A command-line tool to download .ndpi files from an EBRAINS dataset, filtered by diagnosis name.
uvx --from git+https://github.com/HokuMedAI/ebrains-downloader ebrains-downloader --diagnosis Haemangiopericytoma --output /path/to/outputMultiple diagnoses:
uvx --from git+https://github.com/HokuMedAI/ebrains-downloader ebrains-downloader --diagnosis Haemangiopericytoma SchwannomaDiagnosis names containing spaces must be quoted:
uvx --from git+https://github.com/HokuMedAI/ebrains-downloader ebrains-downloader --diagnosis "Fibrous meningioma"git clone https://github.com/HokuMedAI/ebrains-downloader
cd ebrains-downloader
uv run ebrains-downloader --diagnosis Haemangiopericytoma --output /path/to/output| Option | Description | Default |
|---|---|---|
--diagnosis |
Diagnosis name(s) (required, multiple allowed) | — |
--output |
Output directory | downloads |
Downloaded files and the annotation CSV are saved under the output directory:
downloads/
├── annotation.csv
├── Haemangiopericytoma/
│ ├── <uuid>.ndpi
│ └── ...
└── Fibrous meningioma/
├── <uuid>.ndpi
└── ...
Authentication is handled automatically via fairgraph. You will be prompted to log in to your EBRAINS account on first use.
Interrupted downloads are automatically resumed from where they left off.
Please report bugs and feature requests at GitHub Issues.