11,363 research outputs found
A robust method for calculating interface curvature and normal vectors using an extracted local level set
The level-set method is a popular interface tracking method in two-phase flow
simulations. An often-cited reason for using it is that the method naturally
handles topological changes in the interface, e.g. merging drops, due to the
implicit formulation. It is also said that the interface curvature and normal
vectors are easily calculated. This last point is not, however, the case in the
moments during a topological change, as several authors have already pointed
out. Various methods have been employed to circumvent the problem. In this
paper, we present a new such method which retains the implicit level-set
representation of the surface and handles general interface configurations. It
is demonstrated that the method extends easily to 3D. The method is validated
on static interface configurations, and then applied to two-phase flow
simulations where the method outperforms the standard method and the results
agree well with experiments.Comment: 31 pages, 18 figure
Evaluation of 3D gradient filters for estimation of the surface orientation in CTC
The extraction of the gradient information from 3D surfaces plays an important role for many applications including 3D graphics and medical imaging. The extraction of the 3D gradient information is performed by filtering the input data with high pass filters that are typically implemented using 3×3×3 masks. Since these filters extract the
gradient information in small neighborhood, the estimated gradient information will be very sensitive to image noise. The development of a 3D gradient operator that is robust
to image noise is particularly important since the medical datasets are characterized by a relatively low signal to noise ratio. The aim of this paper is to detail the
implementation of an optimized 3D gradient operator that is applied to sample the local curvature of the colon wall in CT data and its influence on the overall performance of
our CAD-CTC method. The developed 3D gradient operator has been applied to extract the local curvature of the colon wall in a large number CT datasets captured with different radiation doses and the experimental results are presented and discussed
A level-set method for the evolution of cells and tissue during curvature-controlled growth
Most biological tissues grow by the synthesis of new material close to the
tissue's interface, where spatial interactions can exert strong geometric
influences on the local rate of growth. These geometric influences may be
mechanistic, or cell behavioural in nature. The control of geometry on tissue
growth has been evidenced in many in-vivo and in-vitro experiments, including
bone remodelling, wound healing, and tissue engineering scaffolds. In this
paper, we propose a generalisation of a mathematical model that captures the
mechanistic influence of curvature on the joint evolution of cell density and
tissue shape during tissue growth. This generalisation allows us to simulate
abrupt topological changes such as tissue fragmentation and tissue fusion, as
well as three dimensional cases, through a level-set-based method. The
level-set method developed introduces another Eulerian field than the level-set
function. This additional field represents the surface density of tissue
synthesising cells, anticipated at future locations of the interface. Numerical
tests performed with this level-set-based method show that numerical
conservation of cells is a good indicator of simulation accuracy, particularly
when cusps develop in the tissue's interface. We apply this new model to
several situations of curvature-controlled tissue evolutions that include
fragmentation and fusion.Comment: 15 pages, 10 figures, 3 supplementary figure
Experimental and computational studies of water drops falling through model oil with surfactant and subjected to an electric field
The behaviour of a single sub-millimetre-size water drop falling through a
viscous oil while subjected to an electric field is of fundamental importance
to industrial applications such as crude oil electrocoalescers. Detailed
studies, both experimental and computational, have been performed previously,
but an often challenging issue has been the characterization of the fluids. As
numerous authors have noted, it is very difficult to have a perfectly clean
water-oil system even for very pure model oils, and the presence of trace
chemicals may significantly alter the interface behaviour. In this work, we
consider a well- characterized water-oil system where controlled amounts of a
surface active agent (Span 80) have been added to the oil. This addition
dominates any trace contaminants in the oil, such that the interface behaviour
can also be well-characterized. We present the results of experiments and
corresponding two-phase- flow simulations of a falling water drop covered in
surfactant and subjected to a monopolar square voltage pulse. The results are
compared and good agreement is found for surfactant concentrations below the
critical micelle concentration.Comment: 7 pages, 9 figures, to be presented at the ICDL 2014 conferenc
A fully automatic CAD-CTC system based on curvature analysis for standard and low-dose CT data
Computed tomography colonography (CTC) is a rapidly evolving noninvasive medical investigation that is viewed by radiologists as a potential screening technique for the detection of colorectal polyps. Due to the technical advances in CT system design, the volume of data required to be processed by radiologists has increased significantly, and as a consequence the manual analysis of this information has become an increasingly time consuming process whose results can be affected by inter- and intrauser variability. The aim of this paper is to detail the implementation of a fully integrated CAD-CTC system that is able to robustly identify the clinically significant polyps in the CT data. The CAD-CTC system described in this paper is a multistage implementation whose main system components are: 1) automatic colon segmentation; 2) candidate surface extraction; 3) feature extraction; and 4) classification. Our CAD-CTC system performs at 100% sensitivity for polyps larger than 10 mm, 92% sensitivity for polyps in the range 5 to 10 mm, and 57.14% sensitivity for polyps smaller than 5 mm with an average of 3.38 false positives per dataset. The developed system has been evaluated on synthetic and real patient CT data acquired with standard and low-dose radiation levels
Extending a serial 3D two-phase CFD code to parallel execution over MPI by using the PETSc library for domain decomposition
To leverage the last two decades' transition in High-Performance Computing
(HPC) towards clusters of compute nodes bound together with fast interconnects,
a modern scalable CFD code must be able to efficiently distribute work amongst
several nodes using the Message Passing Interface (MPI). MPI can enable very
large simulations running on very large clusters, but it is necessary that the
bulk of the CFD code be written with MPI in mind, an obstacle to parallelizing
an existing serial code.
In this work we present the results of extending an existing two-phase 3D
Navier-Stokes solver, which was completely serial, to a parallel execution
model using MPI. The 3D Navier-Stokes equations for two immiscible
incompressible fluids are solved by the continuum surface force method, while
the location of the interface is determined by the level-set method.
We employ the Portable Extensible Toolkit for Scientific Computing (PETSc)
for domain decomposition (DD) in a framework where only a fraction of the code
needs to be altered. We study the strong and weak scaling of the resulting
code. Cases are studied that are relevant to the fundamental understanding of
oil/water separation in electrocoalescers.Comment: 8 pages, 6 figures, final version for to the CFD 2014 conferenc
Automated Fragmentary Bone Matching
Identification, reconstruction and matching of fragmentary bones are basic tasks required to accomplish quantification and analysis of fragmentary human remains derived from forensic contexts. Appropriate techniques for three-dimensional surface matching have received great attention in computer vision literature, and various methods have been proposed for matching fragmentary meshes; however, many of these methods lack automation, speed and/or suffer from high sensitivity to noise. In addition, reconstruction of fragementary bones along with identification in the presence of reference model to compare with in an automatic scheme have not been addressed. In order to address these issues, we used a multi-stage technique for fragment identification, matching and registration.
The study introduces an automated technique for matching of fragmentary human skeletal remains for improving forensic anthropology practice and policy. The proposed technique involves creation of surfaces models for the fragmentary elements which can be done using computerized tomographic scans followed by segmentation. Upon creation of the fragmentary elements models, the models go through feature extraction technique where the surface roughness map of each model is measured using local shape analysis measures. Adaptive thesholding is then used to extract model features. A multi-stage technique is then used to identify, match and register bone fragments to their corresponding template bone model. First, extracted features are used for matching with different template bone models using iterative closest point algorithm with different positions and orientations. The best match score, in terms of minimum root-mean-square error, is used along with the position and orientation and the resulting transformation to register the fragment bone model with the corresponding template bone model using iterative closest point algorithm
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