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首页> 外文期刊>Computers and Electronics in Agriculture >GT-RootS: An integrated software for automated root system measurement from high-throughput phenotyping platform images
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GT-RootS: An integrated software for automated root system measurement from high-throughput phenotyping platform images

机译：GT-ROOTS：来自高吞吐量表型平台图像的自动root系统测量的集成软件

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摘要

GT-RootS (Global Traits of Root System) is an automated Java-based open-source solution we are developing for processing root system images provided by the Rhizoscope, a CIRAD phenotyping platform dedicated to dense cereal plants. Two types of use are proposed. The fully-automated mode applies a predefined standard processing pipeline to a preselected set of images while the semi-automated mode allows the user to interactively check and correct intermediate processing results to a specific image. In both cases, GT-RootS combines a local adaptive thresholding algorithm and a similarity indicator to automatically separate the root system from a complex background without user intervention. A covering house-shaped polygon is then defined in the axis system of the root ellipse from vertical weighted density profiles. This canonical shape is composed of both upper trapezoid and lower rectangular compartments from which upper and lower heights, global width and local offset, root system cone angulation and spatial densities can be easily evaluated and displayed. GT-RootS measurements were compared both to expert evaluations and to two other estimation methods on a set of 64 images of a dense Japonica rice root system of 30-days-old plants. We demonstrate also that GT-RootS satisfies the requirements of high-throughput analyses: short processing time (around 30 images per hour on a low-end computer), measurement accuracy and repeatability, and user bias eradication.
机译：GT-ROOTS（根系的全局特征）是一种自动化的Java的开源解决方案，我们正在开发用于加工由RhizoScope提供的根系系统图像，这是一种专用于致密谷物植物的致态的表型平台。提出了两种类型的使用。完全自动化模式将预定义的标准处理流水线应用于预选的图像集，而半自动模式允许用户以交互地检查和将中间处理结果进行交互地检查和校正特定图像。在这两种情况下，GT根组合了本地自适应阈值算法和相似度指示器，以自动将根系从复杂的背景分离，而无需用户干预。然后在从垂直加权密度分布的根椭圆的轴系统中定义覆盖房屋形多边形。这种规范形状由上梯形和下矩形隔室的组成，并且可以容易地评估和显示上部和下高度，全局宽度和局部偏移，根系锥角和空间密度。将GT-ROOTS测量与专家评估和另外两种其他估算方法进行比较，在30天龄植物的致密粳稻根系中的一组64图像上。我们还证明了GT根符合高通量分析的要求：短路处理时间（在低端计算机上每小时约30张图像），测量精度和可重复性以及用户偏置。

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