TopoAngler: Interactive Topology-Based Extraction of Fishes
TopoAngler: Interactive Topology-Based Extraction of Fishes
复制标题
DOI：
10.1109/tvcg.2017.2743980
复制
发表时间：
2018
影响因子：
5.2
通讯作者：
A. Bock;Harish Doraiswamy;Adam P. Summers;Cláudio T. Silva
中科院分区：
文献类型：
--
作者：
A. Bock;Harish Doraiswamy;Adam P. Summers;Cláudio T. Silva
我们提出了TopOAngler，这是一个可视化框架，能够对Micro-CT扫描中包含的鱼类进行交互式用户引导的分割。CT扫描中固有的噪声，加上鱼类经常断开(有时是断裂)的骨骼结构，使得体积的自动分割变得不切实际。为了克服这一点，我们的框架结合了计算拓扑学的技术和交互式可视界面，使人在IOOP中能够有效地从体积中提取鱼类。在第一步中，使用输入的联接树来创建卷的分层分段。通过使用链接视图，可视化界面允许用户交互地探索这个层次结构，并将个别鱼类的部分收集到一个连贯的子体积中，从而重建整个鱼类。我们的框架主要是为了将其应用于鱼类的CT扫描，作为ScanAllFish项目的一部分，通过与其首席科学家的密切合作而产生。然而，我们预计它也适用于单个数据集包含多个样本的其他生物应用；这是目前实验室普遍遵循的一种常见程序，以增加昂贵的CT扫描仪的吞吐量。
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.