Waxholm Space for Rodent Neuroinformatics

啮齿动物神经信息学沃克斯霍姆空间

• 批准号: 9763673
• 负责人: JAMES C GEE
• 金额: $ 55.07万
• 依托单位: UNIVERSITY OF PENNSYLVANIA
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-09-01 至 2022-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9763673
• 关键词: Address; Adult; Anatomy; Animals; Atlases; Basic Science; Brain; Brain Mapping; Brain imaging; C57BL/6 Mouse; Collection; Communities; Computer software; Data; Data Collection; Development; Disease; Educational workshop; Genetic Variation; Goals; Health; Health Sciences; Histologic; Human; Image Analysis; Imaging technology; Infrastructure; Institutes; International; Lead; Location; Measurement; Methodology; Methods; Modeling; Modernization; Mus; National Institute of Mental Health; Neurosciences; Neurosciences Research; Outcome; Protocols documentation; Publications; Rattus; Research Personnel; Resolution; Resources; Rodent; S-nitro-N-acetylpenicillamine; Science; Scientist; Site; Source; Speed; Standardization; Structure; System; Tennessee; Training; Universities; base; brain research; computerized tools; data resource; data sharing; digital; experience; experimental study; graphical user interface; high resolution imaging; image registration; imaging Segmentation; imaging modality; improved; interest; interoperability; member; multimodality; neuroinformatics; next generation; open source; programs; repaired; technological innovation; tool; user-friendly

Summary Data collections of every variety now abound and continue to grow in the neurosciences but their lack of acces- sibility, especially in an integrative way, to the average investigator presents a persistent and vexing challenge to the field and ultimately limits the potential impact of these resources. To address this undesirable state of the science, the International Neuroinformatics Coordinating Facility (INCF, http://incf.org/) established the Digital At- lasing Program to formulate standards and practices for atlas-based data sharing, and to instantiate these, for the rodent brain initially, in infrastructure, systems and methods capable of serving the scientific goals of the commu- nity. A central outcome has been the development and prototypical implementation of Waxholm Space (WHS), a standard coordinate system for the adult C57BL/6 mouse brain, and its underlying digital atlasing infrastructure (DAI) that allows researchers to query any data resource registered to WHS as an atlas hub. As with its counter- part in human brain studies, the Talairach coordinate system, an essential requirement is the ability to normalize user data into standardized space; the inverse transformation allows standardized data to be accessed in user’s native space. This project brings together leading expertise in brain atlasing at Penn and Duke to develop, evaluate and deploy this critical functionality under community support that would make possible the WHS-based coordination of rodent brain research, which would allow access to data, tools, and analyses from multiple sources. Toward this end, an improved multi-modality atlas defining the canonical coordinate system of WHS will be developed for the mouse and rat, expanding both the range of experimental studies possible and the types of analyses that may be applied to these in the field. This first-of-its-kind analytic capability will be enabled by a suite of tools that accommodate a variety of user backgrounds and needs. These developments will be evaluated through their application to real- world use cases and their practical integration with major community resources. The successful completion of this project will fully realize the value of Waxholm Space in rodent neuroscience research and lead to immediate and broad impact on the field.

概括 现在，神经科学领域的各种数据收集比比皆是，并且还在继续增长，但它们缺乏可访问性。 灵活性，尤其是以综合的方式，对普通研究者来说是一个持续而令人烦恼的挑战 并最终限制这些资源的潜在影响。为了解决这种不良状况 科学，国际神经信息学协调机构（INCF，http://incf.org/）建立了数字At- lasing 计划，制定基于图集的数据共享的标准和实践，并实例化这些标准和实践，以供 啮齿动物的大脑最初是在基础设施、系统和方法中能够服务于社区的科学目标。 本质。一个核心成果是 Waxholm Space (WHS) 的开发和原型实施， 成年 C57BL/6 小鼠大脑的标准坐标系及其底层数字图谱基础设施 (DAI)，允许研究人员查询注册到 WHS 作为图集中心的任何数据资源。与它的反作用一样 在人类大脑研究中，Talairach 坐标系的一个基本要求是标准化的能力 用户数据进入标准化空间；逆变换允许在用户的环境中访问标准化数据 原生空间。 该项目汇集了宾夕法尼亚大学和杜克大学在脑图谱方面的领先专业知识，以开发、评估和部署 这一在社区支持下的关键功能将使基于 WHS 的啮齿动物协调成为可能 大脑研究，这将允许从多个来源获取数据、工具和分析。为此，一个 将为小鼠开发定义 WHS 规范坐标系的改进多模态图集 和大鼠，扩大了可能的实验研究范围和可能应用的分析类型 对于这些在该领域的人。这种史无前例的分析能力将通过一套工具来实现，这些工具可容纳 不同的用户背景和需求。这些发展将通过其实际应用进行评估 世界用例及其与主要社区资源的实际整合。顺利完成 该项目将充分实现沃克斯霍尔姆空间在啮齿动物神经科学研究中的价值，并立即带来 并在该领域产生广泛影响。