domains / families / science / spatial-pipeline

spatial-pipeline

separate

Orchestrates the end-to-end spatial transcriptomics pipeline from Space Ranger / vendor output to spatial domains and statistics, branching FIRST on platform class (imaging in-situ Xenium/MERFISH/CosMx vs sequencing/capture Visium/Visium HD/Slide-seq). Use when deciding segmentation-vs-deconvolution and the QC floors from the platform class, committing the coordinate/image-registration frame and panel identity, deconvolving multi-cell spots against an annotated scRNA reference (never relabeling spot clusters as cell types), building the spatial neighbor graph on PHYSICAL not expression space, gating spatially-variable genes on FDR, or using a real domain method (BANKSY/BayesSpace/STAGATE) rather than clustering the spatial graph alone. Hands off deconvolution and cell-cell communication to the component skills; not a re-teach of any single step.

When to use

• deciding segmentation-vs-deconvolution
• setting QC floors from platform class
• committing coordinate/image-registration frame
• deconvolving multi-cell spots against scRNA reference
• building spatial neighbor graph on physical space
• gating spatially-variable genes on FDR
• using real domain methods like BANKSY or BayesSpace

When not to use

• re-teaching any single step
• inlining deconvolution
• inlining cell-cell communication

Skill page

Source