Guillaume Lobet


I am a FNRS post-doc researcher at the Université de Liège, in Belgium, in the Plant Physiology lab of Pr. Claire Perilleux.

The aim of my current project is to quantify the growth and developmental regulations (allometry) between the root and the shoot in the model plant maize. The project focuses on the events occurring before and after the floral transition.

I develop image analysis and phenotyping tools to help researchers in their scientific workflow. And when I am not implementing image analysis tools, I often play with plant models.

Apart from my daily research activity, I love to reference plant image analysis software and funny plant genes names.

An overview of my research vision can be found in this presentation.

At the moment, I am also a Guest Editor for a Plant Phenomics serie for the journal GigaScience.

About me

guillaume.lobet [at]

Université de Liège
Bât. B22 Physiologie végétale Quartier Vallée 1 Chemin de la Vallée 4 4000 Liège 1 Belgium

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Plant Image Analysis
The Topless Ninja

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The AlloMaize project aims at quantifying the growth and developmental regulations (allometry) between the root and the shoot in the model plant maize (Zea mays). The project focuses on the events occurring before and after the floral transition. As this stage occurs late in the plant development, the size of the different organs, in particular that of the root system, hinder their observation and analysis. Very little information about the root system exists at these stages.

Flowering Interactive Database - FLOR-ID

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The transition to flowering is an essential step of the plant life cycle that is tightly controlled by both endogenous and environmental cues. Its regulation is extremely complex and involves hundreds of genes that are part of highly interconnected pathways. We are currently building a new web-based interactive resource organized around a curated database of the flowering time genes, FLOR-ID. This project is a collaboration with Fred Bouché. Article about the database here (in french) and here (Flowering Highlights).

Root System Markup Language

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Together with researchers from INRIA, CPIB, Juelich, Vienna and Louvain, we created the Root System Markup Language (RSML) that has been designed to alleviate two major bottlenecks: (i) to enable portability of root architecture data between different software tools in an easy and interoperable manner allowing seamless collaborative work, and (ii) to provide a standard format upon which to base central repositories which will soon arise following the expanding worldwide root phenotyping effort. External Diffusion post


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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.

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The Plant Image Analysis website is an online, manually curated, database referencing more than 130 plant image analysis software solutions. The website presents each software in a uniform and concise manner enabling users to identify the available solutions for their experimental needs. The website also enables user feedback, evaluations and new software submissions. The aim of such a toolbox is to help users to find solutions, and to provide developers a way to exchange and communicate about their work.


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GLO-Root Image Analysis (GLO-RIA) is project in collaboration with Ruben Rellan-Alvarez and José Dinneny. It aims at developping imaging solution for the GLO-Root setup. The originality of the project is that it explicitelly combines the informations coming from different channels (soil, structure, reporters). A visualisation of the GLO_Root results is available here. Press release here

Rhizoponic growing setup

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Rhizoponics is an innovative design of hydroponic rhizotrons adapted to Arabidopsis thaliana. The setup allows to simultaneously characterize the RSA and shoot development from seedling to adult stages, i.e. from seed to seed. This system offers the advantages of hydroponics such as control of root environment and easy access to the roots for measurements or sampling. Being completely movable and low cost, it can be used in controlled cabinets.

Modelling tomato inflorescence

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Two recently proposed models help to comprehend the development of the tomato inflorescence, based on the fact that the arrangement of flowers reflects the spatiotemporal balance between maintenance of meristem indeterminancy and acquisition of floral meristem identity. In the model of Prusinkiewicz et al. (2007), an inflorescence is built from meristems that lose their initial « vegetativeness » to become flowers. In the model proposed by Lippman et al. (2008), the branching of the inflorescence depends on the maturation rate of the IM towards FM fate. We combined these two concepts for modelling the tomato inflorescence and gain further insight into the dynamics of the genetic network controling meristem fate.


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The water uptake capacity of a plant is largely influenced by (i) soil exploration (root architecture), (ii) hydraulic conductivity of individual root segments, (iii) quantity and capacity of bulk-to-rhizosphere water flow, and (iv) regulation of stomatal conductance. These factors must be considered simultaneously if we aim to tailor plants towards improved water deficit resistance. PlaNet-Maize is a functional-structural plant model which encompasses the entire soil-plant-atmosphere continuum with a resolution down to individual root segment. The model simulates individual maize plant growth and development, along with water uptake.

Water relations in the soil-plant system

Observing the water flows in the soil-plant system is challenging by nature. Until recently, the techniques used were mainly based on averaged estimation of the soil water content variation, down to the plant level. However, in the past few years, new methods have been developed which enabled a more precise observation of the water flows in the soil-plant system. In order to decrypt the water dynamics in the SPAC, we combined several phenotyping tools into a small platform. The platform enables the in-situ observation of plant architecture (both root and shoot), plant water status and soil water content.

Science Valorisation

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For decades, the only way to valorise one’s research was to publish a manuscript in a peer-reviewed journal. While the paper is still the golden standard for scientific productivity, it is not the only one anymore. Nowadays, researchers have access to a wide variety of means to valorise their research.


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PaperFlow display your publications in a network fashion, trying to make sense of your scientific journey.

Impact CV

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Impact-CV is a small web-based widget that create a CV (or a .bib file) based on an ImpactStory profile.


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Coming soon..

LaTeX thesis template

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LaTeX template for a master/PhD thesis. It is based on the template developed by Eivind Uggedal (available here) and was modified by myself.

Peer-review articles

  • Number of articles: 16
  • As first/last author: 10
  • Scopus h-index: 7
  • Number of citations: 225

Journal names were intentionally left blank. Last update on 2016-04-25.

Integrating roots into a whole plant network of flowering time genes in Arabidopsis thaliana - 2016
Bouché F, D Alioa M, Tocquin P, Lobet G, Detry N, Périlleux C

Environmental Control of Root System Biology - 2016
Rellan-Alvarez R*, Lobet G*, Dinneny J

FLOR-ID, an interactive database of flowering-time gene networks in Arabidopsis thaliana - 2015
Bouché F*, Lobet G*, Tocquin P and Périlleux C

archiDART, an R package for the automated 2D computation of plant root architectural traits - 2015
Delory B, Baudson C, Brostaux Y, Lobet G, du Jardin P, Pagès L and Delaplace P

GLO-Roots, an imaging platform enabling multidimensional characterization of soil grown root systems - 2015
Rellán-Álvarez R, Lobet G, Hildner H, Pradier PL, Sebastian J, Yee C, Yu G, LaRue T, Trontin C, Nieu R, Vogel J and Dinneny J

Root System Markup Language. Toward an unified root architecture description language - 2015
Lobet G, Pound MP, Diener J, Pradal C, Draye X, Godin C, Javaux M, Leitner D, Meunier F, Nacry P, Pridmore TP and Schnepf A

Rhizoponics, a novel hydroponic rhizotron for root system analyses on mature Arabidopsis thaliana plants - 2015
Mathieu L*, Lobet G*, Tocquin P and Périlleux C

Inflorescence architecture in tomato genes functions within a zigzag model - 2014
Périlleux C*, Lobet G* and Tocquin P

Plant Water Uptake in Drying Soils - 2014
Lobet G, Couvreur C, Meunier F, Javaux M and Draye X

A modeling approach to determine the importance of dynamic regulation of plant hydraulic conductivities on the water uptake dynamics in the soil-plant-atmosphere system - 2014
Lobet G, Pagès P and Draye X

Comparative analysis of Cd and Zn impacts on root distribution and morphology of Lolium perenne and Trifolium repens. Implications for phytostabilization - 2014
Lambrechts T, Lequeue G, Lobet G, Godin B, Bielders CL and Lutts S

Root Systems Biology. Bridging regulatory networks to rhizosphere-scale processes - 2013
Hill K, Porco S, Lobet G, Zappala S, Mooney S, Draye X and Bennett MJ

An online database for plant image analysis software tools - 2013
Lobet G, Draye X and Périlleux C

Novel scanning procedure enabling the vectorization of entire rhizotron-grown root systems - 2013
Lobet G and Draye X

A Novel Image Analysis Toolbox Enabling Quantitative Analysis of Root System Architecture - 2011
Lobet G, Pagès L and Draye X

Model-assisted integration of physiological and environmental constraints affecting the dynamic and spatial patterns of root water uptake from soils - 2010
Draye X, Kim YX, Lobet G and Javaux M

Book chapters - thesis

Root water uptake and water flow in the soil-root domain - 2013
Lobet G, Hachez C, Chaumont F, Javaux M and Draye X
Plant Roots, The Hidden Half, 4h edition,

Regulation of water flow in the soil-root domain. New tools and methods. - 2012
Lobet G
Université catholique de Louvain


Root phenotyping data - 2016
Bouché F, D Alioa M, Tocquin P, Lobet G, Detry N, Périlleux C

Maize root emergence - 2015
Lobet G

Rhizotron blueprints - 2012
Lobet G, Draye X

Presentations | view figshare profile

15 - Open Science. A view from the Bench - Feb 2016
Open Belgium Conference, Antwerpen, Belgium

14 - Science Valorisation - Nov 2015
Communiquer sa recherche, ULB, Brussels, Belgium

13 - Structural Root Modelling - Nov 2015
Winter School on Root Phenotyping, Jülich, Germany

12 - Science Valorisation - Jul 2015
Let's Talk Science, Leuven, Belgium

11 - FLOR-ID, an interactive database of flowering gene network in Arabidopsis - Jun 2015
Workshop on Mechanisms Controling Flower Development, Aiguablava, Spain

10 - Plant Image Analysis tools. Current trends and limitations - Apr 2015
Plant Image Analysis Problems and Solution - Madison, Misconsin

9 - Introducing Root System Markup Language - Apr 2015
Modeling plant development from the organ to the whole plant scale - Montpellier

8 - Water relations in the SPAC. What can we learn from functional-structural plant models - Dec 2014
Soil Science Society Belgium - Brussels

7 - Water relations in the soil-plant system. What can we learn from functional-structural plant models - Oct 2014
BASF Top Science Meeting -

6 - Plant Image Analysis tools. Current trends and limitations - Sep 2014
International workshop on Image analysis methods for the plant sciences - Aberythwyth

5 - Modelling water relations in the soil-plant-atmosphere system - Jul 2014
SEB Main Meeting - Manchester

4 - Inflorescence development in tomato. Gene functions within a zigzag model. - Mar 2014
Genetic Variation of Flowering Time Genes and Applications for Crop Improvement - Bielefeld

3 - First steps towards an explicit modeling of aba production and translocation in relation with the water uptake dynamics - Jun 2013
9th International Workshop on Sap Flow - Ghent

2 - A Novel Image Analysis Toolbox Enabling Quantitative Analysis of Root System Architecture. - Sep 2012
International Workshop on Image Analysis Methods for Plant Science - Nottingham

1 - New insights on the role of root radial conductivity on the overall uptake dynamics - Apr 2011
Roots for improving resource acquisition in crops - Grasmere, UK


ImpactStory advisor

ImpactStory is a web-based service that allow researchers to create a profile referencing all their research impact. [My ImpactStory profile]

Ad hoc referee

Plant Physiology, PLoS One, Journal of Experimental Botany, Plant and Soil, Functional Plant Biology, Plant Methods, Annals of Botany, Microscopy and Microanalysis, Plant Signaling and Behavior, Journal of Hydrology, Journal of Visualized Experiments. [My reviewer profile].

Guest Editor

Invited Guest Editor for the Plant Phenomics serie from GigaScience

Scientific meeting organisation

Research advisor

  • 1 PhD student - 6 master theses


Website design and creation

My failures

This is my list of failures. Being a scientist is not always easy and sometimes (often?) what you try does not work, for various reasons. But your failures are, at least, as important as your successes, as they make you think harder about yourself and your work! So, I decided to be proud of them!

The list below is still short, but I am confident it will flourish with time :)

Full disclosure, the idea is not from me and you can read more about it here.

What referees (anonymous) have said about my work

  • (this paper is) neither research nor science
  • (this paper is) not rocket science
  • (his research is) solid, but neither excellent nor innovative

Paper rejections from academic journals

  • 2015: The Plant Cell, Development, Nature Plants,
  • 2016: New Phytologist,

Grants I did not get

  • Helmholtz Young Investigator Group - 2015
  • Fulbright Fellowship - 2012