Tooling

We provide a number of free, open-source libraries and tools alongside webKnossos to aid with data analysis.

webKnossos Wrap Data Format (wkw)

• https://github.com/scalableminds/webknossos-wrap
• Library to read and write wkw datasets
• Available for Python, MATLAB, C/C++, and others

webKnossos Connect

• https://github.com/scalableminds/webknossos-connect
• 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 Cuber

• https://github.com/scalableminds/webknossos-cuber
• Converts image stacks into webKnossos-wrap dataset (*.wkw) and vice-versa
• Supports TIFFs, jpeg, Knossos Cubes, tiled images stacks (e.g. Catmaid)
• Read more about the support data formats

wkNML

• https://github.com/scalableminds/wknml
• Python library for reading and writing webKnossos NML skeleton files

MATLAB NML Functions

• https://github.com/mhlabCodingTeam/SegEM/tree/master/auxiliaryMethods
• MATLAB utilities and function for working with NML skeletons provided as part of the SegEM publication