Huang Xinrui, Li Sha, Gao Song
1 Department of Biophysics, School of Basic Medical Sciences, Peking University , Beijing, China .
2 Department of Medical Physics, School of Foundational Education, Peking University , Beijing, China .
J Comput Biol. 2018 Sep;25(9):1050-1058. doi: 10.1089/cmb.2018.0060. Epub 2018 Jun 21.
Cryo-electron microscopy (Cryo-EM) imaging has the unique potential to bridge the gap between cellular and molecular biology by revealing the structures of large macromolecular assemblies and cellular complexes. Therefore, cryo-EM three-dimensional (3D) reconstruction has been rapidly developed in recent several years and applied widely in life science research; however, it suffers from reduced contrast and low signal-to-noise ratios with a high degree of noise under low electron dose conditions, resulting in failures of many conventional filters. In this article, we explored a modified wavelet shrinkage filter (with optimal wavelet parameters: three-level decomposition, level-1 zeroed out, subband-dependent threshold, soft thresholding, and spline-based discrete dyadic wavelet transform) and extended its application in the cryo-EM field in two aspects: single-particle analysis and cryo-electron tomography. Its performance was assessed with simulation data and real cryo-EM experimental data. Compared with the undenoised results and conventional denoising techniques (e.g., Gaussian, median, and bilateral filters), the modified wavelet shrinkage filter maintained the resolution and contrast but reduced the noise, leading to higher quality images and more accurate measures of the biological structure. We expect that our study can provide benefits to cryo-EM applications: 3D reconstruction, visualization, structural analysis, and interpretation. All these data and programs are available.
冷冻电子显微镜（Cryo-EM）成像通过揭示大型大分子组装体和细胞复合物的结构，具有弥合细胞生物学与分子生物学之间差距的独特潜力。因此，冷冻电子显微镜三维（3D）重建技术在近几年得到了迅速发展，并在生命科学研究中得到了广泛应用；然而，在低电子剂量条件下，它存在对比度降低、信噪比低且噪声程度高的问题，导致许多传统滤波器失效。在本文中，我们探索了一种改进的小波收缩滤波器（具有最佳小波参数：三级分解、一级置零、子带依赖阈值、软阈值处理以及基于样条的离散二进小波变换），并在两个方面扩展了其在冷冻电子显微镜领域的应用：单颗粒分析和冷冻电子断层扫描。使用模拟数据和实际冷冻电子显微镜实验数据对其性能进行了评估。与未去噪结果和传统去噪技术（如高斯滤波器、中值滤波器和双边滤波器）相比，改进的小波收缩滤波器在保持分辨率和对比度的同时降低了噪声，从而得到更高质量的图像和对生物结构更准确的测量。我们期望我们的研究能够为冷冻电子显微镜的应用带来益处：3D重建、可视化、结构分析和解释。所有这些数据和程序均可获取。
