TreeRipper web application: towards a fully automated optical tree recognition software.
TreeRipper web application: towards a fully automated optical tree recognition software.
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DOI：
10.1186/1471-2105-12-178
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发表时间：
2011-05-20
影响因子：
3
通讯作者：
Hughes J
中科院分区：
文献类型：
--
作者：
Hughes J
物种、基因和基因组之间的关系已经像树一样印了世纪。虽然这可能是在20世纪世纪交换和分享系统发育假说的最佳形式，但全球网络现在提供了更快和自动化的方式来传递和分享系统发育知识。然而，需要新的软件来为21世纪重现这些已发表的成果。TreeRipper是一个简单的网站，用于全自动识别多分叉系统发育树（http：//linnaeus.zoology.gla.ac.uk/tagjhughes/treeripper/）。该程序接受一系列的输入图像格式（PNG，JPG/JPEG或GIF）。底层的命令行c++程序遵循一些清理步骤来检测线，删除节点标签，修补断线和拐角，并检测线边缘。然后确定边缘轮廓以检测树的分支长度、尖端标签位置和拓扑结构。光学字符识别（OCR）用于通过免费提供的tesseract-ocr软件将头端标签转换为文本。32%符合TreeRipper先决条件的图像被成功识别，最大的树有115片叶子。尽管已经说明了树生成方法的多样性，使得设计完全自动化的树木识别软件变得困难，但TreeRipper是朝着过去树生成方法的数字化自动化迈出的一步。我们还提供了一个包含100个树图像和相关树文件的数据集，用于培训和/或基准测试未来的软件。TreeRipper是一个基于GNU通用公共许可证v3的开源项目。
Relationships between species, genes and genomes have been printed as trees for over a century. Whilst this may have been the best format for exchanging and sharing phylogenetic hypotheses during the 20th century, the worldwide web now provides faster and automated ways of transferring and sharing phylogenetic knowledge. However, novel software is needed to defrost these published phylogenies for the 21st century. TreeRipper is a simple website for the fully-automated recognition of multifurcating phylogenetic trees (http://linnaeus.zoology.gla.ac.uk/~jhughes/treeripper/). The program accepts a range of input image formats (PNG, JPG/JPEG or GIF). The underlying command line c++ program follows a number of cleaning steps to detect lines, remove node labels, patch-up broken lines and corners and detect line edges. The edge contour is then determined to detect the branch length, tip label positions and the topology of the tree. Optical Character Recognition (OCR) is used to convert the tip labels into text with the freely available tesseract-ocr software. 32% of images meeting the prerequisites for TreeRipper were successfully recognised, the largest tree had 115 leaves. Despite the diversity of ways phylogenies have been illustrated making the design of a fully automated tree recognition software difficult, TreeRipper is a step towards automating the digitization of past phylogenies. We also provide a dataset of 100 tree images and associated tree files for training and/or benchmarking future software. TreeRipper is an open source project licensed under the GNU General Public Licence v3.
影响因子：
3.4
作者：
Smith, Stephen A.;Beaulieu, Jeremy M.;Donoghue, Michael J.
通讯作者：
Donoghue, Michael J.
影响因子：
3
作者：
Han MV;Zmasek CM
通讯作者：
Zmasek CM
影响因子：
5.8
作者：
Laubach, Thomas;von Haeseler, Arndt
通讯作者：
von Haeseler, Arndt