Reference : archiDART: an R package for the automated computation of plant root architectural traits
Scientific journals : Article
Life sciences : Phytobiology (plant sciences, forestry, mycology...)
http://hdl.handle.net/2268/186932
archiDART: an R package for the automated computation of plant root architectural traits
English
Delory, Benjamin mailto [Université de Liège > Agronomie, Bio-ingénierie et Chimie (AgroBioChem) > Biologie végétale >]
Baudson, Caroline mailto [Université de Liège > Agronomie, Bio-ingénierie et Chimie (AgroBioChem) > Biologie végétale >]
Brostaux, Yves mailto [Université de Liège > Agronomie, Bio-ingénierie et Chimie (AgroBioChem) > Statistique, Inform. et Mathém. appliquée à la bioingénierie >]
Lobet, Guillaume mailto [Université de Liège > Département des sciences de la vie > Physiologie végétale >]
du Jardin, Patrick mailto [Université de Liège > Agronomie, Bio-ingénierie et Chimie (AgroBioChem) > Biologie végétale >]
Pagès, Loïc mailto []
Delaplace, Pierre mailto [Université de Liège > Agronomie, Bio-ingénierie et Chimie (AgroBioChem) > Biologie végétale >]
Jan-2016
Plant and Soil
Springer
398
1
351-365
Yes (verified by ORBi)
International
0032-079X
1573-5036
Dordrecht
The Netherlands
[en] Plant root system architecture ; Data Analysis of Root Tracings (DART) ; Root System Markup Language (RSML) ; 2D dynamic analysis ; Root trait
[en] 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.
Fonds de la Recherche Scientifique (Communauté française de Belgique) - F.R.S.-FNRS
http://hdl.handle.net/2268/186932
10.1007/s11104-015-2673-4
The final publication is available at Springer via http://dx.doi.org/10.1007/s11104-015-2673-4

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