Low-field magnetic resonance imaging of roots in intact clayey and silty soils
Abstract
The development of a robust method to non-invasively visualize root morphology in natural soils has been hampered by the opaque, physical, and structural properties of soils. In this work we describe a novel technology, low field magnetic resonance imaging (LF-MRI), for imaging energy sorghum (Sorghum bicolor (L.) Moench) root morphology and architecture in intact soils. The use of magnetic fields much weaker than those used with traditional MRI experiments reduces the distortion due to magnetic material naturally present in agricultural soils. A laboratory based LF-MRI operating at 47 mT magnetic field strength was evaluated using two sets of soil cores: 1) soil/root cores of Weswood silt loam (Udifluventic Haplustept) and a Belk clay (Entic Hapluderts) from a conventionally tilled field, and 2) soil/root cores from rhizotrons filled with either a Houston Black (Udic Haplusterts) clay or a sandy loam purchased from a turf company. The maximum soil water nuclear magnetic resonance (NMR) relaxation time T2 (4 ms) and the typical root water relaxation time T2 (100 ms) are far enough apart to provide a unique contrast mechanism such that the soil water signal has decayed to the point of no longer being detectable during the data collection time period. 2-Dmore »
- Authors:
- Publication Date:
- Research Org.:
- Texas A & M University, College Station, TX (United States). Texas A & M AgriLife Research
- Sponsoring Org.:
- USDOE Advanced Research Projects Agency - Energy (ARPA-E)
- OSTI Identifier:
- 1615698
- Alternate Identifier(s):
- OSTI ID: 1799099
- Grant/Contract Number:
- AR0000823
- Resource Type:
- Published Article
- Journal Name:
- Geoderma
- Additional Journal Information:
- Journal Name: Geoderma Journal Volume: 370 Journal Issue: C; Journal ID: ISSN 0016-7061
- Publisher:
- Elsevier
- Country of Publication:
- Netherlands
- Language:
- English
- Subject:
- 58 GEOSCIENCES; Agriculture; LF-MRI: Low Field Magnetic Resonance Imaging; HF-MRI: High Field Magnetic Resonance Imaging; MR: Magnetic Resonance; MRI: Magnetic Resonance Imaging; NMR; Nuclear Magnetic Resonance; RF: Radio Frequency; SNR: Signal to Noise Ratio; AUTOMAP: Automated Transform by Manifold Approximation; OD: Outside Diameter; AWG: American Wire Gauge; IFFT: Inverse Fast Fourier Transform; FFT: Fast Fourier Transform
Citation Formats
Bagnall, G. Cody, Koonjoo, Neha, Altobelli, Stephen A., Conradi, Mark S., Fukushima, Eiichi, Kuethe, Dean O., Mullet, John E., Neely, Haly, Rooney, William L., Stupic, Karl F., Weers, Brock, Zhu, Bo, Rosen, Matthew S., and Morgan, Cristine L. S. Low-field magnetic resonance imaging of roots in intact clayey and silty soils. Netherlands: N. p., 2020.
Web. doi:10.1016/j.geoderma.2020.114356.
Bagnall, G. Cody, Koonjoo, Neha, Altobelli, Stephen A., Conradi, Mark S., Fukushima, Eiichi, Kuethe, Dean O., Mullet, John E., Neely, Haly, Rooney, William L., Stupic, Karl F., Weers, Brock, Zhu, Bo, Rosen, Matthew S., & Morgan, Cristine L. S. Low-field magnetic resonance imaging of roots in intact clayey and silty soils. Netherlands. https://doi.org/10.1016/j.geoderma.2020.114356
Bagnall, G. Cody, Koonjoo, Neha, Altobelli, Stephen A., Conradi, Mark S., Fukushima, Eiichi, Kuethe, Dean O., Mullet, John E., Neely, Haly, Rooney, William L., Stupic, Karl F., Weers, Brock, Zhu, Bo, Rosen, Matthew S., and Morgan, Cristine L. S. Wed .
"Low-field magnetic resonance imaging of roots in intact clayey and silty soils". Netherlands. https://doi.org/10.1016/j.geoderma.2020.114356.
@article{osti_1615698,
title = {Low-field magnetic resonance imaging of roots in intact clayey and silty soils},
author = {Bagnall, G. Cody and Koonjoo, Neha and Altobelli, Stephen A. and Conradi, Mark S. and Fukushima, Eiichi and Kuethe, Dean O. and Mullet, John E. and Neely, Haly and Rooney, William L. and Stupic, Karl F. and Weers, Brock and Zhu, Bo and Rosen, Matthew S. and Morgan, Cristine L. S.},
abstractNote = {The development of a robust method to non-invasively visualize root morphology in natural soils has been hampered by the opaque, physical, and structural properties of soils. In this work we describe a novel technology, low field magnetic resonance imaging (LF-MRI), for imaging energy sorghum (Sorghum bicolor (L.) Moench) root morphology and architecture in intact soils. The use of magnetic fields much weaker than those used with traditional MRI experiments reduces the distortion due to magnetic material naturally present in agricultural soils. A laboratory based LF-MRI operating at 47 mT magnetic field strength was evaluated using two sets of soil cores: 1) soil/root cores of Weswood silt loam (Udifluventic Haplustept) and a Belk clay (Entic Hapluderts) from a conventionally tilled field, and 2) soil/root cores from rhizotrons filled with either a Houston Black (Udic Haplusterts) clay or a sandy loam purchased from a turf company. The maximum soil water nuclear magnetic resonance (NMR) relaxation time T2 (4 ms) and the typical root water relaxation time T2 (100 ms) are far enough apart to provide a unique contrast mechanism such that the soil water signal has decayed to the point of no longer being detectable during the data collection time period. 2-D MRI projection images were produced of roots with a diameter range of 1.5–2.0 mm using an image acquisition time of 15 min with a pixel resolution of 1.74 mm in four soil types. In addition, we demonstrate the use of a data-driven machine learning reconstruction approach, Automated Transform by Manifold Approximation (AUTOMAP) to reconstruct raw data and improve the quality of the final images. The application of AUTOMAP showed a SNR (Signal to Noise Ratio) improvement of two fold on average. The use of low field MRI presented here demonstrates the possibility of applying low field MRI through intact soils to root phenotyping and agronomy to aid in understanding of root morphology and the spatial arrangement of roots in situ.},
doi = {10.1016/j.geoderma.2020.114356},
journal = {Geoderma},
number = C,
volume = 370,
place = {Netherlands},
year = {Wed Jul 01 00:00:00 EDT 2020},
month = {Wed Jul 01 00:00:00 EDT 2020}
}
https://doi.org/10.1016/j.geoderma.2020.114356
Web of Science
Works referenced in this record:
Soil Water Measurement by a Low-Resolution Nuclear Magnetic Resonance Technique
journal, September 1970
- Prebble, R. E.; Currie, J. A.
- Journal of Soil Science, Vol. 21, Issue 2
Non-invasive imaging of plant roots in different soils using magnetic resonance imaging (MRI)
journal, November 2017
- Pflugfelder, Daniel; Metzner, Ralf; van Dusschoten, Dagmar
- Plant Methods, Vol. 13, Issue 1
Quantitative 3D Analysis of Plant Roots Growing in Soil Using Magnetic Resonance Imaging
journal, January 2016
- van Dusschoten, Dagmar; Metzner, Ralf; Kochs, Johannes
- Plant Physiology, Vol. 170, Issue 3
Combined MRI-PET dissects dynamic changes in plant structures and functions
journal, August 2009
- Jahnke, Siegfried; Menzel, Marion I.; van Dusschoten, Dagmar
- The Plant Journal, Vol. 59, Issue 4
Sample size for measurement of root traits on common bean by image analysis
journal, April 2004
- Araújo, Adelson Paulo; Fernandes, Aurélio Magno; Kubota, Flavio Yuudi
- Pesquisa Agropecuária Brasileira, Vol. 39, Issue 4
EZ-Rhizo: integrated software for the fast and accurate measurement of root system architecture
journal, March 2009
- Armengaud, Patrick; Zambaux, Kevin; Hills, Adrian
- The Plant Journal, Vol. 57, Issue 5
Non-destructive quantification of cereal roots in soil using high-resolution X-ray tomography
journal, January 2012
- Flavel, R. J.; Guppy, C. N.; Tighe, M.
- Journal of Experimental Botany, Vol. 63, Issue 7
In Situ Nuclear Magnetic Resonance Imaging of Roots: Influence of Soil Type, Ferromagnetic Particle Content, and Soil Water 1
journal, November 1987
- Rogers, Hugo H.; Bottomley, Paul A.
- Agronomy Journal, Vol. 79, Issue 6
Root Architecture and Plant Productivity
journal, September 1995
- Lynch, J.
- Plant Physiology, Vol. 109, Issue 1
Rightsizing root phenotypes for drought resistance
journal, February 2018
- Lynch, Jonathan P.
- Journal of Experimental Botany, Vol. 69, Issue 13
MR properties of water in saturated soils and resulting loss of MRI signal in water content detection at 2 tesla
journal, November 1997
- Hall, Laurie D.; Gao Amin, M. H.; Dougherty, Elizabeth
- Geoderma, Vol. 80, Issue 3-4
Developing X-ray Computed Tomography to non-invasively image 3-D root systems architecture in soil
journal, November 2011
- Mooney, S. J.; Pridmore, T. P.; Helliwell, J.
- Plant and Soil, Vol. 352, Issue 1-2
Shovelomics: high throughput phenotyping of maize (Zea mays L.) root architecture in the field
journal, November 2010
- Trachsel, Samuel; Kaeppler, Shawn M.; Brown, Kathleen M.
- Plant and Soil, Vol. 341, Issue 1-2
Belowground plant development measured with magnetic resonance imaging (MRI): exploiting the potential for non-invasive trait quantification using sugar beet as a proxy
journal, September 2014
- Metzner, Ralf; van Dusschoten, Dagmar; Bühler, Jonas
- Frontiers in Plant Science, Vol. 5
Functional–structural root-system model validation using a soil MRI experiment
journal, February 2019
- Koch, Axelle; Meunier, Félicien; Vanderborght, Jan
- Journal of Experimental Botany, Vol. 70, Issue 10
Advances in Non-Destructive Measurement and 3D Visualization Methods for Plant Root Based on Machine Vision
conference, October 2009
- Zhou, Xuecheng; Luo, Xiwen
- 2009 2nd International Conference on Biomedical Engineering and Informatics
Image reconstruction by domain-transform manifold learning
journal, March 2018
- Zhu, Bo; Liu, Jeremiah Z.; Cauley, Stephen F.
- Nature, Vol. 555, Issue 7697
Concepts and Analyses in the CT Scanning of Root Systems and Leaf Canopies: A Timely Summary
journal, December 2015
- Lafond, Jonathan A.; Han, Liwen; Dutilleul, Pierre
- Frontiers in Plant Science, Vol. 6
The relationships between MR parameters and the content of water in packed samples of two soils
journal, April 2000
- Votrubová, Jana; Šanda, Martin; Cı́slerová, Milena
- Geoderma, Vol. 95, Issue 3-4
Modelling root–soil interactions using three–dimensional models of root growth, architecture and function
journal, June 2013
- Dunbabin, Vanessa M.; Postma, Johannes A.; Schnepf, Andrea
- Plant and Soil, Vol. 372, Issue 1-2