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We provide several free, open-source libraries and tools alongside WEBKNOSSOS to aid with data analysis.

WEBKNOSSOS Python Library

  • webknossos-libs
  • Read The Docs
  • Our official Python library for working with WEBKNOSSOS datasets, skeleton and volume annotations and for downloading/uploading data from your WEBKNOSSOS instance through the REST API.
  • Read & write WEBKNOSSOS datasets and *.wkw files (raw image data and volume segmentations)
  • Read & write *.nml files (skeleton annotations)
  • Download, modify and upload datasets to WEBKNOSSOS



  • A WEBKNOSSOS compatible data connector written in Python
  • WEBKNOSSOS-connect serves as an adapter between the WEBKNOSSOS data store interface and other alternative data storage servers (e.g., BossDB) or static files hosted on Cloud Storage (e.g. Neuroglancer Precomputed)

webKnossos Wrap Data Format (wkw)

  • webknossos-wrap
  • Library for low-level read and write operations to wkw datasets
  • Use the WEBKNOSSOS Python API above for easy-to-use, high-level access to wkw datasets
  • Available for Python, MATLAB, C/C++, and others

MATLAB NML Functions

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