Visual tracking for the recovery of multiple interacting plant root systems from X-ray $$\upmu $$ μ CT images

Mairhofer, Stefan; Johnson, James A.; Sturrock, Craig J.; Bennett, Malcolm J.; Mooney, Sacha J.; Pridmore, Tony

doi:10.1007/s00138-015-0733-7

Cited by 19 publications

(18 citation statements)

References 41 publications

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“…Hapca et al (2015) used a statistical approach to map the 3-D distribution of several elements in undisturbed soil by combining 3-D X-ray images with 2-D SEM-EDX data. Mairhofer et al (2016) visualized plant root interactions in undisturbed soil and Ahmed et al (2016) visualized interactions of plant roots, phosphate fertilizers and soil structure over time in 3-D using X-ray imaging.…”

Section: Introductionmentioning

confidence: 99%

Quantitative imaging of the 3-D distribution of cation adsorption sites in undisturbed soil

Keck

Strobel

Gustafsson

et al. 2017

SOIL

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Abstract. Several studies have shown that the distribution of cation adsorption sites (CASs) is patchy at a millimetre to centimetre scale. Often, larger concentrations of CASs in biopores or aggregate coatings have been reported in the literature. This heterogeneity has implications on the accessibility of CASs and may influence the performance of soil system models that assume a spatially homogeneous distribution of CASs. In this study, we present a new method to quantify the abundance and 3-D distribution of CASs in undisturbed soil that allows for investigating CAS densities with distance to the soil macropores. We used X-ray imaging with Ba 2+ as a contrast agent. Ba 2+ has a high adsorption affinity to CASs and is widely used as an index cation to measure the cation exchange capacity (CEC). Eight soil cores (approx. 10 cm 3 ) were sampled from three locations with contrasting texture and organic matter contents. The CASs of our samples were saturated with Ba 2+ in the laboratory using BaCl 2 (0.3 mol L −1 ). Afterwards, KCl (0.1 mol L −1 ) was used to rinse out Ba 2+ ions that were not bound to CASs. Before and after this process the samples were scanned using an industrial X-ray scanner. Ba 2+ bound to CASs was then visualized in 3-D by the difference image technique. The resulting difference images were interpreted as depicting the Ba 2+ bound to CASs only. The X-ray image-derived CEC correlated significantly with results of the commonly used ammonium acetate method to determine CEC in well-mixed samples. The CEC of organic-matter-rich samples seemed to be systematically overestimated and in the case of the clay-rich samples with less organic matter the CEC seemed to be systematically underestimated. The results showed that the distribution of the CASs varied spatially within most of our samples down to a millimetre scale. There was no systematic relation between the location of CASs and the soil macropore structure. We are convinced that the approach proposed here will strongly aid the development of more realistic soil system models.

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Section: Introductionmentioning

confidence: 99%

Quantitative imaging of the 3-D distribution of cation adsorption sites in undisturbed soil

Keck

Strobel

Gustafsson

et al. 2017

SOIL

View full text Add to dashboard Cite

show abstract

mentioning

confidence: 99%

Quantitative imaging of the 3-D distribution of cation adsorption sites in undisturbed soil

Keck¹,

Strobel²,

Gustafsson³

et al. 2017

Preprint

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Several studies have shown that the distribution of cation adsorption sites (CASs) is patchy at a millimetre to centimetre scale. Often, larger concentrations of CASs in biopores or aggregate coatings have been reported in the literature. This heterogeneity has implications on the accessibility of CASs and may influence the performance of soil system models that assume a spatially homogeneous distribution of CASs. In this study, we present a new method to quantify the abundance and 3-D distribution of CASs in undisturbed soil that allows for investigating CAS densities with distance to the soil macropores. We used X-ray imaging with Ba 2+ as a contrast agent. Ba 2+ has a high adsorption affinity to CASs and is widely used as an index cation to measure the cation exchange capacity (CEC). Eight soil cores (approx. 10 cm 3 ) were sampled from three locations with contrasting texture and organic matter contents. The CASs of our samples were saturated with Ba 2+ in the laboratory using BaCl 2 (0.3 mol L −1 ). Afterwards, KCl (0.1 mol L −1 ) was used to rinse out Ba 2+ ions that were not bound to CASs. Before and after this process the samples were scanned using an industrial X-ray scanner. Ba 2+ bound to CASs was then visualized in 3-D by the difference image technique. The resulting difference images were interpreted as depicting the Ba 2+ bound to CASs only. The X-ray image-derived CEC correlated significantly with results of the commonly used ammonium acetate method to determine CEC in well-mixed samples. The CEC of organic-matter-rich samples seemed to be systematically overestimated and in the case of the clay-rich samples with less organic matter the CEC seemed to be systematically underestimated. The results showed that the distribution of the CASs varied spatially within most of our samples down to a millimetre scale. There was no systematic relation between the location of CASs and the soil macropore structure. We are convinced that the approach proposed here will strongly aid the development of more realistic soil system models.

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“…Optionally, multiple trackers can be initiated and run simultaneously (e.g., for multiple plant root systems in the same volume data), by selecting a "New tracker" in the dropdown box above the seed point list (Mairhofer et al, 2015).…”

Section: Set Seed Points At Root Cross Sectionsmentioning

confidence: 99%

X‐Ray Computed Tomography of Crop Plant Root Systems Grown in Soil

et al. 2017

Self Cite

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Non‐destructive methods to quantify the root system architecture of a plant grown in soil are essential to aid our understanding of the factors that impact plant root development in natural environments. With environmental change threatening our ability to sustain agricultural productivity for an expanding global population, the application of these methods has never before seen such an increase in demand. X‐ray computed tomography (CT) based phenotyping techniques permit the spatio‐temporal quantification of roots, helping to identify novel adaptive root architectural responses to abiotic and biotic factors. This protocol reports an integrated workflow from column preparation and plant growth to image and quantification of the root system using novel open source software applications, RooTrak and RooTh. © 2017 by John Wiley & Sons, Inc.

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Visual tracking for the recovery of multiple interacting plant root systems from X-ray $$\upmu $$ μ CT images

Cited by 19 publications

References 41 publications

Quantitative imaging of the 3-D distribution of cation adsorption sites in undisturbed soil

Quantitative imaging of the 3-D distribution of cation adsorption sites in undisturbed soil

Quantitative imaging of the 3-D distribution of cation adsorption sites in undisturbed soil

X‐Ray Computed Tomography of Crop Plant Root Systems Grown in Soil

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