High-throughput three-dimensional visualization of root system architecture of rice using X-ray computed tomography

Abstract

Background: X-ray computed tomography (CT) allows us to visualize root system architecture (RSA) beneath the soil, non-destructively and in a three-dimensional (3-D) form. However, CT scanning, reconstruction processes, and root isolation from X-ray CT volumes, take considerable time. For genetic analyses, such as quantitative trait locus mapping, which require a large population size, a high-throughput RSA visualization method is required.Results: We have developed a high-throughput process flow for the 3-D visualization of rice (Oryza sativa) RSA (consisting of radicle and crown roots), using X-ray CT. The process flow includes use of a uniform particle size, calcined clay to reduce the possibility of visualizing non-root segments, use of a higher tube voltage and current in the X-ray CT scanning to increase root-to-soil contrast, and use of a 3-D median filter and edge detection algorithm to isolate root segments. Using high-performance computing technology, this analysis flow requires only 10 min (33 s, if a rough image is acceptable) for CT scanning and reconstruction, and 2 min for image processing, to visualize rice RSA. This reduced time allowed us to conduct the genetic analysis associated with 3-D RSA phenotyping. In 2-week-old seedlings, 85% and 100% of radicle and crown roots were detected, when 16 cm and 20 cm diameter pots were used, respectively. The X-ray dose per scan was estimated at < 0.09 Gy, which did not impede rice growth. Using the developed process flow, we were able to follow daily RSA development, i.e., 4-D RSA development, of an upland rice variety, over three weeks. Conclusions: We developed a high-throughput process flow for 3-D rice RSA visualization by X-ray CT. The X-ray dose assay on plant growth has shown that this methodology could be applicable for 4-D RSA phenotyping. We named the RSA visualization method ‘RSAvis3D’ and are confident that it represents a potentially efficient application for 3-D RSA phenotyping of various plant species.

RSAtrace3D: robust vectorization software for measuring monocot root system architecture

“…By utilizing software to quantify RSA traits, root segments in the X-ray CT and MRI images are isolated. In the case of X-ray CT, RooTrak [16,17], RootViz3D® [18], Rootine [19], and RSAvis3D [20] were developed as software to segment roots in the soil. Based on the structure information such as root shape and branching, RooTrak and RootViz3D® isolate root segments by tracking the root segments from the point where an operator indicated [16][17][18].…”

“…Based on the structure information such as root shape and branching, RooTrak and RootViz3D® isolate root segments by tracking the root segments from the point where an operator indicated [16][17][18]. In addition, Rootine and RSAvis3D isolate root segments without manual operation; Rootine segments roots using feature detection of the tubular shape of roots, while RSAvis3D segments roots using an edge detection algorithm [19,20]. In the case of MRI, NMRooting software was developed [21].…”

Cost-effective, high-throughput phenotyping system for 3D reconstruction of fruit form

“…Fruit appearance is a key trait for many crops and can condi-2 tion market viability of fruit products and the success of cul-successfully implemented to measure the shape and size of fruits such as strawberries (4, 12), apples (5), carrot (6, 14), mangoes (28), and many others. More recently, methodologies for 3D reconstruction of plant organs have been developed with approaches that vary in speed, scale, cost, and accuracy; including laser scanners, x-ray computed tomography, and reconstruction from sequences of 2D images from digital cameras (8, [29][30][31][32][33][34][35][36][37][38][39][40][41]. Methods that rely on sequences of 2D images are numerous and variable with their own complexities and nuances that provide different strengths and weaknesses (8,27,37,(40)(41)(42)(43)(44).…”

High-throughput visible image transmission design based on the X-CT root 3D reconstruction system

“…In recent years, by continuously adapting and optimizing the imaging terminal, medical CT has reduced the scanning time compared with the past. Using higher voltage and current in a specific X-CT scanner, the contrast between plant roots and soil has increased, making Later, better results obtained in root-soil segmentation [5]. For CT image segmentation or reconstruction at the processing end [6], it is necessary to collect a large amount of data from the host computer and complete, precise algorithm calculations.…”