OpenAIRE is about to release its new face with lots of new content and services.
During September, you may notice downtime in services, while some functionalities (e.g. user registration, login, validation, claiming) will be temporarily disabled.
We apologize for the inconvenience, please stay tuned!
For further information please contact helpdesk[at]

fbtwitterlinkedinvimeoflicker grey 14rssslideshare1
Mairhofer, Stefan; Sturrock, Craig; Wells, Darren M.; Bennett, Malcom J.; Mooney, Sacha J.; Pridmore, Tony (2014)
Publisher: CSIRO Publishing
Languages: English
Types: Article
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.
  • The results below are discovered through our pilot algorithms. Let us know how we are doing!

    • J.-L. Arsenault, S. Pouleur, C. Messier, R. Guay. WinRHIZO™, a root-measuring system with a unique overlap correction method. HortScience, 30:906, 1995.
    • Tjeerd J. Bouma, Kai L. Nielsen, and Bas Koutstaal. Sample preparation and scanning protocol for computerised analysis of root length and diameter. Plant and Soil, 218(1-2):185-196, 2000. ISSN 0032-079X.
    • S. Bouix, M. Martin-Fernandez, L. Ungar, M. Nakamura, M. S, Koo., R. W. McCarley, and M. E, Shenton. On evaluating brain tissue classifiers without a ground truth. Neuroimage, 36(4):1207- 1224, 2007.
    • Deo A. Heeraman, Jan W. Hopmans, and Volker Clausnitzer. Three dimensional imaging of plant roots in situ with x-ray computed tomography. Plant and Soil, 189:167-179, 1997. ISSN 0032-079X.
    • T. Heimann, B. Van Ginneken, M. A. Styner, Y. Arzhaeva, V. Aurich, C. Bauer, A. Beck et al. Comparison and evaluation of methods for liver segmentation from CT datasets. Medical Imaging, IEEE Transactions on,28(8):1251-1265, 2009.
    • Gabor T. Herman. Fundamentals of Computerized Tomography: Image Reconstruction from Projections. Springer Publishing Company, Incorporated, 2nd edition, 2009. ISBN 185233617X, 9781852336172.
    • J. O'Callaghan, J. Wells, S. Richardson, H. Holmes, Y. Yu, S. Walker-Samuel, B. Siow, and M. F. Lythgoe. Is Your System Calibrated? MRI Gradient System Calibration for Pre-Clinical, HighResolution Imaging. PloS one, 9(5), 2014.
    • J. S. Perret, M. E. Al-Belushi, and M. Deadman. Non-destructive visualization and quantification of roots using computed tomography. Soil Biology and Biochemistry, 39(2):391-399, 2007. ISSN 0038- 0717.
    • P. J. Phillips, H. Moon, S. A. Rizvi, and P. J. Rauss. The FERET evaluation methodology for facerecognition algorithms. Pattern Analysis and Machine Intelligence, IEEE Transactions on, 22(10):1090-1104, 2000.
    • Alain Pierret, Yvan Capowiez, Christopher J. Moran, and Andre Kretzschmar. X-ray computed tomography to quantify tree rooting spatial distributions. Geoderma, 90(3-4):307-326, 1999. ISSN 0016-7061.
  • No related research data.
  • No similar publications.

Share - Bookmark

Cite this article

Cookies make it easier for us to provide you with our services. With the usage of our services you permit us to use cookies.
More information Ok