Generator of Root ANAtomy in R

What is GRANAR?

GRANAR is a generator of complete root cross-section network in R.

Upon a small set of anatomical features the GRANAR model is able to reconstruct a generic root cell network for mono and dicotyledon.

Among the few parameters you can modify, there is the aerenchyma proportion, the number and size of the xylem vessels, but also the number of cell layers and the mean size of each cell type.

Once the anatomy is generated, it is possible to look after some functional features related to that anatomy. For instance, hydraulics conductivities can be computed when GRANAR is coupled with MECHA.

Installing GRANAR

GRANAR is a R package

1. Download GRANAR

The source code of GRANAR is available on github: DOI

Another github repository contains example parameter files needed to run GRANAR: granar_examples You do not need your own data to try it out. DOI

2. Install R

The first step before running GRANAR is to install a working version for R! Installation of R are available here:

3. Install required libraries

GRANAR is built upon a handfull of external libraries. You will need to install them before using the model.

These libraries can be install using RStudio. In the Terminal or Console, enter:



In the Terminal or Console enter the following lines:


Feeling adventurous? Check out the source code.

View source code


Input files

GRANAR uses only parameters files as input. Examples of the input files are stored in the modelparameterfolder in the granar_example directory:

  • Zea_mays_1_Heymans_2019.xml : General parameters for maize nodal root anatomy


GRANAR output are stored in a list element and it can be exported under .xml with the same format as CellSet.

 # R script example 
params = read_param_xml(path = "params.xml") # import input parameter for GRANAR 
sim = list() # create an empty list 
sim = create_anatomy(parameters = params) # generate a cell network anatomy
write_anatomy_xml(sim = sim,
                  path = "new_root.xml") # export the data under a .xml file

About us

GRANAR was developed at the Université catholique de Louvain, in the Earth and Life Insititute, in the lab of Guillaume Lobet.

The primary developpers of the model are Adrien Heymans and Guillaume Lobet. Valentin Couvreur provided some technical assistance.

GRANAR is available at:

GRANAR, a computational tool to better understand the functional importance of monocotyledon root anatomy
Adrien Heymans, Valentin Couvreur, Therese LaRue, Ana Paez-Garcia, Guillaume Lobet
Plant Physiology, 2019

GRANAR is released under a GNU General Public Licence v3.0, which means that distribution and use and binary forms, with or without modification, are permitted under the GNU General Public License v3 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 View paper