RooTrak: Automated Recovery of Three-Dimensional Plant Root Architecture in Soil from X-Ray Microcomputed Tomography Images Using Visual Tracking

Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, United Kingdom.
Plant physiology (Impact Factor: 6.84). 12/2011; 158(2):561-9. DOI: 10.1104/pp.111.186221
Source: PubMed


X-ray microcomputed tomography (μCT) is an invaluable tool for visualizing plant root systems within their natural soil environment noninvasively. However, 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 data recovery. We report the development of automatic root segmentation methods and software that view μCT data as a sequence of images through which root objects appear to move as the x-y cross sections are traversed along the z axis of the image stack. Previous approaches have employed significant levels of user interaction and/or fixed criteria to distinguish root and nonroot material. RooTrak exploits multiple, local models of root appearance, each built while tracking a specific segment, to identify new root material. It requires minimal user interaction and is able to adapt to changing root density estimates. The model-guided search for root material arising from the adoption of a visual-tracking framework makes RooTrak less sensitive to the natural ambiguity of x-ray attenuation data. We demonstrate the utility of RooTrak using μCT scans of maize (Zea mays), wheat (Triticum aestivum), and tomato (Solanum lycopersicum) grown in a range of contrasting soil textures. Our results demonstrate that RooTrak can successfully extract a range of root architectures from the surrounding soil and promises to facilitate future root phenotyping efforts.

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    • "The root system descriptions recovered from the experiment performed on the simulated roots is shown in Figure 3. On the left side of each pair is the result obtained using the original extraction method (Mairhofer et al. 2012), while on the right side the proposed mechanism was activated each time it was triggered by two interacting targets. In samples 1-12 there were a total of 3, 2, 2, 4, 1, 1, 2, 2, 3, 3, 2, 1 interactions respectively, interactions were of varying duration with varying degrees of overlap between objects. "
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    ABSTRACT: Root system interaction and competition for resources is an active research area that contributes to our understanding of roots' perception and reaction 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 micro Computed 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 previously not 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 3D descriptions of multiple, interacting root architectures growing in soil from X-ray μCT data. 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. This article is protected by copyright. All rights reserved.
    The Plant Journal 10/2015; DOI:10.1111/tpj.13047 · 5.97 Impact Factor
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    • "However, recent advances in three dimensional (3D) imaging technology such as ground penetrating radar, laser imaging, nuclear magnetic resonance imaging (MRI), neutron radiography (NT), and X-ray computed tomography (CT) have made the observation of undisturbed root systems possible (Macfall et al., 1991; Butnor et al., 2001; Gregory et al., 2003; Kaestner et al., 2006; Perret et al., 2007; Tracy et al., 2010; Moradi et al., 2011; Mairhofer et al., 2012). Innovations in software such as Rootviz, Root track (Tracy et al., 2010; Mairhofer et al., 2012), RootReader3D (Clark et al., 2011), and Avizo (Saoirse et al., 2010), and specific filtering algorithms (Perret et al., 2007) have helped improve 3D image resolution and stream-line the quantification of anatomical parameters such as lateral root length, lateral root number, root-system surface area, and volume of undisturbed root systems. However, accurately isolating roots from root-soil data is complicated by the continuum of water within the root itself, at the root-soil interface, and between soil particles (Lontoc-Roy et al., 2006). "
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    ABSTRACT: Research in the field of plant biology has recently demonstrated that inter- and intra-specific interactions belowground can dramatically alter root growth. Our aim was to answer questions related to the effect of inter- vs. intra-specific interactions on the growth and utilization of undisturbed space by fine roots within three dimensions (3D) using micro X-ray computed tomography. To achieve this, Populus tremuloides (quaking aspen) and Picea mariana (black spruce) seedlings were planted into containers as either solitary individuals, or inter-/intra-specific pairs, allowed to grow for two months, and 3D metrics developed in order to quantify their use of belowground space. In both aspen and spruce, inter-specific root interactions produced a shift in the vertical distribution of the root system volume, and deepened the average position of root tips when compared to intra30 specifically growing seedlings. Inter-specific interactions also increased the minimum distance between root tips belonging to the same root system. There was no effect of belowground interactions on the radial distribution of roots, or the directionality of lateral root growth for either species. In conclusion, we found that significant differences were observed more often when comparing controls (solitary individuals) and paired seedlings (inter- or intra-specific), than when comparing inter- and intra-specifically growing seedlings. This would indicate that competition between neighboring seedlings was more responsible for shifting fine root growth in both species than was neighbor identity. However, significant inter- vs. intra-specific differences were observed, which further emphasizes the importance of biological interactions in competition studies.
    Frontiers in Plant Science 04/2015; 6. DOI:10.3389/fpls.2015.00274 · 3.95 Impact Factor
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    • "Automated software packages for root segmentation are becoming available. The most recent publically available Rootrak (Mairhofer et al. 2012) was tested extensively using our experimental set-up. However, compared to our segmentation and analysis protocols, we found the system sub-optimal. "
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    ABSTRACT: Background and aims Despite the recognised importance of root architecture to plant productivity, our ability to easily observe and quantify root responses to stresses in soil at appropriate mechanistic resolution, remains poor. In this study we examine the impact of P bands on root architecture in heterogeneous soil, trialling a rapid non-destructive analysis technique. Methods We examined fast (<5 min), high resolution (69 μm voxels) x-ray tomography (μCT) to non-destructively observe and quantify wheat (Triticum aestivum L.) roots in a repacked Oxisol, in 3D, with and without a band of P-enriched soil. Results We found that wheat roots displayed localised responses (were plastic) and responded with additional root length within the banded P fertiliser. The seedling root systems also altered 3D root architecture in the band by increasing the number and length of branch roots. Branch root angle was not altered by the P band. The spatial precision of the branching response was striking and raises questions concerning the root sensing and/or response mechanisms.
    12/2014; 385(1-2-1-2):303-310. DOI:10.1007/s11104-014-2191-9
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