Welcome to webKnossos
webKnossos is an open-source tool for exploring large 3D electron-microscopy (EM) and light-microscopy (LM) datasets as well as collaboratively generating annotations. The web-based tool is powered by a specialized data-delivery backend that stores large datasets efficiently on disk and serves many concurrent users. webKnossos has a GPU-accelerated viewer that includes tools for creating and sharing annotations (skeletons and volumes). Powerful user and task management features automatically distribute tasks to human annotators. There are a lot of productivity improvements to make the human part as efficient as possible. webKnossos is also a platform for showcasing datasets alongside a paper 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.
Try webKnossos on a large selection of published datasets: https://webknossos.org/
- 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
- Standalone datastore component for flexible deployments
- Supported dataset formats: WKW (Optimized), KNOSSOS cubes, Neuroglancer Precomputed, and BossDB
- Supported image formats: Grayscale, Segmentation Maps, RGB, Multi-Channel
- Mesh Visualization
- 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
Credits and Help
If you need help with webKnossos, feel free to contact us at firstname.lastname@example.org or write a post in the forum. scalable minds also offers commercial support, managed hosting, and feature development services.