| --- |
| pretty_name: ST-aggregate |
| license: other |
| tags: |
| - spatial-transcriptomics |
| - single-cell |
| - transcriptomics |
| - biology |
| - tabular |
| configs: |
| - config_name: datasets |
| data_files: data/datasets.parquet |
| default: true |
| - config_name: open_matrix_candidates |
| data_files: data/open_matrix_candidates.parquet |
| - config_name: dataset_sources |
| data_files: data/dataset_sources.parquet |
| - config_name: sources |
| data_files: data/sources.parquet |
| - config_name: rights_statements |
| data_files: data/rights_statements.parquet |
| - config_name: source_rights |
| data_files: data/source_rights.parquet |
| - config_name: gene_axis |
| data_files: data/gene_axis.parquet |
| - config_name: distribution_summary |
| data_files: data/distribution_summary.parquet |
| --- |
| |
| # ST-aggregate |
|
|
| ST-aggregate is a rights-aware catalog of human single-cell spatial |
| transcriptomics studies. The public analysis table contains 300 source-backed |
| human datasets representing 200,860,787 cells across CosMx, Xenium, MERFISH, |
| Visium, and related platforms. |
|
|
| > **Important:** this v2 repository is a manually gated federated catalog and |
| > rebuild index. |
| > It does **not** host expression matrices, per-cell metadata, coordinates, or |
| > images. Obtain those objects from the recorded original sources under their |
| > respective terms. |
|
|
| ## Public views |
|
|
| | View | Datasets | Represented cells | |
| |---|---:|---:| |
| | `datasets` | 300 | 200,860,787 | |
| | Human assay-aware primary | 299 | 200,361,575 | |
|
|
| Retired empty records, reserved enums, and three organism-unresolved quarantine |
| records (IDs 15, 68, and 281) are not included. Dataset 133 (499,212 cells) |
| remains in `datasets` but has `assay_aware_primary_candidate=false` because its |
| official archive does not expose a complete measured-feature axis. |
|
|
| The main table intentionally omits internal lifecycle, release-disposition, |
| row-availability, tombstone/replacement, sparse ontology, model-system, panel, |
| and empty publication-link fields. Detailed provenance and rights remain in |
| normalized relationship tables. |
|
|
| ## What is hosted |
|
|
| - compact dataset-level assay, organism, tissue, disease, and cell-count metadata; |
| - 351 links from the 300 datasets to 295 original repository records; |
| - source URLs, accessions, titles, and organism evidence; |
| - 246 rights statements and a complete 295-row source-to-rights relation; |
| - the exact ordered 10,763-gene feature axis; |
| - CSV mirrors, checksums, schema documentation, and sealed-release provenance. |
|
|
| ## Distribution tiers |
|
|
| | Tier | Datasets | Represented cells | Public v2 behavior | |
| |---|---:|---:|---| |
| | `open_matrix_candidate` | 90 | 57,498,711 | Source pointer only; eligible for a separately reviewed future mirror | |
| | `pointer_rebuild_only` | 204 | 141,456,391 | Source pointer and rights metadata only | |
| | `pointer_rebuild_only_pending_biostudies_object_equivalence` | 6 | 1,905,685 | Pointer only pending equivalence evidence | |
|
|
| `open_matrix_candidate` is an eligibility classification, **not** a claim that |
| the matrix is present here. Every row in `matrix_hosted_on_huggingface` is |
| `false` in this release. Manual Hub approval controls access to the catalog but |
| does not replace the original sources' terms. |
|
|
| ## Load |
|
|
| ```python |
| from datasets import load_dataset |
| |
| datasets = load_dataset("deeeech/ST-aggregate", "datasets", split="train") |
| sources = load_dataset("deeeech/ST-aggregate", "sources", split="train") |
| rights = load_dataset("deeeech/ST-aggregate", "rights_statements", split="train") |
| genes = load_dataset("deeeech/ST-aggregate", "gene_axis", split="train") |
| ``` |
|
|
| Join `datasets` to `dataset_sources` by `dataset_id`, then join to |
| `sources` and `source_rights` by `source_id`. Join `source_rights` to |
| `rights_statements` by `rights_id`. |
|
|
| ## Rights and responsible use |
|
|
| There is no blanket license for the third-party source data. The Hub card uses |
| `license: other` because each source retains its own terms. Public availability |
| is not treated as an open-data license: `NOASSERTION` and GEO repository policy |
| records remain pointer/rebuild-only. Review `docs/RIGHTS.md` and the rights |
| tables before downloading or redistributing upstream data. |
|
|
| ## Publication links and citation |
|
|
| All dataset records link to an original repository source. Scholarly-paper DOI |
| and PMID curation is not yet complete, so empty publication-link columns are |
| not included in v2. Repository accessions such as Zenodo record DOIs must not |
| be mistaken for paper citations. |
|
|
| Until ST-aggregate receives a DOI, cite the exact Hugging Face repository |
| revision and cite every upstream study/source used in an analysis. |
|
|
| ## Integrity |
|
|
| This catalog derives from the immutable canonical-v17 publication candidate. |
| Its root-manifest SHA-256 is |
| `15e25994d6438c38784df785694a84c6b885e7643cfc1e9ccc9cef2f3dcb7797`. |
| The ordered gene-axis semantic SHA-256 is |
| `44d473c84980b905f96349c9d66eeda0db515d34d667f1969d0a0b0cadf087db`. |
|
|
| See `release_manifest.json`, `CHECKSUMS.sha256`, `docs/SCHEMA.md`, |
| `docs/PROVENANCE.md`, and `docs/LIMITATIONS.md` for the complete contract. |
|
|
