WEBKNOSSOS

WEBKNOSSOS is an open-source tool for annotating and exploring large 3D image datasets.

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, Zarr, N5
Supported image formats: Grayscale, Segmentation Maps, RGB, Multi-Channel
Support for 3D mesh rendering and ad-hoc mesh 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.

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.

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

scalableminds / webknossos

readme