COMPUTER GRAPHICS & IMAGE PROCESSING SOFTWARE FOR 3 D RECONSTRUCTION

电脑图像

• 批准号: 6282120
• 负责人: STEPHEN J YOUNG
• 金额: $ 5.9万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 1998
• 资助国家: 美国
• 起止时间: 1998-04-01 至 1999-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6282120
• 关键词: bioengineering /biomedical engineering; biomedical equipment development; biomedical resource; biotechnology; building /facility design /renovation; technology /technique

The major goals for these software projects are to design, develop and implement programs for semiautomated segmentation and classification of 3D volumes, and to develop software for the visualization of three-dimensional structure. In the previous years of this project we have developed the program suites, Synu and Ducky, for performing sophisticated three-dimensional visualizations. These programs have been found to be extremely useful by biologists and have been distributed to many investigators throughout the US and internationally. During this year we have focused on improvements in software for segmentation and classification as well as programs for combining volume datasets for use in performing serial tomography and for merging volume correlated datasets acquired from the light and microscope (Perkins et al., 1997). Manual segmentation-tracing programs: In many light and electron microscopic studies, the objects of interest for three-dimensional reconstruction or analysis are delineated by membranes. These membranes are often extremely difficult to define using image processing techniques. Generally it has been found necessary to specify the location of the membranes using an interactive manual tracing method. The program XVOXTRACE developed at NCMIR is specifically designed for manually contouring features of structures in tomographic volumes by tracing with a mouse on planes of the volume along any one of the three major axes. Additional guides are provided to achieve accurate tracing. Thus, as the contours are traced, they can be viewed simultaneously superimposed on selected images from the original tilt series. Pairs of tilt-series images with the contours superimposed may also be displayed as anaglyphic or stereoscopic views. In addition, the accuracy of tracing can be evaluated by examining the contours superimposed on renderings of the volume viewed from an arbitrarily selected orientation. We have developing an improved version of this program which will include stereoscopic volume rendering as well as enhanced contour editing facilities such as automatic contour resplining. Capabilities for panning and zooming on a view of a selected region of the specimen in the volume slice, volume rendering, and tilt displays will also be provided. Semiautomated particle detection: Several on-going NCMIR research projects are interested in defining the three-dimensional distribution of particle-like structures such as synaptic vesicles. In collaboration with Dr. Ioana Martin (Dept. Computer Science, Univ. Indiana, South Bend) we have been developing semiautomated tool for detecting and defining particles. An initial tool was developed based on methods used by Dr. Martin to detect virus particles in two-dimensional electron micrographs. The tool was evaluated to detection of synaptic vesicles in tomographic reconstructions. Although partly successful, we expect that algorithms, currently under development, using three-dimensional information will be considerably more accurate. Measurements based on contours: XDEND is a graphics-based analysis tool developed at NCMIR to obtain measurements of the length, surface area and volume of objects defined as sets of contours such as those produced with XVOXTRACE. In addition, contours can also be derived directly from data volumes in those cases in which the structure can be segmented using simple built-in thresholding. Components of the structure may be resectioned into contours in the transverse, sagittal, or coronal axes to obtain the best orientation for length measurements. The length measurements are based on linear segments interconnecting the centroids of the contours. The program automatically detects branching segments. Objects may be viewed in perspective as contour outlines, centroids or skeletons. XDEND can also be used to reclassify and edit objects after recontouring. We are currently improving this program by providing resectioning along an arbitrary axis, and more accurate skeletonization methods. Software for serial tomography and volume merging We previously developed and implemented a procedure for combining serial section techniques with tomographic reconstruction (Soto et al., 1994). For a fixed tilt range and tilt increment, the resolution of the volume reconstructed by tomography decreases as the thickness of the object under reconstruction is increased. Thus, the resolution obtainable in reconstructions of very thick specimens is relatively poor. To overcome this limitation, we combined tomography with the serial section reconstruction technique to reconstruct large structures with adequate resolution. A series of consecutive sections is cut with a thickness sufficient to achieve the resolution desired in the reconstruction. Each section is reconstructed using tomography. Subsequently, the resulting volumes in the series are aligned and merged into a single volume. We recently developed two programs, MOG and TRANSMOG that are useful in the alignment of serial volumes. Fiducial marks are assigned to features in the raw or segmented sections from the consecutive volumes using the NCMIR fiducial marking tool, FIDO. MOG computes the polynomial function coefficients necessary to align the two sections, including a correction for in-plane warpage that may have occurred between the two volumes. The translations computed by MOG are then applied by TRANSMOG to the remaining sections in the volume. These have programs are also useful for aligning and scaling correlated three-dimensional light and electron microscope data and have been used for this purpose on a collaborative study examining alterations in cardiac muscle in a model of heart failure. Further, this software has also been found useful for assessing changes in structures due to shrinkage. The NCMIR program MOG can be used to obtain numeric estimates of changes in single sections resulting from beam exposure or specimen preparation.

这些软件项目的主要目标是设计、开发 并实施半自动分割程序和 3D 体积的分类，并开发软件 三维结构的可视化。 前几年 在这个项目中，我们开发了程序套件 Synu 和 Ducky， 用于执行复杂的三维可视化。 这些 生物学家发现该程序非常有用，并且已经 已分发给美国各地的许多调查人员 国际上。 今年我们重点改进了 用于分割和分类的软件以及程序 组合用于执行串行断层扫描的体积数据集和 用于合并从光获取的体积相关数据集和 显微镜（Perkins 等，1997）。 手动分段追踪 程序：在许多光和电子显微镜研究中，物体 三维重建或分析感兴趣的是 由膜界定。 这些膜通常非常 使用图像处理技术很难定义。 一般来说它 已发现有必要指定膜的位置 使用交互式手动跟踪方法。 XVOXTACE 程序 NCMIR 开发的产品专为手动轮廓设计 通过鼠标追踪断层摄影体积中的结构特征 在沿着三个主轴之一的体积平面上。 提供了额外的指南来实现准确的跟踪。 因此，作为 轮廓被追踪，可以同时查看 叠加在原始倾斜系列中选定的图像上。 对 具有叠加轮廓的倾斜系列图像也可以是 显示为立体视图或立体视图。 此外， 可以通过检查轮廓来评估追踪的准确性 叠加在从任意角度观看的体积效果图上 选定的方向。 我们已经开发了这个的改进版本 程序将包括立体体积渲染以及 增强的轮廓编辑功能，例如自动轮廓 重新调整。 平移和缩放视图的功能 体积切片中样本的选定区域，体积渲染， 还将提供倾斜显示器。 半自动颗粒 检测：几个正在进行的 NCMIR 研究项目感兴趣的是 定义类粒子的三维分布 突触小泡等结构。 与 Ioana 博士合作 Martin（印第安纳大学南本德分校计算机科学系）我们有 一直在开发用于检测和定义的半自动化工具 颗粒。 最初的工具是根据博士使用的方法开发的。 马丁在二维电子中检测病毒颗粒 显微照片。 该工具被评估用于检测突触小泡 在断层扫描重建中。 尽管部分成功，但我们预计 该算法目前正在开发中，使用三维 信息将会更加准确。 测量基于 轮廓：XDEND 是 NCMIR 开发的基于图形的分析工具 获得长度、表面积和体积的测量值 定义为轮廓集的对象，例如使用 XVOXTRACE。 此外，轮廓也可以直接从 在结构可以分段的情况下的数据量 使用简单的内置阈值。 该结构的组件可以 被切除成横断面、矢状面或冠状面的轮廓 轴以获得长度测量的最佳方向。 这 长度测量基于互连的线性段 轮廓的质心。 程序自动检测 分支段。 物体可以被视为轮廓的透视图 轮廓、质心或骨架。 XDEND 还可用于 重新轮廓后重新分类和编辑对象。 我们目前 通过沿任意方向提供切除来改进该程序 轴，以及更精确的骨架化方法。 串口软件 断层扫描和体积合并我们之前开发并实施 将连续切片技术与断层扫描相结合的程序 重建（Soto 等人，1994）。 对于固定倾斜范围和倾斜 增量，断层扫描重建体积的分辨率 随着重建对象的厚度减小 增加。 因此，在重建中获得的分辨率非常 厚的标本相对较差。 为了克服这个限制，我们 结合断层扫描与连续切片重建技术 以足够的分辨率重建大型结构。 一系列 连续的部分被切割成足够的厚度以实现 重建所需的分辨率。 每个部分都是 使用断层扫描重建。 随后，得到的卷 该系列中的内容被对齐并合并成一个卷。 我们 最近开发了两个程序，MOG 和 TRANSMOG，可用于 系列卷的对齐。 基准标记分配给 连续卷的原始或分段部分中的特征 使用 NCMIR 基准标记工具 FIDO。 MOG 计算 对齐两个部分所需的多项式函数系数， 包括对可能发生的面内翘曲的校正 两卷之间。 MOG 计算出的平移为 由 TRANSMOG 应用到卷中的其余部分。 这些 有程序对于对齐和缩放相关也很有用 三维光和电子显微镜数据 为此用于检查变更的合作研究 心力衰竭模型中的心肌。 另外，这个软件 还发现对于评估结构变化很有用 收缩。 NCMIR 程序 MOG 可用于获取数值 光束照射引起的单个截面变化的估计 或标本制备。