Correlative X-ray and neutron tomography of root systems using cadmium fiducial markers

Abstract

The interactions between plant roots and soil are an area of active research, particularly in terms of water and nutrient uptake. Because noninvasive, in vivo studies are required, tomographic imaging appears an obvious method to use, but no one imaging modality is well suited to capture the complete system. X-ray imaging gives clear insight to soil structure and composition; however, water is comparatively transparent to X-rays and biological matter also displays poor contrast with respect to the pores between soil particles. Neutron imaging presents a complementary view where water and biological matter are better distinguished but the soil minerals are not imaged as clearly as they would be with X-rays. This work aims to develop robust methods for complementary X-ray/neutron tomographic imaging of plant root samples which should lead to new insight into water and nutrient transport in soil. The key challenges of this project are to develop experiments that will meet the requirements of both imaging modalities as well as the biological requirements of the plant samples and to develop ways to register a pair of reconstructed volume images of a sample that will typically have been produced with entirely separate facilities. The use of cadmium fiducial markers for registration has been investigated. Simulations were conducted to investigate the expected registration accuracy as the quantity and distribution of the markers varied. The findings of these simulations were then tested experimentally as plant samples were grown and imaged using neutrons with the IMAT instrument at ISIS Neutron and Muon Source at the STFC Rutherford Appleton Laboratory in Harwell, and with X-rays at µ-VIS X-ray Imaging Centre at the University of Southampton. LAY DESCRIPTION: The interactions between plant roots and soil are an area of active research, particularly in terms of water and nutrient uptake. The samples used in this research are typically imaged so that they can be studied without digging up the roots and destroying the sample in the process. X-ray and neutron imaging techniques have both been used as each can show different materials within the sample. Because neither can show all the components of the system by itself, this work explores methods for combining scans of the same sample to give a more complete image of the system. In particular this work focusses on the use of fiducial markers as a strategy for preparing the samples in such a way that the resulting images can be aligned. The effectiveness of this method was tested in simulation and then in practice. The samples used within this work were imaged using neutrons on the IMAT instrument at ISIS Neutron and Muon Source at the STFC Rutherford Appleton Laboratory in Harwell, and with X-rays at µ-VIS X-ray Imaging Centre at the University of Southampton.

Keywords: CT; Computed tomography; X-ray; crop science; fiducial; imaging; neutron; registration.