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.

Need ground truth for your deep learning project?

Check out your manual annotation services. The easiest way to acquire high-quality annotations. 

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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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.

Follow us on Twitter to get updates on the latest features

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 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.

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.


Automated Neuron Reconstruction

In the following blog post, I will talk more about the steps required for large scale 3D serial-blockface electron microscopy (SBEM) neuron reconstruction. 
Our goal is to create a fully automated neuron reconstruction and Connectome matrix that allows for meaningful biological analyses. The reconstruction is done using our machine-learning neuron reconstruction software Voxelytics...


Introducing webKnossos’ nuclei classifier for Volume EM

When working in nanoscale neuroscience, you are almost always confronted with the difficulty of biological image analysis for large-scale datasets. In order to make scientific discoveries, most of the time you will need to annotate your data either manually or with the help of a Machine Learning system. webKnossos is the perfect tool to annotate large-scale datasets collaboratively. We decided to go one step further and implement the first ...


ML workflows for large-scale reconstruction projects

Reconstructing biological objects (e.g. neurons) from tera- or peta-scale image datasets is a challenging task. webKnossos has some helpful features to assist with large-scale collaborative reconstruction projects.
webKnossos is a web-based platform for visualizing, annotating and sharing large 3D image datasets. One of the most popular use cases ...

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.