CROP, Combining ROot contrasted Phenotypes for more resilient agro ecosystem

The CROP project aims at estimating the beneficial impact of combining contrasted root phenotypes within a single field. We will evaluate the benefit of the combination of water, carbon and nitrogen flow, microbial communities, and yield. To achieve this goal, we will use a set of complementary experimental and modelling tools.


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.

CRootBox / CPlantBox

The focus of CRootBox is the simulation of different types of root architecture, and to provide a generic interface for coupling with soil/environmental models, e.g., in order to determine the impact of specific root architectures on function. CRootBox is currently being extended into a full plant model CPlantBox

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.


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.

Root System Markup Language | RSML

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.


archiDART is an R package that was developed for the automated analysis of plant root system architectures from Root System Markup Language (RSML) files. The package enable the extraction of morphological (length, diameters), dynamic (growth rates, tropisms) and topological (Fitter indices, persistent homology) traits.

Plant Illustrations

The aim of this figshare profile is to collect, in one place, illustrations and pictures of plants, roots, shoots, inflorescences, … All of the illustrations are made by researchers, for researchers. The ultimate goal is to be a resource for the plant science community.

Flowering Interactive Database - FLOR-ID

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).

Some random projects I did and maintain just for fun...

Topless Ninja

Website referencing fun plant gene names. Yes Plant biologists can be funny sometimes.

Conference Bingo

Shiny app to create bingo tables for scientific conferences (plant science theme and others)

Science podcast finder

Shiny app to find science podcast. Based on this article: Science podcasts: analysis of global production and output from 2004 to 2018, MacKenzie (2018), bioRxiv