Visualize, share and annotate your large 3D images online 

Upload your data and share links with colleagues. Collaboratively create skeleton and volume annotations, all from your browser. Optimized for multi-terabyte datasets.

webKnossos is open source and has been published in Nature Methods.

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Published datasets on webKnossos

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 for free.Please contact us to get the dataset uploaded.

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Fast browsing

webKnossos scales seamlessly from giga- to petavoxel datasets. Its storage and streaming technologies provide fast browsing speeds to any of your devices, wherever you are.

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webKnossos supports 2D and 3D datasets with multiple channels. Enhance your data with the flexible layer settings and visualize segments in 3D with the mesh generation feature.

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The unique “flight mode” enables very fast skeleton annotation of neurites. Efficient volume annotation tools accelerate training data generation and proofreading.

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Your datasets are only accessible by you and your chosen collaborators. Once you are ready, share them with the scientific community with a click of a button.

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Custom block


Visualize large EM datasets with segmentations. Automatically generate meshes. Tweak the histogram and other settings to improve the view.


Skeleton annotations for measuring neurons, quantifying objects and marking interesting locations in the dataset.


Volume annotation features for creating segmentations and training data.


The unique flight mode enables fast and precise annotations of neurons.


Support for many image modalities, including fluorescence microscopy, electron microscopy, Micro-CT (µCT) and MRI.


Securely share data with collaborators, reviewers and the scientific community.


Task management features for managing annotation projects with dozens or hundreds of annotators.

We are hiring.

You are passionate about science, and eager to learn? Join our team! 

Used by


webKnossos makes working with large datasets easier and enables global collaboration.

Scalable from giga- to petavoxel datasets

webKnossos scales seamlessly from smaller to the largest image datasets available. Support for 2D and 3D datasets with multiple channels.

Unique annotation modes for faster results

The unique “flight mode” enables very fast skeleton annotation of neurites. Efficient volume annotation tools accelerate training data generation and proof-reading.

Fast browsing no matter where you are

webKnossos storage and streaming technology provide fast browsing speeds to your work computer, home-office laptop, and tablet on-the-go. 

Collaborate, securely

Your datasets are only accessible by you and your chosen collaborators. Once you are ready, publish them with a click of a button.

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Research and webKnossos

Here are some publications that used webKnossos. Click here to see all the references.

Postnatal connectomic development of inhibition in mouse barrel cortex
Anjali Gour, Kevin M. Boergens, Natalie Heike, Yunfeng Hua, Philip Laserstein, Kun Song, Moritz Helmstaedter

Science, 2021

Cell-type specific innervation of cortical pyramidal cells at their apical tufts
Ali Karimi, Jan Odenthal, Florian Drawitsch, Kevin M. Boergens, Moritz Helmstaedter

eLife, 2019

Dense connectomic reconstruction in layer 4 of the somatosensory cortex
Alessandro Motta, Manuel Berning, Kevin M Boergens, Benedikt Staffler, Marcel Beining, Sahil Loomba, Philipp Hennig, Heiko Wissler, Moritz Helmstaedter
Science, 2019


webKnossos supports almost all our connectomics work in the retina. It's the best web-based tool out there for integrated team-based annotation, proofreading, display, and output of serial EM data. The toolset is diverse, powerful, and intuitive. The functionality and ease of use just keep getting better. It has been a pleasure to work with the responsive and science-friendly folks at scalable minds.

David Berson

Professor,Brown University

We are working on systems neuroscience in the mouse olfactory bulb. webKnossos is very useful for safely storing large datasets and managing access across multiple users. It makes it simpler sharing insights with collaborators - by facilitating operations such as looking at the very same data or sharing annotations.

Carles Bosch

Principal Laboratory Research Scientist,Francis Crick Institute


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Read about the latest feature highlights, usage tutorials, and research success stories.


Automated Neuron Reconstruction


How to debug a synapse classifier with webKnossos


ML workflows for large-scale reconstruction projects

Looking for Automated Image Analysis?

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