Techniques and Approaches for Documenting Plant Root Development with X-Ray Computed Tomography

Author(s):  
E. W. Tollner ◽  
E. L. Ramseur ◽  
C. Murphy
2015 ◽  
Vol 42 (5) ◽  
pp. 460 ◽  
Author(s):  
Stefan Mairhofer ◽  
Craig Sturrock ◽  
Darren M. Wells ◽  
Malcolm J. Bennett ◽  
Sacha J. Mooney ◽  
...  

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.


2017 ◽  
Vol 2 (4) ◽  
pp. 270-286 ◽  
Author(s):  
Stefan Mairhofer ◽  
Tony Pridmore ◽  
James Johnson ◽  
Darren M. Wells ◽  
Malcolm J. Bennett ◽  
...  

1999 ◽  
Vol 11 (1) ◽  
pp. 199-211
Author(s):  
J. M. Winter ◽  
R. E. Green ◽  
A. M. Waters ◽  
W. H. Green

2013 ◽  
Vol 19 (S2) ◽  
pp. 630-631
Author(s):  
P. Mandal ◽  
W.K. Epting ◽  
S. Litster

Extended abstract of a paper presented at Microscopy and Microanalysis 2013 in Indianapolis, Indiana, USA, August 4 – August 8, 2013.


Sensors ◽  
2021 ◽  
Vol 21 (2) ◽  
pp. 591
Author(s):  
Manasavee Lohvithee ◽  
Wenjuan Sun ◽  
Stephane Chretien ◽  
Manuchehr Soleimani

In this paper, a computer-aided training method for hyperparameter selection of limited data X-ray computed tomography (XCT) reconstruction was proposed. The proposed method employed the ant colony optimisation (ACO) approach to assist in hyperparameter selection for the adaptive-weighted projection-controlled steepest descent (AwPCSD) algorithm, which is a total-variation (TV) based regularisation algorithm. During the implementation, there was a colony of artificial ants that swarm through the AwPCSD algorithm. Each ant chose a set of hyperparameters required for its iterative CT reconstruction and the correlation coefficient (CC) score was given for reconstructed images compared to the reference image. A colony of ants in one generation left a pheromone through its chosen path representing a choice of hyperparameters. Higher score means stronger pheromones/probabilities to attract more ants in the next generations. At the end of the implementation, the hyperparameter configuration with the highest score was chosen as an optimal set of hyperparameters. In the experimental results section, the reconstruction using hyperparameters from the proposed method was compared with results from three other cases: the conjugate gradient least square (CGLS), the AwPCSD algorithm using the set of arbitrary hyperparameters and the cross-validation method.The experiments showed that the results from the proposed method were superior to those of the CGLS algorithm and the AwPCSD algorithm using the set of arbitrary hyperparameters. Although the results of the ACO algorithm were slightly inferior to those of the cross-validation method as measured by the quantitative metrics, the ACO algorithm was over 10 times faster than cross—Validation. The optimal set of hyperparameters from the proposed method was also robust against an increase of noise in the data and can be applicable to different imaging samples with similar context. The ACO approach in the proposed method was able to identify optimal values of hyperparameters for a dataset and, as a result, produced a good quality reconstructed image from limited number of projection data. The proposed method in this work successfully solves a problem of hyperparameters selection, which is a major challenge in an implementation of TV based reconstruction algorithms.


2021 ◽  
Vol 173 ◽  
pp. 110894
Author(s):  
Ercan Cakmak ◽  
Philip Bingham ◽  
Ross W. Cunningham ◽  
Anthony D. Rollett ◽  
Xianghui Xiao ◽  
...  

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