Research Article | Open Access

Volume 2025 |Article ID 100013 | https://doi.org/10.1016/j.plaphe.2025.100013

VRoot: A VR-Based application for manual root system architecture reconstruction

Dirk N. Baker ,^1,2 Tobias Selzner,³ Jens Henrik Gobbert,¹ Hanno Scharr,⁴ Morris Riedel,^1,2 Ebba þora Hvannberg,² Andrea Schnepf,³ and Daniel Zielasko⁵

¹Jülich Supercomputing Centre, Forschungszentrum Jülich GmbH, Jülich, Germany
²School of Engineering and Natural Sciences, University of Iceland, Reykjavík, Iceland
³Institute of Bio- and Geosciences 3: Agrosphere, Forschungszentrum Jülich GmbH, Jülich, Germany
⁴Institute of Advanced Simulation 8: Data Analytics and Machine Learning, Forschungszentrum Jülich GmbH, Jülich, Germany
⁵Human-Computer Interaction, Trier University, Trier, Germany

Abstract

This article describes an immersive virtual reality reconstruction tool for root system architectures from 3D scans of soil columns. In practical scenarios, experimental conditions will be adapted to fit the need of the data analysis pipeline, including sieving and drying the soil before scanning. Based on previous reports of automatic systems that do not represent what experts would annotate, we developed a virtual reality system to assist with the extraction of root systems in cases in which automated approaches fall short of expert knowledge. The aim of the present study is to evaluate whether our immersive method is superior to classical annotation approaches when tested on synthetic data sets using untrained participants. Our laboratory user study consists of evaluating the root extractions of participants, along with their rating on central user experience and usability measures. We show significant improvement in F1 score across conditions (noisy or clear data) as well as an improved usability. Our study highlights that using virtual reality in root extraction improves accuracy, and we perform an in-depth evaluation of biases that occur when users trace roots in soil volumes.