Datasets:

taejoon89
/

openpath-corpus

license: other
license_name: mixed-public-cc-by-cc0-nih-open
pretty_name: OpenPath Corpus
tags:
  - pathology
  - histopathology
  - whole-slide-imaging
  - digital-pathology
  - self-supervised
  - webdataset
task_categories:
  - image-feature-extraction
size_categories:
  - n>1T
extra_gated_prompt: >-
  Access is granted for research use. By requesting access you agree to (1) cite
  the OpenPath paper and this corpus, and (2) respect the original license and
  attribution terms of every source dataset listed below (in particular the TCGA
  and GTEx attribution statements). The corpus redistributes only public,
  redistributable pathology data.
extra_gated_fields:
  Name: text
  Affiliation: text
  Intended use: text
  I agree to the source-dataset license and attribution terms: checkbox

OpenPath Corpus

Public-only whole-slide histopathology tile corpus used to pre-train OpenPath, a ViT-g/14 pathology foundation model. Tiles are re-extracted at native ~40× (0.5 µm-per-pixel), which is the data lever that lets OpenPath rank #1 on the contamination-free AMC-HCC-ST benchmark among seven foundation models (see the code / model card).

33,991 WebDataset shards (.tar), ~17 TB, ~834 M tiles, 224×224 at native 40×.
Seven public sources (sharded into slots such as tcga_s0…s5):

Source	Shards	License	Notes
TCGA (`tcga_s0…s5`)	20,589	NIH / GDC open-access tier	attribution required (see below)
GTEx (`gtex_s0…s1`)	4,965	GTEx Portal permissive (attribution-only); CC-BY 4.0 DICOM mirror available	attribution required
TCIA (`tcia_s0…s1`)	3,891	CC-BY 3.0 / 4.0 (collection-specific)	pathology collections
ACROBAT	3,318	CC-BY 4.0	breast H&E + IHC
CAMELYON16/17	784	CC0 (public domain)	breast lymph node
SurGen	426	CC-BY 4.0	colorectal
MIDOG (2021 / 2022 / ++)	18	CC-BY 4.0	multi-tumor
Total	33,991	mixed public / redistributable	commercial use permitted

All sources are commercial-use-permitted (CC-BY / CC0 / NIH-open). This corpus does not include any non-commercial (NC) data. PCam / CAMELYON overlap standard patch benchmarks and are therefore excluded from OpenPath's evaluation.

Format & loading

Layout: <source>/tiles/shards/w<id>/*.tar (WebDataset). Each tar entry is a JPEG tile with a JSON sidecar (wsi_id, tile coordinates, magnitude).
Training glob: */tiles/shards/w*/*.tar.

import webdataset as wds
url = "path/to/openpath-corpus/tcga_s0/tiles/shards/w0/000000.tar"
ds = wds.WebDataset(url).decode("pil").to_tuple("jpg", "json")
for img, meta in ds:
    ...  # img: 224×224 PIL RGB, meta: {wsi_id, x, y, mag, ...}

Access & terms (gated)

Gated, manual approval. For research use. When you use the corpus, cite the OpenPath paper and preserve each source's attribution, e.g.:

The results shown here are in whole or part based upon data generated by the TCGA Research Network: https://www.cancer.gov/tcga.

Data were obtained from the GTEx Portal (and/or dbGaP accession phs000424).

Related artifacts

Artifact	Hugging Face repo	Notes
Corpus	`taejoon89/openpath-corpus`	This repository
Checkpoints	`taejoon89/openpath-checkpoints`	teacher checkpoints (`training_0` … `training_345000`); released = `training_316250`
Code	`taejoon89/openpath`	training & evaluation code (also on GitHub)

Citation

@misc{openpath2026,
  title  = {OpenPath: Public-Data Pathology Foundation Models and Leakage-Free Evaluation},
  author = {Tae Joon Jun},
  year   = {2026},
  note   = {https://huggingface.co/taejoon89/openpath}
}

Acknowledgements

This research was supported by a grant of the Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea (grant number: HR21C0198); the Advanced GPU Utilization Support Program funded by the Government of the Republic of Korea, Ministry of Science and ICT; and the National Research Foundation of Korea (NRF) grant funded by the Korean government (MSIT) (grant number: RS-2026-25522634).

License

The corpus redistributes public pathology datasets under their original CC-BY / CC0 / NIH-open terms (all redistributable, commercial use permitted). See the per-source table above and cite/attribute each source accordingly.