Interdisciplinary blog

Computationally Intensive Imaging EPSRC Summer Bursaries 2014

July 1, 2014
by Nathan Soper

Nathan Soper – ‘Application of X-ray Computed Tomography and advanced image processing for novel quantification of plant root growth micro-mechanisms’.

I’ve just finished my 3rd year of Electronic Engineering and am set to be beginning my 4th and final year this September. This internship is based within the Faculty of Engineering and the Environment and more specifically within μ-VIS and under the supervision of Dr Sam D Keyes. In many ways this project is far removed from my previous areas of study, however there is a surprising array of overlap of the skill sets required. This project involves taking many computer vision and engineering techniques and applying them to complex biological systems in order to better understand them.

Specifically this project will involve analysing data sets taken from X-ray images taken of root samples of wheat. With the use of very high resolution X-rays and a large amount of computing grunt, 3D data sets of plant root images can be obtained through a technique known as computer tomography (CT). By taking repeated snapshots through time, the growth of a root through various porous media can be observed and analysed.

As a root grows down through soil or whichever medium within which it is placed, it will move its way around air, soil, water, harder minerals in the ground as well as biological matter. This project will further investigate how this process happens and what factors affect the rate of growth both radially and along the length of the root.

Figure 1 3D rendered image of a root growing through soil, taken from a CT dataset.

Figure 1 3D rendered image of a root growing through soil, taken from a CT dataset.

A sizeable amount of this project will be located in the lab where the samples will be grown, providing plenty of hands on experience in the world of lab based botany. The apparatus for the experiments must also be devised through various CAD and 3D printing methods. All of this must be done before any CT can be done.

Digital Volume Correlation is a “novel technique” that is an extension of previous 2D techniques that allow a 3D volume to be analysed over time. Examining plant roots in 3D in this way is novel and has yet to be extensively researched.

This research could have some very well appreciated applications; being able to better understand how to grow crops such as rice, wheat and maize could vastly improve the yield of arable farms as we better understand how these plants grow. Hopefully this research will be a positive contribution to the field and while be the bedrock for future research projects.

In the future I hope to pursue postgraduate research and so I hope that this summer project will be a good insight into the world of research and I expect to learn many skills that will equip and prepare me for the diverse and complex challenges that this could present.

Categories: Blog. Tags: CII, Computationally Intensive Imaging, epsrc, ian sinclair, idr, interdisciplinary, interdisciplinary research, nathan soper, research, sam keyes, University of Southampton, and vacation bursaries.