Datasets:
metadata
license: other
license_name: ohsu-non-commercial
license_link: https://github.com/ChangLab/miniMTI/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, a molecularly anchored virtual staining framework for multiplex tissue imaging panel reduction.
Paper: bioRxiv 2026.01.21.700911
Code: GitHub
Model: changlab/miniMTI-CRC
Dataset Description
10,000 single-cell image patches randomly sampled (seed=42) from CRC-Orion sample CRC04 (colorectal cancer tissue WSI, RareCyte Orion platform).
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 raw channels)
| Index | Channel |
|---|---|
| 0 | DAPI |
| 1 | CD31 |
| 2 | CD45 |
| 3 | CD68 |
| 4 | CD4 |
| 5 | FOXP3 |
| 6 | CD8a |
| 7 | CD45RO |
| 8 | CD20 |
| 9 | PD-L1 |
| 10 | CD3e |
| 11 | CD163 |
| 12 | E-cadherin |
| 13 | PD-1 |
| 14 | Ki67 |
| 15 | PanCK |
| 16 | aSMA |
| 17 | H&E (R) |
| 18 | H&E (G) |
| 19 | H&E (B) |
Channels 0–16 are immunofluorescence markers. Channels 17–19 are co-registered H&E RGB. The miniMTI model treats each IF channel as a separate marker and the three H&E channels as a single marker (18 markers total).
Usage
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
@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}
}