Abstract
The objective of this study was to develop a flexible and free image processing and analysis solution, based on the Public Domain ImageJ platform, for the segmentation and analysis of complex biological plant root systems in soil from x-ray tomography 3D images. Contrasting root architectures from wheat, barley and chickpea root systems were grown in soil and scanned using a high resolution micro-tomography system. A macro (Root1) was developed that reliably identified with good to high accuracy complex root systems (10% overestimation for chickpea, 1% underestimation for wheat, 8% underestimation for barley) and provided analysis of root length and angle. In-built flexibility allowed the user interaction to (a) amend any aspect of the macro to account for specific user preferences, and (b) take account of computational limitations of the platform. The platform is free, flexible and accurate in analysing root system metrics.
Highlights
Non-destructive observation and measurement of plant root traits in soil represents an important goal for many plant and soil scientists [1]
Wheat and barley varieties were chosen as they represent a range of commercially important crops with geometricaly complex, yet significantly different, root architectures providing a range of challenges to overcome for μCT scanning and subsequent image processing: one a taproot with relatively large root diameters, but with a less variable architecture, 3D analysis of roots in soil compared to highly complex and adaptable wheat and barley root architectures with relatively small diameter roots
Water was maintained to a volumetric water content of 28% w/w daily
Summary
Non-destructive observation and measurement of plant root traits in soil represents an important goal for many plant and soil scientists [1]. This would be achieved in the natural field environment. Past experiences of excavating soil pits and exposing a vertical soil surface under field conditions, and measuring a small fraction of exposed plant roots, have shown that such methodology is sub-optimal [2,3] with only a small portion of the total root system observable and no 3D spatial information retained. Whilst interesting and elegant approaches to monitoring and measuring root growth are developing in soilless transparent media [2,4] omission of soil from such experiments and assays is sub-optimal as it excludes the soil-root interface which is the main reactive surface in plant development in terms of water/nutrient uptake and root development, and is important for all soil biological processes [1,5,6].
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