Three-D Imaging Informatics for High-Resolution Electron Microscopy

高分辨率电子显微镜的三维成像信息学

• 批准号: 8158054
• 负责人: Clement McDonald
• 金额: $ 30.78万
• 依托单位: NATIONAL LIBRARY OF MEDICINE
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/8158054
• 关键词: Electron Microscopy; Resolution; imaging informatics

The Three-D Informatics Group in the NLM Office of High Performance Computing and Communications is developing software for the registration, segmentation, analysis and visualization of 3D data from confocal microscopy, transmission electron tomography, and high resolution dual-beam scanning electron microscopy. These technologies are exploring cell biology at nanometer scales. The Audio Visual Program Development Branch craft individual models, visualizations, and presentations of the processed data from these modalities of microscopy for publication and interactive viewing among our colleagues in the biological sciences. We are conducting this research in partnership with the National Cancer Institutes Laboratory for Cell Biology. These technologies resemble the very successful Visible Human Project (VHP), where cryosectioning, a destructive imaging technique, was used to capture a representation of human anatomy at unprecedented levels of quality and fidelity. Effectively, a human subject was sliced at 1/3 mm intervals and the exposed sections photographed digitally to yield a human anatomical study with pixel resolutions as fine as 350 microns. In a similar approach, dual-beam scanning electron microscopy starts with a fixed cellular sample and ablates the cell using a focused ion beam, slicing the sample at intervals as fine as 15 nanometers. The exposed sections are imaged using a scanning electron microscope. The comparable approaches of these imaging techniques allow the Three-D Informatics Group to apply tools similar to those used on VHP data for registration, segmentation, and image analysis. The very successful VHP Insight Toolkit (ITK) open source software initiative sponsored by NLM and originally funded with other ICs at NIH (NIDCR, NEI, NIMH, NINDS, NCI), the National Science Foundation, and DoD TATRC, are used extensively in this project. We also employ public tools such as 3D Slicer, a software system that uses ITK and is produced Harvards National Alliance for Medical Image Computing (NA-MIC) one of the NIH Roadmap National Centers for Biomedical Computing (NCBCs) funded through NIBIB. During FY2009, the team, led by the programming efforts of Mr. Lowekamp, has provided software tools to NCIs Laboratory of Cell Biology to promote high throughput microscopy and improve their understanding of cellular biology, particularly in the communication of HIV AIDS among dendrite cells, macrophages, and T-Cells. Illuminations from Mr. Bliss of the Audiovisual Program Development Branch have aided in communicating these results and their importance to the community. These results have been published in journals including the Journal of Structural Biology. One of the images that features one of Mr. Lowekamps cell membrane models generated through his software and illuminated by Mr. Bliss was presented on the cover of the November-December 2009 IAVIReport (the publication on AIDS Vaccine Research), volume 13, number 6, with the subtitle Visualizing HIV. The current effort focuses on new processing software for the incoming microscope being acquired by NCI. The new instrument promises far greater resolution, better signal to noise properties, and excellent contrast. Our ability to build effective software tools to extract information will be greatly enhanced by these new developments. This project still in its early stages, but the collaboration has already yielded important results and multiple publications in journals and conferences demonstrating the value of these technologies.

NLM高性能计算和通信办公室中的三-D信息组正在开发用于注册，分割，分析和可视化共聚焦显微镜，传输电子断层扫描和高分辨率双光束扫描电子显微镜的3D数据的软件。 这些技术正在纳米尺度探索细胞生物学。音频视觉程序开发分支机构制作的单个模型，可视化以及来自这些显微镜模式的处理数据的演示，以在我们的生物科学中的同事之间发表和交互式观看。我们正在与国家癌症研究所生物学实验室合作进行这项研究。 这些技术类似于非常成功的可见人类项目（VHP），在该项目中，一种破坏性的成像技术被用来以前所未有的质量和忠诚度来捕获人类解剖结构的表示。有效地，以1/3 mm的间隔将人类受试者切成薄片，并以数字方式拍摄的裸露部分，以产生人类的解剖学研究，其像素分辨率为350微米。在类似的方法中，双光束扫描电子显微镜从固定的细胞样品开始，并使用聚焦的离子束擦洗细胞，以每隔15纳米的良好时间切片样品。使用扫描电子显微镜对暴露部分进行成像。 这些成像技术的可比方法使三-D信息学组可以应用类似于VHP数据中使用的工具进行注册，分割和图像分析。 NLM赞助并最初由NIH（NIDCR，NEI，NIMH，NINDS，NCI，NCI），国家科学基金会和DOD TATRC资助的非常成功的VHP Insight Toolkit（ITK）开源软件计划，最初由NIH（NIDCR，NEI，NIMH，NINDS，NCI）资助。我们还采用了公共工具，例如3D SliCer，这是一种使用ITK的软件系统，该软件系统是Harbards National Alliance for Medical Image Computing（NA-MIC）是NIH路线图国家生物医学计算中心（NCBC）之一，该中心通过Nibib资助。 在2009财年期间，在Lowekamp先生的编程工作的领导下，该团队为NCIS生物学实验室提供了软件工具，以促进高吞吐量显微镜并提高他们对细胞生物学的理解，尤其是在树突状细胞，巨噬细胞，巨噬细胞和T细胞之间的HIV艾滋病交流中。视听计划开发部门Bliss先生的照明有助于传达这些结果及其对社区的重要性。这些结果已发表在包括《结构生物学杂志》在内的期刊上。 2009年11月至12月Iavireport（艾滋病疫苗研究的出版物）的封面上介绍了由他的软件生成并由Bliss先生产生的Lowekamps细胞膜模型之一，并由Bliss先生照亮的图像之一，第13卷，第6卷，第6卷，带有字幕可视化HIV。 当前的工作着重于NCI获取的新处理软件。新仪器有望更大的分辨率，对噪声特性更好的信号以及出色的对比度。这些新开发项目将大大增强我们构建有效的软件工具来提取信息的能力。 该项目仍处于早期阶段，但是该协作已经在期刊和会议上产生了重要的结果和多个出版物，证明了这些技术的价值。