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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.
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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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.
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.
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
Cell-type specific innervation of cortical pyramidal cells at their apical tufts
Ali Karimi, Jan Odenthal, Florian Drawitsch, Kevin M. Boergens, Moritz Helmstaedter
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
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.
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.
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.
Read about the latest feature highlights, usage tutorials, and research success stories.