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.

New: 10GB of storage for free accounts


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 provides 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.

webKnossos in action

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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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.

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


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


Annotation techniques for large-scale volume EM datasets

Generating annotations from volumetric electron microscopic (EM) image datasets is important for the work of many neuroscientists. As these EM datasets massively grow in size to many terabytes, smart tools as well as collaboration workflows are required to obtain high-quality annotations. The resulting annotations can be directly used for visualization or quantification purposes or indirectly, by training or evaluating a Machine Learning (ML) system...


New annotation and usability features in webKnossos

Today I would like to give you an overview of the many new features and UX improvements that we added to webKnossos over the last half-year.

At scalable minds, webKnossos is our primary tool for viewing the results of our automated neuron reconstructions, collaborate on training data annotation, and share the results with colleagues. Many of the new features are therefore inspired by our work in Connectomics and biomedical image reconstruction...


Cross-Dataset Segmentation Models

At scalable minds we work a lot with research labs in the Connectomics field and beyond to help them with automated image analysis and EM dataset reconstructions. We use state-of-the-art machine learning algorithms for automated dense reconstructions of neuron connections in brain tissue. Our alignment and segmentation tools are optimized to handle the terabyte-scale 3D EM datasets...

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