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ANTsX生态系统用于绘制小鼠大脑的地图.

Nicholas J Tustison1, Min Chen2, Fae N Kronman3

  • 1Department of Radiology and Medical Imaging, University of Virginia, Charlottesville, VA, USA. ntustison@virginia.edu.

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概括

研究人员使用ANTsX开发了开源的小鼠大脑映射管道,以整合各种数据集,包括空间转录学和形态学,进入用于创建细胞地图的共同坐标框架.

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科学领域:

  • 神经科学是一个神经科学.
  • 生物信息学是一种生物信息学.
  • 计算生物学 计算生物学

背景情况:

  • 大脑倡议细胞普查网络 (BICCN) 旨在创建一个全面的小鼠大脑细胞地图.
  • 从各种方法 (成像,组织处理,分析) 整合到共享的坐标框架中的各种数据集是一个重大挑战.

研究的目的:

  • 通过使用高级规范化工具生态系统 (ANTsX) 呈现新的小鼠大脑映射管道.
  • 为了使各种神经生物学数据集与共同的协调框架保持一致.
  • 引入新的计算方法,用于发育轨迹插值和自动大脑分片.

主要方法:

  • 使用ANTsX将MERFISH空间转录组学和fMOST形态数据与艾伦共同坐标框架 (CCFv3) 对齐.
  • 将发育性MRI和LSFM数据与发育性CCF (DevCCF) 保持一致.
  • 开发了一种基于速度场的方法,用于跨发育时间点的连续插值.
  • 创建了一个深度学习框架,用于使用最小注释数据进行自动化大脑分片.

主要成果:

  • 成功地将MERFISH和fMOST数据映射到CCFv3,并将发育性MRI/LSFM数据映射到DevCCF.
  • 引入并验证了用于发育间位和自动分片的新计算方法.
  • 所有开发的工作流都是开源的,可重复的.

结论:

  • 提出的管道和方法促进了多模式大脑数据的整合.
  • 这些工具支持创建一本关于小鼠大脑细胞类型的综合参考地图.
  • 为适应这些战略以适应新的数据集和模式提供了指导.