Improvement and Extension of EM3D

描述(申请人提供)：近50年来，透射式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，对于了解细胞的功能和疾病的机制是任何其他成像设备都无法获得的。显微镜提供样品的二维(2D)投影。按照惯例，数据分析是对单个预测进行的。然而，由于缺乏深度信息，2D投影的空间分辨率受到严重限制。在过去的几十年里，层析成像方法已经被开发用于从一系列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。由于电子显微镜可以在组织切片中检测到的大多数细胞和细胞外结构比切片厚度小得多，特定蛋白质的免疫金标记物也是如此，神经科学和其他生物医学领域的细胞生物学家迫切希望将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。主要原因是可用于数据分析的软件包对主流生物学家来说很难使用，而且它们的能力也有限。在过去五年中，该实验室一直在开发一个软件包EM3D，该软件包利用一种创新的方法进行分割和表面模型生成，从而在重建体积的全部尺度上提供空间分辨率。它甚至对新手也很方便，它已经成功地用于从神经肌肉连接的组织切片中解开高度复杂的亚细胞结构，导致了关于突触传递机制的新假说。该应用程序研究的总体目标是为EM3D添加新功能，并为神经科学界和其他生物医学领域的成员创建一个稳定的版本。 其具体目标是：(1)合并EM3D，(2)生成改进的重建算法，(3)开发自动曲面建模方法，(4)制作膜表面模型展平工具，(5)设计自动分区分割程序。

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.