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.
Exploration of large 3D image datasets
Fully browser-based user experience with efficient data streaming
Creation/editing of skeleton and volume annotations
Optimized performance for large datasets and annotations
Sharing and collaboration features
Efficient keyboard shortcuts
Standalone datastore component for flexible deployments
Supported dataset formats: WKW (Optimized), KNOSSOS cubes
Supported image formats: Grayscale, Segmentation Maps, RGB, Multi-Channel
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
If you need help with webKnossos, there is a Community Support forum where members of the community and scalable minds are happy to answer your questions. scalable minds also offers commercial support, managed hosting and feature development services. Please contact us if you want to learn more.