Pen Tablets and WEBKNOSSOS

Tutorial

Today, I want to share helpful tips on using pen tablets for efficient data annotation with WEBKNOSSOS. WEBKNOSSOS offers advanced volume annotation features that simplify cell segmentation with the mouse. However, when dealing with complex shapes that the AI-based quick-select tool may struggle with, using a tablet with its natural pencil-like feel can make a significant difference.

With the newly integrated shortcuts, WEBKNOSSOS has become more tablet-friendly. Let’s explore a workflow for creating efficient volume annotations with a tablet step by step. Alternatively, watch the video version of this tutorial.

Set up your tablet

To streamline your workflow, program your tablet and pen buttons to match the WEBKNOSSOS shortcuts. By doing so, you can focus on your pen without the need of a mouse or keyboard. Here’s an example configuration using a Wacom tablet:

Tablet buttons:

• Left: Brush (ctrl + K, B)
• Middle left: Eraser (ctrl + K, E)
• Middle right: Quick-select (ctrl + K, Q)
• Right: Create new segment (C)

Pen buttons:

• Lower button: Move (ALT)

You can find the full list for keyboard shortcuts in the documentation.

Programming buttons to match the WEBKNOSSOS shortcuts

Annotate your data

Now, let’s dive into the annotation process! In this example, we begin by quick-selecting a cell.

Navigating the dataset and segmenting a cell with the quick-select tool

If the annotation isn’t precise enough, we can easily switch to the eraser tool (middle left button) and erase a corner. Selecting the brush tool is as simple as pressing the left button, allowing us to add small surfaces to the annotation.

Improving the annotation precision with the eraser and brush tools

When ready, pressing the right button creates a new segment, and we can repeat the process for other cells.

Creating new segments and annotating them with the quick-select tool

For increased flexibility, you can additionally use your laptop’s keyboard shortcuts (e.g. “I” and “O” for zooming in and out).

By the way, WEBKNOSSOS also works great with pen input on an iPad. Stay tuned for the next tutorial.

I hope this tutorial has provided you with insights into utilizing tablets for WEBKNOSSOS annotations and make your annotation process faster and more precise. Don’t forget to follow us on Twitter and Mastodon for more tutorials and updates!

PS: some (gaming) computer mice also come with additional, programmable buttons that can be configured in their driver software to perform key combos… I’ll leave you to experimenting what suits you best!