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Getting Started

Welcome to the webKnossos documentation. webKnossos is a tool for exploring large-scale 3D image datasets, creating skeleton annotations and 3D volume segmentations. Since it is a web-based tool, collaboration, crowdsourcing and publication is very easy.

Feel free to drop us a line or create a Pull Request if you have any suggestions for improving the documentation.

Create a Account

Signing up to is the easiest way to get started with webKnossos. Go to and create a new account. Please make sure to enter a correct email address. After you have entered your details, the account will be automatically activated and logged in.

Accounts on are free to use with published datasets. If you wish to use private datasets, there is an upload limit of 10GB. For more data storage, check out the pricing page for paid plans that covers storage costs and provides support services such as dataset conversions. You can also rent a fully-managed dedicated webKnossos server from scalable minds or install webKnossos on your own server.

Explore Published Datasets

On there are already a bunch of published community datasets available for you to explore. To get started, navigate to the Featured Publications tab on your dashboard. There, you find a list of all available public datasets. Click on the dataset name to open the dataset.

The list of available datasets

Once you are in the "View" mode, you are presented with three orthogonal views and one 3D viewport. You can use the following shortcuts to navigate the data. See the full list of gestures and keyboard shortcuts for advanced use.

Shortcut Operation
Left Mouse Drag or Arrow Keys Move In-Plane
SPACE or Mousewheel Move Forward
SHIFT + SPACE or Mousewheel Move Backward
I or ALT + Mousewheel Zoom In
O or ALT + Mousewheel Zoom Out
Scroll Mousewheel (3D View) Zoom In And Out
Right Click Drag (3D View) Rotate 3D View
. (Dot) Toggle Viewport Maximization

You can also change the size of the viewports to see more details in your data and customize your layout.

Explore datasets with customized viewport layouts

Your First Annotation

Click the Create Annotation button while in "View" mode of a dataset to create your first annotation. webKnossos will launch the main annotation screen allowing you to navigate your dataset, place markers to reconstruct skeletons or annotate segments as volume annotations.

Depending on the current tool - selectable in the top bar - various actions can be performed. Note that the most important controls are always shown in the status bar at the bottom of your screen. The first tool is the MOVE tool which allows navigating the dataset by moving the mouse while holding the left mouse button. In the SKELETON tool, a left mouse click can be used to place markers in the data, called nodes. Additionally, the left mouse button can also be used to navigate around, select or drag nodes. The DRAW tool allows to "paint" voxels to create volumetric annotations.

A right mouse click can be used to open a context-sensitive menu with various actions, such as merging two trees or flood-filling a segment. Note that "Classic Controls" can be activated in the settings sidebar which assigns more specialized behaviors to the right click (e.g., dragging with the right mouse button in the draw tool will erase data). Basic movement along the 3rd axis is done with the mouse wheel or by pressing the spacebar keyboard shortcut.

Learn more about the skeleton, volume, and hybrid annotations as well as the interface in the Annotation UI guide.

Editing skeleton and volume annotations in the Annotation UI

Learn More

Now you know the basics of webKnossos. Feel free to explore more features of webKnossos in this documentation.

If you need help with webKnossos, feel free to contact us at or write a post in the forum. scalable minds also offers commercial support, managed hosting, and feature development services.

Read the installation tutorial, if you wish to install webKnossos on your own server.

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