In Situ Root System Architecture Extraction from Magnetic Resonance Imaging for Water Uptake Modeling

By L. Stingaciu, Hannes Schulz, A. Pohlmeier, Sven Behnke, H. Zilken, Mathieu Javaux, Harry Vereecken. 2013

53 citations recorded by the source corpus.

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.

Subfields: Civil and Structural Engineering, Plant Science, Soil Science

View Paper: https://www.semanticscholar.org/paper/e921fb4465ebadd8509c63592200312683fc57af

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Plant Science

1. Achim Walter
2. Frank Liebisch
3. Andreas Hund

In Soil Science

1. Achim Walter
2. Andreas Hund
3. Frank Liebisch

Citations in the corpus

• Root Water Uptake: From Three‐Dimensional Biophysical Processes to Macroscopic Modeling Approaches (2013, unknown): “…2013). he combination of noninvasive methods that enable noninvasive monitoring of the root system, the moisture content distribution around roots and tracer transport towards roots with detailed process models may be used to validate and parameterize these types of model (Stingaciu et al., 2013).”
• Plant phenotyping: from bean weighing to image analysis (2015, methodology): “Other methodologies with the potential to study root system architecture and functioning in the future are nuclear magnetic resonance [104-106], neutron radiography [107] and positron emission tomography [108], which allow segmenting the root from the surrounding substrate.”