layers) usually exhibit novel physicochemical properties, especially in surface-dependent energy storage and catalysis areas. However, the thickness of the commonly reported 2D LDHs is in nanoscale and the bottom-up synthesis of atomically thin LDHs is rarely reported. Herein, high-quality atomically thin layered NiFe-LDHs assembled 3D microspheres were synthesized via a rational designed reaction system, where the formation of atomically thin building blocks was controlled by the synergetic effects of released carbonate anions and butanol. Furthermore, the complexant and solvents played important effects on the process of coprecipitation and the assembling of LDHs. Due to the nature of atomically thin LDHs nanosheets and unique 3D hierarchical structures, the obtained microspheres exhibited excellent electrocatalytic oxygen evolution reaction (OER) activity in alkaline medium with an onset overpotential (0.435 V, which is lower than that of common LDHs) and good durability. The as-prepared 3D NiFe-LDHs microspheres were also firstly used as supercapacitor materials and displayed a high specific capacitance of 1061 F g-1 at the current density of 1 A g-1.

  4. QSAR of Estrogen of Bisphenol A with 3D Vector of Atomic Property Correlation

    Institute of Scientific and Technical Information of China (English)

    CHEN Zhi-Tao; ZHOU Peng; HE Liu; LI Zhi-Liang

    2007-01-01

    Considering atomic property vector and atomic correlative function, the 3-dimensional structural vector of atomic property correlation (3D-VAPC), a novel descriptor,is defined to characterize a 3-dimensional molecular structure by introducing self-adaptability regulation mechanism and the idea of orientating to customers. Characterizing the structures of 25 bisphenol A compounds by this vector, the QSAR models of three kinds of estrogen activities (ER affinities, gene induction and cell proliferation) have high multiple correlation coefficient (Rcum2=0.933, 0.813, 0.959) and cross verification coefficient (Qcum2=0.847, 0.953, 0.798) by support vector machine (SVM), which suits for nonlinear circumstances. The above results show that the models successfully express the correlation between structure and three kinds of estrogen activities. Therefore, 3D-VAPC exactly reflects the molecular structural information and SVM method correctly describes the correlation between information and property of the compounds.

  5. 3D High Resolution l1-SPIRiT Reconstruction on Gadgetron based Cloud

    DEFF Research Database (Denmark)

    Xue, Hui; Kelmann, Peter; Inati, Souheil;

    Applying non-linear reconstruction to high resolution 3D MRI is challenging because of the lengthy computing time needed for those iterative algorithms. To achieve practical processing duration to enable clinical usage of non-linear reconstruction, we have extended previously published Gadgetron...... framework to support distributed computing in a cloud environment. This extension is named GT-Plus. A cloud version of 3D l1-SPIRiT was implemented on the GT-Plus framework. We demonstrate that a 3mins reconstruction could be achieved for 1mm3 isotropic resolution neuro scans with significantly improved...

  6. Generalized recovery algorithm for 3D super-resolution microscopy using rotating point spread functions

    Science.gov (United States)

    Shuang, Bo; Wang, Wenxiao; Shen, Hao; Tauzin, Lawrence J.; Flatebo, Charlotte; Chen, Jianbo; Moringo, Nicholas A.; Bishop, Logan D. C.; Kelly, Kevin F.; Landes, Christy F.

    2016-08-01

    Super-resolution microscopy with phase masks is a promising technique for 3D imaging and tracking. Due to the complexity of the resultant point spread functions, generalized recovery algorithms are still missing. We introduce a 3D super-resolution recovery algorithm that works for a variety of phase masks generating 3D point spread functions. A fast deconvolution process generates initial guesses, which are further refined by least squares fitting. Overfitting is suppressed using a machine learning determined threshold. Preliminary results on experimental data show that our algorithm can be used to super-localize 3D adsorption events within a porous polymer film and is useful for evaluating potential phase masks. Finally, we demonstrate that parallel computation on graphics processing units can reduce the processing time required for 3D recovery. Simulations reveal that, through desktop parallelization, the ultimate limit of real-time processing is possible. Our program is the first open source recovery program for generalized 3D recovery using rotating point spread functions.

  7. A fresh look at 3D microwave ionization curves of hydrogen Rydberg atoms

    CERN Document Server

    Rockwell, G N; Clausen, T; Hoffman, V F; Clausen, Th.

    2001-01-01

    Analytical arguments and numerical simulations suggest that the shapes of 3D microwave ionization curves measured by Koch and collaborators (see P. M. Koch and K. A. H. van Leeuwen, Phys. Rep. {\\bf 255}, 289 (1995)) depend only weakly on the angular momentum of the atoms in the initial microcanonical ensemble, but strongly on the principal quantum number and the magnetic quantum number. Based on this insight, coupled with the computational power of a high-end 60-node Beowulf PC cluster, we present the first 3D quantum calculations of microwave ionization curves in the experimentally relevant parameter regime.

  8. High resolution adaptive imaging of a single atom

    CERN Document Server

    Wong-Campos, J D; Neyenhuis, B; Mizrahi, J; Monroe, C

    2015-01-01

    We report the optical imaging of a single atom with nanometer resolution using an adaptive optical alignment technique that is applicable to general optical microscopy. By decomposing the image of a single laser-cooled atom, we identify and correct optical aberrations in the system and realize an atomic position sensitivity of $\\approx$ 0.5 nm/$\\sqrt{\\text{Hz}}$ with a minimum uncertainty of 1.7 nm, allowing the direct imaging of atomic motion. This is the highest position sensitivity ever measured for an isolated atom, and opens up the possibility of performing out-of-focus 3D particle tracking, imaging of atoms in 3D optical lattices or sensing forces at the yoctonewton (10$^{-24}$ N) scale.

  9. High-resolution noncontact atomic force microscopy.

    Science.gov (United States)

    Pérez, Rubén; García, Ricardo; Schwarz, Udo

    2009-07-01

    original papers authored by many of the leading groups in the field with the goal of providing a well-balanced overview on the state-of-the-art in this rapidly evolving field. These papers, many of which are based on notable presentations given during the Madrid conference, feature highlights such as (1) the development of sophisticated force spectroscopy procedures that are able to map the complete 3D tip-sample force field on different surfaces; (2) the considerable resolution improvement of Kelvin probe force microscopy (reaching, in some cases, the atomic scale), which is accompanied by a thorough, quantitative understanding of the contrast observed; (3) the perfecting of atomic resolution imaging on insulating substrates, which helps reshape our microscopic understanding of surface properties and chemical activity of these surfaces; (4) the description of instrumental and methodological developments that pave the way to the atomic-scale characterization of magnetic and electronic properties of nanostructures, and last but not least (5) the extension of dynamic imaging modes to high-resolution operation in liquids, ultimately achieving atomic resolution. The latter developments are already having a significant impact in the highly competitive field of biological imaging under physiological conditions. This special issue of Nanotechnology would not have been possible without the highly professional support from Nina Couzin, Amy Harvey, Alex Wotherspoon and the entire Nanotechnology team at IOP Publishing. We are thankful for their help in pushing this project forward. We also thank the authors who have contributed their excellent original articles to this issue, the referees whose comments have helped make the issue an accurate portrait of this rapidly moving field, and the entire NC-AFM community that continues to drive NC-AFM to new horizons.

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

    Science.gov (United States)

    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.

  11. Markerless 3D Head Tracking for Motion Correction in High Resolution PET Brain Imaging

    DEFF Research Database (Denmark)

    Olesen, Oline Vinter

    images. Incorrect motion correction can in the worst cases result in wrong diagnosis or treatment. The evolution of a markerless custom-made structured light 3D surface tracking system is presented. The system is targeted at state-of-the-art high resolution dedicated brain PET scanners with a resolution...... significantly. The results were similar to motion correction using an integrated commercial marker-based system. Furthermore, phantom studies were performed supporting the system’s abilities for PET motion correction....

  12. Spatial resolution limits for the isotropic-3D PET detector X’tal cube

    Energy Technology Data Exchange (ETDEWEB)

    Yoshida, Eiji, E-mail: rush@nirs.go.jp; Tashima, Hideaki; Hirano, Yoshiyuki; Inadama, Naoko; Nishikido, Fumihiko; Murayama, Hideo; Yamaya, Taiga

    2013-11-11

    Positron emission tomography (PET) has become a popular imaging method in metabolism, neuroscience, and molecular imaging. For dedicated human brain and small animal PET scanners, high spatial resolution is needed to visualize small objects. To improve the spatial resolution, we are developing the X’tal cube, which is our new PET detector to achieve isotropic 3D positioning detectability. We have shown that the X’tal cube can achieve 1 mm{sup 3} uniform crystal identification performance with the Anger-type calculation even at the block edges. We plan to develop the X’tal cube with even smaller 3D grids for sub-millimeter crystal identification. In this work, we investigate spatial resolution of a PET scanner based on the X’tal cube using Monte Carlo simulations for predicting resolution performance in smaller 3D grids. For spatial resolution evaluation, a point source emitting 511 keV photons was simulated by GATE for all physical processes involved in emission and interaction of positrons. We simulated two types of animal PET scanners. The first PET scanner had a detector ring 14.6 cm in diameter composed of 18 detectors. The second PET scanner had a detector ring 7.8 cm in diameter composed of 12 detectors. After the GATE simulations, we converted the interacting 3D position information to digitalized positions for realistic segmented crystals. We simulated several X’tal cubes with cubic crystals from (0.5 mm){sup 3} to (2 mm){sup 3} in size. Also, for evaluating the effect of DOI resolution, we simulated several X’tal cubes with crystal thickness from (0.5 mm){sup 3} to (9 mm){sup 3}. We showed that sub-millimeter spatial resolution was possible using cubic crystals smaller than (1.0 mm){sup 3} even with the assumed physical processes. Also, the weighted average spatial resolutions of both PET scanners with (0.5 mm){sup 3} cubic crystals were 0.53 mm (14.6 cm ring diameter) and 0.48 mm (7.8 cm ring diameter). For the 7.8 cm ring diameter, spatial

  13. Array diagnostics, spatial resolution, and filtering of undesired radiation with the 3D reconstruction algorithm

    DEFF Research Database (Denmark)

    Cappellin, C.; Pivnenko, Sergey; Jørgensen, E.

    2013-01-01

    This paper focuses on three important features of the 3D reconstruction algorithm of DIATOOL: the identification of array elements improper functioning and failure, the obtainable spatial resolution of the reconstructed fields and currents, and the filtering of undesired radiation and scattering...

  14. The AX-PET project Demonstration of a high resolution axial 3D PET

    CERN Document Server

    Bolle, E; Casella, C; Chesi, E; Clinthorne, N; Cochran, E; De Leo, R; Dissertori, G; Djambazov, G; Fanti, V; Honscheid, K; Huh, S; Johnson, I; Joram, C; Kagan, H; Lustermann, W; Meddi, F; Nappi, E; Nessi-Tedaldi, F; Oliver, J F; Pauss, P; Rafecas, M; Renker, D; Rudge, A; Schinzel, D; Schneider, T; Seguinot, J; Smith, S; Solevi, P; Stapnes, S; Weilhammer, P

    2010-01-01

    The AX-PET is a new geometrical concept for a high resolution 3D PET scanner, based on matrices of axially oriented LYSO crystals interleaved by stacks of WLS, both individually read out by G-APDs. A PET demonstrator, based on two detector modules used in coincidence, is currently under construction.

  15. Interface study of FeMgOFe magnetic tunnel junctions using 3D Atom Probe

    CERN Document Server

    Mazumder, B; Vella, A; Vurpillot, F; Deconihout, B

    2011-01-01

    A detailed interface study was conducted on a Fe/MgO/Fe system using laser assisted 3D atom probe. It exhibits an additional oxide formation at the second interface of the multilayer structure independent of laser wavelength, laser fluence and the thickness of the tunnel barrier. We have shown with the help of simulation that this phenomena is caused by the field evaporation of two layers having two different evaporation

  16. Development of a High Resolution 3D Infant Stomach Model for Surgical Planning

    Science.gov (United States)

    Chaudry, Qaiser; Raza, S. Hussain; Lee, Jeonggyu; Xu, Yan; Wulkan, Mark; Wang, May D.

    Medical surgical procedures have not changed much during the past century due to the lack of accurate low-cost workbench for testing any new improvement. The increasingly cheaper and powerful computer technologies have made computer-based surgery planning and training feasible. In our work, we have developed an accurate 3D stomach model, which aims to improve the surgical procedure that treats the infant pediatric and neonatal gastro-esophageal reflux disease (GERD). We generate the 3-D infant stomach model based on in vivo computer tomography (CT) scans of an infant. CT is a widely used clinical imaging modality that is cheap, but with low spatial resolution. To improve the model accuracy, we use the high resolution Visible Human Project (VHP) in model building. Next, we add soft muscle material properties to make the 3D model deformable. Then we use virtual reality techniques such as haptic devices to make the 3D stomach model deform upon touching force. This accurate 3D stomach model provides a workbench for testing new GERD treatment surgical procedures. It has the potential to reduce or eliminate the extensive cost associated with animal testing when improving any surgical procedure, and ultimately, to reduce the risk associated with infant GERD surgery.

  17. 3D multicolor super-resolution imaging offers improved accuracy in neuron tracing.

    Directory of Open Access Journals (Sweden)

    Melike Lakadamyali

    Full Text Available The connectivity among neurons holds the key to understanding brain function. Mapping neural connectivity in brain circuits requires imaging techniques with high spatial resolution to facilitate neuron tracing and high molecular specificity to mark different cellular and molecular populations. Here, we tested a three-dimensional (3D, multicolor super-resolution imaging method, stochastic optical reconstruction microscopy (STORM, for tracing neural connectivity using cultured hippocampal neurons obtained from wild-type neonatal rat embryos as a model system. Using a membrane specific labeling approach that improves labeling density compared to cytoplasmic labeling, we imaged neural processes at 44 nm 2D and 116 nm 3D resolution as determined by considering both the localization precision of the fluorescent probes and the Nyquist criterion based on label density. Comparison with confocal images showed that, with the currently achieved resolution, we could distinguish and trace substantially more neuronal processes in the super-resolution images. The accuracy of tracing was further improved by using multicolor super-resolution imaging. The resolution obtained here was largely limited by the label density and not by the localization precision of the fluorescent probes. Therefore, higher image resolution, and thus higher tracing accuracy, can in principle be achieved by further improving the label density.

  18. X-Ray Nanofocus CT: Visualising Of Internal 3D-Structures With Submicrometer Resolution

    Science.gov (United States)

    Weinekoetter, Christian

    2008-09-01

    High-resolution X-ray Computed Tomography (CT) allows the visualization and failure analysis of the internal micro structure of objects—even if they have complicated 3D-structures where 2D X-ray microscopy would give unclear information. During the past several years, computed tomography has progressed to higher resolution and quicker reconstruction of the 3D-volume. Most recently it even allows a three-dimensional look into the inside of materials with submicron resolution. With the use of nanofocus® tube technology, nanoCT®-systems are pushing forward into application fields that were exclusive to high cost and rare available synchrotron techniques. The study was performed with the new nanotom, a very compact laboratory system which allows the analysis of samples up to 120 mm in diameter and weighing up to 1 kg with exceptional voxel-resolution down to click, this technique will substitute destructive mechanical slicing and cutting in many applications. The initial CT results obtained with the nanotom® demonstrate that it is now possible to analyze the three-dimensional micro structure of materials and small objects with submicrometer resolution. Any internal difference in material, density or porosity within a sample can be visualized and data like distances can be measured. NanoCT® widely expands the spectrum of detectable micro-structures. The nanotom® opens a new dimension of 3D-microanalysis and will replace more destructive methods—saving costs and time per sample inspected.

  19. Study of a high-resolution, 3-D positioning cadmium zinc telluride detector for PET

    OpenAIRE

    Gu, Y.; Matteson, J. L.; Skelton, R T; Deal, A C; Stephan, E A; Duttweiler, F; Gasaway, T M; Levin, C S

    2011-01-01

    This paper investigates the performance of 1 mm resolution Cadmium Zinc Telluride (CZT) detectors for positron emission tomography (PET) capable of positioning the 3-D coordinates of individual 511 keV photon interactions. The detectors comprise 40 mm × 40 mm × 5 mm monolithic CZT crystals that employ a novel cross-strip readout with interspersed steering electrodes to obtain high spatial and energy resolution. The study found a single anode FWHM energy resolution of 3.06±0.39% at 511 keV thr...

  20. Single-pixel 3D imaging with time-based depth resolution

    CERN Document Server

    Sun, Ming-Jie; Gibson, Graham M; Sun, Baoqing; Radwell, Neal; Lamb, Robert; Padgett, Miles J

    2016-01-01

    Time-of-flight three dimensional imaging is an important tool for many applications, such as object recognition and remote sensing. Unlike conventional imaging approach using pixelated detector array, single-pixel imaging based on projected patterns, such as Hadamard patterns, utilises an alternative strategy to acquire information with sampling basis. Here we show a modified single-pixel camera using a pulsed illumination source and a high-speed photodiode, capable of reconstructing 128x128 pixel resolution 3D scenes to an accuracy of ~3 mm at a range of ~5 m. Furthermore, we demonstrate continuous real-time 3D video with a frame-rate up to 12 Hz. The simplicity of the system hardware could enable low-cost 3D imaging devices for precision ranging at wavelengths beyond the visible spectrum.

  1. Inclusion of high resolution MODIS maps on a 3D tropospheric water vapor GPS tomography model

    Science.gov (United States)

    Benevides, Pedro; Catalao, Joao; Nico, Giovanni; Miranda, Pedro M. A.

    2015-10-01

    Observing the water vapor distribution on the troposphere remains a challenge for the weather forecast. Radiosondes provide precise water vapor profiles of the troposphere, but lack geographical and temporal coverage, while satellite meteorological maps have good spatial resolution but even poorer temporal resolution. GPS has proved its capacity to measure the integrated water vapor in all weather conditions with high temporal sampling frequency. However these measurements lack a vertical water vapor discretization. Reconstruction of the slant path GPS observation to the satellite allows oblique water vapor measurements. Implementation of a 3D grid of voxels along the troposphere over an area where GPS stations are available enables the observation ray tracing. A relation between the water vapor density and the distanced traveled inside the voxels is established, defining GPS tomography. An inverse problem formulation is needed to obtain a water vapor solution. The combination of precipitable water vapor (PWV) maps obtained from MODIS satellite data with the GPS tomography is performed in this work. The MODIS PWV maps can have 1 or 5 km pixel resolution, being obtained 2 times per day in the same location at most. The inclusion of MODIS PWV maps provides an enhanced horizontal resolution for the tomographic solution and benefits the stability of the inversion problem. A 3D tomographic grid was adjusted over a regional area covering Lisbon, Portugal, where a GNSS network of 9 receivers is available. Radiosonde measurements in the area are used to evaluate the 3D water vapor tomography maps.

  2. Insights on the Subduction Process from High-Resolution 3D Models

    Science.gov (United States)

    Jadamec, Margarete

    2015-04-01

    This is an exciting time in geodynamics as the use of unprecedented high-resolution 3D modeling allows us to ask new questions that were previously unattainable. It is now relatively straightforward to run 3D numerical simulations, with local mesh refinement to ~1 km, input data mapped onto over 100 million finite element nodes, and using tens of thousands of compute hours per model, e.g. Jadamec et al. [2012]. With the additional computational resources, comes a new approach to modeling the tectonic problem. For example, mapping tectonic plates onto a high-resolution 3D geodynamic model grid forces the modeler to ask questions much as a field geologist would ask when constructing a geologic map. In this process of moving from textbook models of subduction to using models based on observation, the modeler is forced to explain the more complicated geometries and features in the Earth, allowing for the new computational approaches to be powerful tools for scientific discovery. Subduction modeling of this kind has expanded the classical view of two-dimensional corner flow, e.g. McKenzie [1969], to a slab driven flow that can be quite complex with predictions for upper mantle flow rates that can be over ten times surface plate motions, e.g. Jadamec et al. [2010] and others. In this talk, I will investigate the role of the third-dimension and non-linearity in plate boundary deformation. I will present high-resolution 3D numerical models that examine the effect of observationally based slab geometry, multiple subducting plates, non-linear rheology, and variations in overriding plate thickness on the subduction related deformation of plate margins. Specific examples include the Alaska and Central America subduction systems. In addition, I will highlight future directions in subduction modeling, and how these can be advanced by the increased incorporation of observational data, high-performance computing, focused numerical algorithms, and 3D interactive data visualization.

  3. Correction of a Depth-Dependent Lateral Distortion in 3D Super-Resolution Imaging.

    Directory of Open Access Journals (Sweden)

    Lina Carlini

    Full Text Available Three-dimensional (3D localization-based super-resolution microscopy (SR requires correction of aberrations to accurately represent 3D structure. Here we show how a depth-dependent lateral shift in the apparent position of a fluorescent point source, which we term `wobble`, results in warped 3D SR images and provide a software tool to correct this distortion. This system-specific, lateral shift is typically > 80 nm across an axial range of ~ 1 μm. A theoretical analysis based on phase retrieval data from our microscope suggests that the wobble is caused by non-rotationally symmetric phase and amplitude aberrations in the microscope's pupil function. We then apply our correction to the bacterial cytoskeletal protein FtsZ in live bacteria and demonstrate that the corrected data more accurately represent the true shape of this vertically-oriented ring-like structure. We also include this correction method in a registration procedure for dual-color, 3D SR data and show that it improves target registration error (TRE at the axial limits over an imaging depth of 1 μm, yielding TRE values of < 20 nm. This work highlights the importance of correcting aberrations in 3D SR to achieve high fidelity between the measurements and the sample.

  4. User-Appropriate Viewer for High Resolution Interactive Engagement with 3d Digital Cultural Artefacts

    Science.gov (United States)

    Gillespie, D.; La Pensée, A.; Cooper, M.

    2013-07-01

    Three dimensional (3D) laser scanning is an important documentation technique for cultural heritage. This technology has been adopted from the engineering and aeronautical industry and is an invaluable tool for the documentation of objects within museum collections (La Pensée, 2008). The datasets created via close range laser scanning are extremely accurate and the created 3D dataset allows for a more detailed analysis in comparison to other documentation technologies such as photography. The dataset can be used for a range of different applications including: documentation; archiving; surface monitoring; replication; gallery interactives; educational sessions; conservation and visualization. However, the novel nature of a 3D dataset is presenting a rather unique challenge with respect to its sharing and dissemination. This is in part due to the need for specialised 3D software and a supported graphics card to display high resolution 3D models. This can be detrimental to one of the main goals of cultural institutions, which is to share knowledge and enable activities such as research, education and entertainment. This has limited the presentation of 3D models of cultural heritage objects to mainly either images or videos. Yet with recent developments in computer graphics, increased internet speed and emerging technologies such as Adobe's Stage 3D (Adobe, 2013) and WebGL (Khronos, 2013), it is now possible to share a dataset directly within a webpage. This allows website visitors to interact with the 3D dataset allowing them to explore every angle of the object, gaining an insight into its shape and nature. This can be very important considering that it is difficult to offer the same level of understanding of the object through the use of traditional mediums such as photographs and videos. Yet this presents a range of problems: this is a very novel experience and very few people have engaged with 3D objects outside of 3D software packages or games. This paper

  5. Towards high resolution mapping of 3-D mesoscale dynamics from observations

    Directory of Open Access Journals (Sweden)

    B. Buongiorno Nardelli

    2012-10-01

    Full Text Available The MyOcean R&D project MESCLA (MEsoSCaLe dynamical Analysis through combined model, satellite and in situ data was devoted to the high resolution 3-D retrieval of tracer and velocity fields in the oceans, based on the combination of in situ and satellite observations and quasi-geostrophic dynamical models. The retrieval techniques were also tested and compared with the output of a primitive equation model, with particular attention to the accuracy of the vertical velocity field as estimated through the Q vector formulation of the omega equation. The project focused on a test case, covering the region where the Gulf Stream separates from the US East Coast. This work demonstrated that innovative methods for the high resolution mapping of 3-D mesoscale dynamics from observations can be used to build the next generations of operational observation-based products.

  6. How to get spatial resolution inside probe volumes of commercial 3D LDA systems

    Energy Technology Data Exchange (ETDEWEB)

    Strunck, V.; Sodomann, T.; Mueller, H.; Dopheide, D. [Section of Fluid Flow Measuring Techniques, Physikalisch-Technische Bundesanstalt, Bundesallee 100, 38116, Braunschweig (Germany)

    2004-01-01

    In laser Doppler anemometry (LDA) it is often the aim to determine the velocity profile for a given fluid flow. The spatial resolution of such velocity profiles is limited in principal by the size of the probe volume. The method of using time of flight data from two probe volumes allows improvements of the spatial resolution by at least one order of magnitude and measurements of small-scale velocity profiles inside the measuring volume along the optical axis of commercial available 3D anemometers without moving the probe. No change of the optical set-up is necessary. An increased spatial resolution helps to acquire more precise data in areas where the flow velocity changes rapidly as shown in the vicinity of the stagnation point of a cuboid. In the overlapping region of three measuring volumes a spatially resolved 3D velocity vector profile is obtained in the direction of the optical axis in near plane flow conditions. In plane laminar flows the probe volume is extended by a few millimetres. The limitation of the method to a plane flow is that it would require a two-component LDA in a very special off-axis arrangement, but this arrangement is available in most commercial 3D systems. (orig.)

  7. Optical lens-shift design for increasing spatial resolution of 3D ToF cameras

    Science.gov (United States)

    Lietz, Henrik; Hassan, M. Muneeb; Eberhardt, Jörg

    2017-02-01

    Sensor resolution of 3D time-of-flight (ToF) outdoor-capable cameras is strongly limited because of its large pixel dimensions. Computational imaging permits enhancement of the optical system's resolving power without changing physical sensor properties. Super-resolution (SR) algorithms superimpose several sub-pixel-shifted low-resolution (LR) images to overcome the system's limited spatial sampling rate. In this paper, we propose a novel opto-mechanical system to implement sub-pixel shifts by moving an optical lens. This method is more flexible in terms of implementing SR techniques than current sensor-shift approaches. In addition, we describe a SR observation model that has been optimized for the use of LR 3D ToF cameras. A state-of-the-art iteratively reweighted minimization algorithm executes the SR process. It is proven that our method achieves nearly the same resolution increase as if the pixel area would be halved physically. Resolution enhancement is measured objectively for amplitude images of a static object scene.

  8. 3D cut-cell modelling for high-resolution atmospheric simulations

    CERN Document Server

    Yamazaki, H; Nikiforakis, N

    2015-01-01

    With the recent, rapid development of computer technology, the resolution of atmospheric numerical models has increased substantially. As a result, steep gradients in mountainous terrain are now being resolved in high-resolution models. This results in large truncation errors in those models using terrain-following coordinates. In this study, a new 3D Cartesian coordinate non-hydrostatic atmospheric model is developed. A cut-cell representation of topography based on finite-volume discretization is combined with a cell-merging approach, in which small cut-cells are merged with neighboring cells either vertically or horizontally. In addition, a block-structured mesh-refinement technique achieves a variable resolution on the model grid with the finest resolution occurring close to the terrain surface. The model successfully reproduces a flow over a 3D bell-shaped hill that shows a good agreement with the flow predicted by the linear theory. The ability of the model to simulate flows over steep terrain is demons...

  9. Blind 3D Model Watermarking Based on Multi-Resolution Representation and Fuzzy Logic

    CERN Document Server

    Tamane, Sharvari C

    2012-01-01

    Insertion of a text message, audio data or/and an image into another image or 3D model is called as a watermarking process. Watermarking has variety of applications like: Copyright Protection, Owner Identification, Copy Protection and Data Hiding etc., depending upon the type of watermark insertion algorithm. Watermark remains in the content after applying various attacks without any distortions. The blind watermarking method used in the system is based on a wavelet transform, a fuzzy inference system and a multi-resolution representation (MRR) of the 3d model. The watermark scrambled by Arnold Transform is embedded in the wavelet coefficients at third resolution level of the MRR. Fuzzy logic approach used in the method makes it to approximate the best possible gain with an accurate scaling factor so that the watermark remains invisible. The fuzzy input variables are computed for each wavelet coefficient in the 3D model. The output of the fuzzy system is a single value which is a perceptual value for each cor...

  10. Three-dimensional imaging of dislocations in a nanoparticle at atomic resolution.

    Science.gov (United States)

    Chen, Chien-Chun; Zhu, Chun; White, Edward R; Chiu, Chin-Yi; Scott, M C; Regan, B C; Marks, Laurence D; Huang, Yu; Miao, Jianwei

    2013-04-04

    Dislocations and their interactions strongly influence many material properties, ranging from the strength of metals and alloys to the efficiency of light-emitting diodes and laser diodes. Several experimental methods can be used to visualize dislocations. Transmission electron microscopy (TEM) has long been used to image dislocations in materials, and high-resolution electron microscopy can reveal dislocation core structures in high detail, particularly in annular dark-field mode. A TEM image, however, represents a two-dimensional projection of a three-dimensional (3D) object (although stereo TEM provides limited information about 3D dislocations). X-ray topography can image dislocations in three dimensions, but with reduced resolution. Using weak-beam dark-field TEM and scanning TEM, electron tomography has been used to image 3D dislocations at a resolution of about five nanometres (refs 15, 16). Atom probe tomography can offer higher-resolution 3D characterization of dislocations, but requires needle-shaped samples and can detect only about 60 per cent of the atoms in a sample. Here we report 3D imaging of dislocations in materials at atomic resolution by electron tomography. By applying 3D Fourier filtering together with equal-slope tomographic reconstruction, we observe nearly all the atoms in a multiply twinned platinum nanoparticle. We observed atomic steps at 3D twin boundaries and imaged the 3D core structure of edge and screw dislocations at atomic resolution. These dislocations and the atomic steps at the twin boundaries, which appear to be stress-relief mechanisms, are not visible in conventional two-dimensional projections. The ability to image 3D disordered structures such as dislocations at atomic resolution is expected to find applications in materials science, nanoscience, solid-state physics and chemistry.

  11. On horizontal resolution for seismic acquisition geometries in complex 3D media

    Science.gov (United States)

    Wei, Wei; Fu, Li-Yun

    2014-09-01

    Spatial sampling has a crucial influence on the horizontal resolution of seismic imaging, but how to quantify the influence is still controversial especially in complex media. Most of the studies on horizontal resolution focus on the measurement of wavelet widths for seismic migration, but neglect to evaluate the effect of side-lobe perturbations on spatial resolution. The side-lobe effect, as a migration noise, is important for seismic imaging in complex media. In this article, with focal beam analysis, we define two parameters to represent the horizontal resolution of an acquisition geometry: the width of the main lobe (WML) along the inline and crossline directions and the ratio of the main-lobe amplitude to the total amplitude (RMT) in a focal beam. We provide examples of typical acquisition geometries to show how spatial sampling affects the horizontal resolution, measured in terms of WML and RMT values. WML defines the horizontal resolution to image the target, whereas RMT describes the clarity of the imaging. Migration noise reduces with increasing RMT, indirectly improving both the vertical and horizontal resolutions of seismic imaging. Case studies of seismic migration with 3D seismic data from an oil field of China, demonstrate how the acquisition geometries with different WML and RMT values influence the performance of seismic imaging. Prior WML and RMT analyses to predict the quality of acquired datasets can optimize acquisition geometries before the implementation of seismic acquisition.

  12. Study of a high-resolution, 3D positioning cadmium zinc telluride detector for PET

    Energy Technology Data Exchange (ETDEWEB)

    Gu, Y; Levin, C S [Department of Electrical Engineering, Stanford University, Stanford, CA 94305 (United States); Matteson, J L; Skelton, R T; Deal, A C; Stephan, E A; Duttweiler, F; Gasaway, T M, E-mail: cslevin@stanford.edu [Center for Astrophysics and Space Sciences, University of California, San Diego, La Jolla, CA 92093 (United States)

    2011-03-21

    This paper investigates the performance of 1 mm resolution cadmium zinc telluride (CZT) detectors for positron emission tomography (PET) capable of positioning the 3D coordinates of individual 511 keV photon interactions. The detectors comprise 40 mm x 40 mm x 5 mm monolithic CZT crystals that employ a novel cross-strip readout with interspersed steering electrodes to obtain high spatial and energy resolution. The study found a single anode FWHM energy resolution of 3.06 {+-} 0.39% at 511 keV throughout most of the detector volume. Improved resolution is expected with properly shielded front-end electronics. Measurements made using a collimated beam established the efficacy of the steering electrodes in facilitating enhanced charge collection across anodes, as well as a spatial resolution of 0.44 {+-} 0.07 mm in the direction orthogonal to the electrode planes. Finally, measurements based on coincidence electronic collimation yielded a point spread function with 0.78 {+-} 0.10 mm FWHM, demonstrating 1 mm spatial resolution capability transverse to the anodes-as expected from the 1 mm anode pitch. These findings indicate that the CZT-based detector concept has excellent performance and shows great promise for a high-resolution PET system.

  13. Study of a high-resolution, 3D positioning cadmium zinc telluride detector for PET

    Science.gov (United States)

    Gu, Y.; Matteson, J. L.; Skelton, R. T.; Deal, A. C.; Stephan, E. A.; Duttweiler, F.; Gasaway, T. M.; Levin, C. S.

    2011-03-01

    This paper investigates the performance of 1 mm resolution cadmium zinc telluride (CZT) detectors for positron emission tomography (PET) capable of positioning the 3D coordinates of individual 511 keV photon interactions. The detectors comprise 40 mm × 40 mm × 5 mm monolithic CZT crystals that employ a novel cross-strip readout with interspersed steering electrodes to obtain high spatial and energy resolution. The study found a single anode FWHM energy resolution of 3.06 ± 0.39% at 511 keV throughout most of the detector volume. Improved resolution is expected with properly shielded front-end electronics. Measurements made using a collimated beam established the efficacy of the steering electrodes in facilitating enhanced charge collection across anodes, as well as a spatial resolution of 0.44 ± 0.07 mm in the direction orthogonal to the electrode planes. Finally, measurements based on coincidence electronic collimation yielded a point spread function with 0.78 ± 0.10 mm FWHM, demonstrating 1 mm spatial resolution capability transverse to the anodes—as expected from the 1 mm anode pitch. These findings indicate that the CZT-based detector concept has excellent performance and shows great promise for a high-resolution PET system.

  14. Study of a high-resolution, 3-D positioning cadmium zinc telluride detector for PET

    Science.gov (United States)

    Gu, Y; Matteson, J L; Skelton, R T; Deal, A C; Stephan, E A; Duttweiler, F; Gasaway, T M; Levin, C S

    2011-01-01

    This paper investigates the performance of 1 mm resolution Cadmium Zinc Telluride (CZT) detectors for positron emission tomography (PET) capable of positioning the 3-D coordinates of individual 511 keV photon interactions. The detectors comprise 40 mm × 40 mm × 5 mm monolithic CZT crystals that employ a novel cross-strip readout with interspersed steering electrodes to obtain high spatial and energy resolution. The study found a single anode FWHM energy resolution of 3.06±0.39% at 511 keV throughout most the detector volume. Improved resolution is expected with properly shielded front-end electronics. Measurements made using a collimated beam established the efficacy of the steering electrodes in facilitating enhanced charge collection across anodes, as well as a spatial resolution of 0.44±0.07 mm in the direction orthogonal to the electrode planes. Finally, measurements based on coincidence electronic collimation yielded a point spread function with 0.78±0.10 mm FWHM, demonstrating 1 mm spatial resolution capability transverse to the anodes – as expected from the 1 mm anode pitch. These findings indicate that the CZT-based detector concept has excellent performance and shows great promise for a high-resolution PET system. PMID:21335649

  15. Practical resolution requirements of measurement instruments for precise characterization of autostereoscopic 3D displays

    Science.gov (United States)

    Boher, Pierre; Leroux, Thierry; Collomb-Patton, Véronique; Bignon, Thibault

    2014-03-01

    Different ways to evaluate the optical performances of auto-stereoscopic 3D displays are reviewed. Special attention is paid to the crosstalk measurements that can be performed by measuring, either the precise angular emission at one or few locations on the display surface, or the full display surface emission from very specific locations in front of the display. Using measurements made in the two ways with different instruments on different auto-stereoscopic displays, we show that measurement instruments need to match the resolution of the human eye to obtain reliable results in both cases. Practical requirements in terms of angular resolution for viewing angle measurement instruments and in terms of spatial resolution for imaging instruments are derived and verified on practical examples.

  16. A 3D CZT high resolution detector for x- and gamma-ray astronomy

    DEFF Research Database (Denmark)

    Kuvvetli, Irfan; Budtz-Jørgensen, Carl; Zappettini, A.

    2014-01-01

    At DTU Space we have developed a high resolution three dimensional (3D) position sensitive CZT detector for high energy astronomy. The design of the 3D CZT detector is based on the CZT Drift Strip detector principle. The position determination perpendicular to the anode strips is performed using...... a novel interpolating technique based on the drift strip signals. The position determination in the detector depth direction, is made using the DOI technique based the detector cathode and anode signals. The position determination along the anode strips is made with the help of 10 cathode strips...... layer between the drift strip electrodes and CZT detector material. This method was applied to all the proto type detectors and was a very effective method to reduce the surface leakage current between the strips. The proto type detector was recently investigated at the European Synchrotron Radiation...

  17. Mode-synthesizing atomic force microscopy for 3D reconstruction of embedded low-density dielectric nanostructures

    Institute of Scientific and Technical Information of China (English)

    Pauline Vitry[1; Eric BouriUot[1; Cedric Plassard[1; Yvon Lacroute[1; Eric Calkins[2,3; Laurene Tetard[2,3; Eric Lesniewska[1

    2015-01-01

    Challenges in nanoscale characterization call for non-invasive, yet sensitive subsurface characterization of low-density materials such as polymers. In this work, we present new evidence that mode-synthesizing atomic force microscopy can be used to detect minute changes in low-density materials, such as those engendered in electro-sensitive polymers during electron beam lithography, surpassing all common nanoscale mechanical techniques. Moreover, we propose 3D reconstruction of the exposed polymer regions using successive high-resolution frames acquired at incremental depths inside the sample. In addition, the results clearly show the influence of increasing dwell time on the depth profile of the nano-sized exposed regions. Hence, the simple approach described here can be used for achieving sensitive nanoscale tomography of soft materials with promising applications in material sciences and biology.

  18. High-resolution 3D X-ray imaging of intracranial nitinol stents

    Energy Technology Data Exchange (ETDEWEB)

    Snoeren, Rudolph M.; With, Peter H.N. de [Eindhoven University of Technology (TU/e), Faculty Electrical Engineering, Signal Processing Systems group (SPS), Eindhoven (Netherlands); Soederman, Michael [Karolinska University Hospital, Department of Neuroradiology, Stockholm (Sweden); Kroon, Johannes N.; Roijers, Ruben B.; Babic, Drazenko [Philips Healthcare, Best (Netherlands)

    2012-02-15

    To assess an optimized 3D imaging protocol for intracranial nitinol stents in 3D C-arm flat detector imaging. For this purpose, an image quality simulation and an in vitro study was carried out. Nitinol stents of various brands were placed inside an anthropomorphic head phantom, using iodine contrast. Experiments with objects were preceded by image quality and dose simulations. We varied X-ray imaging parameters in a commercially interventional X-ray system to set 3D image quality in the contrast-noise-sharpness space. Beam quality was varied to evaluate contrast of the stents while keeping absorbed dose below recommended values. Two detector formats were used, paired with an appropriate pixel size and X-ray focus size. Zoomed reconstructions were carried out and snapshot images acquired. High contrast spatial resolution was assessed with a CT phantom. We found an optimal protocol for imaging intracranial nitinol stents. Contrast resolution was optimized for nickel-titanium-containing stents. A high spatial resolution larger than 2.1 lp/mm allows struts to be visualized. We obtained images of stents of various brands and a representative set of images is shown. Independent of the make, struts can be imaged with virtually continuous strokes. Measured absorbed doses are shown to be lower than 50 mGy Computed Tomography Dose Index (CTDI). By balancing the modulation transfer of the imaging components and tuning the high-contrast imaging capabilities, we have shown that thin nitinol stent wires can be reconstructed with high contrast-to-noise ratio and good detail, while keeping radiation doses within recommended values. Experimental results compare well with imaging simulations. (orig.)

  19. High Resolution 3D Earth Observation Data Analysis for Safeguards Activities

    OpenAIRE

    d'Angelo, Pablo; Rossi, Cristian; Minet, Christian; Eineder, Michael; Flory, Michael; Niemeyer, Irmgard

    2014-01-01

    This paper provides an overview of the investigations performed at DLR with respect to the application of high resolution SAR and optical data for 3D analysis in the context of Safeguards. The Research Center Jülich and the adjacent open cut mines were used as main test sites, and a comprehensive stack of ascending and descending TerraSAR data was acquired over two years. TerraSAR data acquisition was performed, and various ways to visualize and analyze stacks of radar images w...

  20. Design of a 3D-IC multi-resolution digital pixel sensor

    Science.gov (United States)

    Brochard, N.; Nebhen, J.; Dubois, J.; Ginhac, D.

    2016-04-01

    This paper presents a digital pixel sensor (DPS) integrating a sigma-delta analog-to-digital converter (ADC) at pixel level. The digital pixel includes a photodiode, a delta-sigma modulation and a digital decimation filter. It features adaptive dynamic range and multiple resolutions (up to 10-bit) with a high linearity. A specific row decoder and column decoder are also designed to permit to read a specific pixel chosen in the matrix and its neighborhood of 4 x 4. Finally, a complete design with the CMOS 130 nm 3D-IC FaStack Tezzaron technology is also described, revealing a high fill-factor of about 80%.

  1. A 3D high-resolution gamma camera for radiopharmaceutical studies with small animals

    CERN Document Server

    Loudos, G K; Giokaris, N D; Styliaris, E; Archimandritis, S C; Varvarigou, A D; Papanicolas, C N; Majewski, S; Weisenberger, D; Pani, R; Scopinaro, F; Uzunoglu, N K; Maintas, D; Stefanis, K

    2003-01-01

    The results of studies conducted with a small field of view tomographic gamma camera based on a Position Sensitive Photomultiplier Tube are reported. The system has been used for the evaluation of radiopharmaceuticals in small animals. Phantom studies have shown a spatial resolution of 2 mm in planar and 2-3 mm in tomographic imaging. Imaging studies in mice have been carried out both in 2D and 3D. Conventional radiopharmaceuticals have been used and the results have been compared with images from a clinically used system.

  2. 3D printing of hydrogels in a temperature controlled environment with high spatial resolution

    Directory of Open Access Journals (Sweden)

    Fischer Benjamin

    2016-09-01

    Full Text Available There is great hope in 3D printing techniques to create patient specific scaffolds for therapeutic applications. The majority of these approaches rely on materials that both give support to cells and effectively mimic a tissue specific microenvironment. Hydrogels provide an exceptional support for cells but their physicochemical properties are not suited for conventional additive layer manufacturing. Their low viscosity and resulting fluidic nature inhibit voluminous 3D deposition and lead to crude printing accuracy. To enhance mechanical features, hydrogels are often chemically modified and/or mixed with additives; however it is not clear whether these changes induce effects on cellular behavior or if in vivo applications are at risk. Certainly it increases the complexity of scaffold systems. To circumvent these obstacles, we aimed for a 3D printing technique which is capable of creating scaffolds out of unmodified, pure hydrogels. Here we present a new method to produce alginate scaffolds in a viscosity- independent manner with high spatial resolution. This is achieved by printing in a sub-zero environment which leads to fast freezing of the hydrogels, thus preserving the printed shape and circumventing any viscosity dependent flows. This enables the user to create scaffolds which are able to reflect soft or stiff cell niches.

  3. Room temperature strong light-matter coupling in 3D THz meta-atoms (Conference Presentation)

    Science.gov (United States)

    Paulillo, Bruno; Manceau, Jean-Michel; Li, Lianhe; Linfield, Edmund; Colombelli, Raffaele

    2016-04-01

    We demonstrate strong light-matter coupling at room temperature in the terahertz (THz) spectral region using 3D meta-atoms with extremely sub-wavelength volumes. Using an air-bridge fabrication scheme, we have implemented sub-wavelength 3D THz micro-resonators that rely on suspended loop antennas connected to semiconductor-filled patch cavities. We have experimentally shown that they possess the functionalities of lumped LC resonators: their frequency response can be adjusted by independently tuning the inductance associated the antenna element or the capacitance provided by the metal-semiconductor-metal cavity. Moreover, the radiation coupling and efficiency can be engineered acting on the design of the loop antenna, similarly to conventional RF antennas. Here we take advantage of this rich playground in the context of cavity electrodynamics/intersubband polaritonics. In the strong light-matter coupling regime, a cavity and a two-level system exchange energy coherently at a characteristic rate called the vacuum Rabi frequency ΩR which is dominant with respect to all other loss mechanisms involved. The signature, in the frequency domain, is the appearance of a splitting between the bare cavity and material system resonances: the new states are called upper and a lower polariton branches. So far, most experimental demonstrations of strong light-matter interaction between an intersubband transition and a deeply sub-wavelength mode in the THz or mid-infrared ranges rely on wavelength-scale or larger resonators such as photonic crystals, diffractive gratings, dielectric micro-cavities or patch cavities. Lately, planar metamaterials have been used to enhance the light-matter interaction and strongly reduce the interaction volume by engineering the electric and magnetic resonances of the individual subwavelength constituents. In this contribution we provide evidence of strong coupling between a THz intersubband transition and an extremely sub-wavelength mode (≈λ/10

  4. 3D imaging provides a high-resolution, volumetric approach for analyzing biofouling.

    Science.gov (United States)

    First, Matthew R; Policastro, Steven A; Strom, Matthew J; Riley, Scott C; Robbins-Wamsley, Stephanie H; Drake, Lisa A

    2014-01-01

    A volumetric approach for determining the fouling burden on surfaces is presented, consisting of a 3D camera imaging system with fine (5 μm) resolution. Panels immersed in an estuary on the southwest coast of Florida, USA were imaged and the data were used to quantify seasonal changes in the biofouling community. Test panels, which were submerged in seawater for up to one year, were analyzed before and after gentle scrubbing to quantify the biovolume of the total fouling community (ie soft and hard organisms) and the hard fouling community. Total biofouling ranged from 0.01 to 1.16 cm(3) cm(-2) throughout the immersion period; soft fouling constituted 22-87% of the total biovolume. In the future, this approach may be used to inform numerical models of fluid-surface interfaces and to evaluate, with high resolution, the morphology of fouling organisms in response to antifouling technologies.

  5. High-resolution 3D analysis of mouse small-intestinal stroma.

    Science.gov (United States)

    Bernier-Latmani, Jeremiah; Petrova, Tatiana V

    2016-09-01

    Here we detail a protocol for whole-mount immunostaining of mouse small-intestinal villi that can be used to generate high-resolution 3D images of all gut cell types, including blood and lymphatic vessel cells, neurons, smooth muscle cells, fibroblasts and immune cells. The procedure describes perfusion, fixation, dissection, immunostaining, mounting, clearing, confocal imaging and quantification, using intestinal vasculature as an example. As intestinal epithelial cells prevent visualization with some antibodies, we also provide an optional protocol to remove these cells before fixation. In contrast to alternative current techniques, our protocol enables the entire villus to be visualized with increased spatial resolution of cell location, morphology and cell-cell interactions, thus allowing for easy quantification of phenotypes. The technique, which takes 7 d from mouse dissection to microscopic examination, will be useful for researchers who are interested in most aspects of intestinal biology, including mucosal immunology, infection, nutrition, cancer biology and intestinal microbiota.

  6. High-resolution laser radar for 3D imaging in artwork cataloging, reproduction, and restoration

    Science.gov (United States)

    Ricci, Roberto; Fantoni, Roberta; Ferri de Collibus, Mario; Fornetti, Giorgio G.; Guarneri, Massimiliano; Poggi, Claudio

    2003-10-01

    A high resolution Amplitude Modulated Laser Radar (AM-LR) sensor has recently been developed, aimed at accurately reconstructing 3D digital models of real targets, either single objects or complex scenes. The sensor sounding beam can be swept linearly across the object or circularly around it, by placing the object on a controlled rotating platform, enabling to obtain respectively linear and cylindrical range maps. Both amplitude and phase shift of the modulating wave of back-scattered light are collected and processed, providing respectively a shade-free, high resolution, photographic-like picture and accurate range data in the form of a range image. The resolution of range measurements depends mainly on the laser modulation frequency, provided that the power of the backscattered light reaching the detector is at least a few nW (current best performances are ~100 μm). The complete object surface can be reconstructed from the sampled points by using specifically developed software tools. The system has been successfully applied to scan different types of real surfaces (stone, wood, alloys, bones), with relevant applications in different fields, ranging from industrial machining to medical diagnostics, to vision in hostile environments. Examples of artwork reconstructed models (pottery, marble statues) are presented and the relevance of this technology for reverse engineering applied to cultural heritage conservation and restoration are discussed. Final 3D models can be passed to numeric control machines for rapid-prototyping, exported in standard formats for CAD/CAM purposes and made available on the Internet by adopting a virtual museum paradigm, thus possibly enabling specialists to perform remote inspections on high resolution digital reproductions of hardly accessible masterpieces.

  7. Improvement of hydrogen uptake in iron and vanadium matrices by doping with 3d atomic impurities

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen, N.B. [Laboratoire de Magnetisme de Bretagne, EA 4522 Universite de Bretagne Occidentale, 6 avenue Victor Le Gorgeu, 29285 Brest Cedex (France); Lebon, A., E-mail: alexandre.lebon@univ-brest.fr [Laboratoire de Magnetisme de Bretagne, EA 4522 Universite de Bretagne Occidentale, 6 avenue Victor Le Gorgeu, 29285 Brest Cedex (France); Vega, A. [Laboratoire de Magnetisme de Bretagne, EA 4522 Universite de Bretagne Occidentale, 6 avenue Victor Le Gorgeu, 29285 Brest Cedex (France); Mokrani, A. [Institut des Materiaux Jean Rouxel, UMR CNRS 6502, Universite de Nantes, 2 rue de la Houssiniere, B.P. 44322 Nantes (France)

    2012-12-25

    Highlights: Black-Right-Pointing-Pointer H trapping is easier in V matrix than in Fe matrix whatever the 3d TM impurity. Black-Right-Pointing-Pointer Sc and Ti are the best impurities to trap atomic H in V matrix. Black-Right-Pointing-Pointer Fe or Mn doping in V enhance the density of H storage. - Abstract: The insertion of hydrogen in V and Fe has been investigated by means of pseudopotential DFT calculations with localized basis sets. In Fe and V matrices we have replaced the central atom by a transition metal impurity X = Sc, Ti, Cr, Mn, Fe, Co and Ni to study the capacity of the environment to trap hydrogen. The dissolution energy and structural rearrangement upon H uptake at the different sites close to the doping impurity are calculated. Optimal electronic environments for H trapping are also determined through the calculation of the Fukui function. In the V matrix, the insertion of hydrogen is promoted by doping with the two impurities located at the left of V in the Periodical Table, that is, Ti and Sc. In the iron matrix, among the elements at its left in the Periodic Table, only Mn improves the H uptake, whereas doping with V and Ti worsen the capability of absorbing hydrogen. Finally, the H-H interaction is found to be strongly dependent upon the metal-hydrogen interaction. Elements like Mn or Fe which shorten the H-X distance, exhibit a strong 3d TM state-1s hydrogen state hybridization that seems to wash out the repulsive H-H Coulomb interaction below the 2.0 Angstrom-Sign limit. Addition of a small percentage of Fe or Mn in binary bcc alloys (V-Ti) is suggested to locally enhance the H storage capacity.

  8. Resolution doubling in 3D-STORM imaging through improved buffers.

    Directory of Open Access Journals (Sweden)

    Nicolas Olivier

    Full Text Available Super-resolution imaging methods have revolutionized fluorescence microscopy by revealing the nanoscale organization of labeled proteins. In particular, single-molecule methods such as Stochastic Optical Reconstruction Microscopy (STORM provide resolutions down to a few tens of nanometers by exploiting the cycling of dyes between fluorescent and non-fluorescent states to obtain a sparse population of emitters and precisely localizing them individually. This cycling of dyes is commonly induced by adding different chemicals, which are combined to create a STORM buffer. Despite their importance, the composition of these buffers has scarcely evolved since they were first introduced, fundamentally limiting what can be resolved with STORM. By identifying a new chemical suitable for STORM and optimizing the buffer composition for Alexa-647, we significantly increased the number of photons emitted per cycle by each dye, providing a simple means to enhance the resolution of STORM independently of the optical setup used. Using this buffer to perform 3D-STORM on biological samples, we obtained images with better than 10 nanometer lateral and 30 nanometer axial resolution.

  9. A 3D Computational Study on the Air-Blast Atomization of a Planar Liquid Layer

    Science.gov (United States)

    Chiodi, Robert; Desjardins, Olivier

    2016-11-01

    The air-blast atomization of a planar liquid layer is a complex fluid phenomenon involving the destabilization of a low speed liquid layer by a high speed gas coflow. While progress has been made in recent years on understanding the instability of the liquid surface, it remains difficult to accurately predict using stability analysis and requires special expertise and equipment to perform thorough experiments. Simulations provide an excellent way to conduct parametric studies to determine the effect of splitter plate geometry and momentum flux ratio on the frequency and wavelengths of instability, however, they are extremely difficult due to the high density ratio and large range of length and time scales present in the flow. Using an accurate conservative level set method in conjunction with a newly reformulated reinitialization equation, we perform 3D simulations of the air-blast atomization of a planar liquid layer and compare them to experiments. We then go on to explore the role momentum flux ratio plays in the longitudinal and transverse wavelengths of instability.

  10. RELAP5-3D Resolution of Known Restart/Backup Issues

    Energy Technology Data Exchange (ETDEWEB)

    Mesina, George L. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Anderson, Nolan A. [Idaho National Lab. (INL), Idaho Falls, ID (United States)

    2014-12-01

    The state-of-the-art nuclear reactor system safety analysis computer program developed at the Idaho National Laboratory (INL), RELAP5-3D, continues to adapt to changes in computer hardware and software and to develop to meet the ever-expanding needs of the nuclear industry. To continue at the forefront, code testing must evolve with both code and industry developments, and it must work correctly. To best ensure this, the processes of Software Verification and Validation (V&V) are applied. Verification compares coding against its documented algorithms and equations and compares its calculations against analytical solutions and the method of manufactured solutions. A form of this, sequential verification, checks code specifications against coding only when originally written then applies regression testing which compares code calculations between consecutive updates or versions on a set of test cases to check that the performance does not change. A sequential verification testing system was specially constructed for RELAP5-3D to both detect errors with extreme accuracy and cover all nuclear-plant-relevant code features. Detection is provided through a “verification file” that records double precision sums of key variables. Coverage is provided by a test suite of input decks that exercise code features and capabilities necessary to model a nuclear power plant. A matrix of test features and short-running cases that exercise them is presented. This testing system is used to test base cases (called null testing) as well as restart and backup cases. It can test RELAP5-3D performance in both standalone and coupled (through PVM to other codes) runs. Application of verification testing revealed numerous restart and backup issues in both standalone and couple modes. This document reports the resolution of these issues.

  11. 3D-information fusion from very high resolution satellite sensors

    Science.gov (United States)

    Krauss, T.; d'Angelo, P.; Kuschk, G.; Tian, J.; Partovi, T.

    2015-04-01

    In this paper we show the pre-processing and potential for environmental applications of very high resolution (VHR) satellite stereo imagery like these from WorldView-2 or Pl'eiades with ground sampling distances (GSD) of half a metre to a metre. To process such data first a dense digital surface model (DSM) has to be generated. Afterwards from this a digital terrain model (DTM) representing the ground and a so called normalized digital elevation model (nDEM) representing off-ground objects are derived. Combining these elevation based data with a spectral classification allows detection and extraction of objects from the satellite scenes. Beside the object extraction also the DSM and DTM can directly be used for simulation and monitoring of environmental issues. Examples are the simulation of floodings, building-volume and people estimation, simulation of noise from roads, wave-propagation for cellphones, wind and light for estimating renewable energy sources, 3D change detection, earthquake preparedness and crisis relief, urban development and sprawl of informal settlements and much more. Also outside of urban areas volume information brings literally a new dimension to earth oberservation tasks like the volume estimations of forests and illegal logging, volume of (illegal) open pit mining activities, estimation of flooding or tsunami risks, dike planning, etc. In this paper we present the preprocessing from the original level-1 satellite data to digital surface models (DSMs), corresponding VHR ortho images and derived digital terrain models (DTMs). From these components we present how a monitoring and decision fusion based 3D change detection can be realized by using different acquisitions. The results are analyzed and assessed to derive quality parameters for the presented method. Finally the usability of 3D information fusion from VHR satellite imagery is discussed and evaluated.

  12. CCTV Coverage Index Based on Surveillance Resolution and Its Evaluation Using 3D Spatial Analysis

    Directory of Open Access Journals (Sweden)

    Kyoungah Choi

    2015-09-01

    Full Text Available We propose a novel approach to evaluating how effectively a closed circuit television (CCTV system can monitor a targeted area. With 3D models of the target area and the camera parameters of the CCTV system, the approach produces surveillance coverage index, which is newly defined in this study as a quantitative measure for surveillance performance. This index indicates the proportion of the space being monitored with a sufficient resolution to the entire space of the target area. It is determined by computing surveillance resolution at every position and orientation, which indicates how closely a specific object can be monitored with a CCTV system. We present full mathematical derivation for the resolution, which depends on the location and orientation of the object as well as the geometric model of a camera. With the proposed approach, we quantitatively evaluated the surveillance coverage of a CCTV system in an underground parking area. Our evaluation process provided various quantitative-analysis results, compelling us to examine the design of the CCTV system prior to its installation and understand the surveillance capability of an existing CCTV system.

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

    Science.gov (United States)

    Fischer, R.; Gerya, T.

    2016-10-01

    Geological-geochemical evidence point towards higher mantle potential temperature and a different type of tectonics (global plume-lid tectonics) in the early Earth (>3.2 Ga) compared to the present day (global plate tectonics). In order to investigate tectono-magmatic processes associated with plume-lid tectonics and crustal growth under hotter mantle temperature conditions, we conduct a series of 3D high-resolution magmatic-thermomechanical models with the finite-difference code I3ELVIS. No external plate tectonic forces are applied to isolate 3D effects of various plume-lithosphere and crust-mantle interactions. Results of the numerical experiments show two distinct phases in coupled crust-mantle evolution: (1) a longer (80-100 Myr) and relatively quiet 'growth phase' which is marked by growth of crust and lithosphere, followed by (2) a short (∼20 Myr) and catastrophic 'removal phase', where unstable parts of the crust and mantle lithosphere are removed by eclogitic dripping and later delamination. This modelling suggests that the early Earth plume-lid tectonic regime followed a pattern of episodic growth and removal also called episodic overturn with a periodicity of ∼100 Myr.

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

    Science.gov (United States)

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

    2015-11-01

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

  15. Technical solutions for a full-resolution autostereoscopic 2D/3D display technology

    Science.gov (United States)

    Stolle, Hagen; Olaya, Jean-Christophe; Buschbeck, Steffen; Sahm, Hagen; Schwerdtner, Armin

    2008-02-01

    Auto-stereoscopic 3D displays capable of high quality, full-resolution images for multiple users can only be created with time-sequential systems incorporating eye tracking and a dedicated optical design. The availability of high speed displays with 120Hz and faster eliminated one of the major hurdles for commercial solutions. Results of alternative display solutions from SeeReal show the impact of optical design on system performance and product features. Depending on the manufacturer's capabilities, system complexity can be shifted from optics to SLM with an impact on viewing angle, number of users and energy efficiency, but also on manufacturing processes. A proprietary solution for eye tracking from SeeReal demonstrates that the required key features can be achieved and implemented in commercial systems in a reasonably short time.

  16. Chromospheric heating and structure as determined from high resolution 3D simulations

    CERN Document Server

    Carlsson, Mats; Gudiksen, Boris V

    2010-01-01

    We have performed 3D radiation MHD simulations extending from the convection zone to the corona covering a box 16 Mm$^3$ at 32 km spatial resolution. The simulations show very fine structure in the chromosphere with acoustic shocks interacting with the magnetic field. Magnetic flux concentrations have a temperature lower than the surroundings in the photosphere but higher in the low chromosphere. The heating is there mostly through ohmic dissipation preferentially at the edges of the flux concentrations. The magnetic field is often wound up around the flux concentrations. When acoustic waves travel up along the field this topology leads to swirling motions seen in chromospheric diagnostic lines such as the calcium infrared triplet.

  17. Can Atomic Force Microscopy Achieve Atomic Resolution in Contact Mode?

    Science.gov (United States)

    Jarvis, M. R.; Pérez, Rubén; Payne, M. C.

    2001-02-01

    Atomic force microscopy operating in the contact mode is studied using total-energy pseudopotential calculations. It is shown that, in the case of a diamond tip and a diamond surface, it is possible for a tip terminated by a single atom to sustain forces in excess of 30 nN. It is also shown that imaging at atomic resolution may be limited by blunting of the tip during lateral scanning.

  18. Feasibility analysis of high resolution tissue image registration using 3-D synthetic data

    Directory of Open Access Journals (Sweden)

    Yachna Sharma

    2011-01-01

    Full Text Available Background: Registration of high-resolution tissue images is a critical step in the 3D analysis of protein expression. Because the distance between images (~4-5μm thickness of a tissue section is nearly the size of the objects of interest (~10-20μm cancer cell nucleus, a given object is often not present in both of two adjacent images. Without consistent correspondence of objects between images, registration becomes a difficult task. This work assesses the feasibility of current registration techniques for such images. Methods: We generated high resolution synthetic 3-D image data sets emulating the constraints in real data. We applied multiple registration methods to the synthetic image data sets and assessed the registration performance of three techniques (i.e., mutual information (MI, kernel density estimate (KDE method [1], and principal component analysis (PCA at various slice thicknesses (with increments of 1μm in order to quantify the limitations of each method. Results: Our analysis shows that PCA, when combined with the KDE method based on nuclei centers, aligns images corresponding to 5μm thick sections with acceptable accuracy. We also note that registration error increases rapidly with increasing distance between images, and that the choice of feature points which are conserved between slices improves performance. Conclusions: We used simulation to help select appropriate features and methods for image registration by estimating best-case-scenario errors for given data constraints in histological images. The results of this study suggest that much of the difficulty of stained tissue registration can be reduced to the problem of accurately identifying feature points, such as the center of nuclei.

  19. Controlling Shear Stress in 3D Bioprinting is a Key Factor to Balance Printing Resolution and Stem Cell Integrity.

    Science.gov (United States)

    Blaeser, Andreas; Duarte Campos, Daniela Filipa; Puster, Uta; Richtering, Walter; Stevens, Molly M; Fischer, Horst

    2016-02-04

    A microvalve-based bioprinting system for the manufacturing of high-resolution, multimaterial 3D-structures is reported. Applying a straightforward fluid-dynamics model, the shear stress at the nozzle site can precisely be controlled. Using this system, a broad study on how cell viability and proliferation potential are affected by different levels of shear stress is conducted. Complex, multimaterial 3D structures are printed with high resolution. This work pioneers the investigation of shear stress-induced cell damage in 3D bioprinting and might help to comprehend and improve the outcome of cell-printing studies in the future.

  20. Atomic resolution images of graphite in air

    Energy Technology Data Exchange (ETDEWEB)

    Grigg, D.A.; Shedd, G.M.; Griffis, D.; Russell, P.E.

    1988-12-01

    One sample used for proof of operation for atomic resolution in STM is highly oriented pyrolytic graphite (HOPG). This sample has been imaged with many different STM`s obtaining similar results. Atomic resolution images of HOPG have now been obtained using an STM designed and built at the Precision Engineering Center. This paper discusses the theoretical predictions and experimental results obtained in imaging of HOPG.

  1. High-resolution modelling of 3D hydrodynamics in coastal archipelagos

    Science.gov (United States)

    Miettunen, Elina; Tuomi, Laura; Ropponen, Janne; Lignell, Risto

    2016-04-01

    Dynamics of the coastal seas are affected by eutrophication, over-fishing, coastal construction and climate change. To enable the sustainable development of these areas, monitoring and modelling of the state of the sea are needed. The Archipelago Sea, located in the northern part of the semi-enclosed and brackish water Baltic Sea, is one of the most complex coastal areas with over 40 000 small islands and islets. It is also very vulnerable area already heavily stressed with eutrophication. Applicable modelling tools are needed to support the decision making and to provide sufficiently reliable information on the effects of the planned actions on the state of the coastal waters. We used 3D hydrodynamic model COHERENS to model the Archipelago Sea area with high spatial resolution of 0.25 nmi. Boundary conditions for this limited area were provided from coarser resolution, 2 nmi, Baltic Sea grid. In order to evaluate the performance of the high-resolution coastal model implementation a comprehensive measurement dataset was gathered, including hydrographic data from three intensive monitoring stations and several more rarely visited monitoring or research stations. The hydrodynamic model was able to simulate the surface temperature and salinity fields and their seasonal variation with good accuracy in this complex area. The sharp depth gradients typical for this area provided some challenges to the modelling. There was some over mixing and related to too strong vertical currents in the steep slopes of the deeper fault lines. Also the water exchange between the more open sea and coastal areas through narrow channels between the islands is not sufficiently well reproduced with the current resolution, leading to too high bottom temperatures.

  2. 3D high spectral and spatial resolution imaging of ex vivo mouse brain

    Energy Technology Data Exchange (ETDEWEB)

    Foxley, Sean, E-mail: sean.foxley@ndcn.ox.ac.uk; Karczmar, Gregory S. [Department of Radiology, University of Chicago, Chicago, Illinois 60637 (United States); Domowicz, Miriam [Department of Pediatrics, University of Chicago, Chicago, Illinois 60637 (United States); Schwartz, Nancy [Department of Pediatrics, Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637 (United States)

    2015-03-15

    Purpose: Widely used MRI methods show brain morphology both in vivo and ex vivo at very high resolution. Many of these methods (e.g., T{sub 2}{sup *}-weighted imaging, phase-sensitive imaging, or susceptibility-weighted imaging) are sensitive to local magnetic susceptibility gradients produced by subtle variations in tissue composition. However, the spectral resolution of commonly used methods is limited to maintain reasonable run-time combined with very high spatial resolution. Here, the authors report on data acquisition at increased spectral resolution, with 3-dimensional high spectral and spatial resolution MRI, in order to analyze subtle variations in water proton resonance frequency and lineshape that reflect local anatomy. The resulting information compliments previous studies based on T{sub 2}{sup *} and resonance frequency. Methods: The proton free induction decay was sampled at high resolution and Fourier transformed to produce a high-resolution water spectrum for each image voxel in a 3D volume. Data were acquired using a multigradient echo pulse sequence (i.e., echo-planar spectroscopic imaging) with a spatial resolution of 50 × 50 × 70 μm{sup 3} and spectral resolution of 3.5 Hz. Data were analyzed in the spectral domain, and images were produced from the various Fourier components of the water resonance. This allowed precise measurement of local variations in water resonance frequency and lineshape, at the expense of significantly increased run time (16–24 h). Results: High contrast T{sub 2}{sup *}-weighted images were produced from the peak of the water resonance (peak height image), revealing a high degree of anatomical detail, specifically in the hippocampus and cerebellum. In images produced from Fourier components of the water resonance at −7.0 Hz from the peak, the contrast between deep white matter tracts and the surrounding tissue is the reverse of the contrast in water peak height images. This indicates the presence of a shoulder in

  3. Spatial resolution in atom probe tomography

    CERN Document Server

    Gault, Baptiste; de Geuser, Frederic; La Fontaine, Alex; Stephenson, Leigh T; Haley, Daniel; Ringer, Simon P

    2015-01-01

    This article addresses gaps in definitions and a lack of standard measurement techniques to assess the spatial resolution in atom probe tomography. This resolution is known to be anisotropic, being better in the depth than laterally. Generally the presence of atomic planes in the tomographic reconstruction is considered as being a sufficient proof of the quality of the spatial resolution of the instrument. Based on advanced spatial distribution maps, an analysis methodology that interrogates the local neighborhood of the atoms within the tomographic reconstruction, it is shown how both the in-depth and the lateral resolution can be quantified. The influences of the crystallography and the temperature are investigated, and models are proposed to explain the observed results. We demonstrate that the absolute value of resolution is specimenspecific.

  4. Low-resolution density maps from atomic models: how stepping "back" can be a step "forward".

    Science.gov (United States)

    Belnap, D M; Kumar, A; Folk, J T; Smith, T J; Baker, T S

    1999-01-01

    Atomic-resolution structures have had a tremendous impact on modern biological science. Much useful information also has been gleaned by merging and correlating atomic-resolution structural details with lower-resolution (15-40 A), three-dimensional (3D) reconstructions computed from images recorded with cryo-transmission electron microscopy (cryoTEM) procedures. One way to merge these structures involves reducing the resolution of an atomic model to a level comparable to a cryoTEM reconstruction. A low-resolution density map can be derived from an atomic-resolution structure by retrieving a set of atomic coordinates editing the coordinate file, computing structure factors from the model coordinates, and computing the inverse Fourier transform of the structure factors. This method is a useful tool for structural studies primarily in combination with 3D cryoTEM reconstructions. It has been used to assess the quality of 3D reconstructions, to determine corrections for the phase-contrast transfer function of the transmission electron microscope, to calibrate the dimensions and handedness of 3D reconstructions, to produce difference maps, to model features in macromolecules or macromolecular complexes, and to generate models to initiate model-based determination of particle orientation and origin parameters for 3D reconstruction.

  5. Study of CT-based positron range correction in high resolution 3D PET imaging

    Energy Technology Data Exchange (ETDEWEB)

    Cal-Gonzalez, J., E-mail: jacobo@nuclear.fis.ucm.es [Grupo de Fisica Nuclear, Dpto. Fisica Atomica, Molecular y Nuclear, Universidad Complutense de Madrid (Spain); Herraiz, J.L. [Grupo de Fisica Nuclear, Dpto. Fisica Atomica, Molecular y Nuclear, Universidad Complutense de Madrid (Spain); Espana, S. [Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA (United States); Vicente, E. [Grupo de Fisica Nuclear, Dpto. Fisica Atomica, Molecular y Nuclear, Universidad Complutense de Madrid (Spain); Instituto de Estructura de la Materia, Consejo Superior de Investigaciones Cientificas (CSIC), Madrid (Spain); Herranz, E. [Grupo de Fisica Nuclear, Dpto. Fisica Atomica, Molecular y Nuclear, Universidad Complutense de Madrid (Spain); Desco, M. [Unidad de Medicina y Cirugia Experimental, Hospital General Universitario Gregorio Maranon, Madrid (Spain); Vaquero, J.J. [Dpto. de Bioingenieria e Ingenieria Espacial, Universidad Carlos III, Madrid (Spain); Udias, J.M. [Grupo de Fisica Nuclear, Dpto. Fisica Atomica, Molecular y Nuclear, Universidad Complutense de Madrid (Spain)

    2011-08-21

    Positron range limits the spatial resolution of PET images and has a different effect for different isotopes and positron propagation materials. Therefore it is important to consider it during image reconstruction, in order to obtain optimal image quality. Positron range distributions for most common isotopes used in PET in different materials were computed using the Monte Carlo simulations with PeneloPET. The range profiles were introduced into the 3D OSEM image reconstruction software FIRST and employed to blur the image either in the forward projection or in the forward and backward projection. The blurring introduced takes into account the different materials in which the positron propagates. Information on these materials may be obtained, for instance, from a segmentation of a CT image. The results of introducing positron blurring in both forward and backward projection operations was compared to using it only during forward projection. Further, the effect of different shapes of positron range profile in the quality of the reconstructed images with positron range correction was studied. For high positron energy isotopes, the reconstructed images show significant improvement in spatial resolution when positron range is taken into account during reconstruction, compared to reconstructions without positron range modeling.

  6. Low-resolution characterization of the 3D structure of the Euglena gracilis photoreceptor.

    Science.gov (United States)

    Barsanti, Laura; Coltelli, Primo; Evangelista, Valtere; Passarelli, Vincenzo; Frassanito, Anna Maria; Vesentini, Nicoletta; Gualtieri, Paolo

    2008-10-24

    This paper deals with the first characterization of the structure of the photoreceptive organelle of the unicellular alga Euglena gracilis (Euglenophyta). This organelle has a three-dimensional organization consisting of up to 50 closely stacked membrane lamellae. Ionically induced unstacking of the photoreceptor lamellae revealed ordered arrays well suited to structural analysis by electron microscopy and image analysis, which ultimately yielded a low-resolution picture of the structure. Each lamella is formed by the photoreceptive membrane protein of the cell assembled within the membrane layer in a hexagonal lattice. The first order diffraction spots in the calculated Fourier transform reveals the presence of 6-fold symmetrized topography (better resolution about 90A). The 2D and 3D structural data are very similar with those recently published on proteorodopsin, a membrane protein used by marine bacterio-plankton as light-driven proton pump. In our opinion these similarity indicate that a photoreceptive protein belonging to the same superfamily of proteorodopsin could form the Euglena photoreceptor.

  7. Acquisition of high-resolution 3D data and processing using Artificial Intelligence

    Science.gov (United States)

    Meng, Hui; Sheng, J.; Yang, W.; Pu, Y.

    1996-11-01

    Holographic PIV (HPIV) is a promising 3D velocity field measurement technique providing high spatial-temporal resolution needed for understanding complex and turbulent flows. An HPIV system, combining in-line recording and off-axis viewing (IROV) holography and Heuristic Morphology Particle Pairing (HMPP) method, is being developed in this work. Unlike 2D PIV, HPIV instantaneously records a volume of particle images through holographic imaging. Its data processing involves special difficulties such as speckle noise, sparse pairs and large data sets. The HMPP algorithm is an adaptive parallel processing scheme applying artificial intelligence searching theory. Based on similar morphology of a particle group at successive instants separated by a small interval, HMPP matches a group of particle images between double exposures and provides velocity vectors for individual particle pairs, providing much higher spatial resolution than conventional correlation algorithm and lower measurement error caused by large velocity gradients. Taking advantages of IROV and HMPP, the system being developed appears highly promising as a practical HPIV configuration.

  8. A Fast Full Tensor Gravity computation algorithm for High Resolution 3D Geologic Interpretations

    Science.gov (United States)

    Jayaram, V.; Crain, K.; Keller, G. R.

    2011-12-01

    We present an algorithm to rapidly calculate the vertical gravity and full tensor gravity (FTG) values due to a 3-D geologic model. This algorithm can be implemented on single, multi-core CPU and graphical processing units (GPU) architectures. Our technique is based on the line element approximation with a constant density within each grid cell. This type of parameterization is well suited for high-resolution elevation datasets with grid size typically in the range of 1m to 30m. The large high-resolution data grids in our studies employ a pre-filtered mipmap pyramid type representation for the grid data known as the Geometry clipmap. The clipmap was first introduced by Microsoft Research in 2004 to do fly-through terrain visualization. This method caches nested rectangular extents of down-sampled data layers in the pyramid to create view-dependent calculation scheme. Together with the simple grid structure, this allows the gravity to be computed conveniently on-the-fly, or stored in a highly compressed format. Neither of these capabilities has previously been available. Our approach can perform rapid calculations on large topographies including crustal-scale models derived from complex geologic interpretations. For example, we used a 1KM Sphere model consisting of 105000 cells at 10m resolution with 100000 gravity stations. The line element approach took less than 90 seconds to compute the FTG and vertical gravity on an Intel Core i7 CPU at 3.07 GHz utilizing just its single core. Also, unlike traditional gravity computational algorithms, the line-element approach can calculate gravity effects at locations interior or exterior to the model. The only condition that must be met is the observation point cannot be located directly above the line element. Therefore, we perform a location test and then apply appropriate formulation to those data points. We will present and compare the computational performance of the traditional prism method versus the line element

  9. Beyond optical molasses: 3D raman sideband cooling of atomic cesium to high phase-space density

    Science.gov (United States)

    Kerman; Vuletic; Chin; Chu

    2000-01-17

    We demonstrate a simple, general purpose method to cool neutral atoms. A sample containing 3x10(8) cesium atoms prepared in a magneto-optical trap is cooled and simultaneously spin polarized in 10 ms at a density of 1.1x10(11) cm (-3) to a phase space density nlambda(3)(dB) = 1/500, which is almost 3 orders of magnitude higher than attainable in free space with optical molasses. The technique is based on 3D degenerate Raman sideband cooling in optical lattices and remains efficient even at densities where the mean lattice site occupation is close to unity.

  10. Zooming in: high resolution 3D reconstruction of differently stained histological whole slide images

    Science.gov (United States)

    Lotz, Johannes; Berger, Judith; Müller, Benedikt; Breuhahn, Kai; Grabe, Niels; Heldmann, Stefan; Homeyer, André; Lahrmann, Bernd; Laue, Hendrik; Olesch, Janine; Schwier, Michael; Sedlaczek, Oliver; Warth, Arne

    2014-03-01

    Much insight into metabolic interactions, tissue growth, and tissue organization can be gained by analyzing differently stained histological serial sections. One opportunity unavailable to classic histology is three-dimensional (3D) examination and computer aided analysis of tissue samples. In this case, registration is needed to reestablish spatial correspondence between adjacent slides that is lost during the sectioning process. Furthermore, the sectioning introduces various distortions like cuts, folding, tearing, and local deformations to the tissue, which need to be corrected in order to exploit the additional information arising from the analysis of neighboring slide images. In this paper we present a novel image registration based method for reconstructing a 3D tissue block implementing a zooming strategy around a user-defined point of interest. We efficiently align consecutive slides at increasingly fine resolution up to cell level. We use a two-step approach, where after a macroscopic, coarse alignment of the slides as preprocessing, a nonlinear, elastic registration is performed to correct local, non-uniform deformations. Being driven by the optimization of the normalized gradient field (NGF) distance measure, our method is suitable for differently stained and thus multi-modal slides. We applied our method to ultra thin serial sections (2 μm) of a human lung tumor. In total 170 slides, stained alternately with four different stains, have been registered. Thorough visual inspection of virtual cuts through the reconstructed block perpendicular to the cutting plane shows accurate alignment of vessels and other tissue structures. This observation is confirmed by a quantitative analysis. Using nonlinear image registration, our method is able to correct locally varying deformations in tissue structures and exceeds the limitations of globally linear transformations.

  11. Computation of a high-resolution MRI 3D stereotaxic atlas of the sheep brain.

    Science.gov (United States)

    Ella, Arsène; Delgadillo, José A; Chemineau, Philippe; Keller, Matthieu

    2017-02-15

    The sheep model was first used in the fields of animal reproduction and veterinary sciences and then was utilized in fundamental and preclinical studies. For more than a decade, magnetic resonance (MR) studies performed on this model have been increasingly reported, especially in the field of neuroscience. To contribute to MR translational neuroscience research, a brain template and an atlas are necessary. We have recently generated the first complete T1-weighted (T1W) and T2W MR population average images (or templates) of in vivo sheep brains. In this study, we 1) defined a 3D stereotaxic coordinate system for previously established in vivo population average templates; 2) used deformation fields obtained during optimized nonlinear registrations to compute nonlinear tissues or prior probability maps (nlTPMs) of cerebrospinal fluid (CSF), gray matter (GM), and white matter (WM) tissues; 3) delineated 25 external and 28 internal sheep brain structures by segmenting both templates and nlTPMs; and 4) annotated and labeled these structures using an existing histological atlas. We built a quality high-resolution 3D atlas of average in vivo sheep brains linked to a reference stereotaxic space. The atlas and nlTPMs, associated with previously computed T1W and T2W in vivo sheep brain templates and nlTPMs, provide a complete set of imaging space that are able to be imported into other imaging software programs and could be used as standardized tools for neuroimaging studies or other neuroscience methods, such as image registration, image segmentation, identification of brain structures, implementation of recording devices, or neuronavigation. J. Comp. Neurol. 525:676-692, 2017. © 2016 Wiley Periodicals, Inc.

  12. Characterization of neurovascular compression in facial neuralgia patients by 3D high-resolution MRI and image fusion technique

    Institute of Scientific and Technical Information of China (English)

    Jing Chen; Xiang-Jun Han; Zi-Yi Guo; Guang Yang; Xiong Wang; Qing-Yu Tang; Yue-Qiong Cheng; Yi Guo; Shui-Xi Fu; Cai-Xiang Chen

    2012-01-01

    Objective:To describe the anatomical characteristics and patterns of neurovascular compression (NVC) in patients suffering trigeminal neuralgia (TN) by3D high-resolution magnetic resonance imaging (MRI) method and image fusion technique.Methods:The anatomic structure of trigeminal nerve, brain stem and blood vessel was observed in100 consecutiveTN patients by 3Dhigh resolutionMRI (3D SPGR, contrast-enhancedT1 3D MP-RAGE andT2/T1 3D FIESTA). The3D image sources were fused and visualized using3D DOCTOR software.Results:One or severalNVC sites, which usually appeared0-9.8 mm away from brain stem, were found on the symptomatic side in93% of theTN cases. Superior cerebellar artery was involved in76% (71/93) of these cases. The other vessels including antero-inferior cerebellar artery, vertebral artery, basilar artery and veins also contributed to the occurrence ofNVC. TheNVC sites were found to be located in the proximal segment in42%of these cases(39/93) and in the distal segment in45% (42/93). Nerve dislocation or distortion was observed in32% (30/93).Conclusions:Various3D high resolutionMRImethods combined with the image fusion technique could provide pathologic anatomic information for the diagnosis and treatment ofTN.

  13. Airborne LIDAR and high resolution satellite data for rapid 3D feature extraction

    Science.gov (United States)

    Jawak, S. D.; Panditrao, S. N.; Luis, A. J.

    2014-11-01

    This work uses the canopy height model (CHM) based workflow for individual tree crown delineation and 3D feature extraction approach (Overwatch Geospatial's proprietary algorithm) for building feature delineation from high-density light detection and ranging (LiDAR) point cloud data in an urban environment and evaluates its accuracy by using very high-resolution panchromatic (PAN) (spatial) and 8-band (multispectral) WorldView-2 (WV-2) imagery. LiDAR point cloud data over San Francisco, California, USA, recorded in June 2010, was used to detect tree and building features by classifying point elevation values. The workflow employed includes resampling of LiDAR point cloud to generate a raster surface or digital terrain model (DTM), generation of a hill-shade image and an intensity image, extraction of digital surface model, generation of bare earth digital elevation model (DEM) and extraction of tree and building features. First, the optical WV-2 data and the LiDAR intensity image were co-registered using ground control points (GCPs). The WV-2 rational polynomial coefficients model (RPC) was executed in ERDAS Leica Photogrammetry Suite (LPS) using supplementary *.RPB file. In the second stage, ortho-rectification was carried out using ERDAS LPS by incorporating well-distributed GCPs. The root mean square error (RMSE) for the WV-2 was estimated to be 0.25 m by using more than 10 well-distributed GCPs. In the second stage, we generated the bare earth DEM from LiDAR point cloud data. In most of the cases, bare earth DEM does not represent true ground elevation. Hence, the model was edited to get the most accurate DEM/ DTM possible and normalized the LiDAR point cloud data based on DTM in order to reduce the effect of undulating terrain. We normalized the vegetation point cloud values by subtracting the ground points (DEM) from the LiDAR point cloud. A normalized digital surface model (nDSM) or CHM was calculated from the LiDAR data by subtracting the DEM from the DSM

  14. High-resolution 3D seismic model of the crustal and uppermost mantle structure in Poland

    Science.gov (United States)

    Grad, Marek; Polkowski, Marcin; Ostaficzuk, Stanisław R.

    2016-01-01

    In the area of Poland a contact between the Precambrian and Phanerozoic Europe and the Carpathians has a complicated structure and a complex P-wave velocity of the sedimentary cover, crystalline crust, Moho depth and the uppermost mantle. The geometry of the uppermost several kilometers of sediments is relatively well recognized from over 100,000 boreholes. The vertical seismic profiling (VSP) from 1188 boreholes provided detailed velocity data for regional tectonic units and for stratigraphic successions from Permian to the Tertiary and Quaternary deposits. These data, however, do not provide information about the velocity and basement depth in the central part of the Trans-European suture zone (TESZ) and in the Carpathians. So, the data set is supplemented by 2D velocity models from 32 deep seismic sounding refraction profiles which also provide information about the crust and uppermost mantle. Together with the results of other methods: vertical seismic profiling, magnetotelluric, allow for the creation of a detailed, high-resolution 3D model for the entire Earth's crust and the uppermost mantle down to a depth of 60 km. The thinnest sedimentary cover in the Mazury-Belarus anteclise is only 0.3 to 1 km thick, which increases to 7 to 8 km along the East European Craton (EEC) margin, and 9 to 12 km in the TESZ. The Variscan domain is characterized by a 1-4 km thick sedimentary cover, while the Carpathians are characterized by very thick sedimentary layers, up to about 20 km. The crystalline crust is differentiated and has a layered structure. The crust beneath the West European Platform (WEP; Variscan domain) is characterized by P-wave velocities of 5.8-6.6 km/s. The upper and middle crusts beneath the EEC are characterized by velocities of 6.1-6.6 km/s, and are underlain by a high velocity lower crust with a velocity of about 7 km/s. A general decrease in velocity is observed from the older to the younger tectonic domains. The TESZ is associated with a steep dip

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

    Energy Technology Data Exchange (ETDEWEB)

    Mondal, Partha P., E-mail: partha@iap.iisc.ernet.in [Nanobioimaging Laboratory, Department of Instrumentation and Applied Physics, Indian Institute of Science, Bangalore 560012 (India); Curthoys, Nikki M.; Hess, Samuel T. [Department of Physics and Astronomy, University of Maine, Orono, Maine 04469 (United States)

    2016-01-15

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

  16. High-resolution 3D dust radiative transfer in galaxies with DART-Ray

    Science.gov (United States)

    Natale, Giovanni; Popescu, Cristina C.; Tuffs, Richard. J.; Debattista, Victor P.; Grootes, Meiert W.

    2015-02-01

    DART-Ray is a 3D ray-tracing dust radiative transfer (RT) code that can be used to derive stellar and dust emission maps of galaxy models and simulations with arbitrary geometries. In addition to the previously published RT algorithm, we have now included in DART-Ray the possibility of calculating the stocastically heated dust emission from each volume element within a galaxy. To show the capabilities of the code, we performed a high-resolution (26 pc) RT calculation for a galaxy N-body+SPH simulation. The simulated galaxy we considered is characterized by a nuclear disc and a flocculent spiral structure. We analysed the derived galaxy maps for the global and local effects of dust on the galaxy attenuation as well as the contribution of scattered radiation to the predicted observed emission. In addition, by performing an additional RT calculation including only the stellar volume emissivity due to young stellar populations (SPs), we derived the contribution to the total dust emission powered by young and old SPs. Full details of this work will be presented in a forthcoming publication.

  17. High Resolution Ultrasonic Method for 3D Fingerprint Representation in Biometrics

    Science.gov (United States)

    Maev, R. Gr.; Bakulin, E. Y.; Maeva, E. Y.; Severin, F. M.

    Biometrics is an important field which studies different possible ways of personal identification. Among a number of existing biometric techniques fingerprint recognition stands alone - because very large database of fingerprints has already been acquired. Also, fingerprints are an important evidence that can be collected at a crime scene. Therefore, of all automated biometric techniques, especially in the field of law enforcement, fingerprint identification seems to be the most promising. Ultrasonic method of fingerprint imaging was originally introduced over a decade as the mapping of the reflection coefficient at the interface between the finger and a covering plate and has shown very good reliability and free from imperfections of previous two methods. This work introduces a newer development of the ultrasonic fingerprint imaging, focusing on the imaging of the internal structures of fingerprints (including sweat pores) with raw acoustic resolution of about 500 dpi (0.05 mm) using a scanning acoustic microscope to obtain images and acoustic data in the form of 3D data array. C-scans from different depths inside the fingerprint area of fingers of several volunteers were obtained and showed good contrast of ridges-and-valleys patterns and practically exact correspondence to the standard ink-and-paper prints of the same areas. Important feature reveled on the acoustic images was the clear appearance of the sweat pores, which could provide additional means of identification.

  18. 3D HIGH RESOLUTION SEISMIC PROSPECTING IN MINING AREAS; XIEQIAO COLLIERY

    Institute of Scientific and Technical Information of China (English)

    CuiRuofei

    1996-01-01

    3D seismic prospecting in mining areas of Xieqiao Colliery is a successfulmodel for an advancement from the resource prospecting to mining prospecting stagein coal fields. Its results have proved that faults with a throw of 5-10 m can be detected in an area with good seismogeologic conditions by using 3D seismic technique.Detection of underground tunnels for the first time utilizing 3D seismic data indicates that subsided columns, gotten and mine goaf can be detected using 3D seismic technique, so it has a broad applied prospect.

  19. High resolution 3-D temperature and salinity fields derived from in situ and satellite observations

    Directory of Open Access Journals (Sweden)

    S. Guinehut

    2012-10-01

    Full Text Available This paper describes an observation-based approach that efficiently combines the main components of the global ocean observing system using statistical methods. Accurate but sparse in situ temperature and salinity profiles (mainly from Argo for the last 10 yr are merged with the lower accuracy but high-resolution synthetic data derived from satellite altimeter and sea surface temperature observations to provide global 3-D temperature and salinity fields at high temporal and spatial resolution. The first step of the method consists in deriving synthetic temperature fields from altimeter and sea surface temperature observations, and salinity fields from altimeter observations, through multiple/simple linear regression methods. The second step of the method consists in combining the synthetic fields with in situ temperature and salinity profiles using an optimal interpolation method. Results show the revolutionary nature of the Argo observing system. Argo observations now allow a global description of the statistical relationships that exist between surface and subsurface fields needed for step 1 of the method, and can constrain the large-scale temperature and mainly salinity fields during step 2 of the method. Compared to the use of climatological estimates, results indicate that up to 50% of the variance of the temperature fields can be reconstructed from altimeter and sea surface temperature observations and a statistical method. For salinity, only about 20 to 30% of the signal can be reconstructed from altimeter observations, making the in situ observing system essential for salinity estimates. The in situ observations (step 2 of the method further reduce the differences between the gridded products and the observations by up to 20% for the temperature field in the mixed layer, and the main contribution is for salinity and the near surface layer with an improvement up to 30%. Compared to estimates derived using in situ observations only, the

  20. High Resolution 3-D temperature and salinity fields derived from in situ and satellite observations

    Directory of Open Access Journals (Sweden)

    S. Guinehut

    2012-03-01

    Full Text Available This paper describes an observation-based approach that combines efficiently the main components of the global ocean observing system using statistical methods. Accurate but sparse in situ temperature and salinity profiles (mainly from Argo for the last 10 years are merged with the lower accuracy but high-resolution synthetic data derived from altimeter and sea surface temperature satellite observations to provide global 3-D temperature and salinity fields at high temporal and spatial resolution. The first step of the method consists in deriving synthetic temperature fields from altimeter and sea surface temperature observations and salinity fields from altimeter observations through multiple/simple linear regression methods. The second step of the method consists in combining the synthetic fields with in situ temperature and salinity profiles using an optimal interpolation method. Results show the revolution of the Argo observing system. Argo observations now allow a global description of the statistical relationships that exist between surface and subsurface fields needed for step 1 of the method and can constrain the large-scale temperature and mainly salinity fields during step 2 of the method. Compared to the use of climatological estimates, results indicate that up to 50 % of the variance of the temperature fields can be reconstructed from altimeter and sea surface temperature observations and a statistical method. For salinity, only about 20 to 30 % of the signal can be reconstructed from altimeter observations, making the in situ observing system mandatory for salinity estimates. The in situ observations (step 2 of the method reduce additionally the error by up to 20 % for the temperature field in the mixed layer and the main contribution is for salinity and the near surface layer with an improvement up to 30 %. Compared to estimates derived using in situ observations only, the merged fields provide a better reconstruction of the high

  1. Detection of 3D tree root systems using high resolution ground penetration radar

    Science.gov (United States)

    Altdorff, D.; Honds, M.; Botschek, J.; Van Der Kruk, J.

    2014-12-01

    Knowledge of root systems and its distribution are important for biomass estimation as well as for the prevention of subsurface distribution network damages. Ground penetration radar (GPR) is a promising technique that enables a non-invasive imaging of tree roots. Due to the polarisation-dependent reflection coefficients and complicated three-dimensional root structure, accurate measurements with perpendicularly polarized antennas are needed. In this study, we show GPR data from two planes and one chestnut at two locations with different soil conditions. Perpendicular 10 x 10 cm grid measurements were made with a shielded 250 MHz antenna in combination with a high precision self-tracking laser theodolite that provides geo-referenced traces with a spatial resolution of ~ 2 cm. After selecting potential root hyperbolas within the perpendicular GPR profiles, the corresponding three-dimensional coordinates were extracted and visualized in planar view to reveal any linear structure that indicates a possible tree root. The coordinates of the selected linear structures were projected back to the surface by means of the laser-theodolite to indicate the locations for groundtruthing. Additionally, we interpolated the measured data into a 3D cube where time slices confirmed the locations of linear reflection events. We validated the indicated predictions by excavation of the soil with a suction dredge. Subsequent georeferencing of the true root distribution and comparison with the selected linear events showed that the approach was able to identify the precise position of roots with a diameter between 3 and 10 cm and a depth of up to 70 cm. However, not all linear events were roots; also mouse channels were found in these depths, since they also generate GPR hyperbolas aligned in linear structures. Roots at a second location at depths of 1 to 1.20 m did not generate identifiable hyperboles, which was probably due to an increased electrical conductivity below 86 cm depth. The

  2. Atomic Resolution Imaging of Halide Perovskites.

    Science.gov (United States)

    Yu, Yi; Zhang, Dandan; Kisielowski, Christian; Dou, Letian; Kornienko, Nikolay; Bekenstein, Yehonadav; Wong, Andrew B; Alivisatos, A Paul; Yang, Peidong

    2016-12-14

    The radiation-sensitive nature of halide perovskites has hindered structural studies at the atomic scale. We overcome this obstacle by applying low dose-rate in-line holography, which combines aberration-corrected high-resolution transmission electron microscopy with exit-wave reconstruction. This technique successfully yields the genuine atomic structure of ultrathin two-dimensional CsPbBr3 halide perovskites, and a quantitative structure determination was achieved atom column by atom column using the phase information of the reconstructed exit-wave function without causing electron beam-induced sample alterations. An extraordinarily high image quality enables an unambiguous structural analysis of coexisting high-temperature and low-temperature phases of CsPbBr3 in single particles. On a broader level, our approach offers unprecedented opportunities to better understand halide perovskites at the atomic level as well as other radiation-sensitive materials.

  3. Atomic Resolution Microscopy of Nitrides in Steel

    DEFF Research Database (Denmark)

    Danielsen, Hilmar Kjartansson

    2014-01-01

    MN and CrMN type nitride precipitates in 12%Cr steels have been investigated using atomic resolution microscopy. The MN type nitrides were observed to transform into CrMN both by composition and crystallography as Cr diffuses from the matrix into the MN precipitates. Thus a change from one...

  4. Robust automatic high resolution segmentation of SOFC anode porosity in 3D

    DEFF Research Database (Denmark)

    Jørgensen, Peter Stanley; Bowen, Jacob R.

    2008-01-01

    Routine use of 3D characterization of SOFCs by focused ion beam (FIB) serial sectioning is generally restricted by the time consuming task of manually delineating structures within each image slice. We apply advanced image analysis algorithms to automatically segment the porosity phase of an SOFC...... anode in 3D. The technique is based on numerical approximations to partial differential equations to evolve a 3D surface to the desired phase boundary. Vector fields derived from the experimentally acquired data are used as the driving force. The automatic segmentation compared to manual delineation...... reveals and good correspondence and the two approaches are quantitatively compared. It is concluded that the. automatic approach is more robust, more reproduceable and orders of magnitude quicker than manual segmentation of SOFC anode porosity for subsequent quantitative 3D analysis. Lastly...

  5. High-Resolution Visual 3D Recontructions for Rapid Archaeological Characterization

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The final output will be geotiffs and a custom 3D texture model format that allows for dynamic level-of-detail rendering. The work discussed in the proposal will...

  6. High-resolution, real-time simultaneous 3D surface geometry and temperature measurement.

    Science.gov (United States)

    An, Yatong; Zhang, Song

    2016-06-27

    This paper presents a method to simultaneously measure three-dimensional (3D) surface geometry and temperature in real time. Specifically, we developed 1) a holistic approach to calibrate both a structured light system and a thermal camera under exactly the same world coordinate system even though these two sensors do not share the same wavelength; and 2) a computational framework to determine the sub-pixel corresponding temperature for each 3D point as well as discard those occluded points. Since the thermal 2D imaging and 3D visible imaging systems do not share the same spectrum of light, they can perform sensing simultaneously in real time: we developed a hardware system that can achieve real-time 3D geometry and temperature measurement at 26 Hz with 768 × 960 points per frame.

  7. Coherent addressing of individual neutral atoms in a 3D optical lattice

    CERN Document Server

    Wang, Yang; Corcovilos, Theodore A; Kumar, Aishwarya; Weiss, David S

    2015-01-01

    We demonstrate arbitrary coherent addressing of individual neutral atoms in a $5\\times 5\\times 5$ array formed by an optical lattice. Addressing is accomplished using rapidly reconfigurable crossed laser beams to selectively ac Stark shift target atoms, so that only target atoms are resonant with state-changing microwaves. The effect of these targeted single qubit gates on the quantum information stored in non-targeted atoms is smaller than $3\\times 10^{-3}$ in state fidelity. This is an important step along the path of converting the scalability promise of neutral atoms into reality.

  8. Adaptive multi-resolution 3D Hartree-Fock-Bogoliubov solver for nuclear structure

    Science.gov (United States)

    Pei, J. C.; Fann, G. I.; Harrison, R. J.; Nazarewicz, W.; Shi, Yue; Thornton, S.

    2014-08-01

    Background: Complex many-body systems, such as triaxial and reflection-asymmetric nuclei, weakly bound halo states, cluster configurations, nuclear fragments produced in heavy-ion fusion reactions, cold Fermi gases, and pasta phases in neutron star crust, are all characterized by large sizes and complex topologies in which many geometrical symmetries characteristic of ground-state configurations are broken. A tool of choice to study such complex forms of matter is an adaptive multi-resolution wavelet analysis. This method has generated much excitement since it provides a common framework linking many diversified methodologies across different fields, including signal processing, data compression, harmonic analysis and operator theory, fractals, and quantum field theory. Purpose: To describe complex superfluid many-fermion systems, we introduce an adaptive pseudospectral method for solving self-consistent equations of nuclear density functional theory in three dimensions, without symmetry restrictions. Methods: The numerical method is based on the multi-resolution and computational harmonic analysis techniques with a multi-wavelet basis. The application of state-of-the-art parallel programming techniques include sophisticated object-oriented templates which parse the high-level code into distributed parallel tasks with a multi-thread task queue scheduler for each multi-core node. The internode communications are asynchronous. The algorithm is variational and is capable of solving coupled complex-geometric systems of equations adaptively, with functional and boundary constraints, in a finite spatial domain of very large size, limited by existing parallel computer memory. For smooth functions, user-defined finite precision is guaranteed. Results: The new adaptive multi-resolution Hartree-Fock-Bogoliubov (HFB) solver madness-hfb is benchmarked against a two-dimensional coordinate-space solver hfb-ax that is based on the B-spline technique and a three-dimensional solver

  9. 3D printing of high-resolution PLA-based structures by hybrid electrohydrodynamic and fused deposition modeling techniques

    Science.gov (United States)

    Zhang, Bin; Seong, Baekhoon; Nguyen, VuDat; Byun, Doyoung

    2016-02-01

    Recently, the three-dimensional (3D) printing technique has received much attention for shape forming and manufacturing. The fused deposition modeling (FDM) printer is one of the various 3D printers available and has become widely used due to its simplicity, low-cost, and easy operation. However, the FDM technique has a limitation whereby its patterning resolution is too low at around 200 μm. In this paper, we first present a hybrid mechanism of electrohydrodynamic jet printing with the FDM technique, which we name E-FDM. We then develop a novel high-resolution 3D printer based on the E-FDM process. To determine the optimal condition for structuring, we also investigated the effect of several printing parameters, such as temperature, applied voltage, working height, printing speed, flow-rate, and acceleration on the patterning results. This method was capable of fabricating both high resolution 2D and 3D structures with the use of polylactic acid (PLA). PLA has been used to fabricate scaffold structures for tissue engineering, which has different hierarchical structure sizes. The fabrication speed was up to 40 mm/s and the pattern resolution could be improved to 10 μm.

  10. Automated detection, 3D segmentation and analysis of high resolution spine MR images using statistical shape models

    Science.gov (United States)

    Neubert, A.; Fripp, J.; Engstrom, C.; Schwarz, R.; Lauer, L.; Salvado, O.; Crozier, S.

    2012-12-01

    Recent advances in high resolution magnetic resonance (MR) imaging of the spine provide a basis for the automated assessment of intervertebral disc (IVD) and vertebral body (VB) anatomy. High resolution three-dimensional (3D) morphological information contained in these images may be useful for early detection and monitoring of common spine disorders, such as disc degeneration. This work proposes an automated approach to extract the 3D segmentations of lumbar and thoracic IVDs and VBs from MR images using statistical shape analysis and registration of grey level intensity profiles. The algorithm was validated on a dataset of volumetric scans of the thoracolumbar spine of asymptomatic volunteers obtained on a 3T scanner using the relatively new 3D T2-weighted SPACE pulse sequence. Manual segmentations and expert radiological findings of early signs of disc degeneration were used in the validation. There was good agreement between manual and automated segmentation of the IVD and VB volumes with the mean Dice scores of 0.89 ± 0.04 and 0.91 ± 0.02 and mean absolute surface distances of 0.55 ± 0.18 mm and 0.67 ± 0.17 mm respectively. The method compares favourably to existing 3D MR segmentation techniques for VBs. This is the first time IVDs have been automatically segmented from 3D volumetric scans and shape parameters obtained were used in preliminary analyses to accurately classify (100% sensitivity, 98.3% specificity) disc abnormalities associated with early degenerative changes.

  11. The new high resolution method of Godunov`s type for 3D viscous flow calculations

    Energy Technology Data Exchange (ETDEWEB)

    Yershov, S.V.; Rusanov, A.V. [Ukranian National Academy of Sciences, Kahrkov (Ukraine)

    1996-12-31

    The numerical method is suggested for the calculations of the 3D viscous compressible flows described by the thin-layer Reynolds-averaged Navier-Stokes equations. The method is based on the Godunov`s finite-difference scheme and it uses the ENO reconstruction suggested by Harten to achieve the uniformly high-order accuracy. The computational efficiency is provided with the simplified multi grid approach and the implicit step written in {delta} -form. The turbulent effects are simulated with the Baldwin - Lomax turbulence model. The application package FlowER is developed to calculate the 3D turbulent flows within complex-shape channels. The numerical results for the 3D flow around a cylinder and through the complex-shaped channels show the accuracy and the reliability of the suggested method. (author)

  12. Dubai 3d Textuerd Mesh Using High Quality Resolution Vertical/oblique Aerial Imagery

    Science.gov (United States)

    Tayeb Madani, Adib; Ziad Ahmad, Abdullateef; Christoph, Lueken; Hammadi, Zamzam; Manal Abdullah Sabeal, Manal Abdullah x.

    2016-06-01

    Providing high quality 3D data with reasonable quality and cost were always essential, affording the core data and foundation for developing an information-based decision-making tool of urban environments with the capability of providing decision makers, stakeholders, professionals, and public users with 3D views and 3D analysis tools of spatial information that enables real-world views. Helps and assist in improving users' orientation and also increase their efficiency in performing their tasks related to city planning, Inspection, infrastructures, roads, and cadastre management. In this paper, the capability of multi-view Vexcel UltraCam Osprey camera images is examined to provide a 3D model of building façades using an efficient image-based modeling workflow adopted by commercial software's. The main steps of this work include: Specification, point cloud generation, and 3D modeling. After improving the initial values of interior and exterior parameters at first step, an efficient image matching technique such as Semi Global Matching (SGM) is applied on the images to generate point cloud. Then, a mesh model of points is calculated using and refined to obtain an accurate model of buildings. Finally, a texture is assigned to mesh in order to create a realistic 3D model. The resulting model has provided enough LoD2 details of the building based on visual assessment. The objective of this paper is neither comparing nor promoting a specific technique over the other and does not mean to promote a sensor-based system over another systems or mechanism presented in existing or previous paper. The idea is to share experience.

  13. DUBAI 3D TEXTUERD MESH USING HIGH QUALITY RESOLUTION VERTICAL/OBLIQUE AERIAL IMAGERY

    Directory of Open Access Journals (Sweden)

    A. T. Madani

    2016-06-01

    Full Text Available Providing high quality 3D data with reasonable quality and cost were always essential, affording the core data and foundation for developing an information-based decision-making tool of urban environments with the capability of providing decision makers, stakeholders, professionals, and public users with 3D views and 3D analysis tools of spatial information that enables real-world views. Helps and assist in improving users’ orientation and also increase their efficiency in performing their tasks related to city planning, Inspection, infrastructures, roads, and cadastre management. In this paper, the capability of multi-view Vexcel UltraCam Osprey camera images is examined to provide a 3D model of building façades using an efficient image-based modeling workflow adopted by commercial software’s. The main steps of this work include: Specification, point cloud generation, and 3D modeling. After improving the initial values of interior and exterior parameters at first step, an efficient image matching technique such as Semi Global Matching (SGM is applied on the images to generate point cloud. Then, a mesh model of points is calculated using and refined to obtain an accurate model of buildings. Finally, a texture is assigned to mesh in order to create a realistic 3D model. The resulting model has provided enough LoD2 details of the building based on visual assessment. The objective of this paper is neither comparing nor promoting a specific technique over the other and does not mean to promote a sensor-based system over another systems or mechanism presented in existing or previous paper. The idea is to share experience.

  14. High-resolution 3D ultrasound jawbone surface imaging for diagnosis of periodontal bony defects: an in vitro study.

    Science.gov (United States)

    Mahmoud, Ahmed M; Ngan, Peter; Crout, Richard; Mukdadi, Osama M

    2010-11-01

    Although medical specialties have recognized the importance of using ultrasonic imaging, dentistry is only beginning to discover its benefit. This has particularly been important in the field of periodontics which studies infections in the gum and bone tissues that surround the teeth. This study investigates the feasibility of using a custom-designed high-frequency ultrasound imaging system to reconstruct high-resolution (3D) surface images of periodontal defects in human jawbone. The system employs single-element focused ultrasound transducers with center frequencies ranging from 30 to 60 MHz. Continuous acquisition using a 1 GHz data acquisition card is synchronized with a high-precision two-dimensional (2D) positioning system of ±1 μm resolution for acquiring accurate measurements of the mandible, in vitro. Signal and image processing algorithms are applied to reconstruct high-resolution ultrasound images and extract the jawbone surface in each frame. Then, all edges are combined and smoothed in order to render a 3D surface image of the jawbone. In vitro experiments were performed to assess the system performance using mandibles with teeth (dentate) or without (nondentate). The system was able to reconstruct 3D images for the mandible's outer surface with superior spatial resolution down to 24 μm, and to perform the whole scanning in images were confirmed with the anatomical structures on the mandibles. All the anatomical landmarks were detected and fully described as 3D images using this novel ultrasound imaging technique, whereas the 2D X-ray radiographic images suffered from poor contrast. These results indicate the great potential of utilizing high-resolution ultrasound as a noninvasive, nonionizing imaging technique for the early diagnosis of the more severe form of periodontal disease.

  15. Fast, background-free, 3D super-resolution optical fluctuation imaging (SOFI).

    Science.gov (United States)

    Dertinger, T; Colyer, R; Iyer, G; Weiss, S; Enderlein, J

    2009-12-29

    Super-resolution optical microscopy is a rapidly evolving area of fluorescence microscopy with a tremendous potential for impacting many fields of science. Several super-resolution methods have been developed over the last decade, all capable of overcoming the fundamental diffraction limit of light. We present here an approach for obtaining subdiffraction limit optical resolution in all three dimensions. This method relies on higher-order statistical analysis of temporal fluctuations (caused by fluorescence blinking/intermittency) recorded in a sequence of images (movie). We demonstrate a 5-fold improvement in spatial resolution by using a conventional wide-field microscope. This resolution enhancement is achieved in iterative discrete steps, which in turn allows the evaluation of images at different resolution levels. Even at the lowest level of resolution enhancement, our method features significant background reduction and thus contrast enhancement and is demonstrated on quantum dot-labeled microtubules of fibroblast cells.

  16. NUMERICAL ANALYSIS OF THE 3-D FLOW FIELD OF PRESSURE ATOMIZERS WITH V-SHAPED CUT AT ORIFICE

    Institute of Scientific and Technical Information of China (English)

    ZHOU Hua

    2011-01-01

    Axisymmetric liquid jets have been studied extensively for more than one century, while non-axisymmetric jets are also very common in engineering applications but attract less concern. Based on Eulerian fluid-fluid model in Fluent software, this article analysizes the 3-D flow fields of pressure atomizers with V-shaped cut at orifice, which will result in a non-axisymmetric liquid jet.Flow rate analysis and jet structure analysis are carried out, the results show that the flow rate can be formulated by adding a correction coefficient to the formula of inviscid axisymmetric jets in atomization regime, when the Weber number is low enough to make the flow fall out of atomization regime, and the jet structure together with the flow rate formula will change. Analysis shows that the evolution of the spray and therefore the structure of the liquid jet are affected much by relative velocity and the local volume fraction of liquid phase.

  17. Orbital evolution of colliding star and pulsar winds in 2D and 3D: dimensionality, resolution, and grid size effects

    CERN Document Server

    Bosch-Ramon, V; Perucho, M

    2014-01-01

    The structure formed by the shocked winds of a massive star and a non-accreting pulsar in a binary system suffers periodic and random variations of orbital and non-linear dynamical origin. The characterization of the evolution of the two-wind interaction region is necessary to understand the non-thermal emission from radio to gamma rays. For the first time, we simulate in 3D the interaction of isotropic stellar and relativistic pulsar winds along one full orbit, on scales well beyond the binary size. We also investigate the impact of grid resolution and size. We carry out, with the code PLUTO, relativistic hydrodynamical simulations in 2 and 3D of the interaction of a slow dense wind and a mildly relativistic wind along one full orbit, up to ~100 times the binary size. The 2-dimensional simulations are carried out with equal and larger grid resolution and size than in 3D. The simulations in 3D confirm previous results in 2D, showing a strong shock induced by Coriolis forces that terminates the pulsar wind in ...

  18. Parameter Estimation of Fossil Oysters from High Resolution 3D Point Cloud and Image Data

    Science.gov (United States)

    Djuricic, Ana; Harzhauser, Mathias; Dorninger, Peter; Nothegger, Clemens; Mandic, Oleg; Székely, Balázs; Molnár, Gábor; Pfeifer, Norbert

    2014-05-01

    A unique fossil oyster reef was excavated at Stetten in Lower Austria, which is also the highlight of the geo-edutainment park 'Fossilienwelt Weinviertel'. It provides the rare opportunity to study the Early Miocene flora and fauna of the Central Paratethys Sea. The site presents the world's largest fossil oyster biostrome formed about 16.5 million years ago in a tropical estuary of the Korneuburg Basin. About 15,000 up to 80-cm-long shells of Crassostrea gryphoides cover a 400 m2 large area. Our project 'Smart-Geology for the World's largest fossil oyster reef' combines methods of photogrammetry, geology and paleontology to document, evaluate and quantify the shell bed. This interdisciplinary approach will be applied to test hypotheses on the genesis of the taphocenosis (e.g.: tsunami versus major storm) and to reconstruct pre- and post-event processes. Hence, we are focusing on using visualization technologies from photogrammetry in geology and paleontology in order to develop new methods for automatic and objective evaluation of 3D point clouds. These will be studied on the basis of a very dense surface reconstruction of the oyster reef. 'Smart Geology', as extension of the classic discipline, exploits massive data, automatic interpretation, and visualization. Photogrammetry provides the tools for surface acquisition and objective, automated interpretation. We also want to stress the economic aspect of using automatic shape detection in paleontology, which saves manpower and increases efficiency during the monitoring and evaluation process. Currently, there are many well known algorithms for 3D shape detection of certain objects. We are using dense 3D laser scanning data from an instrument utilizing the phase shift measuring principle, which provides accurate geometrical basis < 3 mm. However, the situation is difficult in this multiple object scenario where more than 15,000 complete or fragmentary parts of an object with random orientation are found. The goal

  19. High-resolution acoustic imaging at low frequencies using 3D-printed metamaterials

    Directory of Open Access Journals (Sweden)

    S. Laureti

    2016-12-01

    Full Text Available An acoustic metamaterial has been constructed using 3D printing. It contained an array of air-filled channels, whose size and shape could be varied within the design and manufacture process. In this paper we analyze both numerically and experimentally the properties of this polymer metamaterial structure, and demonstrate its use for the imaging of a sample with sub-wavelength dimensions in the audible frequency range.

  20. High-resolution acoustic imaging at low frequencies using 3D-printed metamaterials

    Science.gov (United States)

    Laureti, S.; Hutchins, D. A.; Davis, L. A. J.; Leigh, S. J.; Ricci, M.

    2016-12-01

    An acoustic metamaterial has been constructed using 3D printing. It contained an array of air-filled channels, whose size and shape could be varied within the design and manufacture process. In this paper we analyze both numerically and experimentally the properties of this polymer metamaterial structure, and demonstrate its use for the imaging of a sample with sub-wavelength dimensions in the audible frequency range.

  1. Cerro Negro field, Venezuela: geological images from a high resolution 3-D survey

    Energy Technology Data Exchange (ETDEWEB)

    Woller, Kevin L. [Mobil Technology Co. (WEC)

    1999-07-01

    Following a pilot 3-D survey, Petrolera Cerro Negro acquired and processed a 3-D dynamite survey over the Cerro Negro Field in Venezuela. We designed the survey to achieve high frequency imaging at the relatively shallow (< 1000 m) objectives in the Morichal formation. The data exhibits usable frequencies in the 10-120 Hz range after migration. The results of the survey have satisfied the original objective of imaging the faults and basement structure in the field. Use of continuity measurements on the data has resulted in a photographic quality image of the faults at the basement level. The pattern of the faults indicates an unexpected degree of complexity, indicating a richer structural history than originally thought. The continuity data also shows depositional details in the Morichal, which in accordance with geological history of the area. The operatorship is currently in the process of drilling many horizontal development wells. The patterns of the wells bores and variations in the rock types present a challenge to the usage of the 3-D seismic. The operatorship is working to raise the understanding and utility of the seismic data to another plateau. (author)

  2. Atomic Resolution Imaging and Quantification of Chemical Functionality of Surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Schwarz, Udo [Yale University

    2014-12-10

    The work carried out from 2006-2014 under DoE support was targeted at developing new approaches to the atomic-scale characterization of surfaces that include species-selective imaging and an ability to quantify chemical surface interactions with site-specific accuracy. The newly established methods were subsequently applied to gain insight into the local chemical interactions that govern the catalytic properties of model catalysts of interest to DoE. The foundation of our work was the development of three-dimensional atomic force microscopy (3D-AFM), a new measurement mode that allows the mapping of the complete surface force and energy fields with picometer resolution in space (x, y, and z) and piconewton/millielectron volts in force/energy. From this experimental platform, we further expanded by adding the simultaneous recording of tunneling current (3D-AFM/STM) using chemically well-defined tips. Through comparison with simulations, we were able to achieve precise quantification and assignment of local chemical interactions to exact positions within the lattice. During the course of the project, the novel techniques were applied to surface-oxidized copper, titanium dioxide, and silicon oxide. On these materials, defect-induced changes to the chemical surface reactivity and electronic charge density were characterized with site-specific accuracy.

  3. High-resolution 3D-GRE imaging of the abdomen using controlled aliasing acceleration technique - a feasibility study

    Energy Technology Data Exchange (ETDEWEB)

    AlObaidy, Mamdoh; Ramalho, Miguel; Busireddy, Kiran K.R.; Liu, Baodong; Burke, Lauren M.; Altun, Ersan; Semelka, Richard C. [University of North Carolina at Chapel Hill, Department of Radiology, Chapel Hill, NC (United States); Dale, Brian M. [Siemens Medical Solutions, MR Research and Development, Morrisville, NC (United States)

    2015-12-15

    To assess the feasibility of high-resolution 3D-gradient-recalled echo (GRE) fat-suppressed T1-weighted images using controlled aliasing acceleration technique (CAIPIRINHA-VIBE), and compare image quality and lesion detection to standard-resolution 3D-GRE images using conventional acceleration technique (GRAPPA-VIBE). Eighty-four patients (41 males, 43 females; age range: 14-90 years, 58.8 ± 15.6 years) underwent abdominal MRI at 1.5 T with CAIPIRINHA-VIBE [spatial resolution, 0.76 ± 0.04 mm] and GRAPPA-VIBE [spatial resolution, 1.17 ± 0.14 mm]. Two readers independently reviewed image quality, presence of artefacts, lesion conspicuity, and lesion detection. Kappa statistic was used to assess interobserver agreement. Wilcoxon signed-rank test was used for image qualitative pairwise comparisons. Logistic regression with post-hoc testing was used to evaluate statistical significance of lesions evaluation. Interobserver agreement ranged between 0.45-0.93. Pre-contrast CAIPIRINHA-VIBE showed significantly (p < 0.001) sharper images and lesion conspicuity with decreased residual aliasing, but more noise enhancement and inferior image quality. Post-contrast CAIPIRINHA-VIBE showed significantly (p < 0.001) sharper images and higher lesion conspicuity, with less respiratory motion and residual aliasing artefacts. Inferior fat-suppression was noticeable on CAIPIRINHA-VIBE sequences (p < 0.001). High in-plane resolution abdominal 3D-GRE fat-suppressed T1-weighted imaging using controlled-aliasing acceleration technique is feasible and yields sharper images compared to standard-resolution images using standard acceleration, with higher post-contrast image quality and trend for improved hepatic lesions detection. (orig.)

  4. 3D high resolution tracking of ice flow using mutli-temporal stereo satellite imagery, Franz Josef Glacier, New Zealand

    Science.gov (United States)

    Leprince, S.; Lin, J.; Ayoub, F.; Herman, F.; Avouac, J.

    2013-12-01

    We present the latest capabilities added to the Co-Registration of Optically Sensed Images and Correlation (COSI-Corr) software, which aim at analyzing time-series of stereoscopic imagery to document 3D variations of the ground surface. We review the processing chain and present the new and improved modules for satellite pushbroom imagery, in particular the N-image bundle block adjustment to jointly optimize the viewing geometry of multiple acquisitions, the improved multi-scale image matching based on Semi-Global Matching (SGM) to extract high resolution topography, and the triangulation of multi-temporal disparity maps to derive 3D ground motion. In particular, processes are optimized to run on a cluster computing environment. This new suite of algorithms is applied to the study of Worldview stereo imagery above the Franz Josef, Fox, and Tasman Glaciers, New Zealand, acquired on 01/30/2013, 02/09/2013, and 02/28/2013. We derive high resolution (1m post-spacing) maps of ice flow in three dimensions, where ice velocities of up to 4 m/day are recorded. Images were collected in early summer during a dry and sunny period, which followed two weeks of unsettled weather with several heavy rainfall events across the Southern Alps. The 3D tracking of ice flow highlights the surface response of the glaciers to changes in effective pressure at the ice-bedrock interface due to heavy rainfall, at an unprecedented spatial resolution.

  5. Intelligent Multi-Resolution 3D Modeling, Compression, Registration, Fusion and Recognition Project

    Data.gov (United States)

    National Aeronautics and Space Administration — NASA missions are being designed for multisensor data collection and synthesis using diverse temporal, spatial and spectral resolutions for use by multiple teams of...

  6. Compressive Sensing in High-resolution 3D SAR Tomography of Urban Scenarios

    Directory of Open Access Journals (Sweden)

    Liao Ming-sheng

    2015-04-01

    Full Text Available In modern high resolution SAR data, due to the intrinsic side-looking geometry of SAR sensors, layover and foreshortening issues inevitably arise, especially in dense urban areas. SAR tomography provides a new way of overcoming these problems by exploiting the back-scattering property for each pixel. However, traditional non-parametric spectral estimators, e.g. Truncated Singular Value Decomposition (TSVD, are limited by their poor elevation resolution, which is not comparable to the azimuth and slant-range resolution. In this paper, the Compressive Sensing (CS approach using Basis Pursuit (BP and TWo-step Iterative Shrinkage/Thresholding (TWIST are introduced. Experimental studies with real spotlight-mode TerraSAR-X dataset are carried out using both BP and TWIST, to demonstrate the merits of compressive sensing approaches in terms of robustness, computational efficiency, and super-resolution capability.

  7. Intelligent Multi-Resolution 3D Modeling, Compression, Registration, Fusion and Recognition Project

    Data.gov (United States)

    National Aeronautics and Space Administration — NASA missions are being designed for multi-sensor data collection and synthesis using diverse temporal, spatial and spectral resolutions for use by multiple teams of...

  8. Mapping cardiac fiber orientations from high-resolution DTI to high-frequency 3D ultrasound

    Science.gov (United States)

    Qin, Xulei; Wang, Silun; Shen, Ming; Zhang, Xiaodong; Wagner, Mary B.; Fei, Baowei

    2014-03-01

    The orientation of cardiac fibers affects the anatomical, mechanical, and electrophysiological properties of the heart. Although echocardiography is the most common imaging modality in clinical cardiac examination, it can only provide the cardiac geometry or motion information without cardiac fiber orientations. If the patient's cardiac fiber orientations can be mapped to his/her echocardiography images in clinical examinations, it may provide quantitative measures for diagnosis, personalized modeling, and image-guided cardiac therapies. Therefore, this project addresses the feasibility of mapping personalized cardiac fiber orientations to three-dimensional (3D) ultrasound image volumes. First, the geometry of the heart extracted from the MRI is translated to 3D ultrasound by rigid and deformable registration. Deformation fields between both geometries from MRI and ultrasound are obtained after registration. Three different deformable registration methods were utilized for the MRI-ultrasound registration. Finally, the cardiac fiber orientations imaged by DTI are mapped to ultrasound volumes based on the extracted deformation fields. Moreover, this study also demonstrated the ability to simulate electricity activations during the cardiac resynchronization therapy (CRT) process. The proposed method has been validated in two rat hearts and three canine hearts. After MRI/ultrasound image registration, the Dice similarity scores were more than 90% and the corresponding target errors were less than 0.25 mm. This proposed approach can provide cardiac fiber orientations to ultrasound images and can have a variety of potential applications in cardiac imaging.

  9. Design, modeling and testing of integrated ring extractor for high resolution electrohydrodynamic (EHD) 3D printing

    Science.gov (United States)

    Han, Yiwei; Dong, Jingyan

    2017-03-01

    This paper presents an integrated ring extractor design in electrohydrodynamic (EHD) printing, which can overcome the standoff height limitation in the EHD printing process, and improve printing capability for 3D structures. Standoff height in the EHD printing will affect printing processes and limit the height of the printed structure when the ground electrode is placed under the substrate. In this work, we designed and integrated a ring electrode with the printing nozzle to achieve a self-working printer head, which can start and maintain the printing process without the involvement of the substrate. We applied a FEA method to model the electric field potential distribution and strength to direct the ring extractor design, which provides a similar printing capability with the system using substrate as the ground electrode. We verified the ring electrode design by experiments, and those results from the experiments demonstrated a good match with results from the FEA simulation. We have characterized the printing processes using the integrated ring extractor, and successfully applied this newly designed ring extractor to print polycaprolactone (PCL) 3D structures.

  10. Tunable electronic and magnetic properties in stanene by 3d transition metal atoms absorption

    Science.gov (United States)

    Xing, Dan-Xu; Ren, Ceng-Ceng; Zhang, Shu-Feng; Feng, Yong; Chen, Xin-Lian; Zhang, Chang-Wen; Wang, Pei-Ji

    2017-03-01

    The electronic and magnetic properties of transition metal (TM) atoms (V, Cr, Mn, Fe, Co, Ni) adsorption on stanene are investigated by first-principles calculations. The results indicate that the TM atoms prefer to be relaxed on a H site on stanene except V atom which lies on the valley site. Fe-absorbed stanene is a spin gapless semiconductor with up-spin electron and down-spin hole carriers allowing the coexistence of charge current and the pure spin current. Co-absorbed stanene lies in the half metal phase. The V-, Cr-, Mn-, and Cu-absorbed stanene turn the stanene into metal, while Ni- and Zn-absorbed stanene open a narrow band gap. For V-, Cr-, Mn-, Fe-, and Co-absorbed stanene, the magnetic moment of the TM will survive while the Ni-, Cu-, and Zn-absorbed stanene will be non-magnetic material. These findings may have great potential in the design of new electrically controllable spintronic devices.

  11. Multicolor 3D super-resolution imaging by quantum dot stochastic optical reconstruction microscopy.

    Science.gov (United States)

    Xu, Jianquan; Tehrani, Kayvan F; Kner, Peter

    2015-03-24

    We demonstrate multicolor three-dimensional super-resolution imaging with quantum dots (QSTORM). By combining quantum dot asynchronous spectral blueing with stochastic optical reconstruction microscopy and adaptive optics, we achieve three-dimensional imaging with 24 nm lateral and 37 nm axial resolution. By pairing two short-pass filters with two appropriate quantum dots, we are able to image single blueing quantum dots on two channels simultaneously, enabling multicolor imaging with high photon counts.

  12. Laser 3D printing with sub-microscale resolution of porous elastomeric scaffolds for supporting human bone stem cells.

    Science.gov (United States)

    Petrochenko, Peter E; Torgersen, Jan; Gruber, Peter; Hicks, Lucas A; Zheng, Jiwen; Kumar, Girish; Narayan, Roger J; Goering, Peter L; Liska, Robert; Stampfl, Jürgen; Ovsianikov, Aleksandr

    2015-04-01

    A reproducible method is needed to fabricate 3D scaffold constructs that results in periodic and uniform structures with precise control at sub-micrometer and micrometer length scales. In this study, fabrication of scaffolds by two-photon polymerization (2PP) of a biodegradable urethane and acrylate-based photoelastomer is demonstrated. This material supports 2PP processing with sub-micrometer spatial resolution. The high photoreactivity of the biophotoelastomer permits 2PP processing at a scanning speed of 1000 mm s(-1), facilitating rapid fabrication of relatively large structures (>5 mm(3)). These structures are custom printed for in vitro assay screening in 96-well plates and are sufficiently flexible to enable facile handling and transplantation. These results indicate that stable scaffolds with porosities of greater than 60% can be produced using 2PP. Human bone marrow stromal cells grown on 3D scaffolds exhibit increased growth and proliferation compared to smooth 2D scaffold controls. 3D scaffolds adsorb larger amounts of protein than smooth 2D scaffolds due to their larger surface area; the scaffolds also allow cells to attach in multiple planes and to completely infiltrate the porous scaffolds. The flexible photoelastomer material is biocompatible in vitro and is associated with facile handling, making it a viable candidate for further study of complex 3D-printed scaffolds.

  13. High Resolution 3-D Finite-Volume Coastal Ocean Modeling in Lower Campbell River and Discovery Passage, British Columbia, Canada

    Directory of Open Access Journals (Sweden)

    Yuehua Lin

    2014-03-01

    Full Text Available The 3-D unstructured-grid, Finite-Volume Coastal Ocean Model (FVCOM was used to simulate the flows in Discovery Passage including the adjoining Lower Campbell River, British Columbia, Canada. Challenges in the studies include the strong tidal currents (e.g., up to 7.8 m/s in Seymour Narrows and tailrace discharges, small-scale topographic features and steep bottom slopes, and stratification affected by the Campbell River freshwater discharges. Two applications of high resolution 3-D FVCOM modeling were conducted. One is for the Lower Campbell River extending upstream as far as the John Hart Hydroelectric dam. The horizontal resolution varies from 0.27 m to 32 m in the unstructured triangular mesh to resolve the tailrace flow. The bottom elevation decreases ~14 m within the distance of ~1.4 km along the river. This pioneering FVCOM river modeling demonstrated a very good performance in simulating the river flow structures. The second application is to compute ocean currents immediately above the seabed along the present underwater electrical cable crossing routes across Discovery Passage. Higher resolution was used near the bottom with inter-layer spacing ranging from 0.125 to 0.0005 of total water depth. The model behaves very well in simulating the strong tidal currents in the area at high resolution in both the horizontal and vertical. One year maximum near bottom tidal current along the routes was then analyzed using the model results.

  14. Adsorption of alkali, alkaline-earth, and 3d transition metal atoms on silicene

    Science.gov (United States)

    Sahin, H.; Peeters, F. M.

    2013-02-01

    The adsorption characteristics of alkali, alkaline-earth, and transition metal adatoms on silicene, a graphene-like monolayer structure of silicon are analyzed by means of first-principles calculations. In contrast to graphene, interaction between the metal atoms and the silicene surface is quite strong due to its highly reactive buckled hexagonal structure. In addition to structural properties, we also calculate the electronic band dispersion, net magnetic moment, charge transfer, work function, and dipole moment of the metal adsorbed silicene sheets. Alkali metals, Li, Na, and K, adsorb to hollow sites without any lattice distortion. As a consequence of the significant charge transfer from alkalis to silicene, metalization of silicene takes place. Trends directly related to atomic size, adsorption height, work function, and dipole moment of the silicene/alkali adatom system are also revealed. We found that the adsorption of alkaline-earth metals on silicene is entirely different from their adsorption on graphene. The adsorption of Be, Mg, and Ca turns silicene into a narrow gap semiconductor. Adsorption characteristics of eight transition metals Ti, V, Cr, Mn, Fe, Co, Mo, and W are also investigated. As a result of their partially occupied d orbital, transition metals show diverse structural, electronic, and magnetic properties. Upon the adsorption of transition metals, depending on the adatom type and atomic radius, the system can exhibit metal, half-metal, and semiconducting behavior. For all metal adsorbates, the direction of the charge transfer is from adsorbate to silicene, because of its high surface reactivity. Our results indicate that the reactive crystal structure of silicene provides a rich playground for functionalization at nanoscale.

  15. 3D mechanical measurements with an atomic force microscope on 1D structures

    DEFF Research Database (Denmark)

    Kallesøe, Christian; Larsen, Martin Benjamin Barbour Spanget; Bøggild, Peter;

    2012-01-01

    We have developed a simple method to characterize the mechanical properties of three dimensional nanostructures, such as nanorods standing up from a substrate. With an atomic force microscope the cantilever probe is used to deflect a horizontally aligned nanorod at different positions along...... the nanorod, using the apex of the cantilever itself rather than the tip normally used for probing surfaces. This enables accurate determination of nanostructures' spring constant. From these measurements, Young's modulus is found on many individual nanorods with different geometrical and material structures...... in a short time. Based on this method Young's modulus of carbon nanofibers and epitaxial grown III-V nanowires has been determined....

  16. A Feasibility Study of UV Laser Assisted 3D-Atom Probe Analysis of AlGaN/GaN HEMTs

    Science.gov (United States)

    2013-03-05

    Final Report for AOARD Grant-FA2386-11-1-4031 “A feasibility study of UV laser assisted 3D-atom probe analysis of AlGaN/ GaN HEMTs ” March 5...20-06-2011 to 19-06-2012 4. TITLE AND SUBTITLE A feasibility study of UV laser assisted 3D-atom probe analysis of AlGaN/ GaN HEMTs 5a. CONTRACT...gate region (gate metal, interfacial layer and defects, and AlGaN/ GaN epilayers) of an AFRL HEMT using laser assisted 3-D atom probe (3DAP

  17. Analysis of multiple recording methods for full resolution multi-view autostereoscopic 3D display system incorporating VHOE

    Science.gov (United States)

    Hwang, Yong Seok; Cho, Kyu Ha; Kim, Eun Soo

    2014-03-01

    In this paper, we propose multiple recording process of photopolymer for a full-color multi-view including multiple-view auto-stereoscopic 3D display system based on VHOE (Volume Holographic Optical Element). To overcome the problems such as low resolution, and limited viewing zone of conventional 3D-display without glasses, we designed multiple recording condition of VHOE for multi-view display. It is verified that VHOE may be optically made by angle-multiplexed recording of pre-designed multiple-viewing zone that uniformly is recorded through optimized exposuretime scheduling scheme. Here, VHOE-based backlight system for 4-view stereoscopic display is implemented, in which the output beams that playing a role reference beam from LGP(Light guide plate)t may be sequentially synchronized with the respective stereo images displayed on the LCD panel.

  18. Multi-pulse time delay integration method for flexible 3D super-resolution range-gated imaging.

    Science.gov (United States)

    Xinwei, Wang; Youfu, Li; Yan, Zhou

    2015-03-23

    Constructing flexible regular-shaped range-intensity profiles by the convolution of illuminator laser pulse and sensor gate pulse is crucial for 3D super-resolution range-gated imaging. However, ns-scale rectangular-shaped laser pulse with tunable pulse width is difficult to be obtained, especially for pulsed solid-stated lasers. In this paper we propose a multi-pulse time delay integration (MPTDI) method to reshape range-intensity profiles (RIP) free from the above limitation of pulsed lasers. An equivalent laser pulse temporal shaping model is established to evaluate and optimize the MPTDI method. By using MPTDI, the RIP shape and depth of viewing can both be flexibly changed as desired. Here typical triangular and trapezoidal RIPs are established for 3D imaging under triangular and trapezoidal range-intensity correlation algorithms. In addition, a prototype experiment is demonstrated to prove the feasibility of MPTDI.

  19. Time amplifying techniques towards atomic time resolution

    Institute of Scientific and Technical Information of China (English)

    LI JingZhen

    2009-01-01

    High speed imaging technology has opened applications in many fields,such as collision,detonating,high voltage discharge,disintegration and transfer of phonon and exciton in solid,photosynthesis primitive reaction,and electron dynamics inside atom shell.In principle,all of the transient processes need to be explained theoretically and,st the same time,the time amplifying technique is required for observations of these processes.The present review concerns the atomic time amplifying mechanism of optical information and the extremely-high speed imaging methods,which are expressed in terms of the short time amplifying techniques.It is well-known that for extremely-high speed imaging with the converter tube,the temporal resolution is in the order of sub-picosecond of the streak imaging,and the imaging frequency is 6×10~8-5×10~9 fps(frame per second)of the frame imaging.On the other hand,for the tubeless extremely-high speed imaging,the imaging frequency is 10~7-10~(14) fps,and its mechanism of forming high speed and framing could involve a lot of factors of the light under investigation,for instance,light speed,light parallelism,the parameters of light wave such as amplitude,phase,polarization and wavelength,and even quantum properties of photon.In the cascaded system of electromagnetic wave and particle wave,it is possible to simultaneously realize extremely-high resolution in time and space,which is higher than a kite resolution.Then it would be possible to break the limit of the Heisenberg uncertainty relation of the optical frequency band.

  20. Time amplifying techniques towards atomic time resolution

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    High speed imaging technology has opened applications in many fields,such as collision,detonating, high voltage discharge,disintegration and transfer of phonon and exciton in solid,photosynthesis primitive reaction,and electron dynamics inside atom shell.In principle,all of the transient processes need to be explained theoretically and,at the same time,the time amplifying technique is required for observations of these processes.The present review concerns the atomic time amplifying mechanism of optical information and the extremely-high speed imaging methods,which are expressed in terms of the short time amplifying techniques.It is well-known that for extremely-high speed imaging with the converter tube,the temporal resolution is in the order of sub-picosecond of the streak imaging,and the imaging frequency is 6×10 8 ―5×10 9 fps(frame per second)of the frame imaging.On the other hand,for the tubeless extremely-high speed imaging,the imaging frequency is 10 7 ―10 14 fps,and its mechanism of forming high speed and framing could involve a lot of factors of the light under investigation,for instance,light speed,light parallelism,the parameters of light wave such as amplitude,phase,polari- zation and wavelength,and even quantum properties of photon.In the cascaded system of electro- magnetic wave and particle wave,it is possible to simultaneously realize extremely-high resolution in time and space,which is higher than a kite resolution.Then it would be possible to break the limit of the Heisenberg uncertainty relation of the optical frequency band.

  1. High sensitivity and high resolution element 3D analysis by a combined SIMS–SPM instrument

    Directory of Open Access Journals (Sweden)

    Yves Fleming

    2015-04-01

    Full Text Available Using the recently developed SIMS–SPM prototype, secondary ion mass spectrometry (SIMS data was combined with topographical data from the scanning probe microscopy (SPM module for five test structures in order to obtain accurate chemical 3D maps: a polystyrene/polyvinylpyrrolidone (PS/PVP polymer blend, a nickel-based super-alloy, a titanium carbonitride-based cermet, a reticle test structure and Mg(OH2 nanoclusters incorporated inside a polymer matrix. The examples illustrate the potential of this combined approach to track and eliminate artefacts related to inhomogeneities of the sputter rates (caused by samples containing various materials, different phases or having a non-flat surface and inhomogeneities of the secondary ion extraction efficiencies due to local field distortions (caused by topography with high aspect ratios. In this respect, this paper presents the measured relative sputter rates between PVP and PS as well as in between the different phases of the TiCN cermet.

  2. High-Resolution 3D Bathymetric Mapping for Small Streams Using Low-Altitude Aerial Photography

    Science.gov (United States)

    Dietrich, J. T.; Duffin, J.

    2015-12-01

    Geomorphic monitoring of river restoration projects is a critical component of measuring their success. In smaller streams, with depths less than 2 meters, one of the more difficult variables to map at high-resolution is bathymetry. In larger rivers, bathymetry can be measured with instruments like multi-beam sonar, bathymetric airborne LiDAR, or acoustic doppler current profilers (ADCP). However, these systems are often limited by their minimum operating depths, which makes them ineffective in shallow water. Remote sensing offers several potential solutions for collecting bathymetry, spectral depth mapping and photogrammetric measurement (e.g. Structure-from-Motion (SfM) multi-view photogrammetry). In this case study, we use SfM to produce both high-resolution above water topography and below water bathymetry for two reaches of a stream restoration project on the Middle Fork of the John Day River in eastern Oregon and one reach on the White River in Vermont. We collected low-allitude multispectral (RGB+NIR) aerial photography at all of the sites at altitudes of 30 to 50 meters. The SfM survey was georeferenced with RTK-GPS ground control points and the bathymetry was refraction-corrected using additional RTK-GPS sample points. The resulting raster data products have horizontal resolutions of ~4-8 centimeters for the topography and ~8-15 cm for the bathymetry. This methodology, like many fluvial remote sensing methods, will only work under ideal conditions (e.g. clear water), but it provides an additional tool for collecting high-resolution bathymetric datasets for geomorphic monitoring efforts.

  3. High-resolution direct 3D printed PLGA scaffolds: print and shrink.

    Science.gov (United States)

    Chia, Helena N; Wu, Benjamin M

    2014-12-17

    Direct three-dimensional printing (3DP) produces the final part composed of the powder and binder used in fabrication. An advantage of direct 3DP is control over both the microarchitecture and macroarchitecture. Prints which use porogen incorporated in the powder result in high pore interconnectivity, uniform porosity, and defined pore size after leaching. The main limitations of direct 3DP for synthetic polymers are the use of organic solvents which can dissolve polymers used in most printheads and limited resolution due to unavoidable spreading of the binder droplet after contact with the powder. This study describes a materials processing strategy to eliminate the use of organic solvent during the printing process and to improve 3DP resolution by shrinking with a non-solvent plasticizer. Briefly, poly(lactic-co-glycolic acid) (PLGA) powder was prepared by emulsion solvent evaporation to form polymer microparticles. The printing powder was composed of polymer microparticles dry mixed with sucrose particles. After printing with a water-based liquid binder, the polymer microparticles were fused together to form a network by solvent vapor in an enclosed vessel. The sucrose is removed by leaching and the resulting scaffold is placed in a solution of methanol. The methanol acts as a non-solvent plasticizer and allows for polymer chain rearrangement and efficient packing of polymer chains. The resulting volumetric shrinkage is ∼80% at 90% methanol. A complex shape (honey-comb) was designed, printed, and shrunken to demonstrate isotropic shrinking with the ability to reach a final resolution of ∼400 μm. The effect of type of alcohol (i.e. methanol or ethanol), concentration of alcohol, and temperature on volumetric shrinking was studied. This study presents a novel materials processing strategy to overcome the main limitations of direct 3DP to produce high resolution PLGA scaffolds.

  4. High resolution 3D imaging of living cells with sub-optical wavelength phonons

    Science.gov (United States)

    Pérez-Cota, Fernando; Smith, Richard J.; Moradi, Emilia; Marques, Leonel; Webb, Kevin F.; Clark, Matt

    2016-12-01

    Label-free imaging of living cells below the optical diffraction limit poses great challenges for optical microscopy. Biologically relevant structural information remains below the Rayleigh limit and beyond the reach of conventional microscopes. Super-resolution techniques are typically based on the non-linear and stochastic response of fluorescent labels which can be toxic and interfere with cell function. In this paper we present, for the first time, imaging of live cells using sub-optical wavelength phonons. The axial imaging resolution of our system is determined by the acoustic wavelength (λa = λprobe/2n) and not on the NA of the optics allowing sub-optical wavelength acoustic sectioning of samples using the time of flight. The transverse resolution is currently limited to the optical spot size. The contrast mechanism is significantly determined by the mechanical properties of the cells and requires no additional contrast agent, stain or label to image the cell structure. The ability to breach the optical diffraction limit to image living cells acoustically promises to bring a new suite of imaging technologies to bear in answering exigent questions in cell biology and biomedicine.

  5. Sub-Angstrom Atomic-Resolution Imaging of Heavy Atoms to Light Atoms

    Energy Technology Data Exchange (ETDEWEB)

    O' Keefe, Michael A.; Shao-Horn, Yang

    2003-05-23

    Three decades ago John Cowley and his group at ASU achieved high-resolution electron microscope images showing the crystal unit cell contents at better than 4Angstrom resolution. Over the years, this achievement has inspired improvements in resolution that have enabled researchers to pinpoint the positions of heavy atom columns within the cell. More recently, this ability has been extended to light atoms as resolution has improved. Sub-Angstrom resolution has enabled researchers to image the columns of light atoms (carbon, oxygen and nitrogen) that are present in many complex structures. By using sub-Angstrom focal-series reconstruction of the specimen exit surface wave to image columns of cobalt, oxygen, and lithium atoms in a transition metal oxide structure commonly used as positive electrodes in lithium rechargeable batteries, we show that the range of detectable light atoms extends to lithium. HRTEM at sub-Angstrom resolution will provide the essential role of experimental verification for the emergent nanotech revolution. Our results foreshadow those to be expected from next-generation TEMs with Cs-corrected lenses and monochromated electron beams.

  6. Denoising of high resolution small animal 3D PET data using the non-subsampled Haar wavelet transform

    Energy Technology Data Exchange (ETDEWEB)

    Ochoa Domínguez, Humberto de Jesús, E-mail: hochoa@uacj.mx [Departamento de Ingeniería Eléctrica y computación, Universidad Autónoma de Ciudad Juárez, Ciudad Juárez, Chih. (Mexico); Máynez, Leticia O. [Departamento de Ingeniería Eléctrica y computación, Universidad Autónoma de Ciudad Juárez, Ciudad Juárez, Chih. (Mexico); Vergara Villegas, Osslan O. [Departamento de Ingeniería Industrial, Universidad Autónoma de Ciudad Juárez, Ciudad Juárez, Chih. (Mexico); Mederos, Boris; Mejía, José M.; Cruz Sánchez, Vianey G. [Departamento de Ingeniería Eléctrica y computación, Universidad Autónoma de Ciudad Juárez, Ciudad Juárez, Chih. (Mexico)

    2015-06-01

    PET allows functional imaging of the living tissue. However, one of the most serious technical problems affecting the reconstructed data is the noise, particularly in images of small animals. In this paper, a method for high-resolution small animal 3D PET data is proposed with the aim to reduce the noise and preserve details. The method is based on the estimation of the non-subsampled Haar wavelet coefficients by using a linear estimator. The procedure is applied to the volumetric images, reconstructed without correction factors (plane reconstruction). Results show that the method preserves the structures and drastically reduces the noise that contaminates the image.

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

    Science.gov (United States)

    Fischer, R.; Gerya, T.

    2014-12-01

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

  8. Intraoperative neuronavigation integrated high resolution 3D ultrasound for brainshift and tumor resection control

    Directory of Open Access Journals (Sweden)

    Giovani A.

    2015-06-01

    Full Text Available INTRODUCTION: The link between the neurosurgeon’s knowledge and the scientific improvements made a dramatic change in the field expressed both in impressive drop in the mortality and morbidity rates that were operated in the beginning of the XXth century and in operating with high rates of success cases that were considered inoperable in the past. Neuronavigation systems have been used for many years on surgical orientation purposes especially for small, deep seated lesions where the use of neuronavigation is correlated with smaller corticotomies and with the extended use of transulcal approaches. The major problem of neuronavigation, the brainshift once the dura is opened can be solved either by integrated ultrasound or intraoperative MRI which is out of reach for many neurosurgical departments. METHOD: The procedure of neuronavigation and ultrasonic localization of the tumor is described starting with positioning the patient in the visual field of the neuronavigation integrated 3D ultrasonography system to the control of tumor resection by repeating the ultrasonographic scan in the end of the procedure. DISCUSSION: As demonstrated by many clinical trials on gliomas, the more tumor removed, the better long term control of tumor regrowth and the longer survival with a good quality of life. Of course, no matter how aggressive the surgery, no new deficits are acceptable in the modern era neurosurgery. There are many adjuvant methods for the neurosurgeon to achieve this maximal and safe tumor removal, including the 3T MRI combined with tractography and functional MRI, the intraoperative neuronavigation and neurophysiologic monitoring in both anesthetized and awake patients. The ultrasonography integrated in neuronavigaton comes as a welcomed addition to this adjuvants to help the surgeon achieve the set purpose. CONCLUSION: With the use of this real time imaging device, the common problem of brainshift encountered with the neuronavigation systems

  9. 3D-Information Fusion from Very High Resolution Satellite Sensors

    OpenAIRE

    Krauss, T; P. d'Angelo; G. Kuschk; Tian, J.; T. Partovi

    2015-01-01

    In this paper we show the pre-processing and potential for environmental applications of very high resolution (VHR) satellite stereo imagery like these from WorldView-2 or Pl´eiades with ground sampling distances (GSD) of half a metre to a metre. To process such data first a dense digital surface model (DSM) has to be generated. Afterwards from this a digital terrain model (DTM) representing the ground and a so called normalized digital elevation model (nDEM) representing off-ground ...

  10. High-Resolution Detection of Five Frequencies in a Single 3D Spectrum: HNHCACO - a Bidirectional Coherence Transfer Experiment

    Energy Technology Data Exchange (ETDEWEB)

    Pang Yuxi; Zeng Lei; Kurochkin, Alexander V.; Zuiderweg, Erik R.P. [University of Michigan, Biophysics Research Division (United States)

    1998-02-15

    A new triple-resonance pulse sequence, 3D HNHCACO, is introduced and discussed, which identifies sequential correlations of the backbone nuclei (H{alpha}(i-1), C{alpha}(i-1), C'(i-1), NH(i)) of doubly labeled proteins in H2O. The three-dimensional (3D) method utilizes a recording of 15N and 13C resonances in a single indirect time domain, the 13C' resonance in another indirect time domain, and detects both NH and H{alpha} protons. A bidirectional coherence transfer (NH(i) {r_reversible} N(i) {r_reversible} C'(i-1) {r_reversible} C{alpha}(i-1) {r_reversible} H{alpha}(i-1)) is effectuated, resulting in a single high-resolution 3D spectrum that contains the frequencies of all five backbone nuclei. The experiment was applied to the 12.3 kDa ribonuclease from Bacillus intermedius (Binase)

  11. FIB/SEM tomography with TEM-like resolution for 3D imaging of high-pressure frozen cells.

    Science.gov (United States)

    Villinger, Clarissa; Gregorius, Heiko; Kranz, Christine; Höhn, Katharina; Münzberg, Christin; von Wichert, Götz; Mizaikoff, Boris; Wanner, Gerhard; Walther, Paul

    2012-10-01

    Focused ion beam/scanning electron microscopy (FIB/SEM) tomography is a novel powerful approach for three-dimensional (3D) imaging of biological samples. Thereby, a sample is repeatedly milled with the focused ion beam (FIB) and each newly produced block face is imaged with the scanning electron microscope (SEM). This process can be repeated ad libitum in arbitrarily small increments allowing 3D analysis of relatively large volumes such as eukaryotic cells. High-pressure freezing and freeze substitution, on the other hand, are the gold standards for electron microscopic preparation of whole cells. In this work, we combined these methods and substantially improved resolution by using the secondary electron signal for image formation. With this imaging mode, contrast is formed in a very small, well-defined area close to the newly produced surface. By using this approach, small features, so far only visible in transmission electron microscope (TEM) (e.g., the two leaflets of the membrane bi-layer, clathrin coats and cytoskeletal elements), can be resolved directly in the FIB/SEM in the 3D context of whole cells.

  12. Fast, high-resolution 3D dosimetry utilizing a novel optical-CT scanner incorporating tertiary telecentric collimation.

    Science.gov (United States)

    Sakhalkar, H S; Oldham, M

    2008-01-01

    This study introduces a charge coupled device (CCD) area detector based optical-computed tomography (optical-CT) scanner for comprehensive verification of radiation dose distributions recorded in nonscattering radiochromic dosimeters. Defining characteristics include: (i) a very fast scanning time of approximately 5 min to acquire a complete three-dimensional (3D) dataset, (ii) improved image formation through the use of custom telecentric optics, which ensures accurate projection images and minimizes artifacts from scattered and stray-light sources, and (iii) high resolution (potentially 50 microm) isotropic 3D dose readout. The performance of the CCD scanner for 3D dose readout was evaluated by comparison with independent 3D readout from the single laser beam OCTOPUS-scanner for the same PRESAGE dosimeters. The OCTOPUS scanner was considered the "gold standard" technique in light of prior studies demonstrating its accuracy. Additional comparisons were made against calculated dose distributions from the ECLIPSE treatment-planning system. Dose readout for the following treatments were investigated: (i) a single rectangular beam irradiation to investigate small field and very steep dose gradient dosimetry away from edge effects, (ii) a 2-field open beam parallel-opposed irradiation to investigate dosimetry along steep dose gradients, and (iii) a 7-field intensity modulated radiation therapy (IMRT) irradiation to investigate dosimetry for complex treatment delivery involving modulation of fluence and for dosimetry along moderate dose gradients. Dose profiles, dose-difference plots, and gamma maps were employed to evaluate quantitative estimates of agreement between independently measured and calculated dose distributions. Results indicated that dose readout from the CCD scanner was in agreement with independent gold-standard readout from the OCTOPUS-scanner as well as the calculated ECLIPSE dose distribution for all treatments, except in regions within a few

  13. A high resolution hydrodynamic 3-D model simulation of the malta shelf area

    Directory of Open Access Journals (Sweden)

    A. F. Drago

    Full Text Available The seasonal variability of the water masses and transport in the Malta Channel and proximity of the Maltese Islands have been simulated by a high resolution (1.6 km horizontal grid on average, 15 vertical sigma layers eddy resolving primitive equation shelf model (ROSARIO-I. The numerical simulation was run with climatological forcing and includes thermohaline dynamics with a turbulence scheme for the vertical mixing coefficients on the basis of the Princeton Ocean Model (POM. The model has been coupled by one-way nesting along three lateral boundaries (east, south and west to an intermediate coarser resolution model (5 km implemented over the Sicilian Channel area. The fields at the open boundaries and the atmospheric forcing at the air-sea interface were applied on a repeating "perpetual" year climatological cycle.

    The ability of the model to reproduce a realistic circulation of the Sicilian-Maltese shelf area has been demonstrated. The skill of the nesting procedure was tested by model-modelc omparisons showing that the major features of the coarse model flow field can be reproduced by the fine model with additional eddy space scale components. The numerical results included upwelling, mainly in summer and early autumn, along the southern coasts of Sicily and Malta; a strong eastward shelf surface flow along shore to Sicily, forming part of the Atlantic Ionian Stream, with a presence throughout the year and with significant seasonal modulation, and a westward winter intensified flow of LIW centered at a depth of around 280 m under the shelf break to the south of Malta. The seasonal variability in the thermohaline structure of the domain and the associated large-scale flow structures can be related to the current knowledge on the observed hydrography of the area. The level of mesoscale resolution achieved by the model allowed the spatial and temporal evolution of the changing flow patterns, triggered by

  14. Adaptive Multi-resolution 3D Hartree-Fock-Bogoliubov Solver for Nuclear Structure

    CERN Document Server

    Pei, Junchen; Harrison, Robert; Nazarewicz, Witold; Shi, Yue; Thornton, Scott

    2014-01-01

    Complex many-body systems, such as triaxial and reflection-asymmetric nuclei, weakly-bound halo states, cluster configurations, nuclear fragments produced in heavy-ion fusion reactions, cold Fermi gases, and pasta phases in neutron star crust, they are all characterized by large sizes and complex topologies, in which many geometrical symmetries characteristic of ground-state configurations are broken. A tool of choice to study such complex forms of matter is an adaptive multi-resolution wavelet analysis. This method has generated much excitement since it provides a common framework linking many diversified methodologies across different fields, including signal processing, data compression, harmonic analysis and operator theory, fractals, and quantum field theory. To describe complex superfluid many-fermion systems, we introduce an adaptive pseudo-spectral method for solving self-consistent equations of nuclear density functional theory in three dimensions, without symmetry restrictions. The new adaptive mult...

  15. Biometric assessment of deep-sea vent megabenthic communities using multi-resolution 3D image reconstructions

    Science.gov (United States)

    Thornton, Blair; Bodenmann, Adrian; Pizarro, Oscar; Williams, Stefan B.; Friedman, Ariell; Nakajima, Ryota; Takai, Ken; Motoki, Kaori; Watsuji, Tomo-o.; Hirayama, Hisako; Matsui, Yohei; Watanabe, Hiromi; Ura, Tamaki

    2016-10-01

    This paper describes a method to survey the distribution of megabenthos over multi-hectare regions of the seafloor. Quantitative biomass estimates are made by combining high-resolution 3D image reconstructions, used to model spatial relationships between representative taxa, with lower-resolution reconstructions taken over a wider area in which the distribution of larger predatory animals can be observed. The method is applied to a region of the Iheya North field that was the target of scientific drilling during the IODP Expedition 331 in 2010. An area of 2.5 ha was surveyed 3 years and 4 months after the site was drilled. More than 100,000 organisms from 6 taxa were identified. The visible effects of drilling on the distribution of megabenthos were confined to a 20 m radius of the artificially created hydrothermal discharges, with the associated densities of biomass lower than observed in nearby naturally discharging areas.

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

    Energy Technology Data Exchange (ETDEWEB)

    Le Pogam, Adrien, E-mail: adrien.lepogam@univ-brest.fr [INSERM UMR 1101, LaTIM, Brest (France); Lamare, Frederic [Academic Nuclear Medicine Department, CHU Pellegrin, Bordeaux (France); Hatt, Mathieu [INSERM UMR 1101, LaTIM, Brest (France); Fernandez, Philippe [Academic Nuclear Medicine Department, CHU Pellegrin, Bordeaux (France); Le Rest, Catherine Cheze [INSERM UMR 1101, LaTIM, Brest (France); Academic Nuclear Medicine Department, CHU Poitiers, Poitiers (France); Visvikis, Dimitris [INSERM UMR 1101, LaTIM, Brest (France)

    2013-02-21

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

  17. Single objective light-sheet microscopy for high-speed whole-cell 3D super-resolution.

    Science.gov (United States)

    Meddens, Marjolein B M; Liu, Sheng; Finnegan, Patrick S; Edwards, Thayne L; James, Conrad D; Lidke, Keith A

    2016-06-01

    We have developed a method for performing light-sheet microscopy with a single high numerical aperture lens by integrating reflective side walls into a microfluidic chip. These 45° side walls generate light-sheet illumination by reflecting a vertical light-sheet into the focal plane of the objective. Light-sheet illumination of cells loaded in the channels increases image quality in diffraction limited imaging via reduction of out-of-focus background light. Single molecule super-resolution is also improved by the decreased background resulting in better localization precision and decreased photo-bleaching, leading to more accepted localizations overall and higher quality images. Moreover, 2D and 3D single molecule super-resolution data can be acquired faster by taking advantage of the increased illumination intensities as compared to wide field, in the focused light-sheet.

  18. A Multi-Resolution Approach for an Automated Fusion of Different Low-Cost 3D Sensors

    Directory of Open Access Journals (Sweden)

    Jan Dupuis

    2014-04-01

    Full Text Available The 3D acquisition of object structures has become a common technique in many fields of work, e.g., industrial quality management, cultural heritage or crime scene documentation. The requirements on the measuring devices are versatile, because spacious scenes have to be imaged with a high level of detail for selected objects. Thus, the used measuring systems are expensive and require an experienced operator. With the rise of low-cost 3D imaging systems, their integration into the digital documentation process is possible. However, common low-cost sensors have the limitation of a trade-off between range and accuracy, providing either a low resolution of single objects or a limited imaging field. Therefore, the use of multiple sensors is desirable. We show the combined use of two low-cost sensors, the Microsoft Kinect and the David laserscanning system, to achieve low-resolved scans of the whole scene and a high level of detail for selected objects, respectively. Afterwards, the high-resolved David objects are automatically assigned to their corresponding Kinect object by the use of surface feature histograms and SVM-classification. The corresponding objects are fitted using an ICP-implementation to produce a multi-resolution map. The applicability is shown for a fictional crime scene and the reconstruction of a ballistic trajectory.

  19. High resolution 3D MRI of mouse mammary glands with intra-ductal injection of contrast media.

    Science.gov (United States)

    Markiewicz, Erica; Fan, Xiaobing; Mustafi, Devkumar; Zamora, Marta; Roman, Brian B; Jansen, Sanaz A; Macleod, Kay; Conzen, Suzanne D; Karczmar, Gregory S

    2015-01-01

    The purpose of this study was to use high resolution three-dimensional (3D) magnetic resonance imaging (MRI) to study mouse mammary gland ductal architecture based on intra-ductal injection of contrast agents. Female FVB/N mice age 12-20 weeks (n=12), were used in this study. A 34G, 45° tip Hamilton needle with a 25μL Hamilton syringe was inserted into the tip of the nipple. Approximately 20-25μL of a Gadodiamide/Trypan blue/saline solution was injected slowly over one minute into the nipple and duct. To prevent washout of contrast media from ducts due to perfusion, and maximize the conspicuity of ducts on MRI, mice were sacrificed one minute after injection. High resolution 3D T1-weighted images were acquired on a 9.4T Bruker scanner after sacrifice to eliminate motion artifacts and reduce contrast media leakage from ducts. Trypan blue staining was well distributed throughout the ductal tree. MRI showed the mammary gland ductal structure clearly. In spoiled gradient echo T1-weighted images, the signal-to-noise ratio of regions identified as enhancing mammary ducts following contrast injection was significantly higher than that of muscle (pcontrast media (pcontrast agents to measure metabolism or target receptors in normal ducts and ducts with in situ cancers.

  20. A Multi-Resolution Approach for an Automated Fusion of Different Low-Cost 3D Sensors

    Science.gov (United States)

    Dupuis, Jan; Paulus, Stefan; Behmann, Jan; Plümer, Lutz; Kuhlmann, Heiner

    2014-01-01

    The 3D acquisition of object structures has become a common technique in many fields of work, e.g., industrial quality management, cultural heritage or crime scene documentation. The requirements on the measuring devices are versatile, because spacious scenes have to be imaged with a high level of detail for selected objects. Thus, the used measuring systems are expensive and require an experienced operator. With the rise of low-cost 3D imaging systems, their integration into the digital documentation process is possible. However, common low-cost sensors have the limitation of a trade-off between range and accuracy, providing either a low resolution of single objects or a limited imaging field. Therefore, the use of multiple sensors is desirable. We show the combined use of two low-cost sensors, the Microsoft Kinect and the David laserscanning system, to achieve low-resolved scans of the whole scene and a high level of detail for selected objects, respectively. Afterwards, the high-resolved David objects are automatically assigned to their corresponding Kinect object by the use of surface feature histograms and SVM-classification. The corresponding objects are fitted using an ICP-implementation to produce a multi-resolution map. The applicability is shown for a fictional crime scene and the reconstruction of a ballistic trajectory. PMID:24763255

  1. Petrophysical analysis of limestone rocks by nuclear logging and 3D high-resolution X-ray computed microtomography

    Energy Technology Data Exchange (ETDEWEB)

    Oliveira, M.F.S. [Nuclear Instrumentation Laboratory, COPPE-PEN, UFRJ, P.O. Box 68509, 21941-972 Rio de Janeiro, RJ (Brazil); Lima, I., E-mail: inaya@lin.ufrj.br [Nuclear Instrumentation Laboratory, COPPE-PEN, UFRJ, P.O. Box 68509, 21941-972 Rio de Janeiro, RJ (Brazil); Department of Mechanical Engineering and Energy, IPRJ-UERJ, Nova Friburgo, RJ (Brazil); Ferrucio, P.L.; Abreu, C.J.; Borghi, L. [Geology Department, Geosciences Institute, Rio de Janeiro Federal University, Rio de Janeiro, RJ (Brazil); Lopes, R.T. [Nuclear Instrumentation Laboratory, COPPE-PEN, UFRJ, P.O. Box 68509, 21941-972 Rio de Janeiro, RJ (Brazil)

    2011-10-01

    This study presents the pore-space system analysis of the 2-ITAB-1-RJ well cores, which were drilled in the Sao Jose do Itaborai Basin, in the state of Rio de Janeiro, Brasil. The analysis presented herein has been developed based on two techniques: nuclear logging and 3D high-resolution X-ray computed microtomography. Nuclear logging has been proven to be the technique that provides better quality and more quantitative information about the porosity using radioactive sources. The Density Gamma Probe and the Neutron Sonde used in this work provide qualitative information about bulk density variations and compensated porosity of the geological formation. The samples obtained from the well cores were analyzed by microtomography. The use of this technique in sedimentary rocks allows quantitative evaluation of pore system and generates high-resolution 3D images ({approx}microns order). The images and data obtained by microtomography were integrated with the response obtained by nuclear logging. The results obtained by these two techniques allow the understanding of the pore-size distribution and connectivity, as well as the porosity values. Both techniques are important and they complement each other.

  2. High-resolution, 3D radiative transfer modeling : I. The grand-design spiral galaxy M51

    CERN Document Server

    De Looze, Ilse; Baes, Maarten; Bendo, George J; Cortese, Luca; Boquien, Médéric; Boselli, Alessandro; Camps, Peter; Cooray, Asantha; Cormier, Diane; Davies, Jon I; De Geyter, Gert; Hughes, Thomas M; Jones, Anthony P; Karczewski, Oskar L; Lebouteiller, Vianney; Lu, Nanyao; Madden, Suzanne C; Rémy-Ruyer, Aurélie; Spinoglio, Luigi; Smith, Matthew W L; Viaene, Sebastien; Wilson, Christine D

    2014-01-01

    Context: Dust reprocesses about half of the stellar radiation in galaxies. The thermal re-emission by dust of absorbed energy is considered driven merely by young stars and, consequently, often applied to trace the star formation rate in galaxies. Recent studies have argued that the old stellar population might anticipate a non-negligible fraction of the radiative dust heating. Aims: In this work, we aim to analyze the contribution of young (< 100 Myr) and old (~ 10 Gyr) stellar populations to radiative dust heating processes in the nearby grand-design spiral galaxy M51 using radiative transfer modeling. High-resolution 3D radiative transfer (RT) models are required to describe the complex morphologies of asymmetric spiral arms and clumpy star-forming regions and model the propagation of light through a dusty medium. Methods: In this paper, we present a new technique developed to model the radiative transfer effects in nearby face-on galaxies. We construct a high-resolution 3D radiative transfer model with...

  3. Atomic Resolution Imaging and Quantification of Chemical Functionality of Surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Schwarz, Udo D. [Yale Univ., New Haven, CT (United States). Dept. of Mechanical Engineering and Materials Science; Altman, Eric I. [Yale Univ., New Haven, CT (United States). Dept. of Chemical and Environmental Engineering

    2014-12-10

    The work carried out from 2006-2014 under DoE support was targeted at developing new approaches to the atomic-scale characterization of surfaces that include species-selective imaging and an ability to quantify chemical surface interactions with site-specific accuracy. The newly established methods were subsequently applied to gain insight into the local chemical interactions that govern the catalytic properties of model catalysts of interest to DoE. The foundation of our work was the development of three-dimensional atomic force microscopy (3DAFM), a new measurement mode that allows the mapping of the complete surface force and energy fields with picometer resolution in space (x, y, and z) and piconewton/millielectron volts in force/energy. From this experimental platform, we further expanded by adding the simultaneous recording of tunneling current (3D-AFM/STM) using chemically well-defined tips. Through comparison with simulations, we were able to achieve precise quantification and assignment of local chemical interactions to exact positions within the lattice. During the course of the project, the novel techniques were applied to surface-oxidized copper, titanium dioxide, and silicon oxide. On these materials, defect-induced changes to the chemical surface reactivity and electronic charge density were characterized with site-specific accuracy.

  4. Quantification of gully volume using very high resolution DSM generated through 3D reconstruction from airborne and field digital imagery

    Science.gov (United States)

    Castillo, Carlos; Zarco-Tejada, Pablo; Laredo, Mario; Gómez, Jose Alfonso

    2013-04-01

    Major advances have been made recently in automatic 3D photo-reconstruction techniques using uncalibrated and non-metric cameras (James and Robson, 2012). However, its application on soil conservation studies and landscape feature identification is currently at the outset. The aim of this work is to compare the performance of a remote sensing technique using a digital camera mounted on an airborne platform, with 3D photo-reconstruction, a method already validated for gully erosion assessment purposes (Castillo et al., 2012). A field survey was conducted in November 2012 in a 250 m-long gully located in field crops on a Vertisol in Cordoba (Spain). The airborne campaign was conducted with a 4000x3000 digital camera installed onboard an aircraft flying at 300 m above ground level to acquire 6 cm resolution imagery. A total of 990 images were acquired over the area ensuring a large overlap in the across- and along-track direction of the aircraft. An ortho-mosaic and the digital surface model (DSM) were obtained through automatic aerial triangulation and camera calibration methods. For the field-level photo-reconstruction technique, the gully was divided in several reaches to allow appropriate reconstruction (about 150 pictures taken per reach) and, finally, the resulting point clouds were merged into a unique mesh. A centimetric-accuracy GPS provided a benchmark dataset for gully perimeter and distinguishable reference points in order to allow the assessment of measurement errors of the airborne technique and the georeferenciation of the photo-reconstruction 3D model. The uncertainty on the gully limits definition was explicitly addressed by comparison of several criteria obtained by 3D models (slope and second derivative) with the outer perimeter obtained by the GPS operator identifying visually the change in slope at the top of the gully walls. In this study we discussed the magnitude of planimetric and altimetric errors and the differences observed between the

  5. Overcoming silicon limitations: new 3D-AFM carbon tips with constantly high-resolution for sub-28nm node semiconductor requirements

    Science.gov (United States)

    Foucher, Johann; Schmidt, Sebastian W.; Penzkofer, Christian; Irmer, Bernd

    2012-03-01

    The demands on atomic force microscopy (AFM) as a reference technique for precisely determining surface properties and structural designs of multiple patterns in the semiconductor industry are steadily increasing. With the aim to meet ITRS requirements and simultaneously improve the accuracy of AFM-based critical dimension (CD) measurements at constant resolution, the AFM tip more and more becomes a factor crucially determining the AFM performance. In this context, AFM tip limitations are given by lack of sharpness with too large tip radii/diameter, insufficient wear resistance, and high total cost, which does not conform to production environment needs. One technical approach to overcome these tip limitations is provided by electron beam induced processing (EBIP), which allows for manufacturing AFM tips of desired sharpness, shape, and mechanical stability. Here, we present T-shape-like 3D-AFM tips made of bulk amorphous, high density diamond-like carbon (HDC/DLC), and compare their performance and wear resistance to standard silicon tips. We show the advantages of this approach for the semiconductor industry, in particular on AFM3D technology in order to answer to sub-28 nm nodes requirements, and present tips with 15 nm diameter at 10 nm vertical edge height.

  6. Digitized crime scene forensics: automated trace separation of toolmarks on high-resolution 2D/3D CLSM surface data

    Science.gov (United States)

    Clausing, Eric; Vielhauer, Claus

    2015-03-01

    Locksmith forensics is an important and very challenging part of classic crime scene forensics. In prior work, we propose a partial transfer to the digital domain, to effectively support forensic experts and present approaches for a full process chain consisting of five steps: Trace positioning, 2D/3D acquisition with a confocal 3D laser scanning microscope, detection by segmentation, trace type determination, and determination of the opening method. In particular the step of trace segmentation on high-resolution 3D surfaces thereby turned out to be the part most difficult to implement. The reason for that is the highly structured and complex surfaces to be analyzed. These surfaces are cluttered with a high number of toolmarks, which overlap and distort each other. In Clausing et al., we present an improved approach for a reliable segmentation of relevant trace regions but without the possibility of separating single traces out of segmented trace regions. However, in our past research, especially features based on shape and dimension turned out to be highly relevant for a fully automated analysis and interpretation. In this paper, we consequently propose an approach for this separation. To achieve this goal, we use our segmentation approach and expand it with a combination of the watershed algorithm with a graph-based analysis. Found sub-regions are compared based on their surface character and are connected or divided depending on their similarity. We evaluate our approach with a test set of about 1,300 single traces on the exemplary locking cylinder component 'key pin' and thereby are able of showing the high suitability of our approach.

  7. A simple and high-resolution stereolithography-based 3D bioprinting system using visible light crosslinkable bioinks.

    Science.gov (United States)

    Wang, Zongjie; Abdulla, Raafa; Parker, Benjamin; Samanipour, Roya; Ghosh, Sanjoy; Kim, Keekyoung

    2015-12-22

    Bioprinting is a rapidly developing technique for biofabrication. Because of its high resolution and the ability to print living cells, bioprinting has been widely used in artificial tissue and organ generation as well as microscale living cell deposition. In this paper, we present a low-cost stereolithography-based bioprinting system that uses visible light crosslinkable bioinks. This low-cost stereolithography system was built around a commercial projector with a simple water filter to prevent harmful infrared radiation from the projector. The visible light crosslinking was achieved by using a mixture of polyethylene glycol diacrylate (PEGDA) and gelatin methacrylate (GelMA) hydrogel with eosin Y based photoinitiator. Three different concentrations of hydrogel mixtures (10% PEG, 5% PEG + 5% GelMA, and 2.5% PEG + 7.5% GelMA, all w/v) were studied with the presented systems. The mechanical properties and microstructure of the developed bioink were measured and discussed in detail. Several cell-free hydrogel patterns were generated to demonstrate the resolution of the solution. Experimental results with NIH 3T3 fibroblast cells show that this system can produce a highly vertical 3D structure with 50 μm resolution and 85% cell viability for at least five days. The developed system provides a low-cost visible light stereolithography solution and has the potential to be widely used in tissue engineering and bioengineering for microscale cell patterning.

  8. High-resolution 3D imaging of whole organ after clearing: taking a new look at the zebrafish testis

    Science.gov (United States)

    Frétaud, Maxence; Rivière, Laurie; Job, Élodie De; Gay, Stéphanie; Lareyre, Jean-Jacques; Joly, Jean-Stéphane; Affaticati, Pierre; Thermes, Violette

    2017-01-01

    Zebrafish testis has become a powerful model for reproductive biology of teleostean fishes and other vertebrates and encompasses multiple applications in applied and basic research. Many studies have focused on 2D images, which is time consuming and implies extrapolation of results. Three-dimensional imaging of whole organs recently became an important challenge to better understand their architecture and allow cell enumeration. Several protocols have thus been developed to enhance sample transparency, a limiting step for imaging large biological samples. However, none of these methods has been applied to the zebrafish testis. We tested five clearing protocols to determine if some of them could be applied with only small modifications to the testis. We compared clearing efficiency at both macroscopic and microscopic levels. CUBIC and PACT were suitable for an efficient transparency, an optimal optical penetration, the GFP fluorescence preservation and avoiding meaningful tissue deformation. Finally, we succeeded in whole testis 3D capture at a cellular resolution with both CUBIC and PACT, which will be valuable in a standard workflow to investigate the 3D architecture of the testis and its cellular content. This paves the way for further development of high content phenotyping studies in several fields including development, genetic or toxicology. PMID:28211501

  9. High resolution 3D laser scanner measurements of a strike-slip fault quantify its morphological anisotropy at all scales

    CERN Document Server

    Renard, Francois; Marsan, Davd; Schmittbuhl, Jean

    2008-01-01

    The surface roughness of a recently exhumed strikeslip fault plane has been measured by three independent 3D portable laser scanners. Digital elevation models of several fault surface areas, from 1 m2 to 600 m2, have been measured at a resolution ranging from 5 mm to 80 mm. Out of plane height fluctuations are described by non-Gaussian distribution with exponential long range tails. Statistical scaling analyses show that the striated fault surface exhibits self-affine scaling invariance with a small but significant directional morphological anisotropy that can be described by two scaling roughness exponents, H1 = 0.7 in the direction of slip and H2 = 0.8 perpendicular to the direction of slip.

  10. A High-resolution 3D Geodynamical Model of the Present-day India-Asia Collision System

    Science.gov (United States)

    Kaus, B.; Baumann, T.

    2015-12-01

    We present a high-resolution, 3D geodynamic model of the present-day India-Asia collision system. The model is separated into multiple tectonic blocks, for which we estimate the first order rheological properties and the impact on the dynamics of the collision system. This is done by performing systematic simulations with different rheologies to minimize the misfit to observational constraints such as the GPS-velocity field. The simulations are performed with the parallel staggered grid FD code LaMEM using a numerical resolution of at least 512x512x256 cells to resolve dynamically important shear zones reasonably well. A fundamental part of this study is the reconstruction of the 3D present-day geometry of Tibet and the adjacent regions. Our interpretations of crust and mantle lithosphere geometry are jointly based on a globally available shear wave tomography (Schaeffer and Lebedev, 2013) and the Crust 1.0 model (Laske et al. http://igppweb.ucsd.edu/~gabi/crust1.html). We regionally refined and modified our interpretations based on seismicity distributions and focal mechanisms and incorporated regional receiver function studies to improve the accuracy of the Moho in particular. Results suggest that we can identify at least one "best-fit" solution in terms of rheological model properties that reproduces the observed velocity field reasonably well, including the strong rotation of the GPS velocity around the eastern syntax of the Himalaya. We also present model co-variances to illustrate the trade-offs between the rheological model parameters, their respective uncertainties, and the model fit. Schaeffer, A.J., Lebedev, S., 2013. Global shear speed structure of the upper mantle and transition zone. Geophysical Journal International 194, 417-449. doi:10.1093/gji/ggt095

  11. High-resolution 3D surface displacements from 2004 - 2012 at Santorini volcano, Greece measured by LiDAR-differencing

    Science.gov (United States)

    Parks, M.; Pyle, D. M.; Nissen, E.; Mather, T. A.; Raptakis, C.; Nomikou, P.

    2012-12-01

    In January 2011 Santorini volcano entered a period of unrest characterised by earthquake swarms and caldera-wide uplift. Interferometric Synthetic Aperture Radar (InSAR) measurements indicate vertical motions of 8 - 14 cm across the central volcanic island of Nea Kameni since the onset of unrest. In April 2004, a NERC funded Airborne Research and Survey Facility (ARSF) flight acquired high-resolution (1m per pixel) light detection and ranging laser radar (LiDAR) data over the central volcanic islands of Nea Kameni and Palea Kameni. This survey was repeated in May 2012 to provide an updated digital elevation model (DEM). We apply a new method of differencing pre- and post- deformation LiDAR point clouds using the Iterative Closest Point (ICP) algorithm to produce a high-resolution grid of 3D surface displacements from 2004 - 2012. The 2004 ("source") and 2012 ("target") point clouds are first split into square subsets ("windows") and the displacement for each window is determined by iterating three steps: (1) identifying closest point pairs; (2) calculating the translation and rotation required that best aligns the paired points; (3) applying this transformation to the source cloud. The surface displacement map spans both a period of slow subsidence (from 2004 - 2010), and a subsequent period of inflation (from 2011 - 2012). We shall compare our results with those obtained from simple DEM elevation differencing and from InSAR. To our knowledge, this is the first application of the ICP technique to measuring volcanic deformation. This approach may be implemented at other volcanoes to monitor 3D surface displacements during periods of unrest.

  12. Analysis of structural correlations in a model binary 3D liquid through the eigenvalues and eigenvectors of the atomic stress tensors

    CERN Document Server

    Levashov, Valentin A

    2015-01-01

    It is possible to associate with every atom or molecule in a liquid its own atomic stress tensor. These atomic stress tensors can be used to describe liquids' structures and to investigate the connection between structural and dynamic properties. In particular, atomic stresses allow to address atomic scale correlations relevant to the Green-Kubo expression for viscosity. Previously correlations between the atomic stresses of different atoms were studied using the Cartesian representation of the stress tensors or the representation based on spherical harmonics. In this paper we address structural correlations in a model 3D binary liquid using the eigenvalues and eigenvectors of the atomic stress tensors. Thus correlations relevant to the Green-Kubo expression for viscosity are interpreted in a simple geometric way. On decrease of temperature the changes in the relevant stress correlation function between different atoms are significantly more pronounced than the changes in the pair density function. We demonst...

  13. A High-resolution Vacuum Ultraviolet Laser Photoionization and Photoelectron Study of the Co Atom

    Science.gov (United States)

    Huang, Huang; Wang, Hailing; Luo, Zhihong; Shi, Xiaoyu; Chang, Yih-Chung; Ng, C. Y.

    2016-12-01

    We have measured the vacuum ultraviolet-photoionization efficiency (VUV-PIE) spectrum of Co in the energy range of 63,500-67,000 cm-1, which covers the photoionization transitions of Co(3d74s2 4F9/2) \\to Co+(3d8 3F4), Co(3d74s2 4F7/2) \\to Co+(3d8 3F3), Co(3d74s2 4F9/2) \\to Co+(3d8 3F3), Co(3d74s2 4F9/2) \\to Co+(3d8 3F2), and Co(3d74s2 4F9/2) \\to Co+(3d74s1 5F5). We have also recorded the pulsed field ionization photoelectron spectrum of Co in the same energy range, allowing accurate determinations of ionization energies (IEs) for the photoionization transitions from the Co(3d74s2 4F9/2) ground neutral state to the Co+(3F J ) (J = 4 and 3) and Co+(5F5) ionic states, as well as from the Co(3d74s2 4F7/2) excited neural state to the Co+(3d8 3F3) ionic state. The high-resolution nature of the VUV laser used has allowed the observation of many well-resolved autoionizing resonances in the VUV-PIE spectrum, among which an autoionizing Rydberg series, 3d74s1(5F5)np (n = 19-38), converging to the Co+(3d74s1 5F5) ionic state from the Co(3d74s2 4F9/2) ground neutral state is identified. The fact that no discernible step-like structures are present at these ionization thresholds in the VUV-PIE spectrum indicates that direct photoionization of Co is minor compared to autoionization in this energy range. The IE values, the autoionizing Rydberg series, and the photoionization cross sections obtained in this experiment are valuable for understanding the VUV opacity and abundance measurement of the Co atom in stars and solar atmospheres, as well as for benchmarking the theoretical results calculated in the Opacity Project and the IRON Project, and thus are of relevance to astrophysics.

  14. Investigating Cardiac Motion Patterns Using Synthetic High-Resolution 3D Cardiovascular Magnetic Resonance Images and Statistical Shape Analysis

    Science.gov (United States)

    Biffi, Benedetta; Bruse, Jan L.; Zuluaga, Maria A.; Ntsinjana, Hopewell N.; Taylor, Andrew M.; Schievano, Silvia

    2017-01-01

    Diagnosis of ventricular dysfunction in congenital heart disease is more and more based on medical imaging, which allows investigation of abnormal cardiac morphology and correlated abnormal function. Although analysis of 2D images represents the clinical standard, novel tools performing automatic processing of 3D images are becoming available, providing more detailed and comprehensive information than simple 2D morphometry. Among these, statistical shape analysis (SSA) allows a consistent and quantitative description of a population of complex shapes, as a way to detect novel biomarkers, ultimately improving diagnosis and pathology understanding. The aim of this study is to describe the implementation of a SSA method for the investigation of 3D left ventricular shape and motion patterns and to test it on a small sample of 4 congenital repaired aortic stenosis patients and 4 age-matched healthy volunteers to demonstrate its potential. The advantage of this method is the capability of analyzing subject-specific motion patterns separately from the individual morphology, visually and quantitatively, as a way to identify functional abnormalities related to both dynamics and shape. Specifically, we combined 3D, high-resolution whole heart data with 2D, temporal information provided by cine cardiovascular magnetic resonance images, and we used an SSA approach to analyze 3D motion per se. Preliminary results of this pilot study showed that using this method, some differences in end-diastolic and end-systolic ventricular shapes could be captured, but it was not possible to clearly separate the two cohorts based on shape information alone. However, further analyses on ventricular motion allowed to qualitatively identify differences between the two populations. Moreover, by describing shape and motion with a small number of principal components, this method offers a fully automated process to obtain visually intuitive and numerical information on cardiac shape and motion

  15. Atom pair 2D-fingerprints perceive 3D-molecular shape and pharmacophores for very fast virtual screening of ZINC and GDB-17.

    Science.gov (United States)

    Awale, Mahendra; Reymond, Jean-Louis

    2014-07-28

    Three-dimensional (3D) molecular shape and pharmacophores are important determinants of the biological activity of organic molecules; however, a precise computation of 3D-shape is generally too slow for virtual screening of very large databases. A reinvestigation of the concept of atom pairs initially reported by Carhart et al. and extended by Schneider et al. showed that a simple atom pair fingerprint (APfp) counting atom pairs at increasing topological distances in 2D-structures without atom property assignment correlates with various representations of molecular shape extracted from the 3D-structures. A related 55-dimensional atom pair fingerprint extended with atom properties (Xfp) provided an efficient pharmacophore fingerprint with good performance for ligand-based virtual screening such as the recovery of active compounds from decoys in DUD, and overlap with the ROCS 3D-pharmacophore scoring function. The APfp and Xfp data were organized for web-based extremely fast nearest-neighbor searching in ZINC (13.5 M compounds) and GDB-17 (50 M random subset) freely accessible at www.gdb.unibe.ch .

  16. 3D ToF-SIMS Analysis of Peptide Incorporation into MALDI Matrix Crystals with Sub-micrometer Resolution

    Science.gov (United States)

    Körsgen, Martin; Pelster, Andreas; Dreisewerd, Klaus; Arlinghaus, Heinrich F.

    2016-02-01

    The analytical sensitivity in matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is largely affected by the specific analyte-matrix interaction, in particular by the possible incorporation of the analytes into crystalline MALDI matrices. Here we used time-of-flight secondary ion mass spectrometry (ToF-SIMS) to visualize the incorporation of three peptides with different hydrophobicities, bradykinin, Substance P, and vasopressin, into two classic MALDI matrices, 2,5-dihydroxybenzoic acid (DHB) and α-cyano-4-hydroxycinnamic acid (HCCA). For depth profiling, an Ar cluster ion beam was used to gradually sputter through the matrix crystals without causing significant degradation of matrix or biomolecules. A pulsed Bi3 ion cluster beam was used to image the lateral analyte distribution in the center of the sputter crater. Using this dual beam technique, the 3D distribution of the analytes and spatial segregation effects within the matrix crystals were imaged with sub-μm resolution. The technique could in the future enable matrix-enhanced (ME)-ToF-SIMS imaging of peptides in tissue slices at ultra-high resolution.

  17. 3D scaffolds from vertically aligned carbon nanotubes/poly(methyl methacrylate) composites via atom transfer radical polymerization

    Energy Technology Data Exchange (ETDEWEB)

    Tebikachew, Behabtu; Magina, Sandra [CICECO, Department of Chemistry, University of Aveiro (Portugal); Mata, Diogo; Oliveira, Filipe J.; Silva, Rui F. [CICECO, Department of Materials and Ceramic Engineering, University of Aveiro (Portugal); Barros-Timmons, Ana, E-mail: anabarros@ua.pt [CICECO, Department of Chemistry, University of Aveiro (Portugal)

    2015-01-15

    Vertically aligned carbon nanotubes (VACNTs) synthesized by Thermal Chemical Vapour Deposition (TCVD) were modified using an Ar:O{sub 2} (97:3) plasma to generate oxygen-containing functional groups on the surface for subsequent modification. X-ray photo-emission spectroscopy (XPS) and micro-Raman analyses confirmed the grafting of those functional groups onto the surface of the nanotubes as well as the removal of amorphous carbon produced and deposited on the VACNT forests during the CVD process. The plasma treated VACNT forests were further modified with 2-bromo-2-methylpropionyl bromide, an atom transfer radical polymerization (ATRP) initiator, to grow poly(methyl methacrylate) (PMMA) chains from the forests via ATRP. Scanning transmission electron microscopy (STEM) of the ensuing VACNT/PMMA composites confirmed the coating of the nanotube forests with the PMMA polymer. 3D scaffolds of polymeric composites with honeycomb like structure were then obtained. Compressive tests have shown that the VACNT/PMMA composite has higher compressive strength than the pristine forest. - Highlights: • Vertically aligned carbon nanotubes (VACNTs) were synthesized and plasma modified. • X-ray photo-emission and Raman spectroscopies confirmed the VACNTs modification. • Poly(methyl methacrylate) chains were grown via ATRP from the VACNTs. • STEM of the VACNT/PMMA composites confirmed that PMMA surrounds the nanotubes. • VACNT/PMMA composite has higher compressive strength compared to the pristine forest.

  18. 3D-nanoarchitectured Pd/Ni catalysts prepared by atomic layer deposition for the electrooxidation of formic acid

    Directory of Open Access Journals (Sweden)

    Loïc Assaud

    2014-02-01

    Full Text Available Three-dimensionally (3D nanoarchitectured palladium/nickel (Pd/Ni catalysts, which were prepared by atomic layer deposition (ALD on high-aspect-ratio nanoporous alumina templates are investigated with regard to the electrooxidation of formic acid in an acidic medium (0.5 M H2SO4. Both deposition processes, Ni and Pd, with various mass content ratios have been continuously monitored by using a quartz crystal microbalance. The morphology of the Pd/Ni systems has been studied by electron microscopy and shows a homogeneous deposition of granularly structured Pd onto the Ni substrate. X-ray diffraction analysis performed on Ni and NiO substrates revealed an amorphous structure, while the Pd coating crystallized into a fcc lattice with a preferential orientation along the [220]-direction. Surface chemistry analysis by X-ray photoelectron spectroscopy showed both metallic and oxide contributions for the Ni and Pd deposits. Cyclic voltammetry of the Pd/Ni nanocatalysts revealed that the electrooxidation of HCOOH proceeds through the direct dehydrogenation mechanism with the formation of active intermediates. High catalytic activities are measured for low masses of Pd coatings that were generated by a low number of ALD cycles, probably because of the cluster size effect, electronic interactions between Pd and Ni, or diffusion effects.

  19. 3D-nanoarchitectured Pd/Ni catalysts prepared by atomic layer deposition for the electrooxidation of formic acid.

    Science.gov (United States)

    Assaud, Loïc; Monyoncho, Evans; Pitzschel, Kristina; Allagui, Anis; Petit, Matthieu; Hanbücken, Margrit; Baranova, Elena A; Santinacci, Lionel

    2014-01-01

    Three-dimensionally (3D) nanoarchitectured palladium/nickel (Pd/Ni) catalysts, which were prepared by atomic layer deposition (ALD) on high-aspect-ratio nanoporous alumina templates are investigated with regard to the electrooxidation of formic acid in an acidic medium (0.5 M H2SO4). Both deposition processes, Ni and Pd, with various mass content ratios have been continuously monitored by using a quartz crystal microbalance. The morphology of the Pd/Ni systems has been studied by electron microscopy and shows a homogeneous deposition of granularly structured Pd onto the Ni substrate. X-ray diffraction analysis performed on Ni and NiO substrates revealed an amorphous structure, while the Pd coating crystallized into a fcc lattice with a preferential orientation along the [220]-direction. Surface chemistry analysis by X-ray photoelectron spectroscopy showed both metallic and oxide contributions for the Ni and Pd deposits. Cyclic voltammetry of the Pd/Ni nanocatalysts revealed that the electrooxidation of HCOOH proceeds through the direct dehydrogenation mechanism with the formation of active intermediates. High catalytic activities are measured for low masses of Pd coatings that were generated by a low number of ALD cycles, probably because of the cluster size effect, electronic interactions between Pd and Ni, or diffusion effects.

  20. Detection of latent fingerprints using high-resolution 3D confocal microscopy in non-planar acquisition scenarios

    Science.gov (United States)

    Kirst, Stefan; Vielhauer, Claus

    2015-03-01

    In digitized forensics the support of investigators in any manner is one of the main goals. Using conservative lifting methods, the detection of traces is done manually. For non-destructive contactless methods, the necessity for detecting traces is obvious for further biometric analysis. High resolutional 3D confocal laser scanning microscopy (CLSM) grants the possibility for a detection by segmentation approach with improved detection results. Optimal scan results with CLSM are achieved on surfaces orthogonal to the sensor, which is not always possible due to environmental circumstances or the surface's shape. This introduces additional noise, outliers and a lack of contrast, making a detection of traces even harder. Prior work showed the possibility of determining angle-independent classification models for the detection of latent fingerprints (LFP). Enhancing this approach, we introduce a larger feature space containing a variety of statistical-, roughness-, color-, edge-directivity-, histogram-, Gabor-, gradient- and Tamura features based on raw data and gray-level co-occurrence matrices (GLCM) using high resolutional data. Our test set consists of eight different surfaces for the detection of LFP in four different acquisition angles with a total of 1920 single scans. For each surface and angles in steps of 10, we capture samples from five donors to introduce variance by a variety of sweat compositions and application influences such as pressure or differences in ridge thickness. By analyzing the present test set with our approach, we intend to determine angle- and substrate-dependent classification models to determine optimal surface specific acquisition setups and also classification models for a general detection purpose for both, angles and substrates. The results on overall models with classification rates up to 75.15% (kappa 0.50) already show a positive tendency regarding the usability of the proposed methods for LFP detection on varying surfaces in non

  1. Plant tissues in 3D via X-ray tomography: simple contrasting methods allow high resolution imaging.

    Directory of Open Access Journals (Sweden)

    Yannick M Staedler

    Full Text Available Computed tomography remains strongly underused in plant sciences despite its high potential in delivering detailed 3D phenotypical information because of the low X-ray absorption of most plant tissues. Existing protocols to study soft tissues display poor performance, especially when compared to those used on animals. More efficient protocols to study plant material are therefore needed. Flowers of Arabidopsis thaliana and Marcgravia caudata were immersed in a selection of contrasting agents used to treat samples for transmission electron microscopy. Grayscale values for floral tissues and background were measured as a function of time. Contrast was quantified via a contrast index. The thick buds of Marcgravia were scanned to determine which contrasting agents best penetrate thick tissues. The highest contrast increase with cytoplasm-rich tissues was obtained with phosphotungstate, whereas osmium tetroxide and bismuth tatrate displayed the highest contrast increase with vacuolated tissues. Phosphotungstate also displayed the best sample penetration. Furthermore, infiltration with phosphotungstate allowed imaging of all plants parts at a high resolution of 3 µm, which approaches the maximum resolution of our equipment: 1.5 µm. The high affinity of phosphotungstate for vasculature, cytoplasm-rich tissue, and pollen causes these tissues to absorb more X-rays than the surrounding tissues, which, in turn, makes these tissues appear brighter on the scan data. Tissues with different brightness can then be virtually dissected from each other by selecting the bracket of grayscale to be visualized. Promising directions for the future include in silico phenotyping and developmental studies of plant inner parts (e.g., ovules, vasculature, pollen, and cell nuclei via virtual dissection as well as correlations of quantitative phenotypes with omics datasets. Therefore, this work represents a crucial improvement of previous methods, allowing new directions of

  2. Plant tissues in 3D via X-ray tomography: simple contrasting methods allow high resolution imaging.

    Science.gov (United States)

    Staedler, Yannick M; Masson, David; Schönenberger, Jürg

    2013-01-01

    Computed tomography remains strongly underused in plant sciences despite its high potential in delivering detailed 3D phenotypical information because of the low X-ray absorption of most plant tissues. Existing protocols to study soft tissues display poor performance, especially when compared to those used on animals. More efficient protocols to study plant material are therefore needed. Flowers of Arabidopsis thaliana and Marcgravia caudata were immersed in a selection of contrasting agents used to treat samples for transmission electron microscopy. Grayscale values for floral tissues and background were measured as a function of time. Contrast was quantified via a contrast index. The thick buds of Marcgravia were scanned to determine which contrasting agents best penetrate thick tissues. The highest contrast increase with cytoplasm-rich tissues was obtained with phosphotungstate, whereas osmium tetroxide and bismuth tatrate displayed the highest contrast increase with vacuolated tissues. Phosphotungstate also displayed the best sample penetration. Furthermore, infiltration with phosphotungstate allowed imaging of all plants parts at a high resolution of 3 µm, which approaches the maximum resolution of our equipment: 1.5 µm. The high affinity of phosphotungstate for vasculature, cytoplasm-rich tissue, and pollen causes these tissues to absorb more X-rays than the surrounding tissues, which, in turn, makes these tissues appear brighter on the scan data. Tissues with different brightness can then be virtually dissected from each other by selecting the bracket of grayscale to be visualized. Promising directions for the future include in silico phenotyping and developmental studies of plant inner parts (e.g., ovules, vasculature, pollen, and cell nuclei) via virtual dissection as well as correlations of quantitative phenotypes with omics datasets. Therefore, this work represents a crucial improvement of previous methods, allowing new directions of research to be

  3. High-resolution 3-D imaging of surface damage sites in fused silica with Optical Coherence Tomography

    Energy Technology Data Exchange (ETDEWEB)

    Guss, G; Bass, I; Hackel, R; Mailhiot, C; Demos, S G

    2007-10-30

    In this work, we present the first successful demonstration of a non-contact technique to precisely measure the 3D spatial characteristics of laser induced surface damage sites in fused silica for large aperture laser systems by employing Optical Coherence Tomography (OCT). What makes OCT particularly interesting in the characterization of optical materials for large aperture laser systems is that its axial resolution can be maintained with working distances greater than 5 cm, whether viewing through air or through the bulk of thick optics. Specifically, when mitigating surface damage sites against further growth by CO{sub 2} laser evaporation of the damage, it is important to know the depth of subsurface cracks below the damage site. These cracks are typically obscured by the damage rubble when imaged from above the surface. The results to date clearly demonstrate that OCT is a unique and valuable tool for characterizing damage sites before and after the mitigation process. We also demonstrated its utility as an in-situ diagnostic to guide and optimize our process when mitigating surface damage sites on large, high-value optics.

  4. Methods to improve the resolution of prestack migrated images, with application to a 3D dataset from a fractured reservoir

    Science.gov (United States)

    Perez, Gabriel

    I present three different methods to achieve increased definition in images from conventional seismic data, as illustrated with 3D data from the Fort Worth Basin's Barnett Shale fractured reservoir play, currently one of the hottest exploration and production trends in continental U.S. First, I present a method to correct for wavelet stretch in common-angle prestack migrated data. Wavelet stretch adversely influences contributions to the image from large angle or long offset data. Increasing the fidelity of large angles improves the vertical and lateral resolution in images from seismic data and from derived attributes, and positively impact AVA/AVO analysis. Achieving the greatest potential of this technique demands that I address the increased sensitivity to velocity errors and anisotropy. The other two methods presented here benefit from the balance in spectral content of the imaged data across angles and the increased resolution that are achieved from correcting for wavelet stretch. Then I introduce a new way to define azimuth binning in Kirchhoff prestack migration. This approach avoids mixing the typically weaker side-scattered energy with the stronger reflections from the sagittal plane. With the modified binning, signal and noise events are preferentially imaged in azimuth orientations normal to their apparent strike orientation, in surface- or map-views. This modified azimuthal binning also results in improved detection of out-of-the-plane steeply dipping reflectors, fractures and faults and their orientation, especially when combined with attributes such as curvature and coherence. Finally, I present an approach to measure lateral misalignment in prestack migrated seismic images and then correct for it by applying a warping procedure to these images. Though velocity errors are the most likely source for misalignment between images, it can also result from other imperfections in the imaging procedure. Lateral misalignment is most easily recognized and

  5. 3D micro-particle image modeling and its application in measurement resolution investigation for visual sensing based axial localization in an optical microscope

    Science.gov (United States)

    Wang, Yuliang; Li, Xiaolai; Bi, Shusheng; Zhu, Xiaofeng; Liu, Jinhua

    2017-01-01

    Visual sensing based three dimensional (3D) particle localization in an optical microscope is important for both fundamental studies and practical applications. Compared with the lateral (X and Y) localization, it is more challenging to achieve a high resolution measurement of axial particle location. In this study, we aim to investigate the effect of different factors on axial measurement resolution through an analytical approach. Analytical models were developed to simulate 3D particle imaging in an optical microscope. A radius vector projection method was applied to convert the simulated particle images into radius vectors. With the obtained radius vectors, a term of axial changing rate was proposed to evaluate the measurement resolution of axial particle localization. Experiments were also conducted for comparison with that obtained through simulation. Moreover, with the proposed method, the effects of particle size on measurement resolution were discussed. The results show that the method provides an efficient approach to investigate the resolution of axial particle localization.

  6. Atomic resolution tomography reconstruction of tilt series based on a GPU accelerated hybrid input-output algorithm using polar Fourier transform.

    Science.gov (United States)

    Lu, Xiangwen; Gao, Wenpei; Zuo, Jian-Min; Yuan, Jiabin

    2015-02-01

    Advances in diffraction and transmission electron microscopy (TEM) have greatly improved the prospect of three-dimensional (3D) structure reconstruction from two-dimensional (2D) images or diffraction patterns recorded in a tilt series at atomic resolution. Here, we report a new graphics processing unit (GPU) accelerated iterative transformation algorithm (ITA) based on polar fast Fourier transform for reconstructing 3D structure from 2D diffraction patterns. The algorithm also applies to image tilt series by calculating diffraction patterns from the recorded images using the projection-slice theorem. A gold icosahedral nanoparticle of 309 atoms is used as the model to test the feasibility, performance and robustness of the developed algorithm using simulations. Atomic resolution in 3D is achieved for the 309 atoms Au nanoparticle using 75 diffraction patterns covering 150° rotation. The capability demonstrated here provides an opportunity to uncover the 3D structure of small objects of nanometers in size by electron diffraction.

  7. Repumping and spectroscopy of laser-cooled Sr atoms using the (5s5p)3P2 - (5s4d)3D2 transition

    CERN Document Server

    Mickelson, P G; Anzel, P; DeSalvo, B J; Nagel, S B; Traverso, A J; Yan, M; Killian, T C

    2009-01-01

    We describe repumping and spectroscopy of laser-cooled strontium (Sr) atoms using the (5s5p)3P2 - (5s4d)3D2 transition. Atom number in a magneto-optical trap is enhanced by driving this transition because Sr atoms that have decayed into the (5s5p)3P2 dark state are repumped back into the (5s2)1S0 ground state. Spectroscopy of 84Sr, 86Sr, 87Sr, and 88Sr improves the value of the (5s5p)3P2 - (5s4d)3D2 transition frequency for 88Sr and determines the isotope shifts for the transition.

  8. Repumping and spectroscopy of laser-cooled Sr atoms using the (5s5p)3P2-(5s4d)3D2 transition

    Science.gov (United States)

    Mickelson, P. G.; Martinez de Escobar, Y. N.; Anzel, P.; De Salvo, B. J.; Nagel, S. B.; Traverso, A. J.; Yan, M.; Killian, T. C.

    2009-12-01

    We describe repumping and spectroscopy of laser-cooled strontium (Sr) atoms using the (5s5p)3P2-(5s4d)3D2 transition. Atom number in a magneto-optical trap is enhanced by driving this transition because Sr atoms that have decayed into the (5s5p)3P2 dark state are repumped back into the (5s2)1S0 ground state. Spectroscopy of 84Sr, 86Sr, 87Sr and 88Sr improves the value of the (5s5p)3P2-(5s4d)3D2 transition frequency and determines the isotope shifts for the transition accurately enough to guide laser-cooling experiments with less abundant isotopes.

  9. Statistiscal Experimental Design for Quantitative Atomic Resolution Transmission Electron Microscopy

    NARCIS (Netherlands)

    Van Aert, S.

    2003-01-01

    Statistical experimental design is applied to set up quantitative atomic resolution transmission electron microscopy experiments. In such experiments, observations of the atomic structure of the object under study are always subject to spontaneous fluctuations. As a result of these fluctuations, the

  10. HRTEM Imaging of Atoms at Sub-Angstrom Resolution

    Energy Technology Data Exchange (ETDEWEB)

    O' Keefe, Michael A.; Allard, Lawrence F.; Blom, Douglas A.

    2005-04-06

    John Cowley and his group at Arizona State University pioneered the use of transmission electron microscopy (TEM) for high-resolution imaging. Images were achieved three decades ago showing the crystal unit cell content at better than 4 Angstrom resolution. This achievement enabled researchers to pinpoint the positions of heavy atom columns within the unit cell. Lighter atoms appear as resolution is improved to sub-Angstrom levels. Currently, advanced microscopes can image the columns of the light atoms (carbon, oxygen, nitrogen) that are present in many complex structures, and even the lithium atoms present in some battery materials. Sub-Angstrom imaging, initially achieved by focal-series reconstruction of the specimen exit surface wave, will become common place for next-generation electron microscopes with CS-corrected lenses and monochromated electron beams. Resolution can be quantified in terms of peak separation and inter-peak minimum, but the limits imposed on the attainable resolution by the properties of the micro-scope specimen need to be considered. At extreme resolution the ''size'' of atoms can mean that they will not be resolved even when spaced farther apart than the resolution of the microscope.

  11. 3D tissue-engineered construct analysis via conventional high-resolution microcomputed tomography without X-ray contrast.

    Science.gov (United States)

    Voronov, Roman S; VanGordon, Samuel B; Shambaugh, Robert L; Papavassiliou, Dimitrios V; Sikavitsas, Vassilios I

    2013-05-01

    As the field of tissue engineering develops, researchers are faced with a large number of degrees of freedom regarding the choice of material, architecture, seeding, and culturing. To evaluate the effectiveness of a tissue-engineered strategy, histology is typically done by physically slicing and staining a construct (crude, time-consuming, and unreliable). However, due to recent advances in high-resolution biomedical imaging, microcomputed tomography (μCT) has arisen as a quick and effective way to evaluate samples, while preserving their structure in the original state. However, a major barrier for using μCT to do histology has been its inability to differentiate between materials with similar X-ray attenuation. Various contrasting strategies (hardware and chemical staining agents) have been proposed to address this problem, but at a cost of additional complexity and limited access. Instead, here we suggest a strategy for how virtual 3D histology in silico can be conducted using conventional μCT, and we provide an illustrative example from bone tissue engineering. The key to our methodology is an implementation of scaffold surface architecture that is ordered in relation to cells and tissue, in concert with straightforward image-processing techniques, to minimize the reliance on contrasting for material segmentation. In the case study reported, μCT was used to image and segment porous poly(lactic acid) nonwoven fiber mesh scaffolds that were seeded dynamically with mesenchymal stem cells and cultured to produce soft tissue and mineralized tissue in a flow perfusion bioreactor using an osteogenic medium. The methodology presented herein paves a new way for tissue engineers to identify and distinguish components of cell/tissue/scaffold constructs to easily and effectively evaluate the tissue-engineering strategies that generate them.

  12. X-ray holography with atomic resolution

    Science.gov (United States)

    Tegze, Miklós; Faigel, Gyula

    1996-03-01

    DIFFRACTION methods for crystallographic structure determination suffer from the so-called 'phase problem'; a diffraction pattern provides intensity but not phase information for the scattered beams, and therefore cannot be uniquely inverted to obtain the crystal structure of a sample. Holographic methods1, on the other hand, offer a means of extracting both intensity and phase information. To be useful for crystallographic applications, holography must be implemented with radiation of sufficiently small wavelength to resolve atomic-scale features2. One method, electron-emission holography3-9, uses electron waves and is a powerful tool for studying surface structure; but it cannot image the internal structure of solids because of complications arising from the highly anisotropic nature of electron scattering processes. A proposed alternative method uses X-rays2,10-13, which scatter more isotropically than electrons. Here we demonstrate the efficacy of atomic-scale X-ray holography by obtaining direct images of the three-dimensional arrangement of strontium atoms in the cubic perovskite SrTiO3. With more intense synchrotron sources for illumination, and with the development of improved X-ray detectors, X-ray holography should become a powerful general technique for unambiguous structure determination in condensed matter systems.

  13. Super-resolution microscopy of single atoms in optical lattices

    CERN Document Server

    Alberti, Andrea; Alt, Wolfgang; Brakhane, Stefan; Karski, Michał; Reimann, René; Widera, Artur; Meschede, Dieter

    2015-01-01

    We report on image processing techniques and experimental procedures to determine the lattice-site positions of single atoms in an optical lattice with high reliability, even for limited acquisition time or optical resolution. Determining the positions of atoms beyond the diffraction limit relies on parametric deconvolution in close analogy to methods employed in super-resolution microscopy. We develop a deconvolution method that makes effective use of the prior knowledge of the optical transfer function, noise properties, and discreteness of the optical lattice. We show that accurate knowledge of the image formation process enables a dramatic improvement on the localization reliability. This is especially relevant for closely packed ensembles of atoms where the separation between particles cannot be directly optically resolved. Furthermore, we demonstrate experimental methods to precisely reconstruct the point spread function with sub-pixel resolution from fluorescence images of single atoms, and we give a m...

  14. In vivo application of 3D-line skeleton graph analysis (LSGA) technique with high-resolution magnetic resonance imaging of trabecular bone structure.

    Science.gov (United States)

    Pothuaud, Laurent; Newitt, David C; Lu, Ying; MacDonald, Brian; Majumdar, Sharmila

    2004-05-01

    Over the last several years magnetic resonance (MR) imaging has emerged as a means of measuring in vivo 3D trabecular bone structure. In particular, MR based diagnosis could be used to complement standard bone mineral density (BMD) methods for assessing osteoporosis and evaluating longitudinal changes. The aim of this study was to demonstrate the feasibility of using the 3D-LSGA technique for the evaluation of trabecular bone structure of high-resolution MR images, particularly for assessing longitudinal changes, in vivo. First, the reproducibility of topological 3D-LSGA based measurements was evaluated in a set of seven volunteers, and coefficients of variations ranged from 3.5% to 6%. Second, high-resolution MR images of the radius in 30 postmenopausal women from a placebo controlled drug study (Idoxifene), divided into placebo ( n=9) and treated ( n=21) groups, were obtained at baseline (BL) and after 1 year of treatment (follow-up, FU). In addition, dual X-ray absorptiometry (DXA) measures of BMD were obtained in the distal radius. Standard morphological measurements based on the mean intercept length (MIL) technique as well as 3D-LSGA based measurements were applied to the 3D MR images. Significant changes from BL to FU were detected, in the treated group, using the topological 3D-LSGA based measurements, morphological measures of volume of connected trabeculae and App Tb.N from MIL analysis. The duration of the study was short, and the number of patients remaining in the study was small, hence these results cannot be interpreted with regard to a true therapeutic response. Furthermore, the site (wrist) and the drug (idoxifene) are not optimal for follow-up study. However, this paper demonstrated the feasibility of using 3D-LSGA based evaluation coupled with in vivo high-resolution MR imaging as a complementary approach for the monitoring of trabecular bone changes in individual subjects.

  15. Augmented 3D super-resolution of fluorescence-free nanoparticles using enhanced dark-field illumination based on wavelength-modulation and a least-cubic algorithm

    Science.gov (United States)

    Zhang, Peng; Kim, Kyungsoo; Lee, Seungah; Chakkarapani, Suresh Kumar; Fang, Ning; Kang, Seong Ho

    2016-09-01

    Augmented three-dimensional (3D) subdiffraction-limited resolution of fluorescence-free single-nanoparticles was achieved with wavelength-dependent enhanced dark-field (EDF) illumination and a least-cubic algorithm. Various plasmonic nanoparticles on a glass slide (i.e., gold nanoparticles, GNPs; silver nanoparticles, SNPs; and gold nanorods, GNRs) were imaged and sliced in the z-direction to a thickness of 10 nm. Single-particle images were then compared with simulation data. The 3D coordinates of individual GNP, SNP, and GNR nanoparticles (x, y, z) were resolved by fitting the data with 3D point spread functions using a least-cubic algorithm and collation. Final, 3D super-resolution microscopy (SRM) images were obtained by resolving 3D coordinates and their Cramér-Rao lower bound-based localization precisions in an image space (530 nm × 530 nm × 300 nm) with a specific voxel size (2.5 nm × 2.5 nm × 5 nm). Compared with the commonly used least-square method, the least-cubic method was more useful for finding the center in asymmetric cases (i.e., nanorods) with high precision and accuracy. This novel 3D fluorescence-free SRM technique was successfully applied to resolve the positions of various nanoparticles on glass and gold nanospots (in vitro) as well as in a living single cell (in vivo) with subdiffraction limited resolution in 3D.

  16. Assessment of the 3-d reconstruction and high-resolution geometrical modeling of the human skeletal trunk from 2-D radiographic images.

    Science.gov (United States)

    Delorme, S; Petit, Y; de Guise, J A; Labelle, H; Aubin, C E; Dansereau, J

    2003-08-01

    This paper presents an in vivo validation of a method for the three-dimensional (3-D) high-resolution modeling of the human spine, rib cage, and pelvis for the study of spinal deformities. The method uses an adaptation of a standard close-range photogrammetry method called direct linear transformation to reconstruct the 3-D coordinates of anatomical landmarks from three radiographic images of the subject's trunk. It then deforms in 3-D 1-mm-resolution anatomical primitives (reference bones) obtained by serial computed tomography-scan reconstruction of a dry specimen. The free-form deformation is calculated using dual kriging equations. In vivo validation of this method on 40 scoliotic vertebrae gives an overall accuracy of 3.3 +/- 3.8 mm, making it an adequate tool for clinical studies and mechanical analysis purposes.

  17. Imaging Lithium Atoms at Sub-Angstrom Resolution

    Energy Technology Data Exchange (ETDEWEB)

    O' Keefe, Michael A.; Shao-Horn, Yang

    2005-01-03

    John Cowley and his group at ASU were pioneers in the use of transmission electron microscopy (TEM) for high-resolution imaging. Three decades ago they achieved images showing the crystal unit cell content at better than 4A resolution. Over the years, this achievement has inspired improvements in resolution that have enabled researchers to pinpoint the positions of heavy atom columns within the cell. More recently, this ability has been extended to light atoms as resolution has improved. Sub-Angstrom resolution has enabled researchers to image the columns of light atoms (carbon, oxygen and nitrogen) that are present in many complex structures. By using sub-Angstrom focal-series reconstruction of the specimen exit surface wave to image columns of cobalt, oxygen, and lithium atoms in a transition metal oxide structure commonly used as positive electrodes in lithium rechargeable batteries, we show that the range of detectable light atoms extends to lithium. HRTEM at sub-Angstrom resolution will provide the essential role of experimental verification for the emergent nanotech revolution. Our results foreshadow those to be expected from next-generation TEMs with CS-corrected lenses and monochromated electron beams.

  18. Generation of a cold pulsed beam of Rb atoms by transfer from a 3D magneto-optic trap

    CERN Document Server

    Chanu, Sapam Ranjita; Natarajan, Vasant

    2016-01-01

    We demonstrate a technique for producing a cold pulsed beam of atoms by transferring a cloud of atoms trapped in a three dimensional magneto-optic trap (MOT). The MOT is loaded by heating a getter source of Rb atoms. We show that it is advantageous to transfer with two beams (with a small angle between them) compared to a single beam, because the atoms stop interacting with the beams in the two-beam technique, which results in a Gaussian velocity distribution. The atoms are further cooled in optical molasses by turning off the MOT magnetic field before the transfer beams are turned on.

  19. Breaking the Crowther limit: Combining depth-sectioning and tilt tomography for high-resolution, wide-field 3D reconstructions

    Energy Technology Data Exchange (ETDEWEB)

    Hovden, Robert, E-mail: rmh244@cornell.edu [School of Applied and Engineering Physics and Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, NY 14853 (United States); Ercius, Peter [National Center for Electron Microscopy, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Jiang, Yi [Department of Physics, Cornell University, Ithaca, NY 14853 (United States); Wang, Deli; Yu, Yingchao; Abruña, Héctor D. [Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853 (United States); Elser, Veit [Department of Physics, Cornell University, Ithaca, NY 14853 (United States); Muller, David A. [School of Applied and Engineering Physics and Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, NY 14853 (United States)

    2014-05-01

    To date, high-resolution (<1 nm) imaging of extended objects in three-dimensions (3D) has not been possible. A restriction known as the Crowther criterion forces a tradeoff between object size and resolution for 3D reconstructions by tomography. Further, the sub-Angstrom resolution of aberration-corrected electron microscopes is accompanied by a greatly diminished depth of field, causing regions of larger specimens (>6 nm) to appear blurred or missing. Here we demonstrate a three-dimensional imaging method that overcomes both these limits by combining through-focal depth sectioning and traditional tilt-series tomography to reconstruct extended objects, with high-resolution, in all three dimensions. The large convergence angle in aberration corrected instruments now becomes a benefit and not a hindrance to higher quality reconstructions. A through-focal reconstruction over a 390 nm 3D carbon support containing over 100 dealloyed and nanoporous PtCu catalyst particles revealed with sub-nanometer detail the extensive and connected interior pore structure that is created by the dealloying instability. - Highlights: • Develop tomography technique for high-resolution and large field of view. • We combine depth sectioning with traditional tilt tomography. • Through-focal tomography reduces tilts and improves resolution. • Through-focal tomography overcomes the fundamental Crowther limit. • Aberration-corrected becomes a benefit and not a hindrance for tomography.

  20. Analysis of structural correlations in a model binary 3D liquid through the eigenvalues and eigenvectors of the atomic stress tensors.

    Science.gov (United States)

    Levashov, V A

    2016-03-07

    It is possible to associate with every atom or molecule in a liquid its own atomic stress tensor. These atomic stress tensors can be used to describe liquids' structures and to investigate the connection between structural and dynamic properties. In particular, atomic stresses allow to address atomic scale correlations relevant to the Green-Kubo expression for viscosity. Previously correlations between the atomic stresses of different atoms were studied using the Cartesian representation of the stress tensors or the representation based on spherical harmonics. In this paper we address structural correlations in a 3D model binary liquid using the eigenvalues and eigenvectors of the atomic stress tensors. This approach allows to interpret correlations relevant to the Green-Kubo expression for viscosity in a simple geometric way. On decrease of temperature the changes in the relevant stress correlation function between different atoms are significantly more pronounced than the changes in the pair density function. We demonstrate that this behaviour originates from the orientational correlations between the eigenvectors of the atomic stress tensors. We also found correlations between the eigenvalues of the same atomic stress tensor. For the studied system, with purely repulsive interactions between the particles, the eigenvalues of every atomic stress tensor are positive and they can be ordered: λ1 ≥ λ2 ≥ λ3 ≥ 0. We found that, for the particles of a given type, the probability distributions of the ratios (λ2/λ1) and (λ3/λ2) are essentially identical to each other in the liquids state. We also found that λ2 tends to be equal to the geometric average of λ1 and λ3. In our view, correlations between the eigenvalues may represent "the Poisson ratio effect" at the atomic scale.

  1. True 3D kinematic analysis for slope instability assessment in the Siq of Petra (Jordan), from high resolution TLS

    Science.gov (United States)

    Gigli, Giovanni; Margottini, Claudio; Spizzichino, Daniele; Ruther, Heinz; Casagli, Nicola

    2016-04-01

    released, stratigraphic setting and tectonic activity can be recognized. As a consequence, rock-falls have been occurring, even recently, with unstable rock mass volumes ranging from 0.1 m3 up to over some hundreds m3. Slope instability, acceleration of crack deformation and consequent increasing of rock-fall hazard conditions, could threaten the safety of tourist as well as the integrity of the heritage. 3D surface model coming from Terrestrial Laser Scanner acquisitions was developed almost all over the site of Petra, including the Siq. Comprehensively, a point cloud of five billion points was generated making the site of Petra likely the largest scanned archaeological site in the word. As far as the Siq, the scanner was positioned on the path floor at intervals of not more than 10 meters from each station. The total number of scans in the Siq was 220 with an average point cloud interval of approximately 3 cm. Subsequently, for the definition of the main rockfall source areas, a spatial kinematic analysis for the whole Siq has been performed, by using discontinuity orientation data extracted from the point cloud by means of the software Diana. Orientation, number of sets, spacing/frequency, persistence, block size and scale dependent roughness was obtained combining fieldwork and automatic analysis. This kind of analysis is able to establish where a particular instability mechanism is kinematically feasible, given the geometry of the slope, the orientation of discontinuities and shear strength of the rock. The final outcome of this project was a detail landslide kinematic index map, reporting main potential instability mechanisms for a given area. The kinematic index was finally calibrated for each instability mechanism (plane failure; wedge failure; block toppling; flexural toppling) surveyed in the site. The latter is including the collapse occurred in May 2015, likely not producing any victim, in a sector clearly identified by the susceptibility maps produced by the

  2. High-resolution fiber tract reconstruction in the human brain by means of three-dimensional polarized light imaging (3D-PLI

    Directory of Open Access Journals (Sweden)

    Markus eAxer

    2011-12-01

    Full Text Available Functional interactions between different brain regions require connecting fiber tracts, the structural basis of the human connectome. To assemble a comprehensive structural understanding of neural network elements from the microscopic to the macroscopic dimensions, a multimodal and multiscale approach has to be envisaged. However, the integration of results from complementary neuroimaging techniques poses a particular challenge. In this paper, we describe a steadily evolving neuroimaging technique referred to as three-dimensional polarized light imaging (3D-PLI. It is based on the birefringence of the myelin sheaths surrounding axons, and enables the high-resolution analysis of myelinated axons constituting the fiber tracts. 3D-PLI provides the mapping of spatial fiber architecture in the postmortem human brain at a sub-millimeter resolution, i.e. at the mesoscale. The fundamental data structure gained by 3D-PLI is a comprehensive 3D vector field description of fibers and fiber tract orientations – the basis for subsequent tractography. To demonstrate how 3D-PLI can contribute to unravel and assemble the human connectome, a multiscale approach with the same technology was pursued. Two complementary state-of-the-art polarimeters providing different sampling grids (pixel sizes of 100 μm and 1.6 μm were used. To exemplarily highlight the potential of this approach, fiber orientation maps and 3D fiber models were reconstructed in selected regions of the brain (e.g., Corpus callosum, Internal capsule, Pons. The results demonstrate that 3D-PLI is an ideal tool to serve as an interface between the microscopic and macroscopic levels of organization of the human connectome.

  3. Auger Spectra and Different Ionic Charges Following 3s, 3p and 3d Sub-Shells Photoionization of Kr Atoms

    Directory of Open Access Journals (Sweden)

    Yehia A. Lotfy

    2006-01-01

    Full Text Available The decay of inner-shell vacancy in an atom through radiative and non-radiative transitions leads to final charged ions. The de-excitation decay of 3s, 3p and 3d vacancies in Kr atoms are calculated using Monte-Carlo simulation method. The vacancy cascade pathway resulted from the de-excitation decay of deep core hole in 3s subshell in Kr atoms is discussed. The generation of spectator vacancies during the vacancy cascade development gives rise to Auger satellite spectra. The last transitions of the de-excitation decay of 3s, 3p and 3d holes lead to specific charged ions. Dirac-Fock-Slater wave functions are adapted to calculate radiative and non-radiative transition probabilities. The intensity of Kr^{4+} ions are high for 3s hole state, whereas Kr^{3+} and Kr^{2+} ions have highest intensities for 3p and 3d hole states, respectively. The present results of ion charge state distributions agree well with the experimental data.

  4. 1D-3D Hybrid Modelling - From Multi-Compartment Models to Full Resolution Models in Space and Time

    Directory of Open Access Journals (Sweden)

    Stephan eGrein

    2014-07-01

    Full Text Available Investigation of cellular and network dynamics in the brain by means of modeling & simulation has evolved into a highly interdisciplinary field, that uses sophisticated modeling & simulation approaches to understand distinct areas of brain function. Depending on the underlying complexity, these models vary in level of detail to cope with the attached computational cost. Hence for large network simulations, single neurons are typically reduced to time-dependent signal processors, dismissing spatial aspects of the cells. For single cell or small-world networks, general purpose simulators allow for space and time-dependent simulations of electrical signal processing, based on the cable equation theory. An emerging field in Computational Neuroscience encompasses a new level of detail by incorporating the 3D morphology of cells and organelles into 3D space and time-dependent simulations. Every approach has its advantages and limitations, such as computational cost, integrated and methods-spanning simulation approaches, depending on the network size could establish new ways to investigate the brain. We present a hybrid simulation approach, that makes use of reduced 1D-models using e.g. the NEURON which couples to fully resolved models for simulating cellular and sub-cellular dynamics, including the detailed 3D-morphology of neurons and organelles. To couple 1D- & 3D-simulations, we present a geometry and membrane potential mapping framework, with which graph-based morphologies, e.g. in swc-/hoc-format, are mapped to full surface and volume representations of the neuron; membrane potential data from 1D-simulations are used as boundary conditions for full 3D simulations. Thus, established models and data, based on general purpose 1D-simulators, can be directly coupled to the emerging field of fully resolved highly detailed 3D-modeling approaches. The new framework is applied to investigate electrically active neurons and their intracellular spatio

  5. Finite atomic lattices and resolutions of monomial ideals

    CERN Document Server

    Mapes, Sonja

    2010-01-01

    In this paper we primarily study monomial ideals and their minimal free resolutions by studying their associated LCM lattices. In particular, we formally define the notion of coordinatizing a finite atomic lattice P to produce a monomial ideal whose LCM lattice is P, and we give a complete characterization of all such coordinatizations. We prove that all relations in the lattice L(n) of all finite atomic lattices with n ordered atoms can be realized as deformations of exponents of monomial ideals. We also give structural results for L(n). Moreover, we prove that the cellular structure of a minimal free resolution of a monomial ideal M can be extended to minimal resolutions of certain monomial ideals whose LCM lattices are greater than that of M in L(n).

  6. Atom column indexing: atomic resolution image analysis through a matrix representation.

    Science.gov (United States)

    Sang, Xiahan; Oni, Adedapo A; LeBeau, James M

    2014-12-01

    Here, we report the development of an approach to map atomic resolution images into a convenient matrix representation. Through the combination of two-dimensional Gaussian fitting and the projective standard deviation, atom column locations are projected onto two noncollinear reference lattice vectors that are used to assign each a unique (i, j) matrix index. By doing so, straightforward atomic resolution image analysis becomes possible. Using practical examples, we demonstrate that the matrix representation greatly simplifies categorizing atom columns to different sublattices. This enables a myriad of direct analyses, such as mapping atom column properties and correlating long-range atom column pairs. MATLAB source code can be downloaded from https://github.com/subangstrom/aci.

  7. ATOMIC-FORCE MICROSCOPY AND REAL ATOMIC-RESOLUTION - SIMPLE COMPUTER-SIMULATIONS

    NARCIS (Netherlands)

    KOUTSOS, [No Value; MANIAS, E; TENBRINKE, G; HADZIIOANNOU, G

    1994-01-01

    Using a simple computer simulation for AFM imaging in the contact mode, pictures with true and false atomic resolution are demonstrated. The surface probed consists of two f.c.c. (111) planes and an atomic vacancy is introduced in the upper layer. Changing the size of the effective tip and its regis

  8. Atomic resolution images of solid-liquid interfaces

    OpenAIRE

    Giambattista, Brian; McNairy, W. W.; Slough, C. G.; Johnson, A.; Bell, L. D.; Coleman, R. V.; Schneir, J.; Sonnenfeld, R.; Drake, B; Hansma, P K

    1987-01-01

    A scanning tunneling microscope (STM) can provide atomic-resolution images of solids covered with a variety of liquids, including cryogenic fluids, both polar and nonpolar solvents, conductive aqueous solutions, oils, and even greases. This short overview includes images of solids covered with liquid nitrogen, liquid helium, paraffin oil, silicone oil, microscope immersion oil, silicone vacuum grease, fluorocarbon grease, glycerol, and salt water. These images show atoms, charge-density waves...

  9. Method and phantom to study combined effects of in-plane (x,y) and z-axis resolution for 3D CT imaging.

    Science.gov (United States)

    Goodenough, David; Levy, Josh; Kristinsson, Smari; Fredriksson, Jesper; Olafsdottir, Hildur; Healy, Austin

    2016-09-08

    Increasingly, the advent of multislice CT scanners, volume CT scanners, and total body spiral acquisition modes has led to the use of Multi Planar Reconstruction and 3D datasets. In considering 3D resolution properties of a CT system it is important to note that both the in-plane (x,y) and z-axis (slice thickness) influence the visual-ization and detection of objects within the scanned volume. This study investigates ways to consider both the in-plane resolution and the z-axis resolution in a single phantom wherein analytic or visualized analysis can yield information on these combined effects. A new phantom called the "Wave Phantom" is developed that can be used to sample the 3D resolution properties of a CT image, including in-plane (x,y) and z-axis information. The key development in this Wave Phantom is the incorporation of a z-axis aspect of a more traditional step (bar) resolution gauge phantom. The phantom can be examined visually wherein a cutoff level may be seen; and/or the analytic analysis of the various characteristics of the waveform profile by including amplitude, frequency, and slope (rate of climb) of the peaks, can be extracted from the Wave Pattern using mathematical analysis such as the Fourier transform. The combined effect of changes in in-plane resolution and z-axis (thickness), are shown, as well as the effect of changes in either in-plane resolu-tion, or z-axis thickness. Examples of visual images of the Wave pattern as well as the analytic characteristics of the various harmonics of a periodic Wave pattern resulting from changes in resolution filter and/or slice thickness, and position in the field of view are shown. The Wave Phantom offers a promising way to investigate 3D resolution results from combined effect of in-plane (x-y) and z-axis resolution as contrasted to the use of simple 2D resolution gauges that need to be used with separate measures of z-axis dependency, such as angled ramps. It offers both a visual pattern as well as a

  10. Reconstruction of high-resolution 3D dose from matrix measurements : error detection capability of the COMPASS correction kernel method

    NARCIS (Netherlands)

    Godart, J.; Korevaar, E. W.; Visser, R.; Wauben, D. J. L.; van t Veld, Aart

    2011-01-01

    TheCOMPASS system (IBADosimetry) is a quality assurance (QA) tool which reconstructs 3D doses inside a phantom or a patient CT. The dose is predicted according to the RT plan with a correction derived from 2D measurements of a matrix detector. This correction method is necessary since a direct recon

  11. 3D printing PLGA: a quantitative examination of the effects of polymer composition and printing parameters on print resolution.

    Science.gov (United States)

    Guo, Ting; Holzberg, Timothy; Lim, Casey; Gao, Feng; Gargava, Ankit; Trachtenberg, Jordan; Mikos, Antonios; Fisher, John

    2017-02-28

    In the past few decades, 3D printing has played a significant role in fabricating scaffolds with consistent, complex structure that meets patient-specific needs in future clinical applications. Although many studies have contributed to this emerging field of additive manufacturing, which includes material development and computer-aided scaffold design, current quantitative analyses do not correlate material properties, printing parameters, and printing outcomes to a great extent. A model that correlates these properties has tremendous potential to standardize 3D printing for tissue engineering and biomaterial science. In this study, we printed poly(lactic-co-glycolic acid) (PLGA) utilizing a direct melt extrusion technique without additional ingredients. We investigated PLGA with various lactic acid:glycolic acid (LA:GA) molecular weight ratios and end caps to demonstrate the dependence of the extrusion process on the polymer composition. Micro-computed tomography (microCT) was then used to evaluate printed scaffolds containing different LA:GA ratios, composed of different fiber patterns, and processed under different printing conditions. We built a statistical model to reveal the correlation and predominant factors that determine printing precision. Our model showed a strong linear relationship between the actual and predicted precision under different combinations of printing conditions and material compositions. This quantitative examination establishes a significant foreground to 3D print biomaterials following a systematic fabrication procedure. Additionally, our proposed statistical models can be applied to couple specific biomaterials and 3D printing applications for patient implants with particular requirements.

  12. MTF characterization in 2D and 3D for a high resolution, large field of view flat panel imager for cone beam CT

    Science.gov (United States)

    Shah, Jainil; Mann, Steve D.; Tornai, Martin P.; Richmond, Michelle; Zentai, George

    2014-03-01

    The 2D and 3D modulation transfer functions (MTFs) of a custom made, large 40x30cm2 area, 600- micron CsI-TFT based flat panel imager having 127-micron pixellation, along with the micro-fiber scintillator structure, were characterized in detail using various techniques. The larger area detector yields a reconstructed FOV of 25cm diameter with an 80cm SID in CT mode. The MTFs were determined with 1x1 (intrinsic) binning. The 2D MTFs were determined using a 50.8 micron tungsten wire and a solid lead edge, and the 3D MTF was measured using a custom made phantom consisting of three nearly orthogonal 50.8 micron tungsten wires suspended in an acrylic cubic frame. The 2D projection data was reconstructed using an iterative OSC algorithm using 16 subsets and 5 iterations. As additional verification of the resolution, along with scatter, the Catphan® phantom was also imaged and reconstructed with identical parameters. The measured 2D MTF was ~4% using the wire technique and ~1% using the edge technique at the 3.94 lp/mm Nyquist cut-off frequency. The average 3D MTF measured along the wires was ~8% at the Nyquist. At 50% MTF, the resolutions were 1.2 and 2.1 lp/mm in 2D and 3D, respectively. In the Catphan® phantom, the 1.7 lp/mm bars were easily observed. Lastly, the 3D MTF measured on the three wires has an observed 5.9% RMSD, indicating that the resolution of the imaging system is uniform and spatially independent. This high performance detector is integrated into a dedicated breast SPECT-CT imaging system.

  13. R(2OBBIE-3D, a Fast Robotic High-Resolution System for Quantitative Phenotyping of Surface Geometry and Colour-Texture.

    Directory of Open Access Journals (Sweden)

    António F Martins

    Full Text Available While recent imaging techniques provide insights into biological processes from the molecular to the cellular scale, phenotypes at larger scales remain poorly amenable to quantitative analyses. For example, investigations of the biophysical mechanisms generating skin morphological complexity and diversity would greatly benefit from 3D geometry and colour-texture reconstructions. Here, we report on R(2OBBIE-3D, an integrated system that combines a robotic arm, a high-resolution digital colour camera, an illumination basket of high-intensity light-emitting diodes and state-of-the-art 3D-reconstruction approaches. We demonstrate that R(2OBBIE generates accurate 3D models of biological objects between 1 and 100 cm, makes multiview photometric stereo scanning possible in practical processing times, and enables the capture of colour-texture and geometric resolutions better than 15 μm without the use of magnifying lenses. R(2OBBIE has the potential to greatly improve quantitative analyses of phenotypes in addition to providing multiple new applications in, e.g., biomedical science.

  14. Adsorption of alkali, alkaline-earth, simple and 3d transition metal, and nonmetal atoms on monolayer MoS2

    Directory of Open Access Journals (Sweden)

    X. D. Li

    2015-05-01

    Full Text Available Single adsorption of different atoms on pristine two-dimensional monolayer MoS2 have been systematically investigated by using density functional calculations with van der Waals correction. The adatoms cover alkali metals, alkaline earth metals, main group metal, 3d-transition metals, coinage metal and nonmetal atoms. Depending on the adatom type, metallic, semimetallic or semiconducting behavior can be found in direct bandgap monolayer MoS2. Additionally, local or long-range magnetic moments of two-dimensional MoS2 sheet can also attained through the adsorption. The detailed atomic-scale knowledge of single adsorption on MoS2 monolayer is important not only for the sake of a theoretical understanding, but also device level deposition technological application.

  15. Fast, high-resolution 3D dosimetry utilizing a novel optical-CT scanner incorporating tertiary telecentric collimation

    OpenAIRE

    Sakhalkar, H. S.; Oldham, M

    2008-01-01

    This study introduces a charge coupled device (CCD) area detector based optical-computed tomography (optical-CT) scanner for comprehensive verification of radiation dose distributions recorded in nonscattering radiochromic dosimeters. Defining characteristics include: (i) a very fast scanning time of ~5 min to acquire a complete three-dimensional (3D) dataset, (ii) improved image formation through the use of custom telecentric optics, which ensures accurate projection images and minimizes art...

  16. 3D documentation of footwear impressions and tyre tracks in snow with high resolution optical surface scanning.

    Science.gov (United States)

    Buck, Ursula; Albertini, Nicola; Naether, Silvio; Thali, Michael J

    2007-09-13

    The three-dimensional documentation of footwear and tyre impressions in snow offers an opportunity to capture additional fine detail for the identification as present photographs. For this approach, up to now, different casting methods have been used. Casting of footwear impressions in snow has always been a difficult assignment. This work demonstrates that for the three-dimensional documentation of impressions in snow the non-destructive method of 3D optical surface scanning is suitable. The new method delivers more detailed results of higher accuracy than the conventional casting techniques. The results of this easy to use and mobile 3D optical surface scanner were very satisfactory in different meteorological and snow conditions. The method is also suitable for impressions in soil, sand or other materials. In addition to the side by side comparison, the automatic comparison of the 3D models and the computation of deviations and accuracy of the data simplify the examination and delivers objective and secure results. The results can be visualized efficiently. Data exchange between investigating authorities at a national or an international level can be achieved easily with electronic data carriers.

  17. Super-resolution microscopy of single atoms in optical lattices

    Science.gov (United States)

    Alberti, Andrea; Robens, Carsten; Alt, Wolfgang; Brakhane, Stefan; Karski, Michał; Reimann, René; Widera, Artur; Meschede, Dieter

    2016-05-01

    We report on image processing techniques and experimental procedures to determine the lattice-site positions of single atoms in an optical lattice with high reliability, even for limited acquisition time or optical resolution. Determining the positions of atoms beyond the diffraction limit relies on parametric deconvolution in close analogy to methods employed in super-resolution microscopy. We develop a deconvolution method that makes effective use of the prior knowledge of the optical transfer function, noise properties, and discreteness of the optical lattice. We show that accurate knowledge of the image formation process enables a dramatic improvement on the localization reliability. This allows us to demonstrate super-resolution of the atoms’ position in closely packed ensembles where the separation between particles cannot be directly optically resolved. Furthermore, we demonstrate experimental methods to precisely reconstruct the point spread function with sub-pixel resolution from fluorescence images of single atoms, and we give a mathematical foundation thereof. We also discuss discretized image sampling in pixel detectors and provide a quantitative model of noise sources in electron multiplying CCD cameras. The techniques developed here are not only beneficial to neutral atom experiments, but could also be employed to improve the localization precision of trapped ions for ultra precise force sensing.

  18. High density resolution synchrotron radiation based x-ray microtomography (SR μCT) for quantitative 3D-morphometrics in zoological sciences

    Science.gov (United States)

    Nickel, Michael; Hammel, Jörg U.; Herzen, Julia; Bullinger, Eric; Beckmann, Felix

    2008-08-01

    Zoological sciences widely rely on morphological data to reconstruct and understand body structures of animals. The best suitable methods like tomography allow for a direct representation of 3D-structures. In recent years, synchrotron radiation based x-ray microtomography (SR μCT) placed high resolutions to the disposal of morphologists. With the development of highly brilliant and collimated third generation synchrotron sources, phase contrast SR μCT became widely available. A number of scientific contributions stressed the superiority of phase contrast over absorption contrast. However, here we demonstrate the power of high density resolution methods based on absorption-contrast SRμCT for quantitative 3D-measurements of tissues and other delicate bio-structures in zoological sciences. We used beamline BW2 at DORIS III (DESY, Hamburg, Germany) to perform microtomography on tissue and mineral skeletons of marine sponges (Porifera) which were shock frozen and/or fixed in a glutamate osmium tetroxide solution, followed by critical point drying. High density resolution tomographic reconstructions allowed running quantitative 3D-image analyses in Matlab and ImageJ. By applying contrast and shape rule based algorithms we semi-automatically extracted and measured sponge body structures like mineral spicules, elements of the canal system or tissue structures. This lead to a better understanding of sponge biology: from skeleton functional morphology and internal water flow regimes to body contractility. Our high density resolution based quantitative approach can be applied to a wide variety of biological structures. However, two prerequisites apply: (1) maximum density resolution is necessary; (2) edge effects as seen for example in phase outline contrast SR μCT must not be present. As a consequence, to allow biological sciences to fully exploit the power of SR μCT further increase of density resolution in absorption contrast methods is desirable.

  19. Fusion and Visualization of HiRISE Super-Resolution, Shape-from-Shading DTM with MER Stereo 3D Reconstructions

    Science.gov (United States)

    Gupta, S.; Paar, G.; Muller, J. P.; Tao, Y.; Tyler, L.; Traxler, C.; Hesina, G.; Huber, B.; Nauschnegg, B.

    2014-12-01

    The FP7-SPACE project PRoViDE has assembled a major portion of the imaging data gathered so far from rover vehicles, landers and probes on extra-terrestrial planetary surfaces into a unique database, bringing them into a common planetary geospatial context and providing access to a complete set of 3D vision products. One major aim of PRoViDE is the fusion between orbiter and rover image products. To close the gap between HiRISE imaging resolution (down to 25cm for the OrthoRectified image (ORI), down to 1m for the DTM) and surface vision products, images from multiple HiRISE acquisitions are combined into a super resolution data set (Tao & Muller, 2014), increasing to 5cm resolution the Ortho images. Furthermore, shape-from-shading is applied to one of the ORIs at its original resolution for refinement of the HiRISE DTM, leading to DTM ground resolutions of up to 25 cm. After texture-based co-registration with these refined orbiter 3D products, MER PanCam and NavCam 3D image products can be smoothly pasted into a multi-resolution 3D data representation. Typical results from the MER mission are presented by a dedicated real-time rendering tool which is fed by a hierarchical 3D data structure that is able to cope with all involved scales from global planetary scale down to close-up reconstructions in the mm range. This allows us to explore and analyze the geological characteristics of rock outcrops, for example the detailed geometry and internal features of sedimentary rock layers, to aid paleoenvironmental interpretation. This integrated approach enables more efficient development of geological models of martian rock outcrops. The rendering tool also provides measurement tools to obtain geospatial data of surface points and distances between them. We report on novel scientific use cases and the added value potential of the resultant high-quality data set and presentation means to support further geologic investigations. The research leading to these results has

  20. Single-side access, isotropic resolution and multispectral 3D photoacoustic imaging with rotate-translate scanning of ultrasonic detector array

    CERN Document Server

    Gateau, Jérôme; Chassot, Jean-Marie; Bossy, Emmanuel

    2015-01-01

    Photoacoustic imaging can achieve high-resolution three-dimensional visualization of optical absorbers at penetration depths ~ 1 cm in biological tissues by detecting optically-induced high ultrasound frequencies. Tomographic acquisition with ultrasound linear arrays offers an easy implementation of single-side access, parallelized and high-frequency detection, but usually comes with an image quality impaired by the directionality of the detectors. Indeed, a simple translation of the array perpendicularly to its median imaging plane is often used, but results both in a poor resolution in the translation direction and in strong limited view artifacts. To improve the spatial resolution and the visibility of complex structures while keeping a planar detection geometry, we introduce, in this paper, a novel rotate-translate scanning scheme, and investigate the performance of a scanner implemented at 15 MHz center frequency. The developed system achieved a quasi-isotropic uniform 3D resolution of ~170 um over a cub...

  1. Development status of a CZT spectrometer prototype with 3D spatial resolution for hand x-ray astronomy

    DEFF Research Database (Denmark)

    Auricchio, N.; Caroli, E.; Basili, A.

    2012-01-01

    is based on RENA-3 ASIC and the data handling system uses a custom electronics based on FPGA to provide the ASIC setting, the event handling logic, and the data acquisition. This paper mainly describes the components and the status of the undergoing activities for the construction of the proposed 3D CZT...... of the polarization status of the Crab between 100 and 500 keV. The prototype is made by packing 8 linear modules, each composed of one basic sensitive unit bonded onto a thin supporting ceramic layer. Each unit is a drift strip detector based on a CZT crystal, irradiated transversally to the electric field direction...

  2. 1D-3D hybrid modeling-from multi-compartment models to full resolution models in space and time.

    Science.gov (United States)

    Grein, Stephan; Stepniewski, Martin; Reiter, Sebastian; Knodel, Markus M; Queisser, Gillian

    2014-01-01

    Investigation of cellular and network dynamics in the brain by means of modeling and simulation has evolved into a highly interdisciplinary field, that uses sophisticated modeling and simulation approaches to understand distinct areas of brain function. Depending on the underlying complexity, these models vary in their level of detail, in order to cope with the attached computational cost. Hence for large network simulations, single neurons are typically reduced to time-dependent signal processors, dismissing the spatial aspect of each cell. For single cell or networks with relatively small numbers of neurons, general purpose simulators allow for space and time-dependent simulations of electrical signal processing, based on the cable equation theory. An emerging field in Computational Neuroscience encompasses a new level of detail by incorporating the full three-dimensional morphology of cells and organelles into three-dimensional, space and time-dependent, simulations. While every approach has its advantages and limitations, such as computational cost, integrated and methods-spanning simulation approaches, depending on the network size could establish new ways to investigate the brain. In this paper we present a hybrid simulation approach, that makes use of reduced 1D-models using e.g., the NEURON simulator-which couples to fully resolved models for simulating cellular and sub-cellular dynamics, including the detailed three-dimensional morphology of neurons and organelles. In order to couple 1D- and 3D-simulations, we present a geometry-, membrane potential- and intracellular concentration mapping framework, with which graph- based morphologies, e.g., in the swc- or hoc-format, are mapped to full surface and volume representations of the neuron and computational data from 1D-simulations can be used as boundary conditions for full 3D simulations and vice versa. Thus, established models and data, based on general purpose 1D-simulators, can be directly coupled to the

  3. Synthesis-atomic structure-properties relationships in metallic nanoparticles by total scattering experiments and 3D computer simulations: case of Pt-Ru nanoalloy catalysts.

    Science.gov (United States)

    Prasai, Binay; Ren, Yang; Shan, Shiyao; Zhao, Yinguang; Cronk, Hannah; Luo, Jin; Zhong, Chuan-Jian; Petkov, Valeri

    2015-05-07

    An approach to determining the 3D atomic structure of metallic nanoparticles (NPs) in fine detail and using the unique knowledge obtained for rationalizing their synthesis and properties targeted for optimization is described and exemplified on Pt-Ru alloy NPs of importance to the development of devices for clean energy conversion such as fuel cells. In particular, PtxRu100-x alloy NPs, where x = 31, 49 and 75, are synthesized by wet chemistry and activated catalytically by a post-synthesis treatment involving heating under controlled N2-H2 atmosphere. So-activated NPs are evaluated as catalysts for gas-phase CO oxidation and ethanol electro-oxidation reactions taking place in fuel cells. Both as-synthesized and activated NPs are characterized structurally by total scattering experiments involving high-energy synchrotron X-ray diffraction coupled to atomic pair distribution functions (PDFs) analysis. 3D structure models both for as-synthesized and activated NPs are built by molecular dynamics simulations based on the archetypal for current theoretical modelling Sutton-Chen method. Models are refined against the experimental PDF data by reverse Monte Carlo simulations and analysed in terms of prime structural characteristics such as metal-to-metal bond lengths, bond angles and first coordination numbers for Pt and Ru atoms. Analysis indicates that, though of a similar type, the atomic structure of as-synthesized and respective activated NPs differ in several details of importance to NP catalytic properties. Structural characteristics of activated NPs and data for their catalytic activity are compared side by side and strong evidence found that electronic effects, indicated by significant changes in Pt-Pt and Ru-Ru metal bond lengths at NP surface, and practically unrecognized so far atomic ensemble effects, indicated by distinct stacking of atomic layers near NP surface and prevalence of particular configurations of Pt and Ru atoms in these layers, contribute to the

  4. Atomic Resolution Images of Solid-Liquid Interfaces

    Science.gov (United States)

    Giambattista, Brian; McNairy, W. W.; Slough, C. G.; Johnson, A.; Bell, L. D.; Coleman, R. V.; Schneir, J.; Sonnenfeld, R.; Drake, B.; Hansma, P. K.

    1987-07-01

    A scanning tunneling microscope (STM) can provide atomic-resolution images of solids covered with a variety of liquids, including cryogenic fluids, both polar and nonpolar solvents, conductive aqueous solutions, oils, and even greases. This short overview includes images of solids covered with liquid nitrogen, liquid helium, paraffin oil, silicone oil, microscope immersion oil, silicone vacuum grease, fluorocarbon grease, glycerol, and salt water. These images show atoms, charge-density waves, grains in an evaporated metal film, and even corrosion processes as they occur in real time. The future includes not only basic research in surface science but also applied research in lithography, lubrication, catalysis, corrosion, electrochemistry, and perhaps even biology.

  5. Synthesis-atomic structure-properties relationships in metallic nanoparticles by total scattering experiments and 3D computer simulations: case of Pt-Ru nanoalloy catalysts

    Science.gov (United States)

    Prasai, Binay; Ren, Yang; Shan, Shiyao; Zhao, Yinguang; Cronk, Hannah; Luo, Jin; Zhong, Chuan-Jian; Petkov, Valeri

    2015-04-01

    An approach to determining the 3D atomic structure of metallic nanoparticles (NPs) in fine detail and using the unique knowledge obtained for rationalizing their synthesis and properties targeted for optimization is described and exemplified on Pt-Ru alloy NPs of importance to the development of devices for clean energy conversion such as fuel cells. In particular, PtxRu100-x alloy NPs, where x = 31, 49 and 75, are synthesized by wet chemistry and activated catalytically by a post-synthesis treatment involving heating under controlled N2-H2 atmosphere. So-activated NPs are evaluated as catalysts for gas-phase CO oxidation and ethanol electro-oxidation reactions taking place in fuel cells. Both as-synthesized and activated NPs are characterized structurally by total scattering experiments involving high-energy synchrotron X-ray diffraction coupled to atomic pair distribution functions (PDFs) analysis. 3D structure models both for as-synthesized and activated NPs are built by molecular dynamics simulations based on the archetypal for current theoretical modelling Sutton-Chen method. Models are refined against the experimental PDF data by reverse Monte Carlo simulations and analysed in terms of prime structural characteristics such as metal-to-metal bond lengths, bond angles and first coordination numbers for Pt and Ru atoms. Analysis indicates that, though of a similar type, the atomic structure of as-synthesized and respective activated NPs differ in several details of importance to NP catalytic properties. Structural characteristics of activated NPs and data for their catalytic activity are compared side by side and strong evidence found that electronic effects, indicated by significant changes in Pt-Pt and Ru-Ru metal bond lengths at NP surface, and practically unrecognized so far atomic ensemble effects, indicated by distinct stacking of atomic layers near NP surface and prevalence of particular configurations of Pt and Ru atoms in these layers, contribute to the

  6. High throughput 3D super-resolution microscopy reveals Caulobacter crescentus in vivo Z-ring organization.

    Science.gov (United States)

    Holden, Seamus J; Pengo, Thomas; Meibom, Karin L; Fernandez Fernandez, Carmen; Collier, Justine; Manley, Suliana

    2014-03-25

    We created a high-throughput modality of photoactivated localization microscopy (PALM) that enables automated 3D PALM imaging of hundreds of synchronized bacteria during all stages of the cell cycle. We used high-throughput PALM to investigate the nanoscale organization of the bacterial cell division protein FtsZ in live Caulobacter crescentus. We observed that FtsZ predominantly localizes as a patchy midcell band, and only rarely as a continuous ring, supporting a model of "Z-ring" organization whereby FtsZ protofilaments are randomly distributed within the band and interact only weakly. We found evidence for a previously unidentified period of rapid ring contraction in the final stages of the cell cycle. We also found that DNA damage resulted in production of high-density continuous Z-rings, which may obstruct cytokinesis. Our results provide a detailed quantitative picture of in vivo Z-ring organization.

  7. Development status of a CZT spectrometer prototype with 3D spatial resolution for hard x-ray astronomy

    Science.gov (United States)

    Auricchio, N.; Caroli, E.; Basili, A.; Benassi, G.; Budtz Jørgensen, C.; Curado da Silva, R. M.; Del Sordo, S.; Kuvvetli, I.; Milano, L.; Moscatelli, F.; Stephen, J. B.; Zanichelli, M.; Zappettini, A.

    2012-07-01

    The development of new focusing optics based on wide band Laue lenses operating from ~60 keV up to several hundred keV is particularly challenging. This type of hard X-ray or gamma ray optics requires a high performance focal plane detector in order to exploit to the best their intrinsic capabilities. We describe a three dimensional (3D) position sensitive detector prototype suitable as the basic module for a high efficiency Laue lens focal plane detector. This detector configuration is currently under study for use in a balloon payload dedicated to performing a high significance measurement of the polarization status of the Crab between 100 and 500 keV. The prototype is made by packing 8 linear modules, each composed of one basic sensitive unit bonded onto a thin supporting ceramic layer. Each unit is a drift strip detector based on a CZT crystal, irradiated transversally to the electric field direction. The anode is segmented into 8 detection cells, each comprising one collecting strip and 8 surrounding drift strips. The drift strips are biased by a voltage divider. The cathode is divided into 4 horizontal strips for the reconstruction of the Z interaction position. The detector readout electronics is based on RENA-3 ASIC and the data handling system uses a custom electronics based on FPGA to provide the ASIC setting, the event handling logic, and the data acquisition. This paper mainly describes the components and the status of the undergoing activities for the construction of the proposed 3D CZT prototype and shows the results of the electronics tests.

  8. Galerkin method for unsplit 3-D Dirac equation using atomically$/$kinetically balanced B-spline basis

    CERN Document Server

    Fillion-Gourdeau, F; Bandrauk, A D

    2015-01-01

    A Galerkin method is developed to solve the time-dependent Dirac equation in prolate spheroidal coordinates for an electron-molecular two-center system. The initial state is evaluated from a variational principle using a kinetic/atomic balanced basis, which allows for an efficient and accurate determination of the Dirac spectrum and eigenfunctions. B-spline basis functions are used to obtain high accuracy. This numerical method is used to compute the energy spectrum of the two-center problem and then the evolution of eigenstate wavefunctions in an external electromagnetic field.

  9. Galerkin method for unsplit 3-D Dirac equation using atomically/kinetically balanced B-spline basis

    Energy Technology Data Exchange (ETDEWEB)

    Fillion-Gourdeau, F., E-mail: filliong@CRM.UMontreal.ca [Université du Québec, INRS – Énergie, Matériaux et Télécommunications, Varennes, J3X 1S2 (Canada); Centre de Recherches Mathématiques, Université de Montréal, Montréal, H3T 1J4 (Canada); Lorin, E., E-mail: elorin@math.carleton.ca [School of Mathematics and Statistics, Carleton University, Ottawa, K1S 5B6 (Canada); Centre de Recherches Mathématiques, Université de Montréal, Montréal, H3T 1J4 (Canada); Bandrauk, A.D., E-mail: andre.bandrauk@usherbrooke.ca [Laboratoire de Chimie Théorique, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, J1K 2R1 (Canada); Centre de Recherches Mathématiques, Université de Montréal, Montréal, H3T 1J4 (Canada)

    2016-02-15

    A Galerkin method is developed to solve the time-dependent Dirac equation in prolate spheroidal coordinates for an electron–molecular two-center system. The initial state is evaluated from a variational principle using a kinetic/atomic balanced basis, which allows for an efficient and accurate determination of the Dirac spectrum and eigenfunctions. B-spline basis functions are used to obtain high accuracy. This numerical method is used to compute the energy spectrum of the two-center problem and then the evolution of eigenstate wavefunctions in an external electromagnetic field.

  10. Characterization of a sub-assembly of 3D position sensitive cadmium zinc telluride detectors and electronics from a sub-millimeter resolution PET system

    Science.gov (United States)

    Abbaszadeh, Shiva; Gu, Yi; Reynolds, Paul D.; Levin, Craig S.

    2016-09-01

    Cadmium zinc telluride (CZT) offers key advantages for small animal positron emission tomography (PET), including high spatial and energy resolution and simple metal deposition for fabrication of very small pixel arrays. Previous studies have investigated the intrinsic spatial, energy, and timing resolution of an individual sub-millimeter resolution CZT detector. In this work we present the first characterization results of a system of these detectors. The 3D position sensitive dual-CZT detector module and readout electronics developed in our lab was scaled up to complete a significant portion of the final PET system. This sub-system was configured as two opposing detection panels containing a total of twelve 40~\\text{mm}× 40~\\text{mm}× 5 mm monolithic CZT crystals for proof of concept. System-level characterization studies, including optimizing the trigger threshold of each channel’s comparators, were performed. 68Ge and 137Cs radioactive isotopes were used to characterize the energy resolution of all 468 anode channels in the sub-system. The mean measured global 511 keV photopeak energy resolution over all anodes was found to be 7.35+/- 1.75 % FWHM after correction for photon interaction depth-dependent signal variation. The measured global time resolution was 37 ns FWHM, a parameter to be further optimized, and the intrinsic spatial resolution was 0.76 mm FWHM.

  11. CO tip functionalization in subatomic resolution atomic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Minjung [Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas 78712 (United States); Chelikowsky, James R. [Center for Computational Materials, Institute for Computational Engineering and Sciences, and Departments of Physics and Chemical Engineering, The University of Texas at Austin, Austin, Texas 78712 (United States)

    2015-10-19

    Noncontact atomic force microscopy (nc-AFM) employing a CO-functionalized tip displays dramatically enhanced resolution wherein covalent bonds of polycyclic aromatic hydrocarbon can be imaged. Employing real-space pseudopotential first-principles calculations, we examine the role of CO in functionalizing the nc-AFM tip. Our calculations allow us to simulate full AFM images and ascertain the enhancement mechanism of the CO molecule. We consider two approaches: one with an explicit inclusion of the CO molecule and one without. By comparing our simulations to existing experimental images, we ascribe the enhanced resolution of the CO functionalized tip to the special orbital characteristics of the CO molecule.

  12. Characterization of a high resolution and high sensitivity pre-clinical PET scanner with 3D event reconstruction

    CERN Document Server

    Rissi, M; Bolle, E; Dorholt, O; Hines, K E; Rohne, O; Skretting, A; Stapnes, S; Volgyes, D

    2012-01-01

    COMPET is a preclinical PET scanner aiming towards a high sensitivity, a high resolution and MRI compatibility by implementing a novel detector geometry. In this approach, long scintillating LYSO crystals are used to absorb the gamma-rays. To determine the point of interaction (P01) between gamma-ray and crystal, the light exiting the crystals on one of the long sides is collected with wavelength shifters (WLS) perpendicularly arranged to the crystals. This concept has two main advantages: (1) The parallax error is reduced to a minimum and is equal for the whole field of view (FOV). (2) The P01 and its energy deposit is known in all three dimension with a high resolution, allowing for the reconstruction of Compton scattered gamma-rays. Point (1) leads to a uniform point source resolution (PSR) distribution over the whole FOV, and also allows to place the detector close to the object being imaged. Both points (1) and (2) lead to an increased sensitivity and allow for both high resolution and sensitivity at the...

  13. Optical characterization of auto-stereoscopic 3D displays: interest of the resolution and comparison to human eye properties

    Science.gov (United States)

    Boher, Pierre; Leroux, Thierry; Bignon, Thibault; Collomb-Patton, Véronique

    2014-02-01

    Optical characterization of multi-view auto-stereoscopic displays is realized using high angular resolution viewing angle measurements and imaging measurements. View to view and global qualified binocular viewing space are computed from viewing angle measurements and verified using imaging measurements. Crosstalk uniformity is also deduced and related to display imperfections.

  14. Stability of dislocation structures in copper towards stress relaxation investigated by high angular resolution 3D X-ray diffraction

    DEFF Research Database (Denmark)

    Jakobsen, Bo; Poulsen, Henning Friis; Lienert, Ulrich

    2009-01-01

    A 300 µm thick tensile specimen of OFHC copper is subjected to a tensile loading sequence and deformed to a maximal strain of 3.11%. Using the novel three-dimensional X-ray diffraction method High angular resolution 3DXRD', the evolution of the microstructure within a deeply embedded grain is cha...

  15. Atomic resolution in noncontact AFM by probing cantilever frequency shifts

    Institute of Scientific and Technical Information of China (English)

    Hong Yong Xie

    2007-01-01

    Rutile TiO2(001) quantum dots (or nano-marks) in different shapes were used to imitate uncleaved material surfaces or materials with rough surfaces. By numerical integration of the equation of motion of cantilever for silicon tip scanning along the [110] direction over the rutile TiO2 (001) quantum dots in ultra high vacuum (UHV), scanning routes were explored to achieve atomic resolution from frequency shift image. The tip-surface interaction forces were calculated from Lennard-Jones (12-6) potential by the Hamaker summation method. The calculated results showed that atomic resolution could be achieved by frequency shift image for TiO2 (001) surfaces of rhombohedral quantum dot scanning in a vertical route, and spherical cap quantum dot scanning in a superposition route.

  16. Near-atomic-resolution cryo-EM for molecular virology.

    Science.gov (United States)

    Hryc, Corey F; Chen, Dong-Hua; Chiu, Wah

    2011-08-01

    Electron cryo-microscopy (cryo-EM) is a technique in structural biology that is widely used to solve the three-dimensional structures of macromolecular assemblies, close to their biological and solution conditions. Recent improvements in cryo-EM and single-particle reconstruction methodologies have led to the determination of several virus structures at near-atomic resolution (3.3 - 4.6 Å). These cryo-EM structures not only resolve the Cα backbones and side-chain densities of viral capsid proteins, but also suggest functional roles that the protein domains and some key amino acid residues play. This paper reviews the recent advances in near-atomic-resolution cryo-EM for probing the mechanisms of virus assembly and morphogenesis.

  17. Electron microscopy of gold nanoparticles at atomic resolution

    Science.gov (United States)

    Azubel, Maia; Koivisto, Jaakko; Malola, Sami; Bushnell, David; Hura, Greg L.; Koh, Ai Leen; Tsunoyama, Hironori; Tsukuda, Tatsuya; Pettersson, Mika; Häkkinen, Hannu; Kornberg, Roger D.

    2014-01-01

    Structure determination of gold nanoparticles (AuNPs) is necessary for understanding their physical and chemical properties, and only one AuNP larger than 1 nm in diameter, an Au102NP, has been solved to atomic resolution. Whereas the Au102NP structure was determined by X-ray crystallography, other large AuNPs have proved refractory to this approach. Here we report the structure determination of an Au68NP at atomic resolution by aberration-corrected transmission electron microscopy (AC-TEM), performed with the use of a minimal electron dose, an approach that should prove applicable to metal NPs in general. The structure of the Au68NP was supported by small angle X-ray scattering (SAXS) and by comparison of observed infrared (IR) absorption spectra with calculations by density functional theory (DFT). PMID:25146285

  18. Optical coherence tomography for ultrahigh-resolution 3D imaging of cell development and real-time guiding for photodynamic therapy

    Science.gov (United States)

    Wang, Tianshi; Zhen, Jinggao; Wang, Bo; Xue, Ping

    2009-11-01

    Optical coherence tomography is a new emerging technique for cross-sectional imaging with high spatial resolution of micrometer scale. It enables in vivo and non-invasive imaging with no need to contact the sample and is widely used in biological and clinic application. In this paper optical coherence tomography is demonstrated for both biological and clinic applications. For biological application, a white-light interference microscope is developed for ultrahigh-resolution full-field optical coherence tomography (full-field OCT) to implement 3D imaging of biological tissue. Spatial resolution of 0.9μm×1.1μm (transverse×axial) is achieved A system sensitivity of 85 dB is obtained at an acquisition time of 5s per image. The development of a mouse embryo is studied layer by layer with our ultrahigh-resolution full-filed OCT. For clinic application, a handheld optical coherence tomography system is designed for real-time and in situ imaging of the port wine stains (PWS) patient and supplying surgery guidance for photodynamic therapy (PDT) treatment. The light source with center wavelength of 1310nm, -3 dB wavelength range of 90 nm and optical power of 9mw is utilized. Lateral resolution of 8 μm and axial resolution of 7μm at a rate of 2 frames per second and with 102dB sensitivity are achieved in biological tissue. It is shown that OCT images distinguish very well the normal and PWS tissues in clinic and are good to serve as a valuable diagnosis tool for PDT treatment.

  19. Geomorphology of Late Quaternary Mass Movement Deposits using a Decimetre-Resolution 3D Seismic Volume: Case Studies from Windermere, UK, and Trondheimsfjorden, Norway

    Science.gov (United States)

    Vardy, M. E.; Dix, J. K.; Henstock, T.; Bull, J. M.; Pinson, L.; L'Heureux, J.; Longva, O.; Hansen, L.; Chand, S.; Gutowski, M.

    2009-12-01

    We present results from decimetre resolution 3D seismic volumes acquired over Late Quaternary mass movement deposits in both Lake Windermere, UK, and the Trondheim Harbour area, central Norway. Both deposits were imaged using the 3D Chirp sub-bottom profiler, which combines the known, highly repeatable source waveform of Chirp profilers with the coherent processing and interpretation afforded by true 3D seismic volumes. Reflector morphology from these two volumes are used to identify and map structure on scales of 10s cm to 100s metres. This shows the applicability of the method for the interpretation of failure mechanism, flow morphology and depositional style in these two environments. In Windermere, Younger Dryas deposits have been substantially reworked by the episodic redistribution of sediment from the steep lakesides into the basin. Within the 100 x 400 m 3D seismic volume we identify two small debris flow deposits (1500 m3 and 60,000 m3) and one large (500,000 m3) erosive mass flow deposit. These two depositional mechanisms are distinct. The debris flows have high amplitude, chaotic internal reflections, with a high amplitude reflector representing a lower erosional boundary, discontinuous low amplitude top reflector, and thin out rapidly with distance from the lake margin. The thicker mass flow unit lacks internal structure, and has high amplitude top and base reflectors,. In the Trondheim Harbour we image the down-slope extent of three large slide blocks (which have a net volume > 1 x 106 m3), mobilised by a landslide in 1990, in the 100 x 450 m 3D seismic volume. The morphology of these mass movement deposits is distinct again; demonstrating translational failure along a clear slip plane, leaving well defined slide scars, and forming prominent compressional/extensional structures.

  20. Modeling noncontact atomic force microscopy resolution on corrugated surfaces

    Directory of Open Access Journals (Sweden)

    Kristen M. Burson

    2012-03-01

    Full Text Available Key developments in NC-AFM have generally involved atomically flat crystalline surfaces. However, many surfaces of technological interest are not atomically flat. We discuss the experimental difficulties in obtaining high-resolution images of rough surfaces, with amorphous SiO2 as a specific case. We develop a quasi-1-D minimal model for noncontact atomic force microscopy, based on van der Waals interactions between a spherical tip and the surface, explicitly accounting for the corrugated substrate (modeled as a sinusoid. The model results show an attenuation of the topographic contours by ~30% for tip distances within 5 Å of the surface. Results also indicate a deviation from the Hamaker force law for a sphere interacting with a flat surface.

  1. A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: application to ligand prediction

    Directory of Open Access Journals (Sweden)

    Zaslavskiy Mikhail

    2010-02-01

    Full Text Available Abstract Background Predicting which molecules can bind to a given binding site of a protein with known 3D structure is important to decipher the protein function, and useful in drug design. A classical assumption in structural biology is that proteins with similar 3D structures have related molecular functions, and therefore may bind similar ligands. However, proteins that do not display any overall sequence or structure similarity may also bind similar ligands if they contain similar binding sites. Quantitatively assessing the similarity between binding sites may therefore be useful to propose new ligands for a given pocket, based on those known for similar pockets. Results We propose a new method to quantify the similarity between binding pockets, and explore its relevance for ligand prediction. We represent each pocket by a cloud of atoms, and assess the similarity between two pockets by aligning their atoms in the 3D space and comparing the resulting configurations with a convolution kernel. Pocket alignment and comparison is possible even when the corresponding proteins share no sequence or overall structure similarities. In order to predict ligands for a given target pocket, we compare it to an ensemble of pockets with known ligands to identify the most similar pockets. We discuss two criteria to evaluate the performance of a binding pocket similarity measure in the context of ligand prediction, namely, area under ROC curve (AUC scores and classification based scores. We show that the latter is better suited to evaluate the methods with respect to ligand prediction, and demonstrate the relevance of our new binding site similarity compared to existing similarity measures. Conclusions This study demonstrates the relevance of the proposed method to identify ligands binding to known binding pockets. We also provide a new benchmark for future work in this field. The new method and the benchmark are available at http://cbio.ensmp.fr/paris/.

  2. The effect of spatial micro-CT image resolution and surface complexity on the morphological 3D analysis of open porous structures

    Energy Technology Data Exchange (ETDEWEB)

    Pyka, Grzegorz, E-mail: gregory.pyka@mtm.kuleuven.be [Department of Metallurgy and Materials Engineering, KU Leuven, Kasteelpark Arenberg 44 – PB2450, B-3001 Leuven (Belgium); Kerckhofs, Greet [Department of Metallurgy and Materials Engineering, KU Leuven, Kasteelpark Arenberg 44 – PB2450, B-3001 Leuven (Belgium); Biomechanics Research Unit, Université de Liege, Chemin des Chevreuils 1 - BAT 52/3, B-4000 Liège (Belgium); Schrooten, Jan; Wevers, Martine [Department of Metallurgy and Materials Engineering, KU Leuven, Kasteelpark Arenberg 44 – PB2450, B-3001 Leuven (Belgium)

    2014-01-15

    In material science microfocus X-ray computed tomography (micro-CT) is one of the most popular non-destructive techniques to visualise and quantify the internal structure of materials in 3D. Despite constant system improvements, state-of-the-art micro-CT images can still hold several artefacts typical for X-ray CT imaging that hinder further image-based processing, structural and quantitative analysis. For example spatial resolution is crucial for an appropriate characterisation as the voxel size essentially influences the partial volume effect. However, defining the adequate image resolution is not a trivial aspect and understanding the correlation between scan parameters like voxel size and the structural properties is crucial for comprehensive material characterisation using micro-CT. Therefore, the objective of this study was to evaluate the influence of the spatial image resolution on the micro-CT based morphological analysis of three-dimensional (3D) open porous structures with a high surface complexity. In particular the correlation between the local surface properties and the accuracy of the micro-CT-based macro-morphology of 3D open porous Ti6Al4V structures produced by selective laser melting (SLM) was targeted and revealed for rough surfaces a strong dependence of the resulting structure characteristics on the scan resolution. Reducing the surface complexity by chemical etching decreased the sensitivity of the overall morphological analysis to the spatial image resolution and increased the detection limit. This study showed that scan settings and image processing parameters need to be customized to the material properties, morphological parameters under investigation and the desired final characteristics (in relation to the intended functional use). Customization of the scan resolution can increase the reliability of the micro-CT based analysis and at the same time reduce its operating costs. - Highlights: • We examine influence of the image resolution

  3. WE-F-16A-04: Micro-Irradiator Treatment Verification with High-Resolution 3D-Printed Rodent-Morphic Dosimeters

    Energy Technology Data Exchange (ETDEWEB)

    Bache, S; Belley, M [Duke University Medical Physics Graduate Program, Durham, NC (United States); Benning, R; Adamovics, J [Rider University, Lawrenceville, NJ (United States); Stanton, I; Therien, M [Department of Chemistry, Duke University, Durham, NC (United States); Yoshizumi, T [Department of Radiology, Duke University Medical Center, Durham, NC (United States); Department of Radiation Oncology, Duke University Medical Center, Durham, NC (United States); Oldham, M [Department of Radiation Oncology, Duke University Medical Center, Durham, NC (United States)

    2014-06-15

    Purpose: Pre-clinical micro-radiation therapy studies often utilize very small beams (∼0.5-5mm), and require accurate dose delivery in order to effectively investigate treatment efficacy. Here we present a novel high-resolution absolute 3D dosimetry procedure, capable of ∼100-micron isotopic dosimetry in anatomically accurate rodent-morphic phantoms Methods: Anatomically accurate rat-shaped 3D dosimeters were made using 3D printing techniques from outer body contours and spinal contours outlined on CT. The dosimeters were made from a radiochromic plastic material PRESAGE, and incorporated high-Z PRESASGE inserts mimicking the spine. A simulated 180-degree spinal arc treatment was delivered through a 2 step process: (i) cone-beam-CT image-guided positioning was performed to precisely position the rat-dosimeter for treatment on the XRad225 small animal irradiator, then (ii) treatment was delivered with a simulated spine-treatment with a 180-degree arc with 20mm x 10mm cone at 225 kVp. Dose distribution was determined from the optical density change using a high-resolution in-house optical-CT system. Absolute dosimetry was enabled through calibration against a novel nano-particle scintillation detector positioned in a channel in the center of the distribution. Results: Sufficient contrast between regular PRESAGE (tissue equivalent) and high-Z PRESAGE (spinal insert) was observed to enable highly accurate image-guided alignment and targeting. The PRESAGE was found to have linear optical density (OD) change sensitivity with respect to dose (R{sup 2} = 0.9993). Absolute dose for 360-second irradiation at isocenter was found to be 9.21Gy when measured with OD change, and 9.4Gy with nano-particle detector- an agreement within 2%. The 3D dose distribution was measured at 500-micron resolution Conclusion: This work demonstrates for the first time, the feasibility of accurate absolute 3D dose measurement in anatomically accurate rat phantoms containing variable density

  4. SU-E-CAMPUS-T-05: Validation of High-Resolution 3D Patient QA for Proton Pencil Beam Scanning and IMPT by Polymer Gel Dosimetry

    Energy Technology Data Exchange (ETDEWEB)

    Cardin, A; Avery, S; Ding, X; Kassaee, A; Lin, L [University of Pennsylvania, Philadelphia, PA (United States); Maryanski, M [MGS Research, Inc., Madison, CT (United States)

    2014-06-15

    Purpose: Validation of high-resolution 3D patient QA for proton pencil beam scanning and IMPT by polymer gel dosimetry. Methods: Four BANG3Pro polymer gel dosimeters (manufactured by MGS Research Inc, Madison, CT) were used for patient QA at the Robert's Proton Therapy Center (RPTC, Philadelphia, PA). All dosimeters were sealed in identical thin-wall Pyrex glass spheres. Each dosimeter contained a set of markers for 3D registration purposes. The dosimeters were mounted in a consistent and reproducible manner using a custom build holder. Two proton pencil beam scanning plans were designed using Varian Eclipse™ treatment planning system: 1) A two-field intensity modulated proton therapy (IMPT) plan and 2) one single field uniform dose (SFUD) plan. The IMPT fields were evaluated as a composite plan and individual fields, the SFUD plan was delivered as a single field plan.Laser CT scanning was performed using the manufacturer's OCTOPUS-IQ axial transmission laser CT scanner using a 1 mm slice thickness. 3D registration, analysis, and OD/cm to absorbed dose calibrations were perfomed using DICOM RT-Dose and CT files, and software developed by the manufacturer. 3D delta index, a metric equivalent to the gamma tool, was used for dose comparison. Results: Very good agreement with single IMPT fields and with SFUD was obtained. Composite IMPT fields had a less satisfactory agreement. The single fields had 3D delta index passing rates (3% dose difference, 3 mm DTA) of 98.98% and 94.91%. The composite 3D delta index passing rate was 80.80%. The SFUD passing rate was 93.77%. Required shifts of the dose distributions were less than 4 mm. Conclusion: A formulation of the BANG3Pro polymer gel dosimeter, suitable for 3D QA of proton patient plans is established and validated. Likewise, the mailed QA analysis service provided by the manufacturer is a practical option when required resources are unavailable. We fully disclose that the subject of this research regards a

  5. Scalable, incremental learning with MapReduce parallelization for cell detection in high-resolution 3D microscopy data

    KAUST Repository

    Sung, Chul

    2013-08-01

    Accurate estimation of neuronal count and distribution is central to the understanding of the organization and layout of cortical maps in the brain, and changes in the cell population induced by brain disorders. High-throughput 3D microscopy techniques such as Knife-Edge Scanning Microscopy (KESM) are enabling whole-brain survey of neuronal distributions. Data from such techniques pose serious challenges to quantitative analysis due to the massive, growing, and sparsely labeled nature of the data. In this paper, we present a scalable, incremental learning algorithm for cell body detection that can address these issues. Our algorithm is computationally efficient (linear mapping, non-iterative) and does not require retraining (unlike gradient-based approaches) or retention of old raw data (unlike instance-based learning). We tested our algorithm on our rat brain Nissl data set, showing superior performance compared to an artificial neural network-based benchmark, and also demonstrated robust performance in a scenario where the data set is rapidly growing in size. Our algorithm is also highly parallelizable due to its incremental nature, and we demonstrated this empirically using a MapReduce-based implementation of the algorithm. We expect our scalable, incremental learning approach to be widely applicable to medical imaging domains where there is a constant flux of new data. © 2013 IEEE.

  6. [3D-TOF MR-angiography with high spatial resolution for surgical planning in insular lobe gliomas].

    Science.gov (United States)

    Bykanov, A E; Pitskhelauri, D I; Pronin, I N; Tonoyan, A S; Kornienko, V N; Zakharova, N E; Turkin, A M; Sanikidze, A Z; Shkarubo, M A; Shkatova, A M; Shults, E I

    2015-01-01

    Цель — определение эффективности время-пролетной (3D-TOF) магнитно-резонансной ангиографии (МРА) с высоким разрешением в визуализации медиальных и латеральных лентикулостриарных артерий (ЛСА) и их соотношения с краем опухоли у пациентов с глиомами островковой доли. Материал и методы. Проведен анализ 3D-TOF МРА у 20 пациентов с первично выявленными глиомами головного мозга с вовлечением островковой доли. Всем больным выполнена 3D-TOF МРА без контрастного усиления, а в 6 наблюдениях — до и после него. Результаты. При 3D-TOF МРА до внутривенного контрастирования удавалось определить медиальные ЛСА у 19 (95%) пациентов и латеральные ЛСА — у 18 (90%). 3D-TOF МРА на фоне контрастного усиления позволяет лучше визуализировать как проксимальный, так и дистальный сегмент ЛСА. Выделено три варианта взаимоотношения опухоли и ЛСА: I — опухоль обрастала артерии без их смещения — 2 (10%) случая; II — опухоль смещала артерии медиально без признаков обрастания — 11 (55%); III — опухоль частично обрастала и смещала артерии — 2 (10%). У 5 (25%) пациентов опухоль плохо видна на 3D-TOF МРА из-за отсутствия различий сигнальных хар

  7. Fast 3D contrast enhanced MRI of the liver using temporal resolution acceleration with constrained evolution reconstruction.

    Science.gov (United States)

    Xu, Bo; Spincemaille, Pascal; Chen, Gang; Agrawal, Mukta; Nguyen, Thanh D; Prince, Martin R; Wang, Yi

    2013-02-01

    Time-resolved imaging is crucial for the accurate diagnosis of liver lesions. Current contrast enhanced liver magnetic resonance imaging acquires a few phases in sequential breath-holds. The image quality is susceptible to bolus timing errors, which could result in missing the critical arterial phase. This impairs the detection of malignant tumors that are supplied primarily by the hepatic artery. In addition, the temporal resolution may be too low to reliably separate the arterial phase from the portal venous phase. In this study, a method called temporal resolution acceleration with constrained evolution reconstruction was developed with three-dimensional volume coverage and high-temporal frame rate. Data is acquired using a stack of spirals sampling trajectory combined with a golden ratio view order using an eight-channel coil array. Temporal frames are reconstructed from vastly undersampled data sets using a nonlinear inverse algorithm assuming that the temporal changes are small at short time intervals. Numerical and phantom experimental validation is presented. Preliminary in vivo results demonstrated high spatial resolution dynamic three-dimensional images of the whole liver with high frame rates, from which numerous subarterial phases could be easily identified retrospectively.

  8. Comparison of 3D Maximum A Posteriori and Filtered Backprojection algorithms for high resolution animal imaging in microPET

    Energy Technology Data Exchange (ETDEWEB)

    Chatziioannou, A.; Qi, J.; Moore, A.; Annala, A.; Nguyen, K.; Leahy, R.M.; Cherry, S.R.

    2000-01-01

    We have evaluated the performance of two three dimensional reconstruction algorithms with data acquired from microPET, a high resolution tomograph dedicated to small animal imaging. The first was a linear filtered-backprojection algorithm (FBP) with reprojection of the missing data and the second was a statistical maximum-aposteriori probability algorithm (MAP). The two algorithms were evaluated in terms of their resolution performance, both in phantoms and in vivo. Sixty independent realizations of a phantom simulating the brain of a baby monkey were acquired, each containing 3 million counts. Each of these realizations was reconstructed independently with both algorithms. The ensemble of the sixty reconstructed realizations was used to estimate the standard deviation as a measure of the noise for each reconstruction algorithm. More detail was recovered in the MAP reconstruction without an increase in noise relative to FBP. Studies in a simple cylindrical compartment phantom demonstrated improved recovery of known activity ratios with MAP. Finally in vivo studies also demonstrated a clear improvement in spatial resolution using the MAP algorithm. The quantitative accuracy of the MAP reconstruction was also evaluated by comparison with autoradiography and direct well counting of tissue samples and was shown to be superior.

  9. Atomic resolution imaging and spectroscopy of barium atoms and functional groups on graphene oxide

    Energy Technology Data Exchange (ETDEWEB)

    Boothroyd, C.B., E-mail: ChrisBoothroyd@cantab.net [Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Grünberg Institute, Forschungszentrum Jülich, D-52425 Jülich (Germany); Moreno, M.S. [Centro Atómico Bariloche, 8400 – San Carlos de Bariloche (Argentina); Duchamp, M.; Kovács, A. [Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Grünberg Institute, Forschungszentrum Jülich, D-52425 Jülich (Germany); Monge, N.; Morales, G.M.; Barbero, C.A. [Department of Chemistry, Universidad Nacional de Río Cuarto, X5804BYA Río Cuarto (Argentina); Dunin-Borkowski, R.E. [Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Grünberg Institute, Forschungszentrum Jülich, D-52425 Jülich (Germany)

    2014-10-15

    We present an atomic resolution transmission electron microscopy (TEM) and scanning TEM (STEM) study of the local structure and composition of graphene oxide modified with Ba{sup 2+}. In our experiments, which are carried out at 80 kV, the acquisition of contamination-free high-resolution STEM images is only possible while heating the sample above 400 °C using a highly stable heating holder. Ba atoms are identified spectroscopically in electron energy-loss spectrum images taken at 800 °C and are associated with bright contrast in high-angle annular dark-field STEM images. The spectrum images also show that Ca and O occur together and that Ba is not associated with a significant concentration of O. The electron dose used for spectrum imaging results in beam damage to the specimen, even at elevated temperature. It is also possible to identify Ba atoms in high-resolution TEM images acquired using shorter exposure times at room temperature, thereby allowing the structure of graphene oxide to be studied using complementary TEM and STEM techniques over a wide range of temperatures. - Highlights: • Graphene oxide modified with Ba{sup 2+} was imaged using TEM and STEM at 80 kV. • High-resolution images and spectra were obtained only by heating above 400 °C. • Elemental maps show the distribution of C, Ba, O and Ca on the graphene oxide. • Single Ba atoms were identified in STEM HAADF and HRTEM images.

  10. Application of the Minkowski functionals in 3D to high-resolution MR images of trabecular bone: prediction of the biomechanical strength by nonlinear topological measures

    Science.gov (United States)

    Boehm, Holger F.; Link, Thomas M.; Monetti, Roberto A.; Mueller, Dirk; Rummeny, Ernst J.; Newitt, David; Majumdar, Sharmila; Raeth, Christoph W.

    2004-05-01

    Multi-dimensional convex objects can be characterized with respect to shape, structure, and the connectivity of their components using a set of morphological descriptors known as the Minkowski functionals. In a 3D Euclidian space, these correspond to volume, surface area, mean integral curvature, and the Euler-Poincaré characteristic. We introduce the Minkowski functionals to medical image processing for the morphological analysis of trabecular bone tissue. In the context of osteoporosis-a metabolic disorder leading to a weakening of bone due to deterioration of micro-architecture-the structure of bone increasingly gains attention in the quantification of bone quality. The trabecular architecture of healthy cancellous bone consists of a complex 3D system of inter-connected mineralised elements whereas in osteoporosis the micro-structure is dominated by gaps and disconnections. At present, the standard parameter for diagnosis and assessment of fracture risk in osteoporosis is the bone mineral density (BMD) - a bulk measure of mineralisation irrespective of structural texture characteristics. With the development of modern imaging modalities (high resolution MRI, micro-CT) with spatial resolutions allowing to depict individual trabeculae bone micro-architecture has successfully been analysed using linear, 2- dimensional structural measures adopted from standard histo-morphometry. The preliminary results of our study demonstrate that due to the complex - i.e. the non-linear - network of trabecular bone structures non-linear measures in 3D are superior to linear ones in predicting mechanical properties of trabecular bone from structural information extracted from high resolution MR image data.

  11. Experimental electronic structure and Fermi-surface instability of the correlated 3d sulphide BaVS3 : High-resolution angle-resolved photoemission spectroscopy

    Science.gov (United States)

    Mitrovic, S.; Fazekas, P.; Søndergaard, C.; Ariosa, D.; Barišić, N.; Berger, H.; Cloëtta, D.; Forró, L.; Höchst, H.; Kupčić, I.; Pavuna, D.; Margaritondo, G.

    2007-04-01

    The correlated 3d sulphide BaVS3 exhibits an interesting coexistence of one-dimensional and three-dimensional properties. Our experiments determine the electronic band structure and shed light on this puzzle. High-resolution angle-resolved photoemission measurements in a 4-eV -wide range below the Fermi energy level uncover and investigate the coexistence of a1g wide-band and eg narrow-band d electrons, which lead to the complicated electronic properties of this material. We explore the effects of strong correlations and the Fermi surface instability associated with the metal-insulator transition.

  12. Three-Dimensional (3-D) Atom Probe Tomography of a Cu-Precipitation-Strengthened, Ultrahigh-Strength Carburized Steel

    Science.gov (United States)

    Tiemens, Benjamin L.; Sachdev, Anil K.; Mishra, Raja K.; Olson, Gregory B.

    2012-10-01

    In an effort to reduce material cost, experimental steel alloys were developed that incorporated Cu precipitation in lieu of costly Co alloying additions in secondary hardening carburizing gear steels. This work utilizes three-dimensional atom probe tomography to study one of these prototype alloys and quantify the nanoscale dispersions of body-centered cubic (bcc) Cu and M2C alloy carbides used to strengthen these steels. The temporal evolution of precipitate, size, morphology, and interprecipitate interactions were studied for various tempering times. Findings suggest that Cu precipitation does act as a catalyst for heterogeneous nucleation of M2C carbides at relatively high hardness levels; however, the resultant volume fraction of strengthening carbides was noticeably less than that predicted by thermodynamic equilibrium calculations, indicating a reduced potency compared with Co-assisted precipitation. Microstructural information such as precipitate size and volume fraction was measured at the peak hardness condition and successfully used to recalibrate alloy design models for subsequent alloy design iterations.

  13. Near-interface Si substrate 3d metal contamination during atomic layer deposition processing detected by electron spin resonance

    Science.gov (United States)

    Nguyen, A. P. D.; Stesmans, A.; Hiller, D.; Zacharias, M.

    2012-06-01

    A K- and Q-band electron spin resonance (ESR) study has been carried out on (100)Si/SiO2 entities manufactured by low temperature (150 °C) atomic layer deposition (ALD) of a high-quality SiO2 layer on Si using 3-aminopropyltriethoxysilane, H2O, and ozone in a three-step process. Whereas previous work has demonstrated the high quality of the deposited SiO2 layer, the current ESR analysis reports on the tracing of growth-related contamination of near interface Si substrate layers by two transition metals. This includes, first, detection of the signal of interstitial Cr+ (S = 5/2) impurities in c-Si, characterized by an isotropic central g value of 1.9980 ± 0.0002, an isotropic 53Cr (I = 3/2) hyperfine interaction of splitting Aiso = 11.8 G, and cubic crystal field splitting parameter a = +32.2 G, well in agreement with the known bulk c-Si case; A small anisotropic contribution to the hyperfine interaction has additionally been revealed. The total Cr+ defect density is inferred as ˜5 × 1011 cm-2. Second, a single signal is observed at isotropic g = 2.070 ± 0.001, corresponding to interstitial Fe impurities (Fei)0 (S = 1) positioned in a c-Si matrix. Defect density depth profiling reveals the impurities to be confined to a few μm thick Si substrate top layer, the density decaying exponential-like from the Si/SiO2 interface inward the Si substrate. The total of the results points to a contamination of reactor-environment origin, connected with the layer deposition process. It concerns a weak contamination, in which detection the ESR technique emerges as a powerful technique able to unveil very low levels of contamination of near-surface Si substrate layers.

  14. Assessment of Image Processing and Resolution on Permeability and Drainage Simulations Through 3D Pore-networks Obtained Using X-ray Computed Tomography

    Science.gov (United States)

    Mills, G.; Willson, C. S.; Thompson, K. E.; Rivers, M. L.

    2013-12-01

    Typically, continuum-scale flow parameters are obtained through laboratory experiments. Over the past several years, image-based modeling, which is a direct simulation of flow through the structural arrangements of the voids and solids obtained using X-ray computed tomography (XCT) in a sample porous medium, has become a reliable technique for predicting certain flow parameters. Even though XCT is capable of resolving micron-level details, the voxel resolution of the reconstructed image is still dependent upon a number of factors, including the sample size, X-ray energy and XCT beamline setup. Thus, each imaging experiment requires a tradeoff between the sample size that can be imaged, the voxel resolution, and the length scale of the pore space that can be extracted. In addition, the geometric and topological properties of the void space and 3D pore network structure are dictated by the image processing and the choice of pore network generation method. In this research, image-based pore network models are used to quantitatively assess the impact of image resolution, image processing and the choice of pore network generation methods on simulated parameters. A 5 mm diameter and ~15 mm in length Berea sandstone core was scanned two times. First, a ~12 mm long section of the entire cross-section was scanned at 4.1 micron voxel resolution; next, a ~1.4 mm diameter and ~4.12 mm length section within the 1st domain was scanned at 1 micron voxel resolution. The resulting 3D datasets were filtered and segmented into solid and void space. The low resolution image was filtered and segmented using two different approaches in order to evaluate the potential of each approach in identifying the different solid phases in the original 16 bit dataset. A set of networks were created by varying the pore density on both the high and low resolution datasets in order to assess the impact of these factors on flow simulations. Single-phase permeability and a two-phase drainage pore

  15. A numerical study of super-resolution through fast 3D wideband algorithm for scattering in highly-heterogeneous media

    KAUST Repository

    Létourneau, Pierre-David

    2016-09-19

    We present a wideband fast algorithm capable of accurately computing the full numerical solution of the problem of acoustic scattering of waves by multiple finite-sized bodies such as spherical scatterers in three dimensions. By full solution, we mean that no assumption (e.g. Rayleigh scattering, geometrical optics, weak scattering, Born single scattering, etc.) is necessary regarding the properties of the scatterers, their distribution or the background medium. The algorithm is also fast in the sense that it scales linearly with the number of unknowns. We use this algorithm to study the phenomenon of super-resolution in time-reversal refocusing in highly-scattering media recently observed experimentally (Lemoult et al., 2011), and provide numerical arguments towards the fact that such a phenomenon can be explained through a homogenization theory.

  16. SU-E-T-296: Dosimetric Analysis of Small Animal Image-Guided Irradiator Using High Resolution Optical CT Imaging of 3D Dosimeters

    Energy Technology Data Exchange (ETDEWEB)

    Na, Y; Qian, X; Wuu, C [Columbia University, New York, NY (United States); Adamovics, J [John Adamovics, Skillman, NJ (United States)

    2015-06-15

    Purpose: To verify the dosimetric characteristics of a small animal image-guided irradiator using a high-resolution of optical CT imaging of 3D dosimeters. Methods: PRESAEGE 3D dosimeters were used to determine dosimetric characteristics of a small animal image-guided irradiator and compared with EBT2 films. Cylindrical PRESAGE dosimeters with 7cm height and 6cm diameter were placed along the central axis of the beam. The films were positioned between 6×6cm{sup 2} cubed plastic water phantoms perpendicular to the beam direction with multiple depths. PRESAGE dosimeters and EBT2 films were then irradiated with the irradiator beams at 220kVp and 13mA. Each of irradiated PRESAGE dosimeters named PA1, PA2, PB1, and PB2, was independently scanned using a high-resolution single laser beam optical CT scanner. The transverse images were reconstructed with a 0.1mm high-resolution pixel. A commercial Epson Expression 10000XL flatbed scanner was used for readout of irradiated EBT2 films at a 0.4mm pixel resolution. PDD curves and beam profiles were measured for the irradiated PRESAGE dosimeters and EBT2 films. Results: The PDD agreements between the irradiated PRESAGE dosimeter PA1, PA2, PB1, PB2 and the EB2 films were 1.7, 2.3, 1.9, and 1.9% for the multiple depths at 1, 5, 10, 15, 20, 30, 40 and 50mm, respectively. The FWHM measurements for each PRESAEGE dosimeter and film agreed with 0.5, 1.1, 0.4, and 1.7%, respectively, at 30mm depth. Both PDD and FWHM measurements for the PRESAGE dosimeters and the films agreed overall within 2%. The 20%–80% penumbral widths of each PRESAGE dosimeter and the film at a given depth were respectively found to be 0.97, 0.91, 0.79, 0.88, and 0.37mm. Conclusion: Dosimetric characteristics of a small animal image-guided irradiator have been demonstrated with the measurements of PRESAGE dosimeter and EB2 film. With the high resolution and accuracy obtained from this 3D dosimetry system, precise targeting small animal irradiation can be

  17. Electron impact induced collective and atomic-like single-electron Ga3d → εl excitations in GaAsN alloy

    Energy Technology Data Exchange (ETDEWEB)

    Mikoushkin, V.M., E-mail: V.Mikoushkin@mail.ioffe.ru

    2015-07-01

    Nitride nanolayer of about 4 nm thickness formed on the GaAs (1 0 0) surface by N{sub 2}{sup +} ion bombardment with energy E{sub i} = 2500 eV has been studied in situ by electron energy loss spectroscopy (EELS). Collective (plasmonic) and single-electron excitations were resolved in the EELS spectrum. Analysis of the plasmonic contributions from different chemical phases showed domination of the phase of GaAsN alloy in the nitrated layer. Single-electron excitations were shown to be related to the transitions from core- and valence band states into unoccupied local atomic-like states Ga3d → εl and “GaAs4p” → εl. The model of the atomic-like state formation in a temporary quantum dot near Ga atom was assumed. It has been shown that analysis of collective and single-electron excitations enables synchronous EELS diagnostics of both the chemical composition and unoccupied states of GaAs nitrides.

  18. SU-C-BRE-04: Microbeam-Radiation-Therapy (MRT): Characterizing a Novel MRT Device Using High Resolution 3D Dosimetry

    Energy Technology Data Exchange (ETDEWEB)

    Li, Q [Duke University, Durham, NC (United States); Juang, T; Bache, S [Durham, NC (United States); Chang, S [UNC School of Medicine, Chapel Hill, NC (United States); Oldham, M [Duke University Medical Center, Durham, NC (United States)

    2014-06-15

    Purpose: The feasibility of MRT has recently been demonstrated utilizing a new technology of Carbon-Nano-Tube(CNT) field emission x-ray sources.This approach can deliver very high dose(10's of Gy) in narrow stripes(sub-mm) of radiation which enables the study of novel radiation treatment approaches. Here we investigate the application of highresolution (50um isotropic) PRESAGE/Optical-CT 3D dosimetry techniques to characterize the radiation delivered in this extremely dosimetrically challenging scenario. Methods: The CNT field emission x-ray source irradiator comprises of a linear cathode array and a novel collimator alignment system. This allows a precise delivery of high-energy small beams up to 160 kVp. A cylindrical dosimeter (∼2.2cm in height ∼2.5cm in diameter) was irradiated by CNT MRT delivering 3 strips of radiation with a nominal entrance dose of 32 Gy.A second dosimeter was irradiated with similar entrance dose, with a regular x-ray irradiator collimated to microscopical strip-beams. 50um (isotropic) 3D dosimetry was performed using an in-house optical-CT system designed and optimized for high resolution imaging (including a stray light deconvolution correction).The percentage depth dose (PDD), peak-to-valley ratio (PVR) and beam width (FWHM) data were obtained and analyzed in both cases. Results: High resolution 3D images were successfully achieved with the prototype system, enabling extraction of PDD and dose profiles. The PDDs for the CNT irradiation showed pronounced attenuation, but less build-up effect than that from the multibeam irradiation. The beam spacing between the three strips has an average value of 0.9mm while that for the 13 strips is 1.5 mm at a depth of 16.5 mm. The stray light corrected image shows line profiles with reduced noise and consistent PVR values. Conclusion: MRT dosimetry is extremely challenging due to the ultra small fields involved.This preliminary application of a novel, ultra-high resolution, optical-CT 3D

  19. Real-time high resolution 3D imaging of the lyme disease spirochete adhering to and escaping from the vasculature of a living host.

    Science.gov (United States)

    Moriarty, Tara J; Norman, M Ursula; Colarusso, Pina; Bankhead, Troy; Kubes, Paul; Chaconas, George

    2008-06-20

    Pathogenic spirochetes are bacteria that cause a number of emerging and re-emerging diseases worldwide, including syphilis, leptospirosis, relapsing fever, and Lyme borreliosis. They navigate efficiently through dense extracellular matrix and cross the blood-brain barrier by unknown mechanisms. Due to their slender morphology, spirochetes are difficult to visualize by standard light microscopy, impeding studies of their behavior in situ. We engineered a fluorescent infectious strain of Borrelia burgdorferi, the Lyme disease pathogen, which expressed green fluorescent protein (GFP). Real-time 3D and 4D quantitative analysis of fluorescent spirochete dissemination from the microvasculature of living mice at high resolution revealed that dissemination was a multi-stage process that included transient tethering-type associations, short-term dragging interactions, and stationary adhesion. Stationary adhesions and extravasating spirochetes were most commonly observed at endothelial junctions, and translational motility of spirochetes appeared to play an integral role in transendothelial migration. To our knowledge, this is the first report of high resolution 3D and 4D visualization of dissemination of a bacterial pathogen in a living mammalian host, and provides the first direct insight into spirochete dissemination in vivo.

  20. Real-time high resolution 3D imaging of the lyme disease spirochete adhering to and escaping from the vasculature of a living host.

    Directory of Open Access Journals (Sweden)

    Tara J Moriarty

    2008-06-01

    Full Text Available Pathogenic spirochetes are bacteria that cause a number of emerging and re-emerging diseases worldwide, including syphilis, leptospirosis, relapsing fever, and Lyme borreliosis. They navigate efficiently through dense extracellular matrix and cross the blood-brain barrier by unknown mechanisms. Due to their slender morphology, spirochetes are difficult to visualize by standard light microscopy, impeding studies of their behavior in situ. We engineered a fluorescent infectious strain of Borrelia burgdorferi, the Lyme disease pathogen, which expressed green fluorescent protein (GFP. Real-time 3D and 4D quantitative analysis of fluorescent spirochete dissemination from the microvasculature of living mice at high resolution revealed that dissemination was a multi-stage process that included transient tethering-type associations, short-term dragging interactions, and stationary adhesion. Stationary adhesions and extravasating spirochetes were most commonly observed at endothelial junctions, and translational motility of spirochetes appeared to play an integral role in transendothelial migration. To our knowledge, this is the first report of high resolution 3D and 4D visualization of dissemination of a bacterial pathogen in a living mammalian host, and provides the first direct insight into spirochete dissemination in vivo.

  1. High resolution atomic force microscopy of double-stranded RNA

    Science.gov (United States)

    Ares, Pablo; Fuentes-Perez, Maria Eugenia; Herrero-Galán, Elías; Valpuesta, José M.; Gil, Adriana; Gomez-Herrero, Julio; Moreno-Herrero, Fernando

    2016-06-01

    Double-stranded (ds) RNA mediates the suppression of specific gene expression, it is the genetic material of a number of viruses, and a key activator of the innate immune response against viral infections. The ever increasing list of roles played by dsRNA in the cell and its potential biotechnological applications over the last decade has raised an interest for the characterization of its mechanical properties and structure, and that includes approaches using Atomic Force Microscopy (AFM) and other single-molecule techniques. Recent reports have resolved the structure of dsDNA with AFM at unprecedented resolution. However, an equivalent study with dsRNA is still lacking. Here, we have visualized the double helix of dsRNA under near-physiological conditions and at sufficient resolution to resolve the A-form sub-helical pitch periodicity. We have employed different high-sensitive force-detection methods and obtained images with similar spatial resolution. Therefore, we show here that the limiting factors for high-resolution AFM imaging of soft materials in liquid medium are, rather than the imaging mode, the force between the tip and the sample and the sharpness of the tip apex.Double-stranded (ds) RNA mediates the suppression of specific gene expression, it is the genetic material of a number of viruses, and a key activator of the innate immune response against viral infections. The ever increasing list of roles played by dsRNA in the cell and its potential biotechnological applications over the last decade has raised an interest for the characterization of its mechanical properties and structure, and that includes approaches using Atomic Force Microscopy (AFM) and other single-molecule techniques. Recent reports have resolved the structure of dsDNA with AFM at unprecedented resolution. However, an equivalent study with dsRNA is still lacking. Here, we have visualized the double helix of dsRNA under near-physiological conditions and at sufficient resolution to

  2. Linear Response Equilibrium versus echo-planar encoding for fast high-spatial resolution 3D chemical shift imaging

    Science.gov (United States)

    Fischer, Rudolf Fritz; Baltes, Christof; Weiss, Kilian; Pazhenkottil, Aju; Rudin, Markus; Boesiger, Peter; Kozerke, Sebastian

    2011-07-01

    In this work Linear Response Equilibrium (LRE) and Echo-planar spectroscopic imaging (EPSI) are compared in terms of sensitivity per unit time and power deposition. In addition an extended dual repetition time scheme to generate broad stopbands for improved inherent water suppression in LRE is presented. The feasibility of LRE and EPSI for assessing cholesterol esters in human carotid plaques with high spatial resolution of 1.95 × 1.15 × 1.15 mm 3 on a clinical 3T MR system is demonstrated. In simulations and phantom experiments it is shown that LRE has comparable but lower sensitivity per unit time relative to EPSI despite stronger signal generated. This relates to the lower sampling efficiency in LRE relative to EPSI as a result of limited gradient performance on clinical MR systems. At the same time, power deposition of LRE is significantly reduced compared to EPSI making it an interesting niche application for in vivo high field spectroscopic imaging of metabolites within a limited bandwidth.

  3. Dopant-induced 2D-3D transition in small Au-containing clusters: DFT-global optimisation of 8-atom Au-Ag nanoalloys.

    Science.gov (United States)

    Heiles, Sven; Logsdail, Andrew J; Schäfer, Rolf; Johnston, Roy L

    2012-02-21

    A genetic algorithm (GA) coupled with density functional theory (DFT) calculations is used to perform global optimisations for all compositions of 8-atom Au-Ag bimetallic clusters. The performance of this novel GA-DFT approach for bimetallic nanoparticles is tested for structures reported in the literature. New global minimum structures for various compositions are predicted and the 2D-3D transition is located. Results are explained with the aid of an analysis of the electronic density of states. The chemical ordering of the predicted lowest energy isomers are explained via a detailed analysis of the charge separation and mixing energies of the bimetallic clusters. Finally, dielectric properties are computed and the composition and dimensionality dependence of the electronic polarizability and dipole moment is discussed, enabling predictions to be made for future electric beam deflection experiments.

  4. A combination of pharmacophore modeling, atom-based 3D-QSAR, molecular docking and molecular dynamics simulation studies on PDE4 enzyme inhibitors.

    Science.gov (United States)

    Tripuraneni, Naga Srinivas; Azam, Mohammed Afzal

    2016-11-01

    Phosphodiesterases 4 enzyme is an attractive target for the design of anti-inflammatory and bronchodilator agents. In the present study, pharmacophore and atom-based 3D-QSAR studies were carried out for pyrazolopyridine and quinoline derivatives using Schrödinger suite 2014-3. A four-point pharmacophore model was developed using 74 molecules having pIC50 ranging from 10.1 to 4.5. The best four feature model consists of one hydrogen bond acceptor, two aromatic rings, and one hydrophobic group. The pharmacophore hypothesis yielded a statistically significant 3D-QSAR model, with a high correlation coefficient (R(2 )= .9949), cross validation coefficient (Q(2 )= .7291), and Pearson-r (.9107) at six component partial least square factor. The external validation indicated that our QSAR model possessed high predictive power with R(2) value of .88. The generated model was further validated by enrichment studies using the decoy test. Molecular docking, free energy calculation, and molecular dynamics (MD) simulation studies have been performed to explore the putative binding modes of these ligands. A 10-ns MD simulation confirmed the docking results of both stability of the 1XMU-ligand complex and the presumed active conformation. Outcomes of the present study provide insight in designing novel molecules with better PDE4 inhibitory activity.

  5. R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server.

    Science.gov (United States)

    Cannone, Jamie J; Sweeney, Blake A; Petrov, Anton I; Gutell, Robin R; Zirbel, Craig L; Leontis, Neocles

    2015-07-01

    The RNA 3D Structure-to-Multiple Sequence Alignment Server (R3D-2-MSA) is a new web service that seamlessly links RNA three-dimensional (3D) structures to high-quality RNA multiple sequence alignments (MSAs) from diverse biological sources. In this first release, R3D-2-MSA provides manual and programmatic access to curated, representative ribosomal RNA sequence alignments from bacterial, archaeal, eukaryal and organellar ribosomes, using nucleotide numbers from representative atomic-resolution 3D structures. A web-based front end is available for manual entry and an Application Program Interface for programmatic access. Users can specify up to five ranges of nucleotides and 50 nucleotide positions per range. The R3D-2-MSA server maps these ranges to the appropriate columns of the corresponding MSA and returns the contents of the columns, either for display in a web browser or in JSON format for subsequent programmatic use. The browser output page provides a 3D interactive display of the query, a full list of sequence variants with taxonomic information and a statistical summary of distinct sequence variants found. The output can be filtered and sorted in the browser. Previous user queries can be viewed at any time by resubmitting the output URL, which encodes the search and re-generates the results. The service is freely available with no login requirement at http://rna.bgsu.edu/r3d-2-msa.

  6. A high resolution 3D velocity model beneath the Tokyo Metropolitan area by MeSO-net

    Science.gov (United States)

    Nakagawa, S.; Sakai, S.; Honda, R.; Kimura, H.; Hirata, N.

    2015-12-01

    Beneath the Tokyo metropolitan area, the Philippine Sea Plate (PSP) subducts and causes devastating mega-thrust earthquakes, such as the 1703 Genroku earthquake (M8.0) and the 1923 Kanto earthquake (M7.9). An M7 or greater (M7+) earthquake in this area at present has high potential to produce devastating serious loss of life and property with even greater global economic repercussions. The Central Disaster Management Council of Japan estimates that an M7+ earthquake will cause 23,000 fatalities and 95 trillion yen (about 1 trillion US$) economic loss. We have launched the Special Project for Reducing Vulnerability for Urban Mega Earthquake Disasters in collaboration with scientists, engineers, and social-scientists in nationwide institutions since 2012. We analyze data from the dense seismic array called Metropolitan Seismic Observation network (MeSO-net), which has 296 seismic stations with spacing of 5 km (Sakai and Hirata, 2009; Kasahara et al., 2009). We applied the double-difference tomography method (Zhang and Thurber, 2003) and estimated the velocity structure and the upper boundary of PSP (Nakagawa et al., 2010). The 2011 Tohoku-oki earthquake (M9.0) has activated seismicity also in Kanto region, providing better coverage of ray paths for tomographic analysis. We obtain much higher resolution velocity models from whole dataset observed by MeSO-net between 2008 and 2015. A detailed image of tomograms shows that PSP contacts Pacific plate at a depth of 50 km beneath northern Tokyo bay. A variation of velocity along the oceanic crust suggests dehydration reaction to produce seismicity in a slab, which may related to the M7+ earthquake. Acknowledgement: This study was supported by the Special Project for Reducing Vulnerability for Urban Mega Earthquake Disasters of MEXT, Japan and the Earthquake Research Institute cooperative research program.

  7. Efficient fully 3D list-mode TOF PET image reconstruction using a factorized system matrix with an image domain resolution model

    Science.gov (United States)

    Zhou, Jian; Qi, Jinyi

    2014-01-01

    A factorized system matrix utilizing an image domain resolution model is attractive in fully 3D TOF PET image reconstruction using list-mode data. In this paper, we study a factored model based on sparse matrix factorization that is comprised primarily of a simplified geometrical projection matrix and an image blurring matrix. Beside the commonly-used Siddon's raytracer, we propose another more simplified geometrical projector based on the Bresenham's raytracer which further reduces the computational cost. We discuss in general how to obtain an image blurring matrix associated with a geometrical projector, and provide theoretical analysis that can be used to inspect the efficiency in model factorization. In simulation studies, we investigate the performance of the proposed sparse factorization model in terms of spatial resolution, noise properties and computational cost. The quantitative results reveal that the factorization model can be as efficient as a nonfactored model such as the analytical model while its computational cost can be much lower. In addition we conduct Monte Carlo simulations to identify the conditions under which the image resolution model can become more efficient in terms of image contrast recovery. We verify our observations using the provided theoretical analysis. The result offers a general guide to achieve optimal reconstruction performance based on a sparse factorization model with an only image domain resolution model. PMID:24434568

  8. Efficient fully 3D list-mode TOF PET image reconstruction using a factorized system matrix with an image domain resolution model.

    Science.gov (United States)

    Zhou, Jian; Qi, Jinyi

    2014-02-07

    A factorized system matrix utilizing an image domain resolution model is attractive in fully 3D time-of-flight PET image reconstruction using list-mode data. In this paper, we study a factored model based on sparse matrix factorization that is comprised primarily of a simplified geometrical projection matrix and an image blurring matrix. Beside the commonly-used Siddon's ray-tracer, we propose another more simplified geometrical projector based on the Bresenham's ray-tracer which further reduces the computational cost. We discuss in general how to obtain an image blurring matrix associated with a geometrical projector, and provide theoretical analysis that can be used to inspect the efficiency in model factorization. In simulation studies, we investigate the performance of the proposed sparse factorization model in terms of spatial resolution, noise properties and computational cost. The quantitative results reveal that the factorization model can be as efficient as a non-factored model, while its computational cost can be much lower. In addition we conduct Monte Carlo simulations to identify the conditions under which the image resolution model can become more efficient in terms of image contrast recovery. We verify our observations using the provided theoretical analysis. The result offers a general guide to achieve the optimal reconstruction performance based on a sparse factorization model with an image domain resolution model.

  9. 3D Spectroscopic Instrumentation

    CERN Document Server

    Bershady, Matthew A

    2009-01-01

    In this Chapter we review the challenges of, and opportunities for, 3D spectroscopy, and how these have lead to new and different approaches to sampling astronomical information. We describe and categorize existing instruments on 4m and 10m telescopes. Our primary focus is on grating-dispersed spectrographs. We discuss how to optimize dispersive elements, such as VPH gratings, to achieve adequate spectral resolution, high throughput, and efficient data packing to maximize spatial sampling for 3D spectroscopy. We review and compare the various coupling methods that make these spectrographs ``3D,'' including fibers, lenslets, slicers, and filtered multi-slits. We also describe Fabry-Perot and spatial-heterodyne interferometers, pointing out their advantages as field-widened systems relative to conventional, grating-dispersed spectrographs. We explore the parameter space all these instruments sample, highlighting regimes open for exploitation. Present instruments provide a foil for future development. We give an...

  10. Demonstration of a Novel, Integrated, Multi-Scale Procedure for High-Resolution 3D Reservoir Characterization and Improved CO2-EOR/Sequestration Management, SACROC Unit

    Energy Technology Data Exchange (ETDEWEB)

    Scott R. Reeves

    2007-09-30

    The primary goal of this project was to demonstrate a new and novel approach for high resolution, 3D reservoir characterization that can enable better management of CO{sub 2} enhanced oil recovery (EOR) projects and, looking to the future, carbon sequestration projects. The approach adopted has been the subject of previous research by the DOE and others, and relies primarily upon data-mining and advanced pattern recognition approaches. This approach honors all reservoir characterization data collected, but accepts that our understanding of how these measurements relate to the information of most interest, such as how porosity and permeability vary over a reservoir volume, is imperfect. Ideally the data needed for such an approach includes surface seismic to provide the greatest amount of data over the entire reservoir volume of interest, crosswell seismic to fill the resolution gap between surface seismic and wellbore-scale measurements, geophysical well logs to provide the vertical resolution sought, and core data to provide the tie to the information of most interest. These data are combined via a series of one or more relational models to enable, in its most successful application, the prediction of porosity and permeability on a vertical resolution similar to logs at each surface seismic trace location. In this project, the procedure was applied to the giant (and highly complex) SACROC unit of the Permian basin in West Texas, one of the world's largest CO{sub 2}-EOR projects and a potentially world-class geologic sequestration site. Due to operational scheduling considerations on the part of the operator of the field, the crosswell data was not obtained during the period of project performance (it is currently being collected however as part of another DOE project). This compromised the utility of the surface seismic data for the project due to the resolution gap between it and the geophysical well logs. An alternative approach was adopted that utilized a

  11. Comprehensive Non-Destructive Conservation Documentation of Lunar Samples Using High-Resolution Image-Based 3D Reconstructions and X-Ray CT Data

    Science.gov (United States)

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

    2015-01-01

    Established contemporary conservation methods within the fields of Natural and Cultural Heritage encourage an interdisciplinary approach to preservation of heritage material (both tangible and intangible) that holds "Outstanding Universal Value" for our global community. NASA's lunar samples were acquired from the moon for the primary purpose of intensive scientific investigation. These samples, however, also invoke cultural significance, as evidenced by the millions of people per year that visit lunar displays in museums and heritage centers around the world. Being both scientifically and culturally significant, the lunar samples require a unique conservation approach. Government mandate dictates that NASA's Astromaterials Acquisition and Curation Office develop and maintain protocols for "documentation, preservation, preparation and distribution of samples for research, education and public outreach" for both current and future collections of astromaterials. Documentation, considered the first stage within the conservation methodology, has evolved many new techniques since curation protocols for the lunar samples were first implemented, and the development of new documentation strategies for current and future astromaterials is beneficial to keeping curation protocols up to date. We have developed and tested a comprehensive non-destructive documentation technique using high-resolution image-based 3D reconstruction and X-ray CT (XCT) data in order to create interactive 3D models of lunar samples that would ultimately be served to both researchers and the public. These data enhance preliminary scientific investigations including targeted sample requests, and also provide a new visual platform for the public to experience and interact with the lunar samples. We intend to serve these data as they are acquired on NASA's Astromaterials Acquisistion and Curation website at http://curator.jsc.nasa.gov/. Providing 3D interior and exterior documentation of astromaterial

  12. Sea level history in 3D: Data acquisition and processing for an ultra-high resolution MCS survey across IODP Expedition 313 drillsite

    Science.gov (United States)

    Nedimovic, M. R.; Mountain, G. S.; Austin, J. A., Jr.; Fulthorpe, C.; Aali, M.; Baldwin, K.; Bhatnagar, T.; Johnson, C.; Küçük, H. M.; Newton, A.; Stanley, J.

    2015-12-01

    In June-July 2015, we acquired the first 3D/2D hybrid (short/long streamer) multichannel seismic (MCS) reflection dataset. These data were collected simultaneously across IODP Exp. 313 drillsites, off New Jersey, using R/V Langsethand cover ~95% of the planned 12x50 km box. Despite the large survey area, the lateral and vertical resolution for the 3D dataset is almost a magnitude of order higher than for data gathered for standard petroleum exploration. Such high-resolution was made possible by collection of common midpoint (CMP) lines whose combined length is ~3 times the Earth's circumference (~120,000 profile km) and a source rich in high-frequencies. We present details on the data acquisition, ongoing data analysis, and preliminary results. The science driving this project is presented by Mountain et al. The 3D component of this innovative survey used an athwartship cross cable, extended laterally by 2 barovanes roughly 357.5 m apart and trailed by 24 50-m P-Cables spaced ~12.5 m with near-trace offset of 53 m. Each P-Cable had 8 single hydrophone groups spaced at 6.25 m for a total of 192 channels. Record length was 4 s and sample rate 0.5 ms, with no low cut and an 824 Hz high cut filter. We ran 77 sail lines spaced ~150 m. Receiver locations were determined using 2 GPS receivers mounted on floats and 2 compasses and depth sensors per streamer. Streamer depths varied from 2.1 to 3.7 m. The 2D component used a single 3 km streamer, with 240 9-hydrophone groups spaced at 12.5 m, towed astern with near-trace offset of 229 m. The record length was 4 s and sample rate 0.5 ms, with low cut filter at 2 Hz and high cut at 412 Hz. Receiver locations were recorded using GPS at the head float and tail buoy, combined with 12 bird compasses spaced ~300 m. Nominal streamer depth was 4.5 m. The source for both systems was a 700 in3 linear array of 4 Bolt air guns suspended at 4.5 m towing depth, 271.5 m behind the ship's stern. Shot spacing was 12.5 m. Data analysis to

  13. The influence of the spatial resolution of topographic input data on the accuracy of 3-D UV actinic flux and irradiance calculations

    Directory of Open Access Journals (Sweden)

    P. Weihs

    2011-10-01

    Full Text Available The aim of this study was to investigate the influence of the spatial resolution of a digital elevation map (DEM on the three-dimensional (3-D radiative transfer performance for both spectral ultraviolet (UV irradiance and actinic flux at 305 nm. Model simulations were performed for clear sky conditions for three case studies: the first and second one using three sites in the Innsbruck area and the third one using three sites at the Sonnblick Observatory and surrounding area. It was found that DEM resolution may change the altitude at some locations by up to 500 m, resulting in changes in the sky obscured by the horizon of up to 15%. The geographical distribution of UV irradiance and actinic flux shows that with larger pixel size, uncertainties in UV irradiance and actinic flux determination of up to 100% are possible. These large changes in incident irradiance and actinic flux with changing pixel size are strongly connected to shading effects. The effect of DEM pixel size on irradiance and actinic flux was studied at the six locations, and it was found that significant increases in irradiance and actinic flux with increasing DEM pixel size occurred at one valley location at high solar zenith angles in the Innsbruck area as well as for one steep valley location in the Sonnblick area. This increase in irradiance and actinic flux with increasing DEM resolution is most likely to be connected to shading effects affecting the reflections from the surroundings.

  14. Ultra-high-resolution 3D imaging of atherosclerosis in mice with synchrotron differential phase contrast: a proof of concept study

    Science.gov (United States)

    Bonanno, Gabriele; Coppo, Simone; Modregger, Peter; Pellegrin, Maxime; Stuber, Annina; Stampanoni, Marco; Mazzolai, Lucia; Stuber, Matthias; van Heeswijk, Ruud B.

    2015-07-01

    The goal of this study was to investigate the performance of 3D synchrotron differential phase contrast (DPC) imaging for the visualization of both macroscopic and microscopic aspects of atherosclerosis in the mouse vasculature ex vivo. The hearts and aortas of 2 atherosclerotic and 2 wild-type control mice were scanned with DPC imaging with an isotropic resolution of 15 μm. The coronary artery vessel walls were segmented in the DPC datasets to assess their thickness, and histological staining was performed at the level of atherosclerotic plaques. The DPC imaging allowed for the visualization of complex structures such as the coronary arteries and their branches, the thin fibrous cap of atherosclerotic plaques as well as the chordae tendineae. The coronary vessel wall thickness ranged from 37.4 ± 5.6 μm in proximal coronary arteries to 13.6 ± 3.3 μm in distal branches. No consistent differences in coronary vessel wall thickness were detected between the wild-type and atherosclerotic hearts in this proof-of-concept study, although the standard deviation in the atherosclerotic mice was higher in most segments, consistent with the observation of occasional focal vessel wall thickening. Overall, DPC imaging of the cardiovascular system of the mice allowed for a simultaneous detailed 3D morphological assessment of both large structures and microscopic details.

  15. Advanced Reservoir Characterization and Development through High-Resolution 3C3D Seismic and Horizontal Drilling: Eva South Marrow Sand Unit, Texas County, Oklahoma

    Energy Technology Data Exchange (ETDEWEB)

    Wheeler,David M.; Miller, William A.; Wilson, Travis C.

    2002-03-11

    The Eva South Morrow Sand Unit is located in western Texas County, Oklahoma. The field produces from an upper Morrow sandstone, termed the Eva sandstone, deposited in a transgressive valley-fill sequence. The field is defined as a combination structural stratigraphic trap; the reservoir lies in a convex up -dip bend in the valley and is truncated on the west side by the Teepee Creek fault. Although the field has been a successful waterflood since 1993, reservoir heterogeneity and compartmentalization has impeded overall sweep efficiency. A 4.25 square mile high-resolution, three component three-dimensional (3C3D) seismic survey was acquired in order to improve reservoir characterization and pinpoint the optimal location of a new horizontal producing well, the ESU 13-H.

  16. Mapping 3D fault geometry in earthquakes using high-resolution topography: Examples from the 2010 El Mayor-Cucapah (Mexico) and 2013 Balochistan (Pakistan) earthquakes

    Science.gov (United States)

    Zhou, Yu; Walker, Richard T.; Elliott, John R.; Parsons, Barry

    2016-04-01

    Fault dips are usually measured from outcrops in the field or inferred through geodetic or seismological modeling. Here we apply the classic structural geology approach of calculating dip from a fault's 3-D surface trace using recent, high-resolution topography. A test study applied to the 2010 El Mayor-Cucapah earthquake shows very good agreement between our results and those previously determined from field measurements. To obtain a reliable estimate, a fault segment ≥120 m long with a topographic variation ≥15 m is suggested. We then applied this method to the 2013 Balochistan earthquake, getting dips similar to previous estimates. Our dip estimates show a switch from north to south dipping at the southern end of the main trace, which appears to be a response to local extension within a stepover. We suggest that this previously unidentified geometrical complexity may act as the endpoint of earthquake ruptures for the southern end of the Hoshab fault.

  17. Realtime infiltration process monitoring in macroporous soil - a plot-scale experiment accompanied by high-resolution time-lapse 3D GPR

    Science.gov (United States)

    Jackisch, Conrad; Allroggen, Niklas

    2016-04-01

    Infiltration and quick vertical redistribution of event water through rapid subsurface flow in soil structures is one of the key issues in hydrology. Although the importance of preferential flow is broadly recognised, our theories, observation techniques and modelling approaches lose grounds when the assumption of well-mixed states in REVs collapses. To characterise the combination of advective and diffusive flow is especially challenging. We have shown in earlier studies that a combination of TDR monitoring, dye- and salt-tracer recovery and time-lapse 3D GPR in irrigation experiments provides means to characterise infiltration dynamics at the plot- and hillslope-scale also in highly structured soils. We pinpointed that the spatial and temporal resolution requires special attention and improvement - particularly owing to the facts of high velocity (10-3 ms-1) of advective flow and small scale (10-2 m) of the respective flow structures. We present insights from a novel technique of continuous high-resolution time-lapse 3D GPR measurements during and after a plot-scale (1 m x 1 m) irrigation experiment. Continuous TDR soil moisture measurements, dye tracer excavation and salt-tracer samples are used as qualitative and quantitative references. While classical infiltration experiments either look at spatial patterns or temporal dynamics at singular gauges, we highlight the advantage of combining both to achieve a more complete image of the infiltration process. Although operating at the limits of the techniques this setup enables non-invasive observation of preferential flow processes in the field and allows to explore and characterise macropore matrix exchange.

  18. Ligand-based pharmacophore modeling; atom-based 3D-QSAR analysis and molecular docking studies of phosphoinositide-dependent kinase-1 inhibitors

    Directory of Open Access Journals (Sweden)

    P Kirubakaran

    2012-01-01

    Full Text Available Phosphoinositide-dependent kinase-1 plays a vital role in the PI3-kinase signaling pathway that regulates gene expression, cell cycle growth and proliferation. The common human cancers include lung, breast, blood and prostate possess over stimulation of the phosphoinositide-dependent kinase-1 signaling and making phosphoinositide-dependent kinase-1 an interesting therapeutic target in oncology. A ligand-based pharmacophore and atom-based 3D-QSAR studies were carried out on a set of 82 inhibitors of PDK1. A six point pharmacophore with two hydrogen bond acceptors (A, three hydrogen bond donors (D and one hydrophobic group (H was obtained. The pharmacophore hypothesis yielded a 3D-QSAR model with good partial least square statistics results. The training set correlation is characterized by partial least square factors (R2 = 0.9557, SD = 0.2334, F = 215.5, P = 1.407e-32. The test set correlation is characterized by partial least square factors (Q2 ext = 0.7510, RMSE = 0.5225, Pearson-R =0.8676. The external validation indicated that our QSAR model possess high predictive power with good value of 0.99 and value of 0.88. The docking results show the binding orientations of these inhibitors at active site amino acid residues (Ala162, Thr222, Glu209 and Glu166 of phosphoinositide-dependent kinase-1 protein. The binding free energy interactions of protein-ligand complex have been calculated, which plays an important role in molecular recognition and drug design approach.

  19. Tools for Model Building and Optimization into Near-Atomic Resolution Electron Cryo-Microscopy Density Maps.

    Science.gov (United States)

    DiMaio, F; Chiu, W

    2016-01-01

    Electron cryo-microscopy (cryoEM) has advanced dramatically to become a viable tool for high-resolution structural biology research. The ultimate outcome of a cryoEM study is an atomic model of a macromolecule or its complex with interacting partners. This chapter describes a variety of algorithms and software to build a de novo model based on the cryoEM 3D density map, to optimize the model with the best stereochemistry restraints and finally to validate the model with proper protocols. The full process of atomic structure determination from a cryoEM map is described. The tools outlined in this chapter should prove extremely valuable in revealing atomic interactions guided by cryoEM data.

  20. Advanced double-biprism holography with atomic resolution.

    Science.gov (United States)

    Genz, Florian; Niermann, Tore; Buijsse, Bart; Freitag, Bert; Lehmann, Michael

    2014-12-01

    The optimum biprism position as suggested by Lichte (Ultramicroscopy 64 (1996) 79 [10]) was implemented into a state-of-the-art transmission electron microscope. For a setup optimized for atomic resolution holograms with a width of 30nm and a fringe spacing of 30pm, we investigated the practical improvements on hologram quality. The setup is additionally supplemented by a second biprism as suggested by Harada et al. (Applied Physics Letters 84 (2004) 3229 [12]). In order to estimate the possibilities and limitations of the double biprism setup, geometric optics arguments lead to calculation of the exploitable shadow width, necessary for strong reduction of biprism-induced artefacts. Additionally, we used the double biprism setup to estimate the biprism vibration, yielding the most stable imaging conditions with lowest overall fringe contrast damping. Electron holograms of GaN demonstrate the good match between experiment and simulation, also as a consequence of the improved stability.

  1. The crystal structure of samarosporin I at atomic resolution.

    Science.gov (United States)

    Gessmann, Renate; Axford, Danny; Evans, Gwyndaf; Brückner, Hans; Petratos, Kyriacos

    2012-11-01

    The atomic resolution structures of samarosporin I have been determined at 100 and 293 K. This is the first crystal structure of a natural 15-residue peptaibol. The amino acid sequence in samarosporin I is identical to emerimicin IV and stilbellin I. Samarosporin is a peptide antibiotic produced by the ascomycetous fungus Samarospora rostrup and belongs to peptaibol subfamily 2. The structures at both temperatures are very similar to each other adopting mainly a 3₁₀-helical and a minor fraction of α-helical conformation. The helices are significantly bent and packed in an antiparallel fashion in the centered monoclinic lattice leaving among them an approximately 10-Å channel extending along the crystallographic twofold axis. Only two ordered water molecules per peptide molecule were located in the channel. Comparisons have been carried out with crystal structures of subfamily 2 16-residue peptaibols antiamoebin and cephaibols. The repercussion of the structural analysis of samarosporin on membrane function is discussed.

  2. A Photoisomerizing Rhodopsin Mimic Observed at Atomic Resolution.

    Science.gov (United States)

    Nosrati, Meisam; Berbasova, Tetyana; Vasileiou, Chrysoula; Borhan, Babak; Geiger, James H

    2016-07-20

    The members of the rhodopsin family of proteins are involved in many essential light-dependent processes in biology. Specific photoisomerization of the protein-bound retinylidene PSB at a specified wavelength range of light is at the heart of all of these systems. Nonetheless, it has been difficult to reproduce in an engineered system. We have developed rhodopsin mimics, using intracellular lipid binding protein family members as scaffolds, to study fundamental aspects of protein/chromophore interactions. Herein we describe a system that specifically isomerizes the retinylidene protonated Schiff base both thermally and photochemically. This isomerization has been characterized at atomic resolution by quantitatively interconverting the isomers in the crystal both thermally and photochemically. This event is accompanied by a large pKa change of the imine similar to the pKa changes observed in bacteriorhodopsin and visual opsins during isomerization.

  3. Atomic-resolution structures of prion AGAAAAGA amyloid fibrils

    CERN Document Server

    Zhang, Jiapu

    2011-01-01

    To the best of the author's knowledge, there is little structural data available on the AGAAAAGA palindrome in the hydrophobic region (113-120) of prion proteins due to the unstable, noncrystalline and insoluble nature of the amyloid fibril, although many experimental studies have shown that this region has amyloid fibril forming properties and plays an important role in prion diseases. In view of this, the present study is devoted to address this problem from computational approaches such as local optimization steepest descent, conjugate gradient, discrete gradient and Newton methods, global optimization simulated annealing and genetic algorithms, canonical dual optimization theory, and structural bioinformatics. The optimal atomic-resolution structures of prion AGAAAAGA amyloid fibils reported in this Chapter have a value to the scientific community in its drive to find treatments for prion diseases or at least be useful for the goals of medicinal chemistry.

  4. High-Resolution Geophysical 3D Imaging for Archaeology by Magnetic and EM data: The Case of the Iron Age Settlement of Torre Galli, Southern Italy

    Science.gov (United States)

    Cella, Federico; Fedi, Maurizio

    2015-11-01

    Magnetic and electromagnetic surveying are effective techniques frequently used in archaeology because the susceptibility and the electric resistivity contrast between the cover soil and several buried finds often lead to detectable anomalies. Significant advances were recently achieved by 3D imaging methods of potential field data that provide an estimate of the magnetization distribution within the subsurface. They provide a high-resolution image of the source distribution, thanks to the differentiation of the field and to the stability of the process. These techniques are fast and quite effective in the case of a compact, isolated, and depth-limited source, i.e., just the kind of source generally occurring in archaeological investigations. We illustrate the high-resolution imaging process for a geophysical study carried out at Torre Galli ( Vibo Valentia, Calabria, Italy), one of the most significant sites of the early Iron Age in Italy. Multi-scale derivative analysis of magnetic data revealed the trends of anomalies shaped and aligned with a regular geometry. This allowed us to make an outline of the buried structures, and then to characterize them in terms of size, shape, and depth by means of the imaging technique. Targeted excavations were therefore addressed to the locations selected by our analysis, revealing structures showing exactly the predicted features and confirming the archaeological hypothesis concerning the settlement organization partitioned in terms of functional differentiation: an intermediate area occupied mostly by defensive structures placed between the village, westward, and the necropolis, eastward.

  5. Sea Level History in 3D: Early results of an ultra-high resolution MCS survey across IODP Expedition 313 drillsites

    Science.gov (United States)

    Mountain, G. S.; Kucuk, H. M.; Nedimovic, M. R.; Austin, J. A., Jr.; Fulthorpe, C.; Newton, A.; Baldwin, K.; Johnson, C.; Stanley, J. N.; Bhatnagar, T.

    2015-12-01

    Although globally averaged sea level is rising at roughly 3 mm/yr (and is accelerating), rates of local sea-level change measured at coastlines may differ from this number by a factor of two or more; at some locations, sea level may even be falling. This is due to local processes that can match or even reverse the global trend, making it clear that reliable predictions of future impacts of sea-level rise require a firm understanding of processes at the local level. The history of local sea-level change and shoreline response is contained in the geologic record of shallow-water sediments. We report on a continuing study of sea-level history in sediments at the New Jersey continental margin, where compaction and glacial isostatic adjustment are currently adding 2 mm/yr to the globally averaged rise. We collected 570 sq km of ultra-high resolution 3D MCS data aboard the R/V Langseth in June-July 2015; innovative recording and preliminary results are described by Nedimovic et al. in this same session. The goal was to provide regional context to coring and logging at IODP Exp 313 sites 27-29 that were drilled 750 m into the New Jersey shelf in 2009. These sites recovered a nearly continuous record of post-Eocene sediments from non-marine soils, estuaries, shoreface, delta front, pro-delta and open marine settings. Existing seismic data are good but are 2D high-resolution profiles at line spacings too wide to enable mapping of key nearshore features. The Langseth 3D survey used shallow towing of a tuned air gun array to preserve high frequencies, and twenty-four 50-m PCables each 12.5 apart provided 6.25 x 3.125 m common-midpoint bins along seventy-seven 50-km sail lines. With this especially dense spatial resolution of a pre-stack time migrated volume we expect to map rivers, incised valleys, barrier islands, inlets and bays, pro-delta clinoforms, tidal deltas, sequence boundaries, debris flow aprons, and more. Seismic attributes linked to sedimentary facies and

  6. 3D shaping of electron beams using amplitude masks

    CERN Document Server

    Shiloh, Roy

    2016-01-01

    Shaping the electron wavefunction in three dimensions may prove to be an indispensable tool for research involving atomic-sized particle trapping, manipulation, and synthesis. We utilize computer-generated holograms to sculpt electron wavefunctions in a standard transmission electron microscope in 3D, and demonstrate the formation of electron beams exhibiting high intensity along specific trajectories as well as shaping the beam into a 3D lattice of hot-spots. The concepts presented here are similar to those used in light optics for trapping and tweezing of particles, but at atomic scale resolutions.

  7. 3-D multi-observable probabilistic inversion for the compositional and thermal structure of the lithosphere and upper mantle. II: General methodology and resolution analysis

    Science.gov (United States)

    Afonso, J. C.; Fullea, J.; Yang, Y.; Connolly, J. A. D.; Jones, A. G.

    2013-04-01

    Here we present a 3-D multi-observable probabilistic inversion method, particularly designed for high-resolution (regional) thermal and compositional mapping of the lithosphere and sub-lithospheric upper mantle that circumvents the problems associated with traditional inversion methods. The key aspects of the method are as follows: (a) it exploits the increasing amount and quality of geophysical datasets; (b) it combines multiple geophysical observables (Rayleigh and Love dispersion curves, body-wave tomography, magnetotelluric, geothermal, petrological, gravity, elevation, and geoid) with different sensitivities to deep/shallow, thermal/compositional anomalies into a single thermodynamic-geophysical framework; (c) it uses a general probabilistic (Bayesian) formulation to appraise the data; (d) no initial model is needed; (e) compositional a priori information relies on robust statistical analyses of a large database of natural mantle samples; and (f) it provides a natural platform to estimate realistic uncertainties. In addition, the modular nature of the method/algorithm allows for incorporating or isolating specific forward operators according to available data. The strengths and limitations of the method are thoroughly explored with synthetic models. It is shown that the a posteriori probability density function (i.e., solution to the inverse problem) satisfactorily captures spatial variations in bulk composition and temperature with high resolution, as well as sharp discontinuities in these fields. Our results indicate that only temperature anomalies of ΔT ⪆150°C and large compositional anomalies of ΔMg# > 3 (or bulk ΔAl2O3 > 1.5) can be expected to be resolved simultaneously when combining high-quality geophysical data. This resolving power is sufficient to explore some long-standing problems regarding the nature and evolution of the lithosphere (e.g., vertical stratification of cratonic mantle, compositional versus temperature signatures in seismic

  8. Atomic Resolution Structure of Monomorphic Aβ42 Amyloid Fibrils.

    Science.gov (United States)

    Colvin, Michael T; Silvers, Robert; Ni, Qing Zhe; Can, Thach V; Sergeyev, Ivan; Rosay, Melanie; Donovan, Kevin J; Michael, Brian; Wall, Joseph; Linse, Sara; Griffin, Robert G

    2016-08-03

    Amyloid-β (Aβ) is a 39-42 residue protein produced by the cleavage of the amyloid precursor protein (APP), which subsequently aggregates to form cross-β amyloid fibrils that are a hallmark of Alzheimer's disease (AD). The most prominent forms of Aβ are Aβ1-40 and Aβ1-42, which differ by two amino acids (I and A) at the C-terminus. However, Aβ42 is more neurotoxic and essential to the etiology of AD. Here, we present an atomic resolution structure of a monomorphic form of AβM01-42 amyloid fibrils derived from over 500 (13)C-(13)C, (13)C-(15)N distance and backbone angle structural constraints obtained from high field magic angle spinning NMR spectra. The structure (PDB ID: 5KK3 ) shows that the fibril core consists of a dimer of Aβ42 molecules, each containing four β-strands in a S-shaped amyloid fold, and arranged in a manner that generates two hydrophobic cores that are capped at the end of the chain by a salt bridge. The outer surface of the monomers presents hydrophilic side chains to the solvent. The interface between the monomers of the dimer shows clear contacts between M35 of one molecule and L17 and Q15 of the second. Intermolecular (13)C-(15)N constraints demonstrate that the amyloid fibrils are parallel in register. The RMSD of the backbone structure (Q15-A42) is 0.71 ± 0.12 Å and of all heavy atoms is 1.07 ± 0.08 Å. The structure provides a point of departure for the design of drugs that bind to the fibril surface and therefore interfere with secondary nucleation and for other therapeutic approaches to mitigate Aβ42 aggregation.

  9. Soil process-oriented modelling of within-field variability based on high-resolution 3D soil type distribution maps.

    Science.gov (United States)

    Bönecke, Eric; Lück, Erika; Gründling, Ralf; Rühlmann, Jörg; Franko, Uwe

    2016-04-01

    Today, the knowledge of within-field variability is essential for numerous purposes, including practical issues, such as precision and sustainable soil management. Therefore, process-oriented soil models have been applied for a considerable time to answer question of spatial soil nutrient and water dynamics, although, they can only be as consistent as their variation and resolution of soil input data. Traditional approaches, describe distribution of soil types, soil texture or other soil properties for greater soil units through generalised point information, e.g. from classical soil survey maps. Those simplifications are known to be afflicted with large uncertainties. Varying soil, crop or yield conditions are detected even within such homogenised soil units. However, recent advances of non-invasive soil survey and on-the-go monitoring techniques, made it possible to obtain vertical and horizontal dense information (3D) about various soil properties, particularly soil texture distribution which serves as an essential soil key variable affecting various other soil properties. Thus, in this study we based our simulations on detailed 3D soil type distribution (STD) maps (4x4 m) to adjacently built-up sufficient informative soil profiles including various soil physical and chemical properties. Our estimates of spatial STD are based on high-resolution lateral and vertical changes of electrical resistivity (ER), detected by a relatively new multi-sensor on-the-go ER monitoring device. We performed an algorithm including fuzzy-c-mean (FCM) logic and traditional soil classification to estimate STD from those inverted and layer-wise available ER data. STD is then used as key input parameter for our carbon, nitrogen and water transport model. We identified Pedological horizon depths and inferred hydrological soil variables (field capacity, permanent wilting point) from pedotransferfunctions (PTF) for each horizon. Furthermore, the spatial distribution of soil organic carbon

  10. Reaction-induced porosity and onset of low-temperature carbonation in abyssal peridotites: Insights from 3D high-resolution microtomography

    Science.gov (United States)

    Jöns, Niels; Kahl, Wolf-Achim; Bach, Wolfgang

    2017-01-01

    In a drillcore sample of serpentinized harzburgite from the uppermost oceanic crust (Mid-Atlantic Ridge, ODP Leg 209, Site 1270), we demonstrate using high-resolution 3D-microtomography that micron-sized open cavities are present. The development of porosity is interpreted to result from dissolution of brucite and/or olivine. Petrographic observations indicate that voids are integrated in a network of carbonate veins, the formation of which is linked to changing alkalinity in conjunction with dissolution reactions. Partial carbonate filling of pore spaces indicates that under static conditions low-temperature carbonation leads to clogging of fluid pathways and thus to a reduction in permeability. Electron microprobe analyses show that the inner walls of open voids are lined with Fe-rich precipitates. We propose that the iron in those phases was released by brucite or olivine dissolution and was subsequently oxidized and precipitated as ferric hydroxide. Thermodynamic computations show that this process may be a potential source of catabolic energy for microorganisms inhabiting serpentinites. The proposed carbonation mechanism implies that carbonate precipitation may start soon after exposure of the abyssal peridotites, when dissolution of brucite and weathering of olivine begin, and continue until the phases become inaccessible to seawater. Predicting carbonation rates of abyssal peridotites will hence require understanding of permeability reactions.

  11. New High-Resolution 3D Seismic Imagery of Deformation and Fault Architecture Along Newport-Inglewood/Rose Canyon Fault in the Inner California Borderlands

    Science.gov (United States)

    Holmes, J. J.; Bormann, J. M.; Driscoll, N. W.; Kent, G.; Harding, A. J.; Wesnousky, S. G.

    2014-12-01

    The tectonic deformation and geomorphology of the Inner California Borderlands (ICB) records the transition from a convergent plate margin to a predominantly dextral strike-slip system. Geodetic measurements of plate boundary deformation onshore indicate that approximately 15%, or 6-8 mm/yr, of the total Pacific-North American relative plate motion is accommodated by faults offshore. The largest near-shore fault system, the Newport-Inglewood/Rose Canyon (NI/RC) fault complex, has a Holocene slip rate estimate of 1.5-2.0 mm/yr, according to onshore trenching, and current models suggest the potential to produce an Mw 7.0+ earthquake. The fault zone extends approximately 120 km, initiating from the south near downtown San Diego and striking northwards with a constraining bend north of Mt. Soledad in La Jolla and continuing northwestward along the continental shelf, eventually stepping onshore at Newport Beach, California. In late 2013, we completed the first high-resolution 3D seismic survey (3.125 m bins) of the NI/RC fault offshore of San Onofre as part of the Southern California Regional Fault Mapping project. We present new constraints on fault geometry and segmentation of the fault system that may play a role in limiting the extent of future earthquake ruptures. In addition, slip rate estimates using piercing points such as offset channels will be explored. These new observations will allow us to investigate recent deformation and strain transfer along the NI/RC fault system.

  12. Advanced double-biprism holography with atomic resolution

    Energy Technology Data Exchange (ETDEWEB)

    Genz, Florian, E-mail: florian.genz@physik.tu-berlin.de [Technische Universität Berlin, Institut für Optik und Atomare Physik, Straße des 17. Juni, 10623 Berlin (Germany); Niermann, Tore [Technische Universität Berlin, Institut für Optik und Atomare Physik, Straße des 17. Juni, 10623 Berlin (Germany); Buijsse, Bart; Freitag, Bert [FEI Company, Achtseweg Noord 5, 5651 GG Eindhoven (Netherlands); Lehmann, Michael [Technische Universität Berlin, Institut für Optik und Atomare Physik, Straße des 17. Juni, 10623 Berlin (Germany)

    2014-12-15

    The optimum biprism position as suggested by Lichte (Ultramicroscopy 64 (1996) 79 [10]) was implemented into a state-of-the-art transmission electron microscope. For a setup optimized for atomic resolution holograms with a width of 30 nm and a fringe spacing of 30 pm, we investigated the practical improvements on hologram quality. The setup is additionally supplemented by a second biprism as suggested by Harada et al. (Applied Physics Letters 84 (2004) 3229 [12]). In order to estimate the possibilities and limitations of the double biprism setup, geometric optics arguments lead to calculation of the exploitable shadow width, necessary for strong reduction of biprism-induced artefacts. Additionally, we used the double biprism setup to estimate the biprism vibration, yielding the most stable imaging conditions with lowest overall fringe contrast damping. Electron holograms of GaN demonstrate the good match between experiment and simulation, also as a consequence of the improved stability. - Highlights: • Investigation of optimum biprism position implementation into state-of-the-art TEM. • Reduction of artefacts, especially vignetting in double-biprism electron holography. • Biprism vibration and most stable imaging conditions in double-biprism holography. • Demonstration of the optimized double-biprism setup using a thin GaN-foil.

  13. Non-homogeneous stereological properties of the rat hippocampus from high-resolution 3D serial reconstruction of thin histological sections.

    Science.gov (United States)

    Ropireddy, D; Bachus, S E; Ascoli, G A

    2012-03-15

    Integrating hippocampal anatomy from neuronal dendrites to whole system may help elucidate its relation to function. Toward this aim, we digitally traced the cytoarchitectonic boundaries of the dentate gyrus (DG) and areas CA3/CA1 throughout their entire longitudinal extent from high-resolution images of thin cryostatic sections of adult rat brain. The 3D computational reconstruction identified all isotropic 16 μm voxels with appropriate subregions and layers (http://krasnow1.gmu.edu/cn3/hippocampus3d). Overall, DG, CA3, and CA1 occupied comparable volumes (15.3, 12.2, and 18.8 mm(3), respectively), but displayed substantial rostrocaudal volumetric gradients: CA1 made up more than half of the posterior hippocampus, whereas CA3 and DG were more prominent in the anterior regions. The CA3/CA1 ratio increased from ∼0.4 to ∼1 septo-temporally because of a specific change in stratum radiatum volume. Next we virtually embedded 1.8 million neuronal morphologies stochastically resampled from 244 digital reconstructions, emulating the dense packing of granular and pyramidal layers, and appropriately orienting the principal dendritic axes relative to local curvature. The resulting neuropil occupancy reproduced recent electron microscopy data measured in a restricted location. Extension of this analysis across each layer and subregion over the whole hippocampus revealed highly non-homogeneous dendritic density. In CA1, dendritic occupancy was >60% higher temporally than septally (0.46 vs. 0.28, s.e.m. ∼0.05). CA3 values varied both across subfields (from 0.35 in CA3b/CA3c to 0.50 in CA3a) and layers (0.48, 0.34, and 0.27 in oriens, radiatum, and lacunosum-moleculare, respectively). Dendritic occupancy was substantially lower in DG, especially in the supra-pyramidal blade (0.18). The computed probability of dendrodendritic collision significantly correlated with expression of the membrane repulsion signal Down syndrome cell adhesion molecule (DSCAM). These heterogeneous

  14. Feasibility of filter atomization in high-resolution continuum source atomic absorption spectrometry

    Science.gov (United States)

    Heitmann, Uwe; Becker-Ross, Helmut; Katskov, Dmitri

    2006-03-01

    A prototype spectrometer for high-resolution continuum source atomic absorption spectrometry (HR-CS AAS), built at ISAS Berlin, Germany, was combined with a graphite filter atomizer (GFA), earlier developed at TUT, Pretoria, South Africa. The furnace and auto-sampler units from a commercial AA spectrometer, model AAS vario 6 (Analytik Jena AG, Jena, Germany), were employed in the instrument. Instead of conventional platform tube, the GFA was used to provide low measurement susceptibility to interferences and short determination cycle. The GFA was modified according to the design of the furnace unit and optimal physical parameters of its components (filter and collector) found. Afterwards, optimal GFA was replicated and tested to outline analytical performances of the HR-CS GFA AA spectrometer in view of prospects of multi-element analysis. In particular, reproducibility of performances, repeatability of analytical signals, lifetime, temperature limit and duration of the measurement cycle were examined, and elements available for determination justified. The results show that the peak area of the atomic absorption signal is reproduced in various GFA copies within ± 4% deviation range. The GFA can stand temperatures of 2800 °C with 6 s hold time for 55 temperature cycles, and 2700 °C (8 s) for about 200 cycles. Only the external tube is prone to destruction while the filter and collector do not show any sign of erosion caused by temperature or aggressive matrix. Analytical signals are affected insignificantly by tube aging. Repeatability of the peak area remains within 1.1-1.7% RSD over more than hundred determination cycles. Peak areas are proportional to the sample volume of injected organic and inorganic liquids up to at least 50 μL. The drying stage is combined with hot sampling and cut down to 15-20 s. The list of metals available for determination with full vapor release includes Al, Co, Cr, Ni, Pt as well as more volatile metals. Characteristic masses at

  15. Repumping and spectroscopy of laser-cooled Sr atoms using the (5s5p){sup 3}P{sub 2}-(5s4d){sup 3}D{sub 2} transition

    Energy Technology Data Exchange (ETDEWEB)

    Mickelson, P G; De Escobar, Y N Martinez; Anzel, P; DeSalvo, B J; Nagel, S B; Traverso, A J; Yan, M; Killian, T C, E-mail: killian@rice.ed [Department of Physics and Astronomy, Rice University, Houston, TX 77251 (United States)

    2009-12-14

    We describe repumping and spectroscopy of laser-cooled strontium (Sr) atoms using the (5s5p){sup 3}P{sub 2}-(5s4d){sup 3}D{sub 2} transition. Atom number in a magneto-optical trap is enhanced by driving this transition because Sr atoms that have decayed into the (5s5p){sup 3}P{sub 2} dark state are repumped back into the (5s{sup 2}){sup 1}S{sub 0} ground state. Spectroscopy of {sup 84}Sr, {sup 86}Sr, {sup 87}Sr and {sup 88}Sr improves the value of the (5s5p){sup 3}P{sub 2}-(5s4d){sup 3}D{sub 2} transition frequency and determines the isotope shifts for the transition accurately enough to guide laser-cooling experiments with less abundant isotopes.

  16. Detection and analysis of human serum albumin nanoparticles within phagocytic cells at the resolution of individual live cell or single 3D multicellular spheroid

    Energy Technology Data Exchange (ETDEWEB)

    Afrimzon, Elena; Zurgil, Naomi; Sobolev, Maria; Shafran, Yana [Bar-Ilan University, The Biophysical Interdisciplinary Schottenstein Center for the Research and Technology of the Cellome (Israel); Langer, Klaus; Zlatev, Iavor [Westfälischen Wilhelms-Universität Münster, Institut für Pharmazeutische Technologie und Biopharmazie (Germany); Wronski, Robert; Windisch, Manfred [QPS Austria GmbH (Austria); Briesen, Hagen von [Fraunhofer Institute for Biomedical Engineering IBMT, Department of Cell Biology & Applied Virology (Germany); Schmidt, Reinhold [Medical University of Graz, Department of Neurology (Austria); Pietrzik, Claus [University Medical Center of the Johannes Gutenberg University of Mainz, Institute of Pathobiochemistry (Germany); Deutsch, Mordechai, E-mail: motti.jsc@gmail.com [Bar-Ilan University, The Biophysical Interdisciplinary Schottenstein Center for the Research and Technology of the Cellome (Israel)

    2015-12-15

    Since nanoparticles (NPs) have shown great potential in various biomedical applications, live cell response to NPs should be thoroughly explored prior to their in vivo use. In the current study, live cell array (LCA) methodology and unique cell-based assays were used to study the interaction of magnetite (HSA-Mag NP) loaded human serum albumin NPs with phagocytic cells. The LCA enabled cell culturing during HSA-Mag NP accumulation and monolayer or spheroid formation, concomitantly with on-line monitoring of NP internalization. These platforms were also utilized for imaging intercellular links between living cells preloaded with HSA-Mag NP in 2D and 3D resolution. HSA-Mag NP uptake by cells was quantified by imaging, and analyzed using time-resolved measurements. Image analysis of the individual cells in cell populations showed accumulation of HSA-Mag NP by promonocytes and glial cells in a dose- and time-dependent manner. High variability of NP accumulation in individual cells within cell populations, as well as cell subgroups, was evident in both cell types. Following 24 h interaction, uptake of HSA-Mag NP was about 10 times more efficient in glial cells than in activated promonocytes. The presented assays may facilitate detection and analysis of the amount of NPs within individual cells, as well as the rate of NP accumulation and processing in different subsets of living cells. Such data are crucial for estimating predicted drug dosage delivered by NPs, as well as to study possible mechanisms for NP interference with live cells.

  17. Solution of the neutron transport equation by the collision probability for 3D geometries; Resolution de l`equation du transport pour les neutrons par la methode des probabilites de collision dans le geometries 3D

    Energy Technology Data Exchange (ETDEWEB)

    Oujidi, B.

    1996-09-19

    The TDT code solves the multigroup transport equation by the interface current method for unstructured 2D geometries. This works presents the extension of TDT to the treatment of 3D geometries obtained by axial displacement of unstructured 2D geometries. Three-dimensional trajectories are obtained by lifting the 2D trajectories. The code allows for the definition of macro-domains in the axial direction to be used in the interface-current method. Specular and isotropic reflection or translations boundary conditions can be applied to the horizontal boundaries of the domain. Numerical studies have shown the need for longer trajectory cutoffs for trajectories intersecting horizontal boundaries. Numerical applications to the calculation of local power peaks are given in a second part for: the local destruction of a Pyrex absorbent and inter-assembly (UO{sub 2}-MOX) power distortion due to pellet collapsing at the top of the core. Calculations with 16 groups were performed by coupling TDT to the spectral code APOLLO2. One-group comparisons with the Monte Carlo code TRIMARAN2 are also given. (author). 30 refs.

  18. Solution of the neutron transport equation by the collision probability method for 3D geometries; Resolution de l`equation du transport par les neutrons par la methode des probabilites de collision dans les geometries 3D

    Energy Technology Data Exchange (ETDEWEB)

    Oujidi, B

    1996-09-19

    The TDT code solves the multigroup transport equation by the interface-current method for unstructured 2D geometries. This works presents the extension of TDT to the treatment of 3D geometries obtained by axial displacement of unstructured 2D geometries. Three-dimensional trajectories are obtained by lifting the 2D trajectories. The code allows for the definition of macro-domains in the axial direction to be used in interface-current method. Specular and isotropic reflection or translations boundary conditions can be applied to the horizontal boundaries of the domain. Numerical studies have shown the need for longer trajectory cutoffs for trajectories intersecting horizontal boundaries. Numerical applications to the calculation of local power peaks are given in a second part for: the local destruction of a Pyrex absorbent, inter-assembly (U02-MOX) power distortion due to pellet collapsing at the top of the core. Calculations with 16 groups were performed by coupling TDT to the spectral code APOLLO2. One-group comparisons with the Monte Carlo code TRIMARAN2 are also given. (author) 30 refs.

  19. 3D Animation Essentials

    CERN Document Server

    Beane, Andy

    2012-01-01

    The essential fundamentals of 3D animation for aspiring 3D artists 3D is everywhere--video games, movie and television special effects, mobile devices, etc. Many aspiring artists and animators have grown up with 3D and computers, and naturally gravitate to this field as their area of interest. Bringing a blend of studio and classroom experience to offer you thorough coverage of the 3D animation industry, this must-have book shows you what it takes to create compelling and realistic 3D imagery. Serves as the first step to understanding the language of 3D and computer graphics (CG)Covers 3D anim

  20. 3D video

    CERN Document Server

    Lucas, Laurent; Loscos, Céline

    2013-01-01

    While 3D vision has existed for many years, the use of 3D cameras and video-based modeling by the film industry has induced an explosion of interest for 3D acquisition technology, 3D content and 3D displays. As such, 3D video has become one of the new technology trends of this century.The chapters in this book cover a large spectrum of areas connected to 3D video, which are presented both theoretically and technologically, while taking into account both physiological and perceptual aspects. Stepping away from traditional 3D vision, the authors, all currently involved in these areas, provide th

  1. High-resolution and functional magnetic resonance imaging of the brachial plexus using an isotropic 3D T2 STIR (Short Term Inversion Recovery) SPACE sequence and diffusion tensor imaging

    Energy Technology Data Exchange (ETDEWEB)

    Viallon, M.; Vargas, M.I.; Jlassi, H.; Loevblad, K.O.; Delavelle, J. [University Hospital of Geneva, Department of Radiology, Geneva (Switzerland)

    2008-05-15

    This technical note demonstrates the relevance of the isotropic 3D T2 turbo-spin-echo (TSE) sequence with short-term inversion recovery (STIR) and variable flip angle RF excitations (SPACE: Sampling Perfection with Application optimized Contrasts using different flip angle Evolutions) for high-resolution brachial plexus imaging. The sequence was used in 11 patients in the diagnosis of brachial plexus pathologies involving primary and secondary tumors, and in six volunteers. We show that 3D STIR imaging is not only a reliable alternative to 2D STIR imaging, but it also better evaluates the anatomy, nerve site compression and pathology of the plexus, especially to depict space-occupying tumors along its course. Finally, due to its appropriate contrast we describe how 3D-STIR can be used as a high-resolution mask to be fused with fraction of anisotropy (FA) maps calculated from diffusion tensor imaging (DTI) data of the plexus. (orig.)

  2. 3-D Rat Brain Phantom for High-Resolution Molecular Imaging: Experimental studies aimed at advancing understanding of human brain disease and malfunction, and of behavior problems, may be aided by computer models of small laboratory animals

    NARCIS (Netherlands)

    Beekman, F.J.; Vastenhouw, B.; Van der Wilt, G.; Vervloet, M.; Visscher, R.; Booij, J.; Gerrits, M.; Ji, C.; Ramakers, R.; Van der Have, F.

    2009-01-01

    With the steadily improving resolution of novel small-animal single photon emission computed tomography (SPECT) and positron emission tomography devices, highly detailed phantoms are required for testing and optimizing these systems. We present a three-dimensional (3-D) digital and physical phantom

  3. High-resolution adaptive imaging of a single atom

    Science.gov (United States)

    Wong-Campos, J. D.; Johnson, K. G.; Neyenhuis, B.; Mizrahi, J.; Monroe, C.

    2016-09-01

    Optical imaging systems are used extensively in the life and physical sciences because of their ability to non-invasively capture details on the microscopic and nanoscopic scales. Such systems are often limited by source or detector noise, image distortions and human operator misjudgement. Here, we report a general, quantitative method to analyse and correct these errors. We use this method to identify and correct optical aberrations in an imaging system for single atoms and realize an atomic position sensitivity of ˜0.5 nm Hz-1/2 with a minimum uncertainty of 1.7 nm, allowing the direct imaging of atomic motion. This is the highest position sensitivity ever measured for an isolated atom and opens up the possibility of performing out-of-focus three-dimensional particle tracking, imaging of atoms in three-dimensional optical lattices or sensing forces at the yoctonewton (10-24 N) scale.

  4. Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas.

    Science.gov (United States)

    Petrov, Anton I; Zirbel, Craig L; Leontis, Neocles B

    2013-10-01

    The analysis of atomic-resolution RNA three-dimensional (3D) structures reveals that many internal and hairpin loops are modular, recurrent, and structured by conserved non-Watson-Crick base pairs. Structurally similar loops define RNA 3D motifs that are conserved in homologous RNA molecules, but can also occur at nonhomologous sites in diverse RNAs, and which often vary in sequence. To further our understanding of RNA motif structure and sequence variability and to provide a useful resource for structure modeling and prediction, we present a new method for automated classification of internal and hairpin loop RNA 3D motifs and a new online database called the RNA 3D Motif Atlas. To classify the motif instances, a representative set of internal and hairpin loops is automatically extracted from a nonredundant list of RNA-containing PDB files. Their structures are compared geometrically, all-against-all, using the FR3D program suite. The loops are clustered into motif groups, taking into account geometric similarity and structural annotations and making allowance for a variable number of bulged bases. The automated procedure that we have implemented identifies all hairpin and internal loop motifs previously described in the literature. All motif instances and motif groups are assigned unique and stable identifiers and are made available in the RNA 3D Motif Atlas (http://rna.bgsu.edu/motifs), which is automatically updated every four weeks. The RNA 3D Motif Atlas provides an interactive user interface for exploring motif diversity and tools for programmatic data access.

  5. Atomic resolution of nitrogen-doped graphene on Cu foils

    Science.gov (United States)

    Wang, Chundong; Schouteden, Koen; Wu, Qi-Hui; Li, Zhe; Jiang, Jianjun; Van Haesendonck, Chris

    2016-09-01

    Atomic-level substitutional doping can significantly tune the electronic properties of graphene. Using low-temperature scanning tunneling microscopy and spectroscopy, the atomic-scale crystalline structure of graphene grown on polycrystalline Cu, the distribution of nitrogen dopants and their effect on the electronic properties of graphene were investigated. Both the graphene sheet growth and nitrogen doping were performed using microwave plasma-enhanced chemical vapor deposition. The results indicated that the nitrogen dopants preferentially sit at the grain boundaries of the graphene sheets and confirmed that plasma treatment is a potential method to incorporate foreign atoms into the graphene lattice to tailor the graphene’s electronic properties.

  6. Three dimensional and high resolution magnetic resonance imaging of the inner ear. Normal ears and anomaly scanned with 3D-CISS sequence

    Energy Technology Data Exchange (ETDEWEB)

    Edamatsu, Hideo [Dokkyo Univ., Saitama (Japan). Koshigaya Hospital; Uechi, Yoko; Honjyo, Shiro; Yamashita, Koichi; Tonami, Hisao

    1997-12-01

    The MRI system used in this study was a new scanning sequence, 3D-CISS (Three dimensional-constructive interference in steady state) with 1.5 Tesla. Ten normal ears and one ear with Mondini type anomaly were scanned and reconstructed. In imagings of normal inner ears, the cochlea has three spiral layers; basal, middle and apical turns. Each turn was separated into three parts; the scala vestibuli, osseous spiral lamina and scala tympani. Three semicircular ducts, utricle and saccule were also reconstructed in one frame. In the inner ear of Mondini anomaly, 3D MRI showed cochlear aplasia, hypoplasia of semicircular ducts and widely dilated vestibule. The imaging was identical with findings of ``common cavity``. The anomaly was easily recognized in 3D MRI more than in 2D imagings. The detailed and cubic imagings of the Mondini anomaly in 3D MRI could not be observed with conventional 2D MRI. 3D MRI is not invasive method and can scan a target very quickly. (author)

  7. Creating and Using Interactive, 3D-Printed Models to Improve Student Comprehension of the Bohr Model of the Atom, Bond Polarity, and Hybridization

    Science.gov (United States)

    Smiar, Karen; Mendez, J. D.

    2016-01-01

    Molecular model kits have been used in chemistry classrooms for decades but have seen very little recent innovation. Using 3D printing, three sets of physical models were created for a first semester, introductory chemistry course. Students manipulated these interactive models during class activities as a supplement to existing teaching tools for…

  8. Validation methods for low-resolution fitting of atomic structures to electron microscopy data

    OpenAIRE

    Xu, Xiao-Ping; Volkmann, Niels

    2015-01-01

    Fitting of atomic-resolution structures into reconstructions from electron cryo-microscopy is routinely used to understand the structure and function of macromolecular machines. Despite the fact that a plethora of fitting methods has been developed over recent years, standard protocols for quality assessment and validation of these fits have not been established. Here, we present the general concepts underlying current validation ideas as they relate to fitting of atomic-resolution models int...

  9. Fluorine in shark teeth: its direct atomic-resolution imaging and strengthening function.

    Science.gov (United States)

    Chen, Chunlin; Wang, Zhongchang; Saito, Mitsuhiro; Tohei, Tetsuya; Takano, Yoshiro; Ikuhara, Yuichi

    2014-02-01

    Atomic-resolution imaging of beam-sensitive biominerals is extremely challenging, owing to their fairly complex structures and the damage caused by electron irradiation. Herein, we overcome these difficulties by performing aberration-corrected electron microscopy with low-dose imaging techniques, and report the successful direct atomic-resolution imaging of every individual atomic column in the complex fluorapatite structure of shark tooth enameloid, which can be of paramount importance for teeth in general. We demonstrate that every individual atomic column in shark tooth enameloid can be spatially resolved, and has a complex fluorapatite structure. Furthermore, ab initio calculations show that fluorine atoms can be covalently bound to the surrounding calcium atoms, which improves understanding of their caries-reducing effects in shark teeth.

  10. 3D structure of muscle dihydropyridine receptor

    Directory of Open Access Journals (Sweden)

    Montserrat Samsó

    2015-01-01

    Full Text Available Excitation contraction coupling, the rapid and massive Ca2+ release under control of an action potential that triggers muscle contraction, takes places at specialized regions of the cell called triad junctions. There, a highly ordered supramolecular complex between the dihydropyridine receptor (DHPR and the ryanodine receptor (RyR1 mediates the quasi‐instantaneous conversion from T‐tubule depolarization into Ca2+ release from the sarcoplasmic reticulum (SR. The DHPR has several key modules required for EC coupling: the voltage sensors and II‐III loop in the alpha1s subunit, and the beta subunit. To gain insight into their molecular organization, this review examines the most updated 3D structure of the DHPR as obtained by transmission electron microscopy and image reconstruction. Although structure determination of a heteromeric membrane protein such as the DHPR is challenging, novel technical advances in protein expression and 3D labeling facilitated this task. The 3D structure of the DHPR complex consists of a main body with five irregular corners around its perimeter encompassing the transmembrane alpha 1s subunit besides the intracellular beta subunit, an extended extracellular alpha 2 subunit, and a bulky intracellular II‐III loop. The structural definition attained at 19 Å resolution enabled docking of the atomic coordinates of structural homologs of the alpha1s and beta subunits. These structural features, together with their relative location with respect to the RyR1, are discussed in the context of the functional data.

  11. Submolecular Resolution Imaging of molecules by Atomic Force Microscopy:The influence of the Electrostatic Force

    NARCIS (Netherlands)

    van der Lit, J.; Cicco, F.; Hapala, P.; Jelinek, P.; Swart, Ingmar

    2016-01-01

    The forces governing the contrast in submolecular resolution imaging of molecules with atomic force microscopy (AFM) have recently become a topic of intense debate. Here, we show that the electrostatic force is essential to understand the contrast in atomically resolved AFM images of polar molecules

  12. High-resolution 3-D mapping using terrestrial laser scanning as a tool for geomorphological and speleogenetical studies in caves: An example from the Lessini mountains (North Italy)

    Science.gov (United States)

    Fabbri, Stefano; Sauro, Francesco; Santagata, Tommaso; Rossi, Guido; De Waele, Jo

    2017-03-01

    Terrestrial laser scanning (TLS) is increasingly used in geomorphology for the study of medium- to small scale landforms. A light weight, compact and portable TLS device has been used in the Grotta A Cave (Mt. Lessini, N Italy) to make a detailed 3D model of the underground environment. A total of 16 scans were used to survey the about 150 m long cave in < 6 h. The 3D model of the cave walls makes it possible to carry out morphometric measurements on the different cave environments. The TLS data allowed us to calculate cave volumes and distinguish cupola, phreatic conduit and basalt dike volumes. Wall roughness analysis also allowed recognising smaller-scale morphologies such as megascallops, differential corrosion forms and mineral crusts. These observations have enabled us to discern between different karstification processes and speleogenetic phases, highlighting the importance of condensation-corrosion on the cave passage enlargement in a quantitative way.

  13. Quantitative assessment of cancer vascular architecture by skeletonization of high-resolution 3-D contrast-enhanced ultrasound images: role of liposomes and microbubbles.

    Science.gov (United States)

    Molinari, F; Meiburger, K M; Giustetto, P; Rizzitelli, S; Boffa, C; Castano, M; Terreno, E

    2014-12-01

    The accurate characterization and description of the vascular network of a cancer lesion is of paramount importance in clinical practice and cancer research in order to improve diagnostic accuracy or to assess the effectiveness of a treatment. The aim of this study was to show the effectiveness of liposomes as an ultrasound contrast agent to describe the 3-D vascular architecture of a tumor. Eight C57BL/6 mice grafted with syngeneic B16-F10 murine melanoma cells were injected with a bolus of 1,2-Distearoyl-sn-glycero-3-phosphocoline (DSPC)-based non-targeted liposomes and with a bolus of microbubbles. 3-D contrast-enhanced images of the tumor lesions were acquired in three conditions: pre-contrast, after the injection of microbubbles, and after the injection of liposomes. By using a previously developed reconstruction and characterization image processing technique, we obtained the 3-D representation of the vascular architecture in these three conditions. Six descriptive parameters of these networks were also computed: the number of vascular trees (NT), the vascular density (VD), the number of branches, the 2-D curvature measure, the number of vascular flexes of the vessels, and the 3-D curvature. Results showed that all the vascular descriptors obtained by liposome-based images were statistically equal to those obtained by using microbubbles, except the VD which was found to be lower for liposome images. All the six descriptors computed in pre-contrast conditions had values that were statistically lower than those computed in presence of contrast, both for liposomes and microbubbles. Liposomes have already been used in cancer therapy for the selective ultrasound-mediated delivery of drugs. This work demonstrated their effectiveness also as vascular diagnostic contrast agents, therefore proving that liposomes can be used as efficient "theranostic" (i.e. therapeutic 1 diagnostic) ultrasound probes.

  14. Introductory lecture: Time-resolved chemistry at atomic resolution.

    Science.gov (United States)

    Coppens, Philip; Novozhilova, Irina V

    2003-01-01

    Though time-resolved studies are still at an early stage, the field is rapidly being developed and applied to an increasingly broad spectrum of problems with timescales varying from seconds or more down to femtoseconds. In this overview a number of different techniques are discussed, with emphasis on chemical applications in which information is obtained at the atomic level. The need to correlate with theory, both for calibration of theoretical methods and to obtain related information not accessible experimentally, is stressed.

  15. IZDELAVA TISKALNIKA 3D

    OpenAIRE

    Brdnik, Lovro

    2015-01-01

    Diplomsko delo analizira trenutno stanje 3D tiskalnikov na trgu. Prikazan je razvoj in principi delovanja 3D tiskalnikov. Predstavljeni so tipi 3D tiskalnikov, njihove prednosti in slabosti. Podrobneje je predstavljena zgradba in delovanje koračnih motorjev. Opravljene so meritve koračnih motorjev. Opisana je programska oprema za rokovanje s 3D tiskalniki in komponente, ki jih potrebujemo za izdelavo. Diploma se oklepa vprašanja, ali je izdelava 3D tiskalnika bolj ekonomična kot pa naložba v ...

  16. Seismic attribute detection of faults and fluid pathways within an active strike-slip shear zone: New insights from high-resolution 3D P-Cable™ seismic data along the Hosgri Fault, offshore California

    Science.gov (United States)

    Kluesner, Jared; Brothers, Daniel

    2016-01-01

    Poststack data conditioning and neural-network seismic attribute workflows are used to detect and visualize faulting and fluid migration pathways within a 13.7 km2 13.7 km2 3D P-Cable™ seismic volume located along the Hosgri Fault Zone offshore central California. The high-resolution 3D volume used in this study was collected in 2012 as part of Pacific Gas and Electric’s Central California Seismic Imaging Project. Three-dimensional seismic reflection data were acquired using a triple-plate boomer source (1.75 kJ) and a short-offset, 14-streamer, P-Cable system. The high-resolution seismic data were processed into a prestack time-migrated 3D volume and publically released in 2014. Postprocessing, we employed dip-steering (dip and azimuth) and structural filtering to enhance laterally continuous events and remove random noise and acquisition artifacts. In addition, the structural filtering was used to enhance laterally continuous edges, such as faults. Following data conditioning, neural-network based meta-attribute workflows were used to detect and visualize faults and probable fluid-migration pathways within the 3D seismic volume. The workflow used in this study clearly illustrates the utility of advanced attribute analysis applied to high-resolution 3D P-Cable data. For example, results from the fault attribute workflow reveal a network of splayed and convergent fault strands within an approximately 1.3 km wide shear zone that is characterized by distinctive sections of transpressional and transtensional dominance. Neural-network chimney attribute calculations indicate that fluids are concentrated along discrete faults in the transtensional zones, but appear to be more broadly distributed amongst fault bounded anticlines and structurally controlled traps in the transpressional zones. These results provide high-resolution, 3D constraints on the relationships between strike-slip fault mechanics, substrate deformation, and fluid migration along an active

  17. Marvels of enzyme catalysis at true atomic resolution: distortions, bond elongations, hidden flips, protonation states and atom identities.

    Science.gov (United States)

    Neumann, Piotr; Tittmann, Kai

    2014-12-01

    Although general principles of enzyme catalysis are fairly well understood nowadays, many important details of how exactly the substrate is bound and processed in an enzyme remain often invisible and as such elusive. In fortunate cases, structural analysis of enzymes can be accomplished at true atomic resolution thus making possible to shed light on otherwise concealed fine-structural traits of bound substrates, intermediates, cofactors and protein groups. We highlight recent structural studies of enzymes using ultrahigh-resolution X-ray protein crystallography showcasing its enormous potential as a tool in the elucidation of enzymatic mechanisms and in unveiling fundamental principles of enzyme catalysis. We discuss the observation of seemingly hyper-reactive, physically distorted cofactors and intermediates with elongated scissile substrate bonds, the detection of 'hidden' conformational and chemical equilibria and the analysis of protonation states with surprising findings. In delicate cases, atomic resolution is required to unambiguously disclose the identity of atoms as demonstrated for the metal cluster in nitrogenase. In addition to the pivotal structural findings and the implications for our understanding of enzyme catalysis, we further provide a practical framework for resolution enhancement through optimized data acquisition and processing.

  18. 3D and Education

    Science.gov (United States)

    Meulien Ohlmann, Odile

    2013-02-01

    Today the industry offers a chain of 3D products. Learning to "read" and to "create in 3D" becomes an issue of education of primary importance. 25 years professional experience in France, the United States and Germany, Odile Meulien set up a personal method of initiation to 3D creation that entails the spatial/temporal experience of the holographic visual. She will present some different tools and techniques used for this learning, their advantages and disadvantages, programs and issues of educational policies, constraints and expectations related to the development of new techniques for 3D imaging. Although the creation of display holograms is very much reduced compared to the creation of the 90ies, the holographic concept is spreading in all scientific, social, and artistic activities of our present time. She will also raise many questions: What means 3D? Is it communication? Is it perception? How the seeing and none seeing is interferes? What else has to be taken in consideration to communicate in 3D? How to handle the non visible relations of moving objects with subjects? Does this transform our model of exchange with others? What kind of interaction this has with our everyday life? Then come more practical questions: How to learn creating 3D visualization, to learn 3D grammar, 3D language, 3D thinking? What for? At what level? In which matter? for whom?

  19. Towards automated firearm identification based on high resolution 3D data: rotation-invariant features for multiple line-profile-measurement of firing pin shapes

    Science.gov (United States)

    Fischer, Robert; Vielhauer, Claus

    2015-03-01

    Understanding and evaluation of potential evidence, as well as evaluation of automated systems for forensic examinations currently play an important role within the domain of digital crime scene analysis. The application of 3D sensing and pattern recognition systems for automatic extraction and comparison of firearm related tool marks is an evolving field of research within this domain. In this context, the design and evaluation of rotation-invariant features for use on topography data play a particular important role. In this work, we propose and evaluate a 3D imaging system along with two novel features based on topography data and multiple profile-measurement-lines for automatic matching of firing pin shapes. Our test set contains 72 cartridges of three manufactures shot by six different 9mm guns. The entire pattern recognition workflow is addressed. This includes the application of confocal microscopy for data acquisition, preprocessing covers outlier handling, data normalization, as well as necessary segmentation and registration. Feature extraction involves the two introduced features for automatic comparison and matching of 3D firing pin shapes. The introduced features are called `Multiple-Circle-Path' (MCP) and `Multiple-Angle-Path' (MAP). Basically both features are compositions of freely configurable amounts of circular or straight path-lines combined with statistical evaluations. During the first part of evaluation (E1), we examine how well it is possible to differentiate between two 9mm weapons of the same mark and model. During second part (E2), we evaluate the discrimination accuracy regarding the set of six different 9mm guns. During the third part (E3), we evaluate the performance of the features in consideration of different rotation angles. In terms of E1, the best correct classification rate is 100% and in terms of E2 the best result is 86%. The preliminary results for E3 indicate robustness of both features regarding rotation. However, in future

  20. Simulation studies of atomic resolution X-ray holography

    Indian Academy of Sciences (India)

    Yogesh Kashyap; P S Sarkar; Amar Sinha; B K Godwal

    2004-02-01

    X-ray holography is a new method of structure determination based on measurement of interference of a known reference wave with an unknown object wave (containing information on atomic sites scattering the reference wave) so that phase information is preserved. Unlike X-ray diffraction, it does not demand for translational periodicity in the material. It is based on the idea similar to that of optical holography and has been tested on crystals, quasicrystals, thin films and doped semiconductors for their structure determination. In order to analyse potentials and limitations of this technique, we have carried out theoretical simulation studies on simple structures. In this paper we describe the basic algorithm of hologram generation and reconstruction of atomic positions from generated data. We illustrate this technique using Fe (bcc) single crystal as sample case to demonstrate its capabilities and limitations. Simulations were carried out on the Cu (fcc) structure and on complex structure such as the Al–Pd–Mn quasicrystal. Technical issues such as low signal to noise ratio, twin image problem etc have been discussed briefly to emphasize the need for high intensity X-ray source such as synchrotron for experiments and proper reconstruction algorithm. Finally the scope and potential of this technique have been discussed.

  1. Visualization of arrangements of carbon atoms in graphene layers by Raman mapping and atomic-resolution TEM

    KAUST Repository

    Cong, Chunxiao

    2013-02-01

    In-plane and out-of-plane arrangements of carbon atoms in graphene layers play critical roles in the fundamental physics and practical applications of these novel two-dimensional materials. Here, we report initial results on the edge/crystal orientations and stacking orders of bi-and tri-layer graphene (BLG and TLG) from Raman spectroscopy and transmission electron microscopy (TEM) experiments performed on the same sample. We introduce a new method of transferring graphene flakes onto a normal TEM grid. Using this novel method, we probed the BLG and TLG flakes that had been previously investigated by Raman scattering with high-resolution (atomic) TEM.

  2. Martian terrain - 3D

    Science.gov (United States)

    1997-01-01

    This area of terrain near the Sagan Memorial Station was taken on Sol 3 by the Imager for Mars Pathfinder (IMP). 3D glasses are necessary to identify surface detail.The IMP is a stereo imaging system with color capability provided by 24 selectable filters -- twelve filters per 'eye.' It stands 1.8 meters above the Martian surface, and has a resolution of two millimeters at a range of two meters.Mars Pathfinder is the second in NASA's Discovery program of low-cost spacecraft with highly focused science goals. The Jet Propulsion Laboratory, Pasadena, CA, developed and manages the Mars Pathfinder mission for NASA's Office of Space Science, Washington, D.C. JPL is an operating division of the California Institute of Technology (Caltech). The Imager for Mars Pathfinder (IMP) was developed by the University of Arizona Lunar and Planetary Laboratory under contract to JPL. Peter Smith is the Principal Investigator.Click below to see the left and right views individually. [figure removed for brevity, see original site] Left [figure removed for brevity, see original site] Right

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

    Science.gov (United States)

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

    2014-01-01

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

  4. Collaborative Project. 3D Radiative Transfer Parameterization Over Mountains/Snow for High-Resolution Climate Models. Fast physics and Applications

    Energy Technology Data Exchange (ETDEWEB)

    Liou, Kuo-Nan [Univ. of California, Los Angeles, CA (United States)

    2016-02-09

    Under the support of the aforementioned DOE Grant, we have made two fundamental contributions to atmospheric and climate sciences: (1) Develop an efficient 3-D radiative transfer parameterization for application to intense and intricate inhomogeneous mountain/snow regions. (2) Innovate a stochastic parameterization for light absorption by internally mixed black carbon and dust particles in snow grains for understanding and physical insight into snow albedo reduction in climate models. With reference to item (1), we divided solar fluxes reaching mountain surfaces into five components: direct and diffuse fluxes, direct- and diffuse-reflected fluxes, and coupled mountain-mountain flux. “Exact” 3D Monte Carlo photon tracing computations can then be performed for these solar flux components to compare with those calculated from the conventional plane-parallel (PP) radiative transfer program readily available in climate models. Subsequently, Parameterizations of the deviations of 3D from PP results for five flux components are carried out by means of the multiple linear regression analysis associated with topographic information, including elevation, solar incident angle, sky view factor, and terrain configuration factor. We derived five regression equations with high statistical correlations for flux deviations and successfully incorporated this efficient parameterization into WRF model, which was used as the testbed in connection with the Fu-Liou-Gu PP radiation scheme that has been included in the WRF physics package. Incorporating this 3D parameterization program, we conducted simulations of WRF and CCSM4 to understand and evaluate the mountain/snow effect on snow albedo reduction during seasonal transition and the interannual variability for snowmelt, cloud cover, and precipitation over the Western United States presented in the final report. With reference to item (2), we developed in our previous research a geometric-optics surface-wave approach (GOS) for the

  5. 回火马氏体中合金碳化物的3D原子探针表征Ⅱ.长大%3D ATOM PROBE CHARACTERAZATION OF ALLOY CARBIDES IN TEMPERING MARTENITE Ⅱ. Growth

    Institute of Scientific and Technical Information of China (English)

    刘庆冬; 彭剑超; 刘文庆; 周邦新

    2009-01-01

    The mechanical properties of quench-tempered high-strength low alloy steels are commonly optimized by fine and dispersively distributed alloy carbides. The role of the alloying elements in determining the alloy carbide precipitation sequence is of great significance. The co-addition of carbide-forming elements such as Mo, V and Nb complicates the precipitation behavior. The mutual inter-solutions and growth rates of various MC-and/or M_2C-type carbides are qual-itatively affected by the intrinsic solubility and diffusion at certain tempering condition. However, comprehensive study of the precipitation sequence must be followed with atomic scale resolution techniques. The 3D atom probe (3DAP) is a unique tool capable of obtaining chemical information at the atomic level, offering a powerful method to investigate microstructural and compositional changes occurring at nano-scale. And the sizes, morphology and composition of individual alloy carbide may be visualized and quantified by 3DAP. In this paper, a quenched Nb-V microalloyed steel was chosen to investigate the precipitation behavior of alloy carbide after tempering at 450-650 ℃ for different times. 3DAP, micro hardness test and TEM were applied to characterize the phenomena of hardening and softening during tempering, and the composition evolution and growth behaviors of the alloyed carbides were also studied. The results indicated the second hardening of the 500-600℃ tempering martensite is mainly resulting from precipitation strengthening of alloy carbides. The alloy carbides composition dynamically changed with elevated temperature or prolonged time, that is, the stronger carbide-forming elements replaced or partly replaced the weaker ones. At first V and Nb replaced Mo, and then Nb partly replaced V, and at last the carbides with certain composition were formed. Tempering time has relatively less effect on the carbides composition compared with temperature. When the tempering temperature elevated or

  6. TEHNOLOGIJE 3D TISKALNIKOV

    OpenAIRE

    Kolar, Nataša

    2016-01-01

    Diplomsko delo predstavi razvoj tiskanja skozi čas. Podrobneje so opisani 3D tiskalniki, ki uporabljajo različne tehnologije 3D tiskanja. Predstavljene so različne tehnologije 3D tiskanja, njihova uporaba in narejeni prototipi oz. končni izdelki. Diplomsko delo opiše celoten postopek, od zamisli, priprave podatkov in tiskalnika do izdelave prototipa oz. končnega izdelka.

  7. Atomic resolution probe for allostery in the regulatory thin filament

    Science.gov (United States)

    Williams, Michael R.; Lehman, Sarah J.; Tardiff, Jil C.; Schwartz, Steven D.

    2016-01-01

    Calcium binding and dissociation within the cardiac thin filament (CTF) is a fundamental regulator of normal contraction and relaxation. Although the disruption of this complex, allosterically mediated process has long been implicated in human disease, the precise atomic-level mechanisms remain opaque, greatly hampering the development of novel targeted therapies. To address this question, we used a fully atomistic CTF model to test both Ca2+ binding strength and the energy required to remove Ca2+ from the N-lobe binding site in WT and mutant troponin complexes that have been linked to genetic cardiomyopathies. This computational approach is combined with measurements of in vitro Ca2+ dissociation rates in fully reconstituted WT and cardiac troponin T R92L and R92W thin filaments. These human disease mutations represent known substitutions at the same residue, reside at a significant distance from the calcium binding site in cardiac troponin C, and do not affect either the binding pocket affinity or EF-hand structure of the binding domain. Both have been shown to have significantly different effects on cardiac function in vivo. We now show that these mutations independently alter the interaction between the Ca2+ ion and cardiac troponin I subunit. This interaction is a previously unidentified mechanism, in which mutations in one protein of a complex indirectly affect a third via structural and dynamic changes in a second to yield a pathogenic change in thin filament function that results in mutation-specific disease states. We can now provide atom-level insight that is potentially highly actionable in drug design. PMID:26957598

  8. From 3D view to 3D print

    Science.gov (United States)

    Dima, M.; Farisato, G.; Bergomi, M.; Viotto, V.; Magrin, D.; Greggio, D.; Farinato, J.; Marafatto, L.; Ragazzoni, R.; Piazza, D.

    2014-08-01

    In the last few years 3D printing is getting more and more popular and used in many fields going from manufacturing to industrial design, architecture, medical support and aerospace. 3D printing is an evolution of bi-dimensional printing, which allows to obtain a solid object from a 3D model, realized with a 3D modelling software. The final product is obtained using an additive process, in which successive layers of material are laid down one over the other. A 3D printer allows to realize, in a simple way, very complex shapes, which would be quite difficult to be produced with dedicated conventional facilities. Thanks to the fact that the 3D printing is obtained superposing one layer to the others, it doesn't need any particular work flow and it is sufficient to simply draw the model and send it to print. Many different kinds of 3D printers exist based on the technology and material used for layer deposition. A common material used by the toner is ABS plastics, which is a light and rigid thermoplastic polymer, whose peculiar mechanical properties make it diffusely used in several fields, like pipes production and cars interiors manufacturing. I used this technology to create a 1:1 scale model of the telescope which is the hardware core of the space small mission CHEOPS (CHaracterising ExOPlanets Satellite) by ESA, which aims to characterize EXOplanets via transits observations. The telescope has a Ritchey-Chrétien configuration with a 30cm aperture and the launch is foreseen in 2017. In this paper, I present the different phases for the realization of such a model, focusing onto pros and cons of this kind of technology. For example, because of the finite printable volume (10×10×12 inches in the x, y and z directions respectively), it has been necessary to split the largest parts of the instrument in smaller components to be then reassembled and post-processed. A further issue is the resolution of the printed material, which is expressed in terms of layers

  9. The role of amino acid electron-donor/acceptor atoms in host-cell binding peptides is associated with their 3D structure and HLA-binding capacity in sterile malarial immunity induction

    Energy Technology Data Exchange (ETDEWEB)

    Patarroyo, Manuel E., E-mail: mepatarr@mail.com [Fundacion Instituto de Inmunologia de Colombia (FIDIC), Bogota (Colombia); Universidad Nacional de Colombia, Bogota (Colombia); Almonacid, Hannia; Moreno-Vranich, Armando [Fundacion Instituto de Inmunologia de Colombia (FIDIC), Bogota (Colombia)

    2012-01-20

    Highlights: Black-Right-Pointing-Pointer Fundamental residues located in some HABPs are associated with their 3D structure. Black-Right-Pointing-Pointer Electron-donor atoms present in {beta}-turn, random, distorted {alpha}-helix structures. Black-Right-Pointing-Pointer Electron-donor atoms bound to HLA-DR53. Black-Right-Pointing-Pointer Electron-acceptor atoms present in regular {alpha}-helix structure bound to HLA-DR52. -- Abstract: Plasmodium falciparum malaria continues being one of the parasitic diseases causing the highest worldwide mortality due to the parasite's multiple evasion mechanisms, such as immunological silence. Membrane and organelle proteins are used during invasion for interactions mediated by high binding ability peptides (HABPs); these have amino acids which establish hydrogen bonds between them in some of their critical binding residues. Immunisation assays in the Aotus model using HABPs whose critical residues had been modified have revealed a conformational change thereby enabling a protection-inducing response. This has improved fitting within HLA-DR{beta}1{sup Asterisk-Operator} molecules where amino acid electron-donor atoms present in {beta}-turn, random or distorted {alpha}-helix structures preferentially bound to HLA-DR53 molecules, whilst HABPs having amino acid electron-acceptor atoms present in regular {alpha}-helix structure bound to HLA-DR52. This data has great implications for vaccine development.

  10. Implementation of 3D spatial indexing and compression in a large-scale molecular dynamics simulation database for rapid atomic contact detection

    Directory of Open Access Journals (Sweden)

    Toofanny Rudesh D

    2011-08-01

    Full Text Available Abstract Background Molecular dynamics (MD simulations offer the ability to observe the dynamics and interactions of both whole macromolecules and individual atoms as a function of time. Taken in context with experimental data, atomic interactions from simulation provide insight into the mechanics of protein folding, dynamics, and function. The calculation of atomic interactions or contacts from an MD trajectory is computationally demanding and the work required grows exponentially with the size of the simulation system. We describe the implementation of a spatial indexing algorithm in our multi-terabyte MD simulation database that significantly reduces the run-time required for discovery of contacts. The approach is applied to the Dynameomics project data. Spatial indexing, also known as spatial hashing, is a method that divides the simulation space into regular sized bins and attributes an index to each bin. Since, the calculation of contacts is widely employed in the simulation field, we also use this as the basis for testing compression of data tables. We investigate the effects of compression of the trajectory coordinate tables with different options of data and index compression within MS SQL SERVER 2008. Results Our implementation of spatial indexing speeds up the calculation of contacts over a 1 nanosecond (ns simulation window by between 14% and 90% (i.e., 1.2 and 10.3 times faster. For a 'full' simulation trajectory (51 ns spatial indexing reduces the calculation run-time between 31 and 81% (between 1.4 and 5.3 times faster. Compression resulted in reduced table sizes but resulted in no significant difference in the total execution time for neighbour discovery. The greatest compression (~36% was achieved using page level compression on both the data and indexes. Conclusions The spatial indexing scheme significantly decreases the time taken to calculate atomic contacts and could be applied to other multidimensional neighbor discovery

  11. Metal-graphene interaction studied via atomic resolution scanning transmission electron microscopy.

    Science.gov (United States)

    Zan, Recep; Bangert, Ursel; Ramasse, Quentin; Novoselov, Konstantin S

    2011-03-09

    Distributions and atomic sites of transition metals and gold on suspended graphene were investigated via high-resolution scanning transmission electron microscopy, especially using atomic resolution high angle dark field imaging. All metals, albeit as singular atoms or atom aggregates, reside in the omni-present hydrocarbon surface contamination; they do not form continuous films, but clusters or nanocrystals. No interaction was found between Au atoms and clean single-layer graphene surfaces, i.e., no Au atoms are retained on such surfaces. Au and also Fe atoms do, however, bond to clean few-layer graphene surfaces, where they assume T and B sites, respectively. Cr atoms were found to interact more strongly with clean monolayer graphene, they are possibly incorporated at graphene lattice imperfections and have been observed to catalyze dissociation of C-C bonds. This behavior might explain the observed high frequency of Cr-cluster nucleation, and the usefulness as wetting layer, for depositing electrical contacts on graphene.

  12. Atomic resolution structure of serine protease proteinase K at ambient temperature

    Science.gov (United States)

    Masuda, Tetsuya; Suzuki, Mamoru; Inoue, Shigeyuki; Song, Changyong; Nakane, Takanori; Nango, Eriko; Tanaka, Rie; Tono, Kensuke; Joti, Yasumasa; Kameshima, Takashi; Hatsui, Takaki; Yabashi, Makina; Mikami, Bunzo; Nureki, Osamu; Numata, Keiji; Iwata, So; Sugahara, Michihiro

    2017-01-01

    Atomic resolution structures (beyond 1.20 Å) at ambient temperature, which is usually hampered by the radiation damage in synchrotron X-ray crystallography (SRX), will add to our understanding of the structure-function relationships of enzymes. Serial femtosecond crystallography (SFX) has attracted surging interest by providing a route to bypass such challenges. Yet the progress on atomic resolution analysis with SFX has been rather slow. In this report, we describe the 1.20 Å resolution structure of proteinase K using 13 keV photon energy. Hydrogen atoms, water molecules, and a number of alternative side-chain conformations have been resolved. The increase in the value of B-factor in SFX suggests that the residues and water molecules adjacent to active sites were flexible and exhibited dynamic motions at specific substrate-recognition sites. PMID:28361898

  13. Chemically modified STM tips for atomic-resolution imaging of ultrathin NaCI films

    Institute of Scientific and Technical Information of China (English)

    Zhe Li[1; Koen Schouteden[1; Violeta lancu[1; Ewald Janssens[1; Peter Lievens[1; Chris Van Haesendonck[1; Jorge I. Cerda[2

    2015-01-01

    Cl-functionalized scanning tunneling microscopy (STM) tips are fabricated by modifying a tungsten STM tip in situ on islands of ultrathin NaCI(100) films on Au(111) surfaces. The functionalized tips are used to achieve clear atomic- resolution imaging of NaCI(100) islands. In comparison with bare metal tips, the chemically modified tips yield drastically enhanced spatial resolution as well as contrast reversal in STM topographs, implying that Na atoms, rather than C1 atoms, are imaged as protrusions. STM simulations based on a Green's function formalism reveal that the experimentally observed contrast reversal in the STM topographs is due to the highly localized character of the Cl-pz states at the tip apex. An additional remarkable characteristic of the modified tips is that in dI/dV maps, a Na atom appears as a ring with a diameter that depends crucially on the tip-sample distance.

  14. 3D virtuel udstilling

    DEFF Research Database (Denmark)

    Tournay, Bruno; Rüdiger, Bjarne

    2006-01-01

    3d digital model af Arkitektskolens gård med virtuel udstilling af afgangsprojekter fra afgangen sommer 2006. 10 s.......3d digital model af Arkitektskolens gård med virtuel udstilling af afgangsprojekter fra afgangen sommer 2006. 10 s....

  15. Development of an iterative reconstruction method to overcome 2D detector low resolution limitations in MLC leaf position error detection for 3D dose verification in IMRT

    NARCIS (Netherlands)

    Visser, Ruurd; Godart, J.; Wauben, D. J. L.; Langendijk, J. A.; van't Veld, A. A.; Korevaar, E. W.

    2016-01-01

    The objective of this study was to introduce a new iterative method to reconstruct multi leaf collimator (MLC) positions based on low resolution ionization detector array measurements and to evaluate its error detection performance. The iterative reconstruction method consists of a fluence model, a

  16. An effective hyper-resolution pseudo-3D implementation of small scale hydrological features to improve regional and global climate studies

    Science.gov (United States)

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

    2013-12-01

    Global land surface processes play an important role in the land-atmosphere exchanges of energy, water, and trace gases. As such, correct representation of the different hydrological processes has long been an important research topic in climate modeling. Historically, these processes were presented at a relatively coarse horizontal resolution, focusing mainly on the vertical hydrological response, while lateral exchanges were either disregarded or implemented in a relatively crude manner. Increases in computational power have led to higher resolution regional and global land surface models. For the coming years, it is anticipated that these models will simulate the hydrological response of the earth surface at a 100-1000 meter pixel size, which is stated as hyper-resolution earth surface modeling. At these relatively high resolutions, correct representation of groundwater, including lateral interactions across pixels and with the channel network, becomes important. Next to that, at these high resolutions elevation differences have a larger impact on the hydrological response and therefore need to be represented properly. We will present a new hydrological framework specifically developed to operate at these hyper-resolutions. Our new approach discriminates between differences in the hydrological response of hillslopes, riparian zones, wetlands and flat regions within a given pixel, while interacting with the channel network and the atmosphere. Instead of applying the traditional conceptual approach, these interactions are incorporated using a physically-based approach. In order to be able to differentiate between these different hydrological features, globally available high-resolution 30 meter DEM data were analyzed using a state-of-the-art digital geomorphological identification method. Based on these techniques, local estimates of soil depth, hillslope width functions, channel network density, etc. were also obtained that are used as input to the model In the

  17. Submolecular Resolution Imaging of Molecules by Atomic Force Microscopy: The Influence of the Electrostatic Force

    Science.gov (United States)

    van der Lit, Joost; Di Cicco, Francesca; Hapala, Prokop; Jelinek, Pavel; Swart, Ingmar

    2016-03-01

    The forces governing the contrast in submolecular resolution imaging of molecules with atomic force microscopy (AFM) have recently become a topic of intense debate. Here, we show that the electrostatic force is essential to understand the contrast in atomically resolved AFM images of polar molecules. Specifically, we image strongly polarized molecules with negatively and positively charged tips. A contrast inversion is observed above the polar groups. By taking into account the electrostatic forces between tip and molecule, the observed contrast differences can be reproduced using a molecular mechanics model. In addition, we analyze the height dependence of the various force components contributing to the high-resolution AFM contrast.

  18. 3D laptop for defense applications

    Science.gov (United States)

    Edmondson, Richard; Chenault, David

    2012-06-01

    Polaris Sensor Technologies has developed numerous 3D display systems using a US Army patented approach. These displays have been developed as prototypes for handheld controllers for robotic systems and closed hatch driving, and as part of a TALON robot upgrade for 3D vision, providing depth perception for the operator for improved manipulation and hazard avoidance. In this paper we discuss the prototype rugged 3D laptop computer and its applications to defense missions. The prototype 3D laptop combines full temporal and spatial resolution display with the rugged Amrel laptop computer. The display is viewed through protective passive polarized eyewear, and allows combined 2D and 3D content. Uses include robot tele-operation with live 3D video or synthetically rendered scenery, mission planning and rehearsal, enhanced 3D data interpretation, and simulation.

  19. A Novel 2D Image Compression Algorithm Based on Two Levels DWT and DCT Transforms with Enhanced Minimize-Matrix-Size Algorithm for High Resolution Structured Light 3D Surface Reconstruction

    Science.gov (United States)

    Siddeq, M. M.; Rodrigues, M. A.

    2015-09-01

    Image compression techniques are widely used on 2D image 2D video 3D images and 3D video. There are many types of compression techniques and among the most popular are JPEG and JPEG2000. In this research, we introduce a new compression method based on applying a two level discrete cosine transform (DCT) and a two level discrete wavelet transform (DWT) in connection with novel compression steps for high-resolution images. The proposed image compression algorithm consists of four steps. (1) Transform an image by a two level DWT followed by a DCT to produce two matrices: DC- and AC-Matrix, or low and high frequency matrix, respectively, (2) apply a second level DCT on the DC-Matrix to generate two arrays, namely nonzero-array and zero-array, (3) apply the Minimize-Matrix-Size algorithm to the AC-Matrix and to the other high-frequencies generated by the second level DWT, (4) apply arithmetic coding to the output of previous steps. A novel decompression algorithm, Fast-Match-Search algorithm (FMS), is used to reconstruct all high-frequency matrices. The FMS-algorithm computes all compressed data probabilities by using a table of data, and then using a binary search algorithm for finding decompressed data inside the table. Thereafter, all decoded DC-values with the decoded AC-coefficients are combined in one matrix followed by inverse two levels DCT with two levels DWT. The technique is tested by compression and reconstruction of 3D surface patches. Additionally, this technique is compared with JPEG and JPEG2000 algorithm through 2D and 3D root-mean-square-error following reconstruction. The results demonstrate that the proposed compression method has better visual properties than JPEG and JPEG2000 and is able to more accurately reconstruct surface patches in 3D.

  20. Study on the Method of Gas Atomization for Production of 3 D Printing Metal Powders%气雾化法制备3D打印金属粉末的方法研究∗

    Institute of Scientific and Technical Information of China (English)

    张艳红; 董兵斌

    2016-01-01

    3D打印技术是一种新型的成型技术,其优点在于无需机械加工或任何模具,就可快速地将物体的数字化模型由概念变为实物,从而缩短产品的研制周期,提高生产效率。金属粉末作为金属3D打印最重要的原材料,其制备方法备受人们的关注。本文主要概述了雾化技术的基础原理,综述了气雾化用各类喷嘴结构、气体流场结构及工艺参数对粉末特性的影响,并对3D打印金属粉末制备技术的方法研究和最新进展进行了分析。%3D Printing technology is a new forming technology, it has some advantages:numerical model of object is change quickly from the concept into real without any machining or mold. It shortens the product development cycle and improves pro-duction efficiency. The metal powders is the most important raw material of 3D printing, its preparation method has attracted much attention. In this paper,a basic principle of the atomization technology is provided, the nozzle structures of gas atomiza-tion, effect of gas flow field structure and process parameters on the powder characteristics are all introduced,technology re-search and the latest advances in preparation of 3D printing metal powder are analyzed.

  1. Optimal experimental design for nano-particle atom-counting from high-resolution STEM images

    Energy Technology Data Exchange (ETDEWEB)

    De Backer, A.; De wael, A.; Gonnissen, J.; Van Aert, S., E-mail: sandra.vanaert@uantwerpen.be

    2015-04-15

    In the present paper, the principles of detection theory are used to quantify the probability of error for atom-counting from high resolution scanning transmission electron microscopy (HR STEM) images. Binary and multiple hypothesis testing have been investigated in order to determine the limits to the precision with which the number of atoms in a projected atomic column can be estimated. The probability of error has been calculated when using STEM images, scattering cross-sections or peak intensities as a criterion to count atoms. Based on this analysis, we conclude that scattering cross-sections perform almost equally well as images and perform better than peak intensities. Furthermore, the optimal STEM detector design can be derived for atom-counting using the expression for the probability of error. We show that for very thin objects LAADF is optimal and that for thicker objects the optimal inner detector angle increases.

  2. 3D printing of functional structures

    NARCIS (Netherlands)

    Krijnen, G.J.M.

    2016-01-01

    The technology colloquial known as ‘3D printing’ has developed in such diversity in printing technologies and application fields that meanwhile it seems anything is possible. However, clearly the ideal 3D Printer, with high resolution, multi-material capability, fast printing, etc. is yet to be deve

  3. MISTiC Winds, a Micro-Satellite Constellation Approach to High Resolution Observations of the Atmosphere using Infrared Sounding and 3D Winds Measurements

    Science.gov (United States)

    Maschhoff, K. R.; Polizotti, J. J.; Susskind, J.; Aumann, H. H.

    2015-12-01

    MISTiCTM Winds is an approach to improve short-term weather forecasting based on a miniature high resolution, wide field, thermal emission spectrometry instrument that will provide global tropospheric vertical profiles of atmospheric temperature and humidity at high (3-4 km) horizontal and vertical ( 1 km) spatial resolution. MISTiC's extraordinarily small size, payload mass of less than 15 kg, and minimal cooling requirements can be accommodated aboard a 27U-class CubeSat or an ESPA-Class micro-satellite. Low fabrication and launch costs enable a LEO sun-synchronous sounding constellation that would collectively provide frequent IR vertical profiles and vertically resolved atmospheric motion vector wind observations in the troposphere. These observations are highly complementary to present and emerging environmental observing systems, and would provide a combination of high vertical and horizontal resolution not provided by any other environmental observing system currently in operation. The spectral measurements that would be provided by MISTiC Winds are similar to those of NASA's Atmospheric Infrared Sounder that was built by BAE Systems and operates aboard the AQUA satellite. These new observations, when assimilated into high resolution numerical weather models, would revolutionize short-term and severe weather forecasting, save lives, and support key economic decisions in the energy, air transport, and agriculture arenas-at much lower cost than providing these observations from geostationary orbit. In addition, this observation capability would be a critical tool for the study of transport processes for water vapor, clouds, pollution, and aerosols. Key technical risks are being reduced through laboratory and airborne testing under NASA's Instrument Incubator Program.

  4. Mistic winds, a microsatellite constellation approach to high-resolution observations of the atmosphere using infrared sounding and 3d winds measurements

    Science.gov (United States)

    Maschhoff, K. R.; Polizotti, J. J.; Aumann, H. H.; Susskind, J.

    2016-10-01

    MISTiC Winds is an approach to improve short-term weather forecasting based on a miniature high resolution, wide field, thermal emission spectrometry instrument that will provide global tropospheric vertical profiles of atmospheric temperature and humidity at high (3-4 km) horizontal and vertical ( 1 km) spatial resolution. MISTiC's extraordinarily small size, payload mass of less than 15 kg, and minimal cooling requirements can be accommodated aboard a 27U-class CubeSat or an ESPA-Class micro-satellite. Low fabrication and launch costs enable a LEO sunsynchronous sounding constellation that would collectively provide frequent IR vertical profiles and vertically resolved atmospheric motion vector wind observations in the troposphere. These observations are highly complementary to present and emerging environmental observing systems, and would provide a combination of high vertical and horizontal resolution not provided by any other environmental observing system currently in operation. The spectral measurements that would be provided by MISTiC Winds are similar to those of NASA's AIRS that was built by BAE Systems and operates aboard the AQUA satellite. These new observations, when assimilated into high resolution numerical weather models, would revolutionize short-term and severe weather forecasting, save lives, and support key economic decisions in the energy, air transport, and agriculture arenas-at much lower cost than providing these observations from geostationary orbit. In addition, this observation capability would be a critical tool for the study of transport processes for water vapor, clouds, pollution, and aerosols. Key remaining technical risks are being reduced through laboratory and airborne testing under NASA's Instrument Incubator Program.

  5. MISTiC Winds: A micro-satellite constellation approach to high resolution observations of the atmosphere using infrared sounding and 3D winds measurements

    Science.gov (United States)

    Maschhoff, K. R.; Polizotti, J. J.; Aumann, H. H.; Susskind, J.

    2016-09-01

    MISTiCTM Winds is an approach to improve short-term weather forecasting based on a miniature high resolution, wide field, thermal emission spectrometry instrument that will provide global tropospheric vertical profiles of atmospheric temperature and humidity at high (3-4 km) horizontal and vertical ( 1 km) spatial resolution. MISTiC's extraordinarily small size, payload mass of less than 15 kg, and minimal cooling requirements can be accommodated aboard a 27U-class CubeSat or an ESPA-Class micro-satellite. Low fabrication and launch costs enable a LEO sunsynchronous sounding constellation that would collectively provide frequent IR vertical profiles and vertically resolved atmospheric motion vector wind observations in the troposphere. These observations are highly complementary to present and emerging environmental observing systems, and would provide a combination of high vertical and horizontal resolution not provided by any other environmental observing system currently in operation. The spectral measurements that would be provided by MISTiC Winds are similar to those of NASA's AIRS that was built by BAE Systems and operates aboard the AQUA satellite. These new observations, when assimilated into high resolution numerical weather models, would revolutionize short-term and severe weather forecasting, save lives, and support key economic decisions in the energy, air transport, and agriculture arenas-at much lower cost than providing these observations from geostationary orbit. In addition, this observation capability would be a critical tool for the study of transport processes for water vapor, clouds, pollution, and aerosols. Key remaining technical risks are being reduced through laboratory and airborne testing under NASA's Instrument Incubator Program.

  6. Blender 3D cookbook

    CERN Document Server

    Valenza, Enrico

    2015-01-01

    This book is aimed at the professionals that already have good 3D CGI experience with commercial packages and have now decided to try the open source Blender and want to experiment with something more complex than the average tutorials on the web. However, it's also aimed at the intermediate Blender users who simply want to go some steps further.It's taken for granted that you already know how to move inside the Blender interface, that you already have 3D modeling knowledge, and also that of basic 3D modeling and rendering concepts, for example, edge-loops, n-gons, or samples. In any case, it'

  7. Advanced 3D Object Identification System Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Optra will build an Advanced 3D Object Identification System utilizing three or more high resolution imagers spaced around a launch platform. Data from each imager...

  8. 3D Digital Modelling

    DEFF Research Database (Denmark)

    Hundebøl, Jesper

    wave of new building information modelling tools demands further investigation, not least because of industry representatives' somewhat coarse parlance: Now the word is spreading -3D digital modelling is nothing less than a revolution, a shift of paradigm, a new alphabet... Research qeustions. Based...... on empirical probes (interviews, observations, written inscriptions) within the Danish construction industry this paper explores the organizational and managerial dynamics of 3D Digital Modelling. The paper intends to - Illustrate how the network of (non-)human actors engaged in the promotion (and arrest) of 3......D Modelling (in Denmark) stabilizes - Examine how 3D Modelling manifests itself in the early design phases of a construction project with a view to discuss the effects hereof for i.a. the management of the building process. Structure. The paper introduces a few, basic methodological concepts...

  9. Diffusible iodine-based contrast-enhanced computed tomography (diceCT): an emerging tool for rapid, high-resolution, 3-D imaging of metazoan soft tissues.

    Science.gov (United States)

    Gignac, Paul M; Kley, Nathan J; Clarke, Julia A; Colbert, Matthew W; Morhardt, Ashley C; Cerio, Donald; Cost, Ian N; Cox, Philip G; Daza, Juan D; Early, Catherine M; Echols, M Scott; Henkelman, R Mark; Herdina, A Nele; Holliday, Casey M; Li, Zhiheng; Mahlow, Kristin; Merchant, Samer; Müller, Johannes; Orsbon, Courtney P; Paluh, Daniel J; Thies, Monte L; Tsai, Henry P; Witmer, Lawrence M

    2016-06-01

    Morphologists have historically had to rely on destructive procedures to visualize the three-dimensional (3-D) anatomy of animals. More recently, however, non-destructive techniques have come to the forefront. These include X-ray computed tomography (CT), which has been used most commonly to examine the mineralized, hard-tissue anatomy of living and fossil metazoans. One relatively new and potentially transformative aspect of current CT-based research is the use of chemical agents to render visible, and differentiate between, soft-tissue structures in X-ray images. Specifically, iodine has emerged as one of the most widely used of these contrast agents among animal morphologists due to its ease of handling, cost effectiveness, and differential affinities for major types of soft tissues. The rapid adoption of iodine-based contrast agents has resulted in a proliferation of distinct specimen preparations and scanning parameter choices, as well as an increasing variety of imaging hardware and software preferences. Here we provide a critical review of the recent contributions to iodine-based, contrast-enhanced CT research to enable researchers just beginning to employ contrast enhancement to make sense of this complex new landscape of methodologies. We provide a detailed summary of recent case studies, assess factors that govern success at each step of the specimen storage, preparation, and imaging processes, and make recommendations for standardizing both techniques and reporting practices. Finally, we discuss potential cutting-edge applications of diffusible iodine-based contrast-enhanced computed tomography (diceCT) and the issues that must still be overcome to facilitate the broader adoption of diceCT going forward.

  10. 3D打印技术对著作权制度的冲击与回应%Challenges and Resolutions for Copyright Institution of 3D Printing

    Institute of Scientific and Technical Information of China (English)

    王鑫

    2015-01-01

    The 3D printing bring a lot of significant challenges to Copyright Institution,such as lay Copyright Law great stress on the task that should clear and definite the boundary of "Copy" as quickly as possible,sway some provisions of limitations on Rights under the "Fair Use" regulation,and query the rationality that mitigate or annul a punishment due to the "Technological Neutrality" principle. Based on the Comparative Studies of Regulations on the Protection of Layout-designs of Integrated Circuits, the thesis advises that it is necessary for Copyright Institution to enlarge the content of "Copy",revise the provisions of "Fair Use" and make innovations on technology management process to answer these challenges.%3D打印技术的出现对著作权制度产生了巨大冲击,它不仅加剧了明确作品“复制”行为范围的迫切性,动摇了“合理使用”限制中部分规定的必要性,还使得对于“技术中立”原则引致侵权责任减免的合理性受到质疑。为回应相关技术发展带来的挑战,结合《集成电路布图设计保护条例》保护模式对比探讨,认为有必要适时拓宽“复制”行为范围,进一步规范“合理使用”的行使,创新技术管理模式以完善著作权制度。

  11. A 3D high resolution ex vivo white matter atlas of the common squirrel monkey (Saimiri sciureus) based on diffusion tensor imaging.

    Science.gov (United States)

    Gao, Yurui; Parvathaneni, Prasanna; Schilling, Kurt G; Wang, Feng; Stepniewska, Iwona; Xu, Zhoubing; Choe, Ann S; Ding, Zhaohua; Gore, John C; Chen, Li Min; Landman, Bennett A; Anderson, Adam W

    2016-02-27

    Modern magnetic resonance imaging (MRI) brain atlases are high quality 3-D volumes with specific structures labeled in the volume. Atlases are essential in providing a common space for interpretation of results across studies, for anatomical education, and providing quantitative image-based navigation. Extensive work has been devoted to atlas construction for humans, macaque, and several non-primate species (e.g., rat). One notable gap in the literature is the common squirrel monkey - for which the primary published atlases date from the 1960's. The common squirrel monkey has been used extensively as surrogate for humans in biomedical studies, given its anatomical neuro-system similarities and practical considerations. This work describes the continued development of a multi-modal MRI atlas for the common squirrel monkey, for which a structural imaging space and gray matter parcels have been previously constructed. This study adds white matter tracts to the atlas. The new atlas includes 49 white matter (WM) tracts, defined using diffusion tensor imaging (DTI) in three animals and combines these data to define the anatomical locations of these tracks in a standardized coordinate system compatible with previous development. An anatomist reviewed the resulting tracts and the inter-animal reproducibility (i.e., the Dice index of each WM parcel across animals in common space) was assessed. The Dice indices range from 0.05 to 0.80 due to differences of local registration quality and the variation of WM tract position across individuals. However, the combined WM labels from the 3 animals represent the general locations of WM parcels, adding basic connectivity information to the atlas.

  12. A 3D high resolution ex vivo white matter atlas of the common squirrel monkey (saimiri sciureus) based on diffusion tensor imaging

    Science.gov (United States)

    Gao, Yurui; Parvathaneni, Prasanna; Schilling, Kurt G.; Wang, Feng; Stepniewska, Iwona; Xu, Zhoubing; Choe, Ann S.; Ding, Zhaohua; Gore, John C.; Chen, Li min; Landman, Bennett A.; Anderson, Adam W.

    2016-03-01

    Modern magnetic resonance imaging (MRI) brain atlases are high quality 3-D volumes with specific structures labeled in the volume. Atlases are essential in providing a common space for interpretation of results across studies, for anatomical education, and providing quantitative image-based navigation. Extensive work has been devoted to atlas construction for humans, macaque, and several non-primate species (e.g., rat). One notable gap in the literature is the common squirrel monkey - for which the primary published atlases date from the 1960's. The common squirrel monkey has been used extensively as surrogate for humans in biomedical studies, given its anatomical neuro-system similarities and practical considerations. This work describes the continued development of a multi-modal MRI atlas for the common squirrel monkey, for which a structural imaging space and gray matter parcels have been previously constructed. This study adds white matter tracts to the atlas. The new atlas includes 49 white matter (WM) tracts, defined using diffusion tensor imaging (DTI) in three animals and combines these data to define the anatomical locations of these tracks in a standardized coordinate system compatible with previous development. An anatomist reviewed the resulting tracts and the inter-animal reproducibility (i.e., the Dice index of each WM parcel across animals in common space) was assessed. The Dice indices range from 0.05 to 0.80 due to differences of local registration quality and the variation of WM tract position across individuals. However, the combined WM labels from the 3 animals represent the general locations of WM parcels, adding basic connectivity information to the atlas.

  13. Professional Papervision3D

    CERN Document Server

    Lively, Michael

    2010-01-01

    Professional Papervision3D describes how Papervision3D works and how real world applications are built, with a clear look at essential topics such as building websites and games, creating virtual tours, and Adobe's Flash 10. Readers learn important techniques through hands-on applications, and build on those skills as the book progresses. The companion website contains all code examples, video step-by-step explanations, and a collada repository.

  14. AE3D

    Energy Technology Data Exchange (ETDEWEB)

    2016-06-20

    AE3D solves for the shear Alfven eigenmodes and eigenfrequencies in a torodal magnetic fusion confinement device. The configuration can be either 2D (e.g. tokamak, reversed field pinch) or 3D (e.g. stellarator, helical reversed field pinch, tokamak with ripple). The equations solved are based on a reduced MHD model and sound wave coupling effects are not currently included.

  15. Combined low-temperature scanning tunneling/atomic force microscope for atomic resolution imaging and site-specific force spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Schwarz, Udo; Albers, Boris J.; Liebmann, Marcus; Schwendemann, Todd C.; Baykara, Mehmet Z.; Heyde, Markus; Salmeron, Miquel; Altman, Eric I.; Schwarz, Udo D.

    2008-02-27

    The authors present the design and first results of a low-temperature, ultrahigh vacuum scanning probe microscope enabling atomic resolution imaging in both scanning tunneling microscopy (STM) and noncontact atomic force microscopy (NC-AFM) modes. A tuning-fork-based sensor provides flexibility in selecting probe tip materials, which can be either metallic or nonmetallic. When choosing a conducting tip and sample, simultaneous STM/NC-AFM data acquisition is possible. Noticeable characteristics that distinguish this setup from similar systems providing simultaneous STM/NC-AFM capabilities are its combination of relative compactness (on-top bath cryostat needs no pit), in situ exchange of tip and sample at low temperatures, short turnaround times, modest helium consumption, and unrestricted access from dedicated flanges. The latter permits not only the optical surveillance of the tip during approach but also the direct deposition of molecules or atoms on either tip or sample while they remain cold. Atomic corrugations as low as 1 pm could successfully be resolved. In addition, lateral drifts rates of below 15 pm/h allow long-term data acquisition series and the recording of site-specific spectroscopy maps. Results obtained on Cu(111) and graphite illustrate the microscope's performance.

  16. Combined low-temperature scanning tunneling/atomic force microscope for atomic resolution imaging and site-specific force spectroscopy

    Science.gov (United States)

    Albers, Boris J.; Liebmann, Marcus; Schwendemann, Todd C.; Baykara, Mehmet Z.; Heyde, Markus; Salmeron, Miquel; Altman, Eric I.; Schwarz, Udo D.

    2008-03-01

    We present the design and first results of a low-temperature, ultrahigh vacuum scanning probe microscope enabling atomic resolution imaging in both scanning tunneling microscopy (STM) and noncontact atomic force microscopy (NC-AFM) modes. A tuning-fork-based sensor provides flexibility in selecting probe tip materials, which can be either metallic or nonmetallic. When choosing a conducting tip and sample, simultaneous STM/NC-AFM data acquisition is possible. Noticeable characteristics that distinguish this setup from similar systems providing simultaneous STM/NC-AFM capabilities are its combination of relative compactness (on-top bath cryostat needs no pit), in situ exchange of tip and sample at low temperatures, short turnaround times, modest helium consumption, and unrestricted access from dedicated flanges. The latter permits not only the optical surveillance of the tip during approach but also the direct deposition of molecules or atoms on either tip or sample while they remain cold. Atomic corrugations as low as 1pm could successfully be resolved. In addition, lateral drifts rates of below 15pm/h allow long-term data acquisition series and the recording of site-specific spectroscopy maps. Results obtained on Cu(111) and graphite illustrate the microscope's performance.

  17. High-resolution dynamic atomic force microscopy in liquids with different feedback architectures

    Directory of Open Access Journals (Sweden)

    John Melcher

    2013-02-01

    Full Text Available The recent achievement of atomic resolution with dynamic atomic force microscopy (dAFM [Fukuma et al., Appl. Phys. Lett. 2005, 87, 034101], where quality factors of the oscillating probe are inherently low, challenges some accepted beliefs concerning sensitivity and resolution in dAFM imaging modes. Through analysis and experiment we study the performance metrics for high-resolution imaging with dAFM in liquid media with amplitude modulation (AM, frequency modulation (FM and drive-amplitude modulation (DAM imaging modes. We find that while the quality factors of dAFM probes may deviate by several orders of magnitude between vacuum and liquid media, their sensitivity to tip–sample forces can be remarkable similar. Furthermore, the reduction in noncontact forces and quality factors in liquids diminishes the role of feedback control in achieving high-resolution images. The theoretical findings are supported by atomic-resolution images of mica in water acquired with AM, FM and DAM under similar operating conditions.

  18. Atomic Resolution Imaging at an Ultralow Accelerating Voltage by a Monochromatic Transmission Electron Microscope

    Science.gov (United States)

    Morishita, Shigeyuki; Mukai, Masaki; Suenaga, Kazu; Sawada, Hidetaka

    2016-10-01

    Transmission electron microscopy using low-energy electrons would be very useful for atomic resolution imaging of specimens that would be damaged at higher energies. However, the resolution at low voltages is degraded because of geometrical and chromatic aberrations. In the present study, we diminish the effect of these aberrations by using a delta-type corrector and a monochromator. The dominant residual aberration in a delta-type corrector, which is the sixth-order three-lobe aberration, is counterbalanced by other threefold aberrations. Defocus spread caused by chromatic aberration is reduced by using a monochromated beam with an energy spread of 0.05 eV. We obtain images of graphene and demonstrate atomic resolution at an ultralow accelerating voltage of 15 kV.

  19. Coupling high resolution 3D point clouds from terrestrial LiDAR with high precision displacement time series from GB-InSAR to understand landslide kinematic: example of the La Perraire instability, Swiss Alps.

    Science.gov (United States)

    Michoud, Clément; Baillifard, François; Harald Blikra, Lars; Derron, Marc-Henri; Jaboyedoff, Michel; Kristensen, Lene; Leva, Davide; Metzger, Richard; Rivolta, Carlo

    2014-05-01

    Terrestrial Laser Scanning and Ground-Based Radar Interferometry have changed our perception and interpretation of slope activities for the last 20 years and are now routinely used for monitoring and even early warning purposes. Terrestrial LiDAR allows indeed to model topography with very high point density, even in steep slopes, and to extract 3D displacements of rock masses by comparing successive datasets. GB-InSAR techniques are able to detect mm displacements over large areas. Nevertheless, both techniques suffer of some limitations. The precision of LiDAR devices actually limits its ability to monitor very slow-moving landslides, as well as by the dam resolution and the particular geometry (in azimuth/range) of GB-InSAR data may complicate their interpretations. To overcome those limitations, tools were produced to truly combine strong advantages of both techniques, by coupling high resolution geometrical data from terrestrial LiDAR or photogrammetry with high precision displacement time series from GB-InSAR. We thus developed a new exportation module into the processing chain of LiSAmobile (GB-InSAR) devices in order to wrap radar results from their particular geometry on high resolution 3D point clouds with cm mean point spacing. Furthermore, we also added new importation and visualization functionalities into Coltop3D (software for geological interpretations of laser scanning data) to display those results in 3D and even analyzing displacement time series. This new method has also been optimized to create as few and small files as possible and for time processing. Advantages of coupling terrestrial LiDAR and GB-InSAR data will be illustrated on the La Perraire instability, an active large rockslide involving frequent rockfalls and threatening inhabitant within the Val de Bagnes in the Swiss Alps. This rock mass, monitored by LiDAR and GPS since 2006, is huge enough and long-term movements are big (up to 1.6 m in 6 years) and complex enough to make

  20. Is there a Stobbs factor in atomic-resolution STEM-EELS mapping?

    Energy Technology Data Exchange (ETDEWEB)

    Xin, Huolin L., E-mail: hxin@bnl.gov [Department of Physics, Cornell University, Ithaca, NY 14853 (United States); Dwyer, Christian, E-mail: c.dwyer@fz-juelich.de [Monash Centre for Electron Microscopy, ARC Centre of Excellence for Design in Light Metals, Monash University, Clayton, 3800 Vic (Australia); Department of Materials Engineering, Monash University, Clayton, 3800 Vic (Australia); Muller, David A., E-mail: dm24@cornell.edu [School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853 (United States); Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, NY 14853 (United States)

    2014-04-01

    Recent work has convincingly argued that the Stobbs factor—disagreement in contrast between simulated and experimental atomic-resolution images—in ADF-STEM imaging can be accounted for by including the incoherent source size in simulation. However, less progress has been made for atomic-resolution STEM-EELS mapping. Here we have performed carefully calibrated EELS mapping experiments of a [101] DyScO{sub 3} single-crystal specimen, allowing atomic-resolution EELS signals to be extracted on an absolute scale for a large range of thicknesses. By simultaneously recording the elastic signal, also on an absolute scale, and using it to characterize the source size, sample thickness and inelastic mean free path, we eliminate all free parameters in the simulation of the core-loss signals. Coupled with double channeling simulations that incorporate both core-loss inelastic scattering and dynamical elastic and thermal diffuse scattering, the present work enables a close scrutiny of the scattering physics in the inelastic channel. We found that by taking into account the effective source distribution determined from the ADF images, both the absolute signal and the contrast in atomic-resolution Dy-M{sub 5} maps can be closely reproduced by the double-channeling simulations. At lower energy losses, discrepancies are present in the Sc-L{sub 2,3} and Dy-N{sub 4,5} maps due to the energy-dependent spatial distribution of the background spectrum, core-hole effects, and omitted complexities in the final states. This work has demonstrated the possibility of using quantitative STEM-EELS for element-specific column-by-column atom counting at higher energy losses and for atomic-like final states, and has elucidated several possible improvements for future theoretical work. - Highlights: • This paper present a carefully calibrated experiment, which allows, for the first time, atomic-resolution chemical signals to be extracted on an absolute scale. • By simultaneously recording

  1. Radiochromic 3D Detectors

    Science.gov (United States)

    Oldham, Mark

    2015-01-01

    Radiochromic materials exhibit a colour change when exposed to ionising radiation. Radiochromic film has been used for clinical dosimetry for many years and increasingly so recently, as films of higher sensitivities have become available. The two principle advantages of radiochromic dosimetry include greater tissue equivalence (radiologically) and the lack of requirement for development of the colour change. In a radiochromic material, the colour change arises direct from ionising interactions affecting dye molecules, without requiring any latent chemical, optical or thermal development, with important implications for increased accuracy and convenience. It is only relatively recently however, that 3D radiochromic dosimetry has become possible. In this article we review recent developments and the current state-of-the-art of 3D radiochromic dosimetry, and the potential for a more comprehensive solution for the verification of complex radiation therapy treatments, and 3D dose measurement in general.

  2. 3D Projection Installations

    DEFF Research Database (Denmark)

    Halskov, Kim; Johansen, Stine Liv; Bach Mikkelsen, Michelle

    2014-01-01

    Three-dimensional projection installations are particular kinds of augmented spaces in which a digital 3-D model is projected onto a physical three-dimensional object, thereby fusing the digital content and the physical object. Based on interaction design research and media studies, this article...... contributes to the understanding of the distinctive characteristics of such a new medium, and identifies three strategies for designing 3-D projection installations: establishing space; interplay between the digital and the physical; and transformation of materiality. The principal empirical case, From...... Fingerplan to Loop City, is a 3-D projection installation presenting the history and future of city planning for the Copenhagen area in Denmark. The installation was presented as part of the 12th Architecture Biennale in Venice in 2010....

  3. Atom-counting in High Resolution Electron Microscopy:TEM or STEM - That's the question.

    Science.gov (United States)

    Gonnissen, J; De Backer, A; den Dekker, A J; Sijbers, J; Van Aert, S

    2016-10-27

    In this work, a recently developed quantitative approach based on the principles of detection theory is used in order to determine the possibilities and limitations of High Resolution Scanning Transmission Electron Microscopy (HR STEM) and HR TEM for atom-counting. So far, HR STEM has been shown to be an appropriate imaging mode to count the number of atoms in a projected atomic column. Recently, it has been demonstrated that HR TEM, when using negative spherical aberration imaging, is suitable for atom-counting as well. The capabilities of both imaging techniques are investigated and compared using the probability of error as a criterion. It is shown that for the same incoming electron dose, HR STEM outperforms HR TEM under common practice standards, i.e. when the decision is based on the probability function of the peak intensities in HR TEM and of the scattering cross-sections in HR STEM. If the atom-counting decision is based on the joint probability function of the image pixel values, the dependence of all image pixel intensities as a function of thickness should be known accurately. Under this assumption, the probability of error may decrease significantly for atom-counting in HR TEM and may, in theory, become lower as compared to HR STEM under the predicted optimal experimental settings. However, the commonly used standard for atom-counting in HR STEM leads to a high performance and has been shown to work in practice.

  4. Interaktiv 3D design

    DEFF Research Database (Denmark)

    Villaume, René Domine; Ørstrup, Finn Rude

    2002-01-01

    Projektet undersøger potentialet for interaktiv 3D design via Internettet. Arkitekt Jørn Utzons projekt til Espansiva blev udviklet som et byggesystem med det mål, at kunne skabe mangfoldige planmuligheder og mangfoldige facade- og rumudformninger. Systemets bygningskomponenter er digitaliseret som...... 3D elementer og gjort tilgængelige. Via Internettet er det nu muligt at sammenstille og afprøve en uendelig  række bygningstyper som  systemet blev tænkt og udviklet til....

  5. Unique structure of iC3b resolved at a resolution of 24 Å by 3D-electron microscopy

    Science.gov (United States)

    Alcorlo, Martin; Martínez-Barricarte, Ruben; Fernández, Francisco J.; Rodríguez-Gallego, César; Round, Adam; Vega, M. Cristina; Harris, Claire L.; de Cordoba, Santiago Rodríguez; Llorca, Oscar

    2011-01-01

    Activation of C3, deposition of C3b on the target surface, and subsequent amplification by formation of a C3-cleaving enzyme (C3-convertase; C3bBb) triggers the effector functions of complement that result in inflammation and cell lysis. Concurrently, surface-bound C3b is proteolyzed to iC3b by factor I and appropriate cofactors. iC3b then interacts with the complement receptors (CR) of the Ig superfamily, CR2 (CD21), CR3 (CD11b/CD18), and CR4 (CD11c/CD18) on leukocytes, down-modulating inflammation, enhancing B cell-mediated immunity, and targeting pathogens for clearance by phagocytosis. Using EM and small-angle X-ray scattering, we now present a medium-resolution structure of iC3b (24 Å). iC3b displays a unique conformation with structural features distinct from any other C3 fragment. The macroglobulin ring in iC3b is similar to that in C3b, whereas the TED (thioester-containing domain) domain and the remnants of the CUB (complement protein subcomponents C1r/C1s, urchin embryonic growth factor and bone morphogenetic protein 1) domain have moved to locations more similar to where they were in native C3. A consequence of this large conformational change is the disruption of the factor B binding site, which renders iC3b unable to assemble a C3-convertase. This structural model also justifies the decreased interaction between iC3b and complement regulators and the recognition of iC3b by the CR of the Ig superfamily, CR2, CR3, and CR4. These data further illustrate the extraordinary conformational versatility of C3 to accommodate a great diversity of functional activities. PMID:21788512

  6. Unique structure of iC3b resolved at a resolution of 24 Å by 3D-electron microscopy.

    Science.gov (United States)

    Alcorlo, Martin; Martínez-Barricarte, Ruben; Fernández, Francisco J; Rodríguez-Gallego, César; Round, Adam; Vega, M Cristina; Harris, Claire L; de Cordoba, Santiago Rodríguez; Llorca, Oscar

    2011-08-01

    Activation of C3, deposition of C3b on the target surface, and subsequent amplification by formation of a C3-cleaving enzyme (C3-convertase; C3bBb) triggers the effector functions of complement that result in inflammation and cell lysis. Concurrently, surface-bound C3b is proteolyzed to iC3b by factor I and appropriate cofactors. iC3b then interacts with the complement receptors (CR) of the Ig superfamily, CR2 (CD21), CR3 (CD11b/CD18), and CR4 (CD11c/CD18) on leukocytes, down-modulating inflammation, enhancing B cell-mediated immunity, and targeting pathogens for clearance by phagocytosis. Using EM and small-angle X-ray scattering, we now present a medium-resolution structure of iC3b (24 Å). iC3b displays a unique conformation with structural features distinct from any other C3 fragment. The macroglobulin ring in iC3b is similar to that in C3b, whereas the TED (thioester-containing domain) domain and the remnants of the CUB (complement protein subcomponents C1r/C1s, urchin embryonic growth factor and bone morphogenetic protein 1) domain have moved to locations more similar to where they were in native C3. A consequence of this large conformational change is the disruption of the factor B binding site, which renders iC3b unable to assemble a C3-convertase. This structural model also justifies the decreased interaction between iC3b and complement regulators and the recognition of iC3b by the CR of the Ig superfamily, CR2, CR3, and CR4. These data further illustrate the extraordinary conformational versatility of C3 to accommodate a great diversity of functional activities.

  7. 3D high resolution stratigraphy of early rift deltaic deposits in the Sergipe-Alagoas basin: impact on the reservoir compartmentalization; Estratigrafia de alta resolucao 3D em depositos deltaicos do inicio do rifte da bacia de Sergipe-Alagoas: impacto na compartimentacao de reservatorios

    Energy Technology Data Exchange (ETDEWEB)

    Borba, Claudio [Petroleo Brasileiro S. A. (PETROBRAS/UO-SEAL), Aracaju, SE (Brazil). Unidade de Operacoes de Exploracao e Producao de Sergipe e Alagoas], E-mail: cborba@petrobras.com; Paim, Paulo Sergio Gomes [Universidade do Vale do Rio dos Sinos (UNISINOS), Sao Leopoldo, RS (Brazil)], E-mail: ppaim@unisinos.br; Garcia, Antonio Jorge Vasconcellos [Universidade Federal de Sergipe (UFS), Aracaju, SE (Brazil)], E-mail: garciageo@pq.cnpq.br

    2009-05-15

    A high resolution stratigraphic study applied to reservoir characterization, based on well logs, cuts and cores from the Furado Field, a mature oil field of the Alagoas Sub-basin, was carried out on deltaic strata of the lower portion of the Barra de Itiuba Formation (early rifting of the Sergipe-Alagoas Basin). Three lacustrine systems tracts were recognized within a 3rd order sequence: the low stand systems tract (tectonic pulse initiation) that includes extensive, medium- to coarse-grained fluvial-deltaic sandstones that display good reservoir quality; the transgressive systems tract (tectonic climax), which comprises lacustrine and pro delta shale and distal delta front, fine- to very fine-grained sandstone; and the high stand system tract (tectonic quiescence) that encompasses several cycles of delta front progradation and related poor quality reservoirs relative to those of the low stand system tract. The 4th order sequences are represented by climate-driven transgressive-regressive cycles that constitute independent reservoirs, equivalent to a reservoir zones. This high resolution stratigraphic framework was then used on the building of the 3D geologic model, which honored the systems tracts geometry, and related facies, as well as the paleostructure, including a syn-depositional fault propagation anticline. Several normal faults split the reservoirs at different scales. Their potential impact on reservoir fragmentation was approached through the use of fault juxtaposition and shale gouge ratio diagrams. (author)

  8. Tangible 3D Modelling

    DEFF Research Database (Denmark)

    Hejlesen, Aske K.; Ovesen, Nis

    2012-01-01

    This paper presents an experimental approach to teaching 3D modelling techniques in an Industrial Design programme. The approach includes the use of tangible free form models as tools for improving the overall learning. The paper is based on lecturer and student experiences obtained through...

  9. Shaping 3-D boxes

    DEFF Research Database (Denmark)

    Stenholt, Rasmus; Madsen, Claus B.

    2011-01-01

    Enabling users to shape 3-D boxes in immersive virtual environments is a non-trivial problem. In this paper, a new family of techniques for creating rectangular boxes of arbitrary position, orientation, and size is presented and evaluated. These new techniques are based solely on position data...

  10. 3D Wire 2015

    DEFF Research Database (Denmark)

    Jordi, Moréton; F, Escribano; J. L., Farias

    This document is a general report on the implementation of gamification in 3D Wire 2015 event. As the second gamification experience in this event, we have delved deeply in the previous objectives (attracting public areas less frequented exhibition in previous years and enhance networking) and ha......, improves socialization and networking, improves media impact, improves fun factor and improves encouragement of the production team....

  11. 3D photoacoustic imaging

    Science.gov (United States)

    Carson, Jeffrey J. L.; Roumeliotis, Michael; Chaudhary, Govind; Stodilka, Robert Z.; Anastasio, Mark A.

    2010-06-01

    Our group has concentrated on development of a 3D photoacoustic imaging system for biomedical imaging research. The technology employs a sparse parallel detection scheme and specialized reconstruction software to obtain 3D optical images using a single laser pulse. With the technology we have been able to capture 3D movies of translating point targets and rotating line targets. The current limitation of our 3D photoacoustic imaging approach is its inability ability to reconstruct complex objects in the field of view. This is primarily due to the relatively small number of projections used to reconstruct objects. However, in many photoacoustic imaging situations, only a few objects may be present in the field of view and these objects may have very high contrast compared to background. That is, the objects have sparse properties. Therefore, our work had two objectives: (i) to utilize mathematical tools to evaluate 3D photoacoustic imaging performance, and (ii) to test image reconstruction algorithms that prefer sparseness in the reconstructed images. Our approach was to utilize singular value decomposition techniques to study the imaging operator of the system and evaluate the complexity of objects that could potentially be reconstructed. We also compared the performance of two image reconstruction algorithms (algebraic reconstruction and l1-norm techniques) at reconstructing objects of increasing sparseness. We observed that for a 15-element detection scheme, the number of measureable singular vectors representative of the imaging operator was consistent with the demonstrated ability to reconstruct point and line targets in the field of view. We also observed that the l1-norm reconstruction technique, which is known to prefer sparseness in reconstructed images, was superior to the algebraic reconstruction technique. Based on these findings, we concluded (i) that singular value decomposition of the imaging operator provides valuable insight into the capabilities of

  12. State of the art in atomic resolution off-axis electron holography

    Energy Technology Data Exchange (ETDEWEB)

    Linck, Martin, E-mail: mlinck@lbl.gov [Triebenberg Laboratory, Institute of Structure Physics, Technische Universitaet Dresden, Zum Triebenberg 50, 01328 Dresden (Germany); Freitag, Bert; Kujawa, Stephan [FEI Company, Eindhoven, Building AAE, Achtseweg Noord 5, P.O. Box 80066, 5600 KA Eindhoven (Netherlands); Lehmann, Michael; Niermann, Tore [Institut fuer Optik und Atomare Physik, Technische Universitaet Berlin, Strasse des 17. Juni 135, 10623 Berlin (Germany)

    2012-05-15

    As proposed by Hannes Lichte, to resolve structure-property relations not only the question 'Which atom is where?' but also the question 'Which fields are around?' has to be answered. High-resolution off-axis electron holography opens up an access to these key questions in that it allows accessing the complete exit-wave of the object provided within the information limit of the microscope, i.e. amplitude and phase including atomic details such as position and species, and moreover, information about large area electric potentials and magnetic fields, which a conventional transmission electron microscope is blind for-also when using a Cs-corrector. For an excellent object exit-wave reconstruction, special care has to be taken on the hologram quality, i.e. interference fringe contrast and electron dose. Severe restrictions are given to signal resolution by the limited brightness of the electron source. Utilizing a new high-brightness Schottky field electron emitter in a state-of-the-art transmission electron microscope operated at 300 kV, the phase signal resolution at atomic resolution can significantly be enhanced. An improvement by at least a factor of 2.88 compared to the most recently reported single hologram at atomic resolution is found. To proof the applicability of this setup to real materials science problems, a grain boundary of gold has been investigated holographically. -- Highlights: Black-Right-Pointing-Pointer Impact of the brightness on the reconstructed signal in electron holography. Black-Right-Pointing-Pointer Factor 2.8 gain in signal quality by setup with a high brightness electron gun. Black-Right-Pointing-Pointer Investigation of a grain boundary in gold with a state-of-the-art holography setup. Black-Right-Pointing-Pointer A-posteriori aberration fine-tuning for true one Angstrom resolution in the object wave. Black-Right-Pointing-Pointer Mistilt analysis on the atomic scale by numerical wave optics.

  13. High Resolution Numerical Simulations of Primary Atomization in Diesel Sprays with Single Component Reference Fuels

    Science.gov (United States)

    2015-09-01

    NC. 14. ABSTRACT A high-resolution numerical simulation of jet breakup and spray formation from a complex diesel fuel injector at diesel engine ... diesel fuel injector at diesel engine type conditions has been performed. A full understanding of the primary atomization process in diesel fuel...the capability of a recently adopted high fidelity two phase flow solver in the context of diesel engine sprays. Previous works relating to this

  14. Towards quantitative, atomic-resolution reconstruction of the electrostatic potential via differential phase contrast using electrons

    Energy Technology Data Exchange (ETDEWEB)

    Close, R.; Chen, Z. [School of Physics and Astronomy, Monash University, Clayton, Victoria 3800 (Australia); Shibata, N. [Institute of Engineering Innovation, School of Engineering, University of Tokyo, Tokyo 113-8656 (Japan); Findlay, S.D., E-mail: scott.findlay@monash.edu [School of Physics and Astronomy, Monash University, Clayton, Victoria 3800 (Australia)

    2015-12-15

    Differential phase contrast images in scanning transmission electron microscopy can be directly and quantitatively related to the gradient of the projected specimen potential provided that (a) the specimen can be treated as a phase object and (b) full 2D diffraction patterns as a function of probe position can be obtained. Both are challenging to achieve in atomic resolution imaging. The former is fundamentally limited by probe spreading and dynamical electron scattering, and we explore its validity domain in the context of atomic resolution differential phase contrast imaging. The latter, for which proof-of-principle experimental data sets exist, is not yet routine. We explore the extent to which more established segmented detector geometries can instead be used to reconstruct a quantitatively good approximation to the projected specimen potential. - Highlights: • Atomic-resolution differential phase contrast (DPC) imaging explored via simulation. • Phase-object approximation limits quantification to specimens a few nanometers thick. • Segmented detectors give good estimates of the diffraction pattern's first moment.

  15. Chromatic Aberration Correction for Atomic Resolution TEM Imaging from 20 to 80 kV

    Science.gov (United States)

    Linck, Martin; Hartel, Peter; Uhlemann, Stephan; Kahl, Frank; Müller, Heiko; Zach, Joachim; Haider, Max.; Niestadt, Marcel; Bischoff, Maarten; Biskupek, Johannes; Lee, Zhongbo; Lehnert, Tibor; Börrnert, Felix; Rose, Harald; Kaiser, Ute

    2016-08-01

    Atomic resolution in transmission electron microscopy of thin and light-atom materials requires a rigorous reduction of the beam energy to reduce knockon damage. However, at the same time, the chromatic aberration deteriorates the resolution of the TEM image dramatically. Within the framework of the SALVE project, we introduce a newly developed Cc/Cs corrector that is capable of correcting both the chromatic and the spherical aberration in the range of accelerating voltages from 20 to 80 kV. The corrector allows correcting axial aberrations up to fifth order as well as the dominating off-axial aberrations. Over the entire voltage range, optimum phase-contrast imaging conditions for weak signals from light atoms can be adjusted for an optical aperture of at least 55 mrad. The information transfer within this aperture is no longer limited by chromatic aberrations. We demonstrate the performance of the microscope using the examples of 30 kV phase-contrast TEM images of graphene and molybdenum disulfide, showing unprecedented contrast and resolution that matches image calculations.

  16. Chromatic Aberration Correction for Atomic Resolution TEM Imaging from 20 to 80 kV.

    Science.gov (United States)

    Linck, Martin; Hartel, Peter; Uhlemann, Stephan; Kahl, Frank; Müller, Heiko; Zach, Joachim; Haider, Max; Niestadt, Marcel; Bischoff, Maarten; Biskupek, Johannes; Lee, Zhongbo; Lehnert, Tibor; Börrnert, Felix; Rose, Harald; Kaiser, Ute

    2016-08-12

    Atomic resolution in transmission electron microscopy of thin and light-atom materials requires a rigorous reduction of the beam energy to reduce knockon damage. However, at the same time, the chromatic aberration deteriorates the resolution of the TEM image dramatically. Within the framework of the SALVE project, we introduce a newly developed C_{c}/C_{s} corrector that is capable of correcting both the chromatic and the spherical aberration in the range of accelerating voltages from 20 to 80 kV. The corrector allows correcting axial aberrations up to fifth order as well as the dominating off-axial aberrations. Over the entire voltage range, optimum phase-contrast imaging conditions for weak signals from light atoms can be adjusted for an optical aperture of at least 55 mrad. The information transfer within this aperture is no longer limited by chromatic aberrations. We demonstrate the performance of the microscope using the examples of 30 kV phase-contrast TEM images of graphene and molybdenum disulfide, showing unprecedented contrast and resolution that matches image calculations.

  17. Atomic-Resolution Observations of Semi-Crystalline IntegranularThin Films in Silicon Nitride

    Energy Technology Data Exchange (ETDEWEB)

    Ziegler, Alexander; Idrobo, Juan C.; Cinibulk, Michael K.; Kisielowski, Christian; Browning, Nigel D.; Ritchie, Robert O.

    2005-08-01

    The thin intergranular phase in a silicon nitride (Si3N4)ceramic, which has been regarded for decades as having an entirely amorphous morphology, is shown to have a semi-crystalline structure. Using two different but complementary high-resolution electron microscopy methods, the intergranular atomic structure was directly imaged at the atomic level. These high-resolution images show that the atomic arrangement of the dopand element cerium takes very periodic positions not only along the interface between the intergranular phase and the Si3N4 matrix grains, but it arranges in a semi-crystalline structure that spans the entire width of the intergranular phase between two adjacent matrix grains, in principle connecting the two separate matrix grains. The result will have implications on the approach of understanding the materials properties of ceramics, most significantly on the mechanical properties and the associated computational modeling of the atomic structure of the thin intergranular phase in Si3N4 ceramics.

  18. Correlative atomic force microscopy and localization-based super-resolution microscopy: revealing labelling and image reconstruction artefacts.

    Science.gov (United States)

    Monserrate, Aitor; Casado, Santiago; Flors, Cristina

    2014-03-17

    Hybrid microscopy: A correlative microscopy tool that combines in situ super-resolution fluorescence microscopy based on single-molecule localization and atomic force microscopy is presented. Direct comparison with high- resolution topography allows the authors to improve fluorescence labeling and image analysis in super-resolution imaging.

  19. Unoriented 3d TFTs

    CERN Document Server

    Bhardwaj, Lakshya

    2016-01-01

    This paper generalizes two facts about oriented 3d TFTs to the unoriented case. On one hand, it is known that oriented 3d TFTs having a topological boundary condition admit a state-sum construction known as the Turaev-Viro construction. This is related to the string-net construction of fermionic phases of matter. We show how Turaev-Viro construction can be generalized to unoriented 3d TFTs. On the other hand, it is known that the "fermionic" versions of oriented TFTs, known as Spin-TFTs, can be constructed in terms of "shadow" TFTs which are ordinary oriented TFTs with an anomalous Z_2 1-form symmetry. We generalize this correspondence to Pin+ TFTs by showing that they can be constructed in terms of ordinary unoriented TFTs with anomalous Z_2 1-form symmetry having a mixed anomaly with time-reversal symmetry. The corresponding Pin+ TFT does not have any anomaly for time-reversal symmetry however and hence it can be unambiguously defined on a non-orientable manifold. In case a Pin+ TFT admits a topological bou...

  20. Sub-atomic resolution X-ray crystallography and neutron crystallography: promise, challenges and potential.

    Science.gov (United States)

    Blakeley, Matthew P; Hasnain, Samar S; Antonyuk, Svetlana V

    2015-07-01

    The International Year of Crystallography saw the number of macromolecular structures deposited in the Protein Data Bank cross the 100000 mark, with more than 90000 of these provided by X-ray crystallography. The number of X-ray structures determined to sub-atomic resolution (i.e. ≤1 Å) has passed 600 and this is likely to continue to grow rapidly with diffraction-limited synchrotron radiation sources such as MAX-IV (Sweden) and Sirius (Brazil) under construction. A dozen X-ray structures have been deposited to ultra-high resolution (i.e. ≤0.7 Å), for which precise electron density can be exploited to obtain charge density and provide information on the bonding character of catalytic or electron transfer sites. Although the development of neutron macromolecular crystallography over the years has been far less pronounced, and its application much less widespread, the availability of new and improved instrumentation, combined with dedicated deuteration facilities, are beginning to transform the field. Of the 83 macromolecular structures deposited with neutron diffraction data, more than half (49/83, 59%) were released since 2010. Sub-mm(3) crystals are now regularly being used for data collection, structures have been determined to atomic resolution for a few small proteins, and much larger unit-cell systems (cell edges >100 Å) are being successfully studied. While some details relating to H-atom positions are tractable with X-ray crystallography at sub-atomic resolution, the mobility of certain H atoms precludes them from being located. In addition, highly polarized H atoms and protons (H(+)) remain invisible with X-rays. Moreover, the majority of X-ray structures are determined from cryo-cooled crystals at 100 K, and, although radiation damage can be strongly controlled, especially since the advent of shutterless fast detectors, and by using limited doses and crystal translation at micro-focus beams, radiation damage can still take place. Neutron

  1. Sub-atomic resolution X-ray crystallography and neutron crystallography: promise, challenges and potential

    Directory of Open Access Journals (Sweden)

    Matthew P. Blakeley

    2015-07-01

    Full Text Available The International Year of Crystallography saw the number of macromolecular structures deposited in the Protein Data Bank cross the 100000 mark, with more than 90000 of these provided by X-ray crystallography. The number of X-ray structures determined to sub-atomic resolution (i.e. ≤1 Å has passed 600 and this is likely to continue to grow rapidly with diffraction-limited synchrotron radiation sources such as MAX-IV (Sweden and Sirius (Brazil under construction. A dozen X-ray structures have been deposited to ultra-high resolution (i.e. ≤0.7 Å, for which precise electron density can be exploited to obtain charge density and provide information on the bonding character of catalytic or electron transfer sites. Although the development of neutron macromolecular crystallography over the years has been far less pronounced, and its application much less widespread, the availability of new and improved instrumentation, combined with dedicated deuteration facilities, are beginning to transform the field. Of the 83 macromolecular structures deposited with neutron diffraction data, more than half (49/83, 59% were released since 2010. Sub-mm3 crystals are now regularly being used for data collection, structures have been determined to atomic resolution for a few small proteins, and much larger unit-cell systems (cell edges >100 Å are being successfully studied. While some details relating to H-atom positions are tractable with X-ray crystallography at sub-atomic resolution, the mobility of certain H atoms precludes them from being located. In addition, highly polarized H atoms and protons (H+ remain invisible with X-rays. Moreover, the majority of X-ray structures are determined from cryo-cooled crystals at 100 K, and, although radiation damage can be strongly controlled, especially since the advent of shutterless fast detectors, and by using limited doses and crystal translation at micro-focus beams, radiation damage can still take place

  2. 2D/3D switchable displays

    Science.gov (United States)

    Dekker, T.; de Zwart, S. T.; Willemsen, O. H.; Hiddink, M. G. H.; IJzerman, W. L.

    2006-02-01

    A prerequisite for a wide market acceptance of 3D displays is the ability to switch between 3D and full resolution 2D. In this paper we present a robust and cost effective concept for an auto-stereoscopic switchable 2D/3D display. The display is based on an LCD panel, equipped with switchable LC-filled lenticular lenses. We will discuss 3D image quality, with the focus on display uniformity. We show that slanting the lenticulars in combination with a good lens design can minimize non-uniformities in our 20" 2D/3D monitors. Furthermore, we introduce fractional viewing systems as a very robust concept to further improve uniformity in the case slanting the lenticulars and optimizing the lens design are not sufficient. We will discuss measurements and numerical simulations of the key optical characteristics of this display. Finally, we discuss 2D image quality, the switching characteristics and the residual lens effect.

  3. Recent development of 3D display technology for new market

    Science.gov (United States)

    Kim, Sung-Sik

    2003-11-01

    A multi-view 3D video processor was designed and implemented with several FPGAs for real-time applications and a projection-type 3D display was introduced for low-cost commercialization. One high resolution projection panel and only one projection lens is capable of displaying multiview autostereoscopic images. It can cope with various arrangements of 3D camera systems (or pixel arrays) and resolutions of 3D displays. This system shows high 3-D image quality in terms of resolution, brightness, and contrast so it is well suited for the commercialization in the field of game and advertisement market.

  4. Optofluidic microscope with 3D spatial resolution

    DEFF Research Database (Denmark)

    Vig, Asger Laurberg; Marie, Rodolphe; Jensen, Eric

    2010-01-01

    in the plane perpendicular to the flow direction and the velocity along the flow direction of separated fluorescent labeled polystyrene microspheres with diameters of 1μm, 2.1μm, 3μm and 4μm is determined by the OFM. These results are bench marked against those obtained with a PFF device using conventional...... fluorescence microscope readout. The size separated microspheres are detected by OFM with an accuracy of ≤0.92μm. The position in the height of the channel and the velocity of the separated microspheres are detected with an accuracy of 1.4μm and 0.08 mm/s respectively. Throughout the measurements of the height...... and velocity distribution, the microspheres are observed to move towards the center of the channel in regard to its height....

  5. 3D light robotics

    DEFF Research Database (Denmark)

    Glückstad, Jesper; Palima, Darwin; Villangca, Mark Jayson

    2016-01-01

    As celebrated by the Nobel Prize 2014 in Chemistry light-based technologies can now overcome the diffraction barrier for imaging with nanoscopic resolution by so-called super-resolution microscopy1. However, interactive investigations coupled with advanced imaging modalities at these small scale ...

  6. 3D and beyond

    Science.gov (United States)

    Fung, Y. C.

    1995-05-01

    This conference on physiology and function covers a wide range of subjects, including the vasculature and blood flow, the flow of gas, water, and blood in the lung, the neurological structure and function, the modeling, and the motion and mechanics of organs. Many technologies are discussed. I believe that the list would include a robotic photographer, to hold the optical equipment in a precisely controlled way to obtain the images for the user. Why are 3D images needed? They are to achieve certain objectives through measurements of some objects. For example, in order to improve performance in sports or beauty of a person, we measure the form, dimensions, appearance, and movements.

  7. Characterization of the surface charge distribution on kaolinite particles using high resolution atomic force microscopy

    Science.gov (United States)

    Kumar, Naveen; Zhao, Cunlu; Klaassen, Aram; van den Ende, Dirk; Mugele, Frieder; Siretanu, Igor

    2016-02-01

    Most solid surfaces, in particular clay minerals and rock surfaces, acquire a surface charge upon exposure to an aqueous environment due to adsorption and/or desorption of ionic species. Macroscopic techniques such as titration and electrokinetic measurements are commonly used to determine the surface charge and ζ -potential of these surfaces. However, because of the macroscopic averaging character these techniques cannot do justice to the role of local heterogeneities on the surfaces. In this work, we use dynamic atomic force microscopy (AFM) to determine the distribution of surface charge on the two (gibbsite-like and silica-like) basal planes of kaolinite nanoparticles immersed in aqueous electrolyte with a lateral resolution of approximately 30 nm. The surface charge density is extracted from force-distance curves using DLVO theory in combination with surface complexation modeling. While the gibbsite-like and the silica-like facet display on average positive and negative surface charge values as expected, our measurements reveal lateral variations of more than a factor of two on seemingly atomically smooth terraces, even if high resolution AFM images clearly reveal the atomic lattice on the surface. These results suggest that simple surface complexation models of clays that attribute a unique surface chemistry and hence homogeneous surface charge densities to basal planes may miss important aspects of real clay surfaces.

  8. 3D Surgical Simulation

    Science.gov (United States)

    Cevidanes, Lucia; Tucker, Scott; Styner, Martin; Kim, Hyungmin; Chapuis, Jonas; Reyes, Mauricio; Proffit, William; Turvey, Timothy; Jaskolka, Michael

    2009-01-01

    This paper discusses the development of methods for computer-aided jaw surgery. Computer-aided jaw surgery allows us to incorporate the high level of precision necessary for transferring virtual plans into the operating room. We also present a complete computer-aided surgery (CAS) system developed in close collaboration with surgeons. Surgery planning and simulation include construction of 3D surface models from Cone-beam CT (CBCT), dynamic cephalometry, semi-automatic mirroring, interactive cutting of bone and bony segment repositioning. A virtual setup can be used to manufacture positioning splints for intra-operative guidance. The system provides further intra-operative assistance with the help of a computer display showing jaw positions and 3D positioning guides updated in real-time during the surgical procedure. The CAS system aids in dealing with complex cases with benefits for the patient, with surgical practice, and for orthodontic finishing. Advanced software tools for diagnosis and treatment planning allow preparation of detailed operative plans, osteotomy repositioning, bone reconstructions, surgical resident training and assessing the difficulties of the surgical procedures prior to the surgery. CAS has the potential to make the elaboration of the surgical plan a more flexible process, increase the level of detail and accuracy of the plan, yield higher operative precision and control, and enhance documentation of cases. Supported by NIDCR DE017727, and DE018962 PMID:20816308

  9. TOWARDS: 3D INTERNET

    Directory of Open Access Journals (Sweden)

    Ms. Swapnali R. Ghadge

    2013-08-01

    Full Text Available In today’s ever-shifting media landscape, it can be a complex task to find effective ways to reach your desired audience. As traditional media such as television continue to lose audience share, one venue in particular stands out for its ability to attract highly motivated audiences and for its tremendous growth potential the 3D Internet. The concept of '3D Internet' has recently come into the spotlight in the R&D arena, catching the attention of many people, and leading to a lot of discussions. Basically, one can look into this matter from a few different perspectives: visualization and representation of information, and creation and transportation of information, among others. All of them still constitute research challenges, as no products or services are yet available or foreseen for the near future. Nevertheless, one can try to envisage the directions that can be taken towards achieving this goal. People who take part in virtual worlds stay online longer with a heightened level of interest. To take advantage of that interest, diverse businesses and organizations have claimed an early stake in this fast-growing market. They include technology leaders such as IBM, Microsoft, and Cisco, companies such as BMW, Toyota, Circuit City, Coca Cola, and Calvin Klein, and scores of universities, including Harvard, Stanford and Penn State.

  10. 3D light robotics

    DEFF Research Database (Denmark)

    Glückstad, Jesper; Palima, Darwin; Villangca, Mark Jayson;

    2016-01-01

    As celebrated by the Nobel Prize 2014 in Chemistry light-based technologies can now overcome the diffraction barrier for imaging with nanoscopic resolution by so-called super-resolution microscopy1. However, interactive investigations coupled with advanced imaging modalities at these small scale...... research discipline that could potentially be able to offer the full packet needed for true "active nanoscopy" by use of so-called light-driven micro-robotics or Light Robotics in short....

  11. Fabrication of 3D core-shell multiwalled carbon nanotube@RuO2 lithium-ion battery electrodes through a RuO2 atomic layer deposition process.

    Science.gov (United States)

    Gregorczyk, Keith E; Kozen, Alexander C; Chen, Xinyi; Schroeder, Marshall A; Noked, Malachi; Cao, Anyuan; Hu, Liangbing; Rubloff, Gary W

    2015-01-27

    Pushing lithium-ion battery (LIB) technology forward to its fundamental scaling limits requires the ability to create designer heterostructured materials and architectures. Atomic layer deposition (ALD) has recently been applied to advanced nanostructured energy storage devices due to the wide range of available materials, angstrom thickness control, and extreme conformality over high aspect ratio nanostructures. A class of materials referred to as conversion electrodes has recently been proposed as high capacity electrodes. RuO2 is considered an ideal conversion material due to its high combined electronic and ionic conductivity and high gravimetric capacity, and as such is an excellent material to explore the behavior of conversion electrodes at nanoscale thicknesses. We report here a fully characterized atomic layer deposition process for RuO2, electrochemical cycling data for ALD RuO2, and the application of the RuO2 to a composite carbon nanotube electrode scaffold with nucleation-controlled RuO2 growth. A growth rate of 0.4 Å/cycle is found between ∼ 210-240 °C. In a planar configuration, the resulting RuO2 films show high first cycle electrochemical capacities of ∼ 1400 mAh/g, but the capacity rapidly degrades with charge/discharge cycling. We also fabricated core/shell MWCNT/RuO2 heterostructured 3D electrodes, which show a 50× increase in the areal capacity over their planar counterparts, with an areal lithium capacity of 1.6 mAh/cm(2).

  12. Probing three-dimensional surface force fields with atomic resolution: Measurement strategies, limitations, and artifact reduction

    Directory of Open Access Journals (Sweden)

    Mehmet Z. Baykara

    2012-09-01

    Full Text Available Noncontact atomic force microscopy (NC-AFM is being increasingly used to measure the interaction force between an atomically sharp probe tip and surfaces of interest, as a function of the three spatial dimensions, with picometer and piconewton accuracy. Since the results of such measurements may be affected by piezo nonlinearities, thermal and electronic drift, tip asymmetries, and elastic deformation of the tip apex, these effects need to be considered during image interpretation.In this paper, we analyze their impact on the acquired data, compare different methods to record atomic-resolution surface force fields, and determine the approaches that suffer the least from the associated artifacts. The related discussion underscores the idea that since force fields recorded by using NC-AFM always reflect the properties of both the sample and the probe tip, efforts to reduce unwanted effects of the tip on recorded data are indispensable for the extraction of detailed information about the atomic-scale properties of the surface.

  13. Atomic resolution imaging of beryl: an investigation of the nano-channel occupation.

    Science.gov (United States)

    Arivazhagan, V; Schmitz, F D; Vullum, P E; VAN Helvoort, A T J; Holst, B

    2017-02-01

    Beryl in different varieties (emerald, aquamarine, heliodor etc.) displays a wide range of colours that have fascinated humans throughout history. Beryl is a hexagonal cyclo-silicate (ring-silicate) with channels going through the crystal along the c-axis. The channels are about 0.5 nm in diameter and can be occupied by water and alkali ions. Pure beryl (Be3 Al2 Si6 O18 ) is colourless (variety goshenite). The characteristic colours are believed to be mainly generated through substitutions with metal atoms in the lattice. Which atoms that are substituted is still debated it has been proposed that metal ions may also be enclosed in the channels and that this can also contribute to the crystal colouring. So far spectroscopy studies have not been able to fully answer this. Here we present the first experiments using atomic resolution scanning transmission electron microscope imaging (STEM) to investigate the channel occupation in beryl. We present images of a natural beryl crystal (variety heliodor) from the Bin Thuan Province in Vietnam. The channel occupation can be visualized. Based on the image contrast in combination with ex situ element analysis we suggest that some or all of the atoms that are visible in the channels are Fe ions.

  14. Tip radius preservation for high resolution imaging in amplitude modulation atomic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Ramos, Jorge R., E-mail: jorge.rr@cea.cu [Instituto de Ciencia de Materiales de Madrid, Sor Juana Inés de la Cruz 3, Canto Blanco, 28049 Madrid, España (Spain)

    2014-07-28

    The acquisition of high resolution images in atomic force microscopy (AFM) is correlated to the cantilever's tip shape, size, and imaging conditions. In this work, relative tip wear is quantified based on the evolution of a direct experimental observable in amplitude modulation atomic force microscopy, i.e., the critical amplitude. We further show that the scanning parameters required to guarantee a maximum compressive stress that is lower than the yield/fracture stress of the tip can be estimated via experimental observables. In both counts, the optimized parameters to acquire AFM images while preserving the tip are discussed. The results are validated experimentally by employing IgG antibodies as a model system.

  15. Sample preparation for atomic-resolution STEM at low voltages by FIB

    Energy Technology Data Exchange (ETDEWEB)

    Schaffer, Miroslava, E-mail: mschaffer@SuperSTEM.org [SuperSTEM, STFC Daresbury Laboratories, Keckwick Lane, Warrington WA4 4AD (United Kingdom); Department of Engineering, George Holt Building, Ashton Street, Liverpool L69 3BX (United Kingdom); Schaffer, Bernhard [SuperSTEM, STFC Daresbury Laboratories, Keckwick Lane, Warrington WA4 4AD (United Kingdom); Kelvin Nanocharacterisation Centre, SUPA School of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ, Scotland (United Kingdom); Ramasse, Quentin [SuperSTEM, STFC Daresbury Laboratories, Keckwick Lane, Warrington WA4 4AD (United Kingdom); Department of Engineering, George Holt Building, Ashton Street, Liverpool L69 3BX (United Kingdom)

    2012-03-15

    While FIB sample preparation for transmission electron microscopy is a well established technique, few examples exist of samples of sufficient quality for atomic resolution imaging by aberration corrected (scanning) transmission electron microscopy (STEM). In this work we demonstrate the successful preparation of such samples from five different materials and present the refined lift-out preparation technique, which was applied here. Samples with parallel surfaces and a general thickness between 20 and 40 nm over a range of several {mu}m were repeatedly prepared and analyzed by Cs-corrected STEM at 60 and 100 kV. Here, a novel 'wedge pre-milling' step helps to keep the protective surface layers intact during the whole milling process, allowing features close to or at the sample surface to be analyzed without preparation damage. Another example shows the cross-sectional preparation of a working thin film solar cell device to a final thickness of 10 to 20 nm over {mu}m sized areas in the region of interest, enabling atomic resolution imaging and elemental mapping across general grain boundaries without projection artefacts. All sample preparation has been carried out in modern Dual-Beam FIB microscopes capable of low-kV Ga{sup +} ion milling, but without additional preparation steps after the FIB lift-out procedure. -- Highlights: Black-Right-Pointing-Pointer Suitability of stand-alone FIB preparation for atomic resolution STEM is shown. Black-Right-Pointing-Pointer Reproducible preparation of 10-40 nm thick samples from 5 different materials. Black-Right-Pointing-Pointer Low-kV milling and adjusted procedure for crystalline, homogeneously thin specimen. Black-Right-Pointing-Pointer Wedge pre-milling to protect surface-near features.

  16. Zeeman Effect of Sm Atoms by High-Resolution Diode-Laser Spectroscopy

    Directory of Open Access Journals (Sweden)

    Wei-Guo Jin

    2013-01-01

    Full Text Available High-resolution atomic-beam diode-laser spectroscopy in Sm I has been performed. Zeeman spectra have been measured for the three optical transitions at different external magnetic fields and well resolved at the magnetic fields of stronger than 6.0 mT. Using the known precise Landé -factors of the ground multiplet, the Landé -factors of the upper 4f66s6p   and levels have been determined, and their precision has been improved compared with the reference values.

  17. Toward atomic resolution diffractive imaging of isolated molecules with x-ray free-electron lasers

    CERN Document Server

    Stern, Stephan; Filsinger, Frank; Rouzée, Arnaud; Rudenko, Artem; Johnsson, Per; Martin, Andrew V; Barty, Anton; Bostedt, Christoph; Bozek, John D; Coffee, Ryan N; Epp, Sascha; Erk, Benjamin; Foucar, Lutz; Hartmann, Robert; Kimmel, Nils; Kühnel, Kai-Uwe; Maurer, Jochen; Messerschmidt, Marc; Rudek, Benedikt; Starodub, Dmitri G; Thøgersen, Jan; Weidenspointner, Georg; White, Thomas A; Stapelfeldt, Henrik; Rolles, Daniel; Chapman, Henry N; Küpper, Jochen

    2014-01-01

    We give a detailed account of the theoretical analysis and the experimental results of an x-ray-diffraction experiment on quantum-state selected and strongly laser-aligned gas-phase ensembles of the prototypical large asymmetric rotor molecule 2,5-diiodobenzonitrile, performed at the Linac Coherent Light Source [Phys. Rev. Lett. 112, 083002 (2014)]. This experiment is the first step toward coherent diffractive imaging of structures and structural dynamics of isolated molecules at atomic resolution, i. e., picometers and femtoseconds, using x-ray free-electron lasers.

  18. Measurement of transient atomic displacements in thin films with picosecond and femtometer resolution

    Directory of Open Access Journals (Sweden)

    M. Kozina

    2014-05-01

    Full Text Available We report measurements of the transient structural response of weakly photo-excited thin films of BiFeO3, Pb(Zr,TiO3, and Bi and time-scales for interfacial thermal transport. Utilizing picosecond x-ray diffraction at a 1.28 MHz repetition rate with time resolution extending down to 15 ps, transient changes in the diffraction angle are recorded. These changes are associated with photo-induced lattice strains within nanolayer thin films, resolved at the part-per-million level, corresponding to a shift in the scattering angle three orders of magnitude smaller than the rocking curve width and changes in the interlayer lattice spacing of fractions of a femtometer. The combination of high brightness, repetition rate, and stability of the synchrotron, in conjunction with high time resolution, represents a novel means to probe atomic-scale, near-equilibrium dynamics.

  19. Structure of the SH3 domain of human osteoclast-stimulating factor at atomic resolution

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Liqing, E-mail: chenlq@uah.edu; Wang, Yujun [Laboratory for Structural Biology, University of Alabama in Huntsville, Huntsville, Alabama 35899 (United States); Department of Chemistry, University of Alabama in Huntsville, Huntsville, Alabama 35899 (United States); Graduate Program of Biotechnology, University of Alabama in Huntsville, Huntsville, Alabama 35899 (United States); Wells, David; Toh, Diana; Harold, Hunt [Laboratory for Structural Biology, University of Alabama in Huntsville, Huntsville, Alabama 35899 (United States); Zhou, Jing [Laboratory for Structural Biology, University of Alabama in Huntsville, Huntsville, Alabama 35899 (United States); Department of Chemistry, University of Alabama in Huntsville, Huntsville, Alabama 35899 (United States); Graduate Program of Biotechnology, University of Alabama in Huntsville, Huntsville, Alabama 35899 (United States); DiGiammarino, Enrico [Laboratory for Structural Biology, University of Alabama in Huntsville, Huntsville, Alabama 35899 (United States); Meehan, Edward J. [Laboratory for Structural Biology, University of Alabama in Huntsville, Huntsville, Alabama 35899 (United States); Department of Chemistry, University of Alabama in Huntsville, Huntsville, Alabama 35899 (United States); Graduate Program of Biotechnology, University of Alabama in Huntsville, Huntsville, Alabama 35899 (United States)

    2006-09-01

    The crystal structure of the SH3 domain of human osteoclast-stimulating factor has been determined and refined to the ultrahigh resolution of 1.07 Å. The structure at atomic resolution provides an accurate framework for structure-based design of its inhibitors. Osteoclast-stimulating factor (OSF) is an intracellular signaling protein, produced by osteoclasts themselves, that enhances osteoclast formation and bone resorption. It is thought to act via an Src-related signaling pathway and contains SH3 and ankyrin-repeat domains which are involved in protein–protein interactions. As part of a structure-based anti-bone-loss drug-design program, the atomic resolution X-ray structure of the recombinant human OSF SH3 domain (hOSF-SH3) has been determined. The domain, residues 12–72, yielded crystals that diffracted to the ultrahigh resolution of 1.07 Å. The overall structure shows a characteristic SH3 fold consisting of two perpendicular β-sheets that form a β-barrel. Structure-based sequence alignment reveals that the putative proline-rich peptide-binding site of hOSF-SH3 consists of (i) residues that are highly conserved in the SH3-domain family, including residues Tyr21, Phe23, Trp49, Pro62, Asn64 and Tyr65, and (ii) residues that are less conserved and/or even specific to hOSF, including Thr22, Arg26, Thr27, Glu30, Asp46, Thr47, Asn48 and Leu60, which might be key to designing specific inhibitors for hOSF to fight osteoporosis and related bone-loss diseases. There are a total of 13 well defined water molecules forming hydrogen bonds with the above residues in and around the peptide-binding pocket. Some of those water molecules might be important for drug-design approaches. The hOSF-SH3 structure at atomic resolution provides an accurate framework for structure-based design of its inhibitors.

  20. 3D scanning particle tracking velocimetry

    Science.gov (United States)

    Hoyer, Klaus; Holzner, Markus; Lüthi, Beat; Guala, Michele; Liberzon, Alexander; Kinzelbach, Wolfgang

    2005-11-01

    In this article, we present an experimental setup and data processing schemes for 3D scanning particle tracking velocimetry (SPTV), which expands on the classical 3D particle tracking velocimetry (PTV) through changes in the illumination, image acquisition and analysis. 3D PTV is a flexible flow measurement technique based on the processing of stereoscopic images of flow tracer particles. The technique allows obtaining Lagrangian flow information directly from measured 3D trajectories of individual particles. While for a classical PTV the entire region of interest is simultaneously illuminated and recorded, in SPTV the flow field is recorded by sequential tomographic high-speed imaging of the region of interest. The advantage of the presented method is a considerable increase in maximum feasible seeding density. Results are shown for an experiment in homogenous turbulence and compared with PTV. SPTV yielded an average 3,500 tracked particles per time step, which implies a significant enhancement of the spatial resolution for Lagrangian flow measurements.

  1. Quasi 3D dosimetry (EPID, conventional 2D/3D detector matrices)

    Science.gov (United States)

    Bäck, A.

    2015-01-01

    Patient specific pretreatment measurement for IMRT and VMAT QA should preferably give information with a high resolution in 3D. The ability to distinguish complex treatment plans, i.e. treatment plans with a difference between measured and calculated dose distributions that exceeds a specified tolerance, puts high demands on the dosimetry system used for the pretreatment measurements and the results of the measurement evaluation needs a clinical interpretation. There are a number of commercial dosimetry systems designed for pretreatment IMRT QA measurements. 2D arrays such as MapCHECK® (Sun Nuclear), MatriXXEvolution (IBA Dosimetry) and OCTAVIOUS® 1500 (PTW), 3D phantoms such as OCTAVIUS® 4D (PTW), ArcCHECK® (Sun Nuclear) and Delta4 (ScandiDos) and software for EPID dosimetry and 3D reconstruction of the dose in the patient geometry such as EPIDoseTM (Sun Nuclear) and Dosimetry CheckTM (Math Resolutions) are available. None of those dosimetry systems can measure the 3D dose distribution with a high resolution (full 3D dose distribution). Those systems can be called quasi 3D dosimetry systems. To be able to estimate the delivered dose in full 3D the user is dependent on a calculation algorithm in the software of the dosimetry system. All the vendors of the dosimetry systems mentioned above provide calculation algorithms to reconstruct a full 3D dose in the patient geometry. This enables analyzes of the difference between measured and calculated dose distributions in DVHs of the structures of clinical interest which facilitates the clinical interpretation and is a promising tool to be used for pretreatment IMRT QA measurements. However, independent validation studies on the accuracy of those algorithms are scarce. Pretreatment IMRT QA using the quasi 3D dosimetry systems mentioned above rely on both measurement uncertainty and accuracy of calculation algorithms. In this article, these quasi 3D dosimetry systems and their use in patient specific pretreatment IMRT

  2. 3D printing for dummies

    CERN Document Server

    Hausman, Kalani Kirk

    2014-01-01

    Get started printing out 3D objects quickly and inexpensively! 3D printing is no longer just a figment of your imagination. This remarkable technology is coming to the masses with the growing availability of 3D printers. 3D printers create 3-dimensional layered models and they allow users to create prototypes that use multiple materials and colors.  This friendly-but-straightforward guide examines each type of 3D printing technology available today and gives artists, entrepreneurs, engineers, and hobbyists insight into the amazing things 3D printing has to offer. You'll discover methods for

  3. Intraoral 3D scanner

    Science.gov (United States)

    Kühmstedt, Peter; Bräuer-Burchardt, Christian; Munkelt, Christoph; Heinze, Matthias; Palme, Martin; Schmidt, Ingo; Hintersehr, Josef; Notni, Gunther

    2007-09-01

    Here a new set-up of a 3D-scanning system for CAD/CAM in dental industry is proposed. The system is designed for direct scanning of the dental preparations within the mouth. The measuring process is based on phase correlation technique in combination with fast fringe projection in a stereo arrangement. The novelty in the approach is characterized by the following features: A phase correlation between the phase values of the images of two cameras is used for the co-ordinate calculation. This works contrary to the usage of only phase values (phasogrammetry) or classical triangulation (phase values and camera image co-ordinate values) for the determination of the co-ordinates. The main advantage of the method is that the absolute value of the phase at each point does not directly determine the coordinate. Thus errors in the determination of the co-ordinates are prevented. Furthermore, using the epipolar geometry of the stereo-like arrangement the phase unwrapping problem of fringe analysis can be solved. The endoscope like measurement system contains one projection and two camera channels for illumination and observation of the object, respectively. The new system has a measurement field of nearly 25mm × 15mm. The user can measure two or three teeth at one time. So the system can by used for scanning of single tooth up to bridges preparations. In the paper the first realization of the intraoral scanner is described.

  4. Atomic-resolution structure of cytoskeletal bactofilin by solid-state NMR.

    Science.gov (United States)

    Shi, Chaowei; Fricke, Pascal; Lin, Lin; Chevelkov, Veniamin; Wegstroth, Melanie; Giller, Karin; Becker, Stefan; Thanbichler, Martin; Lange, Adam

    2015-12-01

    Bactofilins are a recently discovered class of cytoskeletal proteins of which no atomic-resolution structure has been reported thus far. The bacterial cytoskeleton plays an essential role in a wide range of processes, including morphogenesis, cell division, and motility. Among the cytoskeletal proteins, the bactofilins are bacteria-specific and do not have a eukaryotic counterpart. The bactofilin BacA of the species Caulobacter crescentus is not amenable to study by x-ray crystallography or solution nuclear magnetic resonance (NMR) because of its inherent noncrystallinity and insolubility. We present the atomic structure of BacA calculated from solid-state NMR-derived distance restraints. We show that the core domain of BacA forms a right-handed β helix with six windings and a triangular hydrophobic core. The BacA structure was determined to 1.0 Å precision (heavy-atom root mean square deviation) on the basis of unambiguous restraints derived from four-dimensional (4D) HN-HN and 2D C-C NMR spectra.

  5. Application of SeaWIFS- and AVHRR-derived data for mesoscale and regional validation of a 3-D high-resolution physical biological model of the Gulf of St. Lawrence (Canada)

    Science.gov (United States)

    Le Fouest, V.; Zakardjian, B.; Saucier, F. J.; Çizmeli, S. A.

    2006-04-01

    We present here a first attempt to validate a regional three-dimensional (3-D) physical-biological coupled model of the Gulf of St. Lawrence with coincident Advanced Very High Resolution Radiometer (AVHRR)-derived sea surface temperature (SST) and Sea-viewing Wide Field-of-view Sensor (SeaWIFS)-derived Chlorophyll- a (Chl- a) data. The analysis focused on comparisons between remotely sensed data and simulated as well as in situ temperature, salinity, Chl- a, and nitrate. Results show that the simulated and AVHRR-derived fields of SST were qualitatively and quantitatively in agreement with in situ measurements. By contrast, marked differences were found between the simulated and SeaWIFS-derived fields of Chl- a, the latter comparing better with the freshwater-associated turbidity simulated by the model. Simulated temperature, salinity, nitrate, and Chl- a data compared well with coincident in situ measurements, and it is then suggested that freshwater-associated turbidity related to the river discharges largely contributed to the Chl- a retrievals by SeaWIFS in the Gulf's waters when using the standard OC4v.4 algorithm and atmospheric correction. Nevertheless, the striking agreement between SeaWIFS-derived ocean colour data and the simulated freshwater-associated turbidity allowed to validate the regional estuarine circulation and associated mesoscale variability. This result brings support to the model's ability to simulate realistic physical and biogeochemical fields in the Gulf of St. Lawrence.

  6. 'Sub-atomic' resolution of non-contact atomic force microscope images induced by a heterogeneous tip structure: a density functional theory study.

    Science.gov (United States)

    Campbellová, Anna; Ondráček, Martin; Pou, Pablo; Pérez, Rubén; Klapetek, Petr; Jelínek, Pavel

    2011-07-22

    A Si adatom on a Si(111)-(7 × 7) reconstructed surface is a typical atomic feature that can rather easily be imaged by a non-contact atomic force microscope (nc-AFM) and can be thus used to test the atomic resolution of the microscope. Based on our first principles density functional theory (DFT) calculations, we demonstrate that the structure of the termination of the AFM tip plays a decisive role in determining the appearance of the adatom image. We show how the AFM image changes depending on the tip-surface distance and the composition of the atomic apex at the end of the tip. We also demonstrate that contaminated tips may give rise to image patterns displaying so-called 'sub-atomic' features even in the attractive force regime.

  7. Reliable planning and monitoring tools by dismantling 3D photographic image of high resolution and document management systems. Application MEDS system; Planificacion fiable y seguimiento del desmantelamiento mediante herramientas 3D, imagen fotografica de alta resolucion y sistemas de gestion documental. Aplicacion del sistema MEDS

    Energy Technology Data Exchange (ETDEWEB)

    Vela Morales, F.

    2010-07-01

    MEDS system (Metric Environment Documentation System) is a method developed by CT3 based engineering documentation generation metric of a physical environment using measurement tools latest technology and high precision, such as the Laser Scanner. With this equipment it is possible to obtain three-dimensional information of a physical environment through the 3D coordinates of millions of points. This information is processed by software that is very useful tool for modeling operations and 3D simulations.

  8. 3D Printing an Octohedron

    OpenAIRE

    Aboufadel, Edward F.

    2014-01-01

    The purpose of this short paper is to describe a project to manufacture a regular octohedron on a 3D printer. We assume that the reader is familiar with the basics of 3D printing. In the project, we use fundamental ideas to calculate the vertices and faces of an octohedron. Then, we utilize the OPENSCAD program to create a virtual 3D model and an STereoLithography (.stl) file that can be used by a 3D printer.

  9. Salient Local 3D Features for 3D Shape Retrieval

    CERN Document Server

    Godil, Afzal

    2011-01-01

    In this paper we describe a new formulation for the 3D salient local features based on the voxel grid inspired by the Scale Invariant Feature Transform (SIFT). We use it to identify the salient keypoints (invariant points) on a 3D voxelized model and calculate invariant 3D local feature descriptors at these keypoints. We then use the bag of words approach on the 3D local features to represent the 3D models for shape retrieval. The advantages of the method are that it can be applied to rigid as well as to articulated and deformable 3D models. Finally, this approach is applied for 3D Shape Retrieval on the McGill articulated shape benchmark and then the retrieval results are presented and compared to other methods.

  10. Implementing an Accurate and Rapid Sparse Sampling Approach for Low-Dose Atomic Resolution STEM Imaging

    Energy Technology Data Exchange (ETDEWEB)

    Kovarik, Libor; Stevens, Andrew J.; Liyu, Andrey V.; Browning, Nigel D.

    2016-10-17

    Aberration correction for scanning transmission electron microscopes (STEM) has dramatically increased spatial image resolution for beam-stable materials, but it is the sample stability rather than the microscope that often limits the practical resolution of STEM images. To extract physical information from images of beam sensitive materials it is becoming clear that there is a critical dose/dose-rate below which the images can be interpreted as representative of the pristine material, while above it the observation is dominated by beam effects. Here we describe an experimental approach for sparse sampling in the STEM and in-painting image reconstruction in order to reduce the electron dose/dose-rate to the sample during imaging. By characterizing the induction limited rise-time and hysteresis in scan coils, we show that sparse line-hopping approach to scan randomization can be implemented that optimizes both the speed of the scan and the amount of the sample that needs to be illuminated by the beam. The dose and acquisition time for the sparse sampling is shown to be effectively decreased by factor of 5x relative to conventional acquisition, permitting imaging of beam sensitive materials to be obtained without changing the microscope operating parameters. The use of sparse line-hopping scan to acquire STEM images is demonstrated with atomic resolution aberration corrected Z-contrast images of CaCO3, a material that is traditionally difficult to image by TEM/STEM because of dose issues.

  11. Low-resolution continuum source simultaneous multi-element electrothermal atomic absorption spectrometry: steps into practice

    Energy Technology Data Exchange (ETDEWEB)

    Katskov, Dmitri, E-mail: katskovda@tut.ac.za

    2015-03-01

    The theory and practical problems of continuum source simultaneous multi-element electrothermal atomic absorption spectrometry (SMET AAS) are discussed by the example of direct analysis of underground water. The experimental methodology is based on pulse vaporization of the sample in a fast heated graphite tube and measurement of transient absorption of continuum spectrum radiation from D{sub 2} and Xe lamps within 200–400 nm wavelengths range with a low resolution spectral instrument and linear charge-coupled device. The setup permits the acquisition of 200 spectra during 1 s atomization pulse. Respective data matrix absorbance vs wavelength/time is employed for the quantification of elements in the sample. The calculation algorithm developed includes broad band and continuum background correction, linearization of function absorbance vs. concentration of atomic vapor and integration of thus modified absorbance at the resonance lines of the elements to be determined. Practical application shows that the method can be employed for the direct simultaneous determination of about 20 elements above microgram per liter level within 3–5 orders of the magnitude concentration range. The investigated sources of measurement errors are mainly associated with the atomization and vapor transportation problems, which are aggravated for the simultaneous release of major and minor sample constituents. Respective corrections concerning the selection of analytical lines, optimal sampling volume, matrix modification and cleaning of the atomizer have been introduced in the SMET AAS analytical technology. Under the optimized experimental conditions the calibration curves in Log-Log coordinates for all the investigated analytes in the single or multi-element reference solutions are approximated by the first order equations. The use of these equations as permanent characteristics of the setup enables instant quantification of Al, Ca, Co, Cr, Cu, Fe, Mg, Mn and Ni in the underground

  12. 高分辨真三维显示中的体素化及均匀化方法%The Voxelization and Homogenization methods of High-Resolution Volumetric 3D Display

    Institute of Scientific and Technical Information of China (English)

    田丰; 夏雪; 田晶; 张文俊; 王鹤

    2013-01-01

    In order to obtain radial uniform luminance and increase the effective numbers of voxels for volumetric 3D display based on projection,a voxelization and homogenization method is proposed.Regarding the problem of high luminance of voxels near central axis,the cause of excessive loss of voxels in the existing sampling methods is analyzed.By replacing three-dimensional sampling with two-dimensional plane-filling algorithm,the voxelization method in radial extent filling is proposed.Homogenization method based on dithering technique is proposed,which helps to correct voxel luminance distortion in cylindrical space.Demonstrated in the experiments,about 60% of the display resolution is retained and the effective voxel number reaches 200 million.The volumetric 3D display prototype is able to show clear and uniform stereo images with all viewing angles under the condition of indoor light.%为了使基于投影的真三维显示获得径向均匀亮度,并提高有效体素数量,提出一种体素化和均匀化方法.针对体素中轴亮度高和外围亮度低的问题,分析了现有体素采样方法导致体素数量损失过多的原因;然后以二维平面填充算法替代三维体素采样,提出基于径向范围填充的体素化方法,以及基于抖动技术的均匀化方法,以修正了柱空间内体素亮度失真.实验结果证明,文中方法保留了约60%的体显示分辨率,有效体素数量达到2亿个,真三维显示样机能够在室内光环境下显示清晰且均匀的全角度立体影像.

  13. ASSESSING 3D PHOTOGRAMMETRY TECHNIQUES IN CRANIOMETRICS

    Directory of Open Access Journals (Sweden)

    M. C. Moshobane

    2016-06-01

    Full Text Available Morphometrics (the measurement of morphological features has been revolutionized by the creation of new techniques to study how organismal shape co-varies with several factors such as ecophenotypy. Ecophenotypy refers to the divergence of phenotypes due to developmental changes induced by local environmental conditions, producing distinct ecophenotypes. None of the techniques hitherto utilized could explicitly address organismal shape in a complete biological form, i.e. three-dimensionally. This study investigates the use of the commercial software, Photomodeler Scanner® (PMSc® three-dimensional (3D modelling software to produce accurate and high-resolution 3D models. Henceforth, the modelling of Subantarctic fur seal (Arctocephalus tropicalis and Antarctic fur seal (Arctocephalus gazella skulls which could allow for 3D measurements. Using this method, sixteen accurate 3D skull models were produced and five metrics were determined. The 3D linear measurements were compared to measurements taken manually with a digital caliper. In addition, repetitive measurements were recorded by varying researchers to determine repeatability. To allow for comparison straight line measurements were taken with the software, assuming that close accord with all manually measured features would illustrate the model’s accurate replication of reality. Measurements were not significantly different demonstrating that realistic 3D skull models can be successfully produced to provide a consistent basis for craniometrics, with the additional benefit of allowing non-linear measurements if required.

  14. Assessing 3d Photogrammetry Techniques in Craniometrics

    Science.gov (United States)

    Moshobane, M. C.; de Bruyn, P. J. N.; Bester, M. N.

    2016-06-01

    Morphometrics (the measurement of morphological features) has been revolutionized by the creation of new techniques to study how organismal shape co-varies with several factors such as ecophenotypy. Ecophenotypy refers to the divergence of phenotypes due to developmental changes induced by local environmental conditions, producing distinct ecophenotypes. None of the techniques hitherto utilized could explicitly address organismal shape in a complete biological form, i.e. three-dimensionally. This study investigates the use of the commercial software, Photomodeler Scanner® (PMSc®) three-dimensional (3D) modelling software to produce accurate and high-resolution 3D models. Henceforth, the modelling of Subantarctic fur seal (Arctocephalus tropicalis) and Antarctic fur seal (Arctocephalus gazella) skulls which could allow for 3D measurements. Using this method, sixteen accurate 3D skull models were produced and five metrics were determined. The 3D linear measurements were compared to measurements taken manually with a digital caliper. In addition, repetitive measurements were recorded by varying researchers to determine repeatability. To allow for comparison straight line measurements were taken with the software, assuming that close accord with all manually measured features would illustrate the model's accurate replication of reality. Measurements were not significantly different demonstrating that realistic 3D skull models can be successfully produced to provide a consistent basis for craniometrics, with the additional benefit of allowing non-linear measurements if required.

  15. Note: High-speed Z tip scanner with screw cantilever holding mechanism for atomic-resolution atomic force microscopy in liquid.

    Science.gov (United States)

    Akrami, Seyed Mohammad Reza; Miyata, Kazuki; Asakawa, Hitoshi; Fukuma, Takeshi

    2014-12-01

    High-speed atomic force microscopy has attracted much attention due to its unique capability of visualizing nanoscale dynamic processes at a solid/liquid interface. However, its usability and resolution have yet to be improved. As one of the solutions for this issue, here we present a design of a high-speed Z-tip scanner with screw holding mechanism. We perform detailed comparison between designs with different actuator size and screw arrangement by finite element analysis. Based on the design giving the best performance, we have developed a Z tip scanner and measured its performance. The measured frequency response of the scanner shows a flat response up to ∼10 kHz. This high frequency response allows us to achieve wideband tip-sample distance regulation. We demonstrate the applicability of the scanner to high-speed atomic-resolution imaging by visualizing atomic-scale calcite crystal dissolution process in water at 2 s/frame.

  16. Local orientation measurements in 3D

    DEFF Research Database (Denmark)

    Juul Jensen, D.

    2005-01-01

    The 3 Dimensional X-Ray Diffraction (3DXRD) method is presented and its potentials illustrated by examples. The 3DXRD method is based on diffraction of high energy X-rays and allows fast and nondestructive 3D characterization of the local distribution of crystallographic orientations in the bulk....... The spatial resolution is about 1x5x5 mu m but diffraction from microstructural elements as small as 100 nm may be monitored within suitable samples. As examples of the use of the 3DXRD method, it is chosen to present results for complete 3D characterization of grain structures, in-situ "filming...

  17. 3D visualization of polymer nanostructure

    Energy Technology Data Exchange (ETDEWEB)

    Werner, James H [Los Alamos National Laboratory

    2009-01-01

    Soft materials and structured polymers are extremely useful nanotechnology building blocks. Block copolymers, in particular, have served as 2D masks for nanolithography and 3D scaffolds for photonic crystals, nanoparticle fabrication, and solar cells. F or many of these applications, the precise 3 dimensional structure and the number and type of defects in the polymer is important for ultimate function. However, directly visualizing the 3D structure of a soft material from the nanometer to millimeter length scales is a significant technical challenge. Here, we propose to develop the instrumentation needed for direct 3D structure determination at near nanometer resolution throughout a nearly millimeter-cubed volume of a soft, potentially heterogeneous, material. This new capability will be a valuable research tool for LANL missions in chemistry, materials science, and nanoscience. Our approach to soft materials visualization builds upon exciting developments in super-resolution optical microscopy that have occurred over the past two years. To date, these new, truly revolutionary, imaging methods have been developed and almost exclusively used for biological applications. However, in addition to biological cells, these super-resolution imaging techniques hold extreme promise for direct visualization of many important nanostructured polymers and other heterogeneous chemical systems. Los Alamos has a unique opportunity to lead the development of these super-resolution imaging methods for problems of chemical rather than biological significance. While these optical methods are limited to systems transparent to visible wavelengths, we stress that many important functional chemicals such as polymers, glasses, sol-gels, aerogels, or colloidal assemblies meet this requirement, with specific examples including materials designed for optical communication, manipulation, or light-harvesting Our Research Goals are: (1) Develop the instrumentation necessary for imaging materials

  18. Atomic resolution crystal structure of Sapp2p, a secreted aspartic protease from Candida parapsilosis.

    Science.gov (United States)

    Dostál, Jiří; Pecina, Adam; Hrušková-Heidingsfeldová, Olga; Marečková, Lucie; Pichová, Iva; Řezáčová, Pavlina; Lepšík, Martin; Brynda, Jiří

    2015-12-01

    The virulence of the Candida pathogens is enhanced by the production of secreted aspartic proteases, which therefore represent possible targets for drug design. Here, the crystal structure of the secreted aspartic protease Sapp2p from Candida parapsilosis was determined. Sapp2p was isolated from its natural source and crystallized in complex with pepstatin A, a classical aspartic protease inhibitor. The atomic resolution of 0.83 Å allowed the protonation states of the active-site residues to be inferred. A detailed comparison of the structure of Sapp2p with the structure of Sapp1p, the most abundant C. parapsilosis secreted aspartic protease, was performed. The analysis, which included advanced quantum-chemical interaction-energy calculations, uncovered molecular details that allowed the experimentally observed equipotent inhibition of both isoenzymes by pepstatin A to be rationalized.

  19. 'Big Bang' tomography as a new route to atomic-resolution electron tomography.

    Science.gov (United States)

    Van Dyck, Dirk; Jinschek, Joerg R; Chen, Fu-Rong

    2012-06-13

    Until now it has not been possible to image at atomic resolution using classical electron tomographic methods, except when the target is a perfectly crystalline nano-object imaged along a few zone axes. The main reasons are that mechanical tilting in an electron microscope with sub-ångström precision over a very large angular range is difficult, that many real-life objects such as dielectric layers in microelectronic devices impose geometrical constraints and that many radiation-sensitive objects such as proteins limit the total electron dose. Hence, there is a need for a new tomographic scheme that is able to deduce three-dimensional information from only one or a few projections. Here we present an electron tomographic method that can be used to determine, from only one viewing direction and with sub-ångström precision, both the position of individual atoms in the plane of observation and their vertical position. The concept is based on the fact that an experimentally reconstructed exit wave consists of the superposition of the spherical waves that have been scattered by the individual atoms of the object. Furthermore, the phase of a Fourier component of a spherical wave increases with the distance of propagation at a known 'phase speed'. If we assume that an atom is a point-like object, the relationship between the phase and the phase speed of each Fourier component is linear, and the distance between the atom and the plane of observation can therefore be determined by linear fitting. This picture has similarities with Big Bang cosmology, in which the Universe expands from a point-like origin such that the distance of any galaxy from the origin is linearly proportional to the speed at which it moves away from the origin (Hubble expansion). The proof of concept of the method has been demonstrated experimentally for graphene with a two-layer structure and it will work optimally for similar layered materials, such as boron nitride and molybdenum disulphide.

  20. Elemental mapping in achromatic atomic-resolution energy-filtered transmission electron microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Forbes, B.D. [School of Physics, University of Melbourne, Parkville, VIC 3010 (Australia); Houben, L. [Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Gruenberg Institute, Forschungszentrum Jülich, D-52425 Jülich (Germany); Mayer, J. [Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Gruenberg Institute, Forschungszentrum Jülich, D-52425 Jülich (Germany); Central Facility for Electron Microscopy, RWTH Aachen University, D-52074 Aachen (Germany); Dunin-Borkowski, R.E. [Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Gruenberg Institute, Forschungszentrum Jülich, D-52425 Jülich (Germany); Allen, L.J., E-mail: lja@unimelb.edu.au [School of Physics, University of Melbourne, Parkville, VIC 3010 (Australia)

    2014-12-15

    We present atomic-resolution energy-filtered transmission electron microscopy (EFTEM) images obtained with the chromatic-aberration-corrected FEI Titan PICO at the Ernst-Ruska Centre, Jülich, Germany. We find qualitative agreement between experiment and simulation for the background-subtracted EFTEM images of the Ti–L{sub 2,3} and O–K edges for a specimen of SrTiO{sub 3} oriented down the [110] zone axis. The simulations utilize the transition potential formulation for inelastic scattering, which permits a detailed investigation of contributions to the EFTEM image. We find that energy-filtered images of the Ti–L{sub 2,3} and O–K edges are lattice images and that the background-subtracted core-loss maps may not be directly interpretable as elemental maps. Simulations show that this is a result of preservation of elastic contrast, whereby the qualitative details of the image are determined primarily by elastic, coherent scattering. We show that this effect places a constraint on the range of specimen thicknesses which could theoretically yield directly useful elemental maps. In general, interpretation of EFTEM images is ideally accompanied by detailed simulations. - Highlights: • Achromatic atomic-resolution EFTEM images were obtained for STO 〈110〉. • Simulations were in qualitative agreement with Ti–L{sub 2,3} and O–K edge maps. • The experimental EFTEM maps are not directly interpretable as elemental maps. • Image intensities are strongly determined by preservation of elastic contrast. • Interpretation of EFTEM images is ideally accompanied by detailed simulations.

  1. GPU加速3D流场特征提取与多分辨率绘制%GPU-Accelerated Feature Extraction and Multi-resolution Visualization for Complex 3D Fluid Field

    Institute of Scientific and Technical Information of China (English)

    徐华勋; 曾亮; 蔡勋; 李思昆

    2009-01-01

    Due to the mutual influence of grid points on the view direction, visualization to a 3D fluid field often has problem of occlusion and cluttering. In this paper, we propose a novel approach for solving the occlusion and cluttering problem based on multi-resolution rendering. By the solution, first, a new fluid feature extraction method is presented by taking advantage of the strong non-linear ability of the neural network. Then based on the flow feature detected, a Voronoi graph method is used to organize field data. Finally, the field data is visualized by the "fisheye views" method. The test result of the visualization effects and performance to our method shows that our proposed approach is feasible and efficient in solving the occlusion and cluttering problem.%由于视线方向上的网格单元前后相互影响,导致3D流场可视化面临遮挡和混乱问题,为此提出一种基于流场特征的多分辨率绘制方法.首先利用基于GPU的BP网络流场特征提取方法对流场典型特征或用户关注的新特征进行选取、训练和识别;在此基础上,利用Voronoi图技术对特征数据构造特征树;最后基于鱼眼视图多分辨率技术进行绘制.对绘制和性能进行测试的实验结果表明,该方法能有效地提取流场特征,降低遮挡和混乱对可视化效果影响.

  2. Intrinsic Resolution of Molecular Electronic Wave Functions and Energies in Terms of Quasi-atoms and Their Interactions.

    Science.gov (United States)

    West, Aaron C; Schmidt, Michael W; Gordon, Mark S; Ruedenberg, Klaus

    2017-02-09

    A general intrinsic energy resolution has been formulated for strongly correlated wave functions in the full molecular valence space and its subspaces. The information regarding the quasi-atomic organization of the molecular electronic structure is extracted from the molecular wave function without introducing any additional postulated model state wave functions. To this end, the molecular wave function is expressed in terms of quasi-atomic molecular orbitals, which maximize the overlap between subspaces of the molecular orbital space and the free-atom orbital spaces. As a result, the molecular wave function becomes the superposition of a wave function representing the juxtaposed nonbonded quasi-atoms and a wave function describing the interatomic electron migrations that create bonds through electron sharing. The juxtaposed nonbonded quasi-atoms are shown to consist of entangled quasi-atomic states from different atoms. The binding energy is resolved as a sum of contributions that are due to quasi-atom formation, quasiclassical electrostatic interactions, and interatomic interferences caused by electron sharing. The contributions are further resolved according to orbital interactions. The various transformations that generate the analysis are determined by criteria that are independent of the working orbital basis used for calculating the molecular wave function. The theoretical formulation of the resolution is quantitatively validated by an application to the C2 molecule.

  3. Influence of spatial and temporal coherences on atomic resolution high angle annular dark field imaging.

    Science.gov (United States)

    Beyer, Andreas; Belz, Jürgen; Knaub, Nikolai; Jandieri, Kakhaber; Volz, Kerstin

    2016-10-01

    Aberration-corrected (scanning) transmission electron microscopy ((S)TEM) has become a widely used technique when information on the chemical composition is sought on an atomic scale. To extract the desired information, complementary simulations of the scattering process are inevitable. Often the partial spatial and temporal coherences are neglected in the simulations, although they can have a huge influence on the high resolution images. With the example of binary gallium phosphide (GaP) we elucidate the influence of the source size and shape as well as the chromatic aberration on the high angle annular dark field (HAADF) intensity. We achieve a very good quantitative agreement between the frozen phonon simulation and experiment for different sample thicknesses when a Lorentzian source distribution is assumed and the effect of the chromatic aberration is considered. Additionally the influence of amorphous layers introduced by the preparation of the TEM samples is discussed. Taking into account these parameters, the intensity in the whole unit cell of GaP, i.e. at the positions of the different atomic columns and in the region between them, is described correctly. With the knowledge of the decisive parameters, the determination of the chemical composition of more complex, multinary materials becomes feasible.

  4. BEAMS3D Neutral Beam Injection Model

    Science.gov (United States)

    McMillan, Matthew; Lazerson, Samuel A.

    2014-09-01

    With the advent of applied 3D fields in Tokamaks and modern high performance stellarators, a need has arisen to address non-axisymmetric effects on neutral beam heating and fueling. We report on the development of a fully 3D neutral beam injection (NBI) model, BEAMS3D, which addresses this need by coupling 3D equilibria to a guiding center code capable of modeling neutral and charged particle trajectories across the separatrix and into the plasma core. Ionization, neutralization, charge-exchange, viscous slowing down, and pitch angle scattering are modeled with the ADAS atomic physics database. Elementary benchmark calculations are presented to verify the collisionless particle orbits, NBI model, frictional drag, and pitch angle scattering effects. A calculation of neutral beam heating in the NCSX device is performed, highlighting the capability of the code to handle 3D magnetic fields. Notice: this manuscript has been authored by Princeton University under Contract Number DE-AC02-09CH11466 with the US Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes.

  5. Near-Atomic Resolution Structure of a Highly Neutralizing Fab Bound to Canine Parvovirus.

    Science.gov (United States)

    Organtini, Lindsey J; Lee, Hyunwook; Iketani, Sho; Huang, Kai; Ashley, Robert E; Makhov, Alexander M; Conway, James F; Parrish, Colin R; Hafenstein, Susan

    2016-11-01

    Canine parvovirus (CPV) is a highly contagious pathogen that causes severe disease in dogs and wildlife. Previously, a panel of neutralizing monoclonal antibodies (MAb) raised against CPV was characterized. An antibody fragment (Fab) of MAb E was found to neutralize the virus at low molar ratios. Using recent advances in cryo-electron microscopy (cryo-EM), we determined the structure of CPV in complex with Fab E to 4.1 Å resolution, which allowed de novo building of the Fab structure. The footprint identified was significantly different from the footprint obtained previously from models fitted into lower-resolution maps. Using single-chain variable fragments, we tested antibody residues that control capsid binding. The near-atomic structure also revealed that Fab binding had caused capsid destabilization in regions containing key residues conferring receptor binding and tropism, which suggests a mechanism for efficient virus neutralization by antibody. Furthermore, a general technical approach to solving the structures of small molecules is demonstrated, as binding the Fab to the capsid allowed us to determine the 50-kDa Fab structure by cryo-EM.

  6. Atomic force microscopy with nanoelectrode tips for high resolution electrochemical, nanoadhesion and nanoelectrical imaging

    Science.gov (United States)

    Nellist, Michael R.; Chen, Yikai; Mark, Andreas; Gödrich, Sebastian; Stelling, Christian; Jiang, Jingjing; Poddar, Rakesh; Li, Chunzeng; Kumar, Ravi; Papastavrou, Georg; Retsch, Markus; Brunschwig, Bruce S.; Huang, Zhuangqun; Xiang, Chengxiang; Boettcher, Shannon W.

    2017-03-01

    Multimodal nano-imaging in electrochemical environments is important across many areas of science and technology. Here, scanning electrochemical microscopy (SECM) using an atomic force microscope (AFM) platform with a nanoelectrode probe is reported. In combination with PeakForce tapping AFM mode, the simultaneous characterization of surface topography, quantitative nanomechanics, nanoelectronic properties, and electrochemical activity is demonstrated. The nanoelectrode probe is coated with dielectric materials and has an exposed conical Pt tip apex of ∼200 nm in height and of ∼25 nm in end-tip radius. These characteristic dimensions permit sub-100 nm spatial resolution for electrochemical imaging. With this nanoelectrode probe we have extended AFM-based nanoelectrical measurements to liquid environments. Experimental data and numerical simulations are used to understand the response of the nanoelectrode probe. With PeakForce SECM, we successfully characterized a surface defect on a highly-oriented pyrolytic graphite electrode showing correlated topographical, electrochemical and nanomechanical information at the highest AFM-SECM resolution. The SECM nanoelectrode also enabled the measurement of heterogeneous electrical conductivity of electrode surfaces in liquid. These studies extend the basic understanding of heterogeneity on graphite/graphene surfaces for electrochemical applications.

  7. Near-atomic resolution structural model of the yeast 26S proteasome.

    Science.gov (United States)

    Beck, Florian; Unverdorben, Pia; Bohn, Stefan; Schweitzer, Andreas; Pfeifer, Günter; Sakata, Eri; Nickell, Stephan; Plitzko, Jürgen M; Villa, Elizabeth; Baumeister, Wolfgang; Förster, Friedrich

    2012-09-11

    The 26S proteasome operates at the executive end of the ubiquitin-proteasome pathway. Here, we present a cryo-EM structure of the Saccharomyces cerevisiae 26S proteasome at a resolution of 7.4 Å or 6.7 Å (Fourier-Shell Correlation of 0.5 or 0.3, respectively). We used this map in conjunction with molecular dynamics-based flexible fitting to build a near-atomic resolution model of the holocomplex. The quality of the map allowed us to assign α-helices, the predominant secondary structure element of the regulatory particle subunits, throughout the entire map. We were able to determine the architecture of the Rpn8/Rpn11 heterodimer, which had hitherto remained elusive. The MPN domain of Rpn11 is positioned directly above the AAA-ATPase N-ring suggesting that Rpn11 deubiquitylates substrates immediately following commitment and prior to their unfolding by the AAA-ATPase module. The MPN domain of Rpn11 dimerizes with that of Rpn8 and the C-termini of both subunits form long helices, which are integral parts of a coiled-coil module. Together with the C-terminal helices of the six PCI-domain subunits they form a very large coiled-coil bundle, which appears to serve as a flexible anchoring device for all the lid subunits.

  8. Radiation damage free two-color X-ray ghost diffraction with atomic resolution

    CERN Document Server

    Li, Zheng; Chapman, Henry; Shih, Yanhua

    2015-01-01

    The X-ray free electron lasers (XFEL) can enable diffractive structural determination of protein crystals or single molecules that are too small and radiation-sensitive for conventional X-ray analysis. However the electronic form factor could have been modified during the ultrashort X-ray pulse due to photoionization and electron cascade caused by the intense X-ray pulse. For general X-ray imaging techniques, to minimize radiation damage effect is of major concern to ensure faithful reconstruction of the structure. Here we show that a radiation damage free diffraction can be achieved with an atomic spatial resolution, by using X-ray parametric down-conversion (PDC), and two-color biphoton ghost imaging. We illustrate that formation of the diffractive patterns satisfies a condition analogous to the Bragg equation, with a resolution that could be as fine as the lattice length scale of several Angstrom. Because the samples are illuminated by the optical photons of low energy, they can be free of radiation damage...

  9. Multiplane 3D superresolution optical fluctuation imaging

    CERN Document Server

    Geissbuehler, Stefan; Godinat, Aurélien; Bocchio, Noelia L; Dubikovskaya, Elena A; Lasser, Theo; Leutenegger, Marcel

    2013-01-01

    By switching fluorophores on and off in either a deterministic or a stochastic manner, superresolution microscopy has enabled the imaging of biological structures at resolutions well beyond the diffraction limit. Superresolution optical fluctuation imaging (SOFI) provides an elegant way of overcoming the diffraction limit in all three spatial dimensions by computing higher-order cumulants of image sequences of blinking fluorophores acquired with a conventional widefield microscope. So far, three-dimensional (3D) SOFI has only been demonstrated by sequential imaging of multiple depth positions. Here we introduce a versatile imaging scheme which allows for the simultaneous acquisition of multiple focal planes. Using 3D cross-cumulants, we show that the depth sampling can be increased. Consequently, the simultaneous acquisition of multiple focal planes reduces the acquisition time and hence the photo-bleaching of fluorescent markers. We demonstrate multiplane 3D SOFI by imaging the mitochondria network in fixed ...

  10. Spectroradiometric characterization of autostereoscopic 3D displays

    Science.gov (United States)

    Rubiño, Manuel; Salas, Carlos; Pozo, Antonio M.; Castro, J. J.; Pérez-Ocón, Francisco

    2013-11-01

    Spectroradiometric measurements have been made for the experimental characterization of the RGB channels of autostereoscopic 3D displays, giving results for different measurement angles with respect to the normal direction of the plane of the display. In the study, 2 different models of autostereoscopic 3D displays of different sizes and resolutions were used, making measurements with a spectroradiometer (model PR-670 SpectraScan of PhotoResearch). From the measurements made, goniometric results were recorded for luminance contrast, and the fundamental hypotheses have been evaluated for the characterization of the displays: independence of the RGB channels and their constancy. The results show that the display with the lower angle variability in the contrast-ratio value and constancy of the chromaticity coordinates nevertheless presented the greatest additivity deviations with the measurement angle. For both displays, when the parameters evaluated were taken into account, lower angle variability consistently resulted in the 2D mode than in the 3D mode.

  11. Novel proposals in widefield 3D microscopy

    Science.gov (United States)

    Sanchez-Ortiga, E.; Doblas, A.; Saavedra, G.; Martinez-Corral, M.

    2010-04-01

    Patterned illumination is a successful set of techniques in high resolution 3D microscopy. In particular, structured illumination microscopy is based on the projection of 1D periodic patterns onto the 3D sample under study. In this research we propose the implementation of a very simple method for the flexible production of 1D structured illumination. Specifically, we propose the insertion of a Fresnel biprism after a monochromatic point source. The biprism produces a pair of twin, fully coherent, virtual point sources. After imaging the virtual sources onto the objective aperture stop, the expected 1D periodic pattern is produced into the 3D sample. The main advantage of using the Fresnel biprism is that by simply varying the distance between the biprism and the point source one can tune the period of the fringes while keeping their contrast.

  12. Atoms

    Institute of Scientific and Technical Information of China (English)

    刘洪毓

    2007-01-01

    Atoms(原子)are all around us.They are something like the bricks (砖块)of which everything is made. The size of an atom is very,very small.In just one grain of salt are held millions of atoms. Atoms are very important.The way one object acts depends on what

  13. Determination of a high spatial resolution geopotential model using atomic clock comparisons

    Science.gov (United States)

    Lion, G.; Panet, I.; Wolf, P.; Guerlin, C.; Bize, S.; Delva, P.

    2017-01-01

    Recent technological advances in optical atomic clocks are opening new perspectives for the direct determination of geopotential differences between any two points at a centimeter-level accuracy in geoid height. However, so far detailed quantitative estimates of the possible improvement in geoid determination when adding such clock measurements to existing data are lacking. We present a first step in that direction with the aim and hope of triggering further work and efforts in this emerging field of chronometric geodesy and geophysics. We specifically focus on evaluating the contribution of this new kind of direct measurements in determining the geopotential at high spatial resolution (≈ 10 km). We studied two test areas, both located in France and corresponding to a middle (Massif Central) and high (Alps) mountainous terrain. These regions are interesting because the gravitational field strength varies greatly from place to place at high spatial resolution due to the complex topography. Our method consists in first generating a synthetic high-resolution geopotential map, then drawing synthetic measurement data (gravimetry and clock data) from it, and finally reconstructing the geopotential map from that data using least squares collocation. The quality of the reconstructed map is then assessed by comparing it to the original one used to generate the data. We show that adding only a few clock data points (less than 1% of the gravimetry data) reduces the bias significantly and improves the standard deviation by a factor 3. The effect of the data coverage and data quality on the results is investigated, and the trade-off between the measurement noise level and the number of data points is discussed.

  14. 3D Spectroscopy in Astronomy

    Science.gov (United States)

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

    2011-09-01

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

  15. Spherical 3D isotropic wavelets

    Science.gov (United States)

    Lanusse, F.; Rassat, A.; Starck, J.-L.

    2012-04-01

    Context. Future cosmological surveys will provide 3D large scale structure maps with large sky coverage, for which a 3D spherical Fourier-Bessel (SFB) analysis in spherical coordinates is natural. Wavelets are particularly well-suited to the analysis and denoising of cosmological data, but a spherical 3D isotropic wavelet transform does not currently exist to analyse spherical 3D data. Aims: The aim of this paper is to present a new formalism for a spherical 3D isotropic wavelet, i.e. one based on the SFB decomposition of a 3D field and accompany the formalism with a public code to perform wavelet transforms. Methods: We describe a new 3D isotropic spherical wavelet decomposition based on the undecimated wavelet transform (UWT) described in Starck et al. (2006). We also present a new fast discrete spherical Fourier-Bessel transform (DSFBT) based on both a discrete Bessel transform and the HEALPIX angular pixelisation scheme. We test the 3D wavelet transform and as a toy-application, apply a denoising algorithm in wavelet space to the Virgo large box cosmological simulations and find we can successfully remove noise without much loss to the large scale structure. Results: We have described a new spherical 3D isotropic wavelet transform, ideally suited to analyse and denoise future 3D spherical cosmological surveys, which uses a novel DSFBT. We illustrate its potential use for denoising using a toy model. All the algorithms presented in this paper are available for download as a public code called MRS3D at http://jstarck.free.fr/mrs3d.html

  16. 3D IBFV : Hardware-Accelerated 3D Flow Visualization

    NARCIS (Netherlands)

    Telea, Alexandru; Wijk, Jarke J. van

    2003-01-01

    We present a hardware-accelerated method for visualizing 3D flow fields. The method is based on insertion, advection, and decay of dye. To this aim, we extend the texture-based IBFV technique for 2D flow visualization in two main directions. First, we decompose the 3D flow visualization problem in a

  17. 3D Elevation Program—Virtual USA in 3D

    Science.gov (United States)

    Lukas, Vicki; Stoker, J.M.

    2016-04-14

    The U.S. Geological Survey (USGS) 3D Elevation Program (3DEP) uses a laser system called ‘lidar’ (light detection and ranging) to create a virtual reality map of the Nation that is very accurate. 3D maps have many uses with new uses being discovered all the time.  

  18. Atomic resolution imaging of YAlO3: Ce in the chromatic and spherical aberration corrected PICO electron microscope.

    Science.gov (United States)

    Jin, Lei; Barthel, Juri; Jia, Chun-Lin; Urban, Knut W

    2017-01-31

    The application of combined chromatic and spherical aberration correction in high-resolution transmission electron microscopy enables a significant improvement of the spatial resolution down to 50 pm. We demonstrate that such a resolution can be achieved in practice at 200kV. Diffractograms of images of gold nanoparticles on amorphous carbon demonstrate corresponding information transfer. The Y atom pairs in [010] oriented yttrium orthoaluminate are successfully imaged together with the Al and the O atoms. Although the 57 pm pair separation is well demonstrated separations between 55 pm and 80 pm are measured. This observation is tentatively attributed to structural relaxations and surface reconstruction in the very thin samples used. Quantification of the resolution limiting effective image spread is achieved based on an absolute match between experimental and simulated image intensity distributions.

  19. Interactive 3D multimedia content

    CERN Document Server

    Cellary, Wojciech

    2012-01-01

    The book describes recent research results in the areas of modelling, creation, management and presentation of interactive 3D multimedia content. The book describes the current state of the art in the field and identifies the most important research and design issues. Consecutive chapters address these issues. These are: database modelling of 3D content, security in 3D environments, describing interactivity of content, searching content, visualization of search results, modelling mixed reality content, and efficient creation of interactive 3D content. Each chapter is illustrated with example a

  20. A 3-D Contextual Classifier

    DEFF Research Database (Denmark)

    Larsen, Rasmus

    1997-01-01

    . This includes the specification of a Gaussian distribution for the pixel values as well as a prior distribution for the configuration of class variables within the cross that is m ade of a pixel and its four nearest neighbours. We will extend this algorithm to 3-D, i.e. we will specify a simultaneous Gaussian...... distr ibution for a pixel and its 6 nearest 3-D neighbours, and generalise the class variable configuration distribution within the 3-D cross. The algorithm is tested on a synthetic 3-D multivariate dataset....

  1. 3D Bayesian contextual classifiers

    DEFF Research Database (Denmark)

    Larsen, Rasmus

    2000-01-01

    We extend a series of multivariate Bayesian 2-D contextual classifiers to 3-D by specifying a simultaneous Gaussian distribution for the feature vectors as well as a prior distribution of the class variables of a pixel and its 6 nearest 3-D neighbours.......We extend a series of multivariate Bayesian 2-D contextual classifiers to 3-D by specifying a simultaneous Gaussian distribution for the feature vectors as well as a prior distribution of the class variables of a pixel and its 6 nearest 3-D neighbours....

  2. 3-D printers for libraries

    CERN Document Server

    Griffey, Jason

    2014-01-01

    As the maker movement continues to grow and 3-D printers become more affordable, an expanding group of hobbyists is keen to explore this new technology. In the time-honored tradition of introducing new technologies, many libraries are considering purchasing a 3-D printer. Jason Griffey, an early enthusiast of 3-D printing, has researched the marketplace and seen several systems first hand at the Consumer Electronics Show. In this report he introduces readers to the 3-D printing marketplace, covering such topics asHow fused deposition modeling (FDM) printing workBasic terminology such as build

  3. 3D for Graphic Designers

    CERN Document Server

    Connell, Ellery

    2011-01-01

    Helping graphic designers expand their 2D skills into the 3D space The trend in graphic design is towards 3D, with the demand for motion graphics, animation, photorealism, and interactivity rapidly increasing. And with the meteoric rise of iPads, smartphones, and other interactive devices, the design landscape is changing faster than ever.2D digital artists who need a quick and efficient way to join this brave new world will want 3D for Graphic Designers. Readers get hands-on basic training in working in the 3D space, including product design, industrial design and visualization, modeling, ani

  4. The application of high-resolution 3D seismic data to model the distribution of mechanical and hydrogeological properties of a potential host rock for the deep storage of radioactive waste in France

    CERN Document Server

    Mari, Jean-Luc

    2014-01-01

    In the context of a deep geological repository of high-level radioactive wastes, the French National Radioactive Waste Management Agency (Andra) has conducted an extensive characterization of the Callovo-Oxfordian argillaceous rock and surrounding formations in the Eastern Paris Basin. As part of this project, an accurate 3D seismic derived geological model is needed. The paper shows the procedure used for building the 3D seismic constrained geological model in depth by combining time-to-depth conversion of seismic horizons, consistent seismic velocity model and elastic impedance in time. It also shows how the 3D model is used for mechanical and hydrogeological studies. The 3D seismic field data example illustrates the potential of the proposed depth conversion procedure for estimating density and velocity distributions, which are consistent with the depth conversion of seismic horizons using the Bayesian Kriging method. The geological model shows good agreement with well log data obtained from a reference we...

  5. 3D bioprinting for engineering complex tissues.

    Science.gov (United States)

    Mandrycky, Christian; Wang, Zongjie; Kim, Keekyoung; Kim, Deok-Ho

    2016-01-01

    Bioprinting is a 3D fabrication technology used to precisely dispense cell-laden biomaterials for the construction of complex 3D functional living tissues or artificial organs. While still in its early stages, bioprinting strategies have demonstrated their potential use in regenerative medicine to generate a variety of transplantable tissues, including skin, cartilage, and bone. However, current bioprinting approaches still have technical challenges in terms of high-resolution cell deposition, controlled cell distributions, vascularization, and innervation within complex 3D tissues. While no one-size-fits-all approach to bioprinting has emerged, it remains an on-demand, versatile fabrication technique that may address the growing organ shortage as well as provide a high-throughput method for cell patterning at the micrometer scale for broad biomedical engineering applications. In this review, we introduce the basic principles, materials, integration strategies and applications of bioprinting. We also discuss the recent developments, current challenges and future prospects of 3D bioprinting for engineering complex tissues. Combined with recent advances in human pluripotent stem cell technologies, 3D-bioprinted tissue models could serve as an enabling platform for high-throughput predictive drug screening and more effective regenerative therapies.

  6. Planetary Torque in 3D Isentropic Disks

    CERN Document Server

    Fung, Jeffrey; Lega, Elena; Velasco, David

    2016-01-01

    Planet migration is inherently a three-dimensional (3D) problem, because Earth-size planetary cores are deeply embedded in protoplanetary disks. Simulations of these 3D disks remain challenging due to the steep requirement in resolution. Using two different hydrodynamics code, FARGO3D and PEnGUIn, we simulate disk-planet interaction for a 1 to 5 Earth-mass planet embedded in an isentropic disk. We measure the torque on the planet and ensure that the measurements are converged both in resolution and between the two codes. We find that the torque is independent of the smoothing length of the planet's potential ($r_{\\rm s}$), and that it has a weak dependence on the adiabatic index of the gaseous disk ($\\gamma$). The torque values correspond to an inward migration rate qualitatively similar to previous linear calculations. We perform additional simulations with explicit radiative transfer using FARGOCA, and again find agreement between 3D simulations and existing torque formulae. We also present the flow pattern...

  7. Planetary Torque in 3D Isentropic Disks

    Science.gov (United States)

    Fung, Jeffrey; Masset, Frédéric; Lega, Elena; Velasco, David

    2017-03-01

    Planetary migration is inherently a three-dimensional (3D) problem, because Earth-size planetary cores are deeply embedded in protoplanetary disks. Simulations of these 3D disks remain challenging due to the steep resolution requirements. Using two different hydrodynamics codes, FARGO3D and PEnGUIn, we simulate disk–planet interaction for a one to five Earth-mass planet embedded in an isentropic disk. We measure the torque on the planet and ensure that the measurements are converged both in resolution and between the two codes. We find that the torque is independent of the smoothing length of the planet’s potential (r s), and that it has a weak dependence on the adiabatic index of the gaseous disk (γ). The torque values correspond to an inward migration rate qualitatively similar to previous linear calculations. We perform additional simulations with explicit radiative transfer using FARGOCA, and again find agreement between 3D simulations and existing torque formulae. We also present the flow pattern around the planets that show active flow is present within the planet’s Hill sphere, and meridional vortices are shed downstream. The vertical flow speed near the planet is faster for a smaller r s or γ, up to supersonic speeds for the smallest r s and γ in our study.

  8. Spherical 3D Isotropic Wavelets

    CERN Document Server

    Lanusse, F; Starck, J -L

    2011-01-01

    Future cosmological surveys will provide 3D large scale structure maps with large sky coverage, for which a 3D Spherical Fourier-Bessel (SFB) analysis in is natural. Wavelets are particularly well-suited to the analysis and denoising of cosmological data, but a spherical 3D isotropic wavelet transform does not currently exist to analyse spherical 3D data. The aim of this paper is to present a new formalism for a spherical 3D isotropic wavelet, i.e. one based on the Fourier-Bessel decomposition of a 3D field and accompany the formalism with a public code to perform wavelet transforms. We describe a new 3D isotropic spherical wavelet decomposition based on the undecimated wavelet transform (UWT) described in Starck et al. 2006. We also present a new fast Discrete Spherical Fourier-Bessel Transform (DSFBT) based on both a discrete Bessel Transform and the HEALPIX angular pixelisation scheme. We test the 3D wavelet transform and as a toy-application, apply a denoising algorithm in wavelet space to the Virgo large...

  9. Improvement of 3D Scanner

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    The disadvantage remaining in 3D scanning system and its reasons are discussed. A new host-and-slave structure with high speed image acquisition and processing system is proposed to quicken the image processing and improve the performance of 3D scanning system.

  10. 3D Printing for Bricks

    OpenAIRE

    ECT Team, Purdue

    2015-01-01

    Building Bytes, by Brian Peters, is a project that uses desktop 3D printers to print bricks for architecture. Instead of using an expensive custom-made printer, it uses a normal standard 3D printer which is available for everyone and makes it more accessible and also easier for fabrication.

  11. Atomic resolution transmission electron microscopy of the intergranular structure of a Y{sub 2}O{sub 3}-silicon nitride ceramic

    Energy Technology Data Exchange (ETDEWEB)

    Ziegler, A.; Kisielowski, C.; Hoffmann, M.J.; Ritchie, R.O.

    2002-05-01

    High-resolution transmission electron microscopy (HRTEM) employing focus-variation phase-reconstruction methods is used to image the atomic structure of grain boundaries in a silicon nitride ceramic at a resolution of 0.8 Angstrom

  12. Organometallic Bonding in an Ullmann-Type On-Surface Chemical Reaction Studied by High-Resolution Atomic Force Microscopy.

    Science.gov (United States)

    Kawai, Shigeki; Sadeghi, Ali; Okamoto, Toshihiro; Mitsui, Chikahiko; Pawlak, Rémy; Meier, Tobias; Takeya, Jun; Goedecker, Stefan; Meyer, Ernst

    2016-10-01

    The on-surface Ullmann-type chemical reaction synthesizes polymers by linking carbons of adjacent molecules on solid surfaces. Although an organometallic compound is recently identified as the reaction intermediate, little is known about the detailed structure of the bonded organometallic species and its influence on the molecule and the reaction. Herein atomic force microscopy at low temperature is used to study the reaction with 3,9-diiododinaphtho[2,3-b:2',3'-d]thiophene (I-DNT-VW), which is polymerized on Ag(111) in vacuum. Thermally sublimated I-DNT-VW picks up a Ag surface atom, forming a CAg bond at one end after removing an iodine. The CAg bond is usually short-lived, and a CAgC organometallic bond immediately forms with an adjacent molecule. The existence of the bonded Ag atoms strongly affects the bending angle and adsorption height of the molecular unit. Density functional theory calculations reveal the bending mechanism, which reveals that charge from the terminus of the molecule is transferred via the Ag atom into the organometallic bond and strengths the local adsorption to the substrate. Such deformations vanish when the Ag atoms are removed by annealing and CC bonds are established.

  13. 3D vision system assessment

    Science.gov (United States)

    Pezzaniti, J. Larry; Edmondson, Richard; Vaden, Justin; Hyatt, Bryan; Chenault, David B.; Kingston, David; Geulen, Vanilynmae; Newell, Scott; Pettijohn, Brad

    2009-02-01

    In this paper, we report on the development of a 3D vision system consisting of a flat panel stereoscopic display and auto-converging stereo camera and an assessment of the system's use for robotic driving, manipulation, and surveillance operations. The 3D vision system was integrated onto a Talon Robot and Operator Control Unit (OCU) such that direct comparisons of the performance of a number of test subjects using 2D and 3D vision systems were possible. A number of representative scenarios were developed to determine which tasks benefited most from the added depth perception and to understand when the 3D vision system hindered understanding of the scene. Two tests were conducted at Fort Leonard Wood, MO with noncommissioned officers ranked Staff Sergeant and Sergeant First Class. The scenarios; the test planning, approach and protocols; the data analysis; and the resulting performance assessment of the 3D vision system are reported.

  14. PLOT3D user's manual

    Science