RootBox

RootBox

Daniel Leitner, University of Vienna, and Andrea Schnepf, Forschungszentrum Jülich GmbH

Website

http://www.csc.univie.ac.at/rootbox/

Description

RootBox is a 3D dynamic L-systems model of root architecture implemented in a flexible Matlab structure. It allows individual modules and algorithms to be easily interchanged and tailored to specific simulations.

The model includes growth of individual roots according to a growth function, branching at predefined branching angles, and root death. The model can produce a variety of different root systems that compare well to observed images of root systems (Leitner et al. 2010a,c). Root system properties such as root length densities can be computed from the model output. Internal functions can readily be altered to specific requirements. This facilitates the coupling with different soil models and model adaptation for specific experimental designs.  Examples of coupling the root growth model with soil models are presented e.g. in Schnepf et al. (2012) who simulated root system phosphate uptake from a rhizotron as affected by root exudation. Leitner et al. (2010b) demonstrated the use of the RootBox model to create a 3D tetrahedral mesh from the root system geometry and the explicit 3D simulation of water and nutrient transport in the soil with static root surfaces as boundaries. Furthermore, RootBox is being used in an algorithm for semi-automated root tracking for the realistic recovery of root system parameters from2Dimages (Leitner et al. 2014).

Scientific articles

Leitner, D., Felderer, B., Vontobel, P., Schnepf, A. Recovering root system traits using image analysis exemplified by two-dimensional neutron radiography images of lupine (2014) Plant Physiology, 164 (1), pp. 24-35.
Link: http://www.plantphysiol.org/content/164/1/24

Dunbabin, V.M., Postma, J.A., Schnepf, A., Pagès, L., Javaux, M., Wu, L., Leitner, D., Chen, Y.L., Rengel, Z., Diggle, A.J. Modelling root-soil interactions using three-dimensional models of root growth, architecture and function (2013) Plant and Soil, 372 (1-2), pp. 93-124.             
Link: http://link.springer.com/article/10.1007/s11104-013-1769-y

Schnepf, A., Leitner, D., Klepsch, S. Modeling phosphorus uptake by a growing and exuding Root system (2012) Vadose Zone Journal, 11 (3).                                                         
Link: https://www.soils.org/publications/vzj/abstracts/11/3/vzj2012.0001

Leitner, D., Klepsch, S., Knieß, A., Schnepf, A. The algorithmic beauty of plant roots - an L-system model for dynamic root growth simulation (2010c) Mathematical and Computer Modelling of Dynamical Systems, 16 (6), pp. 575-587.
Link: http://web.a.ebscohost.com/ehost/detail?sid=6a5db938-753e-4061-8484-596c0d2e30b5%40sessionmgr4001&vid=1&hid=4204&bdata=JnNpdGU9ZWhvc3QtbGl2ZQ%3d%3d#db=aph&AN=55598128

Leitner, D., Schnepf, A., Klepsch, S., Roose, T. Comparison of nutrient uptake between three-dimensional simulation and an averaged root system model (2010b) Plant Biosystems, 144 (2), pp. 443-447.
Link:http://www.tandfonline.com/doi/abs/10.1080/11263501003726334#.UyGsd4Wa-64

Leitner, D., Klepsch, S., Bodner, G., Schnepf, A. A dynamic root system growth model based on L-Systems (2010a) Plant and Soil, 332 (1), pp. 177-192.
Link: http://link.springer.com/article/10.1007/s11104-010-0284-7

Technical information

Operating system: windows, mac

Licence: freeware

Output: L-system strings representing the root system at different times

Export formats: .mat

Other information: Requires Matlab to run