4D X-Ray Computed Tomography in Soil Science: an Overview and Future Perspectives at Mogno/Sirius

Ferreira, Talita R.; Pires, Luiz F.; Reichardt, Klaus

doi:10.1007/s13538-021-01043-x

Cited by 14 publications

(3 citation statements)

References 82 publications

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“…They found significant differences in micro‐structures of microaggregates from different soils, some mostly inorganic with mainly interstitial pores while others comprising more organic components within larger pore spaces accessible for microorganisms. With recent advances in X‐ray sources, image analysis software, available computing power, and storage capacity, it is now possible to do 4D (time series) tomography with scanning times of a few minutes to seconds for a complete scan (Ferreira et al., 2022).…”

Section: Tomographic Approachesmentioning

confidence: 99%

Architecture of soil microaggregates: Advanced methodologies to explore properties and functions

Amelung,

Tang,

Siebers

et al. 2023

J. Plant Nutr. Soil Sci.

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The functions of soils are intimately linked to their three‐dimensional pore space and the associated biogeochemical interfaces, mirrored in the complex structure that developed during pedogenesis. Under stress overload, soil disintegrates into smaller compound structures, conventionally named aggregates. Microaggregates (<250 µm) are recognized as the most stable soil structural units. They are built of mineral, organic, and biotic materials, provide habitats for a vast diversity of microorganisms, and are closely involved in the cycling of matter and energy. However, exploring the architecture of soil microaggregates and their linkage to soil functions remains a challenging but demanding scientific endeavor. With the advent of complementary spectromicroscopic and tomographic techniques, we can now assess and visualize the size, composition, and porosity of microaggregates and the spatial arrangement of their interior building units. Their combinations with advanced experimental pedology, multi‐isotope labeling experiments, and computational approaches pave the way to investigate microaggregate turnover and stability, explore their role in element cycling, and unravel the intricate linkage between structure and function. However, spectromicroscopic techniques operate at different scales and resolutions, and have specific requirements for sample preparation and microaggregate isolation; hence, special attention must be paid to both the separation of microaggregates in a reproducible manner and the synopsis of the geography of information that originates from the diverse complementary instrumental techniques. The latter calls for further development of strategies for synlocation and synscaling beyond the present state of correlative analysis. Here, we present examples of recent scientific progress and review both options and challenges of the joint application of cutting‐edge techniques to achieve a sophisticated picture of the properties and functions of soil microaggregates.

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Section: Tomographic Approachesmentioning

confidence: 99%

Architecture of soil microaggregates: Advanced methodologies to explore properties and functions

Amelung,

Tang,

Siebers

et al. 2023

J. Plant Nutr. Soil Sci.

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“…In addition, X-ray tomography (XCT) and nuclear magnetic resonance imaging (MRI) commonly used in medicine also provide new methods and means for the acquisition of in situ root images (Jahnke et al, 2009). XCT scans the root image by using the characteristics of different attenuation degrees of X-ray passing through the soil and root, and finally obtains the root image (Park et al, 2020;Scotson et al, 2021;Ferreira et al, 2022). MRI is a modern tomographic imaging technology, which mainly transmits radio frequency electromagnetic waves to obtain the MRI information of different positions of objects in the magnetic field to generate images, and uses computers to reconstruct the internal images of objects (Borisjuk et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

A method of cotton root segmentation based on edge devices

Tang

Zhu

et al. 2023

Front. Plant Sci.

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The root is an important organ for plants to absorb water and nutrients. In situ root research method is an intuitive method to explore root phenotype and its change dynamics. At present, in situ root research, roots can be accurately extracted from in situ root images, but there are still problems such as low analysis efficiency, high acquisition cost, and difficult deployment of image acquisition devices outdoors. Therefore, this study designed a precise extraction method of in situ roots based on semantic segmentation model and edge device deployment. It initially proposes two data expansion methods, pixel by pixel and equal proportion, expand 100 original images to 1600 and 53193 respectively. It then presents an improved DeeplabV3+ root segmentation model based on CBAM and ASPP in series is designed, and the segmentation accuracy is 93.01%. The root phenotype parameters were verified through the Rhizo Vision Explorers platform, and the root length error was 0.669%, and the root diameter error was 1.003%. It afterwards designs a time-saving Fast prediction strategy. Compared with the Normal prediction strategy, the time consumption is reduced by 22.71% on GPU and 36.85% in raspberry pie. It ultimately deploys the model to Raspberry Pie, realizing the low-cost and portable root image acquisition and segmentation, which is conducive to outdoor deployment. In addition, the cost accounting is only $247. It takes 8 hours to perform image acquisition and segmentation tasks, and the power consumption is as low as 0.051kWh. In conclusion, the method proposed in this study has good performance in model accuracy, economic cost, energy consumption, etc. This paper realizes low-cost and high-precision segmentation of in-situ root based on edge equipment, which provides new insights for high-throughput field research and application of in-situ root.

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“…For example, the MOGNO beamline at the Sirius synchrotron in the Brazilian Laboratory for Synchrotron Light (LNLS) 16,17,18 is designed to produce fast tomographic images (≥ 1 XCT/s) in a zoom tomography con guration using quasi-monochromatic radiation maximized at one of three selected energies (https://www.lnls.cnpem.br/facilities/mogno-en/). This range of characteristics gives exibility to follow fast, dynamical processes in the rhizosphere over time and at multiple spatial scales 16,19 . And it also gives exibility to select data-collection parameters for acquiring high-resolution in-vivo XCT data while minimizing radiation-induced damage to the roots.…”

Section: Introductionmentioning

confidence: 99%

Monte Carlo simulations of synchrotron X-ray dose effects on root growth during in-vivo tomographic imaging

Moraes

Hesterberg

Neto

et al. 2022

Preprint

Self Cite

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Synchrotron X-ray computed tomography (XCT) has been increasingly applied to study the in-vivo dynamics of root growth and rhizosphere processes. However, minimizing radiation-induced damage to root growth warrants further investigation. Our objective was to develop a robust approach for modeling and evaluating ways to reduce synchrotron X-ray dose effects on root growth during in-vivo imaging. Wheat roots growing in soil were exposed to X-rays during XCT experiments resolved in space (3-D) plus time (4-D). The dose rate and cumulative absorbed dose in roots were modelled with the Monte Carlo code FLUKA considering different experimental conditions using polychromatic and quasi-monochromatic X-ray beam configurations. The most impactful factors affecting damage to roots were incident X-ray energy spectrum, stored current in the accelerator machine, position of the root in the soil, and possibly the number of exposures during the 4-D XCT experiments. Our results imply that radiation dose during in-vivo imaging of plant roots can be diminished by using monochromatic radiation at the highest energy suitable for a given sample thickness and field of view, and by controlling the rotation axis of off-centered roots to increase radiation protection by soil.

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4D X-Ray Computed Tomography in Soil Science: an Overview and Future Perspectives at Mogno/Sirius

Cited by 14 publications

References 82 publications

Architecture of soil microaggregates: Advanced methodologies to explore properties and functions

Architecture of soil microaggregates: Advanced methodologies to explore properties and functions

A method of cotton root segmentation based on edge devices

Monte Carlo simulations of synchrotron X-ray dose effects on root growth during in-vivo tomographic imaging

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