Segmentation of ray and shark tesserae

Please always quote using this URN: urn:nbn:de:0297-zib-54429
  • Rays and sharks are cartilaginous fishes. Most of the cartilaginous skeleton is covered with calcified tiles to improve the stability of the skeleton. These tiles are called tesserae and enclose areas of uncalcified cartilage. Because of the special properties of the tesserae, biologists are interested to understand shape and structure of tessellated cartilage. This thesis presents a segmentation pipeline for the separation of tesserae on the cartilaginous skeleton of rays and sharks. The segmentation pipeline consists of an automatic initial segmentation step followed by manual error corrections by the user. The initial segmentation is based on the contour tree data structure that tracks the evolution of level sets in a dataset during iso-value changes. The presented segmentation concepts are not limited to the segmentation of tesserae but also viable for similar kinds of tiled structures. The input datasets are given as micro-CT scans. The contribution of this thesis is the development of a segmentation pipeline. The pipeline uses a newly developed fast version of the contour-tree-based segmentation algorithm that, after a preprocessing step, does not need to iterate over all voxels in the dataset. Visualizations and computations are done with the software system ZIBAmira. Used algorithms are either implemented as new ZIBAmira modules or they extend already existing ZIBAmira modules.

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Author:David Knötel
Document Type:Master's Thesis
Tag:segmentation, contour tree, watershed, distance map
Granting Institution:Freie Universität Berlin
Advisor:Daniel Baum
Date of final exam:2014/10/24
Year of first publication:2014