TY - JOUR

T1 - archiDART: an R package for the automated computation of plant root architectural traits

AU - Delory, Benjamin M.

AU - Baudson, Caroline

AU - Brostaux, Yves

AU - Lobet, Guillaume

AU - du Jardin, Patrick

AU - Pagès, Loïc

AU - Delaplace, Pierre

PY - 2016/1

Y1 - 2016/1

N2 - 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.

AB - 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.

KW - 2D dynamic analysis

KW - Data Analysis of Root Tracings (DART)

KW - Plant root system architecture

KW - Root System Markup Language (RSML)

KW - Root trait

KW - Plant root system architecture

KW - Data Analysis of Root Tracings (DART)

KW - Root System Markup Language (RSML)

KW - 2D dynamic analysis

KW - Root trait

KW - Biology

KW - Sustainability Science

UR - http://www.scopus.com/inward/record.url?scp=84955184731&partnerID=8YFLogxK

U2 - 10.1007/s11104-015-2673-4

DO - 10.1007/s11104-015-2673-4

M3 - Journal articles

AN - SCOPUS:84955184731

VL - 398

SP - 351

EP - 365

JO - Plant and Soil

JF - Plant and Soil

SN - 0032-079X

IS - 1-2

ER -