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: https://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: https://medium.com/webknossos/from-beamline-to-browser-automating-high-throughput-x-ray-imaging-with-webknossos-at-embl-p14-dc992159574f

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: https://youtu.be/lZS2tOJYErw

Automatically align large volume EM datasets in WEBKNOSSOS.

Run alignment and inspect results directly in the browser.

Watch the tutorial: https://youtu.be/Rt3uG31r2bI

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: https://medium.com/webknossos/custom-model-training-for-mitochondria-detection-in-webknossos-c4a17aeaf27c

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. https://buff.ly/LzXDNn6

Feature highlight 🚀 Surface area

Compute the surface area of your segments in just a few clicks in WEBKNOSSOS.

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 in a data viewport and select "Only show this segment".