WEBKNOSSOS

• Fly through your data for fast skeletonization and proof-reading
• Create 3D training data for automated segmentations efficiently
• Scale data reconstruction projects with crowdsourcing workflows
• Share datasets and annotations with collaborating scientists

Start using WEBKNOSSOS - On your own server - User Documentation - Contact us

Website and hosted version

https://webknossos.org

Features

• Exploration of large 3D image datasets
• Fully browser-based user experience with efficient data streaming
• Creation/editing of skeleton and volume annotations
• Innovative flight mode for fast skeleton annotation
• Optimized performance for large annotations
• User and task management for high-throughput crowdsourcing
• Sharing and collaboration features
• Proof-Reading tools for working with large (over)-segmentations
• Standalone datastore component for flexible deployments
• Supported dataset formats: WKW, Neuroglancer Precomputed, and BossDB, Zarr, N5
• Supported image formats: Grayscale, Segmentation Maps, RGB, Multi-Channel
• Support for 3D mesh rendering and on-the-fly isosurface generation
• Export and streaming of any dataset and annotation as Zarr to third-party tools
• Documented frontend API for user scripts, REST API for backend access
• Open-source development with automated test suite
• Docker-based deployment for production and development
• Detailed Documentation

Publication

Boergens, Berning, Bocklisch, Bräunlein, Drawitsch, Frohnhofen, Herold, Otto, Rzepka, Werkmeister, Werner, Wiese, Wissler and Helmstaedter webKnossos: efficient online 3D data annotation for connectomics. Nature Methods (2017) DOI:10.1038/NMETH.4331.

Read more about the original publication.

Installation

WEBKNOSSOS is open-source, so you can install it on your own server.

Check out the documentation for a tutorial on how to install WEBKNOSSOS on your own server.

For development installations, please see DEV_INSTALL.md file.

Contributions, Contact and Support

We welcome community feedback and contributions! We are happy to have

• general feedback, observations and questions on the image.sc forum,
• feature suggestions and bug reports as issues on GitHub,
• documentation, examples and code contributions as pull requests on GitHub.

For details on community contributions, please refer to our Contributing guide.

Contact us at [email protected].

scalable minds offers commercial hosting, support and development services for WEBKNOSSOS.

Credits

• scalable minds - https://scalableminds.com/
• Max Planck Institute for Brain Research – https://brain.mpg.de/

WEBKNOSSOS was inspired by KNOSSOS.

Thanks

• Browser Stack for letting us test WEBKNOSSOS on a variety of different devices
• CircleCI for letting us run builds and tests on their CI

License

AGPLv3