saha-2026-pub — reproducible code for the SAHA flagship atlas paper

Analysis code for "SAHA: a multimodal subcellular spatial atlas of human anatomy." A frozen, citable snapshot that reproduces the figures of this paper. Organized by figure.

• fig3_germinal_center/ — Fig 3 + Extended Data Fig 4
  • niches_isotype/ (Across-GI): UTAG niches, Ig-isotype maps, pure-IgG fraction, plasma-lineage egress (Fig 3a-f)
  • gc_crossorgan/ (Cross-organ): LN-GC vs GALT-APE-GC — GC detection, DZ/LZ, radial, DE (Fig 3g-l, ED Fig 4)
• fig5_ibd/ — Fig 5 (IBD niche topology)
  • integration/, niche_topology/, build_inputs/

Relationship to other SAHA repos

• SAHA — the org's general/evergreen landing repo (kept separate; not this paper).
• saha-scimap, saha-maxfuse, CONCH pipeline — component/method repos owned by collaborators; they cover Fig 2 (CONCH histology) and Fig 4 (RNA–protein / MaxFuse, scimap).
• saha-data-access — portal / programmatic access.

Data

Large objects (h5ad / rds / zarr) are on Zenodo — not in this repo. Per-figure-panel Source Data tables accompany the manuscript (Nature Source Data requirement), staged separately, not committed here.

Fig 1 (atlas integration) is produced elsewhere; Fig 2 and Fig 4 are the collaborator repos above.