Alignment of spatial transcriptomics data using diffeomorphic metric mapping.
Alignment of spatial transcriptomics data using diffeomorphic metric mapping.
复制标题
使用微分同态度量映射对空间转录组数据进行比对。
DOI：
10.1101/2023.04.11.534630
复制
发表时间：
2023
期刊：
影响因子：
--
通讯作者：
Fan,Jean
中科院分区：
文献类型：
--
作者：
Clifton,Kalen;Anant,Manjari;Aihara,Gohta;Atta,Lyla;Aimiuwu,OsagieK;Kebschull,JustusM;Miller,MichaelI;Tward,Daniel;Fan,Jean
空间转录组学（ST）技术使得能够在薄组织切片内进行高通量基因表达表征。然而，跨部门、样本和技术比较空间观测仍然具有挑战性。为了应对这一挑战，我们开发了STalign，以使用双态度量映射的方式对齐ST数据集，该方式考虑了部分匹配的组织切片和其他局部非线性失真。我们应用STalign在技术内部和跨技术对齐ST数据集，并将ST数据集与3D通用坐标框架对齐。我们表明，STalign在匹配的空间位置上实现了高基因表达和细胞类型对应，这比基于地标的仿射比对有了显着改善。应用STalign将小鼠大脑的ST数据集与艾伦脑图谱的3D通用坐标框架对齐，我们强调了STalign如何用于提升大脑区域注释，并能够询问解剖结构的组成异质性。STalign作为开源Python工具包可在https://github.com/JEFworks-Lab/STalign上获得，作为补充软件，可在https://jef.works/STalign上获得附加文档和教程。
Spatial transcriptomics (ST) technologies enable high throughput gene expression characterization within thin tissue sections. However, comparing spatial observations across sections, samples, and technologies remains challenging. To address this challenge, we developed STalign to align ST datasets in a manner that accounts for partially matched tissue sections and other local non-linear distortions using diffeomorphic metric mapping. We apply STalign to align ST datasets within and across technologies as well as to align ST datasets to a 3D common coordinate framework. We show that STalign achieves high gene expression and cell-type correspondence across matched spatial locations that is significantly improved over landmark-based affine alignments. Applying STalign to align ST datasets of the mouse brain to the 3D common coordinate framework from the Allen Brain Atlas, we highlight how STalign can be used to lift over brain region annotations and enable the interrogation of compositional heterogeneity across anatomical structures. STalign is available as an open-source Python toolkit at https://github.com/JEFworks-Lab/STalign and as supplementary software with additional documentation and tutorials available at https://jef.works/STalign.