| --- |
| pretty_name: STP-Bench |
|
|
| language: |
| - en |
|
|
| license: cc-by-nc-sa-4.0 |
|
|
| tags: |
| - pathology |
| - histopathology |
| - spatial-transcriptomics |
| - virtual-spatial-transcriptomics |
| - spatial-gene-expression-prediction |
| - whole-slide-image |
| - computational-pathology |
| - gene-expression |
| - regression |
| - benchmark |
| - visium |
| - xenium |
|
|
| size_categories: |
| - 100K<n<1M |
| --- |
| |
| # STP-Bench |
|
|
| <p align="center"> |
| <img src="STP-BENCH-dataoverview.jpg" width="100%"> |
| </p> |
|
|
| **STP-Bench** is a comprehensive benchmark dataset for evaluating deep learning models on **spatial transcriptomics prediction from histopathology whole-slide images (WSIs)**. |
|
|
| The dataset accompanies the paper introducing **STP-Bench**, a unified benchmark designed to standardize evaluation across multiple spatial transcriptomics technologies, tissue types, and experimental protocols. |
|
|
| Unlike previous studies that evaluate on a single cohort or technology, STP-Bench aggregates diverse publicly available spatial transcriptomics datasets into a unified benchmark, providing standardized data organization and evaluation protocols for robust and reproducible benchmarking. |
|
|
| --- |
|
|
| ## 📊 Dataset Statistics |
|
|
| STP-Bench consists of two benchmark settings: |
|
|
| - **STP-Bench Internal**: used for model development and benchmark evaluation. |
| - **STP-Bench External**: used to assess model generalization on independent cohorts. |
|
|
| The complete benchmark composition reported in the accompanying paper is summarized below. |
|
|
| | Benchmark | Dataset | Source | Cancer Type | Platform | Slides | Patients | ST Spots | |
| |-----------|---------|--------|-------------|----------|-------:|---------:|---------:| |
| | **Internal** | HEST-PRAD | HEST-1K | PRAD | Visium | 23 | 23 | 62,710 | |
| | | WUSTL-BRCA | WUSTL | IDC | Visium | 47 | 21 | 157,138 | |
| | | NCCHE-Xenium | NCCHE | LUAD | Xenium | 16 | 16 | 34,519 | |
| | | NCCHE-Visium | NCCHE | LUAD | Visium | 43 | 43 | 96,954 | |
| | | HEST-CCRCC | HEST-1K | RCC | Visium | 24 | 24 | 74,220 | |
| | | SMC-GBM | SNU | GBM | Visium | 30 | 17 | 117,036 | |
| | | WUSTL-PDAC | WUSTL | PAAD | Visium | 19 | 14 | 66,447 | |
| | **External** |🔒 MGB-PRAD | MGB | PRAD | Visium | 8 | 8 | 31,438 | |
| | | HEST-IDC | HEST-1K | IDC | Xenium | 4 | 4 | 35,536 | |
| | | Massey-TNBC | Massey | IDC | Visium | 43 | 22 | 55,227 | |
| | | HEST-LUNG | HEST-1K | LUAD | Xenium | 2 | 2 | 5,206 | |
| | | WUSTL-RCC | WUSTL | RCC | Visium | 10 | 10 | 33,090 | |
| | | HEST-GBM | HEST-1K | GBM | Visium | 3 | 3 | 17,763 | |
| | | HEST-PAAD | HEST-1K | PAAD | Xenium | 3 | 3 | 7,571 | |
|
|
| **Internal cohort:** 202 slides, 158 patients, and 609,024 spatial transcriptomics spots. |
|
|
| **External cohort:** 73 slides, 52 patients, and 185,831 spatial transcriptomics spots. |
|
|
| > **🔒 MGB-PRAD is not included in this public Hugging Face release due to institutional data-sharing restrictions.** The accompanying paper reports results on this in-house external cohort for additional generalization evaluation. |
|
|
| --- |
|
|
| ## 📁 Dataset Structure |
|
|
| ``` |
| STP-Bench/ |
| |
| ├── metadata/ |
| │ ├── dataset_metadata.json |
| │ ├── ... |
| │ |
| ├── wsis/ |
| │ ├── slide_001.tif |
| │ ├── ... |
| │ |
| ├── patches/ |
| │ ├── slide_001.h5 |
| │ ├── ... |
| │ |
| └── st/ |
| ├── slide_001.h5 |
| ├── ... |
| ``` |
|
|
| | Directory | Description | |
| |-----------|-------------| |
| | metadata | Dataset metadata and slide annotations | |
| | wsis | Whole-slide H&E images | |
| | patches | Patch-level image features for each slide | |
| | st | Spatial transcriptomics measurements for each slide | |
|
|
| --- |
|
|
| ## 💻 Supporting Code |
|
|
| Benchmark code is available at |
|
|
| **GitHub** |
|
|
| https://github.com/NEXGEM/STpredBench |
|
|
| The repository contains |
|
|
| - preprocessing pipeline |
| - data loading |
| - evaluation scripts |
| - baseline implementations |
| - benchmark splits |
| - training examples |
|
|
| --- |
|
|
| ## ⬇️ Loading Example |
|
|
| ```python |
| from huggingface_hub import snapshot_download |
| |
| snapshot_download( |
| repo_id="nexgem/STP-Bench", |
| repo_type="dataset", |
| local_dir="./STP-Bench" |
| ) |
| ``` |
|
|
| ## 📖 Citation |
|
|
| If you use STP-Bench, please cite |
|
|
| **TBD** |
|
|
| ```bibtex |
| @article{stpbench2026, |
| title={STP-BENCH: A Unified Systematic Benchmark for Virtual Spatial Transcriptomics from Histopathology Images}, |
| author={...}, |
| journal={...}, |
| year={2026} |
| } |
| ``` |
|
|
| --- |
|
|
| ## 📜 License |
|
|
| Please refer to the original licenses of each constituent dataset. |
|
|
| The benchmark organization and preprocessing pipeline are released under the CC BY 4.0 License unless otherwise specified. |
|
|
| --- |
|
|
|
|
|
|
| ## 📬 Contact |
|
|
| **Youngmin Chung** |
| - Sungkyunkwan University, Suwon, Republic of Korea |
| - ymblue@skku.edu |
|
|
| **Ji Hun Ha** |
| - Sungkyunkwan University, Suwon, Republic of Korea |
| - gkwlgns323@skku.edu |
|
|
