Plant and Soil

, Volume 441, Issue 1–2, pp 643–655 | Cite as

A shape-based method for automatic and rapid segmentation of roots in soil from X-ray computed tomography images: Rootine

  • Wei GaoEmail author
  • Steffen Schlüter
  • Sebastian R. G. A. Blaser
  • Jianbo Shen
  • Doris Vetterlein
Methods Paper



X-ray computed tomography (CT) is widely recognized as a powerful tool for in-situ quantification of root system architecture (RSA) in soil. However, employing X-ray CT to identify the spatio-temporal dynamics of RSA still remains a challenge due to non-automatic, time-consuming image processing protocols and their poor recovery of fine roots in soil.


Here we present a new protocol (Rootine) to segment roots rapidly and precisely down to fine roots with two voxels in diameter (90 μm in pots with 70 mm in diameter). This is facilitated by feature detection of the tubular shape of roots, an approach that was originally developed for detecting blood vessels in medical imaging.


In comparison to established root segmentation methods, Rootine produced a more accurate root network, i.e. more roots and less over-segmentation. Root length quantified by X-ray CT showed high correlation with results by root washing combined with 2D light scanning (R2 = 0.92). Tests with different soil materials showed that the recovery of roots depends on signal-to-noise ratio but can be up to 99% for a favorable contrast between fine roots and background.


This new protocol provides great efficiency to study RSA in undisturbed soil. As it is fully automated it has the potential for high-throughput root phenotyping and related modelling.


High-throughput root phenotyping Image analysis Root segmentation Root system architecture (RSA) Tubular root X-ray computed tomography (CT) 



WG and JS are funded by the National Natural Science Foundation of China (31330070, 31772402). The authors thank Dr. John Maximilian Köhne for providing a lot of help during scanning the samples with X-ray CT. Maik Lucas and Ina-Maria Zickenrott supported soil column experiments. We thank Frank Hochholdinger for providing the seeds. We also thank the Chinese Scholarship Council (CSC) for providing a scholarship to WG for visiting Helmholtz Centre for Environmental Research (UFZ). The authors acknowledge Deutsche Forschungsgemeinschaft (DFG) for establishment of SPP 2089.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.Centre for Resources, Environment and Food Security, Department of Plant Nutrition, Key Laboratory of Plant-Soil Interactions, Ministry of Education, No.2 Yuan-ming-yuan West RoadChina Agricultural UniversityBeijingChina
  2. 2.Department of Soil System Science, Helmholtz Centre for Environmental Research – UFZHalle (Saale)Germany
  3. 3.Institute of Agricultural and Nutritional SciencesMartin-Luther-University Halle-WittenbergHalle (Saale)Germany

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