Semi-automatic landmark point annotation for geometric morphometrics
Semi-automatic landmark point annotation for geometric morphometrics
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DOI：
10.1186/s12983-014-0061-1
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发表时间：
2014-08-27
影响因子：
2.8
通讯作者：
Tautz, Diethard
中科院分区：
文献类型：
--
作者：
Bromiley, Paul A.;Schunke, Anja C.;Tautz, Diethard
背景：在以前的工作中，作者描述了一个软件包的三维标志的数字化用于几何形态测量。在本文中，我们描述了这个软件的扩展，允许半自动定位的3D地标，给定的数据库手动注释的训练图像。应用多阶段配准将数据库中的图像块与查询图像对齐，并使用基于数组的投票方案将来自多个数据库图像的结果合并。该软件自动突出显示已被定位与低置信度的点，允许手动correction.Results：评价进行了两个独立的手动地标注释已执行的啮齿动物头骨的微CT图像。这允许在手动和自动注释之间的距离以及手动和自动注释的可重复性方面评估地标准确性。自动标注达到的准确度相当于87.5%的点通过专家手动标注达到的准确度，具有显著更高的可重复性。虽然需要用户输入来产生训练数据，并且在最后的纠错阶段中，该软件能够将使用3D数据的典型地标识别过程中所需的手动注释的数量减少十倍，潜在地允许注释大得多的数据集，从而增加来自后续处理E的结果的统计能力。G. Procrustes/主成分分析。该软件在GNU通用公共许可证下可从我们的网站（www.tina-vision.net）免费获得。
Background: In previous work, the authors described a software package for the digitisation of 3D landmarks for use in geometric morphometrics. In this paper, we describe extensions to this software that allow semi-automatic localisation of 3D landmarks, given a database of manually annotated training images. Multi-stage registration was applied to align image patches from the database to a query image, and the results from multiple database images were combined using an array-based voting scheme. The software automatically highlights points that have been located with low confidence, allowing manual correction.Results: Evaluation was performed on micro-CT images of rodent skulls for which two independent sets of manual landmark annotations had been performed. This allowed assessment of landmark accuracy in terms of both the distance between manual and automatic annotations, and the repeatability of manual and automatic annotation. Automatic annotation attained accuracies equivalent to those achievable through manual annotation by an expert for 87.5% of the points, with significantly higher repeatability.Conclusions: Whilst user input was required to produce the training data and in a final error correction stage, the software was capable of reducing the number of manual annotations required in a typical landmark identification process using 3D data by a factor of ten, potentially allowing much larger data sets to be annotated and thus increasing the statistical power of the results from subsequent processing e. g. Procrustes/principal component analysis. The software is freely available, under the GNU General Public Licence, from our web-site (www.tina-vision.net).