ImagePlane: an automated image analysis pipeline for high-throughput screens using the planarian Schmidtea mediterranea.
ImagePlane: an automated image analysis pipeline for high-throughput screens using the planarian Schmidtea mediterranea.
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ImagePlane：使用涡虫 Schmidtea mediterranea 进行高通量屏幕的自动图像分析管道。
DOI：
10.1089/cmb.2013.0025
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发表时间：
2013
期刊：
影响因子：
--
通讯作者：
Yandell,Mark
中科院分区：
文献类型：
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作者：
Flygare,Steven;Campbell,Michael;Ross,RobertMars;Moore,Barry;Yandell,Mark
ImagePlane是用于自动化、高通量图像分析和信息提取的模块化管道。ImagePlane旨在支持脊椎动物研究，它提供了一种自参数自适应阈值算法；一种可以自动将动物分割成前后/左右象限的算法，用于自动识别基因和蛋白质表达的区域特定差异；以及一种新的算法，用于量化动物的形态，而不受它们的方向和大小的影响。ImagePlane还提供了自动生成报告的方法，其输出可以轻松导入到第三方工具中，如R和Excel。在这里，我们展示了管道的效用，以确定参与干细胞增殖的基因在稻纵卷叶蝉。尽管ImagePlane旨在支持脊椎动物的研究，但它也将被证明对基于细胞的研究很有用。
ImagePlane is a modular pipeline for automated, high-throughput image analysis and information extraction. Designed to support planarian research, ImagePlane offers a self-parameterizing adaptive thresholding algorithm; an algorithm that can automatically segment animals into anterior–posterior/left–right quadrants for automated identification of region-specific differences in gene and protein expression; and a novel algorithm for quantification of morphology of animals, independent of their orientations and sizes. ImagePlane also provides methods for automatic report generation, and its outputs can be easily imported into third-party tools such as R and Excel. Here we demonstrate the pipeline's utility for identification of genes involved in stem cell proliferation in the planarianSchmidtea mediterranea. Although designed to support planarian studies, ImagePlane will prove useful for cell-based studies as well.