Research issues in data modeling for scientific visualization

This article summarizes some topics of modeling as they impinge on the future development of scientific data visualization. The benefits from visualization techniques in analyzing data are well established, but to build on these pioneering efforts, one must recognize modeling as a distinct structural component in the larger context of visualization and problem-solving systems. Volume modeling is the entry way to this arena of future development, and model-based rendering describes how scientists will view the results. Important side developments such as multiresolution modeling and model-based segmentation will contribute structural capability to these systems. All of these components ultimately depend on the mathematical foundations of scattered data modeling and on model validation and standards to incorporate this modeling methodology into effective tools for scientific inquiry.Postprint (published version

Active skeleton for bacteria modeling

The investigation of spatio-temporal dynamics of bacterial cells and their molecular components requires automated image analysis tools to track cell shape properties and molecular component locations inside the cells. In the study of bacteria aging, the molecular components of interest are protein aggregates accumulated near bacteria boundaries. This particular location makes very ambiguous the correspondence between aggregates and cells, since computing accurately bacteria boundaries in phase-contrast time-lapse imaging is a challenging task. This paper proposes an active skeleton formulation for bacteria modeling which provides several advantages: an easy computation of shape properties (perimeter, length, thickness, orientation), an improved boundary accuracy in noisy images, and a natural bacteria-centered coordinate system that permits the intrinsic location of molecular components inside the cell. Starting from an initial skeleton estimate, the medial axis of the bacterium is obtained by minimizing an energy function which incorporates bacteria shape constraints. Experimental results on biological images and comparative evaluation of the performances validate the proposed approach for modeling cigar-shaped bacteria like Escherichia coli. The Image-J plugin of the proposed method can be found online at http://fluobactracker.inrialpes.fr.Comment: Published in Computer Methods in Biomechanics and Biomedical Engineering: Imaging and Visualizationto appear i

Line search multilevel optimization as computational methods for dense optical flow

We evaluate the performance of different optimization techniques developed in the context of optical flowcomputation with different variational models. In particular, based on truncated Newton methods (TN) that have been an effective approach for large-scale unconstrained optimization, we develop the use of efficient multilevel schemes for computing the optical flow. More precisely, we evaluate the performance of a standard unidirectional multilevel algorithm - called multiresolution optimization (MR/OPT), to a bidrectional multilevel algorithm - called full multigrid optimization (FMG/OPT). The FMG/OPT algorithm treats the coarse grid correction as an optimization search direction and eventually scales it using a line search. Experimental results on different image sequences using four models of optical flow computation show that the FMG/OPT algorithm outperforms both the TN and MR/OPT algorithms in terms of the computational work and the quality of the optical flow estimation

Natural Parameterization

The objective of this project has been to develop an approach for imitating physical objects with an underlying stochastic variation. The key assumption is that a set of “natural parameters” can be extracted by a new subdivision algorithm so they reflect what is called the object’s “geometric DNA”. A case study on one hundred wheat grain crosssections (Triticum aestivum) showed that it was possible to extract thirty-six such parameters and to reuse them for Monte Carlo simulation of “new” stochastic phantoms which possessthe same stochastic behavior as the “original” cross-sections