Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People's Republic of China.
Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People's Republic of China; University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China.
J Struct Biol. 2021 Sep;213(3):107770. doi: 10.1016/j.jsb.2021.107770. Epub 2021 Jul 22.
Electron tomography, a powerful imaging tool for studying 3D structures of macromolecular assemblies, always suffers from imperfect reconstruction with limited resolution due to the intrinsic low signal-to-noise ratio (SNR) and inaccessibility to certain tilt angles induced by radiation damage or mechanical limitation. In order to compensate for such insufficient data with low SNR and further improve imaging resolution, prior knowledge constraints about the objects in both real space and reciprocal space are thus exploited during tomographic reconstruction. However, direct Fast Fourier transform (FFT) between real space and reciprocal space remains extraordinarily challenging owing to their inconsistent grid sampling modes, e.g. regular and uniform grid sampling in real space whereas radial or polar grid sampling in reciprocal space. In order to solve such problem, a technique of non-uniform fast Fourier transform (NFFT) has been developed to transform efficiently between non-uniformly sampled grids in real and reciprocal space with sufficient accuracy. In this work, a Non-Uniform fast Fourier transform based Dual-space constraint Iterative reconstruction Method (NUDIM) applicable to biological electron tomography is proposed with a combination of basic concepts from equally sloped tomography (EST) and NFFT based reconstruction. In NUDIM, the use of NFFT can circumvent such grid sampling inconsistency and thus alleviate the stringent equally-sloped sampling requirement in EST reconstruction, while the dual-space constraint iterative procedure can dramatically enhance reconstruction quality. In comparison with conventional reconstruction methods, NUDIM is numerically and experimentally demonstrated to produce superior reconstruction quality with higher contrast, less noise and reduced missing wedge artifacts. More importantly, it is also capable of retrieving part of missing information from a limited number of projections.
电子断层扫描是一种强大的成像工具,可用于研究大分子组装体的 3D 结构,但由于固有低信噪比 (SNR) 和辐射损伤或机械限制导致某些倾斜角度无法获得,因此总是存在不完善的重建和有限的分辨率。为了弥补低 SNR 下的这些不足数据,并进一步提高成像分辨率,可以在断层扫描重建过程中利用关于物体的实空间和倒易空间的先验知识约束。然而,由于它们不一致的网格采样模式(例如实空间中的规则和均匀网格采样,而倒易空间中的径向或极坐标网格采样),在实空间和倒易空间之间进行直接快速傅里叶变换 (FFT) 仍然极具挑战性。为了解决这个问题,已经开发了一种非均匀快速傅里叶变换 (NFFT) 技术,以便在具有足够精度的情况下在实空间和倒易空间中非均匀采样的网格之间进行高效转换。在这项工作中,提出了一种适用于生物电子断层扫描的基于非均匀快速傅里叶变换的双空间约束迭代重建方法 (NUDIM),它结合了同等斜率断层扫描 (EST) 和基于 NFFT 的重建的基本概念。在 NUDIM 中,NFFT 的使用可以避免这种网格采样不一致性,从而减轻 EST 重建中严格的同等斜率采样要求,而双空间约束迭代过程可以显著提高重建质量。与传统的重建方法相比,NUDIM 在数值和实验上都被证明可以产生更高对比度、更少噪声和减少缺失楔形伪影的优越重建质量。更重要的是,它还能够从有限数量的投影中恢复部分缺失信息。