A network-based framework for shape analysis enables accurate characterization of leaf epidermal cells

Jacqueline Nowak,Timon Matz,Zoran Nikoloski,Ryan Christopher Eng,Staffan Persson,Arun Sampathkumar,Matti Waack

doi:10.1038/s41467-020-20730-y

Abstract

Cell shape is crucial for the function and development of organisms. Yet, versatile frameworks for cell shape quantification, comparison, and classification remain underdeveloped. Here, we introduce a visibility graph representation of shapes that facilitates network-driven characterization and analyses across shapes encountered in different domains. Using the example of complex shape of leaf pavement cells, we show that our framework accurately quantifies cell protrusions and invaginations and provides additional functionality in comparison to the contending approaches. We further show that structural properties of the visibility graphs can be used to quantify pavement cell shape complexity and allow for classification of plants into their respective phylogenetic clades. Therefore, the visibility graphs provide a robust and unique framework to accurately quantify and classify the shape of different objects.

Highlights

Cell shape is crucial for the function and development of organisms
In contrast to the visibility graph approach, the Fourier transform analysis performs worse in separating the shapes based on their complexity (Supplementary Fig. 9). These results show that visibility graphs can serve as powerful global descriptors of shape, and is applicable with data from different domains
An extension of the classical descriptors to quantify the number of lobes and necks in cells with complex shapes, like pavement cells in the leaf epidermis, does not result in accurate measurements[6,14,15]

Summary

Introduction

Cell shape is crucial for the function and development of organisms. Yet, versatile frameworks for cell shape quantification, comparison, and classification remain underdeveloped. Despite efforts to devise descriptors that simultaneously identify differences between pavement cells across different taxa and accurately characterize their local shape features[6,14,15], comparative analyses that assess the performance based on a gold standard are rare[6]. Such efforts can be regarded as a necessary step toward understanding the contribution of cellular processes in the emergence of complex cell shapes[16,17,18,19].

Methods

Results

Conclusion