README.md

metadata

license: other
license_name: mixed-per-folder
license_details: >-
  he2mif/ is MIT (MIPHEI-ViT Orion-CRC release); he2st/ is CC BY-NC-SA 4.0
  (HEST-1k); sdk/ redistributes two H&E slides under their original releases'
  terms (ORION-CRC, HEST-1k)
pretty_name: MuPaD examples
tags:
  - pathology
  - computational-pathology
  - virtual-staining
  - multiplex-immunofluorescence
  - spatial-transcriptomics
  - xenium
  - single-cell
size_categories:
  - n<1K

MuPaD examples

Example data for MuPaD (paper code) and the MuPaD SDK (whole-slide inference).

folder	contents	size	licence
he2mif/	ORION-CRC tiles for 5-HE2mIF: 840 H&E / 17-channel mIF / nuclei tiles in the Zenodo 15340874 layout, as one tar	0.4 GB	MIT
he2st/	two HEST-1k Xenium breast slides for 6-HE2ST (NCBI917 train, NCBI920 val): raw HEST files, the 100 µm tile cache and per-cell MUSK features	12.4 GB	CC BY-NC-SA 4.0
sdk/	the two held-out H&E whole-slide images the SDK's end-to-end checks run on: ORION-CRC CRC11 (0.325 µm/px) and HEST-1k NCBI920 (0.087 µm/px); H&E only, see sdk/README.md	6.9 GB	original terms

huggingface-cli download xiangjx/MuPaD-examples --repo-type dataset --include "he2mif/*" --local-dir examples
tar xf examples/he2mif/ORIONCRC_dataset_tile_20x.tar -C examples/he2mif       # tiles ship as one tar
huggingface-cli download xiangjx/MuPaD-examples --repo-type dataset --include "he2st/*"  --local-dir examples

he2mif. Tiles with tissue were sampled uniformly per slide: 600 train, 120 val, 120 test, plus the two demo tiles of 5-HE2mIF/demo.ipynb (a best case, not typical). Point the code at it with ORION_DATA_ROOT=$PWD/examples/he2mif/ORIONCRC_dataset_tile_20x.

he2st. cache/<slide>/ is the tile cache, features/musk/<slide>/emb_cell.npy the per-cell MUSK features, HEST1k/ the raw inputs they were built from (wsis/ st/ xenium_seg/ cells/ metadata/). Rows of expr.npy, emb_cell.npy and every prediction are the same cells in the same order. Set HEST_ROOT=$PWD/examples/he2st/HEST1k HE2ST_CACHE=$PWD/examples/he2st/cache HE2ST_MUSK_FEATURES=$PWD/examples/he2st/features/musk; splits_example.json makes a one-slide smoke run.

sdk. python scripts/e2e_mif_orion.py and python scripts/e2e_expression_ncbi920.py in the SDK download these slides themselves; the ground truth (Orion mIF, Xenium counts) comes from the original ORION-CRC and HEST-1k releases.

Sources: ORION-CRC tiles from the MIPHEI-ViT release (Balezo et al., 2025; MIT); HEST-1k (Jaume et al., NeurIPS 2024; CC BY-NC-SA 4.0, non-commercial, attribution, share-alike).