Electron Tomography: Methods for Three-Dimensional Visualization of Structures in the Cell, 2nd Edition. Edited by Joachim Frank. Springer, Albany, NY; 2006, 455 pages. ISBN 0-387-31234-X (HB)
Electron Tomography: Methods for Three-Dimensional Visualization of Structures in the Cell, 2nd Edition. Edited by Joachim Frank. Springer, Albany, NY; 2006, 455 pages. ISBN 0-387-31234-X (HB)
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DOI：
10.1017/s1431927608080720
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发表时间：
2008-07
影响因子：
2.8
通讯作者：
L. Gan
中科院分区：
文献类型：
--
作者：
L. Gan
电子断层扫描是一种强有力的方法，可以可视化细胞等生物实体的纳米级分辨率三维结构，弥合了X射线结晶学和光学显微镜之间的巨大分辨率差距。随着新的显微镜、样品制备技术和图像分析软件使更广泛的生物界能够接触到电子显微镜，该领域经历了快速增长。最令人兴奋的最新发展之一是电子冷冻断层扫描，电子断层扫描被应用于适当薄的样品，这些样品在液体乙烷中闪速冷冻，然后在低温下成像。如此美丽的技术结合有望揭示生活在其天然细胞环境中的生物分子的天然结构。电子断层摄影术有15个章节，根据断层摄影实验的时间顺序大致分为六个部分：样品准备、成像、倾斜序列对准、重建、降噪和分割。每一章由一位或多位世界专家撰写，格式为评论，引用了过去十年中最相关的论文，其中许多论文是由该书的作者贡献的。几乎没有重叠的材料，所以每一章都可以在不知道其他章节的情况下阅读。大多数插图都是灰度的，但书中间有八页彩色插图。第一章回顾了辐射损伤对塑料埋入试件的影响，其中最臭名昭著的是试件沿光轴方向的收缩。这一章有丰富的数字集合来说明这种辐射诱导的人工制品的外观。第二章综述了超微切割术的最新进展--柱式冷冻或高压冷冻！低温下的样品。它被称为冷冻显微切割术，可能是唯一适合于制备自然冷冻水合组织样本的技术，这些组织足够薄，可以通过电子显微镜成像。第三章回顾了电子成象的物理过程，并说明了透镜缺陷和较厚样品引起的成象退化的影响。第四章简要但全面地回顾了低剂量成像和自动数据收集应考虑的显微镜参数。第五章回顾了基于基准的图像配准的几何结构，并展示了倾斜序列排列不佳如何影响层析图像的例子。这一章特别有价值，因为大多数已发表的断层扫描都是使用胶体金珠对齐的。第六章回顾了基于特征的无基准！对齐，这对于在感兴趣对象附近没有任何基准的样本是强制的。第七章讨论了从二维数据恢复三维结构。文中还讨论了两种流行的层析重建算法，并用模拟图像说明了重建结果。第八章给出了最常见的层析重建方法：加权反投影法的更详细的数学背景。第9章回顾了层析图像作为正交实空间函数之和的表示。这一章是数学上最紧张的一章。第十章讨论了不同倾斜序列捕获方式的几何考虑。文中还讨论了缺失数据对分辨率的影响。第11章介绍了噪声的物理学。文中描述了三种流行的滤波器，并用真实和模拟的层析图像说明了各自的去噪算法的效果。第12章定义了图像分割的概念，讨论了一些半自动分割算法。第13章使用微管和膜作为具有已知特征并且可以自动分割的结构的例子。第14章展示了如何使用来自更高分辨率结构的模板来分割桶形大分子。第15章展示了如何使用图像分类来分割和平均准晶体中的模体，就像成功地在昆虫飞行肌肉上所做的那样。本书是电子断层摄影学学生的必读读物，也是从业者的参考资料。每本书评论显微镜和微观分析
Electron tomography is a powerful method to visualize the nanometer-resolution three-dimensional structure of “unique” biological entities such as cells, bridging the large resolution gap between X-ray crystallography and light microscopy. The field has experienced rapid growth as new microscopes, sample preparation techniques, and image analysis software have made electron microscopy accessible to a broader biological community. One of the most exciting recent developments has been electron cryotomography, where electron tomography is applied to suitably thin specimens that are flash-frozen in liquid ethane and subsequently imaged at cryogenic temperatures. Such a beautiful marriage of technologies promises to reveal the native structures of biological molecules living within their native cellular environments. Electron Tomography has fifteen chapters that are organized roughly into six sections according to the chronological order of a tomography experiment: sample preparation, imaging, tilt series alignment, reconstruction, noise reduction, and segmentation. Each chapter is written by one or more world experts and is formatted as a review, citing the most relevant papers in the past decade, many of which were contributed by the book’s authors. There is almost no overlapping material, so each chapter can be read without knowledge of the others. Most of the figures are grayscale, but there are eight pages of color figures in the middle of the book. The chapters are summarized as follows: Chapter 1 provides an historical perspective on the effects of radiation damage on plastic-embedded specimens, the most infamous being sample shrinkage along the optical axis. This chapter has a rich collection of figures to illustrate the appearance of such radiation-induced artifacts. Chapter 2 reviews the state-of-the-art in ultramicrotomy of plunge-frozen ~or high-pressure frozen! samples at cryogenic temperatures. Cryoultramicrotomy, as it is called, is probably the only technology suitable for preparing native frozen-hydrated samples of tissues thin enough to image by electron microscopy. Chapter 3 reviews the physics of electron image formation and illustrates the effects of image degradation caused by lens imperfections and thicker samples. Chapter 4 briefly but comprehensively reviews lowdose imaging and the microscope parameters that should be considered for automated data collection. Chapter 5 reviews the geometries of fiducial-based image registration and shows examples of how poorly aligned tilt series affect tomograms. This chapter is especially valuable because most published tomograms were aligned using colloidal gold beads. Chapter 6 reviews the algorithms of feature-based ~fiducial-free! alignment, which is mandatory for specimens that do not have any fiducials near the object of interest. Chapter 7 discusses the recovery of 3-D structures from 2-D data. It also discusses two popular algorithms for tomographic reconstruction and illustrates the results with simulated images. Chapter 8 gives a more mathematically detailed background of the most common method of tomographic reconstruction: weighted back-projection. Chapter 9 reviews the representation of the tomogram as a sum of orthogonal real-space functions. This chapter is the most mathematically intense one. Chapter 10 discusses the geometrical considerations for different modes of tilt series acquisition. The effects of missing data on resolution are also discussed. Chapter 11 introduces the physics of noise. Three popular classes of filters are described and the effects of the respective denoising algorithms are illustrated with real and simulated tomograms. Chapter 12 defines the concept of image segmentation and discusses a number of semi-automatic segmentation algorithms. Chapter 13 uses microtubules and membranes as examples of structures that have known features and can be automatically segmented. Chapter 14 shows how to segment barrel-shaped macromolecules using templates derived from higher resolution structures. Chapter 15 shows how image classification can be used to segment and average motifs in paracrystals, as done successfully on insect flight muscle. This book is a must-read for students of electron tomography and serves as a reference for practitioners. Each Book Review MicroscopyAND Microanalysis