WAXHOLM SPACE - MOUSE BRAIN SPATIAL COORDINATE SYSTEM

WAXHOLM SPACE - 小鼠大脑空间坐标系统

• 批准号: 8363171
• 负责人: George ALLAN JOHNSON
• 金额: $ 1.84万
• 依托单位: DUKE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-07-01 至 2012-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8363171
• 关键词: Adult; Atlases; Brain; C57BL/6 Mouse; Collection; Communities; Consensus; Data; Data Set; Documentation; Funding; Future; Grant; Histology; Image; Image Analysis; Label; Magnetic Resonance Imaging; Maps; Methods; Microscopy; Mus; National Center for Research Resources; Neurosciences; Ontology; Phase; Principal Investigator; Protocols documentation; Published Comment; Research; Research Infrastructure; Research Personnel; Resolution; Resources; Source; Specimen; Structure; Sweden; System; Tissues; United States National Institutes of Health; Weight; cost; male; meetings; member; neuroimaging; neuroinformatics; tool; web site

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. Waxholm space (WHS) is a conceptual construct that arose from the first meeting of the Neuroinformatics Coordinating Facility (INCF) advisory board held in Waxholm, Sweden in September 2008. Waxholm space will provide a mouse brain spatial coordinate system that will serve as a reference target for spatial normalization of experimental results attained by the research community. Wide utility will be achieved by incorporation of a comprehensive set of volume image sets acquired on each of seven mice. Those will consist of the following: 1) 3D MR Microscopy images at the highest spatial resolution yet attained (21.5 ¿m) acquired with three different imaging protocols to highlight the widest range of tissue contrast and morphologic structure [1]; 2) Volume Nissl images at 5¿m x 5¿m x 20 ¿m on the same brain reconstructed with minimal distortion and high fidelity [2] and registered to the MR data; 3) a collection of 33 labels derived in the intact specimen on the MR data and transferred to the reconstructed Nissl volume[3, 4]. These data will provide researchers three methods for entering WHS; 1) registration of 3D volume MR images into the target MR reference; 2) registration of conventional histology into the target Nissl; 3) registration of labels into the target labels. SPECIFIC AIMS: We propose here several of the critical milestones necessary to establish WHS: Phase I Completion Feb 1, 2009, We will: -- acquire the canonical dataset on an adult male C57BL/6 mouse; MR data with T1,T2, and T2* weighting at 21.5 ¿m; b) Nissl sections @ 5¿m x 5¿m x 20 ¿m on the same specimen. -- register the MR and Nissl volume and co-align those to a standardized orientation as will be defined by consensus by members of the INCF panel. -- provide and validate labels for at least 33 anatomical structures and validate the ontology of these structures to accepted standards. -- place the canonical data set and the documentation defining WHS on at least one publicly accessible web site with suitable search, imaging, analysis and commenting tools- all of which will be freely available to the neuroscience community. -- define the orientation and best practices for acquisition of future data to facilitate mapping into WHS. Phase II Completion August 1, 2009, we will: -- expand the canonical data set by adding 6 additional data sets with identical acquisition parameters i.e. 3 MR data sets, complete volumetric Nissl data, and labels. -- register all the data to provide a probabilistic atlas -- lace all the data on the freely accessible server. Phase III, We will: -- register representative atlases from at least three other sources to WHS starting initially with the Allen Brain Atlas -- establish the tools and pipelines necessary for registration for MR, Nissl, and labels and validate their use. References 1. Johnson, G.A., et al., NeuroImage, 2007. 37(1): p. 82-89. 2. Bertrand, L. and J. Nissanov, Front Neuroinformatics, 2008. 2: p. 3. 3. Ali, A.A., et al., Neuroimage, 2005. 27(2): p. 425-35. 4. Badea, A., et al., NeuroImage, 2007. 37(3): p. 683-693.

这个子项目是许多利用资源的研究子项目之一 由NIH/NCRR资助的中心拨款提供。子项目的主要支持 而子项目的主要调查员可能是由其他来源提供的， 包括其它NIH来源。 列出的子项目总成本可能 代表子项目使用的中心基础设施的估计数量， NCRR赠款不直接向子项目或子项目工作人员提供资金。 Waxholm空间（英语：Waxholm space，缩写WHS）是2008年9月在瑞典Waxholm召开的神经信息学协调机构（英语：Neuroinformatics Coordinating Facility，缩写INCF）顾问委员会第一次会议上提出的一个概念。Waxholm空间将提供一个小鼠大脑空间坐标系，该坐标系将作为研究团体获得的实验结果空间标准化的参考目标。 广泛的实用性将实现合并的一套全面的体积图像集上获得的每七只小鼠。这些将包括以下内容：1）迄今为止达到的最高空间分辨率的3D MR显微镜图像（21.5 <$m）采用三种不同的成像协议采集，以突出最大范围的组织对比度和形态结构[1]; 2）5 <$m x 5 <$m x 20 <$m的容积Nissl图像m在同一个大脑上，以最小的失真和高保真度重建[2]，并与MR数据配准; 3）在MR数据上的完整标本中导出的33个标记的集合，并转移到重建的Nissl体积[3，4]。这些数据将为研究人员提供三种输入WHS的方法：1）将3D体积MR图像配准到目标MR参考中; 2）将常规组织学配准到目标Nissl中; 3）将标签配准到目标标签中。 具体目标： 我们在这里提出了建立WHS所需的几个关键里程碑： 一期工程于2009年2月1日完工，我们将： --获取成年雄性C57 BL/6小鼠的规范数据集; MR数据，T1、T2和T2* 加权为21.5 μ m; B）相同标本上5 μ m x 5 μ m x 20 μ m的Nissl切片。 --配准MR和Nissl体积，并将其与INCF小组成员一致定义的标准化方向对齐。 --提供并验证至少33个解剖结构的标签，并根据可接受的标准验证这些结构的本体。 - 将规范数据集和定义WHS的文档放在至少一个可公开访问的网站上，并提供适当的搜索，成像，分析和评论工具-所有这些都将免费提供给神经科学界。 --确定未来获取数据的方向和最佳做法，以促进映射到WHS。 二期 完成2009年8月1日，我们将： --通过添加6个具有相同采集参数的额外数据集，即3个MR数据集、完整的体积Nissl数据和标签，扩展规范数据集。 --注册所有数据以提供概率图谱 --将所有数据都放在可自由访问的服务器上。 第三阶段，我们将： --从艾伦脑图谱开始，将至少三个其他来源的代表性图谱注册到WHS --建立MR、Nissl和标签注册所需的工具和管道，并验证其使用。 引用 1. 约翰逊，GA，例如，NeuroImage，2007. 37（1）：第82-89页。 2. 贝特朗湖和J. Nissanov，Front Neuroinformatics，2008。[2]第3页。 3.阿里，助理检察官例如，神经影像，2005年。27（2）：第425- 435页。 4. Badea，A.，例如，NeuroImage，2007. 37（3）：第683-693页。