| --- |
| license: cc-by-4.0 |
| language: |
| - en |
| pretty_name: SpatialAgent Human Expert Reference Data |
| tags: |
| - biology |
| - spatial-transcriptomics |
| - single-cell |
| - gene-panel-design |
| - cell-type-annotation |
| - benchmark |
| size_categories: |
| - 100K<n<1M |
| configs: |
| - config_name: panel_workflows |
| data_files: panel_design/workflows.csv |
| - config_name: annotation_workflows |
| data_files: annotation/workflows.csv |
| --- |
| |
| # SpatialAgent — Human Expert Reference Data |
|
|
| Anonymized reference data produced by human scientists for two spatial-transcriptomics |
| tasks used to benchmark **SpatialAgent**: |
|
|
| 1. **Gene panel design** — expert-designed targeted gene panels for the human |
| **dorsolateral prefrontal cortex (DLPFC / PFC)**. |
| 2. **Cell-type & tissue-niche annotation** — expert annotations of a **developing human |
| heart** MERFISH dataset (228,633 cells × 238 genes). |
|
|
| All scientist identities are removed. Each task uses its **own independent numbering**, so |
| the same person generally has a *different* id in the two tasks (this is intentional — the |
| two studies were anonymized separately). No real names appear anywhere in this repository. |
| Each expert's methodology is documented (by anonymized id) in the `workflows.csv` files. |
|
|
| ## Repository layout |
|
|
| ``` |
| panel_design/ |
| workflows.csv # id (1–10) -> free-text description of the panel-design approach |
| {1..10}.csv # one full panel per expert (ranked gene lists) |
| split/{id}_top{50,100,150}.csv # top-N subsets of each panel |
| annotation/ |
| workflows.csv # id (1–8) -> cell-type & niche annotation approach |
| combined_annotations_anonymized.h5ad # all experts (anonymized) + model/baseline predictions |
| human_annotations_anonymized.h5ad # human experts only (anonymized), no model columns |
| per_expert_raw/ # the original per-expert annotation files, anonymized |
| expert{1,2,5,6,7}.h5ad |
| expert{3,4}.csv |
| expert7_niche.h5ad |
| ``` |
|
|
| See `panel_design/README.md` and `annotation/README.md` for the column-level details of |
| each subset. |
|
|
| ## Panel design (DLPFC) |
|
|
| 10 experts each submitted a ranked panel (typically top 50 / 100 / 150 genes) with a short |
| rationale per gene. Formats are heterogeneous (experts used different tools), so columns |
| differ between files; the common fields are a gene symbol, a ranking/priority, and a |
| free-text reasoning column. `split/` holds the top-50/100/150 truncations used for |
| size-matched evaluation. Workflows range from purely algorithmic (Persist, greedy kNN |
| reconstruction) to literature-driven marker curation — see `panel_design/workflows.csv`. |
|
|
| ## Annotation (developing human heart, MERFISH) |
|
|
| 8 experts annotated the same 228,633 cells. The two combined `.h5ad` objects share an |
| identical cell index and embeddings: |
|
|
| - `X` — log1p-normalized expression (238 genes); `layers['raw_count']` — raw counts. |
| - `obsm` — `X_pca`, `X_umap`, `spatial` (tissue coordinates). |
| - Per-expert columns: `cell_type_tier{1,2,3}_expert{N}`, `tissue_niche_tier{1,2}_expert{N}`, |
| and consolidated `cell_type_expert{N}` / `tissue_niche_expert{N}`. |
| - Consensus reference labels: `cell_type`, `tissue_niche`. |
|
|
| `combined_annotations_anonymized.h5ad` additionally contains model / baseline predictions |
| (`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`) for direct |
| benchmarking; `human_annotations_anonymized.h5ad` is the human-only subset (those columns |
| dropped). `per_expert_raw/` preserves each expert's original file (with their native, |
| heterogeneous column schema) for full transparency. |
|
|
| ### Caveats |
| - **annotation expert 1** did not produce tissue-niche labels (niche fields are empty/NA). |
| - **annotation expert 3**'s labels are of uncertain origin and are likely mis-ordered — use with care. |
| - **annotation expert 8** has no standalone raw file; their annotations exist only inside the combined objects. |
| - **panel expert 3** submitted a previously designed panel for the wrong tissue. |
|
|
| ## License & citation |
|
|
| Released under **CC-BY-4.0** (adjust if your venue requires otherwise). If you use this |
| data, please cite the SpatialAgent paper. The two `workflows.csv` files correspond to the |
| Extended Data tables describing human-scientist workflows. |
|
|
