SlicerMorph: An open and extensible platform to retrieve, visualize and analyse 3D morphology
SlicerMorph: An open and extensible platform to retrieve, visualize and analyse 3D morphology
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DOI：
10.1111/2041-210x.13669
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发表时间：
2021-07-22
影响因子：
6.6
通讯作者：
Maga, A. Murat
中科院分区：
文献类型：
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作者：
Rolfe, Sara;Pieper, Steve;Maga, A. Murat
#ScanAllFishes和oVert等大规模数字化项目正在生成数千种脊椎动物的高分辨率microCT扫描。来自这些项目的数据通过各种开放许可证使用MorphoSource等聚合3D标本库与社区共享。我们预计，随着现有数据和分析方法的融合，生物生物学的定量研究将出现爆炸式增长。虽然数据是可用的，但对大多数生物学家来说，从一系列图像到分析的道路充满了挑战。它涉及到数据格式转换、准确保留数据的空间比例、3D可视化和分割以及获取测量和注释等繁琐任务。当科学家使用带有专有格式的商业软件时，数据交换、协作和可复制性的障碍就会树立起来，这损害了科学界扩大研究参与的努力。我们开发了SlicerMorph作为3D Slicer的扩展，3D Slicer是一个生物医学可视化和分析生态系统，具有广泛的可视化和分割功能，基于成熟的Python脚本开源库，如Visualization Toolkit和Insight Toolkit。除了Slicer的核心功能外，SlicerMorph还为用户提供了方便检索开放访问的3D模型或导入用户自己的3D体积的模块，以注释3D曲线和基于块的地标，生成地标模板，使用地标驱动和无地标方法对3D生物体形式进行几何形态学分析，并根据结果创建3D动画。我们强调如何将这些单独的模块联系在一起，以建立从图像序列到形态空间的完整工作流程。我们的软件开发工作得到了短期课程和研讨会的补充，这些课程和研讨会涵盖了3D成像和形态分析的基础知识，因为它适用于进化生物学中生物体形式和形状的研究。我们的目标是建立一个以Slicer和SlicerMorph为中心的生物生物学家社区，以促进数据和结果的轻松交换以及使用3D标本的合作。我们对同事的建议是，使用一个由大型用户和开发人员社区支持的通用开放平台，确保工具的寿命和可持续性超出最初的开发工作。
Large-scale digitization projects such as #ScanAllFishes and oVert are generating high-resolution microCT scans of vertebrates by the thousands. Data from these projects are shared with the community using aggregate 3D specimen repositories like MorphoSource through various open licenses. We anticipate an explosion of quantitative research in organismal biology with the convergence of available data and the methodologies to analyse them. Though the data are available, the road from a series of images to analysis is fraught with challenges for most biologists. It involves tedious tasks of data format conversions, preserving spatial scale of the data accurately, 3D visualization and segmentations, and acquiring measurements and annotations. When scientists use commercial software with proprietary formats, a roadblock for data exchange, collaboration and reproducibility is erected that hurts the efforts of the scientific community to broaden participation in research. We developed SlicerMorph as an extension of 3D Slicer, a biomedical visualization and analysis ecosystem with extensive visualization and segmentation capabilities built on proven python-scriptable open-source libraries such as Visualization Toolkit and Insight Toolkit. In addition to the core functionalities of Slicer, SlicerMorph provides users with modules to conveniently retrieve open-access 3D models or import users own 3D volumes, to annotate 3D curve and patch-based landmarks, generate landmark templates, conduct geometric morphometric analyses of 3D organismal form using both landmark-driven and landmark-free approaches, and create 3D animations from their results. We highlight how these individual modules can be tied together to establish complete workflow(s) from image sequence to morphospace. Our software development efforts were supplemented with short courses and workshops that cover the fundamentals of 3D imaging and morphometric analyses as it applies to study of organismal form and shape in evolutionary biology. Our goal is to establish a community of organismal biologists centred around Slicer and SlicerMorph to facilitate easy exchange of data and results and collaborations using 3D specimens. Our proposition to our colleagues is that using a common open platform supported by a large user and developer community ensures the longevity and sustainability of the tools beyond the initial development effort.