archiDART v3.0: A new data analysis pipeline allowing the topological analysis of plant root systems

Abstract

Quantifying plant morphology is a very challenging task that requires methods able to capture the geometry and topology of plant organs at various spatial scales. Recently, the use of persistent homology as a mathematical framework to quantify plant morphology has been successfully demonstrated for leaves, shoots, and root systems. In this paper, we present a new data analysis pipeline implemented in the R package archiDART to analyse root system architectures using persistent homology. In addition, we also show that both geometric and topological descriptors are necessary to accurately compare root systems and assess their natural complexity.

Code and data availability

The paper's use-case data and R analysis code are publicly deposited on Zenodo (data/R codes for the use cases; archived archiDART 3.0 source; archiShiny app code), with live code on GitHub and a public web application. These directly reproduce the paper's root-system phenotyping and persistent homology analysis.