Quantification and pattern recognition of necrosis

If you select a particular object or annotations, it will only run in those areas (as shown in your images, Everywhere vs Any annotations vs Current selection). It is up to you what to choose. The overlay shows up everywhere and doesn’t generate anything in and of itself. If you create objects or measurements, and ensure that there are annotations to work inside, it will work inside those annotations if you tell it to.

When scripting, you can also be precise, using the select objects by class option.