Reconstructing root system architectures from non-invasive imaging techniques for the use in functional structural root models

The combination of functional-structural root-system models with root architectures derived from non-invasive imaging is a promising approach for gaining a better understanding of root-soil interaction processes. However, root architectures can often not be fully recovered using imaging, which subsequently affects the assessment of function via the functional-structural root models. In this study, we explored theoretical and actual possibilities of root system reconstruction from MRI and X-ray CT images. Experiments with water-filled capillaries showed the same minimum detectable diameter for both MRI and X-ray CT for the used parameter setup. Experiments with soil-grown lupine roots, however, showed significantly lower root system recovery fractions for MRI than for X-ray CT, from which most roots thicker than 0.2&#160;mm could be recovered. MRI allowed root signal detection below voxel resolution; however, the connection of this signal to a continuous root structure proved difficult for large, crowded root systems. Furthermore, soil moisture levels >30% hampered root system recovery from MRI scans in experiments with pure sand. To overcome the problem of low root system recovery fractions, we developed a new method that uses incomplete root systems as a scaffold onto which missing roots are simulated using information from WinRhizo measurements. Comparisons of root length within subsamples of semi-virtual root systems and root systems derived from X-ray CT scans showed good agreement. Evaluation of hydraulic root architecture measures of incomplete root system scaffolds and semi-virtual root systems proved the importance of using complete root system reconstructions to simulate root water uptake. Semi-virtual root reconstruction thus appears to be a promising technique to complete root systems for subsequent use in functional-structural root models.

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Novel 3D imaging of root systems grown in slab-shaped rhizotrons

10.5194/egusphere-egu2020-21419 ◽

2020 ◽

Author(s):

Sarah Bereswill ◽

Nicole Rudolph-Mohr ◽

Christian Tötzke ◽

Nikolay Kardjilov ◽

André Hilger ◽

...

Keyword(s):

Soil Moisture ◽

Root System ◽

3D Imaging ◽

Neutron Radiography ◽

Root Systems ◽

Root System Architecture ◽

Moisture Distribution ◽

Ph Gradients ◽

Non Invasive ◽

Soil Moisture Distribution

Complex plant-soil interactions can be visualized and quantified by combined application of different non-invasive imaging techniques. Oxygen, carbon dioxide and pH gradients in the rhizosphere can be observed with fluorescent planar optodes, while neutron radiography detects small-scale heterogeneities in soil moisture and its dynamics. Respiration and exudation rates can vary between roots of different types, such as primary and lateral roots, as well as along single roots among the same plant. The 3D root system architecture is therefore a key information when studying rhizosphere processes. It can be captured in detail with neutron tomography, but so far only for plants grown in small, cylindrical containers.Combined non-invasive imaging of biogeochemical dynamics, soil moisture distribution and 3D root system architecture is a technical challenge. Thin, slab-shaped rhizotrons with relatively large vertical and lateral extension are well suited for optical fluorescence imaging, allowing for spatially extended observation of biogeochemical patterns. This rhizotron geometry is, however, unfavorable for standard 3D tomography due to reconstruction artefacts triggered by insufficient neutron transmission when the long side of the sample is aligned parallel to the beam direction.We therefore applied neutron laminography, a method where the rotational axis is tilted, to measure the root systems of maize and lupine plants grown in slab-shaped glass rhizotrons (length&#160;=&#160;150&#160;mm, width&#160;=&#160;150 mm, depth&#160;=&#160;15 mm) in 3D. In parallel, we investigated rhizosphere oxygen dynamics and pH value via fluorescence imaging and assessed soil moisture distribution with neutron radiography.Neutron laminography enabled the 3D reconstruction of the root systems with a nominal spatial resolution of 100 &#181;m/pixel. Reconstruction quality strongly depended on root-soil contrast and hence soil moisture level. After reconstruction of the root system and co-registration with the fluorescence images, first results indicate that observed oxygen concentrations and pH gradients depend on root type and individual distance of the roots from the planar optode.In conclusion, neutron laminography is a novel 3D imaging method for root-soil systems grown in slab-shaped rhizotrons. The method allows for determining the precise 3D position of individual roots within the rhizotron and can be combined with 2D imaging approaches. Following experiments will address X-ray laminography as a possible attractive further application.

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Effect of parameter choice in root water uptake models – the arrangement of root hydraulic properties within the root architecture affects dynamics and efficiency of root water uptake

Hydrology and Earth System Sciences ◽

10.5194/hess-18-4189-2014 ◽

2014 ◽

Vol 18 (10) ◽

pp. 4189-4206 ◽

Cited By ~ 13

Author(s):

M. Bechmann ◽

C. Schneider ◽

A. Carminati ◽

D. Vetterlein ◽

S. Attinger ◽

...

Keyword(s):

Root System ◽

Water Uptake ◽

Root Length ◽

Hydraulic Properties ◽

Three Dimensional ◽

Root Systems ◽

Root Water Uptake ◽

Hydraulic Lift ◽

Hydraulic Redistribution ◽

Young Root

Abstract. Detailed three-dimensional models of root water uptake have become increasingly popular for investigating the process of root water uptake. However, they suffer from a lack of information on important parameters, particularly on the spatial distribution of root axial and radial conductivities, which vary greatly along a root system. In this paper we explore how the arrangement of those root hydraulic properties and branching within the root system affects modelled uptake dynamics, xylem water potential and the efficiency of root water uptake. We first apply a simple model to illustrate the mechanisms at the scale of single roots. By using two efficiency indices based on (i) the collar xylem potential ("effort") and (ii) the integral amount of unstressed root water uptake ("water yield"), we show that an optimal root length emerges, depending on the ratio between roots axial and radial conductivity. Young roots with high capacity for radial uptake are only efficient when they are short. Branching, in combination with mature transport roots, enables soil exploration and substantially increases active young root length at low collar potentials. Second, we investigate how this shapes uptake dynamics at the plant scale using a comprehensive three-dimensional root water uptake model. Plant-scale dynamics, such as the average uptake depth of entire root systems, were only minimally influenced by the hydraulic parameterization. However, other factors such as hydraulic redistribution, collar potential, internal redistribution patterns and instantaneous uptake depth depended strongly on the arrangement on the arrangement of root hydraulic properties. Root systems were most efficient when assembled of different root types, allowing for separation of root function in uptake (numerous short apical young roots) and transport (longer mature roots). Modelling results became similar when this heterogeneity was accounted for to some degree (i.e. if the root systems contained between 40 and 80% of young uptake roots). The average collar potential was cut to half and unstressed transpiration increased by up to 25% in composed root systems, compared to homogenous ones. Also, the least efficient root system (homogenous young root system) was characterized by excessive bleeding (hydraulic lift), which seemed to be an artifact of the parameterization. We conclude that heterogeneity of root hydraulic properties is a critical component for efficient root systems that needs to be accounted for in complex three-dimensional root water uptake models.

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Wyniki analiz spektrometrycznych dwóch dzbanów fenickich z kolekcji gołuchowskiej

Folia Praehistorica Posnaniensia ◽

10.14746/fpp.2017.22.12 ◽

2018 ◽

Vol 22 ◽

pp. 271-285

Author(s):

Michał Krueger ◽

Inga Głuszek

Keyword(s):

Chemical Composition ◽

Western Mediterranean ◽

X Ray ◽

Spectrometric Data ◽

Non Invasive ◽

Fluorescence Spectrometer ◽

Good Agreement

This paper presents results of the spectrometric analyses of two Phoenician jugs from the Gołuchów collection. A non-invasive portable X-ray fluorescence spectrometer (pXRF) has been used to determine the chemical composition of the jugs. The aim of this work was to add new results to a database of spectrometric data of Phoenician pottery from central and western Mediterranean. Good agreement obtained between the chemical results of the two jugs suggest that they could have been made from the same clay.

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Imaging soil structure to measure soil functions and soil health with X-ray computed micro-tomography

Advances in measuring soil health - Burleigh Dodds Series in Agricultural Science ◽

10.19103/as.2020.0079.11 ◽

2021 ◽

pp. 111-138

Author(s):

Alexandra Kravchenko ◽

◽

Andrey Guber ◽

Keyword(s):

Soil Structure ◽

Imaging Techniques ◽

Soil Health ◽

Depth Information ◽

X Ray ◽

Non Invasive ◽

Pore Architecture ◽

Gas Fluxes ◽

X Ray Computed ◽

Micro Tomography

The use of non-invasive imaging techniques expands opportunities to characterize soil health and functioning, complementing the information from the traditional soil structure analyses. Soil pore architecture drives water and gas fluxes, chemical transport, activity and movement of soil biota; and imaging techniques are particularly suitable for quantifying it. Here we discuss the potential for X-ray computed micro-tomography (X-ray µCT) as a tool to characterize key parameters of soil pore architecture, such as measures of macroporosity, pore connectivity, pore shape, and solid-to-pore distance. We also provide a brief overview of the principles behind X-ray µCT, examples of the latest literature that implemented these pore measures for soil characterization, and recommendations for the methods that can be used to determine these characteristics using publicly available software ImagJ. We also assembled a list of resources where in-depth information and comprehensive reviews of the current literature can be found.

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Study of Colonial Manuscripts from San Nicolás Coatepec, México, Through UV&IR Imaging and XRF

MRS Proceedings ◽

10.1557/opl.2012.1375 ◽

2012 ◽

Vol 1374 ◽

pp. 17-25

Author(s):

Jocelyn Alcántara García ◽

José Luis Ruvalcaba Sil ◽

Marie Van der Meeren

Keyword(s):

Imaging Techniques ◽

High Sensitivity ◽

X Ray ◽

Historical Material ◽

Qualitative And Quantitative ◽

Non Invasive ◽

History Of ◽

Material Information ◽

Non Destructive ◽

Suitable Technique

ABSTRACTThe necessity of studying cultural heritage through non-invasive and non-destructive techniques has led to significant advances in the last decade. One of the most recent advancements in this theme in Mexico is the portable X-ray system SANDRA, which was used to study three manuscripts directly related to the history of “San Nicolás Coatepec”, Mexico. X-ray fluorescence was chosen as the suitable technique because it can provide a fast qualitative and quantitative multielemental high sensitivity analysis. The documents were examined globally, using imaging techniques with UV and IR lighting. This research evinced a change in the composition and evolution of writing materials (inks and pigments) and provided information concerning historical use of the documents and its actual legal value as a property document. It also stressed the need of spanning these results to an extensive research attaining other regions of Mexico, in order to fully understand the Mexican documents particularities, aging and deterioration. This, in turn, will provide not only historical material information but also an invaluable scoop to understand deterioration and conservation issues.

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Imaging secondary reaction products at the surface of Vermeer’s Girl with the Pearl Earring by means of macroscopic X-ray powder diffraction scanning

Heritage Science ◽

10.1186/s40494-019-0309-3 ◽

2019 ◽

Vol 7 (1) ◽

Cited By ~ 10

Author(s):

Steven De Meyer ◽

Frederik Vanmeert ◽

Rani Vertongen ◽

Annelies van Loon ◽

Victor Gonzalez ◽

...

Keyword(s):

Powder Diffraction ◽

Imaging Techniques ◽

Relative Sensitivity ◽

Paint Layer ◽

Ground Layer ◽

Reaction Products ◽

Reflection Mode ◽

Secondary Alteration ◽

X Ray ◽

Non Invasive

Abstract The use of non-invasive macroscopic imaging techniques is becoming more prevalent in the field of cultural heritage, especially to avoid invasive procedures that damage valuable artworks. For this purpose, an X-ray powder diffraction scanner (MA-XRPD) capable of visualising crystalline compounds in a highly specific manner was recently developed. Many inorganic pigments present in paintings fall into this category of materials. In this study, the 17th century oil painting Girl with a Pearl Earring (c. 1665) by Johannes Vermeer was analysed with a combination of transmission and reflection mode MA-XRPD. By employing this scanner in reflection mode, the relative sensitivity for compounds that are present at the paint surface could be increased, establishing it as a highly relevant technique for investigating the degradation processes that are ongoing at paint surfaces. Many of the original pigments employed by Vermeer could be identified, along with four secondary alteration products: gypsum (CaSO4·2H2O), anglesite (PbSO4), palmierite (K2Pb(SO4)2) and weddellite (CaC2O4·2H2O). The formation of gypsum was linked to the presence of chalk in the upper glaze layer while the formation of palmierite and weddellite is driven by the presence of lake pigments (and their substrates). In this manner, MA-XRPD can also be used to pinpoint locations relevant for sampling and synchrotron µ-XRPD analysis, which provides information on the microscopic make-up of the paint. A paint cross-section taken from an area rich in palmierite was analysed with synchrotron µ-XRPD, which confirmed the presence of this secondary compound at the interface of the upper paint layer with the ground layer as well as the presence of anglesite in the ground layer. The capacity of MA-XRPD to identify and chart secondary alteration products in a non-invasive manner has only very recently been demonstrated and makes it a highly relevant technique for the assessment of the chemical condition of works of art.

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An approach to modelling tree root architecture in virtual urban growing conditions

10.32920/ryerson.14667894.v1 ◽

2021 ◽

Author(s):

Justin Miron

Keyword(s):

Root Growth ◽

Root System ◽

Root Architecture ◽

Root Systems ◽

System Structure ◽

Tree Roots ◽

System Architectures ◽

Architecture Model ◽

Investigation Methods ◽

Urban Conditions

Understanding the architecture of tree roots is an important component of urban forestry management practice. Tree roots are structurally and functionally important to the survival of trees, and this can be even more so in urban environments where underground space for roots is limited. Tree root architecture models can provide a complementary approach to traditional on-site field investigation methods. Root architecture models are unique in that they can simulate the spatial arrangements of root system structure explicitly, and allow investigators to create hypothetical simulations to test their assumptions about what may be driving root growth. The use of root architecture models in the literature is extensive and may be applied in diverse streams of investigation, but their application to tree root systems is less common. This research demonstrates a root architecture model, Rootbox, as a case study in the application of plant architecture models to simulate tree root growth in urban conditions. Model parameterization was based on conformity of root simulations to tree root architecture reported in the literature. The model is deployed in four hypothetical urban soil scenarios, which are representative of planting sites commonly observed in urban settings. The analysis demonstrates that plausible tree root system architectures – specifically, commonly observed growth attributes - can be produced by Rootbox, but only after several adaptive changes to both the source code/model design are made. Custom soil models can integrate with the simulation to represent urban conditions by modifying both the growth direction and elongation of portions of the root architecture, and thus offer greater control over the output architecture. Rootbox offers a flexible method of simulating the architecture of tree root systems, but further research should focus on optimizing the model’s parameters and functions to enable greater user control over model output.

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Parameterizing complex root water uptake models – the arrangement of root hydraulic properties within the root architecture affects dynamics and efficiency of root water uptake

Hydrology and Earth System Sciences Discussions ◽

10.5194/hessd-11-757-2014 ◽

2014 ◽

Vol 11 (1) ◽

pp. 757-805 ◽

Cited By ~ 4

Author(s):

M. Bechmann ◽

C. Schneider ◽

A. Carminati ◽

D. Vetterlein ◽

S. Attinger ◽

...

Keyword(s):

Root System ◽

Water Uptake ◽

Plant Resistance ◽

Hydraulic Properties ◽

Three Dimensional ◽

Root Systems ◽

Root Water Uptake ◽

Hydraulic Lift ◽

Excessive Bleeding ◽

Single Root

Abstract. Detailed three-dimensional models of root water uptake have become increasingly popular for investigating the process of root water uptake. However they suffer from a lack of information in important parameters, especially distribution of root hydraulic properties. In this paper we explore the role that arrangement of root hydraulic properties and root system topology play for modelled uptake dynamics. We apply microscopic models of single root structures to investigate the mechanisms shaping uptake dynamics and demonstrate the effects in a complex three dimensional root water uptake model. We introduce two efficiency indices, for (a) overall plant resistance and (b) water stress and show that an appropriate arrangement of root hydraulic properties can increase modelled efficiency of root water uptake in single roots, branched roots and entire root systems. The average uptake depth of the complete root system was not influenced by parameterization. However, other factors such as evolution of collar potential, which is related to the plant resistance, root bleeding and redistribution patterns were strongly affected by the parameterization. Root systems are more efficient when they are assembled of different root types, allowing for separation of root function in uptake (short young) roots and transport (longer mature) roots. Results become similar, as soon as this composition is accounted for to some degree (between 40 and 80% of young uptake roots). Overall resistance to root water uptake was decreased up to 40% and total transpiration was increased up to 25% in these composed root systems, compared to homogenous root systems. Also, one parameterization (homogenous young root system) was characterized by excessive bleeding (hydraulic lift), which was accompanied by lowest efficiency. We conclude that heterogeneity of root hydraulic properties is a critical component of complex three dimensional uptake models. Efficiency measures together with information on critical xylem potentials may be useful in parameterizing root property distribution.

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Sicilian Byzantine Icons through the Use of Non-Invasive Imaging Techniques and Optical Spectroscopy: The Case of the Madonna dell’Elemosina

Molecules ◽

10.3390/molecules26247595 ◽

2021 ◽

Vol 26 (24) ◽

pp. 7595

Author(s):

Francesco Armetta ◽

Gabriella Chirco ◽

Fabrizio Lo Celso ◽

Veronica Ciaramitaro ◽

Eugenio Caponetti ◽

...

Keyword(s):

Imaging Techniques ◽

Spectroscopic Techniques ◽

Eastern European ◽

X Ray ◽

Non Invasive ◽

Byzantine Art ◽

Byzantine Icons ◽

Foreign Materials ◽

Infrared Reflectography ◽

First Time

The iconographic heritage is one of the treasures of Byzantine art that have enriched the south of Italy, and Sicily in particular, since the early 16th century. In this work, the investigations of a Sicilian Icon of Greek-Byzantine origin, the Madonna dell’Elemosina, is reported for the first time. The study was carried out using mainly non-invasive imaging techniques (photography in reflectance and grazing visible light, UV fluorescence, infrared reflectography, radiography, and computed tomography) and spectroscopic techniques (X-ray fluorescence and infrared spectroscopy). The identification of the constituent materials provides a decisive contribution to the correct historical and artistic placement of the Icon, a treasure of the Eastern European historical community in Sicily. Some hidden details have also been highlighted. Most importantly, the information obtained enables us to define its conservation state, the presence of foreign materials, and to direct its protection and restoration.

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