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.


In this blog, we introduce new features and share insights into the WEBKNOSSOS development roadmap.

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    New AI-based quick segment tool in WEBKNOSSOS

    FEATURE ARTICLE - June 2023

    We are excited to announce the integration of Meta’s new AI model, SAM: Segment Anything, into WEBKNOSSOS! Learn how to make the best out of the AI option in WEBKNOSSOS. Read more.

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    Automation and interoperability

    TUTORIAL - June 2023

    In this tutorial, we will learn how to download data as a Tiff stack with the WEBKNOSSOS UI, how to automate this process, and how to incorporate an N5 remote dataset into WEBKNOSSOS. Read more.

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    Volume annotations with WEBKNOSSOS

    TUTORIAL - May 2023

    In this tutorial, we will explore the annotation features of WEBKNOSSOS. We will cover everything from opening and annotating a published dataset to utilizing both basic and advanced annotation tools. Read more.

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    Data sharing with WEBKNOSSOS

    TUTORIAL - April 2023

    In this tutorial, you will discover how to efficiently manage and share your data. Read more.

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    Self-hosted data for WEBKNOSSOS

    TUTORIAL - February 2023

    This tutorial explains how to store data externally, by converting data into OME-Zarr and setting up a static file server for use with WEBKNOSSOS. Read more.

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    Organize your data in folders

    FEATURE - February 2023

    The folder structure in WEBKNOSSOS allows you to have your datasets structured, organized, and easily accessible. Read more.

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    Rebranding WEBKNOSSOS

    STORY - February 2023

    Follow our journey of redesigning the branding of WEBKNOSSOS, aligning it more closely with our identity and values. Read more.

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    Feature highlights of WEBKNOSSOS from 2022

    FEATURE - February 2023

    Read all about the top features of 2022: quick-select, interpolation tool, collaborative annotations, and more. Read more.

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    Comparing Array Tomography with Serial Block-face Electron Microscopy

    EXPERIMENT - January 2023

    Array tomography and Serial Block-face Electron Microscopy are two microscopy techniques that work in a similar way and are hard to understand. We playfully explained and compared these techniques using a fig (AT) and a tomato (SBEM). Read more.

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    Reconstructing a kiwi fruit… with SBEM (sort of)

    EXPERIMENT - January 2023

    How would you explain SBEM/volume EM and 3D reconstruction to your grandparents? With a camera, a knife, and a kiwi fruit. Read more.

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    Data Streaming with WEBKNOSSOS Libs

    TUTORIAL - November 2022

    Today, we would like to highlight some features and quality of life improvements WEBKNOSSOS acquired over the summer. They will accelerate your workflows and make the annotating of EM data easier. Read more.

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    Using Zarr Datasets with WEBKNOSSOS

    TUTORIAL - October 2022

    This tutorial explains how to load any Zarr-format-based datasets into WEBKNOSSOS. We support reading Zarr dataset from the local file system, cloud providers such as S3 and Google Cloud, as well as through any web server over HTTP. Read more.

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    Zarr Streaming from WEBKNOSSOS

    TUTORIAL - September 2022

    In this blog post, we will share some progress on streaming any dataset from WEBKNOSSOS to compatible third-party programs through the Zarr interface. Read more.

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    Summer update: annotate faster than ever with these new features

    FEATURE - August 2022

    Today, we would like to highlight some features and quality of life improvements WEBKNOSSOS acquired over the summer. They will accelerate your workflows and make the annotating of EM data easier. Read more.

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    Interview with Carles Bosch on Correlative Multimodal Imaging

    INTERVIEW - July 2022

    Carles Bosch, principal laboratory research scientist at the Sensory Circuits and Neurotechnology Laboratory of the Francis Crick Institute, explains his research on glomerular column circuits in the mouse olfactory bulb. Read more.

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

    INTERVIEW - July 2022

    Daniel Werner, data scientist at scalable minds, tells us about the analysis and reconstruction of 9 vEM datasets he contributed to for a comparative connectomic study among species, by the Max Planck Institute for Brain Research. Read more.

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    How to speed up your annotations using the volume interpolation tool in WEBKNOSSOS

    FEATURE - June 2022

    In this tutorial, we will tell you about the interpolation feature. Draw on one slice, move forward by a few slices, draw again… and WEBKNOSSOS will interpolate the segments between the two annotated slices. Read more.

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    How to debug a synapse classifier with WEBKNOSSOS

    INTERVIEW - October 2021

    Today, we will have a chat with one of our colleagues: Valentin Pinkau. As an experienced data scientist specializing in connectomics, he has some interesting insights to share. Read more

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    Automated Neuron Reconstruction

    CASE STUDY - August 2021

    With the recent publication of the “Dense connectomic reconstruction in layer 4 of the somatosensory cortex“ paper by the Max-Planck-Institute for Brain Research, we showcase WEBKNOSSOS and the ML reconstruction pipeline Voxelytics. Read more

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    Machine learning workflows for large-scale reconstruction projects

    TUTORIAL - July 2021

    Here, we share some tips on how to reconstruct biological objects (e.g. neurons) from tera- or peta-scale image datasets. Read more.

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.

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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.

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.