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README.md
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---
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license: cc-by-4.0
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task_categories:
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- feature-extraction
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- data-mining
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tags:
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- spatial-transcriptomics
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- single-cell
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- h5ad
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- human
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- multi-organ
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- multi-platform
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- MERFISH
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- VisiumHD
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- Xenium
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- 10X-Visium
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- Slide-seqV2
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pretty_name: Human Spatial Transcriptomics Multi-organ Multi-platform Collection
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size_categories:
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- 100M<n<1B
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---
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# Human Spatial Transcriptomics Multi-organ Multi-platform Collection
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This dataset provides a cleaned human spatial transcriptomics collection in `.h5ad` format. The released archive, `Homo_sapiens_h5ad_flat.zip`, contains **1,155 `.h5ad` files** gathered into a flat archive for convenient download and reuse.
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## Dataset Summary
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The collection covers **Homo sapiens** spatial transcriptomics data across multiple organs and experimental platforms. According to the accompanying internal statistics report, the human subset contains **28,050,110 spatial spots** across **1,216 files/slices** in the source statistics. The uploaded archive contains the cleaned `.h5ad` subset as **1,155 files**.
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## Platforms
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| Platform | Spots | Percentage | Files |
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|---|---:|---:|---:|
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| MERFISH | 10,334,462 | 36.84% | 19 |
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| VisiumHD | 8,686,473 | 30.97% | 15 |
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| Xenium | 4,704,330 | 16.77% | 18 |
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| 10X Visium | 3,610,266 | 12.87% | 1,129 |
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| Slide-seqV2 | 714,579 | 2.55% | 35 |
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## Organ Coverage
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The dataset spans a broad set of human tissues and anatomical categories, including unknown/unannotated samples, uterus, colon, lung, liver, prostate, tonsil, ovary, skin, breast, pancreas, heart, lymph node, kidney, brain, thymus, bone marrow, spinal cord, gland, embryo, intestine, placenta, oral mucosa, spleen, blood vessels, head and neck, cervix, stomach, tumor, synovial tissue, muscle, and bladder.
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Top organ categories by spots include:
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| Organ | Spots | Percentage | Files |
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|---|---:|---:|---:|
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| Unknown | 8,733,674 | 31.14% | 30 |
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| Uterus | 2,370,993 | 8.45% | 15 |
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| Colon | 2,307,710 | 8.23% | 45 |
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| Lung | 2,281,167 | 8.13% | 106 |
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| Liver | 1,825,259 | 6.51% | 87 |
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| Prostate | 1,780,803 | 6.35% | 34 |
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| Tonsil | 1,376,446 | 4.91% | 2 |
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| Ovary | 1,216,193 | 4.34% | 43 |
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| Skin | 1,172,313 | 4.18% | 166 |
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| Breast | 979,761 | 3.49% | 68 |
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## Files
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- `Homo_sapiens_h5ad_flat.zip`: flat zip archive containing 1,155 cleaned human `.h5ad` files.
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## Notes
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The uploaded archive includes only the cleaned dataset files. Summary statistics were used to describe the dataset card but are not uploaded as separate files.
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