Root interact with the soil environment in complex ways. We propose a series of tools to mine for patterns in the 3D trajectories of roots.

 

MultiplaneTracking

We propose an ImageJ plugin for direct fitting of root trajectory on a series of tomographic projection data termed MultiplaneTracking. The algorithm is first initiated with a corse tracing that has either been done manually or with existing tools. We used the the Vessel tracking from MeVisal

 

RootHix

The root centrelines were analysed as analogue 3 dimensional signals to extract both the frequency and radius of the Helical patterns present in the root trajectory. First, the background noise of the signal was obtained using a spline regression with 3 anchor points. The background noise was then removed from the raw signal, which resulted in root tracings being centred along the z-axis (Supplementary Information). Centred signals were then analysed for periodic features, and in particular for helical periodicity. The analysis was based on a modification of the Fourier transform that use a set of orthonormal helix forming basis functions. A custom software tool termed RootHix was developed to perform such tasks. Software tools for analysis of root centreline are freely available on GitHub https://github.com/LionelDupuy/RootHix. The repository contains also sample files of lentils roots growing in transparent soil under vairous levels of compression

Detailed information on the mathematical transform used to extract the coefficients of the helix can be found here.