The leading in-browser annotation tool for 3D microscopy data for researchers

webKnossos supports your research with efficient data management and advanced tools to create skeleton and volume annotations. It is optimized to manage petabytes of 3D microscopy image data, as required by Neuroscientists.
webKnossos is developed as an open-source project in collaboration with international research partners.



High Speed Skeleton Annotation

Use Flight mode to quickly capture high-quality skeleton annotations. Organize the UI to fit your needs and discover your data in the easy-to-use viewer.

Create fine-grained skeleton annotations: Mark branch points and overlay 3D mesh structures on your data. Easily organize your skeletons into groups and highlight special interest regions with comments.


Simple Collaboration

As a web-based application, webKnossos makes it extremely easy to share links to your datasets and annotations. Send protected deep links to regions within your dataset for your colleagues to review.

Support your paper publications by publishing your datasets and annotations with webKnossos for everyone to discover. No registration required and immediate access to viewing the original data.

Efficient Volume Annotation

Use webKnossos to create and proof-read dense 3D volume annotations. Advanced tools make it easy to label volume data in order to train a machine learning model. Quickly refine existing annotations and correct mistakes created from automated segmentation systems.

Explore your volume data in 3D through on-the-fly 3D isosurface visualizations.


Dataset Management

webKnossos supports a wide range of common 3D data formats. (Knossos cubes, WKW, Neuroglancer Precomputed, BossDB, Tiff Stacks) Datasets can be hosted on-premise or in our cloud for simplicity.

Work with multi-channel datasets. From simple grayscale and RGB data to (multi-channel) segmentation layers. webKnossos is optimized for working with 3D electron, light, and fluorescence microscopy datasets.

Datasets support access-level control and can be securely shared with colleagues and made available for reviewers.

Project & Task Management

Reconstructing large-scale Connectomics datasets can be daunting. Manage skeleton and volume annotations with advanced project and task management features. Leverage auto-assignments within your team or crowd-sourcing. View and download the aggregated individual results as a whole project.
Fine-grained user access levels and subteams help you manage datasets and tasks within your lab.


Apply for our Pilot Program to help shape future of webKnossos.

Looking for Automated Image Analysis?

Check out Voxelytics and image analysis services from scalable minds. Reconstruct rich information from microscopy images with machine learning-based tools. Automate tasks such as image alignment, registration, dense segmentation, and object detection.