Plant 3D (P3D): A Plant Phenotyping Toolkit for 3D Point Clouds

Ziamtsov, I., Navlakha, S. (March 2020) Plant 3D (P3D): A Plant Phenotyping Toolkit for 3D Point Clouds. Bioinformatics. ISSN 1367-4803 (Public Dataset)

URL: https://pubmed.ncbi.nlm.nih.gov/32232439/
DOI: 10.1093/bioinformatics/btaa220

Abstract

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.

Item Type: Paper
Subjects: bioinformatics
bioinformatics > genomics and proteomics > computers > computer software
organism description > plant
CSHL Authors:
Communities: CSHL labs > Navlakha lab
Depositing User: Adrian Gomez
Date: 31 March 2020
Date Deposited: 02 Apr 2020 18:51
Last Modified: 14 Sep 2020 21:46
Related URLs:
Dataset ID:
  • https://github.com/iziamtso/P3D/
URI: https://repository.cshl.edu/id/eprint/39218

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