Ju Yiwen, Liu Alexander E, Oestreich Kenan, Wang Tina, Topp Christopher N, Ju Tao
Washington University in Saint Louis, St. Louis, USA.
Donald Danforth Plant Science Center, Creve Coeur, USA.
Plant Methods. 2024 Aug 27;20(1):132. doi: 10.1186/s13007-024-01240-0.
The use of 3D imaging techniques, such as X-ray CT, in root phenotyping has become more widespread in recent years. However, due to the complexity of the root structure, analyzing the resulting 3D volumes to obtain detailed architectural root traits remains a challenging computational problem. When it comes to image-based phenotyping of excavated maize root crowns, two types of root features that are notably missing from existing methods are the whorls and soil line. Whorls refer to the distinct areas located at the base of each stem node from which roots sprout in a circular pattern (Liu S, Barrow CS, Hanlon M, Lynch JP, Bucksch A. Dirt/3D: 3D root phenotyping for field-grown maize (zea mays). Plant Physiol. 2021;187(2):739-57. https://doi.org/10.1093/plphys/kiab311 .). The soil line is where the root stem meets the ground. Knowledge of these features would give biologists deeper insights into the root system architecture (RSA) and the below- and above-ground root properties.
We developed TopoRoot+, a computational pipeline that produces architectural traits from 3D X-ray CT volumes of excavated maize root crowns. Building upon the TopoRoot software (Zeng D, Li M, Jiang N, Ju Y, Schreiber H, Chambers E, et al. Toporoot: A method for computing hierarchy and fine-grained traits of maize roots from 3D imaging. Plant Methods. 2021;17(1). https://doi.org/10.1186/s13007-021-00829-z .) for computing fine-grained root traits, TopoRoot + adds the capability to detect whorls, identify nodal roots at each whorl, and compute the soil line location. The new algorithms in TopoRoot + offer an additional set of fine-grained traits beyond those provided by TopoRoot. The addition includes internode distances, root traits at every hierarchy level associated with a whorl, and root traits specific to above or below the ground. TopoRoot + is validated on a diverse collection of field-grown maize root crowns consisting of nine genotypes and spanning across three years. TopoRoot + runs in minutes for a typical volume size of [Formula: see text] on a desktop workstation. Our software and test dataset are freely distributed on Github.
TopoRoot + advances the state-of-the-art in image-based phenotyping of excavated maize root crowns by offering more detailed architectural traits related to whorls and soil lines. The efficiency of TopoRoot + makes it well-suited for high-throughput image-based root phenotyping.
近年来，3D成像技术，如X射线计算机断层扫描（CT），在根系表型分析中的应用越来越广泛。然而，由于根系结构的复杂性，分析由此产生的3D体积以获取详细的根系结构特征仍然是一个具有挑战性的计算问题。在基于图像的挖掘玉米根冠表型分析中，现有方法明显缺少的两种根系特征是轮生体和土线。轮生体是指位于每个茎节基部的不同区域，根系从这里呈圆形萌发（Liu S, Barrow CS, Hanlon M, Lynch JP, Bucksch A. Dirt/3D: 3D root phenotyping for field-grown maize (zea mays). Plant Physiol. 2021;187(2):739 - 57. https://doi.org/10.1093/plphys/kiab311.）。土线是根茎与地面的交汇处。了解这些特征将使生物学家对根系结构（RSA）以及地下和地上根系特性有更深入的了解。
我们开发了TopoRoot+，这是一种计算流程，可从挖掘的玉米根冠的3D X射线CT体积中生成结构特征。在用于计算细粒度根系特征的TopoRoot软件（Zeng D, Li M, Jiang N, Ju Y, Schreiber H, Chambers E, et al. Toporoot: A method for computing hierarchy and fine-grained traits of maize roots from 3D imaging. Plant Methods. 2021;17(1). https://doi.org/10.1186/s13007-021-00829-z.）的基础上，TopoRoot+增加了检测轮生体、识别每个轮生体处的节根以及计算土线位置的能力。TopoRoot+中的新算法提供了一组超出TopoRoot的细粒度特征。这些新增特征包括节间距离、与轮生体相关的每个层次水平的根系特征，以及地上或地下特有的根系特征。TopoRoot+在由9个基因型组成、跨越三年的多种田间种植玉米根冠数据集上得到了验证。对于桌面工作站上典型体积大小为[公式：见原文]的情况，TopoRoot+只需几分钟即可运行。我们的软件和测试数据集可在Github上免费获取。
TopoRoot+通过提供与轮生体和土线相关的更详细的结构特征，推动了基于图像的挖掘玉米根冠表型分析的技术水平。TopoRoot+的效率使其非常适合高通量基于图像的根系表型分析。
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