taejoon89/openpath-corpus

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).

Contents

• 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.