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README.md

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+---
+license: other
+license_name: ohsu-non-commercial
+license_link: https://github.com/ChangLab/cycif-panel-reduction/blob/publication/LICENSE
+tags:
+  - biology
+  - multiplex-imaging
+  - computational-pathology
+  - cycif
+  - colorectal-cancer
+size_categories:
+  - 1K<n<10K
+---
+
+# miniMTI-CRC Example Data
+
+Example single-cell imaging data for testing [miniMTI](https://huggingface.co/changlab/miniMTI-CRC), a molecularly anchored virtual staining framework for multiplex tissue imaging panel reduction.
+
+**Paper:** [bioRxiv 2026.01.21.700911](https://www.biorxiv.org/content/10.64898/2026.01.21.700911v1)
+**Code:** [GitHub](https://github.com/ChangLab/cycif-panel-reduction)
+**Model:** [changlab/miniMTI-CRC](https://huggingface.co/changlab/miniMTI-CRC)
+
+## Dataset Description
+
+10,000 single-cell image patches randomly sampled (seed=42) from CRC-Orion sample CRC04 (colorectal cancer tissue microarray, cyclic immunofluorescence).
+
+### File
+
+- `example_CRC04_10k.h5` — HDF5 file (~178 MB)
+
+### HDF5 Structure
+
+| Dataset    | Shape              | Type   | Description |
+|------------|--------------------|--------|-------------|
+| `images`   | (10000, 32, 32, 20)| uint8  | 17 IF channels + 3 H&E (RGB) channels |
+| `masks`    | (10000, 32, 32)    | bool   | Binary cell segmentation masks |
+| `metadata` | (10000,)           | string | Cell IDs and coordinates: `<sample>-CellID-<id>-x=<x>-y=<y>` |
+
+### Channel Ordering (20 channels)
+
+| Index | Marker      | Index | Marker      |
+|-------|-------------|-------|-------------|
+| 0     | DAPI        | 10    | CD20        |
+| 1     | CD31        | 11    | PD-L1       |
+| 2     | CD45        | 12    | CD3e        |
+| 3     | CD68        | 13    | CD163       |
+| 4     | CD4         | 14    | E-cadherin  |
+| 5     | FOXP3       | 15    | PD-1        |
+| 6     | CD8a        | 16    | Ki67        |
+| 7     | CD45RO      | 17    | H&E (R)     |
+| 8     | CD20        | 18    | H&E (G)     |
+| 9     | PD-L1       | 19    | H&E (B)     |
+
+Channels 0–16 are immunofluorescence markers. Channels 17–19 are co-registered H&E RGB.
+
+## Usage
+
+```python
+from huggingface_hub import hf_hub_download
+
+# Download example data
+path = hf_hub_download(
+    repo_id="changlab/miniMTI-CRC-example",
+    filename="example_CRC04_10k.h5",
+    repo_type="dataset",
+)
+
+# Run inference with miniMTI
+python scripts/inference_example.py --val-file $path --input-channels 17,6,11,13
+```
+
+## Citation
+
+```bibtex
+@article{sims2026minimti,
+  title={miniMTI: minimal multiplex tissue imaging enhances biomarker expression prediction from histology},
+  author={Sims, Z. and Govindarajan, S. and Ait-Ahmad, K. and Ak, C. and Kuykendall, M. and Mills, G. B. and Eksi, E. and Chang, Y. H.},
+  journal={bioRxiv},
+  year={2026},
+  doi={10.64898/2026.01.21.700911}
+}
+```