New annotation features in webKnossos

Hi everyone!
I am happy to present to you some of the new features webKnossos developed over the last half-year. You can try out these features on Don’t hesitate if you have any questions about using them.

Improved annotation capabilities in webKnossos

Combined annotations

Many webKnossos users work with skeleton annotations as well as with dense volume segmentation. webKnossos now supports all skeleton and volume tools in one combined annotation at the same time for convenience! This allows you, for instance, to label volume segments with additional nodes and comments and without being limited to the advantages of either sparse or dense annotation mode.

Annotations at all zoom levels

Moreover, you can now use the volume annotation tools (brush, outline tracer…) at any zoom/magnification level. This is great for getting an overview in an existing annotation layer or for creating a very quick, rough annotation from far out.

Different patterns for different segments

Small patterns/textures help make the segments more distinguishable from one another, which is especially useful when looking at large volume annotations with thousands of segments as produced by automated machine learning pipelines.

Contrast adjustment through histogram slider

EM data by Carles Bosch, Francis Crick Institute

Another handy feature is the histogram slider. Use it to fine-tune the contrast and brightness for both your underlying microscope data or for any of the segmentation and volume layers. (ProTip: Our engineers also like to use the histogram to threshold prediction maps produced by an ML model.)

Last but not least: in cases where you mess up, you can now undo volume annotations to make life easier.


All the best,



Thanks for the update. I love using the histogram sliders to tune the contrast on my scans. I sometimes work with float data and for those I need to move the start and stop handle of the slider almost on top of one another in order to see my data. Any way I can fine tune this?

Hi Mike!
Sure, there is an edit button in the top-right of the histogram. If you click that button, input fields will open where you can manually enter the range of the sliders. Hope this helps!

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@normanrz Thanks for the quick reply. With the inputs I can manually constrain my thresholds to be between 0.1 and 0.34 for my float data and adjust my contrast. That is way more precise than the mouse handles.