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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 skeleton and volume annotations. Powerful user and task management features automatically distribute tasks to human annotators. There are many features to enhance the productivity and efficiency of human annotators. WEBKNOSSOS is also a platform for showcasing datasets alongside a paper publication.

Getting Started

Create a free account on and upload your own datasets or explore the published datasets from the community.



Skeleton Annotations Volume Annotations Flight Mode

Managing Datasets Working on Tasks Showcasing Datasets

Built for Science

WEBKNOSSOS is built for scientists with support by scientists. Our goal is to make image analysis and data exploration accessible and easy to use. While originally designed for the annotation of electron microscopy of neural circuits, we have seen great projects using it to analyze MRI/CT scans, fluorescences microscopy images, and synchrotron datasets.

WEBKNOSSOS' impact on data annotation in neuroscience and Connectomics has been published in Nature Methods, 2017 and many other publications:

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.

Credits and Help

WEBKNOSSOS is 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 community forum. scalable minds also offers commercial support, managed hosting, and image analysis services.