618 research outputs found
Multiscale feature-preserving smoothing of tomographic data
PosterInternational audienceComputer tomography (CT) has wide application in medical imaging and reverse engineering. Due to the limited number of projections used in reconstructing the volume, the resulting 3D data is typically noisy. Contouring such data, for surface extraction, yields surfaces with localised artifacts of complex topology. To avoid such artifacts, we propose a method for feature-preserving smoothing of CT data. The smoothing is based on anisotropic diffusion, with a diffusion tensor designed to smooth noise up to a given scale, while preserving features. We compute these diffusion kernels from the directional histograms of gradients around each voxel, using a fast GPU implementation
Multiscale bilateral filtering for improving image quality in digital breast tomosynthesis
Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/135115/1/mp3283.pd
A multi-level preconditioned Krylov method for the efficient solution of algebraic tomographic reconstruction problems
Classical iterative methods for tomographic reconstruction include the class
of Algebraic Reconstruction Techniques (ART). Convergence of these stationary
linear iterative methods is however notably slow. In this paper we propose the
use of Krylov solvers for tomographic linear inversion problems. These advanced
iterative methods feature fast convergence at the expense of a higher
computational cost per iteration, causing them to be generally uncompetitive
without the inclusion of a suitable preconditioner. Combining elements from
standard multigrid (MG) solvers and the theory of wavelets, a novel
wavelet-based multi-level (WMG) preconditioner is introduced, which is shown to
significantly speed-up Krylov convergence. The performance of the
WMG-preconditioned Krylov method is analyzed through a spectral analysis, and
the approach is compared to existing methods like the classical Simultaneous
Iterative Reconstruction Technique (SIRT) and unpreconditioned Krylov methods
on a 2D tomographic benchmark problem. Numerical experiments are promising,
showing the method to be competitive with the classical Algebraic
Reconstruction Techniques in terms of convergence speed and overall performance
(CPU time) as well as precision of the reconstruction.Comment: Journal of Computational and Applied Mathematics (2014), 26 pages, 13
figures, 3 table
The Data Big Bang and the Expanding Digital Universe: High-Dimensional, Complex and Massive Data Sets in an Inflationary Epoch
Recent and forthcoming advances in instrumentation, and giant new surveys,
are creating astronomical data sets that are not amenable to the methods of
analysis familiar to astronomers. Traditional methods are often inadequate not
merely because of the size in bytes of the data sets, but also because of the
complexity of modern data sets. Mathematical limitations of familiar algorithms
and techniques in dealing with such data sets create a critical need for new
paradigms for the representation, analysis and scientific visualization (as
opposed to illustrative visualization) of heterogeneous, multiresolution data
across application domains. Some of the problems presented by the new data sets
have been addressed by other disciplines such as applied mathematics,
statistics and machine learning and have been utilized by other sciences such
as space-based geosciences. Unfortunately, valuable results pertaining to these
problems are mostly to be found only in publications outside of astronomy. Here
we offer brief overviews of a number of concepts, techniques and developments,
some "old" and some new. These are generally unknown to most of the
astronomical community, but are vital to the analysis and visualization of
complex datasets and images. In order for astronomers to take advantage of the
richness and complexity of the new era of data, and to be able to identify,
adopt, and apply new solutions, the astronomical community needs a certain
degree of awareness and understanding of the new concepts. One of the goals of
this paper is to help bridge the gap between applied mathematics, artificial
intelligence and computer science on the one side and astronomy on the other.Comment: 24 pages, 8 Figures, 1 Table. Accepted for publication: "Advances in
Astronomy, special issue "Robotic Astronomy
Graph- and finite element-based total variation models for the inverse problem in diffuse optical tomography
Total variation (TV) is a powerful regularization method that has been widely
applied in different imaging applications, but is difficult to apply to diffuse
optical tomography (DOT) image reconstruction (inverse problem) due to complex
and unstructured geometries, non-linearity of the data fitting and
regularization terms, and non-differentiability of the regularization term. We
develop several approaches to overcome these difficulties by: i) defining
discrete differential operators for unstructured geometries using both finite
element and graph representations; ii) developing an optimization algorithm
based on the alternating direction method of multipliers (ADMM) for the
non-differentiable and non-linear minimization problem; iii) investigating
isotropic and anisotropic variants of TV regularization, and comparing their
finite element- and graph-based implementations. These approaches are evaluated
on experiments on simulated data and real data acquired from a tissue phantom.
Our results show that both FEM and graph-based TV regularization is able to
accurately reconstruct both sparse and non-sparse distributions without the
over-smoothing effect of Tikhonov regularization and the over-sparsifying
effect of L regularization. The graph representation was found to
out-perform the FEM method for low-resolution meshes, and the FEM method was
found to be more accurate for high-resolution meshes.Comment: 24 pages, 11 figures. Reviced version includes revised figures and
improved clarit
Wavelet-based denoising for 3D OCT images
Optical coherence tomography produces high resolution medical images based on spatial and temporal coherence of the optical waves backscattered from the scanned tissue. However, the same coherence introduces speckle noise as well; this degrades the quality of acquired images.
In this paper we propose a technique for noise reduction of 3D OCT images, where the 3D volume is considered as a sequence of 2D images, i.e., 2D slices in depth-lateral projection plane. In the proposed method we first perform recursive temporal filtering through the estimated motion trajectory between the 2D slices using noise-robust motion estimation/compensation scheme previously proposed for video denoising. The temporal filtering scheme reduces the noise level and adapts the motion compensation on it. Subsequently, we apply a spatial filter for speckle reduction in order to remove the remainder of noise in the 2D slices. In this scheme the spatial (2D) speckle-nature of noise in OCT is modeled and used for spatially adaptive denoising. Both the temporal and the spatial filter are wavelet-based techniques, where for the temporal filter two resolution scales are used and for the spatial one four resolution scales.
The evaluation of the proposed denoising approach is done on demodulated 3D OCT images on different sources and of different resolution. For optimizing the parameters for best denoising performance fantom OCT images were used. The denoising performance of the proposed method was measured in terms of SNR, edge sharpness preservation and contrast-to-noise ratio. A comparison was made to the state-of-the-art methods for noise reduction in 2D OCT images, where the proposed approach showed to be advantageous in terms of both objective and subjective quality measures
Two-stage 2D-to-3D reconstruction of realistic microstructures: Implementation and numerical validation by effective properties
Realistic microscale domains are an essential step towards making modern
multiscale simulations more applicable to computational materials engineering.
For this purpose, 3D computed tomography scans can be very expensive or
technically impossible for certain materials, whereas 2D information can be
easier obtained. Based on a single or three orthogonal 2D slices, the recently
proposed differentiable microstructure characterization and reconstruction
(DMCR) algorithm is able to reconstruct multiple plausible 3D realizations of
the microstructure based on statistical descriptors, i.e., without the need for
a training data set. Building upon DMCR, this work introduces a highly accurate
two-stage reconstruction algorithm that refines the DMCR results under
consideration of microstructure descriptors. Furthermore, the 2D-to-3D
reconstruction is validated using a real computed tomography (CT) scan of a
recently developed beta-Ti/TiFe alloy as well as anisotropic "bone-like"
spinodoid structures. After a detailed discussion of systematic errors in the
descriptor space, the reconstructed microstructures are compared to the
reference in terms of the numerically obtained effective elastic and plastic
properties. Together with the free accessibility of the presented algorithms in
MCRpy, the excellent results in this study motivate interdisciplinary
cooperation in applying numerical multiscale simulations for computational
materials engineering
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