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Low-Field Magnetic Resonance Imaging of Roots in Intact Clayey and Silty Soils



George Bagnall, Cristine` Morgan, Matthew Rosen, Mark Conradi, Stephen Altobelli, Dean Kuethe, Haly Neely, Neha Koonjoo, Bo Zhu, Karl Stupic, John Mullet, Brock Weers, Eiichi Fukushima, William Rooney


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 experiment reduces the distortion due to magnetic material naturally present in agricultural soils. A laboratory based LF-MRI operating at 0.047 T 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. Additionally, 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 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.


MRI, low field, roots, agriculture, AI, phenotyping, agronomy


Bagnall, G. , Morgan, C. , Rosen, M. , Conradi, M. , Altobelli, S. , Kuethe, D. , Neely, H. , Koonjoo, N. , Zhu, B. , Stupic, K. , Mullet, J. , Weers, B. , Fukushima, E. and Rooney, W. (2020), Low-Field Magnetic Resonance Imaging of Roots in Intact Clayey and Silty Soils, Geoderma (Accessed March 2, 2024)
Created June 30, 2020, Updated November 29, 2022