Datasets:

hansen7
/

spatialagent_human

8 human scientists annotated the same developing-human-heart MERFISH dataset (228,633 cells × 238 genes). Identities are removed; experts are numbered 1–8 (this numbering is independent of the panel-design task). Per-expert methodology is in workflows.csv.

Files

File	Contents
`workflows.csv`	`id, cell_type_workflow, niche_workflow` — each expert's approach
`combined_annotations_anonymized.h5ad`	All 8 experts (anonymized) + model/baseline predictions
`human_annotations_anonymized.h5ad`	Human experts only (model/baseline columns dropped)
`per_expert_raw/expert{N}.h5ad` / `.csv`	Each expert's original file, anonymized (native schema)
`per_expert_raw/expert7_niche.h5ad`	Expert 7's tissue-niche annotation (separate source file)

Combined object structure

Both combined .h5ad files share one cell index and embeddings:

X — log1p-normalized expression (238 genes)
layers['raw_count'] — raw counts
obsm — X_pca, X_umap, spatial

Per-expert annotation columns (N = 1..8):

cell_type_tier1_expert{N}        cell_type_tier2_expert{N}     [cell_type_tier3_expert{N}]
tissue_niche_tier1_expert{N}     tissue_niche_tier2_expert{N}
cell_type_expert{N}              tissue_niche_expert{N}        # consolidated single-label

Tier 3 is present only for experts who provided it (cell type: experts 2, 6, 7; niche: expert 7). Expert 6 additionally has cell_type_main_expert6.

Reference / shared columns: cell_type, tissue_niche (consensus labels), plus technical fields (sample_id, batch, n_counts, leiden, and cluster features).

Model/baseline columns (only in combined_annotations_anonymized.h5ad): cell_type_agent, tissue_niche_agent, cell_type_gpt, cell_type_sctab, cell_type_popv, cell_type_biomni_run_{1,2,3}, cell_type_spatialagent_run_4.

Loading

import anndata as ad
adata = ad.read_h5ad("annotation/combined_annotations_anonymized.h5ad")
adata.obs["cell_type_tier1_expert5"]          # one expert's tier-1 cell types
adata.layers["raw_count"]                      # raw counts

Caveats

Expert 1 did not perform tissue-niche annotation (niche fields are empty/NA).
Expert 3's labels are of uncertain origin and likely mis-ordered — use with care.
Expert 8 has no standalone raw file; their annotations live only in the combined objects.
per_expert_raw/ files keep each expert's native, heterogeneous column names (only the filename was anonymized; no scientist name appears in any column or value).