210,652 research outputs found

    EPiK-a Workflow for Electron Tomography in Kepler.

    Get PDF
    Scientific workflows integrate data and computing interfaces as configurable, semi-automatic graphs to solve a scientific problem. Kepler is such a software system for designing, executing, reusing, evolving, archiving and sharing scientific workflows. Electron tomography (ET) enables high-resolution views of complex cellular structures, such as cytoskeletons, organelles, viruses and chromosomes. Imaging investigations produce large datasets. For instance, in Electron Tomography, the size of a 16 fold image tilt series is about 65 Gigabytes with each projection image including 4096 by 4096 pixels. When we use serial sections or montage technique for large field ET, the dataset will be even larger. For higher resolution images with multiple tilt series, the data size may be in terabyte range. Demands of mass data processing and complex algorithms require the integration of diverse codes into flexible software structures. This paper describes a workflow for Electron Tomography Programs in Kepler (EPiK). This EPiK workflow embeds the tracking process of IMOD, and realizes the main algorithms including filtered backprojection (FBP) from TxBR and iterative reconstruction methods. We have tested the three dimensional (3D) reconstruction process using EPiK on ET data. EPiK can be a potential toolkit for biology researchers with the advantage of logical viewing, easy handling, convenient sharing and future extensibility

    MMTF: The Maryland-Magellan Tunable Filter

    Full text link
    This paper describes the Maryland-Magellan Tunable Filter (MMTF) on the Magellan-Baade 6.5-meter telescope. MMTF is based on a 150-mm clear aperture Fabry-Perot (FP) etalon that operates in low orders and provides transmission bandpass and central wavelength adjustable from ~5 to ~15 A and from ~5000 to over ~9200 A, respectively. It is installed in the Inamori Magellan Areal Camera and Spectrograph (IMACS) and delivers an image quality of ~0.5" over a field of view of 27' in diameter (monochromatic over ~10'). This versatile and easy-to-operate instrument has been used over the past three years for a wide variety of projects. This paper first reviews the basic principles of FP tunable filters, then provides a detailed description of the hardware and software associated with MMTF and the techniques developed to observe with this instrument and reduce the data. The main lessons learned in the course of the commissioning and implementation of MMTF are highlighted next, before concluding with a brief outlook on the future of MMTF and of similar facilities which are soon coming on line.Comment: 38 pages, 12 figures, 3 tables, now accepted for publication to the Astronomical Journa

    Automatic alignment for three-dimensional tomographic reconstruction

    Get PDF
    In tomographic reconstruction, the goal is to reconstruct an unknown object from a collection of line integrals. Given a complete sampling of such line integrals for various angles and directions, explicit inverse formulas exist to reconstruct the object. Given noisy and incomplete measurements, the inverse problem is typically solved through a regularized least-squares approach. A challenge for both approaches is that in practice the exact directions and offsets of the x-rays are only known approximately due to, e.g. calibration errors. Such errors lead to artifacts in the reconstructed image. In the case of sufficient sampling and geometrically simple misalignment, the measurements can be corrected by exploiting so-called consistency conditions. In other cases, such conditions may not apply and we have to solve an additional inverse problem to retrieve the angles and shifts. In this paper we propose a general algorithmic framework for retrieving these parameters in conjunction with an algebraic reconstruction technique. The proposed approach is illustrated by numerical examples for both simulated data and an electron tomography dataset

    Nonequilibrium steady states in a vibrated-rod monolayer: tetratic, nematic and smectic correlations

    Get PDF
    We study experimentally the nonequilibrium phase behaviour of a horizontal monolayer of macroscopic rods. The motion of the rods in two dimensions is driven by vibrations in the vertical direction. Aside from the control variables of packing fraction and aspect ratio that are typically explored in molecular liquid crystalline systems, due to the macroscopic size of the particles we are also able to investigate the effect of the precise shape of the particle on the steady states of this driven system. We find that the shape plays an important role in determining the nature of the orientational ordering at high packing fraction. Cylindrical particles show substantial tetratic correlations over a range of aspect ratios where spherocylinders have previously been shown by Bates et al (JCP 112, 10034 (2000)) to undergo transitions between isotropic and nematic phases. Particles that are thinner at the ends (rolling pins or bails) show nematic ordering over the same range of aspect ratios, with a well-established nematic phase at large aspect ratio and a defect-ridden nematic state with large-scale swirling motion at small aspect ratios. Finally, long-grain, basmati rice, whose geometry is intermediate between the two shapes above, shows phases with strong indications of smectic order.Comment: 18 pages and 13 eps figures, references adde

    Fine-To-Coarse Global Registration of RGB-D Scans

    Full text link
    RGB-D scanning of indoor environments is important for many applications, including real estate, interior design, and virtual reality. However, it is still challenging to register RGB-D images from a hand-held camera over a long video sequence into a globally consistent 3D model. Current methods often can lose tracking or drift and thus fail to reconstruct salient structures in large environments (e.g., parallel walls in different rooms). To address this problem, we propose a "fine-to-coarse" global registration algorithm that leverages robust registrations at finer scales to seed detection and enforcement of new correspondence and structural constraints at coarser scales. To test global registration algorithms, we provide a benchmark with 10,401 manually-clicked point correspondences in 25 scenes from the SUN3D dataset. During experiments with this benchmark, we find that our fine-to-coarse algorithm registers long RGB-D sequences better than previous methods

    Long-range nematic order and anomalous fluctuations in suspensions of swimming filamentous bacteria

    Full text link
    We study the collective dynamics of elongated swimmers in a very thin fluid layer by devising long, filamentous, non-tumbling bacteria. The strong confinement induces weak nematic alignment upon collision, which, for large enough density of cells, gives rise to global nematic order. This homogeneous but fluctuating phase, observed on the largest experimentally-accessible scale of millimeters, exhibits the properties predicted by standard models for flocking such as the Vicsek-style model of polar particles with nematic alignment: true long-range nematic order and non-trivial giant number fluctuations.Comment: 6 pages, 4 figures. Supplemental Material: 6 pages, 3 figure

    Mapping carbon nanotube orientation by fast fourier transform of scanning electron micrographs

    Get PDF
    A novel method of applying a two-dimensional Fourier transform (2D-FFT) to SEM was developed to map the CNT orientation in pre-formed arrays. Local 2D-FFTs were integrated azimuthally to determine an orientation distribution function and the associated Herman parameter. This approach provides data rapidly and over a wide range of lengthscales. Although likely to be applicable to a wide range of anisotropic nanoscale structures, the method was specifically developed to study CNT veils, a system in which orientation critically controls mechanical properties. Using this system as a model, key parameters for the 2D-FFT analysis were optimised, including magnification and domain size; a model set of CNT veils were pre-strained to 5%, 10% and 15%, to vary the alignment degree. The algorithm confirmed a narrower orientation distribution function and increasing Herman parameter, with increasing pre-strain. To validate the algorithm, the local orientation was compared to that derived from a common polarised Raman spectroscopy. Orientation maps of the Herman parameter, derived by both methods, showed good agreement. Quantitatively, the mean Herman parameter calculated using the polarised Raman spectroscopy was 0.42 ± 0.004 compared to 0.32 ± 0.002 for the 2D-FFT method, with a correlation coefficient of 0.73. Possible reasons for the modest and systematic discrepancy were discussed

    Radio Galaxy Zoo: Cosmological Alignment of Radio Sources

    Get PDF
    We study the mutual alignment of radio sources within two surveys, FIRST and TGSS. This is done by producing two position angle catalogues containing the preferential directions of respectively 3005930\,059 and 1167411\,674 extended sources distributed over more than 70007\,000 and 1700017\,000 square degrees. The identification of the sources in the FIRST sample was performed in advance by volunteers of the Radio Galaxy Zoo project, while for the TGSS sample it is the result of an automated process presented here. After taking into account systematic effects, marginal evidence of a local alignment on scales smaller than 2.5deg2.5\deg is found in the FIRST sample. The probability of this happening by chance is found to be less than 22 per cent. Further study suggests that on scales up to 1.5deg1.5\deg the alignment is maximal. For one third of the sources, the Radio Galaxy Zoo volunteers identified an optical counterpart. Assuming a flat Λ\LambdaCDM cosmology with Ωm=0.31,ΩΛ=0.69\Omega_m = 0.31, \Omega_\Lambda = 0.69, we convert the maximum angular scale on which alignment is seen into a physical scale in the range [19,38][19, 38] Mpc h701h_{70}^{-1}. This result supports recent evidence reported by Taylor and Jagannathan of radio jet alignment in the 1.41.4 deg2^2 ELAIS N1 field observed with the Giant Metrewave Radio Telescope. The TGSS sample is found to be too sparsely populated to manifest a similar signal
    corecore