Improvement and Extension of EM3D

EM3D的改进和扩展

• 批准号: 6741514
• 负责人: UEL J MCMAHAN
• 金额: $ 49.34万
• 依托单位: STANFORD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2003
• 资助国家: 美国
• 起止时间: 2003-05-01 至 2008-02-29
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6741514
• 关键词: bioimaging /biomedical imaging; computer program /software; computer simulation; computer system design /evaluation; electron microscopy; mathematical model; membrane structure; neurobiology; neuromuscular junction; structural biology; synaptic vesicles; three dimensional imaging /topography; tomography

DESCRIPTION (provided by applicant): The transmission electron microscope has been an important instrument for biomedical research for almost fifty years, revealing fine structural details in tissue sections essential for understanding how cells function and the mechanisms of disease unobtainable by any other imaging device. The microscope provides two-dimensional (2D) projections of specimens. Conventionally, data analysis is done on individual projections. However, spatial resolution in a 2D projection is severely restricted by the absence of depth information. Over the last few decades tomographic methods have been developed to generate 3D volume reconstructions from a series of 2D projections. An obvious advantage of electron microscope tomography (EMT) is that it offers the opportunity to examine the positions and relationships of structures smaller than the thinnest tissue sections that can be cut. Since most cellular and extracellular structures detectable in tissue sections by electron microscopy are much smaller than the section thickness, as are immunogold labels for specific proteins, cell biologists in neuroscience and other biomedical fields are eager to apply EMT to a vast number of previously unapproachable problems. However, few laboratories presently can use EMT on tissue sections. The primary reasons are that the software packages available for data analysis are difficult for mainstream biologists to use, and they also have limited capabilities. Over the last five years this laboratory has been developing a software package, EM3D that utilizes an innovative approach to segmentation and surface-model generation, thereby providing spatial resolution at the full scale of the reconstructed volume. It is convenient to use even for novices, and it has been successfully employed to unravel highly complicated subcellular architecture in tissue sections from neuromuscular junctions leading to novel hypotheses concerning mechanisms of synaptic transmission. The overall goals of the research in this application are to add new features to EM3D and to create a stable release for the neuroscience community and members of other biomedical fields. The specific aims are to: (1) consolidate EM3D, (2) generate an improved reconstruction algorithm, (3) develop a method for automated surface-modeling, (4) make a tool for membrane surface-model flattening, and (5) devise a procedure for automatic compartmental segmentation.

描述（由申请人提供）：近50年来，透射电子显微镜一直是生物医学研究的重要工具，它揭示了组织切片中的精细结构细节，这些细节对于理解细胞的功能和任何其他成像设备无法获得的疾病机制至关重要。显微镜提供标本的二维（2D）投影。传统上，数据分析是在个别预测上进行的。然而，2D投影中的空间分辨率由于缺乏深度信息而受到严重限制。在过去的几十年中，已经开发了断层摄影方法来从一系列2D投影生成3D体积重建。电子显微镜断层扫描（EMT）的一个明显优势是，它提供了检查比可以切割的最薄组织切片更小的结构的位置和关系的机会。由于电子显微镜在组织切片中可检测到的大多数细胞和细胞外结构都比切片厚度小得多，就像特定蛋白质的免疫金标记一样，神经科学和其他生物医学领域的细胞生物学家渴望将EMT应用于大量以前无法解决的问题。然而，目前很少有实验室能够在组织切片上使用EMT。主要原因是主流生物学家难以使用可用于数据分析的软件包，而且它们的功能也有限。在过去的五年里，该实验室一直在开发一个软件包，EM3D，它利用一种创新的方法来分割和表面模型生成，从而提供在重建体积的全尺度的空间分辨率。即使对于新手来说，它也很方便使用，并且已成功用于解开神经肌肉接头组织切片中高度复杂的亚细胞结构，从而提出了有关突触传递机制的新假设。该应用程序研究的总体目标是为EM3D添加新功能，并为神经科学社区和其他生物医学领域的成员创建稳定的版本。 具体目标是：（1）合并EM 3D，（2）生成改进的重建算法，（3）开发用于自动表面建模的方法，（4）制作用于膜表面模型平坦化的工具，以及（5）设计用于自动房室分割的过程。