Semi-automated root image analysis

What is SmartRoot?

SmartRoot is a semi-automated image analysis software which streamlines the quantification of root growth and architecture for complex root systems.

The software combines a vectorial representation of root objects with a powerful tracing algorithm which accommodates to a wide range of image source and quality.

The software supports a sampling-based analysis of root system images, in which detailed information is collected on a limited number of roots selected by the user according to specific research requirements.

SmartRoot is an operating system independent freeware based on ImageJ and uses cross-platform standards (XML, SQL, Java) for communication with data analysis softwares.

SmartRoot is :

  • Semi-automated
  • Platform-independent (Windows, Mac OSX, Linux)
  • Free

SmartRoot works with:

  • Wide range of image type and quality
  • All plant species
  • Mature root systems
  • Time-series

Built in tools :

  • Actions on several traced roots
  • Basic plot generator
  • SQL database export
  • CSV export
  • Various types of root annotations

Measured traits:

  • Root length
  • Root diameter
  • Root insertion angle
  • Lateral density
  • Growth
  • Topology


SmartRoot was developped as an ImageJ plugin. To install it, follow the next steps:

1. Install ImageJ of Fiji

2. Download SmartRoot files

3. Copy the jat files to the `imageJ/plugins` folder

More precise information can be found in the manual or the Quick Start Guide

SmartRoot files Manual Quick Start Guide

Using SmartRoot

Look at the video for a quick start! Or check out the Manual, Quick Start guide or Quick Start image.

Manual Quick Start Guide

Touble using SmartRoot?

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

Get in touch!

SmartRoot + 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

SmartRoot was initially developped by Xavier Draye and Guillaume Lobet at the Université catholique de Louvain.

SmartRoot is still maintained and improved, thanks to numerous user feedbacks and demands, but lso thanks to new developers such as Iko Koevoets from the University of Amsterdam.

How to cite us

A Novel Image Analysis Toolbox Enabling Quantitative Analysis of Root System Architecture. Guillaume Lobet, Loic Pages and Xavier Draye, 2011

View paper

SmartRoot is Open source

SmartRoot 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 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