![]() The complete reconstruction of a root system therefore requires a lot of interactive parameter optimization and interpretation, which is supported by software tools that allow identification of connected root systems (e.g. These local thresholds often vary throughout a sample due to heterogeneities in the substrate and CT-artefacts. Segmentation is usually performed by defining a local threshold for gray values of the CT voxels, classifying them either as root or non-root. Indeed, unaltered RSA can be analyzed by CT, but the segmentation of the root (optical separation of root and soil) is done to a large extent manually and therefore requires a lot of time. ![]() Yet, using CT, the throughput suffers from the bottleneck of rapid and standardized segmentation methods to extract root structures. Moreover, when using destructive methods, in which roots are washed out of the soil, fine roots frequently break off and are washed away, while they can be analyzed in CT scans if the spatial resolution is appropriate. In particular, the possibility to follow the same individual root growing over time and to study dynamic root growth and development processes in pot experiments, and, in addition, the opportunity to explore the unaltered configuration of the 3D RSA interacting with a real field soil matrix, makes CT a unique tool for plant research. so-called ‘shovelomics’ approaches as described in ), CT encompasses various advantages. WinRHIZO, Regent Instruments Inc., Sainte-Foy, Québec, Canada) or custom-made software (e.g. Compared to rather classical, destructive methods, in which roots are first washed out of the soil, imaged and then analyzed with commercially available (e.g. ![]() In the context of root phenotyping, X-ray computed tomography (CT) has become a powerful tool. Increasing the throughput for quantitative characterization of plant root system architecture (RSA) is important for plant breeding and to come to an improved understanding of root–soil interactions. ![]() ConclusionsĪpplication of the presented protocol helps to overcome the segmentation bottleneck and can be considered a step forward to high throughput root phenotyping facilitating appropriate sample sizes desired by science and breeding. Root thickness is a central RSA trait for various physiological research questions such as root growth in compacted soil or under oxygen deficient soil conditions, but hardly assessable in high throughput until today, due to a lack of available protocols. Subsequent to segmentation, a method for the measurement of root thickness distribution has been used. A highly significant ( P < 0.01) and strong correlation (R 2 = 0.84) was found, demonstrating the value of the presented method in the context of field research. Root systems from several crops were sampled in situ and CT-volumes determined with the presented method were compared to root dry matter of washed root samples. To the knowledge of the authors this is the first study approaching to develop a comprehensive segmentation method suitable for comparatively large columns sampled in situ which contain complex, not necessarily connected root systems from multiple plants grown in undisturbed field soil. Resultsīased on commercially available software, this paper presents a protocol that is faster, more standardized and more versatile compared to existing segmentation methods, particularly if used to analyse field samples collected in situ. Using available methods, root segmentation is done to a large extent manually, as it requires a lot of interactive parameter optimization and interpretation and therefore needs a lot of time. Yet, the throughput, which is essential for a more widespread application of CT for basic research or breeding programs, suffers from the bottleneck of rapid and standardized segmentation methods to extract root structures. In pot experiments the growth and development of the same individual root can be followed over time and in addition the unaltered configuration of the 3D root system architecture (RSA) interacting with a real field soil matrix can be studied. Compared to rather classical, destructive methods, CT encompasses various advantages. \): Formation of New Land by the Destabilization of a Colloid Suspension.X-ray computed tomography (CT) has become a powerful tool for root phenotyping.
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