Synchrotron-based 3D X-ray computed tomography reveals root system architecture: Plastic responses to phosphorus placement
We used synchrotron-based X-ray computed tomography (SRXCT) to visualize root distribution in soil cores. X-ray CT is emerging as a leading technique to study plant roots, but SRXCT offers potential advantages compared with conventional X-ray sources, including producing X-rays of higher intensity t...
Saved in:
| Main Authors: | , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2025-05-01
|
| Series: | Geoderma |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S0016706125001375 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850040917819392000 |
|---|---|
| author | Frederik J.T. van der Bom Philipp D. Lösel Andrew M. Kingston Zhe H. Weng Nelly S. Raymond Anton Maksimenko Daniel Hausermann Michael J. Bell Casey L. Doolette Enzo Lombi Peter M. Kopittke |
| author_facet | Frederik J.T. van der Bom Philipp D. Lösel Andrew M. Kingston Zhe H. Weng Nelly S. Raymond Anton Maksimenko Daniel Hausermann Michael J. Bell Casey L. Doolette Enzo Lombi Peter M. Kopittke |
| author_sort | Frederik J.T. van der Bom |
| collection | DOAJ |
| description | We used synchrotron-based X-ray computed tomography (SRXCT) to visualize root distribution in soil cores. X-ray CT is emerging as a leading technique to study plant roots, but SRXCT offers potential advantages compared with conventional X-ray sources, including producing X-rays of higher intensity that are collimated, monochromatic and tuneable; delivering high-resolution data whilst avoiding issues such as beam-hardening and source divergence. We demonstrate the suitability of SRXCT for observing the root system of wheat plants growing in two soils (Calcisol and Ultisol) in response to placement of different phosphorus fertilisers. To optimize scanning quality, we tested the use of an inverse ‘mask’ in front of the soil cores to achieve a more uniform attenuation along the sample, thereby avoiding saturation of the detector along the thinnest parts of the soil cores. Secondly, we developed a deep learning approach for segmentation and quantification of root length and diameter. Our results demonstrate the use of SRXCT as a tool for studying root system architecture in soil at high spatial resolution. The SRXCT method marks a new stride towards advancing our understanding of root structures in unprecedented detail, opening further avenues for exploring plant-soil interactions. |
| format | Article |
| id | doaj-art-d219aea01a264faf89bb5d16c11a6791 |
| institution | DOAJ |
| issn | 1872-6259 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Geoderma |
| spelling | doaj-art-d219aea01a264faf89bb5d16c11a67912025-08-20T02:55:56ZengElsevierGeoderma1872-62592025-05-0145711729910.1016/j.geoderma.2025.117299Synchrotron-based 3D X-ray computed tomography reveals root system architecture: Plastic responses to phosphorus placementFrederik J.T. van der Bom0Philipp D. Lösel1Andrew M. Kingston2Zhe H. Weng3Nelly S. Raymond4Anton Maksimenko5Daniel Hausermann6Michael J. Bell7Casey L. Doolette8Enzo Lombi9Peter M. Kopittke10University of Copenhagen, Department of Plant and Environmental Sciences, Højbakkegård Allé 13, Taastrup 2630, Denmark; The University of Queensland, School of Agriculture and Food Sustainability, Gatton, Queensland 4343, Australia; Corresponding author at: University of Copenhagen, Department of Plant and Environmental Sciences, Højbakkegård Allé 13, Taastrup 2630, Denmark.Department of Materials Physics, Research School of Physics, The Australian National University, Canberra, ACT 2601, AustraliaDepartment of Materials Physics, Research School of Physics, The Australian National University, Canberra, ACT 2601, AustraliaThe University of Queensland, School of Agriculture and Food Sustainability, Gatton, Queensland 4343, AustraliaThe University of Queensland, School of Agriculture and Food Sustainability, Gatton, Queensland 4343, Australia; University of Copenhagen, Department of Geosciences and Natural Resource Management, DK-1350 Copenhagen, DenmarkAustralian Synchrotron, ANSTO, Wurundjeri Country, Clayton, Victoria 3168, AustraliaAustralian Synchrotron, ANSTO, Wurundjeri Country, Clayton, Victoria 3168, AustraliaThe University of Queensland, School of Agriculture and Food Sustainability, Gatton, Queensland 4343, Australia; The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, Gatton, QLD 4343, AustraliaUniversity of South Australia, Future Industries Institute, Mawson Lakes, South Australia 5095, AustraliaUniversity of South Australia, Future Industries Institute, Mawson Lakes, South Australia 5095, Australia; Corresponding author at: University of Copenhagen, Department of Plant and Environmental Sciences, Højbakkegård Allé 13, Taastrup 2630, Denmark.The University of Queensland, School of Agriculture and Food Sustainability, Gatton, Queensland 4343, AustraliaWe used synchrotron-based X-ray computed tomography (SRXCT) to visualize root distribution in soil cores. X-ray CT is emerging as a leading technique to study plant roots, but SRXCT offers potential advantages compared with conventional X-ray sources, including producing X-rays of higher intensity that are collimated, monochromatic and tuneable; delivering high-resolution data whilst avoiding issues such as beam-hardening and source divergence. We demonstrate the suitability of SRXCT for observing the root system of wheat plants growing in two soils (Calcisol and Ultisol) in response to placement of different phosphorus fertilisers. To optimize scanning quality, we tested the use of an inverse ‘mask’ in front of the soil cores to achieve a more uniform attenuation along the sample, thereby avoiding saturation of the detector along the thinnest parts of the soil cores. Secondly, we developed a deep learning approach for segmentation and quantification of root length and diameter. Our results demonstrate the use of SRXCT as a tool for studying root system architecture in soil at high spatial resolution. The SRXCT method marks a new stride towards advancing our understanding of root structures in unprecedented detail, opening further avenues for exploring plant-soil interactions.http://www.sciencedirect.com/science/article/pii/S0016706125001375X-ray computed tomographyRoot system architectureRoot distributionSoil phosphorusSynchrotronImage segmentation |
| spellingShingle | Frederik J.T. van der Bom Philipp D. Lösel Andrew M. Kingston Zhe H. Weng Nelly S. Raymond Anton Maksimenko Daniel Hausermann Michael J. Bell Casey L. Doolette Enzo Lombi Peter M. Kopittke Synchrotron-based 3D X-ray computed tomography reveals root system architecture: Plastic responses to phosphorus placement Geoderma X-ray computed tomography Root system architecture Root distribution Soil phosphorus Synchrotron Image segmentation |
| title | Synchrotron-based 3D X-ray computed tomography reveals root system architecture: Plastic responses to phosphorus placement |
| title_full | Synchrotron-based 3D X-ray computed tomography reveals root system architecture: Plastic responses to phosphorus placement |
| title_fullStr | Synchrotron-based 3D X-ray computed tomography reveals root system architecture: Plastic responses to phosphorus placement |
| title_full_unstemmed | Synchrotron-based 3D X-ray computed tomography reveals root system architecture: Plastic responses to phosphorus placement |
| title_short | Synchrotron-based 3D X-ray computed tomography reveals root system architecture: Plastic responses to phosphorus placement |
| title_sort | synchrotron based 3d x ray computed tomography reveals root system architecture plastic responses to phosphorus placement |
| topic | X-ray computed tomography Root system architecture Root distribution Soil phosphorus Synchrotron Image segmentation |
| url | http://www.sciencedirect.com/science/article/pii/S0016706125001375 |
| work_keys_str_mv | AT frederikjtvanderbom synchrotronbased3dxraycomputedtomographyrevealsrootsystemarchitectureplasticresponsestophosphorusplacement AT philippdlosel synchrotronbased3dxraycomputedtomographyrevealsrootsystemarchitectureplasticresponsestophosphorusplacement AT andrewmkingston synchrotronbased3dxraycomputedtomographyrevealsrootsystemarchitectureplasticresponsestophosphorusplacement AT zhehweng synchrotronbased3dxraycomputedtomographyrevealsrootsystemarchitectureplasticresponsestophosphorusplacement AT nellysraymond synchrotronbased3dxraycomputedtomographyrevealsrootsystemarchitectureplasticresponsestophosphorusplacement AT antonmaksimenko synchrotronbased3dxraycomputedtomographyrevealsrootsystemarchitectureplasticresponsestophosphorusplacement AT danielhausermann synchrotronbased3dxraycomputedtomographyrevealsrootsystemarchitectureplasticresponsestophosphorusplacement AT michaeljbell synchrotronbased3dxraycomputedtomographyrevealsrootsystemarchitectureplasticresponsestophosphorusplacement AT caseyldoolette synchrotronbased3dxraycomputedtomographyrevealsrootsystemarchitectureplasticresponsestophosphorusplacement AT enzolombi synchrotronbased3dxraycomputedtomographyrevealsrootsystemarchitectureplasticresponsestophosphorusplacement AT petermkopittke synchrotronbased3dxraycomputedtomographyrevealsrootsystemarchitectureplasticresponsestophosphorusplacement |