On the evaluation of methods for the recovery of plant root systems from X-ray computed tomography images
X-ray micro computed tomography (µCT) allows non-destructive visualisation of plant root systems within their soil environment and thus offers an alternative to commonly used destructive methodologies for the examination of plant roots and their interaction with the surrounding soil. Various methods...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Published: |
CSIRO Publishing
2014
|
| Subjects: | |
| Online Access: | https://eprints.nottingham.ac.uk/28206/ |
| _version_ | 1848793524570423296 |
|---|---|
| author | Mairhofer, Stefan Sturrock, Craig Wells, Darren M. Bennett, Malcolm J. Mooney, Sacha J. Pridmore, Tony |
| author_facet | Mairhofer, Stefan Sturrock, Craig Wells, Darren M. Bennett, Malcolm J. Mooney, Sacha J. Pridmore, Tony |
| author_sort | Mairhofer, Stefan |
| building | Nottingham Research Data Repository |
| collection | Online Access |
| description | X-ray micro computed tomography (µCT) allows non-destructive visualisation of plant root systems within their soil environment and thus offers an alternative to 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 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 between them. This, however, is a complicated task. Three-dimensional ground truth data is 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 is 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. |
| first_indexed | 2025-11-14T19:01:40Z |
| format | Article |
| id | nottingham-28206 |
| institution | University of Nottingham Malaysia Campus |
| institution_category | Local University |
| last_indexed | 2025-11-14T19:01:40Z |
| publishDate | 2014 |
| publisher | CSIRO Publishing |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | nottingham-282062020-05-04T16:59:23Z https://eprints.nottingham.ac.uk/28206/ 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 X-ray micro computed tomography (µCT) allows non-destructive visualisation of plant root systems within their soil environment and thus offers an alternative to 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 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 between them. This, however, is a complicated task. Three-dimensional ground truth data is 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 is 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. CSIRO Publishing 2014-12-02 Article PeerReviewed Mairhofer, Stefan, Sturrock, Craig, Wells, Darren M., Bennett, Malcolm J., Mooney, Sacha J. and Pridmore, Tony (2014) On the evaluation of methods for the recovery of plant root systems from X-ray computed tomography images. Functional Plant Biology, 42 (5). pp. 460-470. ISSN 1445-4408 Root architecture Root image analysis Segmentation http://www.publish.csiro.au/?paper=FP14071 doi:10.1071/FP14071 doi:10.1071/FP14071 |
| spellingShingle | Root architecture Root image analysis Segmentation Mairhofer, Stefan Sturrock, Craig Wells, Darren M. Bennett, Malcolm J. Mooney, Sacha J. Pridmore, Tony On the evaluation of methods for the recovery of plant root systems from X-ray computed tomography images |
| title | On the evaluation of methods for the recovery of plant root systems from X-ray computed tomography images |
| title_full | On the evaluation of methods for the recovery of plant root systems from X-ray computed tomography images |
| title_fullStr | On the evaluation of methods for the recovery of plant root systems from X-ray computed tomography images |
| title_full_unstemmed | On the evaluation of methods for the recovery of plant root systems from X-ray computed tomography images |
| title_short | On the evaluation of methods for the recovery of plant root systems from X-ray computed tomography images |
| title_sort | on the evaluation of methods for the recovery of plant root systems from x-ray computed tomography images |
| topic | Root architecture Root image analysis Segmentation |
| url | https://eprints.nottingham.ac.uk/28206/ https://eprints.nottingham.ac.uk/28206/ https://eprints.nottingham.ac.uk/28206/ |