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The way that layer.data and and layer.scale interact isn't always obvious when there is an image with non-1s scale and one wants to annotate it with points, shapes, labels, etc.
Making things more confusing, adding a new annotation layer in the GUI passes the scale of the image layer, but that is not the case for programmatic creation.
This came up in a PR I had to a plugin and I wrote up a simple example/explainer: computational-cell-analytics/micro-sam#804 (comment)