Code, weights,
and walkthroughs.
News, preprints, checkpoint downloads, datasets, and a workflow-by-workflow documentation set.
01 · News & releases
News
2026 · 05 · 04
v0.4 ships Stage 2 v5_final and 11-tissue Visium HD index.
NMI 0.71 vs pathologist niche labels. New
best_phase2.pt on the lab page.
release
Read →
2026 · 04 · 22
Multimodal alignment improves zero-shot annotation in Visium HD.
Benchmarks vs scGPT and Geneformer across four tissue types.
preprint
Open ↗
2026 · 05 · 12
External Miyabi quota opens for community reproducibility.
Small allocation for re-running Stage 1.5 and Stage 2 on user splits.
event
Request →
2026 · 03 · 14
v0.3 — Stage 1.5 CPT v3.2-lite bridges scRNA-seq vs Visium HD.
Closes the cross-platform distribution gap measured on the held-out tonsil + breast pair.
release
Read →
02 · Checkpoints & data
Downloads
196 MB
best_model_stage1_5.pt
Stage 1.5 CPT-bridged checkpoint · recommended for scRNA-seq inference.
checkpoint
Get →
214 MB
best_phase2.pt
Stage 2 v5_final · spatial niche + composition + H&E.
checkpoint
Get →
2.1 KB
cell_type_code_mapping.json
786 cell-type vocab used by the annotation head.
json
Get →
17 MB
gene_config_1200.json
Fixed 1200-HVG list. Optional — only needed for fixed gene_mode.
json
Get →
03 · Workflow documentation
Walkthroughs
01 · AnnotatescRNA-seq → e_cell
Cell-type annotation
.h5ad · counts → e_cell (512d) · top-k labels
02 · NicheVisium HD → e_niche
Spatial-niche analysis
spaceranger · H&E → e_niche · neighbour composition
03 · Retrievetext ↔ gene
Cross-modal retrieval
phrase ↔ e_cell · cosine R@k
04 · Describeexpression → text
Cell description generation
single cell → description ≤ 256 tok
04 · Code & citation