Buckets:
| 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 | |
| ```bibtex | |
| @article{stpbench2026, | |
| title={STP-BENCH: A Unified Systematic Benchmark for Virtual Spatial Transcriptomics from Histopathology Images}, | |
| author={Chung, Youngmin and Ha, Ji Hun and Song, Andrew H. and Almagro-P{\'e}rez, Cristina and Seo, Chaeyoung and Suh, Won Jun and Beom, Jeong Won and Oh, Kyoung Bin and Ruppin, Eytan and Mahmood, Faisal and Lee, Joo Sang}, | |
| journal={arXiv preprint arXiv:2609.05956}, | |
| year={2026}, | |
| doi={10.48550/arXiv.2609.05956} | |
| } | |
| ``` | |
| --- | |
| ## 📜 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 | |
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