Volume annotations
Use the AI-based quick-select and the interpolation feature to speed up 3D annotations. Refinewith manual brush and trace tools. Download the annotations to train a machine learning model or for visualization purposes.
Visualize segmented objects as meshes through the integrated mesh generation. Explore dense segmentations with colored and patterned maps.
Skeleton annotations
Create skeleton annotations of neurons or vasculature, represented as line segments, and measure their path lengths. Organize these skeletons into hierarchical groups. Attach comments to nodes to mark interesting locations in your data.
Experience the unique Flight Mode, designed for high-speed tracing of axons or dendrites. Trained annotator crowds achieve impressive tracing speeds of 1.5 ± 0.6 mm/h for axons and 2.1 ± 0.9 mm/h for dendrites in 3D electron microscopy data. For more details, refer to the WEBKNOSSOS paper.
Autosave and history
WEBKNOSSOS automatically saves annotations every 30 seconds and maintains a versioned history of every action across all annotations. Correcting a mistake is as simple as clicking "undo."
In addition, annotation data on WEBKNOSSOS is externally backed up on a daily basis. For users with paid plans, there is an option to back up datasets as well.
Dataset management
Leverage WEBKNOSSOS as a centralized storage solution for all your large-scale image datasets. Say goodbye to scattered data across numerous hard drives or storage servers. WEBKNOSSOS effortlessly scales to handle petabytes of data.
Ensure secure management of datasets within your organization with fine-grained user access levels and the ability to create subteams. WEBKNOSSOS helps you maintain data security while streamlining dataset management.
Interoperability
Download your data and annotations from WEBKNOSSOS to work with them in other tools. WEBKNOSSOS supports standard formats (e.g. TIFF, STL, N5/ZARR, CSV) for exports. Import your remotely stored datasets as Zarr, N5 or Neuroglancer Precomputed directly in WEBKNOSSOS.
Work with the WEBKNOSSOS file formats in Python using our open-source libraries. For more information on tooling and implementation, refer to the documentation
Tasks and project management
Efficiently manage annotation tasks by setting up assignments for your annotators and utilizing auto-assignment to distribute the workload. Monitor the progress of the annotations using monitoring reports, allowing you to stay updated on the status of the tasks. For further processing, easily download all the created annotations in a merged file.If you don't have annotators available, you can directly hire our annotation services through WEBKNOSSOS, ensuring access to professional annotation support.
Routine connectomic reconstructions with WEBKNOSSOS
Sample Preparation and Warping Accuracy for CMI in the Mouse Olfactory Bulb
Embark on a journey with two scientists in London as they navigate the challenges of managing vast datasets from a serial electron microscope. Witness their discovery of WEBKNOSSOS, the tool that will streamline their data analysis and collaboration, even as their research takes them across continents. Watch on YouTube
Make WEBKNOSSOS the central hub for large image data in your lab. Import data from your microscopes. Visualize, manage and collaboratively annotate your data directly in WEBKNOSSOS. Stream your data to other tools for advanced analysis via OME-Zarr support.
Explore remarkable datasets from the scientific community in WEBKNOSSOS.Sign up to build upon the data and create your own annotations.
Your dataset is not in the list?We are happy to host selected public datasets on webknossos.org for free.Please contact us to get the dataset uploaded.
Highlights from our Blog
New AI-based quick segment tool in WEBKNOSSOS
June 2023
Reconstructing a kiwi fruit… with SBEM (sort of)
January 2023
Tutorial on volume annotations with WEBKNOSSOS
May 2023