title: Extracting multiple interacting root systems using X-ray microcomputed tomography.
abstract: Root system interactions and competition for resources are active areas of research that contribute to our understanding of how roots perceive and react to environmental conditions. Recent research has shown this complex suite of processes can now be observed in a natural environment (i.e. soil) through the use of X-ray microcomputed tomography (μCT), which allows non-destructive analysis of plant root systems. Due to their similar X-ray attenuation coefficients and densities, the roots of different plants appear as similar greyscale intensity values in μCT image data. Unless they are manually and carefully traced, it has not previously been possible to automatically label and separate different root systems grown in the same soil environment. We present a technique, based on a visual tracking approach, which exploits knowledge of the shape of root cross-sections to automatically recover from X-ray μCT data three-dimensional descriptions of multiple, interacting root architectures growing in soil. The method was evaluated on both simulated root data and real images of two interacting winter wheat Cordiale (Triticumaestivum L.) plants grown in a single soil column, demonstrating that it is possible to automatically segment different root systems from within the same soil sample. This work supports the automatic exploration of supportive and competitive foraging behaviour of plant root systems in natural soil environments.
authors.affiliation: School of Computer Science, University of Nottingham, Jubilee Campus, Nottingham, NG8 1BB, UK.|Centre for Plant Integrative Biology, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK.
authors.forename: Stefan
authors.initials: S
authors.lastname: Mairhofer
authors.affiliation: Centre for Plant Integrative Biology, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK.|School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK.
authors.forename: Craig J
authors.initials: CJ
authors.lastname: Sturrock
authors.affiliation: Centre for Plant Integrative Biology, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK.|School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK.
authors.forename: Malcolm J
authors.initials: MJ
authors.lastname: Bennett
authors.affiliation: Centre for Plant Integrative Biology, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK.|School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK.
authors.forename: Sacha J
authors.initials: SJ
authors.lastname: Mooney
authors.affiliation: School of Computer Science, University of Nottingham, Jubilee Campus, Nottingham, NG8 1BB, UK.|Centre for Plant Integrative Biology, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK.
authors.forename: Tony P
authors.initials: TP
authors.lastname: Pridmore
mesh_terms: D003198:Computer Simulation; D007091:Image Processing, Computer-Assisted; D018517:Plant Roots / Q000033:anatomy & histology* / Q000254:growth & development; D012984:Software; D014908:Triticum / Q000033:anatomy & histology / Q000254:growth & development; D055114:X-Ray Microtomography / Q000379:methods*
keywords: X-ray computed tomography; multiple target tracking; root system interaction; technical advance