WEBKNOSSOS
@webknossos
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Visualize, share, segment, and annotate your large 3D images online. #opensource #volumeEM #bioimageanalysis #connectomics #zarr Bluesky: @webknossos.org
Joined December 2018
Experience fast 3D microscopy data exploration with WEBKNOSSOS. Annotate your data with AI, explore 3D meshes, collaborate in real-time, manage datasets, and more. Share your research with just one click. Sign up for free at
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🌟Enhancement🌟. Only show selected segments. Toggle the “Hide unlisted segments” setting to pick which segments will be shown.
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Tuesday tips 🐾 for Pros. Did you know you can easily decide whether you want to overwrite while annotating? For example, when using the eraser, just press “Shift” to remove only the active segment. This shortcut also works for the brush and lasso! . Check out the Youtube
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🌟Enhancement🌟. Navigate WEBKNOSSOS faster with the new Command Palette. It allows you to streamline your workflow by quickly searching for tools, jumping to specific datasets, and accessing key features with just a few keystrokes. Activate with 'Ctrl/Cmd + P'
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Tuesday tips 🐾 for Pros. While using the brush, press and hold ‘Shift’ to temporarily activate the segment picker - or ‘Shift + Ctrl’ to switch to the eraser. Check out the Youtube playlist for more tips:
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Working with large datasets? Watch our workflow video to learn how to upload, organize with folders and metadata, set access permissions, and more - making data management seamless.
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Tuesday tips 🐾 for Pros. To move a bounding box, simply make sure the bounding box tool is activated, hold ‘Ctrl’ and drag the box to reposition it.
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🌟Enhancement🌟. You can now edit segment or skeleton tree names by double-clicking their entry in the list - or change their names directly the metadata tab. Plus, you can now double-click on a segment in the segmentation to activate it!
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Tuesday tips 🐾 for Pros. Save your view settings as default! This way, when someone opens your dataset, they’ll see the exact same view as you. Check out the Youtube playlist for more tips:
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Carles Bosch (Francis Crick Institute) discussed at the vEM Data Challenges Symposium how correlative 2-photon and X-ray imaging uncovers neural computation in olfactory circuits, advancing our understanding of brain function. Unfortunately, there was an issue with the.
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🚀 Advancing Retinal Connectomics!.Prof. David Berson from Brown University discussed strategies for large-scale segmentation in retinal connectomics at the vEM Data Challenges Symposium. 🎥 Watch the recorded session here: (.
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Tuesday tips 🐾 for Pros. To change the radius of a node, simply hold 'Shift' and scroll with the mouse wheel.
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Annotate with the basic and smart tools in WEBKNOSSOS, leave a comment, and request feedback. Watch our annotation workflow video and get started for free on
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🚀 Starting in a few hours! Join leading experts as they share insights on handling large #VolumeEM datasets & improving collaborative workflows. 📅 March 6 | 5-7PM CET | Online | Free.🔗 Register now:
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🌟Enhancement🌟. Quickly check a dataset's volume by hovering over the extent icon in the info tab.
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⏳ 4 more days to go! Don't miss our online symposium on #VolumeEM data challenges - practical solutions for massive datasets & collaboration. 📅 March 6, 2025 | 5-7PM CET | Free registration.🔗 Sign up:
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⏳ 4 more days to go! Don't miss our online symposium on #VolumeEM data challenges - practical solutions for massive datasets & collaboration. 📅 March 6, 2025 | 5-7PM CET | Free registration.🔗 Sign up:
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Luke Noon from CIPF will speak at our symposium on vEM data challenges about pioneering vEM workflows beyond the brain. Learn how his team maps liver tissues with innovative annotation & collaboration strategies!. 📅 March 6, 2025 | 5-7PM CET | Free registration.📖 Full abstract
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In our symposium on vEM data challenges, Prof. David Berson from Brown University will explore strategies for large-scale segmentation in retinal connectomics. Register now for free!. 📅 March 6, 2025 | 5-7PM CET.📖 Full abstract and sign up link:
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Tuesday tips 🐾 For Beginners. To make a quick screenshot in WEBKNOSSOS, simply press ‘Q’. If you're using the 4-viewports layout, a screenshot of each viewport will be captured automatically. Check out the Youtube playlist for more tips:
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🐣 New feature 🐣. You can now activate “Selective Visibility” in WEBKNOSSOS to highlight only the active segment or the ones you hover over. This is great to quickly track cell extensions in complex segmentations. Try it out now on
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