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webKnossos

webKnossos is the leading in-browser annotation tool for 3D microscopy data for researchers

Discover webKnossos

webKnossos supports your research with efficient data management and advanced tools to create skeleton and volume annotations.
It is optimized to manage terabytes 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 Annotations

    Use our published Flight mode to quickly capture high-quality skeletons

  • Simple Collaboration

    webKnossos runs in the browser. Share links to annotations and publish datasets

  • Volume Annotation

    Create and proof-read dense volume annotations. 

  • Dataset Management

    Hosted and on-premise data stores with support for a wide range of data formats. 

Hosting

Our hosting solutions get you started with webKnossos today. 

Public Hosting

Free

  • Try out webKnossos for free with any published datasets on webknossos.org
  • Unlimited accounts for your organization
  • Suggest new datasets for publication
  • Community Support
  • All other wK features
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Premium Hosting

From €200per month*

  • Upload and work with your data hosted on scalable minds servers
  • From 100GB of data storage
  • Managed monitoring and backups
  • Help with dataset upload and conversion 
  • Email support
  • Everything from the Public Hosting
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Custom Hosting

From €800per month*

  • On-Premise hosting of your data
  • Unlimited data storage
  • Priority Email & Slack Support
  • Insights about the development roadmap
  • Custom hosting solutions
  • Everything from Premium Hosting

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* VAT not included

Feature Overview

  • Annotations

    • Skeleton & volume annotations

    • High-speed Flight mode

    • Segmentation proofreading

    • Comments, trees & groups 

    • Measurement tools

    • 3D mesh support

    • Mapping support for volumes

    • 3D isosurface visualization

  • Datasets

    • Large-scale dataset management

    • Multi-layer support(e.g., raw, segmentation)

    • On-premise data stores

    • Works with electron, light and fluorescence microscopes

    • Wide range of data sources(WKW, Tiff, Neuroglancer, BOSS)

    • Python and MATLAB libraries

  • Collaboration

Learn more about webKnossos

Check out our recent webKnossos series on the blog. Learn more about new features and tutorials

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Article illustration photo
  • Quantum CEO & our partners
  • Quantum CEO & our partners
  • Quantum CEO & our partners

Looking for Automated AI Image Analysis? 

webKnossos is excellent for viewing, managing and annotating large-scale image datasets but sometimes you need more power to scale.
We offer a wide range of image analysis services for reconstructing rich information from microscope images. We can help with image alignment, dense segmentation, and object detection.
Learn more

Want to work with us?

Learn how webKnossos can work for you. Everything from hosting to feature development.