Introducing webKnossos

The reconstruction of neuronal networks in the brain (Connectomics) is still massively limited by the required amount of human work hours for data analysis. webKnossos is an in-browser annotation tool for 3D electron microscopic data that facilitates user interaction with 3D image data. Together with ever better automated neuron segmentations, webKnossos can push connectomics to efficient large-scale reconstructions. In flight mode, users can go as fast as the human visual system allows – at a speed of 1.5 ± 0.6 mm/h for axons and 2.1 ± 0.9 mm/h for dendrites in 3D electron microscopic data from mammalian cortex. With this, webKnossos provides at least an order of magnitude speed-up.

User-generated skeletons and computer-generated segmentations for efficient circuit reconstruction (webKnossos and SegEM, Berning et al., 2015 Neuron).

Flight mode in webKnossos: tracing along an axon in the cerebral cortex, including the annotation of branch points.


Data sets

Simply import data sets and let webKnossos handle dozens of terabytes with ease. EM connectomics datasets, volume segmentations, and large-scale fluorescence microscopy datasets are supported.

Data sets can be hosted in your local data center or the cloud and are effortlessly streamed to you. All reconstructed skeletons can easily be downloaded for further analysis.

Viewing & Tracing

webKnossos enables real-time flying through large 3D image data. Use different 3D views (orthogonal, oblique and flight mode) to view and trace your data sets. Annotations produce skeleton- and volume-based annotations. Well-trained tracers can reconstruct at a speed of above 1 mm/h.

User management & Collaboration

Do you have large teams and complex structures? webKnossos manages multiple users, projects, and teams with ease. Assign your annotators to tasks based on their experiences level and reconstruct discover large datasets. All work hours are logged for compensation management.

Work collaboratively and simply share URLs to data locations, viewing positions, and skeletons. All tracings and their associated comments are permanent and can be easily shared between scientists, making cross-referencing of relevant locations in very large datasets seamless.

Scriptable Workflows & API

webKnossos is extendable and offers user-side scripting, and an API. Ideal to try out new annotation strategies or viewing support, that can later be integrated into the latest webKnossos release.