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Morphomic Analysis of a Simple Chordate

简单脊索动物的形态分析

基本信息

批准号：
7895085
负责人：
BANGALORE S MANJUNATH
金额：
$ 44.65万
依托单位：
UNIVERSITY OF CALIFORNIA SANTA BARBARA
依托单位国家：
美国
项目类别：
财政年份：
2009
资助国家：
美国
起止时间：
2009-08-01 至 2012-06-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/7895085
关键词：
Address Animal Model Animal Organ Architecture Behavior Biological Biology Biomedical Engineering Cell Count Cell Shape Cell Size Cells Chordata Collection Color Complex Computer Vision Systems Computers Data Detection Development Developmental Biology Developmental Process Dyes Embryo Embryonic Development Engineering Fluorescence Microscopy Future Genes Genetic Genetic Techniques Goals Image Image Analysis Imagery Intervention Laser Scanning Confocal Microscopy Life Manuals Membrane Methodology Methods Modality Modeling Morphogenesis Movement Neural Tube Closure Neuraxis Optics Organ Organism Pattern Recognition Process Research Research Infrastructure Research Personnel Resolution Shapes Snakes Speed Staining method Stains System Talents Testing Time Tissues Wound Healing ascidian base blastomere structure cell behavior cell motility cell type computerized tools imaging informatics imaging modality information processing intercalation knock-down notochord professor programs spatiotemporal three dimensional structure tool

项目摘要

The original application proposed a comprehensive characterization of morphogenesis in both wild type and experimentally manipulated embryos. Emphasis was to be placed on characterizing morphogenesis in both the notochord and the central nervous system. We also proposed to image experimentally manipulated embryos in which key embryogenesis genes were knocked down. In this revised two-year study we will restrict our efforts to the developing notochord in wild-type embryos. Our goal in focusing on the notochord is to establish the methodologies for image capture, segmentation and analysis that will be of broadest potential use to us, and others. In collecting the embryo images for this analysis we will be capturing the embryos in toto and in high resolution. Thus, while we will be focusing on the notochord, the image sets will be amenable to the analysis of other tissues in future studies. The notochord will serve as an ideal model for developing these methods. Besides the universal importance of the notochord for chordate development, the ascidian notochord presents a range of challenges for computer segmentation and analysis, yet it is probably the most tractable tissues in the embryo because of the low and fixed numbers of cells, and the fact that once cell intercalation is completed, the overall arrangement of the cells does not change. In the Preliminary Results section we demonstrated 3D time-lapse imaging of live embryos by both DIC and fluorescence microscopy. In this revised proposal we will continue with both of these imaging methods. As in the original proposal, several approaches for notochord cell segmentation will be pursued and optimized. We have presented preliminary results with two very different approaches for cell boundary detection: network snakes for DIC images; and a watershed-based method for confocal images of live embryos stained with a fluorescent membrane dye. We expect that concentrating on the notochord will allow us to make substantial contributions in only two years while building tools that can later be extended to more challenging tissues. Finally, we will develop tools for the morphometric analysis and visualization of the notochord data.

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