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Python API for working with webKnossos datasets, annotations, and for webKnossos server interaction.

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webKnossos Python Library

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Python API for working with webKnossos datasets, annotations, and for webKnossos server interaction.

For the webKnossos server, please refer to


  • easy-to-use dataset API for reading/writing/editing raw 2D/3D image data and volume annotations/segmentation in webKnossos wrap (*.wkw) format
    • add/remove layers
    • update metadata (datasource-properties.json)
    • up/downsample layers
    • compress layers
    • add/remove magnifications
    • execute any of the wkCuber operations from your code
  • manipulation of webKnossos skeleton annotations (*.nml) as Python objects
    • access to nodes, comments, trees, bounding boxes, metadata, etc.
    • create new skeleton annotation from Graph structures or Python objects
  • interaction, connection & scripting with your webKnossos instance over the REST API
    • up- & downloading annotations and datasets

Please refer to the documentation for further instructions.


The webknossos package requires at least Python 3.7+.

You can install it from pypi, e.g. via pip:

pip install webknossos


See the examples folder or the the documentation.

Contributions & Development

Please see the respective documentation page.


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