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.

Looking for 3D image alignment?

Check out our alignment services. Pre-process your large-scale 2D and 3D microscopy datasets. Automate tasks such as Alignment, Registration, Stitching, Gradient Correction, and Normalization.


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


Fast browsing of large datasets

Work on GB to PB large image datasets from your computer, home-office laptop, or tablet with the powerful storage and streaming technology of WEBKNOSSOS.


Advanced annotation tools for faster results

Work faster with efficient annotation features such as the volume interpolation tool or the flight mode for exceptionally high-speed tracing of axons or dendrites.


Extensive visualization capabilities

Visualize your 2D or 3D datasets with multiple channels. Flexibly adjust contrasts and colors. Load and explore 3D meshes. Visualize your ML predictions, and more.


Secure and efficient collaboration

Work with several colleagues on one annotation. Your datasets are only accessible by you and your chosen collaborators. Once you are ready, publish them with a simple link.

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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

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.

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.

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


WEBKNOSSOS enables extraordinary ease in team annotations of our connectomic datasets. Its web-based format […] has opened doors to cross-university collaborations that are unbound from resource limitations that have historically come with large dataset annotations.Perhaps more importantly than the software itself, I have found the technical support and active engagement with its user community, is what makes WEBKNOSSOS the ideal software today and moving forward. I very much look forward to what webKnossos becomes as the field of connectomics advances.

Gregg Wildenberg

Staff Scientist,The University of Chicago


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 to share 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


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


Reconstructing connectomes from human, macaque, and mouse cortex with Voxelytics

Interview with Daniel Werner - July 2022


Reconstructing a kiwi fruit… with SBEM (sort of)

By Albane de la Villegeorges - January 2023


How to debug a synapse classifier with WEBKNOSSOS

Interview with Valentin Pinkau - October 2021

Looking for Neuron and Connectome reconstruction?

Check out our image analysis services for neuron and connectome reconstructions from volume EM data. Automate tasks such as image alignment, registration, dense segmentation, and object detection.