bioimageio CLI

bioimageio Command Line Interface

bioimageio.core installs a command line interface (CLI) for testing models and other functionality. You can list all the available commands via:

bioimageio --help
usage: bioimageio [-h] {validate-format,test,package,predict,predict-block-artifacts,update-format,update-hashes,add-weights,empty-cache} ...

bioimageio - CLI for bioimage.io resources 🦒

library versions:
  bioimageio.core 0.10.0
  bioimageio.spec 0.5.9.0

spec format versions:
        model RDF 0.5.9
      dataset RDF 0.3.0
     notebook RDF 0.3.0

options:
  -h, --help            show this help message and exit

subcommands:
  {validate-format,test,package,predict,predict-block-artifacts,update-format,update-hashes,add-weights,empty-cache}
    validate-format     Validate the meta data format of a bioimageio resource.
    test                Test a bioimageio resource (beyond meta data formatting).
    package             Save a resource's metadata with its associated files.
    predict             Run inference on your data with a bioimage.io model.
    predict-block-artifacts
                        Command to inspect block artifacts by subtracting the combined, blockwise predictions from a whole sample prediction.

                            Note:
                                - This command intentionally uses a small blocksize (default: 1) to create block artifacts for testing purposes.
                                - Typical sources of block artifacts include:
                                    - Described halo is smaller than the model's receptive field
                                    - Normalization layers inside the network cannot aggregate statistics over the whole sample.
    update-format       Update the metadata format to the latest format version.
    update-hashes       Create a bioimageio.yaml description with updated file hashes.
    add-weights         Add additional weights to a model description by converting from available formats.
    empty-cache         Empty the bioimageio cache directory.

For concrete examples see Get started.

CLI inputs from file

For convenience the command line options (not arguments) may be given in a bioimageio-cli.json or bioimageio-cli.yaml file, e.g.:

# bioimageio-cli.yaml
inputs: inputs/*_{tensor_id}.tiff
outputs: outputs_{model_id}/{sample_id}_{tensor_id}.tiff
overwrite: true
blockwise: true
stats: inputs/dataset_statistics.json