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.​

Demo

Try webKnossos on a large selection of published datasets: 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 tracing​

• Optimized performance for large tracings

• 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

Screenshots

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Credits and Help

webKnossos was developed by scalable minds in collaboration with the Max Planck Institute for Brain Research.

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.