210,652 research outputs found
EPiK-a Workflow for Electron Tomography in Kepler.
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
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
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
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
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
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
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
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 and extended
sources distributed over more than and 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 is found in the FIRST sample. The probability of this happening
by chance is found to be less than per cent. Further study suggests that on
scales up to the alignment is maximal. For one third of the sources,
the Radio Galaxy Zoo volunteers identified an optical counterpart. Assuming a
flat CDM cosmology with , we
convert the maximum angular scale on which alignment is seen into a physical
scale in the range Mpc . This result supports recent
evidence reported by Taylor and Jagannathan of radio jet alignment in the
deg 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
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