Plant 3D (P3D): a plant phenotyping toolkit for 3D point clouds

Abstract

Motivation Developing methods to efficiently analyze 3D point cloud data of plant architectures remain 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 Plant 3D 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/. Contact iziamtso@ucsd.edu or navlakha@cshl.edu Supplementary information Supplementary data are available at Bioinformatics online.

Branch-Pipe: Improving Graph Skeletonization around Branch Points in 3D Point Clouds

“…However, once these challenges are addressed and normal vectors are estimated, our method can be used after the appropriate pre-processing steps are applied. All of our algorithms are available and implemented in P3D, our open-source plant phenotyping toolkit [44].…”

How to make sense of 3D representations for plant phenotyping: a compendium of processing and analysis techniques

“…Maize (Corn) [95] Mango [122] Olive [122] Peach [122] Pine tree [180] Tomato [242] Walnut [122] Methods developed for specific plant applications.…”

“…After the challenging steps of skeletonization, segmentation and/or surface reconstruction, the measurement of traits on either whole plants, or individual plant organs is often relatively straightforward and many different approaches may yield sufficiently good estimates. Measuring these features is important for a large number of tasks [242], including quantifying plant biomass and yield [243], understanding plant response to stressful conditions [196], mapping genotypes and building predictive structural and functional models of plant growth [244].…”

High-Throughput Plant Phenotyping Platform (HT3P) as a Novel Tool for Estimating Agronomic Traits From the Lab to the Field

“…Kar et al (2020) developed an analysis pipeline with outlier detection, missing value imputation, and spatial adjustment for solving the problem of inaccurate and missing phenotypic data. Toolkits tend to be relatively specific, such as Plant 3D (P3D), which specializes in analyzing 3D point cloud data of plant structures (Ziamtsov and Navlakha, 2020). With the advancement of HT3P, their improving high-throughput and efficiency will produce increasingly big data.…”