Counting number of cells and cell segmentation using advection-diffusion equations

summary: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 advection-diffusion equation which gives us at a certain scale the desired information on the number of cells. For solving the problems computationally we use flux-based finite volume level set method developed by Frolkovič and Mikula in [FM1] and semi-implicit co-volume subjective surface method given in [CMSSg, MSSgCVS, MSSgchapter]. Computational experiments on testing and real 2D and 3D embryogenesis images are presented and the results are discussed

Mini-Workshop: Anisotropic Motion Laws

Anisotropic motion laws play a key role in many applications ranging from materials science, biophysics to image processing. All these highly diversified disciplines have made it necessary to develop common mathematical foundations and framworks to deal with anisotropy in geometric motion. The workshop brings together leading experts from various fields to address well-posedness, accuracy, and computational efficiency of the mathematical models and algorithms

Applications of nonlinear diffusion in image processing and computer vision

Nonlinear diffusion processes can be found in many recent methods for image processing and computer vision. In this article, four applications are surveyed: nonlinear diffusion filtering, variational image regularization, optic flow estimation, and geodesic active contours. For each of these techniques we explain the main ideas, discuss theoretical properties and present an appropriate numerical scheme. The numerical schemes are based on additive operator splittings (AOS). In contrast to traditional multiplicative splittings such as ADI, LOD or D'yakonov splittings, all axes are treated in the same manner, and additional possibilities for efficient realizations on parallel and distributed architectures appear. Geodesic active contours lead to equations that resemble mean curvature motion. For this application, a novel AOS scheme is presented that uses harmonie averaging and does not require reinitializations of the distance function in each iteration step

Finite-volume level set method and its adaptive version in completing subjective contours

summary:In this paper we deal with a problem of segmentation (including missing boundary completion) and subjective contour creation. For the corresponding models we apply the semi-implicit finite volume numerical schemes leading to methods which are robust, efficient and stable without any restriction to a time step. The finite volume discretization enables to use the spatial adaptivity and thus improve significantly the computational time. The computational results related to image segmentation with partly missing boundaries and subjective contour extraction are presented

Numerical Solution of Diffusion Models in Biomedical Imaging on Multicore Processors

In this paper, we consider nonlinear partial differential equations (PDEs) of diffusion/advection type underlying most problems in image analysis. As case study, we address the segmentation of medical structures. We perform a comparative study of numerical algorithms arising from using the semi-implicit and the fully implicit discretization schemes. Comparison criteria take into account both the accuracy and the efficiency of the algorithms. As measure of accuracy, we consider the Hausdorff distance and the residuals of numerical solvers, while as measure of efficiency we consider convergence history, execution time, speedup, and parallel efficiency. This analysis is carried out in a multicore-based parallel computing environment

Achieving High Speed CFD simulations: Optimization, Parallelization, and FPGA Acceleration for the unstructured DLR TAU Code

Today, large scale parallel simulations are fundamental tools to handle complex problems. The number of processors in current computation platforms has been recently increased and therefore it is necessary to optimize the application performance and to enhance the scalability of massively-parallel systems. In addition, new heterogeneous architectures, combining conventional processors with specific hardware, like FPGAs, to accelerate the most time consuming functions are considered as a strong alternative to boost the performance. In this paper, the performance of the DLR TAU code is analyzed and optimized. The improvement of the code efficiency is addressed through three key activities: Optimization, parallelization and hardware acceleration. At first, a profiling analysis of the most time-consuming processes of the Reynolds Averaged Navier Stokes flow solver on a three-dimensional unstructured mesh is performed. Then, a study of the code scalability with new partitioning algorithms are tested to show the most suitable partitioning algorithms for the selected applications. Finally, a feasibility study on the application of FPGAs and GPUs for the hardware acceleration of CFD simulations is presented

Primal-dual active set methods for Allen-Cahn variational inequalities

This thesis aims to introduce and analyse a primal-dual active set strategy for solving Allen-Cahn variational inequalities. We consider the standard Allen-Cahn equation with non-local constraints and a vector-valued Allen-Cahn equation with and without non-local constraints. Existence and uniqueness results are derived in a formulation involving Lagrange multipliers for local and non-local constraints. Local Convergence is shown by interpreting the primal-dual active set approach as a semi-smooth Newton method. Properties of the method are discussed and several numerical simulations in two and three space dimensions demonstrate its efficiency. In the second part of the thesis various applications of the Allen-Cahn equation are discussed. The non-local Allen-Cahn equation can be coupled with an elasticity equation to solve problems in structural topology optimisation. The model can be extended to handle multiple structures by using the vector-valued Allen-Cahn variational inequality with non-local constraints. Since many applications of the Allen-Cahn equation involve evolution of interfaces in materials an important extension of the standard Allen-Cahn model is to allow materials to exhibit anisotropic behaviour. We introduce an anisotropic version of the Allen-Cahn variational inequality and we show that it is possible to apply the primal-dual active set strategy efficiently to this model. Finally, the Allen-Cahn model is applied to problems in image processing, such as segmentation, denoising and inpainting. The primal-dual active set method proves exible and reliable for all the applications considered in this thesis