| --- |
| 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). |
|
|
