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@ARTICLE{Stingaciu:188024,
      author       = {Stingaciu, Laura and Schulz, Hannes and Pohlmeier, Andreas
                      and Behnke, Sven and Zilken, Herwig and Javaux, Mathieu and
                      Vereecken, Harry},
      title        = {{I}n {S}itu {R}oot {S}ystem {A}rchitecture {E}xtraction
                      from {M}agnetic {R}esonance {I}maging for {W}ater {U}ptake
                      {M}odeling},
      journal      = {Vadose zone journal},
      volume       = {12},
      number       = {1},
      issn         = {1539-1663},
      address      = {Madison, Wis.},
      publisher    = {SSSA},
      reportid     = {FZJ-2015-01510},
      pages        = {9},
      year         = {2013},
      abstract     = {The three-dimensional root system architecture (RSA) of a
                      lupin plant is constructed using two methods, an automated
                      procedure based on a three-dimensional MRI image, and a
                      semi-manual method based a 3D virtual reality system. The
                      two results show some differences in connectivity of root
                      segments, which affects the distributions of root water
                      uptake and xylem pressures.An automated method for root
                      system architecture reconstruction from three-dimensional
                      volume data sets obtained from magnetic resonance imaging
                      (MRI) was developed and validated with a three-dimensional
                      semimanual reconstruction using virtual reality and a
                      two-dimensional reconstruction using SmartRoot. It was
                      tested on the basis of an MRI image of a 25-d-old lupin
                      (Lupinus albus L.) grown in natural sand with a resolution
                      of 0.39 by 0.39 by 1.1 mm. The automated reconstruction
                      algorithm was inspired by methods for blood vessel detection
                      in MRI images. It describes the root system by a
                      hierarchical network of nodes, which are connected by
                      segments of defined length and thickness, and also allows
                      the calculation of root parameter profiles such as root
                      length, surface, and apex density The obtained root system
                      architecture (RSA) varied in number of branches, segments,
                      and connectivity of the segments but did not vary in the
                      average diameter of the segments (0.137 cm for semimanual
                      and 0.143 cm for automatic RSA), total root surface (127 cm2
                      for semimanual and 124 cm2 for automatic RSA), total root
                      length (293 cm for semimanual and 282 cm for automatic RSA),
                      and total root volume (4.7 cm3 for semimanual and 4.7 cm3
                      for automatic RSA). The difference in performance of the
                      automated and semimanual reconstructions was checked by
                      using the root system as input for water uptake modeling
                      with the Doussan model. Both systems worked well and allowed
                      for continuous water flow. Slight differences in the
                      connectivity appeared to be leading to locally different
                      water flow velocities, which were $30\%$ smaller for the
                      semimanual method.},
      cin          = {IBG-3 / JSC},
      ddc          = {550},
      cid          = {I:(DE-Juel1)IBG-3-20101118 / I:(DE-Juel1)JSC-20090406},
      pnm          = {246 - Modelling and Monitoring Terrestrial Systems: Methods
                      and Technologies (POF2-246) / 41G - Supercomputer Facility
                      (POF2-41G21)},
      pid          = {G:(DE-HGF)POF2-246 / G:(DE-HGF)POF2-41G21},
      typ          = {PUB:(DE-HGF)16},
      UT           = {WOS:000317713300007},
      doi          = {10.2136/vzj2012.0019},
      url          = {https://juser.fz-juelich.de/record/188024},
}