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Tools

We are developing systems for live imaging of plant processes. We develop new substrate that facilitate observation of roots and apply a range of imaging techniques to make quantitative measurements. We have developed OPT and biospeckle imaging systems dedicated to imaging plant root growth. The system will allow accurate acquisition of root morphology, gene expression and protein targetting data to be collected during a live experiment.

Image of a rootWe collaborate with Dr Mike MacDonald (University of Dundee) to develop Single Plane Illumination Method dedicated to root imaging and with Professor Roberto Braga (Federal University of Lavras).

We are constructing a variety of computational tools for extracting quantitative information from live experiments and to analyse the behaviour of developmental biological systems.

Archiroot: Archiroot is a tool dedicated to the measurement and visualisation of whole plant architecture.

ImageJ Balloon Segmentation plugin: This ImageJ 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.

Simul3R: simul3R is a simple Matlab© programme designed to simulate root architectures using elementary branching and expansion functions

CellModeller2: is a C++ / python platform dedicated to multicellular computations (modelling, simulation, analysis, visualisation).

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.

Root imaging sequence

Research

Areas of Interest


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The James Hutton Research Institute is the result of the merger in April 2011 of MLURI and SCRI. This merger formed a new powerhouse for research into food, land use, and climate change.