Botanical Digitization: Application of MorphoLeaf in 2D Shape Visualization, Digital Morphometrics, and Species Delimitation, using Homologous Landmarks of Cucurbitaceae Leaves as a Model.

Abstract

Morphometrics has been applied in several fields of science including botany. Plant leaves are been one of the most important organs in the identification of plants due to its high variability across different plant groups. The differences between and within plant species reflect variations in genotypes, development, evolution, and environment. While traditional morphometrics has contributed tremendously to reducing the problems that come with the identification of plants and delimitation of species based on morphology, technological advancements have led to the creation of deep learning digital solutions that made it easy to study leaves and detect more characters to complement already existing leaf datasets. In this study, we demonstrate the use of MorphoLeaf in generating morphometric dataset from 140 leaf specimens from seven Cucurbitaceae species via scanning of leaves, extracting landmarks, data extraction, landmarks data quantification, and reparametrization and normalization of leaf contours. PCA analysis revealed that blade area, blade perimeter, tooth area, tooth perimeter, height of (each position of the) tooth from tip, and the height of each (position of the) tooth from base are important and informative landmarks that contribute to the variation within the species studied. Our results demonstrate that MorphoLeaf can quantitatively track diversity in leaf specimens, and it can be applied to functionally integrate morphometrics and shape visualization in the digital identification of plants. The success of digital morphometrics in leaf outline analysis presents researchers with opportunities to apply and carry out more accurate image-based researches in diverse areas including, but not limited to, plant development, evolution, and phenotyping.

Plant phenotyping relevance

MorphoLeafによる葉画像のスキャン、ランドマーク抽出、形態計測データ化を中心に、葉の形状形質を定量化するソフトウェア／ワークフローを実証しているため。

Code and data availability

The preprint states its supplementary data (the Cucurbitaceae leaf morphometric dataset from MorphoLeaf analysis) is available online in the authors' GitHub repository, matching an allowed URL.