HISTAI is a comprehensive whole-slide image (WSI) pathological dataset spanning multiple medical specializations. Slides are anonymized and organized into specialized subsets by organ systems or pathology types.
If you wish to support, sponsor, or obtain a commercial license for HISTAI data, please contact us at [email protected].
For details refer to our report:
COMING SOON
This repository contains metadata and references to images hosted separately. Individual slide images are accessible from specialized Hugging Face datasets.
Slides are stored across specialized datasets hosted on Hugging Face. Each specialized dataset contains anonymized slides organized by cases:
histai/<dataset_name>/case_<case_id>/slide_<stain>_<slide_number>.tiff
or
histai/<dataset_name>/case_<case_id>/slide_<magnification>_<stain>_<slide_number>.tiff
Most of the slides are stained with Hematoxylin and Eosin (H&E) and scanned at 20X magnification. If a slide differs in magnification from 20X, this information is embedded in the slide filename, as shown above.
Currently available specialized datasets:
The master repository includes comprehensive metadata in JSON format for each slide/case, containing detailed pathological, clinical, and technical information:
| 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 of the skin. Microscopic description: ... |
additional_info |
Any additional clinical/pathological notes | "A repeat review of the histological specimens was performed, including ... |
age |
Patient age (years) | 37 |
gender |
Patient gender | f |
icd10 |
ICD-10 classification | D22 |
specialization |
Medical specialization or organ system | Skin |
case_mapping |
Reference to slide images | histai/HISTAI-skin-b2/case_13384 |
grossing |
Gross examination details | "Head and neck: One fragment, measuring 2×4 mm, gray, firm, with ... |
| Dataset | Total Slides | Total Cases |
|---|---|---|
| histai/HISTAI-hematologic | 214 | 214 |
| histai/HISTAI-gastrointestinal | 202 | 120 |
| histai/HISTAI-breast | 1,925 | 1,692 |
| histai/HISTAI-thorax | 829 | 657 |
| histai/HISTAI-skin-b2 | 43,757 | 20,621 |
| histai/HISTAI-skin-b1 | 7,710 | 1,778 |
| histai/HISTAI-colorectal-b1 | 5,379 | 998 |
| histai/HISTAI-colorectal-b2 | 94 | 62 |
You can programmatically download slides using:
from huggingface_hub import snapshot_download
snapshot_download(repo_id="histai/<dataset_name>", repo_type="dataset", local_dir="/local_path")
# Ensure you have Git LFS installed
git lfs install
git clone https://huggingface.co/datasets/histai/<dataset_name>
This dataset is licensed under CC BY-NC 4.0 and is intended exclusively for research purposes.
Please cite the following if you use this dataset:
TBD