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Open Mark & Find tool by clicking the button indicated by the arrow below. The icon starts out black but becomes red when Mark & Find is active.
Scan your specimen and focus on the plane that you want to be in the middle of the stack. This might be different to the plane with the most fluorescence. For instance, an adherent cell may have more fluorescence near the coverslip where the cell is flattest, but the middle of the stack might be half way up the nucleus. It might be easiest to use a nuclear stain to locate the middle in this case but you will have to make sure the Begin and End of the stack are beyond the edges of the apical and basal membrane.
Mark the position by clicking the button indicated by the arrow below.