---
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](https://github.com/jinxixiang/MUPAD) (paper code) and the [MuPaD SDK](https://github.com/jinxixiang/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](https://zenodo.org/records/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 |

```bash
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).