Tooling
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
WEBKNOSSOS Cuber
- webknossos-libs/wkcuber
- Read The Docs
- CLI tool for converting (volume) image data into webKnossos-wrap datasets (*.wkw) and vice-versa
- Supports TIFF stacks, jpeg, dm3, Knossos Cubes, tiled images stacks (e.g. Catmaid) and many more
- Read more about the support data formats
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
- https://github.com/mhlabCodingTeam/SegEM/tree/master/auxiliaryMethods
- MATLAB utilities and functions for working with NML skeletons provided as part of the SegEM publication
- Developed by Connectomics Department at Max-Planck-Institute for Brain Research