Improved 3D thinning algorithms for skeleton extraction

In this study, we focused on developing a novel 3D Thinning algorithm to extract one-voxel wide skeleton from various 3D objects aiming at preserving the topological information. The 3D Thinning algorithm was testified on computer-generated and real 3D reconstructed image sets acquired from TEMT and compared with other existing 3D Thinning algorithms. It is found that the algorithm has conserved medial axes and simultaneously topologies very well, demonstrating many advantages over the existing technologies. They are versatile, rigorous, efficient and rotation invariant.<br /

A 3D parallel shrinking algorithm

Shrinking is a frequently used preprocessing step in image processing. This paper presents an efficient 3D parallel shrinking algorithm for transforming a binary object into its topological kernel. The applied strategy is called directional: each iteration step is composed of six subiterations each of which can be executed in parallel. The algorithm makes easy implementation possible, since deletable points are given by 3 x 3 x 3 matching templates. The topological correctness of the algorithm is proved for (26,6) binary pictures

2D parallel thinning and shrinking based on sufficient conditions for topology preservation

Thinning and shrinking algorithms, respectively, are capable of extracting medial lines and topological kernels from digital binary objects in a topology preserving way. These topological algorithms are composed of reduction operations: object points that satisfy some topological and geometrical constraints are removed until stability is reached. In this work we present some new sufficient conditions for topology preserving parallel reductions and fiftyfour new 2D parallel thinning and shrinking algorithms that are based on our conditions. The proposed thinning algorithms use five characterizations of endpoints

A 3D Sequential Thinning Scheme Based on Critical Kernels

International audienceWe propose a new generic sequential thinning scheme based on the critical kernels framework. From this scheme, we derive sequential algorithms for obtaining ultimate skeletons and curve skeletons. We prove some properties of these algorithms, and we provide the results of a quantitative evaluation that compares our algorithm for curve skeletons with both sequential and parallel ones

How sufficient conditions are related for topology-preserving reductions

A crucial issue in digital topology is to ensure topology preservation for reductions acting on binary pictures (i.e., operators that never change a white point to black one). Some sufficient conditions for topology-preserving reductions have been proposed for pictures on the three possible regular partitionings of the plane (i.e., the triangular, the square, and the hexagonal grids). In this paper, the relationships among these conditions are stated

On parallel thinning algorithms: minimal non-simple sets, P-simple points and critical kernels

International audienceCritical kernels constitute a general framework in the category of abstract complexes for the study of parallel homotopic thinning in any dimension. In this article, we present new results linking critical kernels to minimal non-simple sets (MNS) and P-simple points, which are notions conceived to study parallel thinning in discrete grids. We show that these two previously introduced notions can be retrieved, better understood and enriched in the framework of critical kernels. In particular, we propose new characterizations which hold in dimensions 2, 3 and 4, and which lead to efficient algorithms for detecting P-simple points and minimal non-simple sets

clDice -- a Novel Topology-Preserving Loss Function for Tubular Structure Segmentation

Accurate segmentation of tubular, network-like structures, such as vessels, neurons, or roads, is relevant to many fields of research. For such structures, the topology is their most important characteristic; particularly preserving connectedness: in the case of vascular networks, missing a connected vessel entirely alters the blood-flow dynamics. We introduce a novel similarity measure termed centerlineDice (short clDice), which is calculated on the intersection of the segmentation masks and their (morphological) skeleta. We theoretically prove that clDice guarantees topology preservation up to homotopy equivalence for binary 2D and 3D segmentation. Extending this, we propose a computationally efficient, differentiable loss function (soft-clDice) for training arbitrary neural segmentation networks. We benchmark the soft-clDice loss on five public datasets, including vessels, roads and neurons (2D and 3D). Training on soft-clDice leads to segmentation with more accurate connectivity information, higher graph similarity, and better volumetric scores.Comment: * The authors Suprosanna Shit and Johannes C. Paetzold contributed equally to the wor