PlantCV v2: Image analysis software for high-throughput plant phenotyping

Abstract

Systems for collecting image data in conjunction with computer vision techniques are a powerful tool for increasing the temporal resolution at which plant phenotypes can be measured non-destructively. Computational tools that are flexible and extendable are needed to address the diversity of plant phenotyping problems. We previously described the Plant Computer Vision (PlantCV) software package, which is an image processing toolkit for plant phenotyping analysis. The goal of the PlantCV project is to develop a set of modular, reusable, and repurposable tools for plant image analysis that are open-source and community-developed. Here we present the details and rationale for major developments in the second major release of PlantCV. In addition to overall improvements in the organization of the PlantCV project, new functionality includes a set of new image processing and normalization tools, support for analyzing images that include multiple plants, leaf segmentation, landmark identification tools for morphometrics, and modules for machine learning.

Plant phenotyping relevance

植物画像から表現型を抽出するオープンソース解析ソフトウェアの開発・改良が中心であり、植物フェノタイピング手法論文に該当する。

Code and data availability

The paper explicitly states that scripts, notebooks, SQL schema, and simple input data for its figures/results are on GitHub, that Setaria images come from publicly available datasets on the PlantCV data page, and that PlantCV v2.1 is archived on Zenodo.