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Python package to work with webKnossos datasets and annotations

Project description

webKnossos Python Library

PyPI version Supported Python Versions Build Status Documentation Code Style

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.


AGPLv3 Copyright scalable minds

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