PhenoPhyte: a flexible affordable method to quantify 2D phenotypes from imagery.
PhenoPhyte: a flexible affordable method to quantify 2D phenotypes from imagery.
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DOI：
10.1186/1746-4811-8-45
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发表时间：
2012-11-06
期刊：
影响因子：
5.1
通讯作者：
Shyu CR
中科院分区：
文献类型：
--
作者：
Green JM;Appel H;Rehrig EM;Harnsomburana J;Chang JF;Balint-Kurti P;Shyu CR
复杂植物表型的准确表征对于通过正向或反向遗传学将生物学功能分配给基因至关重要。它也可以是至关重要的，在确定处理，基因型，或环境条件对植物生长或对昆虫或病原体的易感性的影响。虽然已经开发了表征复杂表型的技术，但大多数技术都不具有成本效益，或者过于不精确或主观，无法可靠地区分复杂性状（如生长，颜色变化或抗病性）中的细微差异。我们设计了一种廉价的成像协议，便于自动量化的二维视觉表型，使用计算机视觉和图像处理算法应用于标准的数字图像。该协议允许在实验室和现场对植物进行非破坏性成像，并且由于自动颜色和尺度归一化，可以在次优成像条件下使用。我们设计了基于网络的工具PhenoPhyte处理图像坚持这一协议，并证明了它的能力，以衡量各种二维性状（如生长，叶面积和食草动物）使用图像从几个物种（拟南芥和芜菁）。然后，我们提供了一个更复杂的例子来衡量玉米南方叶枯病的抗病性。PhenoPhyte是一个新的具有成本效益的网络应用程序，用于使用简单的成像协议从数字图像中半自动量化二维性状。这个工具的有用性证明了在多个物种的各种特性。我们表明，数字表型可以减少人类在性状量化中的主观性，从而提高准确性和精度，这对于区分和量化细微的表型变异以及理解基因功能和/或治疗效果至关重要。
Accurate characterization of complex plant phenotypes is critical to assigning biological functions to genes through forward or reverse genetics. It can also be vital in determining the effect of a treatment, genotype, or environmental condition on plant growth or susceptibility to insects or pathogens. Although techniques for characterizing complex phenotypes have been developed, most are not cost effective or are too imprecise or subjective to reliably differentiate subtler differences in complex traits like growth, color change, or disease resistance. We designed an inexpensive imaging protocol that facilitates automatic quantification of two-dimensional visual phenotypes using computer vision and image processing algorithms applied to standard digital images. The protocol allows for non-destructive imaging of plants in the laboratory and field and can be used in suboptimal imaging conditions due to automated color and scale normalization. We designed the web-based tool PhenoPhyte for processing images adhering to this protocol and demonstrate its ability to measure a variety of two-dimensional traits (such as growth, leaf area, and herbivory) using images from several species (Arabidopsis thaliana and Brassica rapa). We then provide a more complicated example for measuring disease resistance of Zea mays to Southern Leaf Blight. PhenoPhyte is a new cost-effective web-application for semi-automated quantification of two-dimensional traits from digital imagery using an easy imaging protocol. This tool’s usefulness is demonstrated for a variety of traits in multiple species. We show that digital phenotyping can reduce human subjectivity in trait quantification, thereby increasing accuracy and improving precision, which are crucial for differentiating and quantifying subtle phenotypic variation and understanding gene function and/or treatment effects.