Atomic force microscopy (AFM) is a powerful and increasingly accessible technology that has a wide range of bio-imaging applications. AFM is capable of producing detailed three-dimensional topographical images with high signal-to-noise ratio, which enables the structural features of individual molecules to be studied without the need for ensemble averaging. Here, a software tool Trace_y, designed to reconstruct the three-dimensional surface envelopes of individual helical filament structures from topographical AFM images, is presented. Workflow using Trace_y is demonstrated on the structural analysis of individual helical amyloid protein fibrils where the assembly mechanism of heterogeneous, complex and diverse fibril populations due to structural polymorphism is not understood. The algorithms presented here allow structural information encoded in topographical AFM height images to be extracted and understood as three-dimensional (3D) contact point clouds. This approach will facilitate the use of AFM in structural biology to understand molecular structures and behaviors at individual molecule level.

中文翻译：

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Trace_y：通过三维接触点重建原子力显微镜对单个螺旋丝进行结构分析的软件算法


原子力显微镜 （AFM） 是一种功能强大且日益普及的技术，具有广泛的生物成像应用。AFM 能够产生具有高信噪比的详细三维形貌图像，这使得无需集成平均即可研究单个分子的结构特征。在这里，提出了一种软件工具Trace_y，旨在从形貌 AFM 图像中重建单个螺旋丝结构的三维表面包络。在单个螺旋淀粉样蛋白原纤维的结构分析中演示了使用 Trace_y 的工作流程，其中由于结构多态性导致的异质、复杂和多样化原纤维群的组装机制尚不清楚。这里介绍的算法允许提取在形貌 AFM 高度图像中编码的结构信息，并将其理解为三维 （3D） 接触点云。这种方法将有助于在结构生物学中使用 AFM 来了解单个分子水平的分子结构和行为。