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Low-field magnetic resonance imaging of roots in intact clayey and silty soils



Mark S. Conradi, Stephen A. Altobelli, Dean O. Kuethe, Matthew S. Rosen, Neha Koonjoo, Bo Zhu, Karl F. Stupic, William L. Rooney, John E. Mullet, Brock Weers, G. Cody Bagnall, Haly Neely, Eiichi Fukushima, Cristine Morgan


The development of a robust method to non-invasively visualize root morphology in natural soils has been hampered by the opaque nature, chemical composition, and physical structure of soils. We describe here a novel technology—low field magnetic resonance imaging (LF-MRI)—for the imaging of energy sorghum root morphology and architecture in intact soils. Our use of magnetic fields much weaker than those used in traditional MRI instruments results in significantly reduced distortion from magnetic material naturally present agricultural soils. A laboratory based LF-MRI operating at a magnetic field strength of 0.047 T (47 mT) was evaluated using two sets of soil cores: 1) soil/root cores of Weswood silt loam and a Belk clay from a conventionally tilled field, and 2) soil/root cores from rhizotrons filled with either a Houston Black clay or a silt loam. The more than an order of magnitude difference between the measured maximum soil water NMR relaxation time T2 (4 ms) and the typical root water T2 (85 ms) provide a unique contrast mechanism whereby the soil water signal is filtered out of the image during the data collection. 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 scanner data and improve the quality of the final images. The application of AUTOMAP showed a SNR improvement of more than a factor of two on average. The use of low field MRI in intact soils may be a compelling new tool for root phenotyping and agronomy to aid in understanding of root morphology and the spatial arrangement of roots in situ.


MRI, plants, roots, low-field MRI, NMR
Created March 27, 2020, Updated April 13, 2020