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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:



Skeleton Annotations Volume Annotations Flight Mode

Managing Datasets Working on Tasks Showcasing Datasets

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, feel free to contact us at or write a post in the forum. scalable minds also offers commercial support, managed hosting, and feature development services.

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