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

Metzner R, Eggert A, van Dusschoten D, Pflugfelder D, Gerth S, Schurr U, Uhlmann N, Jahnke S - Plant Methods (2015)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Wilhelm-Jonen- Str., 52425 Jülich, Germany.

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.

No MeSH data available.


Related in: MedlinePlus

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.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC4359488&req=5

Fig1: 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.

Mentions: An example of a CT image with a spatial resolution of 28 μm (voxel size) is shown in Figure 1a which was obtained from a bean plant growing in a small pot. Roots that grew at the inner surface of the pot can be directly recognized by removing the pot material from the image without special segmentation efforts (Figure 1a). Due to their elongated shape they can be distinguished visually from sand grains and darker areas where air or water filled pores and finer soil particles were located. The ability to image both soil structures and plant roots is a very intriguing feature of CT [3,40,41]. However, roots developing as a 3D structure in a soil filled pot have to be detected by signal contrast based on X-ray attenuation which may be low between particular soil structures such as water filled pores and the roots [3,28]. Segmentation of the roots from the soil background is therefore a major step in extracting root structures and traits from CT images. So far many different approaches exist for this step in data analysis, exploiting different algorithms and filters in manual [19,40,42] or automated fashion [43,44]. However, a standard procedure remains yet to be defined. Figure 1b shows the result of a root segmentation procedure applied here to the dataset partly shown in Figure 1a. The segmentation follows an image analysis procedure including threshold filtering for manually selected grey values and for objects of a size and (cylindrical) shape typical for roots [45]. For the root segmentation procedure the spatial resolution of the images had to be reduced by a factor of 2 in each dimension because otherwise it would not have been possible to run the analysis on a standard workstation-sized computer with enhanced memory. The 3D rendered image of the segmented root system (Figure 1b) shows not only the roots at the soil surface but also a range of roots of variable diameter deep in the soil core. The 3D visualization allowed identification of primary, basal and hypocotyl-borne roots [46] by tracing them back to their respective origin (data not shown). In this way, the lowest root tips were identified as belonging to basal roots or the primary root (Figure 1b) while the thinner roots in the upper part of Figure 1b were lateral roots of each of these root types. The high spatial resolution of CT shown here also enables a precise mapping of root diameters.Figure 1


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

Metzner R, Eggert A, van Dusschoten D, Pflugfelder D, Gerth S, Schurr U, Uhlmann N, Jahnke S - Plant Methods (2015)

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.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4359488&req=5

Fig1: 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.
Mentions: An example of a CT image with a spatial resolution of 28 μm (voxel size) is shown in Figure 1a which was obtained from a bean plant growing in a small pot. Roots that grew at the inner surface of the pot can be directly recognized by removing the pot material from the image without special segmentation efforts (Figure 1a). Due to their elongated shape they can be distinguished visually from sand grains and darker areas where air or water filled pores and finer soil particles were located. The ability to image both soil structures and plant roots is a very intriguing feature of CT [3,40,41]. However, roots developing as a 3D structure in a soil filled pot have to be detected by signal contrast based on X-ray attenuation which may be low between particular soil structures such as water filled pores and the roots [3,28]. Segmentation of the roots from the soil background is therefore a major step in extracting root structures and traits from CT images. So far many different approaches exist for this step in data analysis, exploiting different algorithms and filters in manual [19,40,42] or automated fashion [43,44]. However, a standard procedure remains yet to be defined. Figure 1b shows the result of a root segmentation procedure applied here to the dataset partly shown in Figure 1a. The segmentation follows an image analysis procedure including threshold filtering for manually selected grey values and for objects of a size and (cylindrical) shape typical for roots [45]. For the root segmentation procedure the spatial resolution of the images had to be reduced by a factor of 2 in each dimension because otherwise it would not have been possible to run the analysis on a standard workstation-sized computer with enhanced memory. The 3D rendered image of the segmented root system (Figure 1b) shows not only the roots at the soil surface but also a range of roots of variable diameter deep in the soil core. The 3D visualization allowed identification of primary, basal and hypocotyl-borne roots [46] by tracing them back to their respective origin (data not shown). In this way, the lowest root tips were identified as belonging to basal roots or the primary root (Figure 1b) while the thinner roots in the upper part of Figure 1b were lateral roots of each of these root types. The high spatial resolution of CT shown here also enables a precise mapping of root diameters.Figure 1

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Wilhelm-Jonen- Str., 52425 Jülich, Germany.

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.

No MeSH data available.


Related in: MedlinePlus