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Innovation and Improvement for In Situ Root Measurements


Fine roots (generally < 2 mm in diameter) play a critical role in the carbon and nutrient cycles of ecosystems. Their production, distribution within the soil, and turnover must be measured to have a full understanding of how an ecosystem is responding to perturbations such as climate change (Reference 2, 10 and 11). Currently, the best method available for quantifying fine roots is minirhizotrons (Reference 12), which are used to periodically collect images of intact roots with a camera inserted in a transparent tube installed in the soil. Current analysis of the collected images is difficult, labor-intensive, and subject to operator biases. Quantification and analysis is a particular challenge in certain environments such as rocky soils and wetland ecosystems (Reference 13). Grant applications are sought for technology innovation to improve current minirhizotron technologies and produce rapid assessments and measurements of in situ fine root measurements. Improvements should be aimed at developing an integrated high-throughput system that captures and processes images in real time and produces an automated replicable and artifact-free analysis of the images. Key capabilities should include state-of-the-art analytical operations, immediate detection and extraction of features (see item 2 below), and use of image-processing filters for comparing images while keeping pace with the rate of image capture. Specific technology developments should include one or more of the following criteria: (1) Advanced Image Collection System New, low-cost imaging-camera designs and automated acquisition systems with increased versatility in soil imaging and field conditions. Device flexibility of usage and portability are also sought (Reference 13). (2) Automated Image Analysis Software improvements to develop new image-processing algorithms and automated solutions that can reduce the amount of manual intervention required for each image analysis. A reliable, automated minirhizotron image analysis system would make possible more consistency and greater data intensity. An example of a minirhizotron analysis system is RootFly (, but this program has proven inadequate for truly automated analysis, especially in systems where there is little contrast between roots and the background soil matrix. Specific high resolution root parameters that should be captured by automated analysis include, but are not limited to: root length, root diameter, color, turnover rates, and fungal presence. Innovative methods for automated analysis of fine root and fungal dynamics (i.e., production, mortality, and turnover calculate between sampling dates) are also highly desired. (3) Three-dimensional Scaling and Image Analysis Current analysis methods cannot adequately scale 2-dimensional minirhizotron images to three-dimensional data. There is potential for automated analysis of root edge resolution in order to quantify the image depth of field, or whether a particular root was in focus and therefore within a given depth of field (Reference 13). (4) Other Non-Destructive Belowground Assessment Tools Additionally, desired measurement characteristics could include other non-destructive, remote quantification or visualizations of fine roots in soil such as ground penetrating radar (References 15 and 16) microscopic or high-resolution X-ray imaging of roots (Reference 14), and portable X-ray tomography (i.e., Such a system could be deployed using the minirhizotron tubes that have been installed in many experimental sites, or newer, miniaturized approaches that are minimally invasive to the experimental system (e.g. soil environment) could be developed.
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