Plum Fabian, Labonte David
Department of Bioengineering, Imperial College London, London, UK.
PeerJ. 2021 Apr 12;9:e11155. doi: 10.7717/peerj.11155. eCollection 2021.
We present , an open-source platform for the creation of digital 3D models of arthropods and small objects. consists of a scanner and a Graphical User Interface, and enables the automated generation of Extended Depth Of Field images from multiple perspectives. These images are then masked with a novel automatic routine which combines random forest-based edge-detection, adaptive thresholding and connected component labelling. The masked images can then be processed further with a photogrammetry software package of choice, including open-source options such as , to create high-quality, textured 3D models. We demonstrate how these 3D models can be rigged to enable realistic digital specimen posing, and introduce a novel simple yet effective method to include semi-realistic representations of approximately planar and transparent structures such as wings. As a result of the exclusive reliance on generic hardware components, rapid prototyping and open-source software, costs only a fraction of available comparable systems. The resulting accessibility of will (i) drive the development of novel and powerful methods for machine learning-driven behavioural studies, leveraging synthetic data; (ii) increase accuracy in comparative morphometric studies as well as extend the available parameter space with area and volume measurements; (iii) inspire novel forms of outreach; and (iv) aid in the digitisation efforts currently underway in several major natural history collections.
我们展示了一个用于创建节肢动物和小物体数字3D模型的开源平台。它由一台扫描仪和一个图形用户界面组成,并能够从多个视角自动生成扩展景深图像。然后,这些图像会通过一种新颖的自动程序进行掩膜处理,该程序结合了基于随机森林的边缘检测、自适应阈值处理和连通组件标记。接着,可以使用选择的摄影测量软件包(包括诸如之类的开源选项)对掩膜后的图像进行进一步处理,以创建高质量的、有纹理的3D模型。我们展示了如何对这些3D模型进行骨骼绑定以实现逼真的数字标本摆姿,并介绍了一种新颖、简单但有效的方法来纳入近似平面和透明结构(如翅膀)的半逼真表示。由于完全依赖通用硬件组件、快速原型制作和开源软件,该平台的成本仅为现有可比系统的一小部分。该平台的可及性将(i)推动利用合成数据进行机器学习驱动的行为研究的新颖且强大方法的发展;(ii)提高比较形态计量学研究的准确性,并通过面积和体积测量扩展可用参数空间;(iii)激发新颖的外展形式;以及(iv)协助目前在几个主要自然历史收藏机构中正在进行的数字化工作。