Arbour J H
Department of Biology, Middle Tennessee State University, Murfreesboro, 37132, TN, USA.
Integr Org Biol. 2023 Aug 17;5(1):obad030. doi: 10.1093/iob/obad030. eCollection 2023.
Contrast enhanced computed-tomography imaging like diffusible iodine-based contrast-enhanced computed tomography (diceCT) can provide detailed information on muscle architecture important to comparative analyses of functional morphology, using non-destructive approaches. However, manual segmentation of muscle fascicles/fibers is time-consuming, and automated approaches are at times inaccessible and unaffordable. Here, we introduce GoodFibes, an R package for reconstructing muscle architecture in 3D from diceCT image stacks. GoodFibes uses textural analysis of image grayscale values to track straight or curved fiber paths through a muscle image stack. Accessory functions provide quality checking, fiber merging, and 3D visualization and export capabilities. We demonstrate the utility and effectiveness of GoodFibes using two datasets, from an ant and bat diceCT scans. In both cases, GoodFibes provides reliable measurements of mean fiber length compared to traditional approaches, and is as effective as currently available software packages. This open-source, free to use software package will help to improve access to tools in the analysis of muscle fiber anatomy using diceCT scans. The flexible and transparent R-language environment allows other users to build on the functions described here and permits direct statistical analysis of the resulting fiber metrics. We hope that this will increase the number of comparative and evolutionary studies incorporating these rich and functionally important datasets.
像基于可扩散碘的对比增强计算机断层扫描（diceCT）这样的对比增强计算机断层扫描成像，可以使用无损方法提供有关肌肉结构的详细信息，这对于功能形态学的比较分析很重要。然而，手动分割肌肉束/纤维很耗时，而自动化方法有时难以获得且成本高昂。在这里，我们介绍GoodFibes，一个用于从diceCT图像堆栈中三维重建肌肉结构的R包。GoodFibes使用图像灰度值的纹理分析来跟踪穿过肌肉图像堆栈的直线或曲线纤维路径。辅助功能提供质量检查、纤维合并以及三维可视化和导出功能。我们使用来自蚂蚁和蝙蝠diceCT扫描的两个数据集展示了GoodFibes的实用性和有效性。在这两种情况下，与传统方法相比，GoodFibes都能提供可靠的平均纤维长度测量值，并且与目前可用的软件包一样有效。这个开源、免费使用的软件包将有助于改善使用diceCT扫描分析肌肉纤维解剖结构时工具的可及性。灵活且透明的R语言环境允许其他用户在此处描述的功能基础上进行构建，并允许对所得纤维指标进行直接统计分析。我们希望这将增加纳入这些丰富且功能重要的数据集的比较和进化研究的数量。
