Lights, camera, pliman! An R package for plant image analysis

Abstract

Abstract Manual measurements of quantitative traits are time consuming and error prone. Therefore, high‐throughput phenotyping methods that allow a rapid and accurate assessment are vital to a growing range of researchers such as agronomists, breeders, phytopathologists, geneticists, ecologists and biologists. Here, I describe the pliman R package, a collection of functions designed (but not limited) to conduct plant image analysis. The package will help researchers to (a) manipulate, segment and compute image indexes based on Red, Green, Blue, Red‐Edge and Near‐Infrared bands; (b) measure leaf area and shape; (c) quantify plant disease severity; (d) count and extract features (e.g. area, perimeter, radius, circularity and eccentricity) of objects such as grains, leaves, pods, pollen and cells; and (e) compute RGB indexes for each object in an image. In this paper, I describe the main features implemented in the package, guiding the user along a gentle learning curve with practical and reproducible examples. The results of validation studies implemented to count objects in different scenarios (combination of seed sizes, background colour and image resolution), measure leaf area, and quantify plant disease severity have shown that pliman measurements are highly concordant with existing ‘gold standard’ tools. The pliman package offers a flexible, intuitive and richly documented working environment for image‐based phenotyping, being an interesting alternative to free and commercial ‘point‐and‐click’ solutions. R users will find the package fairly easy to use and will be surprised at how the setting of a few arguments will allow processing thousands of images while they enjoy a cup of coffee.

Plant phenotyping relevance

植物画像解析用Rパッケージを開発し、葉面積・形状・病害重症度などの表現型抽出機能と検証結果を中核として扱っているため。

Code and data availability

植物フェノタイピング解析を再現する公開資産であることを、入力本文と直接リンクから確認できなかったため保留しました。

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