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 skeleton and volume annotations. Powerful user and task management features automatically distribute tasks to human annotators. WEBKNOSSOS is also a platform for showcasing datasets alongside a paper publication.

Features¶

Exploration of large 2D, 3D, 4D image datasets as found in electron-microscopy, synchrotron, CT, MRI, Micro/Nano-CT, and light microscopy
Fully browser-based user experience. No installation required
Efficient 3D data streaming for quick loading speeds
Creation/editing of skeleton (line-segments) and 3D volumetric annotations
Innovative flight mode for fast skeleton annotation
User and task management for high-throughput collaboration in the lab or crowdsourcing
Easy Sharing. Share your datasets and annotations securely with others using web links
Fine-grained access permission and and user roles for secure collaboration
AI Quick Select tool to speed up segmentation
Standalone datastore component for flexible deployments
Supported dataset formats: Zarr, WKW (Optimized), KNOSSOS cubes, Neuroglancer Precomputed, N5, and image stacks (some formats will be converted on upload)
Supported image formats: Grayscale, Segmentation Maps, RGB, Multi-Channel
Supports Time Series datasets
3D Mesh Visualization
Integrated Synapse and Connectome Viewer
Python library with documentation for API access and integration in custom analysis workflows
Frontend API for user scripting
Developed as an open-source project with automated testing
Deployable with Docker for production and development

Screenshots¶

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 hello@webknossos.org or write a post in the community forum. scalable minds also offers commercial support, managed hosting, and image analysis services.