Visualizing three-dimensional root networks using computed tomography

Kaestner, Anders; Schneebeli, Martin; Graf, Frank

doi:10.1016/j.geoderma.2006.04.009

Cited by 95 publications

(93 citation statements)

References 33 publications

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“…diameter of up to 200 μm; Watt et al (2008)). Furthermore, the material density range of plant roots is similar to those of the pore-water and organic matter fractions that constitute the surrounding soil (Kaestner et al 2006). Consequently, automated segmentation using standard computer vision algorithms is difficult to apply and does not yield reliable results (Coleman and Colbert 2007).…”

Section: D Image Analysismentioning

confidence: 99%

“…Until recently, the majority of canonical methods for investigating roots in situ involve either root washing that results in a loss of root material and of spatially resolved data (Berntson and Woodward 1992;Dittmer 1938;Pagliai and De Nobili 1993;Sierra et al 2003;Smucker et al 1982) or rhizoboxes which constrain the observed root system to a 2D plane (Dinkelaker et al 1993;Gibeaut et al 1997;Schmidt et al 2011;Wenzel et al 2001). More recently, a number of studies have demonstrated the utility of X-ray-based, non-destructive tomographic imaging (μCT) for visualising undisturbed plant root systems in real soils (Aylmore 1993;Dunbabin et al 2013;Gregory and Hinsinger 1999;Gregory et al 2003;Heeraman et al 1997;Kaestner et al 2006;Perret et al 2007;Pierret et al 2005;Stuppy et al 2003). Increasingly, the imaging of plants at multiple time intervals is being incorporated into μCT studies, allowing longitudinal quantification of root trait development in relation to key soil parameters .…”

Section: Introductionmentioning

confidence: 99%

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Imaging the interaction of roots and phosphate fertiliser granules using 4D X-ray tomography

et al. 2015

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Aims Plant root system architecture adapts to the prevailing soil environment and the distribution of nutrients. Many species respond to localised regions of high nutrient supply, found in the vicinity of fertiliser granules, by elevating branching density in these areas. However, observation of these adaptations is frequently limited to plants cultured in idealised materials (e.g., hydrogels) which have a structure-less, homogenous matrix, which are spatially limited and in the case of rhizotron observation provide only 2D data that are not fully quantitative. Methods In this study, in vivo, time resolved, microfocus X-ray CT imaging (μCT) in 3D was used to visualise, quantify and assess root/fertiliser interactions of wheat plants in an agricultural soil during the entire plant life cycle. Two contrasting fertilisers [Triple superphosphate (TSP) and struvite (Crystal Green®)] were applied according to 3 different treatments, each providing an equivalent of 80 kg P 2 O 5 ha −1 (struvite only, TSP only and a 50:50 mixture) to each plant. μCT scans (60 μm spatial resolution) of the plant roots were obtained over 14 weeks.Results This is the first time that in situ root/soil/ fertiliser interactions have been visualised in 3D from plant germination through to maturity. Results show that lateral roots tend to pass within a few millimetres of the phosphorus (P) source. At this length scale, roots are able to access the P diffusing from the granule. Conclusions Quantitative analysis of root/fertiliser interactions has shown that rooting density correlates with granule volume-loss for a slow release, struvite fertiliser.

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Section: D Image Analysismentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Imaging the interaction of roots and phosphate fertiliser granules using 4D X-ray tomography

et al. 2015

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“…Digitized measurements can then be used in software to create 3D root system reconstructions [20][21][22]; in fractal branching modeling, which simulates the growth of root systems utilizing statistical relationships among root parts [12]; or for root-density based modeling [23]. Automatic methods have focused on in situ methods such as X-ray computed tomography (CT) scanning for small root systems [24] and ground-penetrating radar (GPR) for large root systems [25].…”

Section: Introductionmentioning

confidence: 99%

Tree Root System Characterization and Volume Estimation by Terrestrial Laser Scanning and Quantitative Structure Modeling

Smith¹,

Astrup²,

Raumonen

et al. 2014

Forests

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Abstract:The accurate characterization of three-dimensional (3D) root architecture, volume, and biomass is important for a wide variety of applications in forest ecology and to better understand tree and soil stability. Technological advancements have led to increasingly more digitized and automated procedures, which have been used to more accurately and quickly describe the 3D structure of root systems. Terrestrial laser scanners (TLS) have successfully been used to describe aboveground structures of individual trees and stand structure, but have only recently been applied to the 3D characterization of whole root systems. In this study, 13 recently harvested Norway spruce root systems were mechanically pulled from the soil, cleaned, and their volumes were measured by OPEN ACCESSForests 2014, 5 3275 displacement. The root systems were suspended, scanned with TLS from three different angles, and the root surfaces from the co-registered point clouds were modeled with the 3D Quantitative Structure Model to determine root architecture and volume. The modeling procedure facilitated the rapid derivation of root volume, diameters, break point diameters, linear root length, cumulative percentages, and root fraction counts. The modeled root systems underestimated root system volume by 4.4%. The modeling procedure is widely applicable and easily adapted to derive other important topological and volumetric root variables.

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“…Para detectar estruturas com tais dimensões, técnicas com maior resolução são necessárias, a exemplo dos métodos não invasivos para visualização e quantificação das raízes em 3D (Kaestner et al, 2006;Mairhofer et al, 2012).…”

Section: Resultsunclassified

“…Na realidade, o crescimento das raízes depende da estrutura do solo, porém a estruturação do solo também depende das raízes, e descobrir o limiar onde o ambiente do solo controla a distribuição espacial das raízes e como o crescimento da raiz modifica a estrutura do solo, é trabalho bem complexo (Kaestner et al, 2006).…”

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Distribuição espacial das raízes de cafeeiro e dos poros de dois Latossolos sob manejo conservacionista

Carducci

Oliveira²,

Lima³

et al. 2014

Rev. bras. eng. agríc. ambient.

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R E S U M OO objetivo deste trabalho foi avaliar o efeito do sistema de manejo que emprega práticas de conservação do solo na distribuição do sistema radicular de cafeeiros e na estrutura de dois Latossolos após seis anos de implantação da lavoura na região do Alto São Francisco, MG. Foram abertas três trincheiras aleatórias e longitudinais à linha de plantio (0,70 x 1,50 m) em um Latossolo gibbsítico e em um Latossolo caulinítico ambos sob sistema de manejo do solo que emprega práticas conservacionistas. A avaliação do sistema radicular foi feita pelo método do perfil cultural e análise digital de imagens 2D, com posterior confecção de mapas de superfície das variáveis radiculares analisadas por meio da krigagem. Amostras de solo com estrutura preservada foram coletadas para quantificar a distribuição do diâmetro de poros 3D obtida por tomografia computada de raios-X. As raízes e poros foram classificados em: 1, >1 e ≤ 3 e > 3 mm de diâmetro. O sistema radicular dos cafeeiros de ambos os solos em estudo mesmo sobre o mesmo sistema de manejo apresentaram boa ramificação na direção horizontal e vertical. A maior concentração de raízes ocorreu na profundidade de 0,20-0,34 m no Latossolo caulinítico. No Latossolo gibbsítico, a distribuição radicular foi uniformizada especialmente na direção vertical do perfil do solo atingindo maiores profundidade. A maior ocorrência de raízes finas ocorreu no Latossolo gibsítico na profundidade de 0,80-0,94 m. Spatial distribution of coffee roots and pores of two Latosols under conservationist management A B S T R A C TThe aim of this study was to evaluate the effect of management system employing soil conservation practices in the coffee root system distribution and in the structure of two Latosols after six years in the crop establishment in Alto São Francisco Valley, MG. Three random trenches were made lengthwise along the row planting (0.70 x 1.50 m) in a gibbsitic Latosol and a kaolinitc Latosol both under soil management system employing soil conservationist practices. The root system evaluation was done by crop profile methods and 2D image analyze, with subsequent surface mapping of the root variables analyzed by kriging. Intact soil cores were sampled for pore diameter distribution analysed by X-ray CT scan. The roots and pores were classified by diameter:1, > 1 and ≤ 3 and > 3 mm. The coffee root system in both soils under study on the same management system showed good branching in horizontal and vertical direction. The highest root concentration occurred at 0.20-0.34 m depth in kaolinitic Latosol. In gibbsitic Latosol the root distribution was uniform, especially in the vertical soil profile reaching greater depths. The highest occurrence of fine roots in the gibbsitic Latosol occurred at 0.80-0.94 m depth.Palavras-chave: morfologia radicular análise de imagem tomografia computada de raios-X krigagem Coffea arabica L. Key words:roots morphology image analyze X-ray CT scan kriging Coffea arabica L. Revista Brasileira de Engenharia Agrícola e AmbientalCampina Grande, PB, ...

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Visualizing three-dimensional root networks using computed tomography

Cited by 95 publications

References 33 publications

Imaging the interaction of roots and phosphate fertiliser granules using 4D X-ray tomography

Imaging the interaction of roots and phosphate fertiliser granules using 4D X-ray tomography

Tree Root System Characterization and Volume Estimation by Terrestrial Laser Scanning and Quantitative Structure Modeling

Distribuição espacial das raízes de cafeeiro e dos poros de dois Latossolos sob manejo conservacionista

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