Ziamtsov, I., Navlakha, S. (March 2020) Plant 3D (P3D): A Plant Phenotyping Toolkit for 3D Point Clouds. Bioinformatics. ISSN 1367-4803 (Public Dataset)
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 bioinformatics > computational biology > algorithms bioinformatics > computational biology bioinformatics > genomics and proteomics > computers > computer software bioinformatics > computational biology > algorithms > machine learning 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: | 01 Feb 2024 19:52 |
| Related URLs: | |
| Dataset ID: |
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| URI: | https://repository.cshl.edu/id/eprint/39218 |
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