Developing X-ray Computed Tomography to non-invasively image 3-D root systems architecture in soil

Abstract

Background The need to observe roots in their natural undisturbed state within soil, both spatially and temporally, is a challenge that continues to occupy researchers studying the rhizosphere. Scope This paper reviews how over the last 30 years the application of X-ray Computed Tomography (CT) has demonstrated considerable promise for root visualisation studies. We describe how early CT work demonstrated that roots could be visualised within soils, but was limited by resolution (ca. 1 mm). Subsequent work, utilising newer micro CT scanners, has been able to achieve higher resolutions (ca. 50 μm) and enhance imaging capability in terms of detecting finer root material. However the overlap in the attenuation density of root material and soil pore space has been a major impediment to the uptake of the technology. We then outline how sophisticated image processing techniques, frequently based on object tracking methods, have demonstrated great promise in overcoming these obstacles. This, along with the concurrent advances in scan and reconstruction times, image quality and resolution (ca. 0.5 μm) have opened up new opportunities for the application of X-ray CT in experimental studies of root and soil interactions. Conclusions We conclude that CT is well placed to contribute significantly to unravelling the complex interactions between roots and soil.

Accelerating genetic gains in legumes for the development of prosperous smallholder agriculture: integrating genomics, phenotyping, systems modelling and agronomy

“…• Non-destructively visualizes opaque root structures by measuring the attenuation of ionizing radiation as it passes through the root • A series of projections are acquired and combined to reconstruct a 3D image of the root system Mairhofer et al (2012), Mooney et al (2012) Rhizophonics (University of Liège, Belgium)…”

Analyzing Lateral Root Development: How to Move Forward

“…For example, the x-ray CT technique can be used to study root architectures under varying nutrient, moisture, temperature, and soil density conditions in a physiologically relevant way over time. Drawbacks of the system, such as imaging time, imaging area, and a 3D image reconstruction approach, are being overcome with improvements in instrumentation (scan time and image quality) and development of new software (Mairhofer et al, 2011;Mooney et al, 2011).…”

Quantitative 3D Analysis of Plant Roots Growing in Soil Using Magnetic Resonance Imaging

“…Computed tomography (CT; both x-ray and neutron) has been proposed to overcome the mentioned difficulties with studying roots in natural soil. CT has been successfully used to obtain high-resolution images of roots (Moradi et al, 2009;Flavel et al, 2012;Mooney et al, 2012). High resolution is necessary for segmenting roots due to a poor contrast between roots and soil (Jassogne et al, 2009;Mairhofer et al, 2012;Mairhofer et al, 2013).…”