archiDART v 3 . 0 : A new data analysis pipeline allowing the

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. This article is included in the gateway. RPackage This article is included in the Global Open Data for gateway. Agriculture and Nutrition This article is included in the Interactive Figures