bioimageio.core
bioimageio.core is a python package that implements prediction with bioimage.io models
including standardized pre- and postprocessing operations.
Such models are represented as bioimageio.spec resource descriptions.
In addition bioimageio.core provides functionality to convert model weight formats and compute selected dataset statistics used for preprocessing.
Documentation
Here you find the bioimageio.core documentation.
Examples
Notebooks that save and load resource descriptions and validate their format (using bioimageio.spec, a dependency of bioimageio.core)
Use the described resources in Python with bioimageio.core
Presentations
Set up Development Environment
To set up a development environment run the following commands:
conda create -n core python=$(grep -E '^requires-python' pyproject.toml | grep -oE '[0-9]+\.[0-9]+')
conda activate core
pip install -e .[dev,partners]
Joint development of bioimageio.spec and bioimageio.core
Assuming spec-bioimage-io is cloned to the parent folder a joint development environment can be created with the following commands:
conda create -n core python=$(grep -E '^requires-python' pyproject.toml | grep -oE '[0-9]+\.[0-9]+')
conda activate core
pip install -e .[dev,partners] -e ../spec-bioimage-io[dev]
Logging level
bioimageio.spec and bioimageio.core use loguru for logging, hence the logging level
may be controlled with the LOGURU_LEVEL environment variable.
The bioimageio CLI has logging enabled by default.
To activate logging when using bioimageio.spec/bioimageio.core as a library, add
from loguru import logger
logger.enable("bioimageio")
Changelog
See changelog.md
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