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Visualizing three-dimensional root networks using Computed Tomography
Abstract
We describe a method to reconstruct the root network from a three-dimensional image generated with computed tomography. The X-ray absorption of roots and the interface of the air–soil material is very similar and the contrast extremely low. The method consists of three steps: contrast enhancement using a non-linear diffusion filter, thresholding based on Rosin's method and extraction of the main features using a morphological connectivity algorithm. With this approach, we are also capable of reconstructing fine roots with high fidelity, which is shown with a performance experiment using artificial images with increasing noise. The method is applied to an X-ray microtomography data set of two alder roots, grown for 4 months in a natural moraine soil. To simplify the soil material, the bare roots were transferred into a Plexiglas receptacle filled with quartz sand. The reconstructed image is compared with a photograph of the real roots.
... It is known that the plant root system is usually related to soil physical and chemical attributes, plant genetics and water content, so the roots has a fundamental importance in the interactions that occur between soil and living organisms (Costa et al., 2012;Mairhofer et al., 2012). In this way, the plant roots influence the stability, shape (roughness) and geometry (area) of soil aggregates, i.e., may interfere on the pores size and distribution, altering air-water, nutrient dynamics and protection of soil carbon (Kaestner, Schneebeli, & Graf, 2006;Carducci et al., 2014;Silva et al., 2013;Zinn, Lal, Bigham, & Resck, 2007). ...
... The low bulk density and high porosity values can be observed, even after three years of cultivation, yet in important to know that the management system conduct after 2014 was no-tillage system (Figure 1) Kohn et al., 2016;Stanck et al., 2017). This maintenance of the newly pores and structure alleviation in the past may be related to the presence of large volume of flaxseed roots, that acted by stabilizing the soil structure (Kaestner et al., 2006;Chen et al., 2018;Carducci et al., 2014) (Figures 3, 4 and 5). density and high porosity values can be observed, even after three years of cultivation, yet in important to know that the management system conduct after 2014 was no-tillage system (Figure 1) Kohn et al., 2016;Stanck et al., 2017). ...
... density and high porosity values can be observed, even after three years of cultivation, yet in important to know that the management system conduct after 2014 was no-tillage system (Figure 1) Kohn et al., 2016;Stanck et al., 2017). This maintenance of the newly pores and structure alleviation in the past may be related to the presence of large volume of flaxseed roots, that acted by stabilizing the soil structure (Kaestner et al., 2006;Chen et al., 2018;Carducci et al., 2014) (Figures 3, 4 and 5). The presence of larger aggregates with visible pores results in a better porosity (Figure 1, Table 3 and 4), which gives the roots a good development in length and volume occupying even the smallest pores spaces (Table 7; Figure 4) The presence of larger aggregates with visible pores results in a better porosity (Figure 1, Table 3 and 4), which gives the roots a good development in length and volume occupying even the smallest pores spaces (Table 7; Figure 4) agreeing with Kaestner et al. (2006) and Silva et al. (2016), who found in their studies a high spatial dependence on the roots growth and the pores system, although it is not yet clear scientifically the limits where one effect begins (roots) and the other ends (structure). ...
Our goal was to evaluate the root development of flaxseed and its relationship with soil aggregation and organic carbon storage in two sowing seasons under soil conservationist management, in Santa Catarina state, Brazil. We used three flaxseed genotypes: Aguará and Caburé from Argentina, and Gold from Brazil, sowings in April and May in a no-tillage system under Haplumbrept. In the flowering stage, the root system was evaluated by image analyze using a Safira software. Root distribution maps were used by geostatistical kriging. At the harvest stage, soil blocks were sampled for analyze the aggregates morphometry by image with Quantporo software and the soil organic carbon. Undisturbed soil were sampled to determine the physical attributes. The experimental design was in randomized blocks with three repetitions, anova was performed by Fisher and the means compared by Tukey test. No physical impediments were found for the roots performance in the Haplumbrept under conservationist management system, these favored the irregularity of the aggregates surface observed by the low values of aspect and roughness in the different tested diameter ranges. Both Caburé and Aguará genotypes showed good roots spatial distribution in the soil profile in both sowing seasons with an increase in carbon storage in the smallest diameter aggregates (here considered the aggregates of 4.76-1 mm). Caburé genotype is the best genotype adapted to the edaphoclimatic conditions evaluated because had a greater roots volume, area and length below to 0.15 m depth.
... The artificial water structures approach in this work is similar to the work presented by Kaestner et al. on XTM of 3D root networks. 40 In this work, XTM data is simulated by adding background noise from XTM scans acquired with different imaging conditions to ground truth structures, instead of adding artificial noise to the ground truth structures as done in. 40 The water feature ground truth mask contains 3D structures simulating water accumulations in individual pores as spheres with diameter sizes in pixels of (60, 40,20,10,9,8,7,6,5,4,3,2,1) and water accumulations in the throats connecting different pores to larger clusters as columns with diameter sizes in pixels of (13,12,11,10,9,8,7,6,5,4, 3, 2, 1) as shown in the 3D rendering in Fig. 2a. ...
... 40 In this work, XTM data is simulated by adding background noise from XTM scans acquired with different imaging conditions to ground truth structures, instead of adding artificial noise to the ground truth structures as done in. 40 The water feature ground truth mask contains 3D structures simulating water accumulations in individual pores as spheres with diameter sizes in pixels of (60, 40,20,10,9,8,7,6,5,4,3,2,1) and water accumulations in the throats connecting different pores to larger clusters as columns with diameter sizes in pixels of (13,12,11,10,9,8,7,6,5,4, 3, 2, 1) as shown in the 3D rendering in Fig. 2a. The ground truth binary structures are then multiplied with a value that represents mean GSV difference between water and void domain based on CNR analysis. ...
... 40 In this work, XTM data is simulated by adding background noise from XTM scans acquired with different imaging conditions to ground truth structures, instead of adding artificial noise to the ground truth structures as done in. 40 The water feature ground truth mask contains 3D structures simulating water accumulations in individual pores as spheres with diameter sizes in pixels of (60, 40,20,10,9,8,7,6,5,4,3,2,1) and water accumulations in the throats connecting different pores to larger clusters as columns with diameter sizes in pixels of (13,12,11,10,9,8,7,6,5,4, 3, 2, 1) as shown in the 3D rendering in Fig. 2a. The ground truth binary structures are then multiplied with a value that represents mean GSV difference between water and void domain based on CNR analysis. ...
Improvements in synchrotron based operando X-ray tomographic microscopy (XTM) of polymer electrolyte fuel cells (PEFCs) have paved the way for 4D imaging studies of the water distribution in the gas diffusion layer (GDL). In order to capture the full water dynamics in 4D, a decrease of the scan time towards 0.1 s is aspired, posing significant challenges in image processing for quantitative water detection. In this work, ex situ and in situ X-ray tomographic microscopy experiments were conducted to study the influence of imaging parameters and image denoising settings on image quality and water detectability in the GDL. The image quality is quantified for scan times between 50 ms and 12.8 s at the TOMCAT beamline of the Swiss Light Source. Denoising strategies for a broad range of image qualities were identified, which enable high in situ water detectability rate of 96% at a scan time of 1.6 s and 88% at subsecond scan time as short as 0.4 s. The presented methodology can be transferred to other PEFC or similar XTM imaging setups and image processing pipelines to verify their water detection capabilities.
... The imaging of plant roots in soil using X-ray CT relies on sufficient contrast in X-ray attenuation between growth medium solids, air-filled pores, soil water, plant material and organic matter. The attenuation of these materials varies with several factors including soil type, soil moisture content, the proximity of roots to organic matter or air-filled pores and root water status (Kaestner et al. 2006). ...
... Ground penetrating radar (GPR) is a non-destructive testing method used to detect changes in physical properties within the shallow subsurface (Daniels 1996). The operating principles of a GPR system are based on the theory of electromagnetic (EM) fields, which is described by Maxwell's equations (Jol 2008). In addition, GPR effectiveness relies on the response of the investigated materials to the EM fields, which is ruled by the constitutive equations (Jol 2008). ...
... The operating principles of a GPR system are based on the theory of electromagnetic (EM) fields, which is described by Maxwell's equations (Jol 2008). In addition, GPR effectiveness relies on the response of the investigated materials to the EM fields, which is ruled by the constitutive equations (Jol 2008). Therefore, the combination of the EM theory with the physical properties of the material is essential for a quantitative description of the GPR signal. ...
This paper provides an overview of the existing literature on the subject of the assessment and monitoring of tree roots and their interactions with the soil. An overview of tree root system architectures is given, and the main issues in terms of tree health and stability, as well as the impact of trees on the built environment, are discussed. An overview of the main destructive and non-destructive testing methods is presented, and a lack of available research-based outputs in the fields of tree root interconnectivity and soil interaction is highlighted. The effectiveness of non-destructive methods in these areas is demonstrated, in particular that of ground-penetrating radar. The paper references recent developments in estimating tree root mass density and health.
... During the last two decades, increasing interest in root architecture characterization has led to the application of 3D visualization techniques such as neutron computed tomography, magnetic resonance imaging (Metzner et al., 2015) and X-ray micro computed tomography (X-ray μCT) (Heeraman et al., 1997;Gregory et al., 2003;Kaestner et al., 2006;Mairhofer et al., 2013) for plant root research. The T increasing availability of affordable X-ray μCT scanners in particular sparked the research on plant root visualization (Pierret et al., 1999;Kaestner et al., 2006;Perret et al., 2007;Mooney et al., 2012;Mairhofer et al., 2013). ...
... During the last two decades, increasing interest in root architecture characterization has led to the application of 3D visualization techniques such as neutron computed tomography, magnetic resonance imaging (Metzner et al., 2015) and X-ray micro computed tomography (X-ray μCT) (Heeraman et al., 1997;Gregory et al., 2003;Kaestner et al., 2006;Mairhofer et al., 2013) for plant root research. The T increasing availability of affordable X-ray μCT scanners in particular sparked the research on plant root visualization (Pierret et al., 1999;Kaestner et al., 2006;Perret et al., 2007;Mooney et al., 2012;Mairhofer et al., 2013). The extraction of roots from reconstructed CT volumes necessarily requires image processing which, depending on the complexity of the environment, may be very involved. ...
... The extraction of roots from reconstructed CT volumes necessarily requires image processing which, depending on the complexity of the environment, may be very involved. Next to manual segmentation (Pierret et al., 2002;Ahmed et al., 2016), single CT-grey value threshold based methodologies are still often used (Kaestner et al., 2006;Perret et al., 2007;Flavel et al., 2017). However, small roots are then frequently not discernible from surrounding soil because of partial volume effects (PVE) . ...
Increasing interest in plant-root phenotyping has stimulated the development of X-ray μCT-based root/soil segmentation protocols. However, most scanning and CT volume processing protocols were only applied for detection of simple and small juvenile roots. We tested a new methodology for its ability to extract large mature maize roots from X-ray μCT volumes of undisturbed soil monoliths (10 × 20 × 15 cm) and compared its performance with two existing (semi-)automated segmentation algorithms. The X-ray μCT based root assessments were validated by means of the measured root biomass. Segmentation of maize root systems proved to be particularly challenging because regardless of soil type, within-sample vertical gradients in X-ray attenuation caused an overlap in CT-reconstructed grey values of roots, water and mineral phases. However, in contrast to the two existing algorithms, a new alternative methodology did allow for relatively fast and accurate segmentation of the mature roots. This was evidenced by a highly significant correlation between the CT-derived root volume and its measured root biomass. Despite the large size of the investigated soil monoliths, roots could be resolved down to a diameter of 200 μm. This methodology opens up new possibilities for investigating large and complex root systems, and may become an invaluable new tool in plant breeding research.
... As such, the resulting grey value is an intermediate value, potentially corresponding to those of lower density materials, which hinders straightforward segmentation. Partly due to this effect, accurate quantitative information can only be obtained if the feature's size exceeds the voxel size/resolution at least two times (Rogasik et al., 2003;Kaestner et al., 2006). The impact of this effect will thus diminish with increasing feature's size. ...
... During the last two decades, increasing interest in root architecture characterization has led to the application of 3D visualization techniques such as neutron computed tomography, magnetic resonance imaging (Metzner et al., 2015) and X-ray micro computed tomography (X-ray µCT) (Heeraman et al., 1997;Gregory et al., 2003;Kaestner et al., 2006;Mairhofer et al., 2013) for plant root research. The increasing availability of affordable X-ray µCT scanners in particular sparked the research on plant root visualization (Pierret et al., 1999;Kaestner et al., 2006;Perret et al., 2007;Mooney et al., 2012;Mairhofer et al., 2013). ...
... During the last two decades, increasing interest in root architecture characterization has led to the application of 3D visualization techniques such as neutron computed tomography, magnetic resonance imaging (Metzner et al., 2015) and X-ray micro computed tomography (X-ray µCT) (Heeraman et al., 1997;Gregory et al., 2003;Kaestner et al., 2006;Mairhofer et al., 2013) for plant root research. The increasing availability of affordable X-ray µCT scanners in particular sparked the research on plant root visualization (Pierret et al., 1999;Kaestner et al., 2006;Perret et al., 2007;Mooney et al., 2012;Mairhofer et al., 2013). The extraction of roots from reconstructed CT volumes necessarily requires image processing which, depending on the complexity of the environment, may be very involved. ...
... (Boundless, 2016)) impact on the image quality found in MRI Koebernick et al., 2014). Whilst the majority of X-ray CT studies have been carried out on agricultural plant species such as wheat (Jenneson et al., 1999;Gregory et al., 2003;Mooney et al., 2006), maize (Lontoc-Roy et al., 2006), soybean (Tollner et al., 1994), potato (Han et al., 2008) and tomato , a few studies can be found on tree roots (Pierret et al., 1999;Kaestner et al., 2006;Paya et al., 2015) and grasses (Pfeifer et al., 2015). As yet, no research has been carried out on the root architecture of alpine species under natural soil conditions using the X-ray CT. ...
... Not being able to detect the thinner roots on the present 3D images was not due to the limitations of the X-ray CT technology, rather the issue of resolution, sample size and the heterogenic soil matrix. In general, in homogeneous background the minimum resolution should be set twice as high as the cored sample is long in millimeters and set even higher if the background is heterogenic (Kaestner et al., 2006). A higher resolution setting however would have resulted in a prohibitively prolonged scanning and segmenting time. ...
... A higher resolution setting however would have resulted in a prohibitively prolonged scanning and segmenting time. The method suggested by Kaestner et al. (2006) was successful at detecting roots with a diameter < 0.5 mm in homogeneous background, however roots in heterogeneous soil matrix (e.g. Fig. 5a-c) remained challenging. ...
Glacial forefields host young, poorly developed soils with highly unstable environmental conditions. Root system contribution to soil stabilization is a well-known phenomenon. Identifying the functional traits and root morphology of pioneer vegetation that establish on forefields can provide information useful in the practical application of plants in land restoration of high altitude mountain sites.
This study aims to gather information on the root morphology and biomechanical characteristics of the 10 most dominant pioneer plant species of the forefield of Lys Glacier (NW Italian Alps).
X-ray Computed Tomography (X-ray CT) was used to visualize and quantify non-destructively the root architecture of the studied species. Samples were cored directly from the forefield. Data on root traits such as total root length, rooting depth, root diameter, root length density and number of roots in relation to diameter classes as well as plant height were determined and compared between species. Roots were also tested for their tensile strength resistance.
X-ray CT technology allowed us to visualize the 3D root architecture of species intact in their natural soil system. X-ray CT technology provided a visual representation of root–soil interface and information on the exact position, orientation and elongation of the root system in the soil core. Root architecture showed high variability among the studied species. For all species the majority of roots consisted of roots smaller than 0.5 mm in diameter. There were also considerable differences found in root diameter and total root length although these were not statistically significant. However, significant differences were found in rooting depth, root length density, plant height and root tensile strength between species and life forms (dwarf shrub, forb, graminoid). In all cases, root tensile strength decreased with increasing root diameter. The highest tensile strength was recorded for graminoids such as Luzula spicata (L.) DC. and Poa laxa Haenke and the lowest for Epilobium fleischeri Hochst.
The differences in root properties among the studied species highlight the diverse adaptive and survival strategies plants employ to establish on and thrive in the harsh and unstable soil conditions of a glacier forefield. The data determined in this study could provide a significant contribution to a database that allow those who are working in land restoration and preservation of high altitude mountain sites to employ native species in a more efficient, effective and informed manner.
... In the past 20 years, there has been a rapid increase in the use of three-dimensional (3D) visualization technology. For instance, neutron-stimulated radiation computed tomography (NSECT) [57], magnetic resonance imaging (MRI) [33,44], and X-ray electronic computed tomography (CT) [22,27,34,40,60,62] have all contributed to the advancement of non-destructive testing (NDT) research. Microfocal and nanofocal CT devices use a small X-ray beam to create object images. ...
... Image segmentation is a classic challenge in computer vision due to the complexity of the image and its A c c e p t e d m a n u s c r i p t ACCEPTED MANUSCRIPT 5 susceptibility to environmental influences. Manual segmentation is generally based on grayscale differences using threshold segmentation of grayscale images [1,19,34,48,50]. However, due to the presence of the partial volume effect (PVE) [35] and the small difference in density with the surrounding medium, roots are usually not distinguishable from the surrounding soil [51]. ...
This study aimed to enhance the understanding of root-soil interaction at a microscale level and its implications for practical land management, ecosystem restoration, and engineered solutions on vegetated slopes. Specifically, the interaction between tall fescue roots and sand was investigated using four-dimensional (4D) CT scanning. The growth process of tall fescue roots in sand was tracked on the 2nd, 4th, 6th, and 8th days after seed transplantation. To accurately segment root-soil CT images and overcome challenges such as the partial volume effect (PVE) and the similarity of root water grayscale in CT images, a semi-automatic segmentation process was employed. The analysis focused on examining the evolution of three-dimensional root parameters throughout the growth process. The findings highlighted the significant influence of initial porosity on tall fescue root development, the global decrease in saturation with root growth, and the predominant impact of pore distribution on local saturation distribution. The study revealed that the root system's influence on saturation, on the eighth day after transplantation, extended up to 800 pixels (8 mm) from the root surface. These results have practical implications for optimizing planting density and providing effective planting strategies for vegetated slope design in engineering applications.
... Root channels form after the roots die and rot away (Fig. 5 A 1 ). 3D images based on CT scans indicate that most root channels are thin and long irregular cylinders as shown in Figs. 5 A 2a , 5 A 2b and 5 A 2c (Kaestner et al., 2006;Li et al., 2016;Bai, 2022). They vary in length from centimeters to meters (Sun, 2005) and are generally circular or subcircular with diameters ranging from 0.1 to 5 mm (Lei, 1986). ...
... They vary in length from centimeters to meters (Sun, 2005) and are generally circular or subcircular with diameters ranging from 0.1 to 5 mm (Lei, 1986). Root channels are typically aligned vertically or sub- (Kaestner et al., 2006;Danjon and Reubens, 2008) as plant roots tend to grow downward to reach water (Liu, 1985). Surrounding particles of these pores are laterally pushed away during the growth of plant roots, creating a compressed zone along and around the root channels (Fig. 5 A 3 ) (Wang, 2010). ...
... In a study of tree roots, Pierret (1999) [142] used CT on chestnut (Aesculus hippocastanum) and maple (Acer pseudoplatanus) trees for the distribution of tree roots under undisturbed soils and proposed a series of methods from field sampling to spatial analysis. Kaestner (2006) [143] reconstructed the high-fidelity fine roots of alders (Alnus incana (L.) Moench) using an improved algorithm based on diffusion filter to enhance the contrast between roots and sand. Jassogne (2008) [144] used RootViz (developed by Davidson, www.rootviz3d.org, ...
... In a study of tree roots, Pierret (1999) [142] used CT on chestnut (Aesculus hippocastanum) and maple (Acer pseudoplatanus) trees for the distribution of tree roots under undisturbed soils and proposed a series of methods from field sampling to spatial analysis. Kaestner (2006) [143] reconstructed the high-fidelity fine roots of alders (Alnus incana (L.) Moench) using an improved algorithm based on diffusion filter to enhance the contrast between roots and sand. Jassogne (2008) [144] used RootViz (developed by Davidson, www.rootviz3d.org, ...
As an important part of the urban environment, trees have certain risks while living in harmony with humans. For example, the failure of trees in extreme weather may cause casualties and damage to public and private; the decline and death of old and valuable trees can have an impact on the diversity and cultural value of trees. This paper outlines the theories related to tree risk and the development of tree risk assessment, evaluates the advantages and disadvantages of various tree risk assessment methods in existing studies, and explains some factors affecting the bearing capacity and related applications using knowledge of tree mechanics. Approaches in modern probing techniques are applied to study the response and loading of tree crowns and branches under wind loads, the application of different non-destructive testing techniques in visual assessment for detecting internal defects and root distribution of trees, and the role and impact of objective quantitative test results on tree risk assessment. Finally, the future development direction of tree risk assessment is predicted, which provides an important reference for research on tree risk assessment.
... The authors also took into account the misclassification in the segmentation process due to the presence of root branches and solved this error by using top-hat filtering which extracts areas of interest darker than the adjacent voxels. In another example, Kaestner et al. (2006) extracted not only the large roots but also the fine roots in a homogeneous sandy substrate, by combining global thresholding method with the non-linear diffusion filter, and the morphological dilation filter, based on the root continuity assumption. The hybrid filters used by Kaestner et al. (2006) can identify roots not only on their grey colour, but also upon other properties such as morphological connectivity. ...
... In another example, Kaestner et al. (2006) extracted not only the large roots but also the fine roots in a homogeneous sandy substrate, by combining global thresholding method with the non-linear diffusion filter, and the morphological dilation filter, based on the root continuity assumption. The hybrid filters used by Kaestner et al. (2006) can identify roots not only on their grey colour, but also upon other properties such as morphological connectivity. In another example, Lontoc-Roy et al. (2006) examined the primary roots of maize by manually assigning different thresholds for a variety of soil columns under various X-ray CT conditions to the global thresholding method. ...
Despite the critical importance of roots within soils for supporting plant growth, the assessment of root distribution in soils remains difficult and much is unknown regarding their behaviour. In this review, we examine X-ray computed tomography (CT) as a non-invasive method for examining root distribution in soils. X-ray CT enables three-dimensional reconstruction of soil cores to accurately estimate a wide range of features within the soil, including roots, not only examining changes spatially but also temporally. With the development of high-end X-ray CT systems and image processing algorithms, this approach can now be used to examine a range of factors, including root system architecture, soil-root interactions, soil pore architecture, soil biophysical interactions, and soil microorganism behaviour. In addition, we examine the use of synchrotron-based X-ray CT which has been used to provide better resolution, larger sample analysis, faster scanning, and images with greater contrast compared to conventional systems.
... Studies using X-ray tomography to analyse root growth over time, show large differences in total X-ray dose received by plants [9][10][11][12][13][14][15]. Several aware that the dose may affect root growth [16] or use older plants (e.g. ...
... Several aware that the dose may affect root growth [16] or use older plants (e.g. [11,17]), assuming a reduced sensitivity of older plants to radiation exposure. Only two recent studies working with X-ray CT included a control treatment without scanning to evaluate potential harmful effects of X-ray dose [10,18]-both have been working with cereals. ...
X-ray CT is a powerful technology to study root growth in soil in-situ. Root systems can be studied in its true 3D geometry over time. Hence, the same plant can be scanned multiple times during development. A downside is the potential of X-rays to interfere with biological processes and therefore plant growth. The aim of this study is to evaluate the influence of cumulative X-ray dose on Vicia faba and Hordeum vulgare during a growth period of 17 days. One control treatment without X-ray scanning was compared to two treatments being scanned every two and four days, respectively. Scanned treatments received a maximum cumulative dose of less than 8 Gy. Plant species differed in their susceptibility to X-ray dose. For Vicia faba, mean total root length was reduced significantly. Leave growth was reduced as well. Number and length of second order laterals was reduced significantly, as well as length of first order laterals. Hordeum vulgare showed no negative impact of X-ray dose on any of the root parameters. Large differences between the two species investigated were detected in respect to susceptibility to X-ray dose. Results indicate that for X-ray CT studies involving temporal resolution a control treatment without scanning is required.
... A study of soil microbial functioning through X-ray CT analysis would be a commanding tool in understanding the role of soil pore geometry on SOM degradation as the tomographic technique is not harmful to the microbial community (Bouckaert et al., 2013). However, many researchers (De Gryze et al., Kaestner et al., 2006) reported that phase separation/segmentation became very difficult as the X-ray attenuation coefficients of SOM become in-between air/waterfilled pores and mineral matrix. Consequently, in-situ measurement of low concentrations of SOM in cultivable mineral soils (i.e., 5 % wt. ...
X-ray computed tomography (X-ray CT) is a non-destructive method of soil analysis which can provide three-dimensional (3D) view, quantitative information of the internal organization of the soil. In this paper, we discuss the potential application of X-ray CT in characterization of soil properties like porosity and pore size distribution (PSD), root architecture, soil phase classification, water and solute transport in soil, and highlight the research during last 10–15 years. Here, we review the recent development of X-ray CT in soil science, use of artificial intelligence and machine learning in image analysis, point out the major challenges associated with its use, discuss few improvements to overcome these difficulties and elaborate the possible future technological developments for non-invasive/destructive soil characterization by integrating X-ray CT with recently available complementary techniques.
... The variation in RSA at soil depth largely reflects the distribution of soil nutrients at soil depth. The dynamic nature of the root structure, as it adapts to the environment and its own requirements, plays a crucial role in optimizing the growth and development of forest trees [20,21]. Conducting a comprehensive and detailed investigation of RSA has significant implications for the understanding of soil-plant systems. ...
Aims: Changes in root system architecture (RSA) and soil depth affect the root decomposition rate. However, due to soil opacity, many variables of RSA have not been well studied or even measured. Methods: To investigate the effects of soil depth and the characteristics of RSA on the root decomposition rate, soil samples (Soil cores were collected in October 2020 from Cunninghamia lanceolata and Pinus taeda plantations, which were 40 years old) were obtained using a soil auger and had a diameter of 10 cm and a length of 60 cm. Samples were taken from six different soil depths, ranging from 0 to 60 cm with a 10 cm interval between each depth. The RSA in the in-situ soil cores was analyzed using computed tomography scans and Avizo. Results: Root volume and the number of root throats were significantly higher at the 0–10 cm soil depth than at the 10–60 cm soil depth, but root length was significantly lower at the 50–60 cm soil depth (p < 0.05). Structural equation modeling showed that different stand types influenced root biomass and thus the root decomposition rate directly or indirectly through the characteristics of the stand types. RSA, i.e., root thickness and breadth, affected root biomass indirectly and then affected the root decomposition rate. Root biomass contributed the most to the root decomposition rate in the Cunninghamia lanceolata (20.19%) and Pinus taeda (32.26%) plantations. The contribution of the RSA variables to the root decomposition rate exceeded 50% at the 20–30 cm and 40–50 cm soil depths. Conclusions: Our findings suggested that the influence of the RSA variables on the root decomposition rate varies with soil depth. This deserves more consideration in our future studies on root decomposition and RSA.
... X-rays have both destructive as well as simulative effects on plants depend upon the amount of doses given. Several researchers tested on x-rays by keeping dose very low on older plants as they aware about doses may affect plant growth (Perret et al., 2007;Kaestner et al., 2006). Blaser et al., (2018) uses x-ray CT of less than 8 Gy on two hosts, Vicia faba and Hordeum vulgare and recorded that in Vicia faba reduces root length, leaf growth, number and length of first, second order laterals while Hordeum vulgare donot show any negative impact of xray dose on root parameters. ...
... The variation in root structure at soil depth largely re ects the distribution of soil nutrients at the soil depth. Changes in the root structure according to the environment and its own needs help to optimize the growth and development of the forest tree (Kaestner et al. 2006;Peng and Chen 2021). A better and more in-depth study of root structure has far-reaching implications for the study of soil-plant systems. ...
Aims
Changes in root structure and soil depth affect root decomposition. However, due to soil opacity, many variables of root structure have not been well studied and even measured.
Methods
To investigate the effects of soil depth and the characteristics of root structure on root decomposition, soil samples (In-situ soil core of 10cm diameter and 60cm length drilled by soil auger in October 2020) were collected in Cunninghamia lanceolata and Pinus taeda plantations (40 years), at six soil depths (0-60cm, every 10cm). The root structure in the in-situ soil cores was analyzed using CT scans and specialized analysis software.
Results
Root volume, shape, and connectivity were significantly higher in the 0–10 cm soil depth than in the 10-60cm soil depths, but root length and tortuosity were significantly lower than in the 50-60cm soil depth (p༜0.05). The SEM shows that different stand types influenced root biomass and thus root decomposition directly or indirectly through the characteristics of stand types. Root structure variables affected root biomass and thus root decomposition indirectly. Root biomass contributed the most to root decomposition in Cunninghamia lanceolata (20.19%) and Pinus taeda (32.26%) plantations. The contribution of root structure variables to root decomposition exceeded 50% in the 20–30 cm and 40–50 cm soil depths.
Conclusions
Our findings suggested that the contribution and influence of root structure variables on root decomposition rate varies with soil depth. It deserves more consideration in our future studies.
... Many of them involve pre-and post-processing of the image. These are used to enhance the contrast between roots and soil matrix and to reduce noise by applying different filters like Gaussian and Non-local means filters Kaestner et al., 2006;Koebernick et al., 2014;Lucas et al., 2019b). In addition, post-processing filters can be applied to remove misclassified features, e.g. by applying size or median filters (Gao et al., 2019a;Lucas et al., 2019b). ...
Growing roots interact with soil, and its structure, across a range of spatial and temporal scales, and thus adapt to the local environment (Downie et al., 2015). Several factors influence the development of roots, and as such, shape the root system architecture (RSA). Well-known examples of these are water stress, mechanical impedance, pore connectivity and porosity (Bengough et al., 2011; Correa et al., 2019; Lucas et al., 2019a). However, it is not just physical but also biological and chemical factors such as the availability of nitrogen that can change the growth of roots and their RSA (Flavel et al., 2014; Gao, Blaser, et al., 2019b; Nwankwo et al., 2018). Due to all these factors, perhaps not surprisingly root growth in artificial soil, such as gel media and indeed sieved soil, shows significantly different root growth when compared to roots developed in undisturbed soil (Hargreaves et al., 2009). In this chapter we review how rhizosphere research with X-ray CT has developed within the last three decades and show X-ray imaging is an excellent tool to investigate changes in root architecture in soil over time.
... Many of them involve pre-and post-processing of the image. These are used to enhance the contrast between roots and soil matrix and to reduce noise by applying different filters like Gaussian and Non-local means filters Kaestner et al., 2006;Koebernick et al., 2014;Lucas et al., 2019b). In addition, post-processing filters can be applied to remove misclassified features, e.g. by applying size or median filters (Gao et al., 2019a;Lucas et al., 2019b). ...
The output of CT imaging (after reconstruction) of soil samples are grayscale images with a series of gray values corresponding to soil components with different densities. Most current techniques to quantify the soil pore system rely on binary images, with the target objects or foreground pixels (e.g. pores) labelled as 1 and the background (e.g. soil) labelled as 0. This means the grayscale images need to be segmented to binary images before further quantification. However, because of the partial volume effect and noise in the images, in most cases the histogram of the grayscale image does not exhibit clear, distinct peaks, which makes image segmentation a very challenging task. Many filtering techniques have been developed to smooth image noise and enhance the contrast between the target and background, which can greatly help image segmentation if correctly used. Numerous image segmentation techniques have also been developed to deal with specific problems in a variety of disciplines. In soil science, a range of global and local segmentation methods have been used and their performances compared and summarized in previous studies. Recently, artificial intelligence (AI) has been used to segment soil CT images and showed great potential in extracting not only soil pore space, but also other soil components. In this chapter, we briefly summarize the widely used traditional global and local segmentation methods and then present a new segmentation protocol that combines machine learning and deep learning strategies to segment pore space in soil aggregate images. The results of the AI-based method are very promising, and we propose the AI techniques will soon be extensively used in the processing of the soil CT images.
... Interestingly, Pierret et al. (1999) were amongst the first to identify one of the major imaging challenges concerned with root segmentation. Later, Kaestner et al. (2006) endeavored to provide the solution by applying a non-linear diffusion filter to smoothen the images followed by conveying a threshold value extracted from Rosin's (2001) algorithm, and concluded that a phenotyping dilation operation could be used to eradicate misclassified objects. This method could perceive primary roots and fine lateral roots as well. ...
The phenotyping of plant roots is a challenging task and poses a major lacuna in plant root research. Roots rhizospheric zone is affected by several environmental cues among which salinity, drought, heavy metal and soil pH are key players. Among biological factors, fungal, nematode and bacterial interactions with roots are vital for improving nutrient uptake efficiency in plants. The subterranean nature of a plant root and the limited number of approaches for root phenotyping offers a great challenge to the plant breeders to select a desirable root trait under different stress conditions. Identification of key root traits can provide a basic understanding for generating crop plants with enhanced ability to withstand various biotic or abiotic stresses. For instance, crops with improved soil exploration potential, phosphate uptake efficiency, water use efficiency and others. Laboratory methods such as hydroponics, rhizotron, rhizoslide and luminescence observatory for roots do not provide precise and desired root quantification attributes. Though 3D imaging by X-ray computed tomography (X-ray-CT) and magnetic resonance imaging techniques are complex, however, it provides the most applicable and practically relevant data for quantifying root system architecture traits. This review outlines the current developments in root studies including recent approaches viz. X-ray-CT, MRI, thermal infrared imaging and minirhizotron. Although root phenotyping is a laborious procedure, it offers multiple advantages by removing discrepancies and providing the actual practical significance of plant roots for breeding programs.
... Other applications of X-ray CT involve characterization of the root system (Gregory et al., 2003;Heeraman et al., 1997;Kaestner et al., 2006;Lontoc-Roy et al., 2006;Perret et al., 2007, Tracy et al., 2012. For example, Gregory et al. (2003) measured the length and diameter of wheat and rapeseed roots. ...
... 3D measurement requires digging out the root system, so time-series data cannot be collected. Because root point data obtained by non-destructive methods, such as groundpenetrating radars [47], do not indicate connections, it is difficult to convert them into RSA data without a connection algorithm [48]. Recently, we devised a connection algorithm for point data of Cryptomeria japonica roots [13]. ...
Three-dimensional (3D) root system architecture (RSA) is a predominant factor in anchorage failure in trees. Only a few studies have used 3D laser scanners to evaluate RSA, but they do not check the accuracy of measurements. 3D laser scanners can quickly obtain RSA data, but the data are collected as a point cloud with a large number of points representing surfaces. The point cloud data must be converted into a set of interconnected axes and segments to compute the root system traits. The purposes of this study were: (i) to propose a new method for easily obtaining root point data as 3D coordinates and root diameters from point cloud data acquired by 3D laser scanner measurement; and (ii) to compare the accuracy of the data from main roots with intensive manual measurement. We scanned the excavated root systems of two Pinus thunbergii Parl. trees using a 3D laser scanner and neuTube software, which was developed for reconstructing the neuronal structure, to convert the point cloud data into root point data for reconstructing RSA. The reconstruction and traits of the RSA calculated from point cloud data were similar in accuracy to intensive manual measurements. Roots larger than 7 mm in diameter were accurately measured by the 3D laser scanner measurement. In the proposed method, the root point data were connected as a frustum of cones, so the reconstructed RSAs were simpler than the 3D root surfaces. However, the frustum of cones still showed the main coarse root segments correctly. We concluded that the proposed method could be applied to reconstruct the RSA and calculate traits using point cloud data of the root system, on the condition that it was possible to model both the stump and ovality of root sections.
... However, there are several disadvantages of X-ray CT technology emerged during our work, which remain to be considered or resolved in such researches of future. At first, the detection limitation of CT scanning was about 2-3 times the side length of voxel (Kaestner et al., 2006), that means the small roots whose diameter less than about 200 μm could not be recognized. However, the traditional approach by human eyes can recognize these small roots with ease. ...
Conspecific seagrass living in differing environments may develop different root system acclimation patterns. We applied X-ray computed tomography (CT) for imaging and quantifying roots systems of Zostera japonica collected from typical oligotrophic and eutrophic sediments in two coastal sites of northern China, and determined sediment physicochemical properties that might influence root system morphology, density, and distribution. The trophic status of sediments had little influence on the Z. japonica root length, and diameters of root and rhizome. However, Z. japonica in oligotrophic sediment developed the root system with longer rhizome node, deeper rhizome distribution, and larger allocation to below-ground tissues in order to acquire more nutrients and relieve the N deficiency. And the lower root and rhizome densities of Z. japonica in eutrophic sediment were mainly caused by fewer shoots and shorter longevity, which was resulted from the more serious sulfide inhibition. Our results systematically revealed the effect of sediment trophic status on the phenotypic plasticity, quantity, and distribution of Z. japonica root system, and demonstrated the feasibly of X-ray CT in seagrass root system research.
... The limit for the smallest observable root is a function of the quality of the image (signal-to-noise ratio) and resolution [6]. The smallest observable object is generally considered to be of a size of twice the spatial resolution, and this may even not be sufficient if the image is noisy and background is not homogeneous [22]. In other words, the smallest observable object should be larger than 2 pixels/voxels. ...
Plant roots change their morphological traits in order to adapt themselves to different environmental conditions, resulting in alteration of the root system architecture. To understand this mechanism, it is essential to visualize morphology of the entire root system. To reveal effects of long-term alteration of gravity environment on root system development, we have performed an experiment in the International Space Station using Arabidopsis plants and obtained dried root systems grown in rockwool slabs. X-ray computed tomography (CT) technique using industrial X-ray scanners has been introduced to visualize root system architecture of crop species grown in soil in 3D non-invasively. In the case of the present study, however, root system of Arabidopsis is composed of finer roots compared with typical crop plants and rockwool is also composed of fibers having similar dimension to that of the roots. A higher spatial resolution imaging method is required for distinguishing roots from rockwool. Therefore, in the present study, we tested refraction-contrast X-ray micro-CT using coherent X-ray optics available at the beamline of the synchrotron radiation facility SPring-8 for bio-imaging. We have found that wide field of view but with low resolution obtained at the experimental Hutch 3 of this beamline provided an overview map of the root systems, while narrow field of view but with high resolution obtained at the experimental Hutch 1 provided extended architecture of the secondary roots, by clear distinction between roots and individual rockwool fibers, resulting in successful tracing of these roots from their basal regions.
... Morphological filters possess effective noise suppression with reduced geometrical feature blurring [7]. [8] extracts the main features using a morphological filter algorithm to reconstruct fine roots with high fidelity. WinRHIZO, EZ-RHIZO, and ROOTEDGE are software tools designed for the measurement of root system architecture [9][10][11]. ...
Research on rice (Oryza sativa) roots demands the automatic analysis of root architecture during image processing. It is challenging for a digital filter to identify the roots from the obscure and cluttered background. The original Frangi algorithm, presented by Alejandro F. Frangi in 1998, is a successful low-pass filter dedicated to blood vessel image enhancement. Considering the similarity between vessels and roots, the Frangi filter algorithm is applied to outline the roots. However, the original Frangi only enhances the tube-like primary roots but erases the lateral roots during filtering. In this paper, an improved Frangi filtering algorithm (IFFA), designed for plant roots, is proposed. Firstly, an automatic root phenotyping system is designed to fulfill the high-throughput root image acquisition. Secondly, multilevel image thresholding, connected components labeling, and width correction are used to optimize the output binary image. Thirdly, to enhance the local structure, the Gaussian filtering operator in the original Frangi is redesigned with a truncated Gaussian kernel, resulting in more discernible lateral roots. Compared to the original Frangi filter and commercially available software, IFFA is faster and more accurate, achieving a pixel accuracy of 97.48%. IFFA is an effective morphological filtering approach to enhance the roots of rice for segmentation and further biological research. It is convincing that IFFA is suitable for different 2-D plant root image processing and morphological analysis.
... The imaging of plant roots in soil using X-ray CT relies on sufficient contrast in X-ray attenuation between growth medium solids, air-filled pores, soil water, plant material and organic matter. The attenuation of these materials varies with several factors including soil type, soil moisture content, the proximity of roots to organic matter or air-filled pores and root water status (Kaestner, et al., 2006). ...
Evidence suggests that trees and forests around the world are constantly being threatened by disease and environmental pressures. Over the last decade, new pathogens spread rapidly in European forests, and quarantine measures have mostly been unable to contain outbreaks. As a result, millions of trees were infected, and many of these have already died. It is therefore vital to identify infected trees in order to track, control and prevent disease spread.
In addressing these challenges, the available methods often include cutting of branches and trees or incremental coring of trees. However, not only do the tree itself and its surrounding environment suffer from these methods, but they also are costly, laborious and time-consuming.
In recent years the application of non-invasive testing techniques has been accepted and valued in this particular area. Given its flexibility, rapidity of data collection and cost-efficiency, Ground Penetrating Radar (GPR) has been increasingly used in this specific area of research. Consequently, this PhD Thesis aims at addressing a major challenge within the context of early identification of tree decay and tree disease control using GPR. In more detail, two main topics are addressed, namely the characterisation of the internal structure of tree trunks, and the assessment of tree root systems’ architecture. As a result, a comprehensive methodology for the assessment of both tree trunks and roots using GPR is presented, which includes the implementation of novel algorithms and GPR signal processing approaches for the characterisation of tree trunks’ internal structure and the three-dimensional mapping of tree root systems. Results of this research project were promising and will contribute towards the establishment of novel tree evaluation approaches.
... Some techniques have also been developed to investigate root architecture in 3-D (e.g. Kaestner et al., 2006) and the interplay between roots and soil (e.g. Krebs, 1994;Moran et al., 2000). . ...
... X-ray CT is a non-destructive structural imaging method that allows 3D reconstruction of scanned objects at 1-2 mm lat-eral resolution, which is widely used in the field of medical diagnostic, material, and earth sciences (Cnudde et al., 2006). With a spatial resolution typically around the micron level, Micro-CT has been applied in plants since the late 1990s (Pierret et al., 1999;Kaestner et al., 2006;Tracy et al., 2010). Recent improvements of Micro-CT have boosted the scanning resolution to the sub-micron level, which is now called high-resolution X-ray CT (HRXCT) (Dhondt et al., 2010). ...
In multicellular and even single-celled organisms, individual components are interconnected at multiscale levels to produce enormously complex biological networks that help these systems maintain homeostasis for development and environmental adaptation. Systems biology studies initially adopted network analysis to explore how relationships between individual components give rise to complex biological processes. Network analysis has been applied to dissect the complex connectivity of mammalian brains across different scales in time and space in The Human Brain Project. In plant science, network analysis has similarly been applied to study the connectivity of plant components at the molecular, subcellular, cellular, organic, and organism levels. Analysis of these multiscale networks contributes to our understanding of how genotype determines phenotype. In this review, we summarized the theoretical framework of plant multiscale networks and introduced studies investigating plant networks by various experimental and computational modalities. We next discussed the currently available analytic meth-odologies and multi-level imaging techniques used to map multiscale networks in plants. Finally, we highlighted some of the technical challenges and key questions remaining to be addressed in this emerging field. multiscale network, connectivity, cytoskeleton, membrane contact site, organelle interaction, multicellularity, con-nectome, cytoarchitecture, topological analysis, multi-level imaging techniques
... Finally, in order to reduce noise in the grayscale values while preserving the edges of the pores and organic features, different smoothing algorithms were tested using image filtering tools on Matlab, including Gaussian 3D filtering, 3D median filtering, guided image filtering and anisotropic diffusion (quadratic and exponential). The quadratic anisotropic diffusion tool imdiffusefilt was found to be best suited for filtering out noise without losing the signal: the method enhances the contrast between matrix and darker elements by using strong gradients in the image as barriers to the smoothing effect and thus preserving the edges (Kaestner et al., 2006). ...
Subsurface structures and especially the interactions between pores, roots and other organic matter elements have a strong impact on ecosystem functioning. Yet despite recent progress in the application of X-ray Computed Microtomography (µCT) to soil structure in agricultural science, applications to the more complex and heterogeneous substrates found in natural soils, specifically wetland soils, remain sparse. We apply X-ray µCT to a complex heterogenous soil and develop a robust segmentation method to quantify the pores, live roots and necromass. This approach significantly improves the detection of the organic matter elements, and gives us unprecedented detail and resolution in the segmentation of pores, live roots and necromass at a high spatial resolution (62.5 µm in this study). We identify several situations where pores and organic matter interact in the soil, including the disconnected air spaces (aerenchyma) that run within the Spartina stem and roots, tubular-shaped pores left behind by decaying roots, and lateral roots deploying within structural fragilities in the sediment. The capacity of X-ray µCT to distinguish the connected live root system from the necromass opens possibilities for applications to determine key wetland soil functions such as soil cohesivity, soil nutrient exchanges and soil carbon dynamics.
... To overcome these physical barriers, several phenotyping methods have been proposed, each of which employs a different trade-off in terms of accuracy, coverage, throughput, and cost [18,34]. These methods are based, for example, on ground-penetrating radar [55][56][57], electric resistivity tomography [56,58,59], minirhizotrons [60][61][62][63][64], shovelomics [65,66], soil coring [67], X-ray tomography [68][69][70][71], magnetic resonance imaging [42,72,73], and 3D laser scanning [74,75]. ...
Numerous types of biological branching networks, with varying shapes and sizes, are used to acquire and distribute resources. Here, we show that plant root and shoot architectures share a fundamental design property. We studied the spatial density function of plant architectures, which specifies the probability of finding a branch at each location in the 3-dimensional volume occupied by the plant. We analyzed 1645 root architectures from four species and discovered that the spatial density functions of all architectures are population-similar. This means that despite their apparent visual diversity, all of the roots studied share the same basic shape, aside from stretching and compression along orthogonal directions. Moreover, the spatial density of all architectures can be described as variations on a single underlying function: a Gaussian density truncated at a boundary of roughly three standard deviations. Thus, the root density of any architecture requires only four parameters to specify: the total mass of the architecture and the standard deviations of the Gaussian in the three x , y , z growth directions. Plant shoot architectures also follow this design form, suggesting that two basic plant transport systems may use similar growth strategies.
... To better understand the role of morphology of roots in soil, high-resolution imaging methods, such as micro-CT (Kaestner et al., 2006;Tracy et al., 2010) can be used to investigate natural roots and thus obtain a 3D reconstruction for bioinspired design insights. Mishra et al. (2018) used imaging capture of Zea mays roots via an optical microscope. ...
It has been 10 years since the publication of the first article looking at plants as a biomechatronic system and as model for robotics. Now, roboticists have started to look at plants differently and consider them as a model in the field of bioinspired robotics. Despite plants have been seen traditionally as passive entities, in reality they are able to grow, move, sense, and communicate. These features make plants an exceptional example of morphological computation - with probably the highest level of adaptability among all living beings. They are a unique model to design robots that can act in- and adapt to- unstructured, extreme, and dynamically changing environments exposed to sudden or long-term events. Although plant-inspired robotics is still a relatively new field, it has triggered the concept of growing robotics: an emerging area in which systems are designed to create their own body, adapt their morphology, and explore different environments. There is a reciprocal interest between biology and robotics: plants represent an excellent source of inspiration for achieving new robotic abilities, and engineering tools can be used to reveal new biological information. This way, a bidirectional biology-robotics strategy provides mutual benefits for both disciplines. This mini-review offers a brief overview of the fundamental aspects related to a bioengineering approach in plant-inspired robotics. It analyses the works in which both biological and engineering aspects have been investigated, and highlights the key elements of plants that have been milestones in the pioneering field of growing robots.
... Mooney et al. [5] applied CT to visualize and quantify root lodging of wheat within different kinds of soil. Kaestner et al. [6] presented a method which including three steps to realize the reconstruction of the root network. Lontoc-Roy et al. [7] used CT to scan maize root systems in different soil surroundings, and an algorithm was developed in MATLAB based on CT histograms to segment root from surrounding soil, ultimately, they reconstructed the maize root systems. ...
... When the main lateral angle of oleander root system is 45 degrees and 60 degrees, the performance of reducing slope surface displacement is decent with the increase of fractal dimension of root system, and this change feature is corresponding to the result of digital simulation. The form of oleander root system with lateral root angle of 90 degree is single, the arrangement is regular, it is not conducive to forming a winding network structure in soil and the performance of reducing surface displacement is not so obvious (Danjon et al. 2008;Kaestner et al. 2006;Tasser and Tappeiner 2005). For oleander root system with lateral root angle of 30 degree, because of the angle is small, the distribution in the soil is small, the contact with soil is not sufficient, so the performance of soilreinforcement is bad (Liang 2015). ...
Based on the box-counting dimension method of fractal theory, a set of computing image fractal dimension software Fractal 1.0 was developed which can be used to determine the root fractal dimension of plants. By combining the theory of fractal with the finite element theory, the effects of root system fractal dimension on the amount of displacement taking place on the surface of slope were studied. By analyzing the relationship between them from different aspects, the results indicate that fractal dimension can be regarded as the parameter of root system, the effects of different root systems on the stability of soil in slope surface were quantitatively characterized through integrating fractal dimension with finite element method.
... Peat samples were scanned at 70 kV and 250 µA with voxel resolution of 38.8 µm for total of 1700 images per column, and run time of 30 min. Image segmentation of roots in peat was difficult to achieve because of similar particle density, and the quality of CT scanning depends on density separation (Heeraman, Hopmans, and Clausnitzer 1997;Kaestner, Schneeneli, and Graf 2006). ...
The objective was to refine protocols to quantify rooting of plant cuttings and the water/air microenvironment of substrates using x-ray computed tomography (CT). Poinsettia (Euphorbia pulcherrima) cuttings were propagated in three substrates (peat, rockwool, and phenolic foam) at varied moisture levels. In Experiment 1, adventitious rooting occurred in cuttings grown in rockwool or foam from 12% to 86% volumetric water content (VWC) and 12% to 80% volumetric air content (VAC). The highest root growth occurred in rockwool at 59% VWC and 33% VAC. There was an advantage to quantifying root growth by CT in rockwool and foam, in contrast to peat, because of clear differences in material density between root and substrate during image processing. In Experiment 2, root growth was quantified in peat by two-dimensional image scans under similar growth chamber environments, with rapid root growth from 52% to 63% VWC and 16% to 26% VAC. In Experiment 3, CT was used to quantify the substrate microenvironment at 0.5 cm slices to further describe the environment at the base of the plant cutting. Rapid rooting occurred in microenvironments above 56% VWC and 14% VAC, whereas the low 3% VAC in foam at high moisture may limit root growth.
Abbreviations: volumetric water content (VWC), volumetric air content (VAC), volumetric solid content (VSC)
... Furthermore, the non-destructive X-ray CT scanning technique has been applied to analyse the distribution and architectures of root networks (Haling et al. 2013;Mooney et al. 2012). In general, homogeneous sandy soils (Flavel et al. 2012;Mooney et al. 2012;Pierret et al. 1999) have constituted the optimum medium for the non-destructive visualisation (Kaestner et al. 2006;Mairhofer et al. 2013) and quantification of root networks using X-ray CT scanning. At a smaller scale, microfocus X-ray CT scanning allows the precise study of the 3-D rhizosphere in non-homogeneous in situ samples (Aravena et al. 2011;Seignez et al. 2010). ...
The objectives of this study were to visualise and quantify the soil macropore networks and root architectures within intact soil columns under different ecosystems and to investigate the influences of roots on soil macropore network characteristics. Intact soil columns with diameters of 110 mm and lengths of 400 mm were taken from alpine Kobresia meadow, interspace meadow patches of Potentilla fruticosa shrubs, Potentilla fruticosa shrubs and Artemisia sphaerocephala shrubs in the Qinghai Lake watershed of the NE Qinghai–Tibet Plateau. A Philips medical X-ray CT scanner was used to simultaneously visualise and quantify the soil macropore networks and root architectures. The results showed that macropores and taproots were concentrated in the top 0–150 mm. The root volume density of the P. fruticosa shrub was greater than that of the interspace meadow patches of P. fruticosa shrub and that of the alpine Kobresia meadow. The macroporosity and the root volume density of the soils under the P. fruticosa shrub patches were significantly greater than those in the soils under the other sites. The root volume density was significantly correlated with the macroporosity for the A. sphaerocephala shrubs (R² = 0.88) and the P. fruticosa shrubs (R² = 0.73). There were significant positive correlations between the volume density, branch density and mean angle of the roots and those of the macropores. Shrub roots invasion played an important role in the formation of macropores. The root volume density was the most important factor for the quantified characteristics and distributions of the macropores.
... In order to capture 3D RSA for pots >30 mm diameter, and at the same time detect the fine roots (root diameter ≤ 2 or 3 times of the image resolution), the segmentation method to extract roots from CT images is of critical importance. Established methods can generally be grouped into three categories: (1) global thresholding based on the histogram of the image (Kaestner et al. 2006;Kuka et al. 2013), (2) region growing by adaptive local thresholding (Flavel et al. 2012;Gregory et al. 2003), and (3) root tracking based on level sets (Mairhofer et al. 2012;Tabb et al. 2018). The overlapping attenuation values of root and soil matrix makes global thresholding an inadequate method (Helliwell et al. 2013;Mooney et al. 2012). ...
AimsX-ray computed tomography (CT) is widely recognized as a powerful tool for in-situ quantification of root system architecture (RSA) in soil. However, employing X-ray CT to identify the spatio-temporal dynamics of RSA still remains a challenge due to non-automatic, time-consuming image processing protocols and their poor recovery of fine roots in soil.Methods
Here we present a new protocol (Rootine) to segment roots rapidly and precisely down to fine roots with two voxels in diameter (90 μm in pots with 70 mm in diameter). This is facilitated by feature detection of the tubular shape of roots, an approach that was originally developed for detecting blood vessels in medical imaging.ResultsIn comparison to established root segmentation methods, Rootine produced a more accurate root network, i.e. more roots and less over-segmentation. Root length quantified by X-ray CT showed high correlation with results by root washing combined with 2D light scanning (R2 = 0.92). Tests with different soil materials showed that the recovery of roots depends on signal-to-noise ratio but can be up to 99% for a favorable contrast between fine roots and background.Conclusions
This new protocol provides great efficiency to study RSA in undisturbed soil. As it is fully automated it has the potential for high-throughput root phenotyping and related modelling.
... These pore-network models have substantially improved our understanding of some fundamental biogeochemical processes and transport processes occurring in soil which would remain unknown otherwise, such as the impact of pore geometry on microbial inhabitation (Young and Ritz 2000), the relationship between pore structure and resident time of solute (Bijeljic and Blunt 2006), reactive solute transport (Li et al. 2006) and the dynamics of water-air interfacial area (Hassanizadeh et al. 2002). However, idealising the soil as a network is not a realistic representation and could give rise to considerable errors when used to calculate the physical and biochemical properties of structured soils (Zhang et al. 2016c;Hussain et al. 2013 The last decade has seen an increased application of X-ray micro-tomography in soil research (Baveye et al. 2010;Van Loo et al. 2014;Akhtar et al. 2011;Dal Ferro et al. 2013;Elliot et al. 2010;Kaestner et al. 2006). The X-ray tomography is based on variation of the attenuation of X-ray within an object (Bouckaert et al. 2013;Lin et al. 2016) and can provide 3D visualization at resolution as fine as one micron (Ostadi et al. 2010). ...
Pore-scale simulation and tomography have been used in a combination over the past decade to study some fundamental physical and biogeochemical processes in soil that are difficult or impossible to measure, one of which is water flow in unsaturated soil. Considering that an important application of pore-scale simulation in soil is to elucidate how convective water flow distributes soluble nutrients through the heterogeneous pore space when water flow is in steady state, we propose an alternative model in this paper to simulate unsaturated water flow at pore scale. The model is quasi-static, consisting of two steps. The first one is to determine water distribution in the pore geometry using a morphological model; once the water distribution is known under a pressure, the water–air interface is fixed in space. The second step is to simulate water flow numerically by solving the Stokes equations in which the water–air interface is treated as a boundary. We test the water flow model against analytical solution of thin water film flow over a non-slip solid wall, and then combine it with the morphological model to simulate water flow in 3D soil structures acquired using X-ray tomography at resolution of 10 µm. As a validation, we compare the permeability calculated by the model under different saturations with those estimated by the van Genuchten formula using the saturated permeability and water retention parameters obtained from the morphological model. We also discuss the pros and cons of the model and its implications in unsaturated soil modelling.
... The primary challenge in using SRXCT descriptions of the rhizosphere to parameterise models and/or understand root hair morphology is the deleterious occlusion of hairs by the non-gaseous soil phases (Keyes et al. 2013;Daly et al. 2016;Koebernick et al. 2017). This is a small-scale instance of the root occlusion problem known from plant-scale imaging, whereby the overlapping X-ray attenuation of roots and water or organic matter phases can render roots indistinguishable in CT data (Heeraman et al. 1997;Kaestner et al. 2006;Lontoc-Roy et al. 2006;Mooney et al. 2012). Figure 2 shows cross sections of nodal roots and representative detail of root hairs for two rice plants (Oryza sativa cv. ...
The rhizosphere is a zone of fundamental importance for understanding the dynamics of nutrient acquisition by plant roots. The canonical difficulty of experimentally investigating the rhizosphere led long ago to the adoption of mathematical models, the most sophisticated of which now incorporate explicit representations of root hairs and rhizosphere soil. Mathematical upscaling regimes, such as homogenisation, offer the possibility of incorporating into larger-scale models the important mechanistic processes occurring at the rhizosphere scale. However, we lack concrete descriptions of all the features required to fully parameterise models at the rhizosphere scale. By combining synchrotron X-ray computed tomography (SRXCT) and a novel root growth assay, we derive a three-dimensional description of rhizosphere soil structure suitable for use in multi-scale modelling frameworks. We describe an approach to mitigate sub-optimal root hair detection via structural root hair growth modelling. The growth model is explicitly parameterised with SRXCT data and simulates three-dimensional root hair ideotypes in silico, which are suitable for both ideotypic analysis and parameterisation of 3D geometry in mathematical models. The study considers different hypothetical conditions governing root hair interactions with soil matrices, with their respective effects on hair morphology being compared between idealised and image-derived soil/root geometries. The studies in idealised geometries suggest that packing arrangement of soil affects hair tortuosity more than the particle diameter. Results in field-derived soil suggest that hair access to poorly mobile nutrients is particularly sensitive to the physical interaction between the growing hairs and the phase of the soil in which soil water is present (i.e. the hydrated textural phase). The general trends in fluid-coincident hair length with distance from the root, and their dependence on hair/soil interaction mechanisms, are conserved across Cartesian and cylindrical geometries.
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The online version of this article (doi:10.1007/s11538-017-0350-x) contains supplementary material, which is available to authorized users.
... De premières études tomographiques se sont intéressées aux stries de croissances et à la densité du bois actuel (Onoe et al., 1983 ;Taylor et al., 1984 ;Funt & Bryan, 1987 ;Lindgren,1991 ;Fromm et al., 2001). Dans les années 1990 et 2000, un certain nombre d'études se sont penchées sur le cas des systèmes racinaires (Heeraman et al., 1997 ;Pierret et al., 1999 ;Gregory et al., 2003 ;Kaestner et al., 2006 ;Tracy et al., 2010 ;Flavel et al., 2012 ;Mairhofer et al., 2012 ;Mooney et al., 2012). Ces A-B, fruits pyritisés de l'Eocène inférieur (London Clay Flora). ...
La transition Crétacé inférieur-Crétacé supérieur (environ 100 millions d’années) marque une période cruciale pour l’évolution de certaines plantes à graines. Elle correspond à la rapide radiation des plantes à fleurs et à la réorganisation écologique des Angiospermes et des conifères. Cependant, notre connaissance des plantes à graines durant le Crétacé moyen et en Laurasie reste encore très partielle. Pendant la dernière décennie, la microtomographie synchrotron s’est avérée une technique d’imagerie très performante pour l’étude des structures internes de divers fossiles. Jusqu’à maintenant, les applications de cette technique n’ont été que très limitées en paléobotanique.C’est dans ce contexte que cette thèse s’est intéressée : (1) au développement de nouvelles approches d’imagerie par tomographie, utiles en paléobotanique, et sur différents types de préservation ; (2) à l’utilisation de ces nouvelles approches pour compléter notre connaissance de la morpho-anatomie, la systématique, la diversité, et l’écologie des plantes à graines laurasiatiques du Crétacé moyen. Ainsi, un peu plus d’une centaine de spécimens (e.g. inflorescences, fleurs, fruits, et grains de pollen d’Angiospermes ; cônes and axes feuillés de conifères) provenant de gisements paléontologiques français ont été étudiés par tomographie synchrotron.Pour la première fois, de nombreuses fleurs très diversifiées sont décrites dans les dépôts cénomaniens du Gard (Sud-Est de la France). Elles montrent une remarquable préservation en trois dimensions. Dans certains cas, toutes les unités florales du périanthe, de l’androcée, et du gynécée sont préservées. Un nouveau protocole combinant microtomographie par contraste de phase de propagation et nano-holotomographie a été développé pour étudier des petits spécimens isolés tels que des fleurs préservées sous forme de fusain ou de lignite (taille de voxel proche de 50 nm). Les données tomographiques permettent de décrire les fleurs de la morphologie générale à la paroi des grains de pollen, in situ, dans les étamines. Certaines de ces fleurs montrent des structures florales inédites. Elles sont majoritairement attribuées à des Lauraceae.De plus, des nodules siliceux, opaques, denses, et contenant des inclusions végétales sont ici signalés dans les dépôts cénomaniens de Charente-Maritime (Ouest de la France). Ils contiennent d’abondants restes de conifères (e.g. Brachyphyllum, Frenelopsis, Geinitzia et Glenrosa). Ils sont préservés sous forme de perminéralisation siliceuse et en trois dimensions. L’essentiel des tissus est préservé. Ce travail propose un protocole tomographique multi-échelles, haute résolution et haute énergie, utile à l’étude d’inclusions végétales contenues à l’intérieur de nodules rocheux de grande dimension. Le conifère Glenrosa est décrit pour la première fois, de la morphologie générale des structures végétatives et reproductives à l’histologie. Nous discutons la systématique et la paléoécophysiologie de ce genre. Les caractéristiques xéromorphes de Glenrosa suggèrent que ce conifère était probablement adapté pour tolérer des conditions difficiles induites par les milieux côtiers. Ce travail soutient que pendant le Cénomanien, les environnements les plus ouverts sur la mer étaient dominés par les conifères alors que les milieux littoraux plus internes et protégés montraient quant à eux des flores à dominante angiospermienne.Pour conclure, cette recherche doctorale contribue considérablement à notre connaissance des Angiospermes et des conifères de la Laurasie, pendant le Crétacé moyen. De plus, les nouvelles approches tomographiques proposées dans ce travail pourront être reproductibles pour l’étude d’autres flores, ou d’autres spécimens paléontologiques, quelle que soit leur origine géographique et stratigraphique.
... The primary challenge in using SRXCT descriptions of the rhizosphere to parameterise models and/or understand root hair morphology is the deleterious occlusion of hairs by the non-gaseous soil phases (Keyes et al. 2013;Daly et al. 2016;Koebernick et al. 2017). This is a small-scale instance of the root occlusion problem known from plant-scale imaging, whereby the overlapping X-ray attenuation of roots and water or organic matter phases can render roots indistinguishable in CT data (Heeraman et al. 1997;Kaestner et al. 2006;Lontoc-Roy et al. 2006;Mooney et al. 2012). Figure 2 shows cross sections of nodal roots and representative detail of root hairs for two rice plants (Oryza sativa cv. ...
Background: the rhizosphere is a zone of fundamental importance for understanding the dynamics of nutrient acquisition by plant roots. The canonical difficulty of experimentally investigating the rhizosphere led long ago to the adoption of mathematical models, the most sophisticated of which now incorporate explicit representations of root hairs and rhizosphere soil. Mathematical upscaling regimes, such as homogenisation, offer the possibility of incorporating into larger scale models the important mechanistic processes occurring at the rhizosphere scale. However, we lack concrete descriptions of all the features required to fully parameterise models at the rhizosphere scale.
Scope : by combining Synchrotron X-ray Computed Tomography (SRXCT) and a novel root growth assay, we derive a three-dimensional description of rhizosphere soil structure suitable for use in multi-scale modelling frameworks. We describe an approach to mitigate sub-optimal root-hair detection via structural root-hair growth modelling. The growth model is explicitly parameterized with SRXCT data, and simulates three-dimensional root hair ideotypes in silico, which are suitable for both ideotypic analysis and parameterisation of 3D geometry in mathematical models.
Conclusions: the study considers different hypothetical conditions governing root hair interactions with soil matrices, with their respective effects on hair morphology being compared between idealized and image-derived soil/root geometries. The studies in idealised geometries suggest that packing arrangement of soil affects hair tortuosity more than the particle diameter. Results:in field-derived soil suggest that hair access to poorly-mobile nutrients is particularly sensitive to the physical interaction between the growing hairs and the phase of the soil in which soil water is present (i.e. the hydrated textural phase). The general trends in fluid-coincident hair length with distance from the root, and their dependence on hair/soil interaction mechanisms, are conserved across Cartesian and cylindrical geometries.<br/
... The more advanced noise reduction algorithm with use of anisotropic diffusion filter was proposed in (Heinzl et al. 2007), while in (Huang et al. 2003) the authors used 3D Gaussian filter for noise reduction. Another feature extraction algorithm was presented in (Kaestner et al. 2006), where the authors used non-linear diffusion filter to enhance the contrast and then the adaptive thresholding procedure for overall enhancement of measurement data and availability of features extraction from them. Several studies of feature extraction from CT scans were performed using wavelet analysis. ...
The proposed method of processing of X-ray Computed Tomography (CT) data is based on its three-dimensional (3D) wavelet analysis, which allows for detection and localization of sudden changes in voxels of CT data array. The applied wavelet transform can be considered as filtering using sets of low-pass and high-pass filters over directions of a domain. The internal damage, which initially has different spectrum than the healthy regions of a structure, are emphasized after the wavelet analysis and depending on its intensity in the CT data array the wavelet coefficients become different for them. The tests were performed on the carbon fibre reinforced composite plate. The water-jet method was used for cutting of a circular hole inside. During the cutting process several delaminations in various layers occurred. Moreover, during the manufacturing process several air pockets in the matrix appeared. Application of the proposed processing algorithm allows not only for detection and localization of internal damage but also its classification by a type. It is possible due to analysing the magnitude of wavelet coefficients after wavelet-based decomposition and characteristic shape and dimensions of various types of damage. This allows for automation of the examination process.
... A powerful computer is than used to stack these images creating a virtual three-dimensional object allowing the analysis of its internal structure 1 . Despite its original development for medical diagnosis (Hounsfield, 1976), computed tomography have long been used for several other scientific purposes (Staedler et al., 2013), including studies in the broad field of Plant Sciences (Heeraman et al., 1997;Kaestner et al., 2006;Brodersen et al., 2012;Gee, 2013;Breteron et al., 2015;Cochard et al., 2015 and others). ...
The complex endophytic structure formed by parasitic plant species often represents a challenge in the study of the host-parasite interface. Even with the large amounts of anatomical slides, a three-dimensional comprehension of the structure may still be difficult to obtain. In the present study we applied the High Resolution X-ray Computed Tomography (HRXCT) analysis along with usual plant anatomy techniques in order to compare the infestation pattern of two mistletoe species of the genus Phoradendron. Additionally, we tested the use of contrasting solutions in order to improve the detection of the parasite’s endophytic tissue. To our knowledge, this is the first study to show the three-dimensional structure of host-mistletoe interface by using HRXCT technique. Results showed that Phoradendron perrottetii growing on the host Tapirira guianensis forms small woody galls with a restricted endophytic system. The sinkers were short and eventually grouped creating a continuous interface with the host wood. On the other hand, the long sinkers of P. bathyoryctum penetrate deeply into the wood of Cedrela fissilis branching in all directions throughout the woody gall area, forming a spread-out infestation pattern. The results indicate that the HRXCT is indeed a powerful approach to understand the endophytic system of parasitic plants. The combination of three-dimensional models of the infestation with anatomical analysis provided a broader understanding of the host-parasite connection. Unique anatomic features are reported for the sinkes of P. perrottetii, while the endophytic tissue of P. bathyoryctum conformed to general anatomy observed for other species of this genus. These differences are hypothesized to be related to the three-dimensional structure of each endophytic system and the communication stablished with the host.
... Computed microtomographic (CMT) imaging has been widely used in the fields of soil science, hydrology, petroleum engineering, and environmental engineering. In petroleum engineering, the focus has often been on extraction of porosity, pore morphology, network information, and relative permeability estimates for use in pore network simulators (e.g., Coles et al., 1998;Lindquist and Venkatarangan, 1999;Turner et al., 2004;Prodanović et al., 2007), whereas in soils and hydrology research, more work has focused on multiphase variables and on estimating properties such as fluid saturation and distribution (e.g., Hopmans, 1999, 2000;Perret et al., 2000); on describing soil structural features such as macropores (e.g., Anderson et al., 1990;Peth et al., 2008;Luo et al., 2010), root structure (e.g., Kaestner et al., 2006;Tracy et al., 2010), and plant uptake mechanisms (e.g., Scheckel et al., 2007). We refer to Taina et al. (2008) for an extensive review of tomography applications in soil science, and to Werth et al. (2010) for contaminant hydrology-type applications. ...
Crop production under stressful and fragile agro-ecologies is really formidable challenge. Under changing climate, the development of crop stress resilience is further challenging owing to its intricacies and linkage among abiotic and biotic stress responses and unprecedented prevalence of climatic vulnerabilities. Root mediated stress modulation and rhizosphere engineering is one of the novel approaches for improved crop growth and productivity under resource poor stressful environments. Holistic understanding and harnessing/tapping of inherent root associated traits including versatile root architecture and complex plant–microbe interactions in consonance with enhanced root exudation potential is one of the frontier areas of crop science research. Crop plants with wider root adaptability and root growth plasticity is quite essential for scavenging more quantities of essential nutrients under marginal and degraded lands. But the extent of employing root adaptability with differential exudation of organic compounds to drive selective plant–microbe interactions is merely exploited as source for crop resilience particularly under imminent multiple stresses. “Root microbiome” being integral reservoir of microbes is controlled by stress and cultivar specific root exudation and reported to evoke various cellular, biochemical, and molecular processes to improve the metabolic capability of crop under stressful environment. A systematic study of structure and function of root microbiome in accordance with expression of related candidate genes as directed by crop adaptability and environmental factors is critical for devising reliable crop production strategies to improve productivity. Conventional efforts to manage unabated crop stresses and to attain potential crop yields are not withstanding and long lasting. Comprehensive understanding of root adaptive mechanisms coupled with genetic and modern biotechnological approaches besides integrated and innovative fertilization practices are the need of the hour to yield economically feasible and environmentally sustainable results. In this backdrop this chapter deals with various root associated traits such as root architecture, root exudation potential, and root microbiome which are majorly important for developing crop stress resilience.KeywordsCrop stressesNutrient uptakeRoot architectureRoot exudationRoot microbiomeRhizosphere efficiency
The phenotyping of plant roots is a challenging
task and poses a major lacuna in plant root research. Roots
rhizospheric zone is afected by several environmental cues
among which salinity, drought, heavy metal and soil pH are
key players. Among biological factors, fungal, nematode and
bacterial interactions with roots are vital for improving nutrient uptake efciency in plants. The subterranean nature of
a plant root and the limited number of approaches for root
phenotyping ofers a great challenge to the plant breeders
to select a desirable root trait under diferent stress conditions. Identifcation of key root traits can provide a basic
understanding for generating crop plants with enhanced
ability to withstand various biotic or abiotic stresses. For
instance, crops with improved soil exploration potential,
phosphate uptake efciency, water use efciency and others.Laboratory methods such as hydroponics, rhizotron, rhizoslide and luminescence observatory for roots do not provide
precise and desired root quantifcation attributes. Though
3D imaging by X-ray computed tomography (X-ray-CT)
and magnetic resonance imaging techniques are complex,
however, it provides the most applicable and practically relevant data for quantifying root system architecture traits.
This review outlines the current developments in root studies
including recent approaches viz. X-ray-CT, MRI, thermal
infrared imaging and minirhizotron. Although root phenotyping is a laborious procedure, it ofers multiple advantages
by removing discrepancies and providing the actual practical
signifcance of plant roots for breeding programs.
Plant phenotype plays an important role in genetics, botany, and agronomy, while the currently popular methods for phenotypic trait measurement have some limitations in aspects of cost, performance, and space-time coverage. With the rapid development of imaging technology, computing power, and algorithms, computer vision has thoroughly revolutionized the plant phenotyping and is now a major tool for phenotypic analysis. Based on the above reasons, researchers are devoted to developing image-based plant phenotyping methods as a complementary or even alternative to the manual measurement. However, the use of computer vision technology to analyze plant phenotypic traits can be affected by many factors such as research environment, imaging system, research object, feature extraction, model selection, and so on. Currently, there is no review paper to compare and analyze these methods thoroughly. Therefore, this review introduces the typical plant phenotyping methods based on computer vision in detail, with their principle, applicable range, results, and comparison. This paper extensively reviews 200+ papers of plant phenotyping in the light of its technical evolution, spanning over twenty years (from 2000 to 2020). A number of topics have been covered in this paper, including imaging technologies, plant datasets, and state-of-the-art phenotyping methods. In this review, we categorize the plant phenotyping into two main groups: plant organ phenotyping and whole-plant phenotyping. Furthermore, for each group, we analyze each research of these groups and discuss the limitations of the current approaches and future research directions.
Three- and four-dimensional imaging techniques are a prerequisite for spatially resolving the form-structure-function relationships in plants. However, choosing the right imaging method is a difficult and time-consuming process as the imaging principles, advantages and limitations, as well as the appropriate fields of application first need to be compared. The present study aims to provide an overview of three imaging methods that allow for imaging opaque, large and thick (>5 mm, up to several centimeters), hierarchically organized plant samples that can have complex geometries. We compare light microscopy of serial thin sections followed by 3D reconstruction (LMTS3D) as an optical imaging technique, micro-computed tomography (µ-CT) based on ionizing radiation, and magnetic resonance imaging (MRI) which uses the natural magnetic properties of a sample for image acquisition. We discuss the most important imaging principles, advantages, and limitations, and suggest fields of application for each imaging technique (LMTS, µ-CT, and MRI) with regard to static (at a given time; 3D) and dynamic (at different time points; quasi 4D) structural and functional plant imaging.
Due to the availability of commercial laboratory systems and the emergence of user facilities at synchrotron radiation sources, studies of microcomputed tomography or microCT have increased exponentially. MicroComputed Technology provides a complete introduction to the technology, describing how to use it effectively and understand its results. The first part of the book focuses on methodology, covering experimental methods, data analysis, and visualization approaches. The second part addresses various microCT applications, including porous solids, microstructural evolution, soft tissue studies, multimode studies, and indirect analyses. The author presents a sufficient amount of fundamental material so that those new to the field can develop a relative understanding of how to design their own microCT studies. One of the first full-length references dedicated to microCT, this book provides an accessible introduction to field, supplemented with application examples and color images.
R OOTS have an extreme impact on soil properties and parameters are essential toward successful crop management. The study aims at modifying simple and quick method to identify key parameters of root structure by using medical X-ray CT)X-ray computed tomography) scanning technique and assesses its potentials.The results reveal that the modified simple procedures made it possible to isolate the root from the soil and partially overcome the problem of partial volume effect, and the main taproot was shown located at 0 to 30 mm depth. This procedure presented appropriate technique for segmenting large amounts of data. The modified method reduced the duration of the experiment and the risk of sample disturbance compared with the conventional methods to derive the architecture and the functional imaging. Results of plant growth parameters were closely related to the morphological parameters measured using the medical X-ray CT techniques.This approach enabledobservingroot growth manner and how individual roots overcome obstacles on their way. The technique modification shows great potential to provide new fundamental insights into soil-plant interactions and increase understanding of soil plant relationship. 13
X-ray computed tomography (CT) combined with a quantitative analysis of the resulting volume images is a fruitful technique in soil science. However, the variations in X-ray attenuation due to different soil components keep the segmentation of single components within these highly heterogeneous samples a challenging problem. Particularly demanding are bio-pores due to their elongated shape and the low gray value difference to the surrounding soil structure.
Recently, variational models in connection with algorithms from convex optimization were successfully applied for image segmentation. In this paper we apply these methods for the first time for the segmentation of bio-pores in CT images of soil samples. We introduce a novel convex model which enforces smooth boundaries of bio-pores and takes the varying attenuation values in the depth into account. Segmentation results are reported for different real-world 3D data sets as well as for simulated data. These results are compared with two gray value thresholding methods, namely indicator kriging and a global thresholding procedure, and with a morphological approach. Pros and cons of the methods are assessed by considering geometric features of the segmented bio-pore systems. The variational approach features well-connected smooth pores while not detecting smaller or shallower pores. This is an advantage in cases where the main bio-pores network is of interest and where infillings, e.g., excrements of earthworms, would result in losing pore connections as observed for the other thresholding methods.
We propose a visual object tracking framework for the extraction of multiple interacting plant root systems from three-dimensional X-ray micro computed tomography images of plants grown in soil. Our method is based on a level set framework guided by a greyscale intensity distribution model to identify object boundaries in image cross-sections. Root objects are followed through the data volume, while updating the tracker’s appearance models to adapt to changing intensity values. In the presence of multiple root systems, multiple trackers can be used, but need to distinguish target objects from one another in order to correctly associate roots with their originating plants. Since root objects are expected to exhibit similar greyscale intensity distributions, shape information is used to constrain the evolving level set interfaces in order to lock trackers to their correct targets. The proposed method is tested on root systems of wheat plants grown in soil.
Soil structure affects plant growth in many ways. Roots grow most rapidly in very friable soil, but their uptake of water and nutrients may be limited by inadequate contact with the solid and liquid phases of the soil. This contact is much more intimate in hard soil, but then the growth of the roots is strongly inhibited, so that their foraging ability is poor, and the plant may eventually become short of water or nutrients. However, many soils, even if hard, contain continuous macropores that provide niches for the roots to grow in. The presence of such macropores increases the extent of the root system, but because the roots are clumped within them, the rate at which the roots can extract water and nutrients from the soil between the macropores is considerably slowed. These macropores also provide niches for microorganisms, both symbiotic and pathogenic, so that the response of roots to different tillage treatments may differ markedly on this account alone. Soil structure not only affects the ability of roots to grow and to supply the leaves with water and nutrients; if adverse, it also induces them to send hormonal signals that slow the growth of the shoot, even if they are currently able to take up adequate water and nutrients.
Computer axial tomography (CAT) is one of the most adequate non-destructive techniques for the investigation of the internal structure of a large category of objects. This method, based on the attenuation of X- or gamma-ray, generates digital images which map the numerical values of the linear attenuation coefficient of a section or of the entire volume of the investigated sample. Depending on the energy of the utilized radiation as well as on the effective atomic number of the sample, CAT can furnish, with a spatial resolution of 0.01–0.5 mm, quantitative as well as qualitative information concerning local density or chemical composition of the sample. In geosciences, CAT has been successfully applied to the investigation of bulk density, moisture content or macroporosity of the soil, soil–plant–water system, oil sand or shales, small scale heterogeneities in siltstone or sandstone, diamonds in kimberlite, mineralization layers in manganese nodules, local structure of marine sediments or coal composition. The method has also been used for the investigation of the rock mechanical properties, rock permeability, fracture network, two or three-phase flow or residual oil distribution in carbonate cores. A review of the actual applications of CAT in soil science, sedimentology, coal geology as well as rock mechanics is presented. All these applications reveal the great potential of CAT in geoscience investigations.
X-ray Computed Tomography (CT) is a non-invasive technique that allows forthree-dimensional, nondestructive imaging of heterogeneous materials. Todate, few studies have examined the potential of CT to quantify plant rootsin situ. Pre-germinated bean plants were grown for 14 days in PVC containers(10 cm long5.0 cm internal diameter) containing a sandy soil medium ina growth chamber under optimum growing conditions. The stems of the beanplants were excised and their root systems imaged with a high-energyindustrial tomography unit (420 kV). Forty individual horizontal tomograms,each 200 m thick were combined into a 3-D data set for a total rootingdepth of 0.8 cm starting at the base of the hypocotyl. This volumetric dataset was analyzed for root volume through estimation of relative fractions ofroot and soil matrix within each voxel for the entire 3-D data set. Therendering of iso-attenuation surfaces illustrated the spatial arrangement ofroots with diameters equal and larger than 0.36 mm. In addition, bean rootsystems were destructively sampled at 1-cm depth increments and analyzed fordry weight, total root length and root diameter. Destructive root samplingyielded a root length per unit volume (Lv) between 44 and 60 cm cm-3soil, whereas the CT-measured Lv was about 76 cm cm-3.
Most thresholding algorithms have difficulties processing images with unimodal distributions. In this paper an algorithm, based on finding a corner in the histogram plot, is proposed that is capable of performing bilevel thresholding of such images. Its effectiveness is demonstrated on synthetic data as well as a variety of real data, showing its successful application to edges, corners, difference images, optic flow, texture difference images, polygonal approximation of curves, and image segmentation.
In a fractal branching pattern the same rules govern branching at each subsequent level. The initial size (diameter) and the essential branching rules thus contain the information required to construct the whole pattern. If root branching patterns have fractal characteristics, measurement of the proximal root diameter at the stem base and the branching rules as observed anywhere in the root system, would be enough to predict total root length, root diameter distribution and root length per unit dry weight (specific root length).
A ‘pipe stem’ model is used to derive algebraic relations between total root size and proximal root diameter for two classes of branching patterns, determinate and proportionate. To predict total root length from the proximal root diameter, at least information is needed on the minimum root diameter, the average length of internal and external links (segments) and the proportionality factor between total cross sectional areas before and after branching. For the length of the longest root or the specific root length further information on the branching rules is needed, as it is highest for determinate and proportionate branching rules, respectively.
If root systems have scale-independent branching rules, the total number of links in the root system can be predicted from
the ratio of the largest and smallest root diameter. In Paper I we presented an algebraic model for a dicho-syntomous pattern
(the simplest form of proportionate branching forming two equal branches at each node) and a herringbone branching model (the
simplest form of determinate branching rules). Here, we present a recursive computer model and its results to analyze intermediate
patterns, derived from allotomous proportionate branching (with unequal branches). The numerical and algebraic model gave
the same results when applied to the same situation and parameter values.
For practical applications of the relations found, a test is required on whether or not the underlying assumptions are met.
To illustrate such a test, measurements of the branching pattern were made on Mondriaan's Red Tree painting. For patterns
such as this tree a slight dependency of the proportionality factor on root diameter and random variability of several parameters
may have to be included.
A new theoretical and experimental framework that permits an accurate determination of aggregate-size stability distribution is presented. The size-stability distribution in addition to estimating aggregate-size distribution distinguishes between amounts of stable and unstable macroaggregates (>250 micrometer). The determination of aggregate-size stability distribution involves the assumptions that soil aggregates can be categorized in terms of their size and water stability (slaking resistance). Experimentally this procedure involves the slaked and capillary-wetted pretreatments; and a subsequent slaking treatment of aggregates >250 micrometer in size. We also propose the stable aggregates index (SAI) and the stable macroaggregates index (SMaI) for studying soil stability based on aggregate resistance to slaking. These indices account for the total weighted average of stable aggregates and the total weighted average of stable macroaggregates, respectively. Both the SAI and the SMaI indices were shown to be sensitive to the effects of vegetation on soil stability under different riparian buffer communities. The SAI and the SMaI indices were higher in surface soils under cool-season grass than any of the other treatments. These soils samples are well aggregated with SAI = 74% and SMaI = 56% followed by SAI = 55% and SMaI = 37% under existing riparian forest, SAI = 40% and SMaI = 21% under 7-yr switchgrass and SAI = 36% and SMaI = 18% under cropped system.
A quantitative model of wheat root systems is developed that links the size and distribution of the root system to the capture of water and nitrogen (which are assumed to be evenly distributed with depth) during grain filling, and allows estimates of the economic consequences of this capture to be assessed. A particular feature of the model is its use of summarizing concepts, and reliance on only the minimum number of parameters (each with a clear biological meaning). The model is then used to provide an economic sensitivity analysis of possible target characteristics for manipulating root systems. These characteristics were: root distribution with depth, proportional dry matter partitioning to roots, resource capture coefficients, shoot dry weight at anthesis, specific root weight and water use efficiency. From the current estimates of parameters it is concluded that a larger investment by the crop in fine roots at depth in the soil, and less proliferation of roots in surface layers, would improve yields by accessing extra resources. The economic return on investment in roots for water capture was twice that of the same amount invested for nitrogen capture. DEFRA
Current streambank restoration efforts focus on providing bank stability, enhancing water quality, and improving woody habitat using native vegetation rather than traditional engineering techniques. However, in most cases harsh site conditions limit restoration success. A two-year field study was conducted at Twentymile Creek, in northern Mississippi, investigating edaphic factors governing the survival of black willow (Salix nigra) cuttings used for streambank restoration. Low height growth, above-ground biomass production, and average leaf area were observed in willow cuttings grown in plots subjected to moisture deficits. However, sediment texture emerged as the dominant factor determining willow post growth, health, and survival. Shoot biomass, leaf biomass, and total above-ground biomass were 15-, 10-, and 14-fold greater for large willow cuttings (posts) grown in plots with sandy sediments relative to those grown in plots with similar moisture and soil redox potential but with silt and clay sediments. Average leaf size, average leaf mass and specific leaf area were all lower in fine textured plots. Under moisture conditions present at our sites, coarse-grained sediment (sand) was more conducive to willow growth, biomass production, and survival than were fine-grained sediments (silt/clay). Our results strongly suggest that soil texture and moisture conditions can determine restoration success. Therefore, it is critical that site conditions are factored into the selection of project locations prior to the initiation of willow planting restoration projects.
Relations between anisotropic diffusion and robust statistics are described in this paper. Specifically, we show that anisotropic diffusion can be seen as a robust estimation procedure that estimates a piecewise smooth image from a noisy input image. The "edge-stopping" function in the anisotropic diffusion equation is closely related to the error norm and influence function in the robust estimation framework. This connection leads to a new "edge-stopping" function based on Tukey's biweight robust estimator that preserves sharper boundaries than previous formulations and improves the automatic stopping of the diffusion. The robust statistical interpretation also provides a means for detecting the boundaries (edges) between the piecewise smooth regions in an image that has been smoothed with anisotropic diffusion. Additionally, we derive a relationship between anisotropic diffusion and regularization with line processes. Adding constraints on the spatial organization of the line processes allows us to develop new anisotropic diffusion equations that result in a qualitative improvement in the continuity of edges.
A quantitative model of wheat root systems is developed that links the size and distribution of the root system to the capture of water and nitrogen (which are assumed to be evenly distributed with depth) during grain filling, and allows estimates of the economic consequences of this capture to be assessed. A particular feature of the model is its use of summarizing concepts, and reliance on only the minimum number of parameters (each with a clear biological meaning). The model is then used to provide an economic sensitivity analysis of possible target characteristics for manipulating root systems. These characteristics were: root distribution with depth, proportional dry matter partitioning to roots, resource capture coefficients, shoot dry weight at anthesis, specific root weight and water use efficiency. From the current estimates of parameters it is concluded that a larger investment by the crop in fine roots at depth in the soil, and less proliferation of roots in surface layers, would improve yields by accessing extra resources. The economic return on investment in roots for water capture was twice that of the same amount invested for nitrogen capture.
Glomalin is a recently discovered glypoproteinaceous substance produced by arbuscular mycorrhizal fungi (AMF) that plays an important role in structuring soil. We quantified soil fungal hyphal length and glomalin content at vegetated and open microsites in Stipa tenacissima steppes of SE Spain. Soils underneath the canopy of S. tenacissima had higher glomalin pools compared to open microsites. We also found significant differences between sites, suggesting the presence of landscape level heterogeneity in glomalin concentration. Soil fungal hyphal length also differed significantly among the sites, but there was no significant effect of microsite. Water-stable aggregates (1 - 2 mm diameter; WSA 1-2 mm), however, while differing among sites, did not vary as a function of microsite. Furthermore, WSA 1-2 mm was negatively correlated with glomalin fractions, as well as soil organic C. Carbonates were likely the major binding agents in these carbonate-rich (average carbonate content: 71%) soils, and not organic C (including glomalin). AMF-mediated stabilization of soil aggregates did not contribute to the formation and maintenance of fertile islands underneath the canopy of S. tenacissima. q 2003 Elsevier Ltd. All rights reserved.
Plant roots are subjected to mechanical impedance when soil pore space cannot accommodate the extending root system. The paper examines briefly the theoretical aspects of the combined effects of stress and moisture history in modifying both the pore space available for root growth and soil strength that limits the ability of roots to deform the soil. A root extension model that requires cyclic changes in root apex geometry to overcome pore space confinement is described. Cells in the growth zone of roots are analysed as pressurized thin-walled structures of simple geometrical shape made of a polymeric elastomer reinforced by a network of symmetrical inextensible fibrils. Such structures exhibit somewhat unexpected but unique changes in shape governed by both fibril arrangement and contact stresses acting on the external surfaces. A simplified model of a root apex can be constructed from these structural units and the behaviour of this model lends support to the proposed variable root apex geometry routine evolved by roots to penetrate compact soils. This analysis highlights the crucial role played by physical factors in the growth processes of roots and the disparate models described provide the basis for the development of a comprehensive quantitative model of root proliferation.
Glomalin is a recently discovered glypoproteinaceous substance produced by arbuscular mycorrhizal fungi (AMF) that plays an important role in structuring soil. We quantified soil fungal hyphal length and glomalin content at vegetated and open microsites in Stipa tenacissima steppes of SE Spain. Soils underneath the canopy of S. tenacissima had higher glomalin pools compared to open microsites. We also found significant differences between sites, suggesting the presence of landscape level heterogeneity in glomalin concentration. Soil fungal hyphal length also differed significantly among the sites, but there was no significant effect of microsite. Water-stable aggregates (1–2 mm diameter; WSA1–2mm), however, while differing among sites, did not vary as a function of microsite. Furthermore, WSA1–2mm was negatively correlated with glomalin fractions, as well as soil organic C. Carbonates were likely the major binding agents in these carbonate-rich (average carbonate content: 71%) soils, and not organic C (including glomalin). AMF-mediated stabilization of soil aggregates did not contribute to the formation and maintenance of fertile islands underneath the canopy of S. tenacissima.
This paper presents the use of x-ray tomography imaging to reconstruct a three-dimensional (3D) digital representation of individual particles in a granular system. The granular system is represented by the mass center coordinates and the morphology representation of each particle. An automated procedure using pattern recognition to identify related particle cross sections in adjacent serial images was developed. Procedures to calculate quantities needed for subsequent simulation of particle behavior including the volume and the momentum of inertia of each particle are also presented. The developments described in the paper enable modeling and simulation of the behavior, and experimental observations of the particle kinematics of real microstructures of granular materials in a true 3D platform.
A new version of the Perona and Malik theory for edge detection and image restoration is proposed. This new version keeps all the improvements of the original model and avoids its drawbacks: it is proved to be stable in presence of noise, with existence and uniqueness results. Numerical experiments on natural images are presented.
Plant roots are subjected to mechanical impedance when soil pore space cannot accommodate the extending root system. The paper examines briefly the theoretical aspects of the combined effects of stress and moisture history in modifying both the pore space available for root growth and soil strength that limits the ability of roots to deform the soil. A root extension model that requires cyclic changes in root apex geometry to overcome pore space confinement is described. Cells in the growth zone of roots are analysed as pressurized thin-walled structures of simple geometrical shape made of a polymeric elastomer reinforced by a network of symmetrical inextensible fibrils. Such structures exhibit somewhat unexpected but unique changes in shape governed by both fibril arrangement and contact stresses acting on the external surfaces. A simplified model of a root apex can be constructed from these structural units and the behaviour of this model lends support to the proposed variable root apex geometry routine evolved by roots to penetrate compact soils. This analysis highlights the crucial role played by physical factors in the growth processes of roots and the disparate models described provide the basis for the development of a comprehensive quantitative model of root proliferation.
The role of the rhizosphere in relation to mineral nutrition is discussed within a quantitative framework using the Barber-Cushman model as a starting point. The uptake or release of nutrients by roots growing in soil leads to concentration gradients forming in the soil: the zone so affected is termed the rhizosphere. The nature of these gradients depends on three factors: the rate of uptake/release; the mobility of the nutrient in soil; and the rate of conversion between available and unavailable forms. The interplay between these factors determines the amount of mineral nutrients acquired by the plant and it is the complexity of the interplay which demands the use of mathematical models in order to understand which factors most limit uptake. Despite extensive experimental evidence of root-mediated changes to the physical, chemical and biological status of rhizosphere soil, the quantitative significance of these changes for mineral nutrition has not been assessed. The problems of making this quantitative transition are reviewed.
Plants require roots to supply water, nutrients and oxygen for growth. The spatial distribution of roots in relation to the
macropore structure of the soil in which they are growing influences how effective they are at accessing these resources.
A method for quantifying root-macropore associations from horizontal soil sections is illustrated using two black vertisols
from the Darling Downs, Queensland, Australia. Two-dimensional digital images were obtained of the macropore structure and
root distribution for an area 55 × 55 mm at a resolution of 64 μm. The spatial distribution of roots was quantified over a
range of distances using the K-function. In all specimens, roots were shown to be clustered at short distances (1–10 mm) becoming
more random at longer distances. Root location in relation to macropores was estimated using the function describing the distance
of each root to the nearest macropore. From this function, a summary variable, termed the macropore sheath, was defined. The
macropore sheath is the distance from macropores within which 80% of roots are located. Measured root locations were compared
to random simulations of root distribution to establish if there was a preferential association between roots and macropores.
More roots were found in and around macropores than expected at random.
The mechanical and physiological bases for root growth against high mechanical impedance are reviewed. The best estimates of maximum axial root growth pressure (max) in completely impeded pea roots appear to be from 0.5 to 0.6 MPa, which results from a turgor pressure of about 0.8 MPa. When roots are incompletely impeded, a range of responses has been reported. Roots do not change elongation rate in a simple mechanical way in response to changes in mechanical impedance. Instead, ethylene might play a key role in mediating an increase in root diameter and a decrease in elongation rate. These changes persist for some hours or days after impedance is removed. Differences between species in their ability to penetrate strong soil layers are not related to differences in max, but appear to be due to differences in root diameter. In rice, differences between cultivars in the ability of their roots to penetrate strong wax layers are not related to their elongation rates through uniformly strong media. Differences between species or cultivars in their ability to penetrate strong layers may be due to differences in the tendency of roots to deflect or buckle when they grow from a weak to a strong environment.
X-ray micro-tomography is a well-established technique for non-invasive imaging and evaluation of heterogeneous materials. An inexpensive X-ray micro-tomography system has been designed and built for the specific purposes of examining root growth and root/soil interactions. The system uses a silver target X-ray source with a focal spot diameter of 80 m, an X-ray image intensifier with a sampling aperture of about 100 m, and a sample with a diameter of 25 mm. Pre-germinated wheat and rape seeds were grown for up to 8–10 days in plastic containers in a sandy loam soil sieved to < 250="">m, and imaged with the X-ray system at regular intervals. The quality of 3 D image obtained was good allowing the development and growth of both root axes and some first-order laterals to be observed. The satisfactory discrimination between soil and roots enabled measurements of root diameter (wheat values were 0.48–1.22 mm) in individual tomographic slices and, by tracking from slice to slice, root lengths were also measured. The measurements obtained were generally within 10% of those obtained from destructive samples measured manually and with a flat-bed scanner. Further developments of the system will allow more detailed examination of the root:soil interface.
The aim of this work was to exemplify the specific contribution of both two- and three-dimensional (3D) X-ray computed tomography to characterise earthworm burrow systems. To achieve this purpose we used 3D mathematical morphology operators to characterise burrow systems resulting from the activity of an anecic ( Aporrectodea nocturna), and an endogeic species ( Allolobophora chlorotica), when both species were introduced either separately or together into artificial soil cores. Images of these soil cores were obtained using a medical X-ray tomography scanner. Three-dimensional reconstructions of burrow systems were obtained using a specifically developed segmentation algorithm. To study the differences between burrow systems, a set of classical tools of mathematical morphology (granulometries) were used. So-called granulometries based on different structuring elements clearly separated the different burrow systems. They enabled us to show that burrows made by the anecic species were fatter, longer, more vertical, more continuous but less sinuous than burrows of the endogeic species. The granulometry transform of the soil matrix showed that burrows made by A. nocturna were more evenly distributed than those of A. chlorotica. Although a good discrimination was possible when only one species was introduced into the soil cores, it was not possible to separate burrows of the two species from each other in cases where species were introduced into the same soil core. This limitation, partly due to the insufficient spatial resolution of the medical scanner, precluded the use of the morphological operators to study putative interactions between the two species
Axial X-ray computed tomography (CT) scanning provides a convenient means of recording the three-dimensional form of soil structure. The technique has been used for nearly two decades, but initial development has concentrated on qualitative description of images. More recently, increasing effort has been put into quantifying the geometry and topology of macropores likely to contribute to preferential flow in soils.Here we describe a novel technique for tracing connected macropores in the CT scans. After object extraction, three-dimensional mathematical morphological filters are applied to quantify the reconstructed structure. These filters consist of sequences of so-called erosions and/or dilations of a 32-face structuring element to describe object sizes, distances and volumes of influence. The tracing and quantification methodologies were tested on a set of undisturbed soil cores collected in a Swiss pre-alpine meadow where a new earthworm species (Aporrectodea nocturna) was accidentally introduced. Given the reduced number of samples analysed in this study, the results presented only illustrate the potential of the method to reconstruct and quantify macropores. Our results suggest that the introduction of the new species induced very limited change to the soil structure; for example, no difference in total macropore length or mean diameter was observed. However, in the zone colonised by the new species, individual macropores tended to have a longer average length, be more vertical and be further apart at some depth.Overall, the approach proved well suited to the analysis of the three-dimensional architecture of macropores. It provides a framework for the analysis of complex structures, which are less satisfactorily observed and described using 2D imaging.
Thinning on binary images is an iterative layer by layer erosion until only the “skeletons” of the objects are left. This paper presents an efficient parallel thinning algorithm which produces either curve skeletons or surface skeletons from 3D binary objects. It is important that a curve skeleton is extracted directly (i.e., without creating a surface skeleton). The strategy which is used is called directional: each iteration step is composed of a number of subiterations each of which can be executed in parallel. One iteration step of the proposed algorithm contains 12 subiterations instead of the usual six. The algorithm makes easy implementation possible, since deletable points are given by 3×3×3 matching templates. The topological correctness for (26, 6) binary pictures is proved.
Poor root development due to constraining soil conditions could be an important factor influencing health of urban trees. Therefore, there is a need for efficient techniques to analyze the spatial distribution of tree roots. An analytical procedure for describing tree rooting patterns from X-ray computed tomography (CT) data is described and illustrated. Large irregularly shaped specimens of undisturbed sandy soil were sampled from Various positions around the base of trees using field impregnation with epoxy resin, to stabilize the cohesionless soil. Cores approximately 200 mm in diameter by 500 mm in height were extracted from these specimens. These large core samples were scanned with a medical X-ray CT device, and contiguous images of soil slices (2 mm thick) were thus produced. X-ray CT images are regarded as regularly-spaced sections through the soil although they are not actual 2D sections but matrices of voxels similar to 0.5 mm x 0.5 mm x 2 mm. The images were used to generate the equivalent of horizontal root contact maps from which three-dimensional objects, assumed to be roots, were reconstructed. The resulting connected objects were used to derive indices of the spatial organization of roots, namely: root length distribution, root length density, root growth angle distribution, root spatial distribution, and branching intensity. The successive steps of the method, from sampling to generation of indices of tree root organization, are illustrated through a case study examining rooting patterns of valuable urban trees. (C) 1999 Elsevier Science B.V. All rights reserved.
An X-ray micro-tomography system has been designed that is dedicated to the low-dose imaging of radiation sensitive living organisms and has been used to image the early development of the first few days of plant development immediately after germination. The system is based on third-generation X-ray micro-tomography system and consists of an X-ray tube, two-dimensional X-ray detector and a mechanical sample manipulation stage. The X-ray source is a 50kVp X-ray tube with a silver target with a filter to centre the X-ray spectrum on 22keV.A 100mm diameter X-ray image intensifier (XRII) is used to collect the two-dimensional projection images. The rotation tomography table incorporates a linear translation mechanism to eliminate ring artefact that is commonly associated with third-generation tomography systems. Developing maize seeds (Triticum aestivum) have been imaged using the system with a cubic voxel linear dimension of 100 microm, over a diameter of 25mm and the root lengths and volumes measured. The X-ray dose to the plants was also assessed and found to have no effect on the plant root development.
The root system of a plant is as complicated as the shoot in its diversity, in its reactions with the matrix of substances, and with the myriad organisms that surround it. Laboratory studies blind us to the complexity found by careful study of roots in soil. This complexity is illustrated in the much-studied corn root system, covering the changes along the framework roots: the surface tissues and their interactions with the soil, the water-conducting xylem, whose gradual elaboration dictates the water status of the root. A conspicuous manifestation of the changes is the rhizosheath, whose microflora differs from that on the mature bare zones. The multitude of fine roots is the most active part of the system in acquiring water and nutrients, with its own multitude of root tips, sites of intense chemical activity, that strongly modify the soil they contact, mobilize reluctant ions, immobilize toxic ions, coat the soil particles with mucilage, and select the microflora.
We lack a thorough conceptual and functional understanding of fine roots. Studies that have focused on estimating the quantity of fine roots provide evidence that they dominate overall plant root length. We need a standard procedure to quantify root length/biomass that takes proper account of fine roots. Here we investigated the extent to which root length/biomass may be underestimated using conventional methodology, and examined the technical reasons that could explain such underestimation. Our discussion is based on original X-ray-based measurements and on a literature review spanning more than six decades. We present evidence that root-length recovery depends strongly on the observation scale/spatial resolution at which measurements are carried out; and that observation scales/resolutions adequate for fine root detection have an adverse impact on the processing times required to obtain precise estimates. We conclude that fine roots are the major component of root systems of most (if not all) annual and perennial plants. Hence plant root systems could be much longer, and probably include more biomass, than is widely accepted.
Two different formal definitions of gray-scale reconstruction are presented. The use of gray-scale reconstruction in various image processing applications discussed to illustrate the usefulness of this transformation for image filtering and segmentation tasks. The standard parallel and sequential approaches to reconstruction are reviewed. It is shown that their common drawback is their inefficiency on conventional computers. To improve this situation, an algorithm that is based on the notion of regional maxima and makes use of breadth-first image scannings implemented using a queue of pixels is introduced. Its combination with the sequential technique results in a hybrid gray-scale reconstruction algorithm which is an order of magnitude faster than any previously known algorithm.<
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Nonlinear diffusion filtering in image processing is usually
performed with explicit schemes. They are only stable for very small
time steps, which leads to poor efficiency and limits their practical
use. Based on a discrete nonlinear diffusion scale-space framework we
present semi-implicit schemes which are stable for all time steps. These
novel schemes use an additive operator splitting (AOS), which guarantees
equal treatment of all coordinate axes. They can be implemented easily
in arbitrary dimensions, have good rotational invariance and reveal a
computational complexity and memory requirement which is linear in the
number of pixels. Examples demonstrate that, under typical accuracy
requirements, AOS schemes are at least ten times more efficient than the
widely used explicit schemes
Influence of soil pollution by heavy metals on the water relations of young forest ecosystems
- M Menon
Menon, M., 2006. Influence of soil pollution by heavy metals on the
water relations of young forest ecosystems. PhD thesis, Swiss
Federal Institute of Technology.
Characteristics and frunctions of root systems
- Fitter
Fitter, A., 2002. Characteristics and frunctions of root systems. In:
Waisl, et al. (Ed.), pp. 15-32.
- E A Paul
- F E Clark
Paul, E.A., Clark, F.E., 1996. Soil Microbiology and Biochemistry,
2nd edition. Academic Press, San Diego.
How do roots penetrate soil?
- L J Clark
- W R Whalley
- P B Barraclough
Clark, L.J., Whalley, W.R., Barraclough, P.B., 2003. How do roots
penetrate soil? Plant Soil 255, 93-104.
How do roots penetrate soil?
- Clark