Network feature-based phenotyping of leaf venation robustly reconstructs the latent space

Abstract

Abstract Despite substantial variation in leaf vein architectures among angiosperms, a typical hierarchical network pattern is shared within clades. Functional demands constrain the network structure of leaf venation, generating a biased distribution in the morphospace. Although network structures and their diversity are crucial for understanding angiosperm venation, previous studies have relied on simple morphological measurements (e.g., length, diameter, branching angles, and areole area) and their derived statistics to quantify phenotypes. In this study, we developed a simple, high-throughput phenotyping workflow for the quantification of vein networks and identified leaf venation-specific morphospace patterns. The proposed method involves four processes: leaf image acquisition using a feasible system, leaf vein segmentation based on a deep neural network model, network extraction as an undirected graph, and network feature calculation. To demonstrate the proposed method, we applied it to images of non-chemically treated leaves of five species for classification based on network features alone, with an accuracy of 90.6%. By dimensionality reduction, a one-dimensional morphospace, along which venation shows variation in loopiness, was identified for both untreated and cleared leaf images, suggesting that patterns of venation are determined by a functional trade-off. The proposed network feature-based method is a useful morphological descriptor, providing a quantitative representation of the topological aspects of venation and enabling inverse mapping to leaf vein structures. Accordingly, our approach is promising for analyses of the functional and structural properties of veins. Author Summary Leaf venation exhibits diverse network structures among taxa and conservation within taxa, reflecting complex evolutionary processes involving functional, developmental, and structural constraints. We used network features to characterize hierarchical and complex venation patterns. We analyzed 479 non-chemically treated leaves of five species and demonstrated that network features contain sufficient information for species classification. Furthermore, we identified biased distribution patterns in the leaf venation morphospace by characterizing leaf samples from both untreated and cleared leaf images. These results improve our understanding of morphological constraints and functional trade-offs shaping divergence in leaf venation. Our approach provides a basis for similar analyses in various fields targeting reticulate networks, which are ubiquitous in nature, including biomimetics, generative design, and microfluidics.

Plant phenotyping relevance

葉画像から葉脈ネットワークを抽出し、形態特徴を定量化する高スループット表現型解析ワークフローを開発・実証しており、フェノタイピング手法が中心である。

Code and data availability

The paper's cleared-leaf phenotyping analysis is built directly on the public NMNS Cleared Leaf Database (4,095 images; 328 filtered for the cleared leaf dataset and 20 high-resolution images for U-Net training). No author code, trained model checkpoints, or untreated-leaf dataset deposit is described with a public URL