Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK.
Tumour Cell Biology Laboratory, The Francis Crick Institute, London, UK.
Life Sci Alliance. 2021 Jan 27;4(3). doi: 10.26508/lsa.202000880. Print 2021 Mar.
Diverse extracellular matrix patterns are observed in both normal and pathological tissue. However, most current tools for quantitative analysis focus on a single aspect of matrix patterning. Thus, an automated pipeline that simultaneously quantifies a broad range of metrics and enables a comprehensive description of varied matrix patterns is needed. To this end, we have developed an ImageJ plugin called TWOMBLI, which stands for The Workflow Of Matrix BioLogy Informatics. This pipeline includes metrics of matrix alignment, length, branching, end points, gaps, fractal dimension, curvature, and the distribution of fibre thickness. TWOMBLI is designed to be quick, versatile and easy-to-use particularly for non-computational scientists. TWOMBLI can be downloaded from https://github.com/wershofe/TWOMBLI together with detailed documentation and tutorial video. Although developed with the extracellular matrix in mind, TWOMBLI is versatile and can be applied to vascular and cytoskeletal networks. Here we present an overview of the pipeline together with examples from a wide range of contexts where matrix patterns are generated.
在正常组织和病理组织中都观察到不同的细胞外基质模式。然而，目前大多数定量分析工具都集中在基质模式的单一方面。因此，需要一种能够同时定量多种指标并能够全面描述各种基质模式的自动化流水线。为此，我们开发了一个名为 TWOMBLI 的 ImageJ 插件，它代表基质生物信息学的工作流程。该流水线包括基质对齐、长度、分支、端点、间隙、分形维数、曲率以及纤维厚度分布的度量。TWOMBLI 的设计目的是快速、通用且易于使用，特别是对于非计算科学家。TWOMBLI 可以从 https://github.com/wershofe/TWOMBLI 下载，同时提供详细的文档和教程视频。尽管 TWOMBLI 是为细胞外基质开发的，但它用途广泛，可以应用于血管和细胞骨架网络。在这里，我们概述了该流水线，并提供了广泛的背景下生成基质模式的示例。
