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!
“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...
All AI analysis workflows in WEBKNOSSOS are now fully documented.
Our step-by-step tutorials cover:
Alignment
Automated segmentation
Custom model training
Explore the documentation: docs.webknossos.org/webknossos/a...
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 hello@webknossos.org.
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!
