Patch-type Segmentation of Voxel Shapes using Simplified Surface Skeletons

We present a new method for decomposing a 3D voxel shape into disjoint segments using the shape’s simplified surface-skeleton. The surface skeleton of a shape consists of 2D manifolds inside its volume. Each skeleton point has a maximally inscribed ball that touches the boundary in at least two contact points. A key observation is that the boundaries of the simplified fore- and background skeletons map one-to-one to increasingly fuzzy, soft convex, respectively concave, edges of the shape. Using this property, we build a method for segmentation of 3D shapes which has several desirable properties. Our method segments both noisy shapes and shapes with soft edges which vanish over low-curvature regions. Multiscale segmentations can be obtained by varying the simplification level of the skeleton. We present a voxel-based implementation of our approach and illustrate it on several realistic examples.

Fast and robust curve skeletonization for real-world elongated objects

We consider the problem of extracting curve skeletons of three-dimensional, elongated objects given a noisy surface, which has applications in agricultural contexts such as extracting the branching structure of plants. We describe an efficient and robust method based on breadth-first search that can determine curve skeletons in these contexts. Our approach is capable of automatically detecting junction points as well as spurious segments and loops. All of that is accomplished with only one user-adjustable parameter. The run time of our method ranges from hundreds of milliseconds to less than four seconds on large, challenging datasets, which makes it appropriate for situations where real-time decision making is needed. Experiments on synthetic models as well as on data from real world objects, some of which were collected in challenging field conditions, show that our approach compares favorably to classical thinning algorithms as well as to recent contributions to the field.Comment: 47 pages; IEEE WACV 2018, main paper and supplementary materia

Skeletonization and segmentation of binary voxel shapes

Preface. This dissertation is the result of research that I conducted between January 2005 and December 2008 in the Visualization research group of the Technische Universiteit Eindhoven. I am pleased to have the opportunity to thank a number of people that made this work possible. I owe my sincere gratitude to Alexandru Telea, my supervisor and first promotor. I did not consider pursuing a PhD until my Master’s project, which he also supervised. Due to our pleasant collaboration from which I learned quite a lot, I became convinced that becoming a doctoral student would be the right thing to do for me. Indeed, I can say it has greatly increased my knowledge and professional skills. Alex, thank you for our interesting discussions and the freedom you gave me in conducting my research. You made these four years a pleasant experience. I am further grateful to Jack vanWijk, my second promotor. Our monthly discussions were insightful, and he continuously encouraged me to take a more formal and scientific stance. I would also like to thank Prof. Jan de Graaf from the department of mathematics for our discussions on some of my conjectures. His mathematical rigor was inspiring. I am greatly indebted to the Netherlands Organisation for Scientific Research (NWO) for funding my PhD project (grant number 612.065.414). I thank Prof. Kaleem Siddiqi, Prof. Mark de Berg, and Dr. Remco Veltkamp for taking part in the core doctoral committee and Prof. Deborah Silver and Prof. Jos Roerdink for participating in the extended committee. Our Visualization group provides a great atmosphere to do research in. In particular, I would like to thank my fellow doctoral students Frank van Ham, Hannes Pretorius, Lucian Voinea, Danny Holten, Koray Duhbaci, Yedendra Shrinivasan, Jing Li, NielsWillems, and Romain Bourqui. They enabled me to take my mind of research from time to time, by discussing political and economical affairs, and more trivial topics. Furthermore, I would like to thank the senior researchers of our group, Huub van de Wetering, Kees Huizing, and Michel Westenberg. In particular, I thank Andrei Jalba for our fruitful collaboration in the last part of my work. On a personal level, I would like to thank my parents and sister for their love and support over the years, my friends for providing distractions outside of the office, and Michelle for her unconditional love and ability to light up my mood when needed

The fully connected N-dimensional skeleton: probing the evolution of the cosmic web

A method to compute the full hierarchy of the critical subsets of a density field is presented. It is based on a watershed technique and uses a probability propagation scheme to improve the quality of the segmentation by circumventing the discreteness of the sampling. It can be applied within spaces of arbitrary dimensions and geometry. This recursive segmentation of space yields, for a $d$-dimensional space, a $d-1$ succession of $n$-dimensional subspaces that fully characterize the topology of the density field. The final 1D manifold of the hierarchy is the fully connected network of the primary critical lines of the field : the skeleton. It corresponds to the subset of lines linking maxima to saddle points, and provides a definition of the filaments that compose the cosmic web as a precise physical object, which makes it possible to compute any of its properties such as its length, curvature, connectivity etc... When the skeleton extraction is applied to initial conditions of cosmological N-body simulations and their present day non linear counterparts, it is shown that the time evolution of the cosmic web, as traced by the skeleton, is well accounted for by the Zel'dovich approximation. Comparing this skeleton to the initial skeleton undergoing the Zel'dovich mapping shows that two effects are competing during the formation of the cosmic web: a general dilation of the larger filaments that is captured by a simple deformation of the skeleton of the initial conditions on the one hand, and the shrinking, fusion and disappearance of the more numerous smaller filaments on the other hand. Other applications of the N dimensional skeleton and its peak patch hierarchy are discussed.Comment: Accepted for publication in MNRA