Recovering complete plant root system architectures from soil via X-ray μ-Computed Tomography.
Recovering complete plant root system architectures from soil via X-ray μ-Computed Tomography.
复制标题
通过X射线μ计算的断层扫描从土壤中恢复完整的植物根系体系。
DOI：
10.1186/1746-4811-9-8
复制
发表时间：
2013-03-20
期刊：
影响因子：
5.1
通讯作者：
Pridmore TP
中科院分区：
文献类型：
--
作者：
Mairhofer S;Zappala S;Tracy S;Sturrock C;Bennett MJ;Mooney SJ;Pridmore TP
x射线微计算机断层扫描（μCT）提供了可视化植物根系在其自然环境-土壤中生长的三维结构的能力。然而，从x射线CT数据中恢复根构型描述是具有挑战性的。根与土壤的x射线衰减值重叠，根物质的衰减值不同。任何成功的根识别方法都必须明确地针对根材料，并能够适应根属性的局部变化。RooTrak通过将水平集方法与视觉跟踪框架相结合来满足这些要求，并已被证明能够在x射线μCT图像中从土壤中分割出各种植物根系。该方法提供了高质量的根系描述，但从上到下跟踪根系，因此忽略了向上生长（斜向）的分支。我们提出了一个扩展到RooTrak，它允许它提取斜向根。另一个向后看的步骤重新审视了之前的图像，标记出可能向上生长的根。然后对这些情况进行跟踪，从而使根系得到更有效和更完整的恢复。结果表明，根的提取有明显的改善，没有关键的建筑特征将被低估。RooTrak采用的视觉跟踪框架提供了在x射线CT图像中将根与土壤分离所需的焦点和灵活性，并且可以扩展到检测斜向根。扩展后的软件工具可以对植物根系结构进行更完整的描述，并支持更精确的建筑特征计算。
X-ray micro-Computed Tomography (μCT) offers the ability to visualise the three-dimensional structure of plant roots growing in their natural environment – soil. Recovery of root architecture descriptions from X-ray CT data is, however, challenging. The X-ray attenuation values of roots and soil overlap, and the attenuation values of root material vary. Any successful root identification method must both explicitly target root material and be able to adapt to local changes in root properties. RooTrak meets these requirements by combining the level set method with a visual tracking framework and has been shown to be capable of segmenting a variety of plant roots from soil in X-ray μCT images. The approach provides high quality root descriptions, but tracks root systems top to bottom and so omits upward-growing (plagiotropic) branches. We present an extension to RooTrak which allows it to extract plagiotropic roots. An additional backward-looking step revisits the previous image, marking possible upward-growing roots. These are then tracked, leading to efficient and more complete recovery of the root system. Results show clear improvement in root extraction, without which key architectural traits would be underestimated. The visual tracking framework adopted in RooTrak provides the focus and flexibility needed to separate roots from soil in X-ray CT imagery and can be extended to detect plagiotropic roots. The extended software tool produces more complete descriptions of plant root structure and supports more accurate computation of architectural traits.
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影响因子：
4.9
作者：
Clark, LJ;Whalley, WR;Barraclough, PB
通讯作者：
Barraclough, PB
影响因子：
3.8
作者：
Mooney, SJ
通讯作者：
Mooney, SJ
影响因子：
9.7
作者：
Perret, J. S.;Al-Belushi, M. E.;Deadman, M.
通讯作者：
Deadman, M.
影响因子：
6.4
作者：
RUFELT, H
通讯作者：
RUFELT, H
影响因子：
6.1
作者：
Kaestner, Anders;Schneebeli, Martin;Graf, Frank
通讯作者：
Graf, Frank