TopoAngler: Interactive Topology-Based Extraction of Fishes

Abstract

We present TopoAngler, a visualization framework that enables an interactive user-guided segmentation of fishes contained in a micro-CT scan. The inherent noise in the CT scan coupled with the often disconnected (and sometimes broken) skeletal structure of fishes makes an automatic segmentation of the volume impractical. To overcome this, our framework combines techniques from computational topology with an interactive visual interface, enabling the human-in-the-Ioop to effectively extract fishes from the volume. In the first step, the join tree of the input is used to create a hierarchical segmentation of the volume. Through the use of linked views, the visual interface then allows users to interactively explore this hierarchy, and gather parts of individual fishes into a coherent sub-volume, thus reconstructing entire fishes. Our framework was primarily developed for its application to CT scans of fishes, generated as part of the ScanAllFish project, through close collaboration with their lead scientist. However, we expect it to also be applicable in other biological applications where a single dataset contains multiple specimen; a common routine that is now widely followed in laboratories to increase throughput of expensive CT scanners.

Wasserstein Distances, Geodesics and Barycenters of Merge Trees

“…In that context, Topological Data Analysis (TDA) [32] forms a family of generic, robust, and efficient techniques whose utility has been demonstrated in a number of visualization tasks [55] for revealing the implicit structural patterns present in complex datasets. Examples of popular application fields include turbulent combustion [23,51,65], material sciences [40,53,54], nuclear energy [71], fluid dynamics [61], bioimaging [4,20,26], quantum chemistry [16,47,76] or astrophysics [103,105]. Among the data abstractions developed in TDA (see Sec.…”

Denoising with discrete Morse theory

“…Note that our algorithm bears resemblance with strategies used for simplification of merge and split trees [9,10,32] since they both have their origin rooted at Morse theory and employ similar techniques for simplification of trees. Although persistence threshold can be used as a simplification parameter of contour trees [6,42], our goal and scenario are entirely different. Algorithm 1 operates on the dual graph with tetrahedra as nodes and triangles as edges, ergo bypassing the need for computation of contour tree.…”

Mergemaps: Treemaps for Scientific Data

“…From a data analysis perspective, merge trees have been used in various interesting applications. Bock et al [3] used it for extracting fishes from micro-CT scans, Valsangkar et al [35] track cyclones by understanding how their contours join and split, Doraiswamy et al [8] identify congestion in New York roads.…”