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README.md

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+---
+license: other
+tags:
+- single-cell
+- rna-seq
+- scRNA-seq
+- h5ad
+- anndata
+- genomics
+- benchmark
+- shape-analysis
+size_categories:
+- 1M<n<10M
+task_categories:
+- tabular-classification
+- tabular-regression
+pretty_name: scShapeBench
+---
+
+# scShapeBench
+
+A benchmark dataset for single-cell shape analysis, containing **2,547,517 cells** across **105 real-world single-cell RNA-seq datasets** in AnnData (`.h5ad`) format.
+
+## Dataset Summary
+
+scShapeBench is a curated collection of real-world single-cell gene expression datasets assembled for benchmarking computational methods in single-cell shape analysis. Each dataset is stored as an individual AnnData file with precomputed PCA embeddings and Leiden clustering.
+
+- **Total cells:** 2,547,517
+- **Total datasets:** 105
+- **Total size:** ~116 GB
+- **Format:** AnnData (.h5ad)
+- **Data type:** Real-world (synthetic data to be added in a future release)
+
+## Dataset Structure
+
+```
+scShapeBench/
+├── data/
+│   ├── SCD-0001.h5ad
+│   ├── SCD-0002.h5ad
+│   ├── ...
+│   └── SCD-0112.h5ad
+├── cell_metadata.csv    # Combined cell-level metadata (2.5M rows)
+├── gene_metadata.csv    # Combined gene-level metadata
+├── dataset_index.csv    # Per-file summary: dimensions, size
+├── croissant.json       # Croissant 1.1 metadata
+└── README.md
+```
+
+### File Naming
+
+Files are named `SCD-XXXX.h5ad` where XXXX is a zero-padded index. The numbering is not contiguous (e.g., SCD-0031, SCD-0032, SCD-0034–0036 are absent).
+
+### Per-File Contents
+
+Each `.h5ad` file contains:
+
+| Component | Description |
+|-----------|-------------|
+| `X` | Gene expression matrix (cells × genes), log-normalized |
+| `obs` | Cell metadata: `n_genes`, `leiden` (cluster assignment) |
+| `var` | Gene metadata: `gene_ids`, `feature_types`, `genome`, `n_cells`, `highly_variable`, etc. |
+| `obsm['X_pca']` | Precomputed PCA embeddings |
+| `uns` | Clustering and HVG parameters |
+
+### Dataset Index
+
+The `dataset_index.csv` file provides per-file summary statistics:
+
+| Column | Description |
+|--------|-------------|
+| `file_id` | Dataset identifier (e.g., SCD-0001) |
+| `filename` | Filename |
+| `n_cells` | Number of cells |
+| `n_genes` | Number of genes |
+| `file_size_bytes` | File size in bytes |
+
+Dataset sizes range from 1,163 cells (SCD-0006) to 434,340 cells (SCD-0037).
+
+## Usage
+
+```python
+import scanpy as sc
+import pandas as pd
+
+# Load a single dataset
+adata = sc.read_h5ad("data/SCD-0001.h5ad")
+print(adata)
+
+# Browse available datasets
+index = pd.read_csv("dataset_index.csv")
+print(index.sort_values("n_cells", ascending=False).head())
+
+# Load cell metadata across all datasets
+cell_meta = pd.read_csv("cell_metadata.csv")
+print(cell_meta.groupby("file_id").size())
+```
+
+## Croissant Metadata
+
+This dataset includes a `croissant.json` file conforming to the [Croissant 1.1](https://docs.mlcommons.org/croissant/) metadata standard. This enables programmatic discovery and loading of dataset metadata through compatible tools.
+
+## Citation
+
+<!-- Add citation information here when available -->
+
+## License
+
+License to be determined.