@webknossos.org.bsky.social
Visualize, share, segment, and annotate your large 3D images online.
🌟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! 🔬
24.04.2025 12:17 — 👍 19 🔁 12 💬 0 📌 0
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 ! …
23.04.2025 07:19 — 👍 39 🔁 9 💬 3 📌 4Working 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.
11.04.2025 13:13 — 👍 1 🔁 0 💬 0 📌 0Tuesday 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...
13.03.2025 14:10 — 👍 0 🔁 0 💬 0 📌 0
🚀 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
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: https://buff.ly/4ha0pL7!
