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. 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.

Getting Started

Sign up for a free account on https://webknossos.org/ and either upload one of your own datasets, or work with a large selection of published community datasets.

Features

• Exploration of large 3D image datasets as found in electron-microscopy, synchrotron, CT, MRI, Micro/Nano-CT
• 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. Every dataset and annotation can be securely shared as a web link with others
• 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
• 3D Mesh Visualization
• Integrated Synapse and Connectome Viewer
• Documented Python library for API access and integration in custom analysis workflows
• Documented frontend API for user scripting, REST API for backend access
• Open-source development with automated test suite
• Docker-based deployment 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.