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The Use of CT Scanning and MRI to investigate soil, water and pathogen interactions
(
2000-present/ Research Team: J. Perret, M. Deadman, M. Al-Belushi, S. Goddard)

 

 

The use of CAT scanning technology for non-medical investigations is in its infancy.  The application of these techniques to agricultural sciences is similarly very new.  This proposal aims to utilize the state of the art equipment at SQU Hospital to examine, non-destructively, the interactions between plant, pathogen and soil.  The project consists of two phases.  In Phase I, validation of results from scanning will be achieved through destructive sampling of replicate plants grown under optimal conditions.  In Phase II, stress conditions will be imposed through water deficit and pathogen action.  Root growth in the test crops (cucumber, bean, wheat) will be assessed and visualized over time to create a three dimensional model of developmental changes effected by stress. This would appear to be the first attempt to visualize root growth under pathogenic and water stresses using CAT analysis and MRI.  The results could have major implications for variety selection, irrigation management and plant breeding.  Information on root structure (length, diameter, tortuosity, surface area etc) has an affect on disease escape and could provide important indicators for disease resistance.  Information about irrigation management could affect the pathogen profile distribution in the soil, also influencing disease escape.

 The analysis of the root system will be carried out in two stages: i) visualization of the roots in 2-D, 3-D, and 4-D (i.e., visualization at different times) and ii) quantification of geometrical characteristics of the root systems.Computer codes in the PV-WAVE programming language will be developed for the visualization and quantification of the roots.  The PV-WAVE language is a comprehensive programming environment that integrates state-of-the-art numerical and graphical analyses.  This programming language is widely used for analyzing and visualizing technical data in many fields, such as medical imaging, remote sensing and engineering.  PV-WAVE is an ideal tool for working with large arrays such as our CAT scan data or MRI data, because of its array-oriented operators and ability to display and process data in the ASCII and Binary formats.

Visualization of the CAT scan matrices is an important step towards the understanding and analysis of the complex root structure.  In order to generate images, programs in PV-WAVE will be developed to convert the matrices in DICOM format (output of the CAT scanner at Sultan Qaboos University’s hospital) into the ASCII and BINARY formats.  Each pixel value will be scaled to a range of 0-255 to form the image.  In this context, an image is a two-dimensional array of pixels for which each element is attributed to a color depending on its value.  To enhance or mask portions of the image, a binary threshold will be used for better detection of the roots.  Visualization of cross-sectional images will be used to examine size and distribution of roots in horizontal planes.  Longitudinal views will be used for visualizing the distribution of the roots along the length of the pot.  Three-dimensional imagery has recently been possible with the aid of powerful stereotactic radiosurgery computer programs.  However, these softwares are very expensive and not offered on typical medical scanners.  Since 3-D imaging is critical to depict the actual distribution of the root system, we will develop our own three-dimensional reconstructive methodology.  

 

Programs in PV-WAVE will be developed to generate three-dimensional models of the roots entirely based on the CAT scan data and MRI data.   These algorithms will permit a three-dimensional image to be reconstructed from multiple contiguous scans.  Since the pots containing the plants will be scanned over time, the root development will also be visualized in 4-D.  Longitudinal views will be used for visualizing the distribution of the roots along the length of the pot.  Three-dimensional imagery has recently been possible with the aid of powerful stereotactic radiosurgery computer programs.  However, these softwares are very expensive and not offered on typical medical scanners.  Since 3-D imaging is critical to depict the actual distribution of the root system, we will develop our own three-dimensional reconstructive methodology.  Programs in PV-WAVE will be developed to generate three-dimensional models of the roots entirely based on the CAT scan data and MRI data.   These algorithms will permit a three-dimensional image to be reconstructed from multiple contiguous scans.  Since the pots containing the plants will be scanned over time, the root development will also be visualized in 4-D.  (Click here for more info)


© 2000 Johan Perret