Feature highlight 🚀 Pen mode skeleton Enable Pen mode for the skeleton tool to place nodes continuously while drawing with the mouse. This is especially useful for quickly placing many nodes within a single section. Sketch skeletons quickly and smoothly!

Feature highlight 🚀 Selective visibility When Hide unlisted segments is enabled, only segments added to the segment list are shown. Individual segments can still be hidden by toggling their visibility in the list. Additionally, you can right-click a segment and select "Only show this segment".

Feature highlight 🚀 Mesh opacity Adjust the opacity of 3D meshes for selected segments. This is useful for revealing internal structures, such as cell organelles.

Feature highlight 🚀 Surface area Compute the surface area of your segments in just a few clicks in WEBKNOSSOS.

Feature highlight 🚀 Splitting segments manually with the split segment toolkit Use the split segment toolkit to draw a curved 3D surface and split a segment along this interface. This is particularly useful for correcting ground truth within a bounding box. www.youtube.com/watch?v=iABt...

Feature highlight 🚀 Voxel Pipette tool The former Segment Picker has been generalized into the Voxel Pipette tool. It displays data values for all visible layers in a tooltip. To pick a segment ID, hold Shift and the tool will have its previous behavior.

Feature highlight 🚀 Live update for shared annotations Shared annotations now update live. See changes from collaborators as they happen. Support for simultaneous editing is coming soon!

Feature highlight 🚀 Command palette Navigate WEBKNOSSOS more efficiently with the Command Palette. Quickly search for tools, jump to datasets, and access key actions using just a few keystrokes. Let us know if you want more actions accessible through the command palette.

Feature highlight 🚀 Multiple points for split operation The proofreading tool now supports multiple reference points: define several segments around a desired split, and the tool automatically selects an optimal split point. Get more reliable splits with less manual tweaking!

Feature highlight 🚀 Viewport rotation Rotate orthogonal viewports freely in WEBKNOSSOS to trace objects from the best angle. Use keyboard shortcuts to rotate each viewport. Try rotating viewports in WEBKNOSSOS now and accelerate your tracing workflow!

Last year brought many great new features to WEBKNOSSOS ✨ Over the next days, we’ll share a series of feature highlights. Stay tuned!

Our Method of the Year 2025 is...drumroll please...EM-based connectomics!! Our Editorial introduces our choice and highlights six Comments and other related content in this special issue. Please join us in celebrating EM-based connectomics! 🎉🧠🔬 www.nature.com/articles/s41...

🌟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.

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...

#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

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

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...

🌟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...

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...

🌟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...

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...

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

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

🌟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.

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...

🌟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 😎

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...

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

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!

🌟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'

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...

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! 🔬

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 ! …

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.

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.

🌟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!

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...

@Norman Rzepka introduced @WEBKNOSSOS at our vEM Data Challenges Symposium! 🙌 He showcased fast 3D data visualization, efficient annotations, AI-driven segmentation, and seamless collaboration🔬✨ 🎥 Watch the recorded session here:

@LukeNoon from CIPF shared insights into his research at the vEM Data Challenges Symposium on mapping liver & peripheral tissues using innovative annotation & collaboration strategies. 🎥 Watch the recorded session here: youtu.be/1sMQFpRGMLs?....

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. Unfortunately, there was an issue with the recording. A previous video of a similar talk:

🚀 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: (youtu.be/vO8lro_wlz8?...)

Tuesday tips 🐾 for Pros To change the radius of a node, simply hold 'Shift' and scroll with the mouse wheel.

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 webknossos.org! www.youtube.com/watch?v=FfqN...

🚀 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: buff.ly/TZRYGcL.

🌟Enhancement🌟 Quickly check a dataset's volume by hovering over the extent icon in the info tab.

⏳ 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: buff.ly/LaZw4aA.

@normanrz.com from scalable minds will introduce WEBKNOSSOS at our symposium on vEM data challenges. Learn more about fast annotations, AI-driven segmentation & seamless collaboration! 📅 March 6, 2025 | 5-7PM CET | Free registration 📖 Full abstract and sign up link: https://buff.ly/42gkyv4

@carlesbosch.bsky.social from the Francis Crick Institute presents his work at our symposium on vEM data challenges, showcasing how correlative 2-photon and X-ray imaging reveals neural computation in olfactory circuits. 📅 March 6, 2025 | 5-7PM CET | Free registration | https://buff.ly/42gkyv4

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 and peripheral tissues with innovative annotation & collaboration strategies! 📅 March 6, 2025 | 5-7PM CET | Online www.eventbrite.de/e/volume-em-...

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 and get reminders! 📅 March 6, 2025 | 5-7PM CET | Free registration 📖 Full abstract and sign up link: https://buff.ly/42gkyv4