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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.
Highlights
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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 provide 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
Professor,Brown University
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 sharing 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
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Blog
Read about the latest feature highlights, usage tutorials, and research success stories.
Automated Neuron Reconstruction
How to debug a synapse classifier with webKnossos
ML workflows for large-scale reconstruction projects