Plant 3D (P3D): a plant phenotyping toolkit for 3D point clouds
Plant 3D (P3D): a plant phenotyping toolkit for 3D point clouds
复制标题
DOI：
10.1093/bioinformatics/btaa220
复制
发表时间：
2020-03
期刊：
影响因子：
5.8
通讯作者：
Illia Ziamtsov;Saket Navlakha
中科院分区：
文献类型：
--
作者：
Illia Ziamtsov;Saket Navlakha
开发有效分析植物结构三维点云数据的方法对于许多表型应用仍然具有挑战性。在这里，我们描述了一个工具，解决四个核心表型任务：云点分类成茎和层点；茎点的图形骨架化；单个椎板分割；还有整片叶子的标签。这四项任务对于许多下游表型目标至关重要，例如量化植物生物量，对植物形状进行形态学分析，以及揭示基因型与表型之间的关系。P3D工具提供了一个直观的图形用户界面，一个快速的3D渲染引擎，用于可视化具有数百万云点的植物，以及用于3D架构分析的几种图论和机器学习算法。可用性和实现P3D是开源的，并在c++中实现。源代码和Windows安装程序免费提供：https://github.com/iziamtso/P3D/。
MOTIVATION Developing methods to efficiently analyze 3D point cloud data of plant architectures remains challenging for many phenotyping applications. Here, we describe a tool that tackles four core phenotyping tasks: classification of cloud points into stem and lamina points; graph skeletonization of the stem points; segmentation of individual lamina; and whole leaf labeling. These four tasks are critical for numerous downstream phenotyping goals, such as quantifying plant biomass, performing morphological analyses of plant shapes, and uncovering genotype to phenotype relationships. The P3D tool provides an intuitive graphical user interface, a fast 3D rendering engine for visualizing plants with millions of cloud points, and several graph-theoretic and machine learning algorithms for 3D architecture analyses. AVAILABILITY AND IMPLEMENTATION P3D is open-source and implemented in C ++. Source code and Windows installer are freely available at: https://github.com/iziamtso/P3D/.