In this paper, we introduce a set of methods for processing and analyzing long time series of 3D images representing embryo evolution. The images are obtained by in vivo scanning using a confocal microscope where one of the channels represents the cell nuclei and the other one the cell membranes. Our image processing chain consists of three steps: image filtering, object counting (center detection) and segmentation. The corresponding methods are based on numerical solution of nonlinear PDEs, namely...

This paper studies a family of finite volume schemes for the hyperbolic scalar conservation law $u_t+{\nabla }_g·f(x,u)=0$ on a closed Riemannian manifold M. For an initial value in BV(M) we will show that these schemes converge with a $h^{\frac{1}{4}}$ convergence rate towards the entropy solution. When M is 1-dimensional the schemes are TVD and we will show that this improves the convergence rate to $h^{\frac{1}{2}}.$

We study a two-grid scheme fully discrete in time and space for solving the Navier-Stokes system. In the first step, the fully non-linear problem is discretized in space on a coarse grid with mesh-size H and time step k. In the second step, the problem is discretized in space on a fine grid with mesh-size h and the same time step, and linearized around the velocity uH computed in the first step. The two-grid strategy is motivated by the fact that under suitable assumptions, the contribution of uH...

We propose a 1D adaptive numerical scheme for hyperbolic conservation laws based on the numerical density of entropy production (the amount of violation of the theoretical entropy inequality). This density is used as an a posteriori error which provides information if the mesh should be refined in the regions where discontinuities occur or coarsened in the regions where the solution remains smooth. As due to the Courant-Friedrich-Levy stability condition the time step is restricted and leads to...

In this paper, we first construct a model for free surface flows that takes into account the air entrainment by a system of four partial differential equations. We derive it by taking averaged values of gas and fluid velocities on the cross surface flow in the Euler equations (incompressible for the fluid and compressible for the gas). The obtained system is conditionally hyperbolic. Then, we propose a mathematical kinetic interpretation of this system to finally construct a two-layer kinetic scheme...

We consider the system of partial differential equations governing the one-dimensional flow of two superposed immiscible layers of shallow water. The difficulty in this system comes from the coupling terms involving some derivatives of the unknowns that make the system nonconservative, and eventually nonhyperbolic. Due to these terms, a numerical scheme obtained by performing an arbitrary scheme to each layer, and using time-splitting or other similar techniques leads to instabilities in...

This study concerns some asymptotic models used to compute the flow outside and inside fractures in a bidimensional porous medium. The flow is governed by the Darcy law both in the fractures and in the porous matrix with large discontinuities in the permeability tensor. These fractures are supposed to have a small thickness with respect to the macroscopic length scale, so that we can asymptotically reduce them to immersed polygonal fault interfaces and the model finally consists in a coupling between...

We develop a method for counting number of cells and extraction of approximate cell centers in 2D and 3D images of early stages of the zebra-fish embryogenesis. The approximate cell centers give us the starting points for the subjective surface based cell segmentation. We move in the inner normal direction all level sets of nuclei and membranes images by a constant speed with slight regularization of this flow by the (mean) curvature. Such multi- scale evolutionary process is represented by a geometrical...

This contribution deals with the numerical simulation of dislocation dynamics. Dislocations are described by means of the evolution of a family of closed or open smooth curves $\Gamma \left(t\right):S\to {ℝ}^2$, $t\geqq 0$. The curves are driven by the normal velocity $v$ which is the function of curvature $\kappa$ and the position. The evolution law reads as: $v=-\kappa +F$. The motion law is treated using direct approach numerically solved by two schemes, i. e., backward Euler semi-implicit and semi-discrete method of lines. Numerical stability is improved...

The interaction between dislocation dipolar loops plays an important role in the computation of the dislocation dynamics. The analytical form of the interaction force between two loops derived in the present paper from Kroupa’s formula of the stress field generated by a single dipolar loop allows for faster computation.

In this paper, we describe an efficient method for 3D image segmentation. The method uses a PDE model – the so called generalized subjective surface equation which is an equation of advection-diffusion type. The main goal is to develop an efficient and stable numerical method for solving this problem. The numerical solution is based on semi-implicit time discretization and flux-based level set finite volume space discretization. The space discretization is discussed in details and we introduce three...

This paper is concerned with the finite volume approximation of the p-laplacian equation with homogeneous Dirichlet boundary conditions on rectangular meshes. A reconstruction of the norm of the gradient on the mesh’s interfaces is needed in order to discretize the p-laplacian operator. We give a detailed description of the possible nine points schemes ensuring that the solution of the resulting finite dimensional nonlinear system exists and is unique. These schemes, called admissible, are locally...

This paper is concerned with the finite volume approximation of the p-Laplacian equation with homogeneous Dirichlet boundary conditions on rectangular meshes. A reconstruction of the norm of the gradient on the mesh's interfaces is needed in order to discretize the p-Laplacian operator. We give a detailed description of the possible nine points schemes ensuring that the solution of the resulting finite dimensional nonlinear system exists and is unique. These schemes, called admissible, are locally...

This paper is concerned with the numerical approximation of Cauchy problems for one-dimensional nonconservative hyperbolic systems. The theory developed by Dal Maso et al. [J. Math. Pures Appl.74 (1995) 483–548] is used in order to define the weak solutions of the system: an interpretation of the nonconservative products as Borel measures is given, based on the choice of a family of paths drawn in the phase space. Even if the family of paths can be chosen arbitrarily, it is natural to require this...

This paper is devoted to the numerical simulation of wave breaking. It presents the results of a numerical workshop that was held during the conference LOMA04. The objective is to compare several mathematical models (compressible or incompressible) and associated numerical methods to compute the flow field during a wave breaking over a reef. The methods will also be compared with experiments.

This paper is devoted to the numerical simulation of wave breaking. It presents the results of a numerical workshop that was held during the conference LOMA04. The objective is to compare several mathematical models (compressible or incompressible) and associated numerical methods to compute the flow field during a wave breaking over a reef. The methods will also be compared with experiments.

We consider the Pn model to approximate the time dependent transport equation in one dimension of space. In a diffusive regime, the solution of this system is solution of a diffusion equation. We are looking for a numerical scheme having the diffusion limit property: in a diffusive regime, it has to give the solution of the limiting diffusion equation on a mesh at the diffusion scale. The numerical scheme proposed is an extension of the Godunov type scheme proposed by Gosse to solve the P1 model...

We study the use of a GPU for the numerical approximation of the curvature dependent flows of graphs - the mean-curvature flow and the Willmore flow. Both problems are often applied in image processing where fast solvers are required. We approximate these problems using the complementary finite volume method combined with the method of lines. We obtain a system of ordinary differential equations which we solve by the Runge-Kutta-Merson solver. It is a robust solver with an automatic choice of the...

This paper concerns with the finite volume scheme for nonlinear tensor diffusion in image processing. First we provide some basic information on this type of diffusion including a construction of its diffusion tensor. Then we derive a semi-implicit scheme with the help of so-called diamond-cell method (see [Coirier1] and [Coirier2]). Further, we prove existence and uniqueness of a discrete solution given by our scheme. The proof is based on a gradient bound in the tangential direction by a gradient...