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: https://webknossos.org/
Exploration of large 3D image datasets
Fully browser-based user experience with efficient data streaming
Creation/editing of skeleton and volume annotations
Optimized performance for large annotations
User and task management for high-throughput crowdsourcing
Sharing and collaboration features
Standalone datastore component for flexible deployments
Supported image formats: Grayscale, Segmentation Maps, RGB, Multi-Channel
Documented frontend API for user scripts, REST API for backend access
Open-source development with automated test suite
Docker-based deployment for production and development
If you need help with webKnossos, feel free to contact us at [email protected] or write a post in the forum. scalable minds also offers commercial support, managed hosting and feature development services.