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--- |
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license: mit |
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tags: |
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- pathology |
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- histology |
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- cell-phenotyping |
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- foundation-models |
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- benchmark |
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pretty_name: "PathoCell Benchmark Datasets" |
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--- |
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# PathoCell: A Benchmark for Foundational Models in Computational Pathology |
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This repository contains the datasets for **PathoCellBench** (formerly PhenoBench), a comprehensive benchmark designed to evaluate the cell phenotyping capabilities of pathology Foundation Models. |
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The benchmark suite includes four key datasets, all processed into the efficient LMDB (Lightning Memory-Mapped Database) format to facilitate large-scale experimentation. |
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## Datasets Included |
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This collection consolidates the following datasets: |
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* **[PathoCell](https://huggingface.co/datasets/FabianReith/phenobench/tree/main/data/phenocell)** (formerly PhenoCell): Our new, challenging benchmark dataset for H&E cell phenotyping with 14 granular cell types. |
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* **[PanNuke](https://huggingface.co/datasets/FabianReith/phenobench/tree/main/data/pannuke)**: A pan-cancer nucleus segmentation and classification dataset. **Note: This dataset requires a one-time setup step after downloading (see instructions below).** |
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* **[Lizard](https://huggingface.co/datasets/FabianReith/phenobench/tree/main/data/lizard)**: A large-scale nucleus segmentation and classification dataset in colon histology. |
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* **[ARCTIQUE](https://huggingface.co/datasets/FabianReith/phenobench/tree/main/data/arctique)**: A colorectal cancer histology dataset for tile-based classification. |
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--- |
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## **IMPORTANT**: Setup Instructions for the PanNuke Dataset |
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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. |
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After downloading the repository, navigate into the PanNuke `lmdb` directory and run the `cat` command as shown below. |
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# 1. Navigate to the correct directory |
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cd data/pannuke/pannuke_lmdb/ |
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# 2. Run the cat command to merge the parts into a single file |
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cat data.mdb.part_* > data.mdb |
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# 3. Verify the new file 'data.mdb' has been created. |
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# You can now optionally delete the .part files to save space. |
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# rm data.mdb.part_* |
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The other datasets (`PathoCell`, `Lizard`, and `ARCTIQUE`) are ready to use immediately after download and do not require this step. |
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--- |
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## How to Use |
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You can download the entire dataset collection using the Hugging Face `datasets` library. |
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from datasets import load_dataset |
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# Download all the dataset files |
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# Note: This does not load the LMDB files into memory, it only downloads the raw files. |
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# Remember to run the reassembly command for PanNuke after downloading. |
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dataset_path = load_dataset("FabianReith/phenobench", cache_dir="./huggingface_data") |
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print(f"Dataset downloaded to: {dataset_path.cache_files}") |
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After reassembly, you can use your own custom data loader to read from the resulting `.mdb` files. |
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## Dataset Structure |
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The data is organized into folders, one for each of the four datasets. |
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```` |
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/ |
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├── data/ |
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│ ├── arctique/ |
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│ │ ├── arctique_lmdb/ |
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│ │ │ ├── data.mdb |
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│ │ │ └── lock.mdb |
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│ │ └── ... (other metadata files) |
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│ │ |
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│ ├── lizard/ |
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│ │ ├── lizard_lmdb/ |
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│ │ │ ├── data.mdb |
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│ │ │ └── lock.mdb |
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│ │ └── ... |
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│ │ |
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│ ├── pannuke/ |
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│ │ ├── pannuke_lmdb/ (Requires reassembly) |
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│ │ │ ├── data.mdb.part_aa |
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│ │ │ ├── data.mdb.part_ab |
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│ │ │ └── ... |
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│ │ └── ... |
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│ │ |
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│ └── phenocell/ (PathoCell legacy name) |
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│ ├── phenocell/ |
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│ │ ├── data.mdb |
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│ │ └── lock.mdb |
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│ └── ... |
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│ |
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├── pathocell_hdf/ |
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│ └── ... (contains the PathoCell dataset in HDF5 format) |
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│ |
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├── .gitattributes |
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└── README.md |
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```` |
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## Citation Information |
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If you use our benchmark or the **PathoCell** dataset in your research, please cite our work. |
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*TODO* |
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Please also ensure you cite the original papers for the **PanNuke**, **Lizard**, and **ARCTIQUE** datasets if you use them. |
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## License |
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This dataset collection is licensed under the **MIT License**. |
