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WEBKNOSSOS

@webknossos.org

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Visualize, share, segment, and annotate your large 3D images online.

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WEBKNOSSOS @webknossos.org · Nov 25

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 webknossos.org!

WEBKNOSSOS @webknossos.org · 1h

🌟Enhancements🌟

The proofreading tool got smarter: you can now define multiple segments around a desired split, and it will automatically pick the optimal split point.

WEBKNOSSOS @webknossos.org · 2d

Tuesday tips 🐾 for Beginners

Need to undo changes and return to a previous version? Simply access the menu and select 'Restore older version’.

Check out the Youtube Playlist for more tips: youtube.com/playlist?lis...

Reposted by WEBKNOSSOS

Carles Bosch @carlesbosch.bsky.social · 16d

#Nanoimaging symposium @crick.ac.uk!

At #CrickXrays25 we'll tackle:
💫synchrotron upgrades
📈current limits in throughput, volume, resolution
🧪sample preparation for X-ray PC imaging
🧠♥️applications in neuroscience and tissue life science

🗓️13th October 2025
🇬🇧🌐 London & online
tinyurl.com/crickxrays25

Hard X-ray imaging of biological soft tissues symposium 2025

tinyurl.com

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WEBKNOSSOS @webknossos.org · 21d

🌟Enhancements🌟

Shared annotations got a big upgrade: they now update live—see your collaborators’ changes as they happen. Simultaneous editing is on the horizon 👀

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WEBKNOSSOS @webknossos.org · 23d

Tuesday tips 🐾 for Beginners

Sort your trees by name or by creation time by clicking the button in the right sidebar.

Check out the Youtube Playlist for more tips: youtube.com/playlist?lis...

WEBKNOSSOS @webknossos.org · Sep 4

🌟Enhancements🌟

Use Ctrl + Shift + Left, Ctrl + Shift + Right, Ctrl + Shift + Up and Ctrl + Shift + Down to rotate in 90 degree increments

Learn more about keyboard shortcuts: docs.webknossos.org/webknossos/u...

WEBKNOSSOS @webknossos.org · Sep 2

Tuesday tips 🐾 for Beginners

Did you know about the 3D viewport settings? You can choose whether to display the planes, only wireframes, or all views along with the data. You can also toggle the dataset and layer borders.
Check out the Youtube playlist for more tips: www.youtube.com/playlist?lis...

Today I learned - Tips for WEBKNOSSOS pros

Few tips and tricks to use on webknossos.org

www.youtube.com

WEBKNOSSOS @webknossos.org · Aug 14

🌟Enhancements🌟

ICYMI: Webknossos viewports are now rotatable.

Use keyboard shortcuts to rotate the orthogonal viewport. Try Shift + Left, Shift + Right, Shift + Up and Shift + Down.

Learn more about keyboard shortcuts: docs.webknossos.org/webknossos/u...

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WEBKNOSSOS @webknossos.org · Aug 12

Tuesday tips 🐾 for Beginners

Did you know you can use the shortcuts K and L to toggle the sidebars in WEBKNOSSOS? You can also use '.' to maximize a viewport.

Check out the Youtube Playlist for more tips: youtube.com/playlist?lis...

WEBKNOSSOS @webknossos.org · Jul 31

🌟Big new feature🌟

Rotate the viewports. You can now freely rotate the orthogonal viewports. Trace your objects in the best angle.

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WEBKNOSSOS @webknossos.org · Jul 29

Tuesday tips 🐾 for Beginners

Did you know that you can toggle crosshairs and scalebars on or off in WEBKNOSSOS? Simply go to the settings in the left sidebar and customize your view.

Check out the Youtube Playlist for more tips: buff.ly/M3nCDIL

WEBKNOSSOS @webknossos.org · Jul 24

🌟Enhancement🌟

If you copy the position to your clipboard (e.g. from Webknossos, an email from a colleague or your notes), you can now paste the position anywhere in the Webknossos UI. No need to activate the position control.

WEBKNOSSOS @webknossos.org · Jul 22

Tuesday tips 🐾 for Beginners

Did you know you can create bounding boxes? They help define regions of interest, export specific data, and more!

Check out the Youtube Playlist for more tips: youtube.com/playlist?lis...

WEBKNOSSOS @webknossos.org · Jul 17

🌟Enhancement🌟

Make the 3D meshes of your segments translucent. Great for revealing inner segments, such as as cell organelles. Also, translucent meshes look really cool 😎

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WEBKNOSSOS @webknossos.org · Jul 15

Tuesday tips 🐾 for Beginners

Did you know you can customize skeleton colors? Let WEBKNOSSOS choose a color for your tree or select your preferred shade by right-clicking and choosing 'Change Tree Color'.

Check out the Youtube Playlist for more tips: youtube.com/playlist?lis...

WEBKNOSSOS @webknossos.org · Jun 26

🌟Enhancement🌟

Only show selected segments. Toggle the “Hide unlisted segments” setting to pick which segments will be shown.

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WEBKNOSSOS @webknossos.org · Jun 24

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!

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WEBKNOSSOS @webknossos.org · Jun 5

🌟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'

WEBKNOSSOS @webknossos.org · Jun 3

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: www.youtube.com/playlist?lis...

Reposted by WEBKNOSSOS

Paolo Ronchi @paoloronchi.bsky.social · Apr 24

If you want to learn the latest developments in volumeEM from the experts, with hands-on experience on our instruments @embl.org, this course is for you! 🔬

EMBL Events @events.embl.org · Apr 10

🔬 The practical course #EMBOvEM is open for registration 👉 https://s.embl.org/vem25-01-bl

You will gain theoretical and hands-on knowledge on the three main techniques for volume EM – microtome-based serial block-face SEM, focused ion beam SEM, and array tomography.

#vEM #Microscopy

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Reposted by WEBKNOSSOS

Helene Schmidt @helenelab.bsky.social · Apr 23

Super happy that our papers #2 and #3 from our 3-person lab just went online on bioRxiv! First large-scale 3D EM dataset from mouse hippocampus CA1 www.biorxiv.org/content/10.1... - check out the beautiful data on webknossos wklink.org/7023 ! …

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WEBKNOSSOS @webknossos.org · Apr 11

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.

WEBKNOSSOS @webknossos.org · Apr 8

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.

WEBKNOSSOS @webknossos.org · Apr 3

🌟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!

WEBKNOSSOS @webknossos.org · Apr 1

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: www.youtube.com/playlist?lis...