archiDART

What is archiDART?

archiDART is an R package that was developed for the automated analysis of plant root system architectures using Data Analysis of Root Tracings (DART) and Root System Markup Language (RSML) files.

This R package is the result of an international collaboration between the Ecosystem Functioning and Services lab of the Leuphana University Lüneburg (Germany), the Earth and Life Institute of the Catholic University of Louvain-la-Neuve (Belgium), the Forschungszentrum Jülich GmbH (IBG-3, Germany), the Plant Biology Unit of Gembloux Agro-Bio Tech (University of Liège, Belgium), the French National Institute for Agricultural Research (Centre PACA UR 1115 PSH, France), and the Donald Danforth Plant Science Center (USA).

archiDART is:

an R package
Open source
Flexible
Easy to use
Free
Examplified in a web application

archiDART works with:

Root System Markup Language data
Data from the DART software

Built in analysis:

Root system traits
Time series
Lateral root distribution
Root growth directions and trajectories
Topological indices
Persistent homology

Installation

archiDART was developped as an R package. To install it, follow the next steps:

1. Install R

1. Install R-Studio (optional)

2. In the R terminal, type in: install.packages(archiDART)

3. In the R terminal, type in: library(archiDART)

More information can be found in the manual provided with the R package.

Manual

Using archiDART

We created a web application to show the basic capabilities of archiDART. Check it out!

Manual Web application

Trouble using archiDART?

You need some help? You want to propose some new features? You found a bug? Just get in touch with us!

Get in touch!

archiDART + RSML =

RootSystemML is a file format to represent root architectural data. It has been designed to overcome two major challenges:

1. To enable portability of root architecture data between different software tools in an easy and interoperable manner allowing seamless collaborative work.

2. To provide a standard format upon which to base central repositories which will soon arise following the expanding worldwide root phenotyping effort.

RSML allows to store 2D or 3D image metadata, plant and root properties and geometries, continuous functions along individual root paths and a suite of annotations at the image, plant or root scales, at one or several time points. The plant ontologies are used to describe botanical entities that are relevant at the scale of root system architecture.

RSML website RSML paper

About us

archiDART was initially developped by Benjamin Delory.

archiDART is still maintained and improved, thanks to numerous user feedbacks and demands, but also thanks to new developers such as Guillaume Lobet from the Forschungszentrum Juelich.

How to cite us

Delory BM, Baudson C, Brostaux Y, Lobet G, du Jardin P, Pagès L, Delaplace P (2016). archiDART: an R package for the automated computation of plant root architectural traits. Plant and Soil, 398, 351-365.

View paper

archiDART is Open source

archiDART is free to use and released under a GPL licence. It means that redistribution and use in source and binary forms, with or without modification, are permitted under the GNU General Public License v2 and provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

Source code on GitHub