7,716 research outputs found
Confocal microscopy of colloidal particles: towards reliable, optimum coordinates
Over the last decade, the light microscope has become increasingly useful as
a quantitative tool for studying colloidal systems. The ability to obtain
particle coordinates in bulk samples from micrographs is particularly
appealing. In this paper we review and extend methods for optimal image
formation of colloidal samples, which is vital for particle coordinates of the
highest accuracy, and for extracting the most reliable coordinates from these
images. We discuss in depth the accuracy of the coordinates, which is sensitive
to the details of the colloidal system and the imaging system. Moreover, this
accuracy can vary between particles, particularly in dense systems. We
introduce a previously unreported error estimate and use it to develop an
iterative method for finding particle coordinates. This individual-particle
accuracy assessment also allows comparison between particle locations obtained
from different experiments. Though aimed primarily at confocal microscopy
studies of colloidal systems, the methods outlined here should transfer readily
to many other feature extraction problems, especially where features may
overlap one another.Comment: Accepted by Advances in Colloid and Interface Scienc
A Modified Cross Correlation Algorithm for Reference-free Image Alignment of Non-Circular Projections in Single-Particle Electron Microscopy
In this paper we propose a modified cross correlation method to align images
from the same class in single-particle electron microscopy of highly
non-spherical structures. In this new method, First we coarsely align
projection images, and then re-align the resulting images using the cross
correlation (CC) method. The coarse alignment is obtained by matching the
centers of mass and the principal axes of the images. The distribution of
misalignment in this coarse alignment can be quantified based on the
statistical properties of the additive background noise. As a consequence, the
search space for re-alignment in the cross correlation method can be reduced to
achieve better alignment. In order to overcome problems associated with false
peaks in the cross correlations function, we use artificially blurred images
for the early stage of the iterative cross correlation method and segment the
intermediate class average from every iteration step. These two additional
manipulations combined with the reduced search space size in the cross
correlation method yield better alignments for low signal-to-noise ratio images
than both classical cross correlation and maximum likelihood(ML) methods.Comment: 29page
Classical and all-floating FETI methods for the simulation of arterial tissues
High-resolution and anatomically realistic computer models of biological soft
tissues play a significant role in the understanding of the function of
cardiovascular components in health and disease. However, the computational
effort to handle fine grids to resolve the geometries as well as sophisticated
tissue models is very challenging. One possibility to derive a strongly
scalable parallel solution algorithm is to consider finite element tearing and
interconnecting (FETI) methods. In this study we propose and investigate the
application of FETI methods to simulate the elastic behavior of biological soft
tissues. As one particular example we choose the artery which is - as most
other biological tissues - characterized by anisotropic and nonlinear material
properties. We compare two specific approaches of FETI methods, classical and
all-floating, and investigate the numerical behavior of different
preconditioning techniques. In comparison to classical FETI, the all-floating
approach has not only advantages concerning the implementation but in many
cases also concerning the convergence of the global iterative solution method.
This behavior is illustrated with numerical examples. We present results of
linear elastic simulations to show convergence rates, as expected from the
theory, and results from the more sophisticated nonlinear case where we apply a
well-known anisotropic model to the realistic geometry of an artery. Although
the FETI methods have a great applicability on artery simulations we will also
discuss some limitations concerning the dependence on material parameters.Comment: 29 page
Capturing Nucleation at 4D Atomic Resolution
Nucleation plays a critical role in many physical and biological phenomena
ranging from crystallization, melting and evaporation to the formation of
clouds and the initiation of neurodegenerative diseases. However, nucleation is
a challenging process to study in experiments especially in the early stage
when several atoms/molecules start to form a new phase from its parent phase.
Here, we advance atomic electron tomography to study early stage nucleation at
4D atomic resolution. Using FePt nanoparticles as a model system, we reveal
that early stage nuclei are irregularly shaped, each has a core of one to few
atoms with the maximum order parameter, and the order parameter gradient points
from the core to the boundary of the nucleus. We capture the structure and
dynamics of the same nuclei undergoing growth, fluctuation, dissolution,
merging and/or division, which are regulated by the order parameter
distribution and its gradient. These experimental observations differ from
classical nucleation theory (CNT) and to explain them we propose the order
parameter gradient (OPG) model. We show the OPG model generalizes CNT and
energetically favours diffuse interfaces for small nuclei and sharp interfaces
for large nuclei. We further corroborate this model using molecular dynamics
simulations of heterogeneous and homogeneous nucleation in liquid-solid phase
transitions of Pt. We anticipate that the OPG model is applicable to different
nucleation processes and our experimental method opens the door to study the
structure and dynamics of materials with 4D atomic resolution.Comment: 42 pages, 5 figures, 12 supplementary figures and one supplementary
tabl
Image Sampling with Quasicrystals
We investigate the use of quasicrystals in image sampling. Quasicrystals
produce space-filling, non-periodic point sets that are uniformly discrete and
relatively dense, thereby ensuring the sample sites are evenly spread out
throughout the sampled image. Their self-similar structure can be attractive
for creating sampling patterns endowed with a decorative symmetry. We present a
brief general overview of the algebraic theory of cut-and-project quasicrystals
based on the geometry of the golden ratio. To assess the practical utility of
quasicrystal sampling, we evaluate the visual effects of a variety of
non-adaptive image sampling strategies on photorealistic image reconstruction
and non-photorealistic image rendering used in multiresolution image
representations. For computer visualization of point sets used in image
sampling, we introduce a mosaic rendering technique.Comment: For a full resolution version of this paper, along with supplementary
materials, please visit at
http://www.Eyemaginary.com/Portfolio/Publications.htm
EIT Reconstruction Algorithms: Pitfalls, Challenges and Recent Developments
We review developments, issues and challenges in Electrical Impedance
Tomography (EIT), for the 4th Workshop on Biomedical Applications of EIT,
Manchester 2003. We focus on the necessity for three dimensional data
collection and reconstruction, efficient solution of the forward problem and
present and future reconstruction algorithms. We also suggest common pitfalls
or ``inverse crimes'' to avoid.Comment: A review paper for the 4th Workshop on Biomedical Applications of
EIT, Manchester, UK, 200
- …