1. 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.
2. 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.
3. 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.
4. 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.

中文翻译：

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SlicerMorph：一个开放且可扩展的平台，用于检索、可视化和分析 3D 形态

1. #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显微 CT 扫描。来自这些项目的数据使用聚合 3D 样本库（如 MorphoSource）通过各种开放许可与社区共享。随着可用数据的融合和分析它们的方法，我们预计生物生物学的定量研究将出现爆炸式增长。
2. 尽管数据可用，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挑战。它涉及繁琐的数据格式转换任务，准确地保留数据的空间尺度，3D 可视化和分割，以及获取测量和注释。当科学家使用专有格式的商业软件时，就会为数据交换、协作和可重复性设置障碍，从而损害科学界扩大参与研究的努力。
3. 我们开发了 SlicerMorph 作为 3D Slicer 的扩展，这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，建立在经过验证的可编写 Python 脚本的开源库（例如 Visualization Toolkit 和 Insight Toolkit）之上。除了 Slicer 的核心功能外，SlicerMorph 还为用户提供了模块来方便地检索开放访问的 3D 模型或导入用户自己的 3D 体积、注释 3D 曲线和基于补丁的地标、生成地标模板、进行 3D 有机体的几何形态测量分析使用地标驱动和无地标方法形成表格，并根据其结果创建 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。
4. 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，以使用 3D 标本促进数据和结果的轻松交换和协作。我们对同事的建议是，使用由大型用户和开发人员社区支持的通用开放平台可确保工具在初始开发工作之后的寿命和可持续性。