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 3 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.

中文翻译：

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基于 X 射线计算机断层扫描的水稻根系结构的高通量三维可视化。

背景 X 射线计算机断层扫描 (CT) 允许我们以非破坏性的三维 (3-D) 形式可视化土壤下方的根系结构 (RSA)。然而，CT 扫描、重建过程和从 X 射线 CT 体积中分离根部需要相当长的时间。对于需要大量种群规模的遗传分析，例如数量性状位点作图，需要高通量的 RSA 可视化方法。结果 我们开发了一种高通量工艺流程，用于使用 X 射线 CT 对水稻 (Oryza sativa) RSA（由胚根和冠根组成）进行 3-D 可视化。工艺流程包括使用均匀的粒度、煅烧粘土以减少可视化非根段的可能性、在 X 射线 CT 扫描中使用更高的管电压和电流以增加根与土壤的对比度，并使用 3-D 中值滤波器和边缘检测算法来隔离根段。该分析流程采用高性能计算技术，CT扫描重建仅需10分钟（33秒，如果可以接受粗糙图像），图像处理2分钟，即可实现水稻RSA可视化。这缩短的时间使我们能够进行与 3-D RSA 表型相关的遗传分析。在 2 周龄幼苗中，分别使用 16 厘米和 20 厘米直径的花盆，检测到 85% 和 100% 的胚根和冠根。每次扫描的 X 射线剂量估计为 < 0.09 Gy，这不会阻碍水稻的生长。使用开发的工艺流程，我们能够在 3 周内跟踪陆地水稻品种的每日 RSA 开发，即 4-D RSA 开发。结论 我们开发了一种通过 X 射线 CT 进行 3-D 水稻 RSA 可视化的高通量工艺流程。植物生长的 X 射线剂量测定表明，该方法可适用于 4-D RSA 表型分析。我们将 RSA 可视化方法命名为“RSAvis3D”，并相信它代表了对各种植物物种进行 3-D RSA 表型分析的潜在有效应用。