Direct comparison of MRI and X-ray CT technologies for 3D imaging of root systems in soil: potential and challenges for root trait quantification

Abstract

BackgroundRoots are vital to plants for soil exploration and uptake of water and nutrients. Root performance is critical for growth and yield of plants, in particular when resources are limited. Since roots develop in strong interaction with the soil matrix, tools are required that can visualize and quantify root growth in opaque soil at best in 3D. Two modalities that are suited for such investigations are X-ray Computed Tomography (CT) and Magnetic Resonance Imaging (MRI). Due to the different physical principles they are based on, these modalities have their specific potentials and challenges for root phenotyping. We compared the two methods by imaging the same root systems grown in 3 different pot sizes with inner diameters of 34 mm, 56 mm or 81 mm.ResultsBoth methods successfully visualized roots of two weeks old bean plants in all three pot sizes. Similar root images and almost the same root length were obtained for roots grown in the small pot, while more root details showed up in the CT images compared to MRI. For the medium sized pot, MRI showed more roots and higher root lengths whereas at some spots thin roots were only found by CT and the high water content apparently affected CT more than MRI. For the large pot, MRI detected much more roots including some laterals than CT.ConclusionsBoth techniques performed equally well for pots with small diameters which are best suited to monitor root development of seedlings. To investigate specific root details or finely graduated root diameters of thin roots, CT was advantageous as it provided the higher spatial resolution. For larger pot diameters, MRI delivered higher fractions of the root systems than CT, most likely because of the strong root-to-soil contrast achievable by MRI. Since complementary information can be gathered with CT and MRI, a combination of the two modalities could open a whole range of additional possibilities like analysis of root system traits in different soil structures or under varying soil moisture.Electronic supplementary materialThe online version of this article (doi:10.1186/s13007-015-0060-z) contains supplementary material, which is available to authorized users.

Quantitative 3D Analysis of Plant Roots Growing in Soil Using Magnetic Resonance Imaging

“…1B). As MRI, root analysis with x-ray CT also acquires, with current root segmentation procedures, similar fractions of roots compared to WinRHIZO (Flavel et al, 2012;Metzner et al, 2015). Koebernick et al (2014) reported a detection of near 100% for roots of Vicia faba regarding only roots .500 mm.…”

X‐ray computed tomography and its potential in ecological research: A review of studies and optimization of specimen preparation

“…Samples are certainly more easily prepared for MRI than X‐ray CT, in particular for those studies which require metal‐based staining for soft tissue imaging (Metscher, 2009a, 2013). Nevertheless, magnetic resonance scanning systems are limited in resolution (Metscher, 2013; Metzner et al., 2015) and often have prohibitive costs of operation (Ziegler et al., 2011). Furthermore, air spaces routinely found in biological samples can cause artifacts in MRI (Jasanoff & Sun, 2002; Wecker, Hörnschemeyer, & Hoehn, 2002; Ziegler et al., 2011).…”

Root Phenotyping Pipeline for Cereal Plants

“…Several root screening approaches involve the application of three-dimensional (3D) imaging techniques. The most promising technique for noninvasive 3D imaging in soil is X-ray computed tomography (CT) and magnetic resonance imaging (MRI) (Metzner et al 2015). There are also other applicable approaches that include selective plane illumination microscopy (SPIM) and optical projection omography (OPT) that are adapted for plants grown in transparent media (Downie et al 2012).…”