core-bioimage-io-widgets

This is a QT UI widget for creating BioImage.io models' specs, and building model.zip files compatible with BioImage model zoo.

installation

Dependecies:

• PyQt5
• qtpy
• markdown
• PyYaml
• bioimageio.core

To install the project, clone the github repository and install it via pip:

git clone https://github.com/juglab/core-bioimage-io-widgets.git
cd core-bioimage-io-widgets
pip install -e .

To run widget issue this command:

bioimageio-widget

napari

You can use this widget inside your napari plugin to export your model in a compatible format with the bioimage.io model zoo.
To do that:

• Import the BioImageModelWidget into your plugin's code
• Create a new instance of the imported widget and show it!
• Either fill-up the model's specs through the ui or you can pass your model's data to the widget instance via load_specs method.
• Finally you can export your model with the Build button provided by the widget.

    from core_bioimage_io_widgets.widgets import BioImageModelWidget

    # Populate the model data dictionary
    # The data format follows the spec-bioimage-io model's rdf:
    # https://github.com/bioimage-io/spec-bioimage-io/blob/gh-pages/model_spec_latest.md
    model_data = {
        "format_version": "0.4.9",
        "type": "model",
        "timestamp": dt.datetime.now().isoformat(),
        "name": "My Model",
        "description": "Some descriptions.",
        "license": "BSD-3-Clause",
        "documentation": "./path/to/file.md",
        "weights": {"keras_hdf5": {"source": str(weights)}},
        "authors": authors,
        "test_inputs": [inputs],
        "test_outputs": [outputs],
        "cite": cite,
        ...
    }

    # Create an instance of bioimage.io core ui widget
    # and pass the model data to it:
    bioimageio_win = BioImageModelWidget()
    bioimageio_win.show()
    bioimageio_win.load_specs(model_data)