HistoGauge: A Benchmark for Foundational Models in Computational Pathology

This repository contains the datasets for HistoGauge (formerly PhenoBench), a comprehensive benchmark designed to evaluate the cell phenotyping capabilities of pathology Foundation Models.

The benchmark suite includes four key datasets, all processed into the efficient LMDB (Lightning Memory-Mapped Database) format to facilitate large-scale experimentation.

Datasets Included

This collection consolidates the following datasets:

PathoCell (formerly PhenoCell): Our new, challenging benchmark dataset for H&E cell phenotyping with 14 granular cell types.
PanNuke: A pan-cancer nucleus segmentation and classification dataset. Note: This dataset requires a one-time setup step after downloading (see instructions below).
Lizard: A large-scale nucleus segmentation and classification dataset in colon histology.
ARCTIQUE: A colorectal cancer histology dataset for tile-based classification.

IMPORTANT: Setup Instructions for the PanNuke Dataset

Due to repository file size limits, the large database file for the PanNuke dataset (data.mdb) was split into smaller parts. Before you can use this dataset, you must reassemble these parts into a single file.

After downloading the repository, navigate into the PanNuke lmdb directory and run the cat command as shown below.

# 1. Navigate to the correct directory
cd data/pannuke/pannuke_lmdb/

# 2. Run the cat command to merge the parts into a single file
cat data.mdb.part_* > data.mdb

# 3. Verify the new file 'data.mdb' has been created.
#    You can now optionally delete the .part files to save space.
#    rm data.mdb.part_*

The other datasets (PathoCell, Lizard, and ARCTIQUE) are ready to use immediately after download and do not require this step.

How to Use

You can download the entire dataset collection using the Hugging Face datasets library.

from datasets import load_dataset

# Download all the dataset files
# Note: This does not load the LMDB files into memory, it only downloads the raw files.
# Remember to run the reassembly command for PanNuke after downloading.
dataset_path = load_dataset("FabianReith/phenobench", cache_dir="./huggingface_data")

print(f"Dataset downloaded to: {dataset_path.cache_files}")

After reassembly, you can use your own custom data loader to read from the resulting .mdb files.

Dataset Structure

The data is organized into folders, one for each of the four datasets.

/
└── data/
    ├── arctique/
    │   ├── arctique_lmdb/
    │   │   ├── data.mdb
    │   │   └── lock.mdb
    │   └── ... (other metadata files)
    │
    ├── lizard/
    │   ├── lizard_lmdb/
    │   │   ├── data.mdb
    │   │   └── lock.mdb
    │   └── ...
    │
    ├── pannuke/
    │   ├── pannuke_lmdb/    (Requires reassembly)
    │   │   ├── data.mdb.part_aa
    │   │   ├── data.mdb.part_ab
    │   │   └── ...
    │   └── ...
    │
    └── pathocell/
        ├── pathocell_lmdb/
        │   ├── data.mdb
        │   └── lock.mdb
        └── ...

Citation Information

If you use our benchmark or the PathoCell dataset in your research, please cite our work.

TODO

Please also ensure you cite the original papers for the PanNuke, Lizard, and ARCTIQUE datasets if you use them.

License

This dataset collection is licensed under the MIT License.

Datasets:

Kainmueller-Lab
/

phenobench

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