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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 3.8.

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.


AGPLv3 Copyright scalable minds

Test Data Credits

Excerpts for testing purposes have been sampled from:

  • Dow Jacobo Hossain Siletti Hudspeth (2018). Connectomics of the zebrafish's lateral-line neuromast reveals wiring and miswiring in a simple microcircuit. eLife. DOI:10.7554/eLife.33988
  • Zheng Lauritzen Perlman Robinson Nichols Milkie Torrens Price Fisher Sharifi Calle-Schuler Kmecova Ali Karsh Trautman Bogovic Hanslovsky Jefferis Kazhdan Khairy Saalfeld Fetter Bock (2018). A Complete Electron Microscopy Volume of the Brain of Adult Drosophila melanogaster. Cell. DOI:10.1016/j.cell.2018.06.019. License: CC BY-NC 4.0
  • Bosch Ackels Pacureanu et al (2022). Functional and multiscale 3D structural investigation of brain tissue through correlative in vivo physiology, synchrotron microtomography and volume electron microscopy. Nature Communications. DOI:10.1038/s41467-022-30199-6

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