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
