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

Background: Roots 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.

Results: Both 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.

Conclusions: Both 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.

Keywords: Common bean (Phaseolus vulgaris L.) 3D imaging; Magnetic Resonance Imaging (MRI); Non-destructive; Root system architecture; Roots in soil; X-ray Computed Tomography (CT).

Figure 1

CT and MRI images of soil and bean roots in a small pot. The same plant grown in a soil filled pot with an inner diameter (I.D.) of 34 mm and a height of 200 mm was imaged sequentially with X-ray Computed Tomography (CT) and Magnetic Resonance Imaging (MRI). (a) Shows the upper part of the soil column below the pot material imaged with CT (gray-scale) measured with voxel size of 28 × 28 × 28 μm³ with the roots of a bean plant (Phaseolus vulgaris L.) highlighted (red). (b) The root system segmented from the same CT image as in (a) on a voxel size of 56 × 56 × 56 μm³. (c) Shows the same root system imaged one day later with MRI and a voxel size of 333 × 333 × 1000 μm³ with the last value representing the vertical dimension. Arrowheads denote the same roots in both images. DAS: days after sowing Scale bar: 10 mm.

Figure 2

MRI and CT images of a bean root system in a medium soil filled pot. The same plant grown in a soil filled pot with an I.D. of 56 mm and a height of 200 mm was imaged sequentially by MRI and CT. (a) MRI image measured with a voxel size 375 × 375 × 1000 μm³. The CT image (b) shows the root system measured of the same plant segmented on a voxel size of 68 × 68 × 68 μm³. Roots in the lowest part of the pot could not be segmented and are therefore not shown. (c) CT-MRI co-registration: the CT image is in red and the MRI image in grey. Arrowheads highlight roots visible in CT but not in MRI. Box highlights area where few roots are visible in CT. Scale bar: 10 mm.

Figure 3

MRI and CT images of a bean root system in a large pot. The same plant grown in a soil filled pot with an I.D. of 81 mm and a height of 300 mm was imaged sequentially with MRI and CT. (a) MRI image shows the roots system in the whole pot with a voxel size of 521 × 521 × 1000 μm³. Root systems of the same plant segmented from CT data (b) on a voxel size of 99 × 99 × 99 μm³. Since the CT dataset was not complete only data of the upper ~75 mm of the pot could be reconstructed and are shown here. The orange colored ring denotes the volume measured also by CT. Arrowheads highlight the same roots in both images. Scale bar: 20 mm.