Running a volume EM core facility? Deliver aligned and segmented datasets with reproducible AI workflows in WEBKNOSSOS - from alignment to custom model training. Support your users with documented, scalable analysis pipelines.

Segmentation errors often reflect gaps in the training data. Review the ground truth, add missing examples, retrain, and iterate. Custom model training gives you direct control over model behavior. Guidelines for ground truth annotation: buff.ly/w41Ip9e

🌟Enhancement🌟 Open datasets or jump straight to annotations - right from the command palette. Press Ctrl/Cmd + P from anywhere in the UI, then scroll or start typing to find what you need.

“And from a facility perspective, everything is automated. No one has to manually convert, upload, organize, or assign permissions.” At EMBL P14, reconstructed tomography datasets are automatically converted and transferred to WEBKNOSSOS through the API. Read more: medium.com/webknossos/f...

WEBKNOSSOS AI Grant 🔬 We are offering compute credits to support selected research projects applying AI segmentation to volume EM datasets. Interested? Send us a link to your dataset in WEBKNOSSOS and a short description of your analysis goals at [email protected].

Run automated alignment in WEBKNOSSOS and improve the results with manual matches when needed. Maintain control over challenging areas while keeping the workflow efficient. www.youtube.com/watch?v=8IEl...

Train or refine custom segmentation models directly in WEBKNOSSOS. Annotate ground truth, train the model, test on a small region, iterate, and run on the full dataset.

Dataset showcase ✨ In this study, Chen et al. (ScienceAdvances, 2025) investigate the ultrastructure and function of lamellar Schwann cells in Pacinian corpuscles, revealing their active role in mechanosensory processing. Explore the segmented dataset in WEBKNOSSOS: wklink.org/3248

At the EMBL P14 beamline, tomography datasets are automatically transferred into WEBKNOSSOS minutes after reconstruction. Angelika Svetlove explains how the team built this pipeline - and why analysis, not acquisition, is now the main bottleneck. Read the interview:

New Web Page - Volume EM Industrial Partners www.volumeem.org/industrial-p... We’re excited to introduce our newly curated Industrial Partners page, showcasing organizations recognized by the volumeEM Community as key contributors in the field.

Run pre-trained segmentation models for SEM data in WEBKNOSSOS. Test on small bounding boxes, inspect merge and split errors, and run on the full dataset once validated. View the tutorial: youtu.be/lZS2tOJYErw

Cleaning up bounding boxes just got a bit easier: multi-select (hold Ctrl/Cmd) + delete is now supported in WEBKNOSSOS.

Automatically align large volume EM datasets in WEBKNOSSOS. Run alignment and inspect results directly in the browser. Watch the tutorial: buff.ly/Edriq64

We annotated ground truth data and trained an instance segmentation model for mitochondria detection on a 140 GB mouse cortex dataset (Motta et al., 2019) in WEBKNOSSOS. See the workflow and results: medium.com/webknossos/c...

New feature 🐣 CSV export for trees! In WEBKNOSSOS, go to the Skeleton tab. Under "More actions", select "Download visible trees CSV" and check your downloads folder. Your trees are ready for analysis!

AI workflows for volume EM in WEBKNOSSOS. Align large EM datasets, run pre-trained segmentation models, train custom models on your own ground truth, and and move from small test regions to full-dataset segmentation. All workflows are now documented with step-by-step tutorials. buff.ly/LzXDNn6

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.