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webKnossos is the leading in-browser annotation tool for 2D/3D microscopy data for life sciences

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 unique 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 


Our hosting solutions get you started with webKnossos today. 

Public Hosting


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

Premium Hosting

From €250per 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

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


webKnossos Support Subscription

Hands-on support services for your locally installed instance of webKnossos

    Regular installation of updates and migrations
    Help with dataset upload and conversion 
    Premium email support

From 200€ per month*

* VAT not included

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Feature Overview

  • Annotations

    • Skeleton & volume annotations

    • High-speed Flight mode

    • Merge and split segmentations

    • Comments, trees & groups 

    • Measurement tools

    • 3D mesh generation and visualization

    • ID Mapping support for segmentations

  • Datasets

    • Support for peta-scale datasets

    • Electron, light, fluorescence microscopy and MRI/CT

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

    • On-premise data connectors

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

    • Python and MATLAB libraries for import/export

  • Collaboration

webKnossos was developed in collaboration with the Max Planck Institute for Brain Research.


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

Selected users of webKnossos

  • Quantum CEO & our partners
  • 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.

Want to work with us?

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

About scalable minds

scalable minds is a software engineering company with a strong focus on solutions utilizing powerful AI methods for our clients and research partners. We are experts for large-scale image analysis.
Our team consists of currently 16 exceptional software engineers and data scientists. We all share the passion for artificial intelligence, brain research and solving technical challenges.
We are not afraid to tackle complex challenges. Get in touch with us to learn more.

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