The structures of roots play an essential role in plant growth, development, and stress responses. Minirhizotron imaging is one of the widely used approaches to capture and analyze root systems. After segmenting minirhizotron images, every individual root is separated from each other and the background. Root traits, like root lengths and diameter distributions, can provide information about the health of the plants. Current methods to analyze minirhizotron images usually rely on manually annotated labels and commercial software tools, which are time and labor-consuming. Unfortunately, these current methods usually generate a statistical analysis of the input image rather than the features of each root. In this work, we propose a pipeline to automatically use deep neural networks to segment roots from the background and then extract root features like lengths and diameter distributions from the individual segmented root. In detail, we first use a pre-trained U-Net to segment the roots in the minirhizotron images. Then, we separate each individual root with the help of connected component analysis. Finally, we extract the features like diameter distribution or root lengths of every individual root with morphological operations, like skeletonization. For evaluation, we conduct experiments on synthetic roots, which are made of strings and threads, and compare results against a benchmark root dataset (PRMI) of real switchgrass roots and compare the estimated results with the existing commercial software.
Purpose
Root system architectures are complex and challenging to characterize effectively for agronomic and ecological discovery.
Methods
We propose a new method, Spatial and Texture Analysis of Root SystEm distribution with Earth mover’s Distance (STARSEED), for comparing root system distributions that incorporates spatial information through a novel application of the Earth Mover’s Distance (EMD).
Results
We illustrate that the approach captures the response of sesame root systems for different genotypes and soil moisture levels. STARSEED provides quantitative and visual insights into changes that occur in root architectures across experimental treatments.
Conclusion
STARSEED can be generalized to other plants and provides insight into root system architecture development and response to varying growth conditions not captured by existing root architecture metrics and models. The code and data for our experiments are publicly available: https://github.com/GatorSense/STARSEED.
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