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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.
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 webknossos.org for free.Please contact us to get the dataset uploaded.
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You will receive monthly insights about the latest tools and techniques for biological image analysis, updates on webKnossos’ new features and links to recent scientific discoveries.
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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
10.1126/science.abb4534
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
10.7554/eLife.46876
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
10.1126/science.aay3134
Testimonials
"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
Sidney A. Fox and Dorothea Doctors Fox Professor of Ophthalmology and Visual Science at Brown University
"scalable minds are an amazing team: highly professional, expert software design, 100% achievers. They have been essential for our development of efficient human-machine interaction with large-scale image data of brain circuits. The software they built for us is world-leading in our field."
Moritz Helmstaedter
Director - Max Planck Institute for Brain Research
Blog
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 ...