Plant and Soil

, Volume 398, Issue 1–2, pp 351–365 | Cite as

archiDART: an R package for the automated computation of plant root architectural traits

  • Benjamin M. Delory
  • Caroline Baudson
  • Yves Brostaux
  • Guillaume Lobet
  • Patrick du Jardin
  • Loïc Pagès
  • Pierre Delaplace
Regular Article

Abstract

Background and aims

In order to analyse root system architectures (RSAs) from captured images, a variety of manual (e.g. Data Analysis of Root Tracings, DART), semi-automated and fully automated software packages have been developed. These tools offer complementary approaches to study RSAs and the use of the Root System Markup Language (RSML) to store RSA data makes the comparison of measurements obtained with different (semi-) automated root imaging platforms easier. The throughput of the data analysis process using exported RSA data, however, should benefit greatly from batch analysis in a generic data analysis environment (R software).

Methods

We developed an R package (archiDART) with five functions. It computes global RSA traits, root growth rates, root growth directions and trajectories, and lateral root distribution from DART-generated and/or RSML files. It also has specific plotting functions designed to visualise the dynamics of root system growth.

Results

The results demonstrated the ability of the package’s functions to compute relevant traits for three contrasted RSAs (Brachypodium distachyon [L.] P. Beauv., Hevea brasiliensis Müll. Arg. and Solanum lycopersicum L.).

Conclusions

This work extends the DART software package and other image analysis tools supporting the RSML format, enabling users to easily calculate a number of RSA traits in a generic data analysis environment.

Keywords

Plant root system architecture Data Analysis of Root Tracings (DART) Root System Markup Language (RSML) 2D dynamic analysis Root trait 

Notes

Acknowledgments

Delory B.M. (Research Fellow) and Lobet G. (Postdoctoral Researcher) are financially supported by the Belgian National Fund for Scientific Research. The authors would like to thank Jacques Le Bot (INRA, Centre PACA, UR 1115 PSH) for providing the vectorized root system of the tomato plant used in this paper, and Pierre Tocquin (University of Liège, PhytoSYSTEMS) and three anonymous reviewers for their helpful comments on the manuscript.

Conflict of interest

The authors declare that they have no conflict of interest.

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Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Benjamin M. Delory
    • 1
  • Caroline Baudson
    • 1
  • Yves Brostaux
    • 2
  • Guillaume Lobet
    • 3
  • Patrick du Jardin
    • 1
  • Loïc Pagès
    • 4
  • Pierre Delaplace
    • 1
  1. 1.Plant BiologyUniversity of Liège – Gembloux Agro-Bio TechGemblouxBelgium
  2. 2.Applied Statistics, Computer Science and ModelingUniversity of Liège – Gembloux Agro-Bio TechGemblouxBelgium
  3. 3.Laboratory of Plant Physiology, PhytoSYSTEMSUniversity of LiègeLiègeBelgium
  4. 4.INRA, Centre PACA, UR 1115 PSH, Domaine Saint-Paul, Site AgroparcAvignonFrance

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