Volume annotations with WEBKNOSSOS


Albane le Tournoulx de la Villegeorges
4 min readMay 15, 2023


In this tutorial, we will explore the annotation features of WEBKNOSSOS. We will cover everything from opening and annotating a published dataset to utilizing both basic and advanced annotation tools. Additionally, I will explain a few things about meshes and provide insights into the layer system of WEBKNOSSOS. Let’s get started!

If you already have an account, go to the “featured publications” page. Alternatively, sign up for free in less than a minute on webknossos.org.

Select a dataset from the list of publications to start annotating a demo dataset. You can also open one of your own datasets (if you want to learn how to upload a dataset to WEBKNOSSOS, watch our tutorial on how to upload your own data).


Click on “create annotation” to begin. Navigate through the dataset and zoom in to find the cell you want to annotate.

Creating an annotation and navigating through the data.

Select the brush tool to create your first volume annotation. Brush over a segment. Use the eraser tool to correct mistakes.

Brushing and erasing a segment.

Create a new segment by selecting a new segment ID. Use the trace tool to draw more precise contours.

Creating segments with new segment IDs and annotating cells with the trace tool.


Now, let’s explore the smart tools of WEBKNOSSOS. Choose the quick-select tool and turn on the AI option. Draw a rectangle around the cell you want to segment. Create and annotate new segments by pressing the keyboard shortcut “C”.

Turning on the AI option of the quick-select tool and annotating a few cells.

Quick tip: When dealing with long and complex shapes, try drawing multiple rectangles on different areas. The annotations will merge and your complex shape will be segmented in no time.

Tracing multiple rectangles using the quick-select tool for precise annotation

Now, annotate a segment on a new slice. Skip a few sections forward and annotate again. To interpolate the two sections, click the interpolation tool. All the slices in between the two original ones have now been automatically annotated by WEBKNOSSOS.

Annotating a slice, skipping a few sections forward, annotating again, and clicking the interpolation tool: all slices in between the two have been automatically annotated.

Repeat this super fast workflow as much as you need. The combination of these two tools enables highly efficient 3D annotation.

Repeating the process of annotating slices using the quick-select tool and interpolating the annotations.


To create a 3D mesh, right-click on your annotation and click on “compute mesh”. Hide the planes in the 3D viewport to fully enjoy your 3D mesh.

Computing a 3D mesh.

To have a look at even more impressive meshes, go to the featured publication and choose a dataset with an existing mesh file. Right-click on a segment and choose “load mesh”. Maximize the 3D viewport and enjoy the view!

Loading meshes from a featured publication.


WEBKNOSSOS works with a layer system, similar to Photoshop. You will usually have the “raw data” layer at the top, as well as optional additional color layers. You can change the opacity of the layers and use the histograms to adjust the contrast of your data.

Turning on a color layer, changing the opacity, and adjusting the contrast with the histogram.

Then, you will find the segmentation layers for volume and skeleton annotations. You can toggle the visibility and set the opacity of the annotations as needed. Once a volume annotation layer is active, you can start annotating.

Toggling the visibility of the annotation layers.

I hope this tutorial has helped you to better understand the volume annotation capabilities of WEBKNOSSOS. Don’t hesitate to try out what you’ve learned on webknossos.org. For more tutorials and updates on new features, follow us on Twitter or Mastodon!