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Spatial Report Generation (Visium)
Assemble an auditable final spatial transcriptomics report from upstream OmniObjects (DB-free).
Generate Final Report
Report Title
Clustered AnnData (required)
-- select spatial_anndata_clustered --
Markers Table (required)
-- select spatial_markers_table --
Marker Summary (required)
-- select spatial_marker_summary --
Approved Thresholds (required)
-- select spatial_qc_thresholds_approved --
Optional inputs
QC Plots Summary / Bundle
(none)
Spatial Analysis Summary
(none)
Workflow Runner output.json
(none)
Top markers per cluster
Include QC section (if QC object provided)
Include spatial analysis section (if analysis object provided)
Include provenance (object IDs)
Generate Report
Produces
report/report.md
and
report/report.json
plus OmniObject outputs.