There are 2 segmentation modes in the Pixel Editor: Semantic Segmentation and Instance Segmentation.

Semantic Segmentation

The Pixel Editor is in Semantic Segmentation mode by default.

When in Semantic Segmentation mode, all the instances you create that are assigned to the same class will count as one instance.

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See for yourself

Create an instance and assign it a class. Next, create other instances and assign them the same class. The instances you created count as one instance.

Instance Segmentation

When in Instance Segmentation mode, each instance you create will count as one instance.

To set the segmentation mode to Instance Segmentation, turn the Semantic/Instance segmentation mode on by sliding the toggle to the right in the left panel.