32,221 research outputs found
3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries
Recent advances in electron microscopy have enabled the imaging of single
cells in 3D at nanometer length scale resolutions. An uncharted frontier for in
silico biology is the ability to simulate cellular processes using these
observed geometries. Enabling such simulations requires watertight meshing of
electron micrograph images into 3D volume meshes, which can then form the basis
of computer simulations of such processes using numerical techniques such as
the Finite Element Method. In this paper, we describe the use of our recently
rewritten mesh processing software, GAMer 2, to bridge the gap between poorly
conditioned meshes generated from segmented micrographs and boundary marked
tetrahedral meshes which are compatible with simulation. We demonstrate the
application of a workflow using GAMer 2 to a series of electron micrographs of
neuronal dendrite morphology explored at three different length scales and show
that the resulting meshes are suitable for finite element simulations. This
work is an important step towards making physical simulations of biological
processes in realistic geometries routine. Innovations in algorithms to
reconstruct and simulate cellular length scale phenomena based on emerging
structural data will enable realistic physical models and advance discovery at
the interface of geometry and cellular processes. We posit that a new frontier
at the intersection of computational technologies and single cell biology is
now open.Comment: 39 pages, 14 figures. High resolution figures and supplemental movies
available upon reques
Convex optimization problem prototyping for image reconstruction in computed tomography with the Chambolle-Pock algorithm
The primal-dual optimization algorithm developed in Chambolle and Pock (CP),
2011 is applied to various convex optimization problems of interest in computed
tomography (CT) image reconstruction. This algorithm allows for rapid
prototyping of optimization problems for the purpose of designing iterative
image reconstruction algorithms for CT. The primal-dual algorithm is briefly
summarized in the article, and its potential for prototyping is demonstrated by
explicitly deriving CP algorithm instances for many optimization problems
relevant to CT. An example application modeling breast CT with low-intensity
X-ray illumination is presented.Comment: Resubmitted to Physics in Medicine and Biology. Text has been
modified according to referee comments, and typos in the equations have been
correcte
OPED reconstruction algorithm for limited angle problem
The structure of the reconstruction algorithm OPED permits a natural way to
generate additional data, while still preserving the essential feature of the
algorithm. This provides a method for image reconstruction for limited angel
problems. In stead of completing the set of data, the set of discrete sine
transforms of the data is completed. This is achieved by solving systems of
linear equations that have, upon choosing appropriate parameters, positive
definite coefficient matrices. Numerical examples are presented.Comment: 17 page
Implementation of an Optimal First-Order Method for Strongly Convex Total Variation Regularization
We present a practical implementation of an optimal first-order method, due
to Nesterov, for large-scale total variation regularization in tomographic
reconstruction, image deblurring, etc. The algorithm applies to -strongly
convex objective functions with -Lipschitz continuous gradient. In the
framework of Nesterov both and are assumed known -- an assumption
that is seldom satisfied in practice. We propose to incorporate mechanisms to
estimate locally sufficient and during the iterations. The mechanisms
also allow for the application to non-strongly convex functions. We discuss the
iteration complexity of several first-order methods, including the proposed
algorithm, and we use a 3D tomography problem to compare the performance of
these methods. The results show that for ill-conditioned problems solved to
high accuracy, the proposed method significantly outperforms state-of-the-art
first-order methods, as also suggested by theoretical results.Comment: 23 pages, 4 figure
Efficient Resolution of Anisotropic Structures
We highlight some recent new delevelopments concerning the sparse
representation of possibly high-dimensional functions exhibiting strong
anisotropic features and low regularity in isotropic Sobolev or Besov scales.
Specifically, we focus on the solution of transport equations which exhibit
propagation of singularities where, additionally, high-dimensionality enters
when the convection field, and hence the solutions, depend on parameters
varying over some compact set. Important constituents of our approach are
directionally adaptive discretization concepts motivated by compactly supported
shearlet systems, and well-conditioned stable variational formulations that
support trial spaces with anisotropic refinements with arbitrary
directionalities. We prove that they provide tight error-residual relations
which are used to contrive rigorously founded adaptive refinement schemes which
converge in . Moreover, in the context of parameter dependent problems we
discuss two approaches serving different purposes and working under different
regularity assumptions. For frequent query problems, making essential use of
the novel well-conditioned variational formulations, a new Reduced Basis Method
is outlined which exhibits a certain rate-optimal performance for indefinite,
unsymmetric or singularly perturbed problems. For the radiative transfer
problem with scattering a sparse tensor method is presented which mitigates or
even overcomes the curse of dimensionality under suitable (so far still
isotropic) regularity assumptions. Numerical examples for both methods
illustrate the theoretical findings
- …