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Specifications for bioimage.io

This repository contains the specifications of the standard format defined by the bioimage.io community for the content (i.e., models, datasets and applications) in the bioimage.io website. Each item in the content is always described using a YAML 1.2 file named rdf.yaml or bioimageio.yaml. This rdf.yaml \ bioimageio.yaml--- along with the files referenced in it --- can be downloaded from or uploaded to the bioimage.io website and may be produced or consumed by bioimage.io-compatible consumers (e.g., image analysis software like ilastik).

These are the latest format specifications that bioimage.io-compatible resources should comply to.

Note that the Python package PyYAML does not support YAML 1.2 . We therefore use and recommend ruyaml. For differences see https://ruamelyaml.readthedocs.io/en/latest/pyyaml.

Please also note that the best way to check whether your rdf.yaml file is fully bioimage.io-compliant, is to call bioimageio.core.test_description from the bioimageio.core Python package. The bioimageio.core Python package also provides the bioimageio command line interface (CLI) with the test command:

bioimageio test path/to/your/rdf.yaml

Documentation

The bioimageio.spec documentation is hosted at https://bioimage-io.github.io/spec-bioimage-io.

Key dates

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  • Released:
Newer release available (0.5.14.1)

Owner

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Credits

Author: Fynn Beuttenmüller

Requires

Python >=3.8

Provides Extra

dev docs

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