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

ABSTRACT 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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Available from: Susan Zappala, Sep 29, 2015
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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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    • "In the case of pots, expensive magnetic resonance imaging technologies represent one noninvasive approach to capture highresolution details of root architecture (Schulz et al., 2013), similar to the capabilities of x-ray microcomputed tomography (mCT) systems. X-ray systems allow capturing of the root architecture at a fine scale in containers with a wide variety of soil types (Mairhofer et al., 2012; Mooney et al., 2012). It has been shown that x-ray mCT paired with specifically designed algorithms has sufficient resolution to recover the root structure in many cases (Mairhofer et al., 2013). "
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    ABSTRACT: Current plant phenotyping technologies to characterize agriculturally relevant traits have been primarily developed for use in laboratory and/or greenhouse conditions. In the case of root architectural traits, this limits phenotyping efforts, largely, to young plants grown in specialized containers and growth media. Hence, novel approaches are required to characterize mature root systems of older plants grown under actual soil conditions in the field. Imaging methods able to address the challenges associated with characterizing mature root systems are rare due, in part, to the greater complexity of mature root systems, including the larger size, overlap and diversity of root components. Our imaging solution combines a field imaging protocol and algorithmic approach to analyze mature root systems grown in the field. Via two case studies, we demonstrate how image analysis can be utilized to estimate localized root traits that reliably capture heritable architectural diversity as well as environmentally induced architectural variation of both monocot and dicot plants. In the first study we show that our algorithms and traits (including 13 novel traits inaccessible to manual estimation) can differentiate nine maize genotypes 8 weeks after planting. The second study focuses on a diversity panel of 188 cowpea genotypes to identify which traits are sufficient to differentiate genotypes even when comparing plants whose harvesting date differs up to 14 days. Overall, we find that automatically derived traits can increase both the speed and reproducibility of the trait-estimation pipeline under field conditions.
    Plant physiology 09/2014; DOI:10.1104/pp.114.243519 · 6.84 Impact Factor
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