Environmental Microscopy

Discover how environmental microscopes could reveal the life of biological organisms in soil. The study exploits recent advances in transparent soils, mesofluidics, and light-sheet imaging. More details here (Liu et al 2021)



Estimation of bacterial attachement rate

The colonisation of plant roots by bacteria is affected by a range of factors. Bacterial use chemotaxis to sense root exudates and migrate toward sources of nutrients released by the roots. Such behaviours have been well studies for a range of rhizobacteria. What happens following contact between plant roots and bacteria is less well quantified. Estimation of the attachement rate of bacteria on plant roots is a difficult parameter to establish in experimentally because it is almost impossible to tracking the movement of bacteria in soil . We have recently developped a mathematical framwork to estimate the attachement rate and growth rate of Pseudomonas fluorescens. using standard colonisation assays. Details can be found here (Caroll et al 2020)



Helical patterns in root trajectories


Root  interact with the soil environment in complex ways. We propose a series of tools to mine for patterns in the trajectories of roots. First, we propose an ImageJ plugin for direct fitting of root trajectory on a series of tomographic projection data termed MultiplaneTracking. We also propose a series of tools to extract both the frequency and radius of the Helical patterns present in the root trajectory, bot also to identify sites where the root is deflected from its trajectory, for example due to interaction with the granular media. You can access such tools using this link. (Dupuy)





Phosphatase activity tracer


Zymography is a powerful techniques to quantify phosphatase activity along the root using quantitative imaging. This page provides an imageJ plugin that extract the profiles of phosphatase activity along the root. The plugin is initiated with a coarse outline of the root centerline. An algorithm is then used to refine the position of the centerline along the root. The profile of activity is then extracted perpendicular to the centerline and exported as a CSV file. Python scripts are also provided to post-proces the data. scripts consists of an optimisation algorithm to find the enter of the root more accurately but also the fitting of models to extract key features of the profile. (Dupuy)


 Software for root phenotyping

(Dupuy et al)This page provides various tools to manage and analyse root phenotyping data.


rootgame screenshot

The root game

Like a challenge? Try to see if you can be a good root and capture water, nitrogen, phosphorus from the soil, and also break through hard layer of soil. This is the RootGame! Imagine you are driving a root growing in soil trying to get as many soil goodies as you can. But be carefully, it's not how much you are getting that matters, but how healthy and balance your diet is!



Model based root phenotyping

This page provides various tools to obtain root growth parameters from root growth data.

(Kalogiros et al)


Transparent Soil

Lettuce root grown in transparent soil

Understanding of soil processes is essential for addressing the global issues of food security, disease transmission and climate change. However, techniques for observing soil biology are lacking. This page provide some information on newly developped Transparent Soil. The material provide substrate for root, bacteria and other soil organisms that is heterogeneous, porous, transparent and suitable for live in situ 3D imaging. THe material is constructed from particles of the transparent polymer, Nafion, and a solution with matching optical properties. We also use minerals and fluorescent dyes that are adsorbed onto the Nafion particles for nutrient supply and imaging of pore size and geometry. 

(L. Dupuy and H. Downie)


rhizobact3Colonisation of the root tip by bacteria

Bacteria are ubiquitous to the root environment, but it is unclear how bacterial communities establish along the root. This model describes how bacteria establish and maintain at the of tip of the root. The model use Smoothed Particle Hydrodynamics to simulate the flow of bacteria along the root. This page provide the source code for the simulation tool as well as an executable that allows exploration of model behaviour Rhizobact.
(Dupuy and Silk)


Assemble a root phenotyping plateform with flatbed scanners

This page gives a short description of how to build your own root phenotyping plateform using scanners. It provides also some programs to run the scanners and analyse the images.
(Adu et al)


RhizoCamIconHow to build your own Rhizotron Camera

Equipment for carrying out rhizontron imaging is sometime expansive and not very modular. This page gives a short description of how to build your own Rhizotron Camera using webcams. The instrument is cheap, easy to assemble and scripts are provided as example of how to control the webcam with python



Model of the developpment of root systems are often based on architecutral model and the simulation of thousands of meristems simultaneously. Here we propose to represent the growth of root systems using PDEs that describe the dynamics of the density distribution of root apical meristems. MWaves is a python program that simulate the dynamics of root meristems distribution in soil. It uses the finite volume method to solve the equations of conservation of the meristem quantities.



ImageJ Balloon Segmentation pluginballoonplugin root

This ImageJ Balloon Segmentation plugin has been developed to extract cell architectures from live imaging datasets. It uses a physical "balloon inflation" algorithm for finding the cell boundaries from RGB images.

(Author: L. Dupuy)


SimulDens is a MatlabĀ© program that reconstruct root architectures from mappings of branching density. This program was developed to show that plant architectural processes can be represented by continuous variable, as an alternative to representing explicitly the whole network of interconnected branches.




CellModeller is python module for 2D multicellular analysis and computing. It consist fundamentally of a generic data structure (multiscale graph representation) and elementary methods or operations to both query and modify such objects (e.g get the neighbour of a cell or modify the concentration of its
constituents). The behaviour and properties of each entity in the structure (vertex, wall, cell ...) can be controlled through user specified models, using python scripting language.

(Dupuy and Mackenzie)



simul3R is a simple MatlabĀ© program designed to simulate root architectures using elementary branching and expansion functions.



Archiroot logoArchiroot

Archiroot is a simple free software for the measurment and visualisation of root architecture. It uses simple measurment of root angle and length to reconstruct complete 3D architectures.

(Author: L. Dupuy)


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