Software Tools and Resources


img1 Canopy Reconstruction recovers accurate and useful models of plants in three dimensions from multiple colour images captured using a low-cost camera.


rsml_logo RootSystemML is a file format representing root architectural data. It has been designed to enable portability of root architecture data between different software tools and to provide a standard format upon which to base root architecture repositories.

rootnav RootNav is a software tool for quantification of root system architectures in a range of plant species, grown and imaged in a variety of ways. Measurements can be exported directly, or saved in a database, where additional traits can be calculated later using a simple plug-in system.

roottrace RootTrace is a tool providing automatic and high throughput measurements of root length and curvature, over time, from sequences of images of plated seedlings. RootTrace is available as open source from SourceForge and is supported by a series of novel image acquisition robots, detailed schematics of these machines are also publically available.

rootrak RooTrak is a tool for separating plant roots from soil in X-ray CT data. Variations in the X-ray attenuation values of root material and the overlap in attenuation values between roots and soil caused by water and organic materials represent major challenges to image segmentation. RooTrak can successfully extract a range of root architectures from the surrounding soil, providing automatic measurement of roots in their natural environment.

cell-o-tape CellSeT provides quantitative data on the geometric and radiometric properties of cell networks imaged using confocal laser microscopy. The global structure of the network is extracted and used to guide analysis of individual elements, providing greater robustness to local noise and imaging artefacts than previous approaches. CellSeT provides a rich framework for the molecular, cellular and tissue scale analysis of confocal images via its extensible plug-in architecture

cell-o-tape Cell-o-Tape is a tool to count and measure individual neighbouring cells along a defined file in confocal laser scanning microscope images. The tool builds on the raw data to detect a significant change in cell length along the file. This facility can be used, for example, to provide an estimate of the position of transition into the elongation zone of an Arabidopsis root, traditionally a location sensitive to the subjectivity of the experimenter.

psc-colocalization-plugin PSC Colocalization Plugin a protein colocalization plugin for ImageJ which calculates correlation coefficients over areas of interest and was created to support quantitative measurement of protein colocalisation in confocal laser microscope images.