Flexible isosurfaces: Simplifying and displaying scalar topology using the contour tree

The contour tree is an abstraction of a scalar field that encodes the nesting relationships of isosurfaces. We show how to use the contour tree to represent individual contours of a scalar field, how to simplify both the contour tree and the topology of the scalar field, how to compute and store geometric properties for all possible contours in the contour tree, and how to use the simplified contour tree as an interface for exploratory visualization

Complete characterization of sink-strengths for 1D to 3D mobilities of defect clusters.II. Bridging between limiting cases with effective sink-strengths calculations

In a companion paper, we proposed new analytical expressions of cluster sink-strengths (CSS) indispensable to any complete parameterization of rate equations cluster dynamics accounting for reaction between defect clusters populations having a 1D-mobility. In this second paper, we first establish simulation setup rules for truly converged estimates of effective CSS by Kinetic Monte-Carlo, and then we grid on a wide set of radii, rotation energies, diffusion coefficients and concentrations of both reaction partners. Symmetric roles of some parameters are used to infer a generic form for a semi-analytical expression of CSS depending on all these interaction parameters: it is composed of the various analytical limiting cases established and fitted transition functions that allow a gradual switching between them. The analysis of the residuals shows that the overall agreement is reasonably good: it is only in the transition zones that discrepancies are located and this is due to the asymmetry of the actual transition functions. The expression can be easily extended to temperatures at least a few hundred degrees around the reference. But further extending the CSS evaluations to much smaller diffusion coefficients ratios, we see that the domain for 1D-1D mobility is very extended: for a $10^{-3}$ ratio the computed CSS is still not correctly described by the 1D-CSS with respect to a fixed sink (1D-0), but rather by the established 1D-1D expression. For our typical sets of conditions, it is only when approaching a ratio of $10^{-6}$ that the 1D-0 CSS starts to become more relevant. This highlights the counter-intuitive fact that the growth kinetics of moderately trapped 1D mobile loops, whose effective mobility is greatly reduced, may not be described by 1D-0 kinetics but rather by appropriately corrected 1D-1D CSS which have completely different order of magnitude and kinetic orders.Comment: 21 pages, 12 figure

VolRoverN: Enhancing Surface and Volumetric Reconstruction for Realistic Dynamical Simulation of Cellular and Subcellular Function

Establishing meaningful relationships between cellular structure and function requires accurate morphological reconstructions. In particular, there is an unmet need for high quality surface reconstructions to model subcellular and synaptic interactions among neurons and glia at nanometer resolution. We address this need with VolRoverN, a software package that produces accurate, efficient, and automated 3D surface reconstructions from stacked 2D contour tracings. While many techniques and tools have been developed in the past for 3D visualization of cellular structure, the reconstructions from VolRoverN meet specific quality criteria that are important for dynamical simulations. These criteria include manifoldness, water-tightness, lack of self- and object-object-intersections, and geometric accuracy. These enhanced surface reconstructions are readily extensible to any cell type and are used here on spiny dendrites with complex morphology and axons from mature rat hippocampal area CA1. Both spatially realistic surface reconstructions and reduced skeletonizations are produced and formatted by VolRoverN for easy input into analysis software packages for neurophysiological simulations at multiple spatial and temporal scales ranging from ion electro-diffusion to electrical cable models