No cell is an island: characterising the leaf epidermis using epidermalmorph, a new R package.

Abstract

The leaf epidermis is the interface between a plant and its environment. The epidermis is highly variable in morphology, with links to both phylogeny and environment, and this diversity is relevant to several fields, including physiology, functional traits, palaeobotany, taxonomy and developmental biology. Describing and measuring leaf epidermal traits remains challenging. Current approaches are either extremely labour-intensive and not feasible for large studies or limited to measurements of individual cells. Here, we present a method to characterise individual cell size, shape (including the effect of neighbouring cells) and arrangement from light microscope images. We provide the first automated characterisation of cell arrangement (from traced images) as well as multiple new shape characteristics. We have implemented this method in an R package, epidermalmorph, and provide an example workflow using this package, which includes functions to evaluate trait reliability and optimal sampling effort for any given group of plants. We demonstrate that our new metrics of cell shape are independent of gross cell shape, unlike existing metrics. epidermalmorph provides a broadly applicable method for quantifying epidermal traits that we hope can be used to disentangle the fundamental relationships between form and function in the leaf epidermis.

Plant phenotyping relevance

葉の表皮細胞の形状・配置などの植物形質を顕微鏡画像から自動定量する手法とRパッケージを開発しており、方法が研究の中心である。

Code and data availability

The paper's authors publicly released their analysis code, the epidermalmorph R package, on GitHub with documentation and tutorials, including example data ('podocarps') in the package. The expanded phenotype dataset is not yet available (request_only), but the code asset qualifies as public and paper-specific.