IMAGE BASED PHENOTYPING

基于图像的表型分析

• 批准号: 8172261
• 负责人: ROSS T WHITAKER
• 金额: $ 11.59万
• 依托单位: UNIVERSITY OF UTAH
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-09-15 至 2011-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8172261
• 关键词: Algorithms; Animal Experimentation; Autistic Disorder; Biological Process; Biomedical Computing; Collaborations; Complex; Computer Retrieval of Information on Scientific Projects Database; Computer software; Congenital Heart Defects; Development; Funding; Genes; Genetic; Goals; Grant; Growth; Hand; Health Sciences; Human Genetics; Image; Imagery; Institutes; Institution; Investments; Laboratories; Length; Measurement; Metric; Microscope; Minor; Modeling; Molecular Abnormality; Mus; Mutation; Oregon; Pathology; Pattern; Pediatric Neoplasm; Phenotype; Preparation; Process; Protocols documentation; Research; Research Personnel; Resources; Skeleton; Source; Specimen; Structure; Time; United States National Institutes of Health; Universities; Utah; Work; base; density; human disease; image processing; imaging Segmentation; imaging modality; insight; interest; morphometry; mouse model; positional cloning; research study; shape analysis; skeletal; software systems; tool

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. This project started with the laboratory of Dr. Mario Capecchi at the University of Utah's Eccles Institute of Human Genetics. Dr. Capecchi's laboratory was investigating the phenotypic expression of specific, induced genetic abnormalities in mice, a model that has been shown to provide insight into the ontogeny of congenital human disease. Conventional analysis of mouse skeletal structure requires sacrificing the research animal and a labor-intensive, time-consuming process of skeleton preparation and physical inspection under a dissecting microscope. Many tens or even hundreds of specimens are often required for a meaningful statistical analysis, which represents an enormous investment of time and money. The goal of the Center for Integrative Biomedical Computing collaboration with the Capecchi lab is to develop a faster, non-invasive protocol for skeletal analysis that uses semi-automated image processing of three-dimensional micro-CT rather than hand measurements of prepared skeletal specimens. We are continuing the development of a set of image segmentation, measurement and visualization algorithms and software systems for quantitative morphometry that allow us to experiment with new metrics such as the analysis of shape that would not be possible with prepared skeletal specimens. Furthermore, we expect that our tools will allow for more precise and repeatable measurements for length, density and volume, and therefore give insight into genetic alterations that have previously been described as pleiotropic (partially penetrant) or that have been misinterpreted as minor effects. Over the years this project has gained interest from collaborators working with other imaging modalities and various pathologies including childhood tumors, autism, and heart defects. In particular, collaborative work with the Charles Keller laboratory (University of Oregon Health Sciences Center) is extending the shape analysis work. The work of the CIBC with Dr. Keller has focused primarily on skeletal phenotypes using mouse mice models that have been created through genetic knock outs. The process has been to segment sets of 3D microCT images using Seg3D and to analyze and visualize the results using the CIBC software: ShapeWorks, SCIRun and/or ImageVis3D. This work represents an ongoing strategy of reverse genetics in the mouse as a way of determining the contribution of a single gene to a complex biological process, such as developmental patterning.

该副本是利用众多研究子项目之一 由NIH/NCRR资助的中心赠款提供的资源。子弹和 调查员（PI）可能已经从其他NIH来源获得了主要资金， 因此可以在其他清晰的条目中代表。列出的机构是 对于中心，这不一定是调查员的机构。 该项目始于犹他大学人类遗传学研究所Mario Capecchi博士的实验室。 Capecchi博士的实验室正在研究小鼠特异性诱导的遗传异常的表型表达，该模型已被证明可以洞悉先天性人类疾病的个体。小鼠骨骼结构的常规分析需要牺牲研究动物，并在解剖显微镜下进行骨骼制备和物理检查的劳动密集型，耗时的过程。有意义的统计分析通常需要许多数十个甚至数百个标本，这代表了时间和金钱的巨大投资。与Capecchi Lab的综合生物医学计算中心合作中心的目标是开发一种用于骨骼分析的更快的非侵入性协议，该方案使用了三维微型CT的半自动图像处理，而不是对准备好的骨骼样品的手动测量。我们正在继续开发一组图像分割，测量和可视化算法和软件系统，以实现定量形态计量学，这使我们能够尝试使用新的指标，例如使用准备好的骨骼标本的形状分析，而形状分析是不可能的。此外，我们预计我们的工具将允许对长度，密度和体积进行更精确，可重复的测量，因此可以深入了解以前被描述为多效性（部分渗透剂）或被误解为较小效果的遗传变化。 多年来，该项目引起了与其他成像方式和各种病理的合作者的兴趣，包括儿童肿瘤，自闭症和心脏缺陷。 特别是，与查尔斯·凯勒（Charles Keller）实验室（俄勒冈大学健康科学中心）的合作合作正在扩展形状分析工作。 CIBC与Keller博士的工作主要专注于使用遗传敲门效果创建的小鼠模型的骨骼表型。 该过程是使用SEG3D段组合的3D Microct图像集，并使用CIBC软件分析和可视化结果：ShapeWorks，Scirun和/或ImageVis3D。 这项工作代表了小鼠反向遗传学的持续策略，是确定单个基因对复杂生物学过程（例如发育模式）的贡献的一种方式。