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The webknossos Python package provides an API for working with WEBKNOSSOS datasets, annotations, and for WEBKNOSSOS server interaction. To get started, check out the installation instructions and the code examples, such as


  • 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

Source Code

The webknossos Python package is open-source on GitHub. Feel free to report bugs there or open pull requests with your features and fixes.


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