StereoMorph: an R package for the collection of 3D landmarks and curves using a stereo camera set-up
StereoMorph: an R package for the collection of 3D landmarks and curves using a stereo camera set-up
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DOI：
10.1111/2041-210x.12326
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发表时间：
2015-03-01
影响因子：
6.6
通讯作者：
Westneat, Mark W.
中科院分区：
文献类型：
--
作者：
Olsen, Aaron M.;Westneat, Mark W.
生物学和古生物学中解剖学的定量三维测量是理解形态、功能和生态多样性背后的进化过程的关键。然而，从大量样品或现场收集3D形态测量数据目前受到方法的限制，这些方法要么太昂贵，要么太耗时，要么缺乏便携性。我们推出了一个新的R包StereoMorph，用于使用两个标准数码相机快速准确地收集3D地标和曲线。StereoMorph提供了一套完整的工具，用于使用立体相机设置收集3D地标和曲线的每一步。这包括图像处理和优化功能，用于使用棋盘图案进行自动相机校准，易于使用的应用程序，用于数字化照片中的地标和曲线，以及用于重建3D点和曲线的工具。图像处理工具和数字化应用程序也很容易适用于2D形态测量，使2D标志和曲线能够使用棋盘图案自动数字化和缩放。我们包括五个例子，演示StereoMorph的关键功能：自动检测棋盘角，相机校准，测试校准精度，数字化照片和3D曲线重建。与成本低于1500美元的设置，我们表明，它是可能实现的平均重建误差小于30微米。一旦相机组装好，标本可以像2D形态测量一样快速拍照，而数字化需要两到三倍的时间来数字化一张照片。最后，我们将提供一个附带的教程，详细介绍使用StereoMorph收集3D地标和曲线所需的所有步骤。此外，我们还提供了一个网络博客，为更新和用户问题和建议提供平台。
Quantitative, three-dimensional measurements of anatomy in biology and paleontology are key to understanding the evolutionary processes underlying morphological, functional and ecological diversification. However, the collection of 3D morphometric data from a large number of samples or in the field is currently limited by methods that are either too costly, too time-consuming or lack portability. We present a new R package, StereoMorph, for the rapid and accurate collection of 3D landmarks and curves using two standard digital cameras. StereoMorph provides a complete set of tools for every step in the collection of 3D landmarks and curves using a stereo camera set-up. This includes image processing and optimization functions for automated camera calibration using a checkerboard pattern, an easy-to-use application for digitizing landmarks and curves from photographs, and tools for reconstructing points and curves in 3D. The image processing tools and digitizing application are readily applicable to 2D morphometrics as well, enabling 2D landmarks and curves to be digitized and scaled automatically using a checkerboard pattern. We include five examples that demonstrate key functionalities of StereoMorph: automated detection of checkerboard corners, camera calibration, testing calibration accuracy, digitizing photographs and 3D curve reconstruction. With a set-up costing less than $1500, we show that it is possible to achieve a mean reconstruction error of less than 30 microns. Once the cameras are assembled, specimens can be photographed as quickly as with 2D morphometrics while digitizing takes two to three times as long as digitizing a single photograph. We conclude by presenting an accompanying tutorial which details all of the steps required to collect 3D landmarks and curves using StereoMorph. Additionally, we present a web blog that will provide a platform for updates and user questions and suggestions.