spatial-scribe

Drive SpatialScribe - a spatial-transcriptomics cell-type annotation copilot - end-to-end on your own imaging-based spatial data, compute, and Anthropic key. Use when annotating a Xenium, CosMx, MERSCOPE, Atera, or .h5ad section; running the panel-adequacy check ("which cell types can my panel resolve?"), the QC funnel, or a reference match; deciding supervised annotation vs unsupervised clustering from the reference-to-panel match; clustering and consensus cell-type annotation with per-cell confidence and abstention; malignant/tumour calling, spatial niches, neighborhood enrichment, or gene programs; self-verifying an annotation; or exporting an annotated .h5ad + a self-contained HTML report + a re-runnable script. Also use to launch the SpatialScribe web app or to drive its grounded Claude copilot in plain language. Triggers on "SpatialScribe", "annotate my Xenium/CosMx section", "panel check", "spatial annotation QC", "reference match", "should I cluster or annotate", "run_copilot".