| --- |
| license: mit |
| pretty_name: TCGA-mini |
| size_categories: |
| - 1K<n<10K |
| tags: |
| - pathology |
| - whole-slide-imaging |
| - tcga |
| - medical-imaging |
| --- |
| |
| # TCGA-mini |
|
|
| `TCGA-mini` is a curated whole-slide imaging (WSI) dataset composed of TCGA `.svs` pathology slides. |
|
|
| - Number of slides: `1319` (`.svs`) |
| - Location in repo: `slides/` |
| - Storage footprint on the Hub: about `1.42 TiB` (`1450.94 GiB`, Git LFS-backed) |
|
|
| ## Dataset structure |
|
|
| ```text |
| TCGA-mini/ |
| ├── README.md |
| └── slides/ |
| ├── TCGA-xxxx-xxxx-xxZ-00-DX1.svs |
| └── ... |
| ``` |
|
|
| ## Data format |
|
|
| - File type: Aperio whole-slide image files (`.svs`) |
| - Naming: Original TCGA-style slide identifiers are preserved |
| - Labels/annotations: Not included in this repo |
|
|
| ## Download |
|
|
| Download all slides: |
|
|
| ```bash |
| hf download W8Yi/TCGA-mini \ |
| --repo-type dataset \ |
| --include "slides/*.svs" \ |
| --local-dir ./TCGA-mini |
| ``` |
|
|
| Download a single slide: |
|
|
| ```bash |
| hf download W8Yi/TCGA-mini \ |
| --repo-type dataset \ |
| --include "slides/TCGA-06-0743-01Z-00-DX1.svs" \ |
| --local-dir ./TCGA-mini |
| ``` |
|
|
| ## Quick usage example (OpenSlide) |
|
|
| ```python |
| from openslide import OpenSlide |
| |
| slide = OpenSlide("TCGA-mini/slides/TCGA-06-0743-01Z-00-DX1.svs") |
| print("levels:", slide.level_count) |
| print("dimensions:", slide.dimensions) |
| ``` |
|
|
| ## Intended use |
|
|
| This dataset is intended for research and educational use in computational pathology and WSI pipelines. |
| It is not intended for clinical diagnosis or direct patient care. |
|
|
| ## Source and attribution |
|
|
| Slides originate from The Cancer Genome Atlas (TCGA) program. |
| Users are responsible for complying with all applicable TCGA/GDC data-use and publication policies. |
|
|
| ## Limitations |
|
|
| - No train/val/test split is provided |
| - No labels or clinical tables are included in this repo |
| - Whole-slide files are very large and require substantial storage and I/O throughput |
|
|
| ## Citation |
|
|
| If you use this dataset, please cite: |
|
|
| 1. This Hugging Face dataset repository: `W8Yi/TCGA-mini` |
| 2. The TCGA program and relevant data source publications |
|
|
