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Recovering complete plant root system architectures from soil via X-ray ?-computed tomography

Mairhofer, Stefan; Zappala, Susan; Tracy, Saoirse; Sturrock, Craig; Bennett, Malcolm J.; Mooney, Sacha J.; Pridmore, Tony

Recovering complete plant root system architectures from soil via X-ray ?-computed tomography Thumbnail


Stefan Mairhofer

Susan Zappala

Saoirse Tracy

Sacha J. Mooney

Professor of Computer Science


Background: X-ray micro-Computed Tomography (μCT) offers the ability to visualise the three-dimensional
structure of plant roots growing in their natural environment – soil. Recovery of root architecture descriptions from X-ray CT data is, however, challenging. The X-ray attenuation values of roots and soil overlap, and the attenuation values of root material vary. Any successful root identification method must both explicitly target root material and be able to adapt to local changes in root properties.
RooTrak meets these requirements by combining the level set method with a visual tracking framework and has been shown to be capable of segmenting a variety of plant roots from soil in X-ray μCT images. The approach provides high quality root descriptions, but tracks root systems top to bottom and so omits upward-growing (plagiotropic) branches.
Results: We present an extension to RooTrak which allows it to extract plagiotropic roots. An additional backwardlooking
step revisits the previous image, marking possible upward-growing roots. These are then tracked, leading to efficient and more complete recovery of the root system. Results show clear improvement in root extraction, without which key architectural traits would be underestimated.
Conclusions: The visual tracking framework adopted in RooTrak provides the focus and flexibility needed to
separate roots from soil in X-ray CT imagery and can be extended to detect plagiotropic roots. The extended
software tool produces more complete descriptions of plant root structure and supports more accurate computation of architectural traits.
Keywords: Root systems architecture, 3D, X-ray Computed Tomography, Image analysis, Root phenotyping


Mairhofer, S., Zappala, S., Tracy, S., Sturrock, C., Bennett, M. J., Mooney, S. J., & Pridmore, T. (2013). Recovering complete plant root system architectures from soil via X-ray ?-computed tomography. Plant Methods, 9, Article 8.

Journal Article Type Article
Publication Date Mar 20, 2013
Deposit Date Apr 10, 2014
Publicly Available Date Apr 10, 2014
Journal Plant Methods
Electronic ISSN 1746-4811
Publisher Springer Verlag
Peer Reviewed Peer Reviewed
Volume 9
Article Number 8
Public URL
Publisher URL


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