| | --- |
| | license: mit |
| | tags: |
| | - pathology |
| | - histology |
| | - cell-phenotyping |
| | - foundation-models |
| | - benchmark |
| | pretty_name: "HistoGauge Benchmark Datasets" |
| | --- |
| | |
| | # 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](https://huggingface.co/datasets/FabianReith/phenobench/tree/main/data/pathocell)** (formerly PhenoCell): Our new, challenging benchmark dataset for H&E cell phenotyping with 14 granular cell types. |
| | * **[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).** |
| | * **[Lizard](https://huggingface.co/datasets/FabianReith/phenobench/tree/main/data/lizard)**: A large-scale nucleus segmentation and classification dataset in colon histology. |
| | * **[ARCTIQUE](https://huggingface.co/datasets/FabianReith/phenobench/tree/main/data/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**. |
