Three dimensional imaging of plant roots in situ with X-ray Computed Tomography

Heeraman, D. A.; Hopmans, Jan W.; Clausnitzer, V.

doi:10.1023/b:plso.0000009694.64377.6f

Cited by 145 publications

(129 citation statements)

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“…For plants grown in soil, x-ray CT techniques and magnetic resonance imaging (Heeraman et al, 1997;Nagel et al, 2009;Tracy et al, 2010;Lucas et al, 2011;Zhu et al, 2011) have recently increased our capabilities to visualize root system architecture in situ nondestructively. For example, the x-ray CT technique can be used to study root architectures under varying nutrient, moisture, temperature, and soil density conditions in a physiologically relevant way over time.…”

Section: How To Image Root Systems?mentioning

confidence: 99%

“…As mentioned above, this can be downscaled using x-ray CT, although the low-throughput and sample size:resolution trade-off remain a constraint . Less extensively, magnetic resonance imaging has been used in a similar way to study root architecture in situ, as has neutron tomography (Heeraman et al, 1997). In all these approaches, however, cost, effort, the limited throughput, and accessibility (e.g., limited availability of synchrotron beam time for neutron tomography) are still major drawbacks.…”

Section: Root System Architecture In the Soilmentioning

confidence: 99%

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Analyzing Lateral Root Development: How to Move Forward

et al. 2012

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Roots are important to plants for a wide variety of processes, including nutrient and water uptake, anchoring and mechanical support, storage functions, and as the major interface between the plant and various biotic and abiotic factors in the soil environment. Therefore, understanding the development and architecture of roots holds potential for the manipulation of root traits to improve the productivity and sustainability of agricultural systems and to better understand and manage natural ecosystems. While lateral root development is a traceable process along the primary root and different stages can be found along this longitudinal axis of time and development, root system architecture is complex and difficult to quantify. Here, we comment on assays to describe lateral root phenotypes and propose ways to move forward regarding the description of root system architecture, also considering crops and the environment.Root system architecture is a key determinant of nutrient and water use efficiency and describes, on a macro scale, the organization of the primary root and root-and stemderived branches where they are present in monocots and dicots (Hochholdinger et al., 2004;De Smet et al., 2006;Hochholdinger and Zimmermann, 2008;Pé ret et al., 2009;Coudert et al., 2010

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Section: How To Image Root Systems?mentioning

confidence: 99%

Section: Root System Architecture In the Soilmentioning

confidence: 99%

Analyzing Lateral Root Development: How to Move Forward

et al. 2012

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“…Imaging techniques for the visualization of soilgrown root systems in two and three dimensions include x-ray computed tomography (Heeraman et al, 1997;Tracy et al, 2010;Mooney et al, 2012), neutron radiography (NR; Oswald et al, 2008), and magnetic resonance imaging (Pohlmeier et al, 2008). NR is one of the most suitable techniques to investigate roots grown in soil, because it allows a high throughput, provides a strong contrast between roots and soil, and therefore requires little effort for image processing.…”

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confidence: 99%

Recovering Root System Traits Using Image Analysis Exemplified by Two-Dimensional Neutron Radiography Images of Lupine

et al. 2013

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Root system traits are important in view of current challenges such as sustainable crop production with reduced fertilizer input or in resource-limited environments. We present a novel approach for recovering root architectural parameters based on imageanalysis techniques. It is based on a graph representation of the segmented and skeletonized image of the root system, where individual roots are tracked in a fully automated way. Using a dynamic root architecture model for deciding whether a specific path in the graph is likely to represent a root helps to distinguish root overlaps from branches and favors the analysis of root development over a sequence of images. After the root tracking step, global traits such as topological characteristics as well as root architectural parameters are computed. Analysis of neutron radiographic root system images of lupine (Lupinus albus) grown in mesocosms filled with sandy soil results in a set of root architectural parameters. They are used to simulate the dynamic development of the root system and to compute the corresponding root length densities in the mesocosm. The graph representation of the root system provides global information about connectivity inside the graph. The underlying root growth model helps to determine which path inside the graph is most likely for a given root. This facilitates the systematic investigation of root architectural traits, in particular with respect to the parameterization of dynamic root architecture models.

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“…Of these, HRCT and SRXTM are the most useful methods to visualize both internal and external morphology and anatomy in a noninvasive and nondestructive manner, and are useable for a range of specimen sizes. HRCT has been used in plant sciences to examine structure and morphology of extant flowers and fruits (1; see also the Digital Morphology digital library of the University of Texas at Austin, www.digimorph.org), density of extant woods (2,3), spatial distribution of root systems (4)(5)(6), and light interception of the tree canopy (7,8). In paleobotany, CT has been used in a few cases to reveal internal structures, including in Paleozoic charophytes (9), silicified Cycadeoidea stems and Araucaria mirabilis cones from the Jurassic (10), an undescribed Cretaceous gymnosperm fructification (11,12), a Paleogene hymenophyllaceous fern rhizome (13), and Eocene myrtaceous fruits (14).…”

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confidence: 99%

Virtual taphonomy using synchrotron tomographic microscopy reveals cryptic features and internal structure of modern and fossil plants

Smith

Collinson

Rudall

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

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While more commonly applied in zoology, synchrotron radiation X-ray tomographic microscopy (SRXTM) is well-suited to nondestructive study of the morphology and anatomy of both fossil and modern plants. SRXTM uses hard X-rays and a monochromatic light source to provide high-resolution data with little beam-hardening, resulting in slice data with clear boundaries between materials. Anatomy is readily visualized, including various planes of section from a single specimen, as clear as in traditional histological sectioning at low magnifications. Thus, digital sectioning of rare or difficult material is possible. Differential X-ray attenuation allows visualization of different layers or chemistries to enable virtual 3-dimensional (3D) dissections of material. Virtual potential fossils can be visualized and digital tissue removal reveals cryptic underlying morphology. This is essential for fossil identification and for comparisons between assemblages where fossils are preserved by different means. SRXTM is a powerful approach for botanical studies using morphology and anatomy. The ability to gain search images in both 2D and 3D for potential fossils gives paleobotanists a tool-virtual taphonomy-to improve our understanding of plant evolution and paleobiogeography.anatomy ͉ morphology ͉ palaeobotany ͉ synchrotron radiation X-ray tomographic microscopy V arious methods now exist for visualizing plant material in 3-dimension (3D). Confocal laser-scanning microscopy, electron tomography, and optical coherence microscopy are used for imaging thin (often sectioned) and (semi-)transparent material (1), in conjunction with modern computer programs for 3D reconstruction. Complementing this, other techniques for examining larger specimens or to avoid sectioning ''difficult'' material include neutron imaging, nuclear magnetic resonance (NMR) imaging, X-ray computed tomography (CT), highresolution X-ray computed tomography (HRCT), and synchrotron radiation X-ray tomographic microscopy (SRXTM). Of these, HRCT and SRXTM are the most useful methods to visualize both internal and external morphology and anatomy in a noninvasive and nondestructive manner, and are useable for a range of specimen sizes. HRCT has been used in plant sciences to examine structure and morphology of extant flowers and fruits (1; see also the Digital Morphology digital library of the University of Texas at Austin, www.digimorph.org), density of extant woods (2, 3), spatial distribution of root systems (4-6), and light interception of the tree canopy (7,8). In paleobotany, CT has been used in a few cases to reveal internal structures, including in Paleozoic charophytes (9), silicified Cycadeoidea stems and Araucaria mirabilis cones from the Jurassic (10), an undescribed Cretaceous gymnosperm fructification (11, 12), a Paleogene hymenophyllaceous fern rhizome (13), and Eocene myrtaceous fruits (14).Recently, SRXTM has become increasingly used in biology, especially in paleontology (e.g., 15-20; see ref. 19 for comparative review of the various methods mentioned...

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Three dimensional imaging of plant roots in situ with X-ray Computed Tomography

Cited by 145 publications

References 0 publications

Analyzing Lateral Root Development: How to Move Forward

Analyzing Lateral Root Development: How to Move Forward

Recovering Root System Traits Using Image Analysis Exemplified by Two-Dimensional Neutron Radiography Images of Lupine

Virtual taphonomy using synchrotron tomographic microscopy reveals cryptic features and internal structure of modern and fossil plants

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