Abstract from repository: "Transcriptional and epigenetic profiling of single-cells has advanced our knowledge of the molecular bases of gastrulation and early organogenesis. However, current approaches rely on dissociating cells from tissues, thereby losing the crucial spatial context that is necessary for understanding cell and tissue interactions during development. Here, we apply an image-based...

Description from GitHub: "Data processing and analysis scripts for our spatial profiling of mouse embryos using seqFISH as described in 'Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis'."