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

2015 ◽  
Vol 42 (5) ◽  
pp. 460 ◽  
Author(s):  
Stefan Mairhofer ◽  
Craig Sturrock ◽  
Darren M. Wells ◽  
Malcolm J. Bennett ◽  
Sacha J. Mooney ◽  
...  
Keyword(s):  
Computed Tomography ◽  
Plant Root ◽  
Ground Truth ◽  
Real Data ◽  
Root Systems ◽  
Ground Truth Data ◽  
X Ray ◽  
Computed Tomography Images ◽  
X Ray Computed ◽  
Plant Root Systems

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.

X‐Ray Computed Tomography of Crop Plant Root Systems Grown in Soil

2017 ◽  
Vol 2 (4) ◽  
pp. 270-286 ◽  
Author(s):  
Stefan Mairhofer ◽  
Tony Pridmore ◽  
James Johnson ◽  
Darren M. Wells ◽  
Malcolm J. Bennett ◽  
...  
Keyword(s):  
Computed Tomography ◽  
Plant Root ◽  
Root Systems ◽  
Crop Plant ◽  
X Ray ◽  
X Ray Computed ◽  
Plant Root Systems

scholarly journals The Application of Contrast Media for In Vivo Feature Enhancement in X-Ray Computed Tomography of Soil-Grown Plant Roots

2017 ◽  
Vol 23 (3) ◽  
pp. 538-552 ◽  
Author(s):  
Samuel D. Keyes ◽  
Neil J. Gostling ◽  
Jessica H. Cheung ◽  
Tiina Roose ◽  
Ian Sinclair ◽  
...  
Keyword(s):  
Contrast Media ◽  
Plant Root ◽  
Root Systems ◽  
System Architectures ◽  
X Ray ◽  
Iodinated Contrast ◽  
Seminal Roots ◽  
X Ray Computed ◽  
Plant Root Systems

AbstractThe use of in vivo X-ray microcomputed tomography (μCT) to study plant root systems has become routine, but is often hampered by poor contrast between roots, soil, soil water, and soil organic matter. In clinical radiology, imaging of poorly contrasting regions is frequently aided by the use of radio-opaque contrast media. In this study, we present evidence for the utility of iodinated contrast media (ICM) in the study of plant root systems using μCT. Different dilutions of an ionic and nonionic ICM (Gastrografin 370 and Niopam 300) were perfused into the aerial vasculature of juvenile pea plants via a leaf flap (Pisum sativum). The root systems were imaged via μCT, and a variety of image-processing approaches used to quantify and compare the magnitude of the contrast enhancement between different regions. Though the treatment did not appear to significantly aid extraction of full root system architectures from the surrounding soil, it did allow the xylem and phloem units of seminal roots and the vascular morphology within rhizobial nodules to be clearly visualized. The nonionic, low-osmolality contrast agent Niopam appeared to be well tolerated by the plant, whereas Gastrografin showed evidence of toxicity. In summary, the use of iodine-based contrast media allows usually poorly contrasting root structures to be visualized nondestructively using X-ray μCT. In particular, the vascular structures of roots and rhizobial nodules can be clearly visualized in situ.

scholarly journals Visualization Ability of Phase-Contrast Synchrotron-Based X-Ray Imaging Using an X-Ray Interferometer in Soft Tissue Tumors

2021 ◽  
Vol 20 ◽  
pp. 153303382110101
Author(s):  
Thet-Thet Lwin ◽  
Akio Yoneyama ◽  
Hiroko Maruyama ◽  
Tohoru Takeda
Keyword(s):  
Computed Tomography ◽  
Soft Tissue ◽  
Spatial Resolution ◽  
Phase Contrast ◽  
Soft Tissue Tumors ◽  
X Ray ◽  
3 Dimensional ◽  
Computed Tomography Images ◽  
X Ray Imaging ◽  
X Ray Computed

Phase-contrast synchrotron-based X-ray imaging using an X-ray interferometer provides high sensitivity and high spatial resolution, and it has the ability to depict the fine morphological structures of biological soft tissues, including tumors. In this study, we quantitatively compared phase-contrast synchrotron-based X-ray computed tomography images and images of histopathological hematoxylin-eosin-stained sections of spontaneously occurring rat testicular tumors that contained different types of cells. The absolute densities measured on the phase-contrast synchrotron-based X-ray computed tomography images correlated well with the densities of the nuclear chromatin in the histological images, thereby demonstrating the ability of phase-contrast synchrotron-based X-ray imaging using an X-ray interferometer to reliably identify the characteristics of cancer cells within solid soft tissue tumors. In addition, 3-dimensional synchrotron-based phase-contrast X-ray computed tomography enables screening for different structures within tumors, such as solid, cystic, and fibrous tissues, and blood clots, from any direction and with a spatial resolution down to 26 μm. Thus, phase-contrast synchrotron-based X-ray imaging using an X-ray interferometer shows potential for being useful in preclinical cancer research by providing the ability to depict the characteristics of tumor cells and by offering 3-dimensional information capabilities.

scholarly journals Computation of permeability of a non-crimp carbon textile reinforcement based on X-ray computed tomography images

2016 ◽  
Vol 81 ◽  
pp. 289-295 ◽  
Author(s):  
Ilya Straumit ◽  
Christoph Hahn ◽  
Elisabeth Winterstein ◽  
Bernhard Plank ◽  
Stepan V. Lomov ◽  
...  
Keyword(s):  
Computed Tomography ◽  
X Ray ◽  
Computed Tomography Images ◽  
X Ray Computed

Automatic Knot Detection in Coarse-Resolution Cone-Beam Computed Tomography Images of Softwood Logs

2019 ◽  
Vol 69 (3) ◽  
pp. 185-187
Author(s):  
Magnus Fredriksson ◽  
Julie Cool ◽  
Stavros Avramidis
Keyword(s):  
Computed Tomography ◽  
Exploratory Study ◽  
Ct Scanning ◽  
Detection Algorithm ◽  
Cone Beam ◽  
X Ray ◽  
Coarse Resolution ◽  
Computed Tomography Images ◽  
X Ray Computed ◽  
Accurate Position

Abstract X-ray computed tomography (CT) scanning of sawmill logs is associated with costly and complex machines. An alternative scanning solution was developed, but its data have not been evaluated regarding detection of internal features. In this exploratory study, a knot detection algorithm was applied to images of four logs to evaluate its performance in terms of knot position and size. The results were a detection rate of 67 percent, accurate position, and inaccurate size. Although the sample size was small, it was concluded that automatic knot detection in coarse resolution CT images of softwoods is feasible, albeit for knots of sufficient size.

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