Virtual microscopy of zebrafish as a community resource

斑马鱼的虚拟显微镜作为社区资源

• 批准号: 7993610
• 负责人: Keith Chi Cheng
• 金额: $ 13.19万
• 依托单位: PENNSYLVANIA STATE UNIV HERSHEY MED CTR
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-02-05 至 2011-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7993610
• 关键词: 3-Dimensional; Address; Adolescent; Adult; Affect; Aging; Anatomy; Animals; Applications Grants; Area; Atlases; Biological Models; Biological Process; Books; Chemicals; Collection; Communicable Diseases; Communities; Computers; Databases; Development; Diagnostic; Disadvantaged; Discipline; Disease; Disease model; Distant; Educational process of instructing; Embryo; Fishes; Funding; Gene Expression; Genes; Genetic; Glass; Growth; Growth and Development function; Histologic; Histology; Image; In Situ; Individual; Information Networks; Institutes; Internet; Investigation; Larva; Lead; Learning; Longevity; Mails; Malignant Neoplasms; Messenger RNA; Microscope; Microscopic; Microscopy; Mission; Modeling; Monoclonal Antibody R24; Mus; Oils; Oligonucleotides; Online Systems; Optics; Oregon; Organogenesis; Paraffin; Pathology; Pattern; Phenotype; Plastics; Play; Principal Investigator; Registries; Research; Research Infrastructure; Research Personnel; Resolution; Resources; Role; Sampling; Scanning; Side; Slice; Slide; Source; Staging; Staining method; Stains; Structure; Terminology; Time; Tissues; Transgenic Organisms; Travel; United States National Institutes of Health; Universities; Work; Zebrafish; base; digital; digital imaging; functional genomics; human disease; improved; interest; lens; mutant; programs; reconstruction; tumor registry; virtual; working group; zebrafish development

DESCRIPTION (provided by applicant): NIH-sponsored zebrafish and Aquatic Models working groups have recommended the creation of web based anatomy, histology and pathology atlases as a community resource. The principal investigators propose to generate and digitize reference glass slides for web-based virtua/microscopy and 3D at as of the zebrafish. This atlas will be available through the Zebrafish Information Network (ZFIN) of the University of Oregon (http://zfin.org/ZFIN/). In virtual microscopy, any computer with a web browser and fast internet connection can function as a microscope, using annotated virtual slide files on a remote server. Virtual slides are GB size, compressed composites of high magnification image tiles or strips; image packets are sent to the remote user according to user-chosen field-of-view and magnification. In the 3D anatomy atlas, selected anatomical structures can be viewed and rotated. The atlases will include normal, and some abnormal, embryos, larvae, juveniles and adults. The experimental features of the zebrafish have made it a premier model for functional genomics. High-throughput mutant, antisense knockdowns ("morphants"), fluorescent transgenic, and chemical screens have already yielded thousands of potential models of human disease affecting a variety of biological functions at a variety of stages of growth and development. A web-based, comprehensive reference atlas of normal zebrafish would greatly facilitate this work. Remote annotation of and access to such atlases will facilitate the growth of the atlas as a resource, as well as individual and collaborative investigations. Specific Aim 1 is to generate a registry of serial, stained paraffin and plastic sections of normal zebrafish embryos, larvae, juveniles, and adults. Specific aim 2 is to scan these sections to create virtual slides. Illustrative pairs of annotated fields will be generated. Specific Aim 3 is to digitally outline histologically identifiable structures in zebrafish embryos, larvae, juveniles, and adults for 3D reconstructions. The resultant infrastructure will be complementary to, adaptable to, and coordinated with those of other model systems. The atlas will support the zebrafish community across multiple disciplines, and address the missions of nearly all Institutes of the NIH.

描述(由申请者提供)：NIH赞助的斑马鱼和水生模型工作组建议创建基于网络的解剖学、组织学和病理学地图集作为社区资源。主要研究人员建议生成并数字化基于网络的Virtua/显微镜和3D斑马鱼的参考玻片。这份地图集将通过俄勒冈大学斑马鱼信息网(http://zfin.org/ZFIN/).)提供在虚拟显微镜中，任何有网络浏览器和快速互联网连接的计算机都可以像显微镜一样工作，使用远程服务器上带注释的虚拟幻灯片文件。虚拟幻灯片是GB大小的高倍率图像块或条带的压缩组合；图像包根据用户选择的视场和放大倍数发送到远程用户。在3D解剖图集中，可以查看和旋转选定的解剖结构。这些地图集将包括正常的和一些异常的胚胎、幼虫、幼虫和成虫。斑马鱼的实验特征使其成为功能基因组学的首选模型。高通量突变体、反义基因敲除(“变异体”)、荧光转基因和化学筛选已经产生了数千种潜在的人类疾病模型，在生长和发育的不同阶段影响各种生物功能。一份基于网络的、全面的普通斑马鱼参考地图集将极大地促进这项工作。这类地图集的远程注释和查阅将有助于地图集作为一种资源的发展，以及个人和协作调查。具体目标1是建立正常斑马鱼胚胎、幼体、幼体和成体的连续染色石蜡和塑料切片的登记。具体目标2是扫描这些部分以创建虚拟幻灯片。将生成说明性的带注释的字段对。具体目标3是数字化勾勒斑马鱼胚胎、幼体、幼体和成体的组织可识别结构，用于3D重建。由此产生的基础设施将是对其他模型系统的补充、适应和协调。该地图集将支持跨多个学科的斑马鱼群落，并解决几乎所有NIH研究所的任务。