With this setup you can manually align the planes of a z-stack. If you have imported your z-stack and there are bigger shifts between individual planes of the stack, this setup helps you to make a coarse alignment of your z-stack before an automated alignment, e.g. via Z-Stack Alignment with ROI.

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1

Alignment Controls Section
Here you have your controls to align the z-planes in the stack manually. For more information, see Alignment Controls Section.

2

Image View
Displays your selected z-plane and the following plane with different colors. The current plane is displayed in cyan and the following z-plane is displayed in red.

3

View Options
Here you have your standard view options (Dimensions Tab and Display Tab).