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 webknossos.org Account

Signing up to webknossos.org is the easiest way to get started with webKnossos. Go to webknossos.org 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 webknossos.org 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, checkout the pricing page for paid plans that covers storage costs and provide 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 webknossos.org 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 orthongonal 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 Tracing button from the view mode of a dataset to create your first annotation. webKnossos will launch the main annotation screen allowing you to navigate your dataset and place markers to reconstruct skeletons.

Drag the mouse while pressing the left mouse button to navigate the dataset. Right-click in the data to place markers, called nodes. Basic movement in the dataset 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 Tracing UI guide.

Editing skeleton and volume annotations in the Tracing 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 hello@scalableminds.com. 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.