RootAnalyzer: A Cross-Section Image Analysis Tool for Automated Characterization of Root Cells and Tissues.
RootAnalyzer: A Cross-Section Image Analysis Tool for Automated Characterization of Root Cells and Tissues.
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DOI：
10.1371/journal.pone.0137655
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发表时间：
2015
期刊：
影响因子：
3.7
通讯作者：
Miklavcic SJ
中科院分区：
文献类型：
--
作者：
Chopin J;Laga H;Huang CY;Heuer S;Miklavcic SJ
植物根系解剖特征的形态是影响植物有效吸收水分和养分的关键因素。现有的根部解剖特征表型鉴定技术通常基于人工或半自动分割和注释根部横截面的显微图像。在这篇文章中，我们提出了一个全自动化的工具，以下称为RootAnalyzer，用于有效地从根横截面图像中提取和分析解剖特征。RootAnalyzer使用一系列图像处理技术，如局部阈值和最近邻识别，将植物根从图像的背景中分割出来，对皮层、中柱、内胚层和表皮进行分类和表征，并随后产生关于根细胞和组织的形态属性的统计数据。我们使用RootAnalyzer对15幅小麦植株图像和1幅玉米植株图像进行了分析，并与人工获取的地面真实数据进行了对比。对比结果表明，RootAnalyzer能够完全刻画大部分根组织区域，准确率在90%以上。
The morphology of plant root anatomical features is a key factor in effective water and nutrient uptake. Existing techniques for phenotyping root anatomical traits are often based on manual or semi-automatic segmentation and annotation of microscopic images of root cross sections. In this article, we propose a fully automated tool, hereinafter referred to as RootAnalyzer, for efficiently extracting and analyzing anatomical traits from root-cross section images. Using a range of image processing techniques such as local thresholding and nearest neighbor identification, RootAnalyzer segments the plant root from the image’s background, classifies and characterizes the cortex, stele, endodermis and epidermis, and subsequently produces statistics about the morphological properties of the root cells and tissues. We use RootAnalyzer to analyze 15 images of wheat plants and one maize plant image and evaluate its performance against manually-obtained ground truth data. The comparison shows that RootAnalyzer can fully characterize most root tissue regions with over 90% accuracy.