Editing and working with the configuration file

The configuration file (config.yaml) is the central record of files in your project, as well as the settings for your models. As a YAML file, it can be edited manually, but the GUI provides an easy way to edit it without needing to know the YAML format. In this guide, we will show you how to edit the configuration file using the GUI.

Editing the configuration

After creating your DeepLabCut project, you’ll be shown the main GUI window, where you can manage your project from the Project Management Tab.

• Locate the Configuration File: At the top of the main window, you’ll find the file path to the configuration file.

• Edit the File: Click on Edit config.yaml.

  • A Configuration Editor window will open, displaying all the configuration details.

  • You will need to modify some of these settings to align with your experiment.

  • For example:

    • Update or define the bodyparts you wish to track.

    • Optional: Outline the skeleton structure.

Step-by-step configuration walkthrough

Defining & updating bodyparts

• Locate the Bodyparts Section: In the Configuration Editor, find the bodyparts category.

• Modify the List: Click on the arrow next to bodyparts to expand the list. Here, you can:

  • Update the list with the names of the bodyparts relevant to your study.

  • Add more entries by right-clicking on a row number and selecting Insert.

Defining the skeleton

• Navigate to the Skeleton Section: Scroll down to the skeleton category.

• Adjust the Skeleton List: Click on the arrow to expand this section.

  • You can then update the list of bodypart pairs: i.e. the connections that define the skeleton structure of your model.

  • In the list of bodypart pairs, each pair has an index. (ranging from 0 to the total number of pairs in the skeleton).

  • Each item of the pair (also indexed; 0 or 1) has a value: the name of the bodypart.

  • Each pair of two bodyparts represents a connection, where all connections together make the skeleton.

Tip

Spend some time visualizing how the chosen bodyparts can be connected effectively to form a coherent, visually helpful skeleton.

Saving changes

• Save the Configuration: Once you’re satisfied with the modifications, click Save. This will store your changes and return you to the main GUI window.

Next steps

Head over the guide for the Labeling GUI, which will show you how to label your data using the napari-based labeling GUI.