HISTAI is a comprehensive, open-source Whole Slide Image (WSI) dataset designed to advance research and development in digital pathology. It provides a diverse, multimodal, and richly annotated collection comprising over 112,000 slides from multiple organ systems and pathological specializations. Each slide includes extensive clinical, pathological, and technical metadata, enabling a wide range of research applications from diagnostic modeling to multimodal analyses.
If you wish to support, sponsor, or obtain a commercial license for HISTAI data, please contact us at models@hist.ai.
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Metadata Repository: HISTAI-metadata [START HERE]
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Individual Specialized Subsets:
A detailed research paper describing the HISTAI dataset is available:
HISTAI: An Open-Source, Large-Scale Whole Slide Image Dataset for Computational Pathology Dmitry Nechaev, Alexey Pchelnikov, Ekaterina Ivanova 📖 Read on arXiv
If you use HISTAI in your research, please cite:
@misc{nechaev2025histaiopensourcelargescaleslide,
title = {HISTAI: An Open-Source, Large-Scale Whole Slide Image Dataset for Computational Pathology},
author = {Dmitry Nechaev and Alexey Pchelnikov and Ekaterina Ivanova},
year = {2025},
eprint = {2505.12120},
archivePrefix = {arXiv},
primaryClass = {eess.IV},
url = {https://arxiv.org/abs/2505.12120}
}Slides are organized by cases within specialized subsets following this naming convention:
histai/<dataset_name>/case_<case_id>/slide_<stain>_<slide_number>.tiff
or
histai/<dataset_name>/case_<case_id>/slide_<magnification>_<stain>_<slide_number>.tiff
- Standard magnification: 20X (explicitly mentioned if differs)
- Staining: Primarily Hematoxylin and Eosin (H&E)
- Scanners used: Primarily Leica Aperio GT450, AT2, some Hamamatsu, and 3DHISTECH systems.
Detailed metadata accompanies each slide, provided in JSON format. Fields include:
| Field | Description | Example |
|---|---|---|
diagnosis |
Incoming clinical notes | Benign skin neoplasms |
conclusion |
Final pathological conclusion | Intradermal melanocytic nevus of the skin |
diff_diagnosis |
Differential diagnostic notes (if available) | |
micro_protocol |
Microscopic description | Skin: Intradermal melanocytic nevus |
additional_info |
Supplementary clinical/pathological notes | "A repeat review of histological specimens was performed..." |
age |
Patient age (years) | 37 |
gender |
Patient gender | f |
icd10 |
ICD-10 codes | D22 |
specialization |
Medical specialization or organ system | Skin |
case_mapping |
References to slide images | histai/HISTAI-skin-b2/case_13384 |
grossing |
Gross examination details | "Head and neck: One fragment, 2×4 mm, gray, firm..." |
| Dataset | Total Slides | Total Cases |
|---|---|---|
| HISTAI-hematologic | 214 | 214 |
| HISTAI-gastrointestinal | 202 | 120 |
| HISTAI-breast | 1,925 | 1,692 |
| HISTAI-thorax | 829 | 657 |
| HISTAI-skin-b2 | 43,757 | 20,621 |
| HISTAI-skin-b1 | 7,710 | 1,778 |
| HISTAI-colorectal-b1 | 5,379 | 998 |
| HISTAI-colorectal-b2 | 94 | 62 |
| HISTAI-mixed | 52,691 | 21,137 |
Total slides: 112,801 Total cases: 47,279 Magnification: 20X (110,338 slides), 40X (2,463 slides) Stains: H&E (92,536 slides), IHC (16,920 slides), Other (3,345 slides)
from huggingface_hub import snapshot_download
snapshot_download(repo_id="histai/<dataset_name>", repo_type="dataset", local_dir="/local_path")git lfs install
git clone https://huggingface.co/datasets/histai/<dataset_name>The HISTAI dataset is licensed under CC BY-NC 4.0 and intended for research purposes only. For commercial use, contact models@hist.ai.
- SPIDER: Multi-organ supervised dataset with annotations.
- Hibou: Vision models for digital pathology.
Authors: Dmitry Nechaev, Alexey Pchelnikov, Ekaterina Ivanova Emails: dmitry@hist.ai, alex@hist.ai, kate@hist.ai