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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

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.
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Fig3: 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.

Mentions: Root traits calculated from CT and MRI root images of the volumes shown in Figures1,2and3


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)

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

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

Fig3: 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.
Mentions: Root traits calculated from CT and MRI root images of the volumes shown in Figures1,2and3

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