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💎 Oldy but goldy: the AI quick-select tool. Click a structure or drag a box and WEBKNOSSOS segments it for you. Set the prediction depth to label many sections at once, in 2D or 3D. #WEBKNOSSOS

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WEBKNOSSOS @webknossos.org · 16/09/2026

💎 Oldy but goldy: viewport navigation in WEBKNOSSOS. Rotate the orthogonal viewports freely for the best angle, jump into Flight mode, and rearrange, maximise or reset your layout any time. #WEBKNOSSOS

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WEBKNOSSOS @webknossos.org · 08/09/2026

New feature 🐣 Layer transforms (translation, rotation, and scaling) can now be edited live while viewing or annotating data. Try it out on webknossos.org!

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WEBKNOSSOS @webknossos.org · 03/09/2026

Got your data in WEBKNOSSOS and a coding agent like Claude? Turn it into a beautiful flythrough video. Let the AI write code to control camera moves, layer opacities and more, and show your audience what you actually see. Learn how in our blog post: home.webknossos.org/blog/creatin...

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WEBKNOSSOS @webknossos.org · 01/09/2026

Around WEBKNOSSOS in 80 seconds 🌍 Experience fast 3D microscopy data exploration. Annotate with AI, explore 3D meshes, collaborate in real time, manage datasets, and share your research with one click. Sign up for free at webknossos.org!

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WEBKNOSSOS @webknossos.org · 01/09/2026

💎 Oldy but goldy: dataset management in WEBKNOSSOS. Organise datasets into folders with per-folder permissions, recognize them at a glance with thumbnails, and attach metadata and tags to datasets. #WEBKNOSSOS

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WEBKNOSSOS @webknossos.org · 25/08/2026

💎 Oldy but goldy: the bounding box tool in WEBKNOSSOS. Create & resize a box, move it with Ctrl, fine-tune the values in the sidebar — then export the data inside, register segments, or auto-generate boxes for AI training. #WEBKNOSSOS

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WEBKNOSSOS @webknossos.org · 20/08/2026

Maximum Intensity Project is now available in WEBKNOSSOS 🐣 MIP renders your dataset directly in the 3D viewport, by projecting a layer through the volume and keeping the brightest value along each ray. Read the article: home.webknossos.org/blog/mip

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WEBKNOSSOS @webknossos.org · 18/08/2026

💎 Oldy but goldy: animations in WEBKNOSSOS. Render a video where the EM data shrinks to reveal your 3D meshes — with camera path, resolution and mesh options. Perfect for talks and papers. #WEBKNOSSOS

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WEBKNOSSOS @webknossos.org · 11/08/2026

💎 Oldy but goldy: 3D meshes in WEBKNOSSOS. Generate them ad-hoc or precompute them, adjust per-segment opacity to reveal organelles, export as STL, and click a mesh to jump straight to that spot in 2D.

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WEBKNOSSOS @webknossos.org · 04/08/2026

💎 Oldy but goldy: the segments list in WEBKNOSSOS. Organise segments into groups, run batch actions across a whole group, give them custom colors, and read stats — count, volume, surface area, bbox — with CSV export.

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WEBKNOSSOS @webknossos.org · 09/07/2026

Meet the WEBKNOSSOS Assistant 🤵‍♂️ Ask questions in natural language and get clear answers instantly. Available directly in WEBKNOSSOS through the Help button and throughout our documentation.

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WEBKNOSSOS @webknossos.org · 07/07/2026

Nuclei and soma detection are now available in WEBKNOSSOS! Try it on webknossos.org.

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WEBKNOSSOS @webknossos.org · 01/07/2026

The WEBKNOSSOS Python docs are now available via llms.txt. Use your favorite AI assistant to explore the API, learn workflows, and find answers directly from the documentation. docs.webknossos.org/llms.txt

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WEBKNOSSOS @webknossos.org · 19/06/2026

Working on correlative microscopy workflows? Use skeletons to align landmarks and combine light microscopy and vEM data directly in WEBKNOSSOS. Example dataset (Drawitsch et al., eLife 2018): webknossos.org/links/tNaRtC...

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WEBKNOSSOS @webknossos.org · 17/06/2026

You can now customize your keyboard shortcuts in WEBKNOSSOS! Go to the user menu → Keyboard Shortcuts to add or edit them. Tip: it also gives you a full overview of all available shortcuts.

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WEBKNOSSOS @webknossos.org · 04/06/2026

Creating animations in WEBKNOSSOS? You can now include skeletons in your renders. Generate clearer videos for publications, presentations, or sharing your reconstructions. Try it out at webknossos.org now!

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WEBKNOSSOS @webknossos.org · 02/06/2026

“Students weren’t just annotating - they were thinking critically about what they observed.” In this course, students used WEBKNOSSOS to explore real EM data, segment organelles, analyze cellular asymmetry, and develop biological hypotheses from their own observations. Read more: buff.ly/MckCdVY

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WEBKNOSSOS @webknossos.org · 28/05/2026

Segment cells in 3D with the Quick Select tool in WEBKNOSSOS! Just click inside a process and WEBKNOSSOS automatically segments it across multiple sections. Adjust the number of Z sections in the toolbar settings (top right).

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WEBKNOSSOS @webknossos.org · 21/05/2026

Automatically sample bounding boxes for ML training in WEBKNOSSOS. Choose the magnification, number, and size of boxes, and review the generated boxes to adjust any that landed in empty regions. Learn how to choose suitable box sizes and counts for ML training: docs.webknossos.org/webknossos/a...

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WEBKNOSSOS @webknossos.org · 20/05/2026

"We can produce up to 12 tomograms per hour, and beam time can run for 24 hours straight. So a single user can easily generate multiple terabytes in one session." Read more on how Angelika Svetlove used WEBKNOSSOS to efficiently handle such massive images: medium.com/webknossos/f...

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WEBKNOSSOS @webknossos.org · 18/05/2026

Did you know you can view and work with time series (N-dimensional) datasets in WEBKNOSSOS? You can even inspect statistics for a specific time point.

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WEBKNOSSOS @webknossos.org · 15/05/2026

We spoke with @inperience.bsky.social from Miami University about using WEBKNOSSOS in a cell biology course built around real C. elegans vEM data. 48 students annotated cells, generated AI training data, and even contributed to a biological discovery. Read the interview: buff.ly/MckCdVY

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WEBKNOSSOS @webknossos.org · 28/04/2026

Managing a connectomics or volume EM project? Validate segmentation on small regions before scaling to the full dataset. Iterate until results are satisfactory.

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WEBKNOSSOS @webknossos.org · 22/04/2026

Start with a small test bounding box. Validate the segmentation, inspect errors, and only then run the model on the full dataset. A controlled workflow for large-scale EM analysis.

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WEBKNOSSOS @webknossos.org · 16/04/2026

Create figures for your paper with WEBKNOSSOS 🖼️ Customize the view to match your needs: set display modes, adjust the layout, load meshes and edit colors and transparency. These are just a few of the available options for generating publication-ready images. Try it out yourself on webknossos.org!

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WEBKNOSSOS @webknossos.org · 15/04/2026

“Users can leave Hamburg and continue inspecting their datasets the same day without transferring large volumes of data.” At the P14 beamline, tomography datasets appear in WEBKNOSSOS minutes after reconstruction, allowing users to explore them remotely in the browser. medium.com/webknossos/f...

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WEBKNOSSOS @webknossos.org · 09/04/2026

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.

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WEBKNOSSOS @webknossos.org · 01/04/2026

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

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WEBKNOSSOS @webknossos.org · 31/03/2026

🌟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.

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WEBKNOSSOS @webknossos.org · 26/03/2026

“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...

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WEBKNOSSOS @webknossos.org · 25/03/2026

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 hello@webknossos.org.

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WEBKNOSSOS @webknossos.org · 23/03/2026

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...

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WEBKNOSSOS @webknossos.org · 19/03/2026

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.

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WEBKNOSSOS @webknossos.org · 18/03/2026

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

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WEBKNOSSOS @webknossos.org · 05/03/2026

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

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WEBKNOSSOS @webknossos.org · 04/03/2026

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

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WEBKNOSSOS @webknossos.org · 02/03/2026

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

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WEBKNOSSOS @webknossos.org · 26/02/2026

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...

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WEBKNOSSOS @webknossos.org · 25/02/2026

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!

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WEBKNOSSOS @webknossos.org · 23/02/2026

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

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WEBKNOSSOS @webknossos.org · 09/02/2026

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!

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WEBKNOSSOS @webknossos.org · 05/02/2026

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".

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WEBKNOSSOS @webknossos.org · 04/02/2026

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

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WEBKNOSSOS @webknossos.org · 02/02/2026

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

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WEBKNOSSOS @webknossos.org · 28/01/2026

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.

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WEBKNOSSOS @webknossos.org · 26/01/2026

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!

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WEBKNOSSOS @webknossos.org · 21/01/2026

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.

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WEBKNOSSOS @webknossos.org · 19/01/2026

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!

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WEBKNOSSOS @webknossos.org · 15/01/2026

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!

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