title: Quantitative 3D Analysis of Plant Roots Growing in Soil Using Magnetic Resonance Imaging.
abstract: Precise measurements of root system architecture traits are an important requirement for plant phenotyping. Most of the current methods for analyzing root growth require either artificial growing conditions (e.g. hydroponics), are severely restricted in the fraction of roots detectable (e.g. rhizotrons), or are destructive (e.g. soil coring). On the other hand, modalities such as magnetic resonance imaging (MRI) are noninvasive and allow high-quality three-dimensional imaging of roots in soil. Here, we present a plant root imaging and analysis pipeline using MRI together with an advanced image visualization and analysis software toolbox named NMRooting. Pots up to 117 mm in diameter and 800 mm in height can be measured with the 4.7 T MRI instrument used here. For 1.5 l pots (81 mm diameter, 300 mm high), a fully automated system was developed enabling measurement of up to 18 pots per day. The most important root traits that can be nondestructively monitored over time are root mass, length, diameter, tip number, and growth angles (in two-dimensional polar coordinates) and spatial distribution. Various validation measurements for these traits were performed, showing that roots down to a diameter range between 200 μm and 300 μm can be quantitatively measured. Root fresh weight correlates linearly with root mass determined by MRI. We demonstrate the capabilities of MRI and the dedicated imaging pipeline in experimental series performed on soil-grown maize (Zea mays) and barley (Hordeum vulgare) plants.
authors.affiliation: IBG-2: Plant Sciences, Forschungszentrum Jülich, 52425 Jülich, Germany (D.v.D, R.M., J.K., J.A.P., D.P., J.B., U.S., S.J.). d.van.dusschoten@fz-juelich.de.
authors.forename: Dagmar
authors.identifier: http://orcid.org/0000-0002-6251-1231
authors.initials: D
authors.lastname: van Dusschoten
authors.affiliation: IBG-2: Plant Sciences, Forschungszentrum Jülich, 52425 Jülich, Germany (D.v.D, R.M., J.K., J.A.P., D.P., J.B., U.S., S.J.).
authors.forename: Ralf
authors.identifier: http://orcid.org/0000-0001-6164-1141
authors.initials: R
authors.lastname: Metzner
authors.affiliation: IBG-2: Plant Sciences, Forschungszentrum Jülich, 52425 Jülich, Germany (D.v.D, R.M., J.K., J.A.P., D.P., J.B., U.S., S.J.).
authors.forename: Johannes
authors.initials: J
authors.lastname: Kochs
authors.affiliation: IBG-2: Plant Sciences, Forschungszentrum Jülich, 52425 Jülich, Germany (D.v.D, R.M., J.K., J.A.P., D.P., J.B., U.S., S.J.).
authors.forename: Johannes A
authors.identifier: http://orcid.org/0000-0002-5222-6648
authors.initials: JA
authors.lastname: Postma
authors.affiliation: IBG-2: Plant Sciences, Forschungszentrum Jülich, 52425 Jülich, Germany (D.v.D, R.M., J.K., J.A.P., D.P., J.B., U.S., S.J.).
authors.forename: Daniel
authors.initials: D
authors.lastname: Pflugfelder
authors.affiliation: IBG-2: Plant Sciences, Forschungszentrum Jülich, 52425 Jülich, Germany (D.v.D, R.M., J.K., J.A.P., D.P., J.B., U.S., S.J.).
authors.forename: Jonas
authors.identifier: http://orcid.org/0000-0002-4463-2291
authors.initials: J
authors.lastname: Bühler
authors.affiliation: IBG-2: Plant Sciences, Forschungszentrum Jülich, 52425 Jülich, Germany (D.v.D, R.M., J.K., J.A.P., D.P., J.B., U.S., S.J.).
authors.forename: Ulrich
authors.identifier: http://orcid.org/0000-0003-0369-8777
authors.initials: U
authors.lastname: Schurr
authors.affiliation: IBG-2: Plant Sciences, Forschungszentrum Jülich, 52425 Jülich, Germany (D.v.D, R.M., J.K., J.A.P., D.P., J.B., U.S., S.J.).
authors.forename: Siegfried
authors.identifier: http://orcid.org/0000-0002-4086-2567
authors.initials: S
authors.lastname: Jahnke
mesh_terms: D001467:Hordeum / Q000033:anatomy & histology / Q000254:growth & development; D021621:Imaging, Three-Dimensional / Q000379:methods* / Q000706:statistics & numerical data; D008279:Magnetic Resonance Imaging / Q000379:methods* / Q000706:statistics & numerical data; D010641:Phenotype; D018517:Plant Roots / Q000033:anatomy & histology / Q000254:growth & development*; D012984:Software; D012987:Soil; D003313:Zea mays / Q000033:anatomy & histology / Q000254:growth & development
chemical_list: D012987:Soil