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Usage¤

💁 Recommendations¤

  • Use the bioimageio.core Python package to not only validate the format of your bioimageio.yaml/rdf.yaml file, but also test and deploy it (e.g. model inference).
  • bioimageio.spec keeps evolving. Try to use and upgrade to the most current format version! Note: The command line interface bioimageio (part of bioimageio.core) has the update-format command to help you with that.

Examples¤

We provide some bioimageio.yaml/rdf.yaml example files to describe models, applications, notebooks and datasets; more examples are available at bioimage.io. There is also an example notebook demonstrating how to programmatically access the models, applications, notebooks and datasets descriptions in Python. For integration of bioimageio resources we recommend the bioimageio.core Python package.

⌨ bioimageio command-line interface (CLI)¤

The bioimageio CLI has moved to bioimageio.core.

🖥 Installation¤

bioimageio.spec can be installed with either conda or pip. We recommend installing bioimageio.core instead to get access to the Python programmatic features available in the BioImage.IO community:

conda install -c conda-forge bioimageio.core

or

pip install -U bioimageio.core

Still, for a lighter package or just testing, you can install the bioimageio.spec package solely:

conda install -c conda-forge bioimageio.spec

or

pip install -U bioimageio.spec

🏞 Environment variables¤

Todo

link to settings in dev docs