STITCHING LATERALLY ADJACENT TOMOGRAMS

缝合横向相邻的断层图

• 批准号: 8362538
• 负责人: DAVID N MASTRONARDE
• 金额: $ 3.19万
• 依托单位: UNIVERSITY OF COLORADO
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-05-01 至 2012-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8362538
• 关键词: 3-Dimensional; Area; Cell physiology; Cells; Cellular Structures; Funding; Goals; Grant; Image; Individual; Measures; National Center for Research Resources; Pancreas; Plastics; Positioning Attribute; Principal Investigator; Process; Research; Research Infrastructure; Resources; Running; Series; Source; Tomogram; United States National Institutes of Health; cost; programs; tool

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. There are practical limits to the size of the area that can be reconstructed in a single tomogram from a plastic section, even with tilt series taken by montaging overlapping camera frames. To reconstruct larger areas, it is necessary to generate tomograms from adjacent, overlapping areas and stitch them together. The primary impetus for this effort is the Visible Cell Project, which aims to reconstruct a significant fraction of a pancreatic cell. For this project, it was determined that the necessary area could be acquired in a 3x3 array of overlapping tomograms, referred to as a supermontage (each tomogram is itself generated from a 3x3 montage of 2Kx2K camera frames). The strategy for stitching these tomograms was to adapt existing tools in IMOD where possible and develop new ones where necessary. Stitching is carried out by running three new programs. The first program sets up a file for carrying information about the supermontage through the processing sequence, finds the overall shifts needed to align each pair of adjacent overlapping volumes, and cross-correlates small subvolumes at an array of positions in each overlap zone to measure the local deviations from perfect alignment. The second program takes this information about the relationships between adjacent pairs of volumes and resolves it into transformations that will best align all of the volumes. These transformations include some nonlinear warping of the volumes in the overlap zones. The primary goal of this warping is to reduce the 3-D stitching problem to a 2-D one so that the final stitching can be done by the existing program from blending 2-D montaged images. The third program manages the final steps of the process: warping each individual volume, matching image intensities between volumes, stacking them into a single file, and running the montage-blending program with some special parameters appropriate for this situation. With these programs, a 3x3 supermontage has been stitched seamlessly.

该副本是利用资源的众多研究子项目之一 由NIH/NCRR资助的中心赠款提供。对该子弹的主要支持 而且，副投影的主要研究员可能是其他来源提供的 包括其他NIH来源。 列出的总费用可能 代表subproject使用的中心基础架构的估计量， NCRR赠款不直接向子弹或副本人员提供的直接资金。 该区域的大小实际上是可以从塑料部分中重建的区域的大小，即使倾斜序列是通过蒙蒂格重叠的相机框架进行的倾斜系列。 为了重建较大的区域，有必要从相邻的重叠区域生成断层图并将它们缝合在一起。 这项工作的主要动力是可见的细胞项目，该项目旨在重建大量胰腺细胞。 对于这个项目，确定可以在3x3重叠的横线图中获取必要区域，该层次被称为超大型（每个断层图本身）本身是从2kx2k摄像头框架的3x3蒙太奇生成的）。 缝制这些断层图的策略是在可能的情况下调整IMOD中现有工具，并在必要时开发新工具。 缝线是通过运行三个新程序进行的。 第一个程序设置了一个文件，用于通过处理序列携带有关超大型的信息，找到对齐每对相邻的重叠卷所需的总体移位，并在每个重叠区域的一系列位置上交叉校正小的子vol，以测量与完美镇定的局部偏差。 第二个程序将这些信息采用了有关相邻卷之间关系的信息，并将其解析为最能使所有卷都充分对齐的转换。 这些转换包括重叠区域中体积的一些非线性翘曲。 这种翘曲的主要目的是将3D缝合问题减少到2-D缝制问题，以便通过将2-D型蒙特图像融合到现有程序可以完成最终缝线。 第三个程序管理过程的最后一步：扭曲每个单独的卷，匹配卷之间的图像强度，将它们堆叠到一个文件中，并使用适合这种情况的一些特殊参数运行蒙太奇融合程序。 有了这些程序，3x3超大型人数已无缝缝制。