This repository contains workflow implementations and their high level descriptions in the form of workflow RDFs.
A BioImage.IO-compatible workflow Resource Description File (RDF) is a YAML file with a set of specifically defined fields.
You can find detailed field definitions here:
The specifications are also available as json schemas:
The BioImage.IO command line tool makes it easy to work with BioImage.IO RDFs.
The bioimageio command of the bioimageio.core package is further extended by this repository's bioimageio.workflows package:
type
$ bioimageio run-workflow --help
bioimageio.workflows can be installed with either pip or conda (recommended):
# pip
pip install -U bioimageio.workflows
# conda
conda install -c conda-forge bioimageio.workflows
in development start server:
python -m bioimageio.workflows.server start-server
start a submodule:
python -m bioimageio.workflows.server start-submodule-service stardist
For boolean environment variables possible, are case-insensitive, positive values are: "true", "yes", "1". Any other value is interpreted as "false".
| Name | Default | Description | defined in |
|---|---|---|---|
| BIOIMAGEIO_SERVER_URL | "http://127.0.0.1:9527" | Use to overwrite the default server address. | bioimageio.workflows |
| BIOIMAGEIO_SERVER_<env name>_URL | <BIOIMAGEIO_SERVER_URL> | Workflow/conda environment specific server url, e.g. 'BIOIMAGEIO_SERVER_STARDIST_URL'. | bioimageio.workflows |
| BIOIMAGEIO_USE_REMOTE_DEFAULT_ENV | "false" | If "true" bioimageio.workflows will execute any workflow defined in the default environment remotely via the hypha server and not locally. | bioimageio.workflows |
| BIOIMAGEIO_AUTOSTART_SERVER | "true" | If "true" a hypha server will be launched automatically if connecting to a local server url (http://localhost:...) fails. | bioimageio.workflows |
| BIOIMAGE_SERVER_CONDA_ENV | "bioimageio_wf_env_default" | Conda environment to start server in. Only applies if 'BIOIMAGEIO_AUTOSTART_SERVER' is "true". | bioimageio.workflows |
| BIOIMAGEIO_AUTOSTART_ENV_SERVICES | "true" | If "true" the required submodule service is started automatically when required for the first time. Conda environment names follow the pattern 'bioimageio_wf_env_'. | bioimageio.workflows |
| BIOIMAGEIO_AUTOINSTALL_SUBMODULE_ENVS | "true" | If "true" missing mamba environments are installed if necessary. Only applies if 'BIOIMAGEIO_AUTOSTART_ENV_SERVICES' is "true". | bioimageio.workflows |
| BIOIMAGEIO_USE_CACHE | "true" | Enables simple URL to file cache. | bioimageio.spec |
| BIOIMAGEIO_CACHE_PATH | generated tmp folder | File path for simple URL to file cache; changes of URL source are not detected. | bioimageio.spec |
| BIOIMAGEIO_CACHE_WARNINGS_LIMIT | "3" | Maximum number of warnings generated for simple cache hits. | bioimageio.spec |