Introducing Root System Markup Language, a new toolbox to link experimental data with simulation

<p>The number of image analysis tools supporting the extraction of architectural features of root systems and of explicit 3D root models has increased in recent years. We describe the Root System Markup Language (RSML), which has been designed to overcome two major challenges: (1) to enable portability of root architecture data between different software tools (modelling-imaging-data analysis) in an easy and interoperable manner, allowing seamless collaborative work; and (2) to provide a standard format upon which to base central repositories that will soon arise following the expanding worldwide root phenotyping effort. RSML follows the XML standard to store two- or three-dimensional 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 scale at one or several time points. Plant ontologies are used to describe botanical entities that are relevant at the scale of root system architecture. An XML schema describes the features and constraints of RSML, and open-source packages have been developed in several languages (R, Excel, Java, Python and C++) to enable researchers to integrate RSML files into popular research workflow.</p

Structural Root Modelling

<p>Presentation on structural root modelling. </p

Image of random root systems

Image of random root system

Science Valorisation

<p>Lab presentation presenting the different tools to valorise science outputs. Featuring ImpactStory, Altmetrics, figshare and many others</p> <p> </p> <p>[Updated on November 19th 2015]</p

Benchmarking in image analysis tools: a tale of caution

How we should be careful when using automated image analysis pipeline

Open Science: A view from the Bench

<div>My personal views on open science. About open data, open code and open pubiblishing.</div><div><br></div>Presentation for the Open Belgium Conference in 2016

Scans of maize root systems grown in rhizotrons

Scans of maize root systems grown in rhizotron

Simulated dicot root systems

Library of simulated dicot root systems, with different architectural properties (genotypes). Each genotype was represented by 10 simulations. The different genotypes were based on a standard parameter set (mock) and had one parameter changed: growth rates (slow vs. fast), inter-lateral distances (dense vs sparse) or gravitropisms (steep vs shallow). <div><br></div><div>These root systems were used in web application: https://plantmodelling.shinyapps.io/archidart/</div

Rhizotron holder

Blueprint for a rhizotron holder to put in greenhouse. Cheap, easy to build and does not require much space

Picture of succulent plant

Succulent plant showing a nice leaf patterning in a Fibonacci spira