“ a common goal in ST analysis is to connect and integrate information from both gene expression and cellular or transcript locations “

Spatial transcriptomic technologies

  • 从原理分
    • imaging-based spatial transcriptomics technologies
      • FISH
      • ISS
    • sequencing-based spatial transcriptomics technologies

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  • 从分辨率分
    • Spots
    • Single-cell
    • Subcellular

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Identification of cell types from ST data

Cell type identification and localization is probably the most basic task for ST data analysis.

  • unsupervised clustering combined with manual or automatic annotation is a common approach to identify cell types in an unbiased manner

Characterizing spatial patterns of transcriptomic profiles

Subcellular structure analysis

Understanding how cells communicate with the tissue environment

整体思路

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image-20231107171210919

基于图像的分析，如细胞分割和形态定量，可用于研究组织选定部分中的细胞复杂性。

基于基因表达的分析包括几种方法，如聚类，空间网络构建和细胞类型富集，以可视化基因表达模式。

  • 降维聚类
  • 表达差异分析
  • 结合功能分析

RF

10x Visium空间转录组分析思路_哔哩哔哩_bilibili

2022最新空间转录组（spatial transcriptomics）数据分析指南_哔哩哔哩_bilibili