Data Export through Python¶

The WEBKNOSSOS Python library makes it very easy to download/upload any of your organization's datasets, and annotations. For detailed info, please refer to the webknossos-libs documentation website for guides and tutorials.

There are also quick start instructions for Python download available directly from the WEBKNOSSOS UI.

Example Snippets¶

The WEBKNOSSOS Python library can be installed using pip. We recommend to use a virtual environment, e.g. with uv.

pip install webknossos

Downloading Annotations¶

import webknossos as wk

with wk.webknossos_context(
    token="<your_api_token>",
    url="https://webknossos.org"
):
    annotation = wk.Annotation.download("<annotation_id>")

Downloading Datasets¶

import webknossos as wk

with wk.webknossos_context(token="<your_api_token>", url="https://webknossos.org"):
    # Get a reference to the dataset without downloading it. 
    # Image data will be streamed when being accessed.
    remote_dataset = wk.Dataset.open_remote(
        dataset_id="<dataset_id>",
    )

    # You can access dataset layers via keys and as attributes.
    color_layer = remote_dataset.get_layer("color")

Authentication¶

The WEBKNOSSOS requires you to authenticate yourself via an API Token to access your data. You can find your API Token in your user profile settings.