WAXHOLM SPACE - MOUSE BRAIN SPATIAL COORDINATE SYSTEM

WAXHOLM SPACE - 小鼠大脑空间坐标系统

• 批准号: 7956935
• 负责人: George ALLAN JOHNSON
• 金额: $ 1.64万
• 依托单位: DUKE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-07-01 至 2010-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7956935
• 关键词: Adult; Atlases; Brain; C57BL/6 Mouse; Collection; Communities; Computer Retrieval of Information on Scientific Projects Database; Consensus; Data; Data Set; Documentation; Funding; Future; Grant; Histology; Image; Image Analysis; Institution; Label; Magnetic Resonance Imaging; Maps; Methods; Microscopy; Mus; Neurosciences; Ontology; Phase; Protocols documentation; Published Comment; Research; Research Personnel; Resolution; Resources; Source; Specimen; Structure; Sweden; System; Tissues; United States National Institutes of Health; Weight; 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. 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. 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.

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 瓦克斯霍尔姆空间(WHS)是2008年9月在瑞典瓦克斯霍尔姆举行的神经信息学协调设施(INCF)顾问委员会第一次会议上提出的一个概念结构。瓦克斯霍尔姆空间将提供一个小鼠大脑空间坐标系，作为研究界获得的实验结果空间标准化的参考目标。通过纳入在七只小鼠身上分别获得的一套全面的体积图像集，将实现广泛的实用。这些图像将包括：1)用三种不同成像协议获得的最高空间分辨率(21.5？m)的3D MR显微镜图像，以突出最广泛的组织对比度和形态结构[1]；2)同一大脑上5？m x 5？m x 20？m的体积Nissl图像，以最小的失真和高保真重建并注册到MR数据；3)从完整的MR标本中获得的33个标记的集合，并将其传输到重建的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)将传统组织学配准到目标Nissl中；3)将标签配准到目标标签中。 具体目标： 我们在此提出建立WHS所需的几个关键里程碑： 第一阶段完成2009年2月1日，我们将： --获取成年雄性C57BL/6小鼠的标准数据集；T1、T2和T2*权重为21.5？m的MR数据；b)同一标本上的Nissl切片：5？m x 5？m x 20？m。 -登记MR和Nissl卷，并按照INCF小组成员将以协商一致方式定义的标准化方向共同调整这些卷。 --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的文件放在至少一个公开可访问的网站上，并使用适当的搜索、成像、分析和评论工具--所有这些都将向神经科学界免费提供。 --确定获取未来数据的方向和最佳做法，以便于绘制成世界卫生组织的地图。 第二阶段完成2009年8月1日，我们将： --通过添加另外6个具有相同采集参数的数据集来扩展规范数据集，即3个MR数据集、完整的体积尼氏数据和标签。 --登记所有数据，以提供概率图谱 --在可自由访问的服务器上捆绑所有数据。 第三阶段，我们会： --将至少三个其他来源的代表性地图集登记到WHS，最初从艾伦脑地图集开始 --建立注册MR、NISSL和标签所需的工具和管道，并验证其使用。 参考文献 1.约翰逊，G.A.等人，《神经影像》，2007年。37(1)：第82-89页。 2.Bertrand，L.和J.Nissanov，前沿神经信息学，2008。2：第3页。 3.阿里，A.A.等人，《神经影像》，2005年。27(2)：第425-35页。 4.Badea，A.等人，《神经影像》，2007年。37(3)：第683-693页。