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On the evaluation of methods for the recovery of plant root systems from X-ray computed tomography images

Mairhofer, Stefan; Sturrock, Craig; Wells, Darren M.; Bennett, Malcolm J.; Mooney, Sacha J.; Pridmore, Tony P.

On the evaluation of methods for the recovery of plant root systems from X-ray computed tomography images Thumbnail


Stefan Mairhofer

Principal Research Fellow

Professor of Soil Physics

Professor of Computer Science


© CSIRO 2015. X-ray microcomputed tomography (μCT) allows nondestructive visualisation of plant root systems within their soil environment and thus offers an alternative to the commonly used destructive methodologies for the examination of plant roots and their interaction with the surrounding soil. Various methods for the recovery of root system information from X-ray computed tomography (CT) image data have been presented in the literature. Detailed, ideally quantitative, evaluation is essential, in order to determine the accuracy and limitations of the proposed methods, and to allow potential users to make informed choices among them. This, however, is a complicated task. Three-dimensional ground truth data are expensive to produce and the complexity of X-ray CT data means that manually generated ground truth may not be definitive. Similarly, artificially generated data are not entirely representative of real samples. The aims of this work are to raise awareness of the evaluation problem and to propose experimental approaches that allow the performance of root extraction methods to be assessed, ultimately improving the techniques available. To illustrate the issues, tests are conducted using both artificially generated images and real data samples.

Journal Article Type Article
Acceptance Date Oct 1, 2014
Online Publication Date Dec 2, 2014
Publication Date Dec 2, 2014
Deposit Date Jan 27, 2015
Publicly Available Date Jan 27, 2015
Journal Functional Plant Biology
Print ISSN 1445-4408
Electronic ISSN 1445-4416
Publisher CSIRO Publishing
Peer Reviewed Peer Reviewed
Volume 42
Issue 5
Pages 460-470
Keywords Root architecture, Root image analysis, Segmentation
Public URL
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